H3K27ac • Neuron NGBEPEL4GLYM5OX3 • Nott 2019 Enhancer Neuron Enhancer Show metadata identifier NGBEPEL4GLYM5OX3 data_source Nott_2019 Download track Download number_of_intervals 141,642 bp_covered 130,290,144 output_type enhancer peaks genome_build hg38 cell_type Neuron biosample_type Tissue biosample_term_id CL:0000540 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Enhancer file_format bed bed3-lifted file_size 2,302,799 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_NeuN_enhancers_lifted.bed.gz processed_file_md5 9adca47b36ff7da3bfb0a78ad4d80e16 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_NeuN_enhancers_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_NeuN_enhancers_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/enhancers/NeuN_enhancers.sorted.bigBed -P FILER2/Annotationtracks/Downloads/Nott_2019/enhancers/NeuN_enhancers.sorted.bigBed raw_file_md5 220511817dcfb6f010e3bfd50875a22b data_category Enhancer Genomic feature type H3K27ac enhancer peaks track_description version=2019;Original_cell_type=neurons;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 4yo, 18yo;sexes=M;ethnicities=His, Caucasian;brain_regions=Parietal Cortex, Temporal Cortex;pat system_category Nervous life_stage Adult, Child track_name Nott_2019 Neuron Enhancer H3K27ac-histone-mark enhancer peaks (bed3-lifted) [Life stage: Adult, Child] [Enhancer]
H3K4me3 • PU.1+ Microglia NGBEPEL4PJUJAKTB • Nott 2019 Histone ChIP-seq PU.1+ Microglia Histone Show metadata identifier NGBEPEL4PJUJAKTB data_source Nott_2019 Download track Download number_of_intervals 20,198 bp_covered 32,595,591 output_type peaks genome_build hg38 cell_type PU.1+ Microglia biosample_type Tissue biosample_term_id CL:0000129 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay Histone ChIP-seq file_format bed bed3-lifted file_size 355,521 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz processed_file_md5 f92f4fd2120e31029a90242f93fc8053 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K4me3/PU1_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K4me3/PU1_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz raw_file_md5 7ff57c82eac5365d4ba73d1b36b08655 data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K4me3 peaks track_description version=2019;Original_cell_type=PU1_optimal_peak_IDR_ENCODE.H3K4me3;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=4yo;sexes=M;ethnicities=His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic;dataSource_pubmed_id=31727856;in_trackHub=yes;dataSource_a system_category Nervous life_stage Child track_name Nott_2019 PU.1+ Microglia Histone ChIP-seq H3K4me3 peaks (bed3-lifted) [Life stage: Child] [Histone ChIP-seq peaks]
H3K27ac • Neuron NGBEPELCBNAG2EFC • Nott 2019 Super-enhancer Neuron Enhancer Show metadata identifier NGBEPELCBNAG2EFC data_source Nott_2019 Download track Download number_of_intervals 1,170 bp_covered 98,328,897 output_type super-enhancer peaks genome_build hg38 cell_type Neuron biosample_type Tissue biosample_term_id CL:0000540 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Super-enhancer file_format bed bed6-lifted file_size 29,680 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_NEUN_superEnhancer_L1_lifted.bed.gz processed_file_md5 7e0e8eb72bfe649022b85c472cf0ff4f wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_NEUN_superEnhancer_L1_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_NEUN_superEnhancer_L1_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/Super_enhancers/NEUN_superEnhancer_L1.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/Super_enhancers/NEUN_superEnhancer_L1.gz raw_file_md5 c9e8e569c8137b41a055488b927275ea data_category Enhancer Genomic feature type H3K27ac super-enhancer peaks track_description version=2019;Original_cell_type=neurons;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 4yo, 18yo;sexes=M;ethnicities=His, Caucasian;brain_regions=Parietal Cortex, Temporal Cortex;pat system_category Nervous life_stage Adult, Child track_name Nott_2019 Neuron Super-enhancer H3K27ac-histone-mark super-enhancer peaks (bed6-lifted) [Life stage: Adult, Child] [Enhancer]
H3K27ac • PU.1+ Microglia NGBEPELCYWMCR5BJ • Nott 2019 Histone ChIP-seq PU.1+ Microglia Histone Show metadata identifier NGBEPELCYWMCR5BJ data_source Nott_2019 Download track Download number_of_intervals 48,791 bp_covered 82,267,056 output_type peaks genome_build hg38 cell_type PU.1+ Microglia biosample_type Tissue biosample_term_id CL:0000129 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Histone ChIP-seq file_format bed bed3-lifted file_size 822,603 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz processed_file_md5 dcbea562195c6dc5e6592df34e88227e wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K27/PU1_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K27/PU1_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz raw_file_md5 2eb92bd0cca0d176b2059df8a9847683 data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K27ac peaks track_description version=2019;Original_cell_type=PU1_optimal_peak_IDR_ENCODE.H3K27;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 18yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Parietal Cortex, Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology, system_category Nervous life_stage Adult, Child track_name Nott_2019 PU.1+ Microglia Histone ChIP-seq H3K27ac peaks (bed3-lifted) [Life stage: Adult, Child] [Histone ChIP-seq peaks]
H3K27ac • Oligodendrocyte NGBEPELDE7AUCBD4 • Nott 2019 Super-enhancer Oligodendrocyte Enhancer Show metadata identifier NGBEPELDE7AUCBD4 data_source Nott_2019 Download track Download number_of_intervals 1,152 bp_covered 76,371,866 output_type super-enhancer peaks genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Super-enhancer file_format bed bed6-lifted file_size 29,170 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_OLIG2_superEnhancer_L1_lifted.bed.gz processed_file_md5 3a9ffa8958fb78570266e2cb951eb6c3 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_OLIG2_superEnhancer_L1_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_OLIG2_superEnhancer_L1_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/Super_enhancers/OLIG2_superEnhancer_L1.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/Super_enhancers/OLIG2_superEnhancer_L1.gz raw_file_md5 6d6ef51d95473ed9c6980986c55ecf02 data_category Enhancer Genomic feature type H3K27ac super-enhancer peaks track_description version=2019;Original_cell_type=oligodendrocytes;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 4yo, 18yo;sexes=M;ethnicities=His, Caucasian;brain_regions=Parietal Cortex, Temporal C system_category Nervous life_stage Adult, Child track_name Nott_2019 Oligodendrocyte Super-enhancer H3K27ac-histone-mark super-enhancer peaks (bed6-lifted) [Life stage: Adult, Child] [Enhancer]
Neuron NGBEPELH4UIPYVWM • Nott 2019 ATAC-seq Neuron Accessible chromatin Show metadata identifier NGBEPELH4UIPYVWM data_source Nott_2019 Download track Download number_of_intervals 55,932 bp_covered 26,306,624 output_type accessible chromatin region genome_build hg38 cell_type Neuron biosample_type Tissue biosample_term_id CL:0000540 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody Not applicable assay ATAC-seq file_format bed bed3-lifted file_size 943,524 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz processed_file_md5 021f5f79663b653312674edba82d0333 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/ATAC/NeuN_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/ATAC/NeuN_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz raw_file_md5 001cd49abd5da350109e6c9eed7b8e56 data_category Accessible chromatin Genomic feature type ATAC-seq accessible chromatin region track_description version=2019;Original_cell_type=NeuN_optimal_peak_IDR_ENCODE.ATAC;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 4yo, 8yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type IIa, Focal cortical dysplasia type Ic, Ne system_category Nervous life_stage Child track_name Nott_2019 Neuron ATAC-seq accessible chromatin region (bed3-lifted) [Life stage: Child] [Accessible chromatin]
H3K27ac • Neuron NGBEPELI5ERYXM7L • Nott 2019 Histone ChIP-seq Neuron Histone Show metadata identifier NGBEPELI5ERYXM7L data_source Nott_2019 Download track Download number_of_intervals 148,066 bp_covered 157,234,772 output_type peaks genome_build hg38 cell_type Neuron biosample_type Tissue biosample_term_id CL:0000540 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Histone ChIP-seq file_format bed bed3-lifted file_size 2,416,796 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz processed_file_md5 2b2caaea48f1970d0509c0615c7ad141 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_NeuN_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K27/NeuN_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K27/NeuN_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz raw_file_md5 67c6c2e06a3fe6497af988d5f0a89200 data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K27ac peaks track_description version=2019;Original_cell_type=NeuN_optimal_peak_IDR_ENCODE.H3K27;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 18yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Parietal Cortex, Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology system_category Nervous life_stage Adult, Child track_name Nott_2019 Neuron Histone ChIP-seq H3K27ac peaks (bed3-lifted) [Life stage: Adult, Child] [Histone ChIP-seq peaks]
Astrocyte NGBEPELJZCPD6ZU6 • Nott 2019 ATAC-seq Astrocyte Accessible chromatin Show metadata identifier NGBEPELJZCPD6ZU6 data_source Nott_2019 Download track Download number_of_intervals 52,436 bp_covered 21,812,881 output_type accessible chromatin region genome_build hg38 cell_type Astrocyte biosample_type Tissue biosample_term_id CL:0000127 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody Not applicable assay ATAC-seq file_format bed bed3-lifted file_size 879,849 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz processed_file_md5 3114be2d4ea871dc1d150abfc9bf5cbb wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/ATAC/LHX2_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/ATAC/LHX2_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz raw_file_md5 5cc00f19995ccdb1bfd453840794abb6 data_category Accessible chromatin Genomic feature type ATAC-seq accessible chromatin region track_description version=2019;Original_cell_type=LHX2_optimal_peak_IDR_ENCODE.ATAC;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=12yo, 14yo, 4yo;sexes=M;ethnicities=Caucasian, HIs, His;brain_regions=Frontal Cortex, Temporal Cortex;pathologies_dx=Cystic encephalomalacia , Focal cortical dysplasi system_category Nervous life_stage Child track_name Nott_2019 Astrocyte ATAC-seq accessible chromatin region (bed3-lifted) [Life stage: Child] [Accessible chromatin]
H3K27ac • Astrocyte NGBEPELKO22X6KHC • Nott 2019 Super-enhancer Astrocyte Enhancer Show metadata identifier NGBEPELKO22X6KHC data_source Nott_2019 Download track Download number_of_intervals 460 bp_covered 40,754,317 output_type super-enhancer peaks genome_build hg38 cell_type Astrocyte biosample_type Tissue biosample_term_id CL:0000127 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Super-enhancer file_format bed bed6-lifted file_size 12,061 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_LHX2_superEnhancer_L1_lifted.bed.gz processed_file_md5 1ceed625460a0038575b3fb312a81b7d wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_LHX2_superEnhancer_L1_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_LHX2_superEnhancer_L1_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/Super_enhancers/LHX2_superEnhancer_L1.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/Super_enhancers/LHX2_superEnhancer_L1.gz raw_file_md5 8e0635a999a1fee313d4e48646a9dddc data_category Enhancer Genomic feature type H3K27ac super-enhancer peaks track_description version=2019;Original_cell_type=astrocyte;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 12yo, 4yo;sexes=M;ethnicities=HIs, His, Caucasian;brain_regions=Temporal Cortex, Frontal Cort system_category Nervous life_stage Child track_name Nott_2019 Astrocyte Super-enhancer H3K27ac-histone-mark super-enhancer peaks (bed6-lifted) [Life stage: Child] [Enhancer]
H3K27ac • Oligodendrocyte NGBEPELKVRL7TVOO • Nott 2019 Histone ChIP-seq Oligodendrocyte Histone Show metadata identifier NGBEPELKVRL7TVOO data_source Nott_2019 Download track Download number_of_intervals 73,122 bp_covered 106,184,364 output_type peaks genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Histone ChIP-seq file_format bed bed3-lifted file_size 1,220,856 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz processed_file_md5 e02c0ff47978f0df61e6b214f0d8c075 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K27/Olig2_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K27/Olig2_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz raw_file_md5 47dcef5d7d90621cea37887ec9b62bb8 data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K27ac peaks track_description version=2019;Original_cell_type=Olig2_optimal_peak_IDR_ENCODE.H3K27;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 18yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Parietal Cortex, Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative patholog system_category Nervous life_stage Adult, Child track_name Nott_2019 Oligodendrocyte Histone ChIP-seq H3K27ac peaks (bed3-lifted) [Life stage: Adult, Child] [Histone ChIP-seq peaks]
H3K27ac • Oligodendrocyte NGBEPELLKCUVYQSF • Nott 2019 Enhancer Oligodendrocyte Enhancer Show metadata identifier NGBEPELLKCUVYQSF data_source Nott_2019 Download track Download number_of_intervals 66,626 bp_covered 80,769,948 output_type enhancer peaks genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Enhancer file_format bed bed3-lifted file_size 1,103,602 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_Olig_enhancers_lifted.bed.gz processed_file_md5 f50a9bd858ae376d3c86439a26ea17bd wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_Olig_enhancers_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/formatted_output_Olig_enhancers_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Enhancer/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/enhancers/Olig2_enhancers.sorted.bigBed -P FILER2/Annotationtracks/Downloads/Nott_2019/enhancers/Olig2_enhancers.sorted.bigBed raw_file_md5 b8ac27702659800eef5ae21725412556 data_category Enhancer Genomic feature type H3K27ac enhancer peaks track_description version=2019;Original_cell_type=oligodendrocytes;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 4yo, 18yo;sexes=M;ethnicities=His, Caucasian;brain_regions=Parietal Cortex, Temporal C system_category Nervous life_stage Adult, Child track_name Nott_2019 Oligodendrocyte Enhancer H3K27ac-histone-mark enhancer peaks (bed3-lifted) [Life stage: Adult, Child] [Enhancer]
H3K4me3 • PU.1+ Microglia NGBEPELMB5KOIJ77 • Nott 2019 PLAC-seq PU.1+ Microglia Chromatin interactions Show metadata identifier NGBEPELMB5KOIJ77 data_source Nott_2019 Download track Download number_of_intervals 209,462 bp_covered 1,047,930,022 output_type chromatin interactions genome_build hg38 cell_type PU.1+ Microglia biosample_type Tissue biosample_term_id CL:0000129 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay PLAC-seq file_format bed bed4+19 interact file_size 5,078,905 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/05/2025 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Microglia_PLAC_seq_lifted.bed.gz processed_file_md5 62cba4990f7f7d222c810fbfe81d1d82 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Microglia_PLAC_seq_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Microglia_PLAC_seq_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/PLAC/Microglia.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed -P FILER2/Annotationtracks/Downloads/Nott_2019/PLAC/Microglia.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed raw_file_md5 1644aa6e30619631d51f3e32e3a04c45 data_category Chromatin interactions Genomic feature type PLAC-seq H3K4me3 chromatin interactions track_description version=2019;Original_cell_type=microglia;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;value_description=score/1000;ages=17yo, 5mo, 7yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Frontal Cortex, Parietal Cortex, Temporal Cortex;pathologies_dx=Anoxic ischemic encephalopathy , system_category Nervous life_stage Child track_name Nott_2019 PU.1+ Microglia PLAC-seq H3K4me3-histone-mark chromatin interactions (bed4+19 interact) [Life stage: Child] [Chromatin interactions]
H3K4me3 • Oligodendrocyte NGBEPELMCU66SP4A • Nott 2019 PLAC-seq Oligodendrocyte Chromatin interactions Show metadata identifier NGBEPELMCU66SP4A data_source Nott_2019 Download track Download number_of_intervals 123,720 bp_covered 619,509,026 output_type chromatin interactions genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay PLAC-seq file_format bed bed4+19 interact file_size 2,740,059 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/05/2025 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Olig_PLAC_seq_lifted.bed.gz processed_file_md5 3c1513aa325204df9aa3d7b62c0a13cb wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Olig_PLAC_seq_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_Olig_PLAC_seq_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/PLAC/Olig2.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed -P FILER2/Annotationtracks/Downloads/Nott_2019/PLAC/Olig2.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed raw_file_md5 6d3da0354f58d89182e2706ad0f8c734 data_category Chromatin interactions Genomic feature type PLAC-seq H3K4me3 chromatin interactions track_description version=2019;Original_cell_type=oligodendrocytes;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;value_description=score/1000;ages=14yo, 4yo, 6yo;sexes=F, M;ethnicities=Caucasian, His, Pacific Islander;brain_regions=Frontal Cortex, Temporal Cortex;pathologies_dx=Focal cortical dysplas system_category Nervous life_stage Child track_name Nott_2019 Oligodendrocyte PLAC-seq H3K4me3-histone-mark chromatin interactions (bed4+19 interact) [Life stage: Child] [Chromatin interactions]
Oligodendrocyte NGBEPELO5LCQ5SXA • Nott 2019 ATAC-seq Oligodendrocyte Accessible chromatin Show metadata identifier NGBEPELO5LCQ5SXA data_source Nott_2019 Download track Download number_of_intervals 38,476 bp_covered 21,024,569 output_type accessible chromatin region genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody Not applicable assay ATAC-seq file_format bed bed3-lifted file_size 655,864 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz processed_file_md5 6b2c4ffe6b3231aad4c075865a59f6ed wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/ATAC/Olig2_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/ATAC/Olig2_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz raw_file_md5 67c32af1e8a65fea0af9a2c4214f9d9a data_category Accessible chromatin Genomic feature type ATAC-seq accessible chromatin region track_description version=2019;Original_cell_type=Olig2_optimal_peak_IDR_ENCODE.ATAC;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology;dataSource_pubmed_id=3 system_category Nervous life_stage Child track_name Nott_2019 Oligodendrocyte ATAC-seq accessible chromatin region (bed3-lifted) [Life stage: Child] [Accessible chromatin]
H3K27ac • Astrocyte NGBEPELPRTGXPUEM • Nott 2019 Histone ChIP-seq Astrocyte Histone Show metadata identifier NGBEPELPRTGXPUEM data_source Nott_2019 Download track Download number_of_intervals 70,902 bp_covered 92,528,824 output_type peaks genome_build hg38 cell_type Astrocyte biosample_type Tissue biosample_term_id CL:0000127 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Histone ChIP-seq file_format bed bed3-lifted file_size 1,174,896 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz processed_file_md5 16d17f95ad4755e6b660faf3576c2946 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K27_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K27/LHX2_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K27/LHX2_optimal_peak_IDR_ENCODE.H3K27.sorted.bigBed.gz raw_file_md5 0176dc7dea4e18131e9b56a9c475050b data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K27ac peaks track_description version=2019;Original_cell_type=LHX2_optimal_peak_IDR_ENCODE.H3K27;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=12yo, 14yo, 4yo;sexes=M;ethnicities=Caucasian, HIs, His;brain_regions=Frontal Cortex, Temporal Cortex;pathologies_dx=Cystic encephalomalacia , Focal cortical dysplas system_category Nervous life_stage Child track_name Nott_2019 Astrocyte Histone ChIP-seq H3K27ac peaks (bed3-lifted) [Life stage: Child] [Histone ChIP-seq peaks]
H3K4me3 • Neuron NGBEPELPW2WHHWWJ • Nott 2019 PLAC-seq Neuron Chromatin interactions Show metadata identifier NGBEPELPW2WHHWWJ data_source Nott_2019 Download track Download number_of_intervals 186,454 bp_covered 932,689,358 output_type chromatin interactions genome_build hg38 cell_type Neuron biosample_type Tissue biosample_term_id CL:0000540 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay PLAC-seq file_format bed bed4+19 interact file_size 4,057,893 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/05/2025 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_NeuN_PLAC_seq_lifted.bed.gz processed_file_md5 9cdbbf6226ae92fa18c32d6d04b1c19a wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_NeuN_PLAC_seq_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/formatted_output_NeuN_PLAC_seq_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/PLAC-seq/bed4plus19_interact/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/PLAC/NeuN.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed -P FILER2/Annotationtracks/Downloads/Nott_2019/PLAC/NeuN.5k.2.peaks_interactions_ucsc_genome_browser.inter.bed raw_file_md5 44c933050983d29d3835459ceb4de1b7 data_category Chromatin interactions Genomic feature type PLAC-seq H3K4me3 chromatin interactions track_description version=2019;Original_cell_type=neurons;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;value_description=score/1000;ages=14yo, 4yo, 6yo, 8yo;sexes=F, M;ethnicities=Caucasian, His, Pacific Islander;brain_regions=Frontal Cortex, Temporal Cortex;pathologies_dx=Focal cortical dysplasia t system_category Nervous life_stage Child track_name Nott_2019 Neuron PLAC-seq H3K4me3-histone-mark chromatin interactions (bed4+19 interact) [Life stage: Child] [Chromatin interactions]
H3K4me3 • Oligodendrocyte NGBEPELQJ2SLIT4P • Nott 2019 Histone ChIP-seq Oligodendrocyte Histone Show metadata identifier NGBEPELQJ2SLIT4P data_source Nott_2019 Download track Download number_of_intervals 28,955 bp_covered 36,629,556 output_type peaks genome_build hg38 cell_type Oligodendrocyte biosample_type Tissue biosample_term_id CL:0000128 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay Histone ChIP-seq file_format bed bed3-lifted file_size 502,272 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz processed_file_md5 5ae5731610e1added5813376bec1b094 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_Olig2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K4me3/Olig2_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K4me3/Olig2_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz raw_file_md5 b8aef318b4f04272a76456c27c0a8a0c data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K4me3 peaks track_description version=2019;Original_cell_type=Olig2_optimal_peak_IDR_ENCODE.H3K4me3;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology;dataSource_pubmed_i system_category Nervous life_stage Child track_name Nott_2019 Oligodendrocyte Histone ChIP-seq H3K4me3 peaks (bed3-lifted) [Life stage: Child] [Histone ChIP-seq peaks]
H3K27ac • PU.1+ Microglia NGBEPELTEX7FTWNU • Nott 2019 Super-enhancer PU.1+ Microglia Enhancer Show metadata identifier NGBEPELTEX7FTWNU data_source Nott_2019 Download track Download number_of_intervals 627 bp_covered 36,383,399 output_type super-enhancer peaks genome_build hg38 cell_type PU.1+ Microglia biosample_type Tissue biosample_term_id CL:0000129 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K27ac assay Super-enhancer file_format bed bed6-lifted file_size 16,103 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_PU1_superEnhancer_L1_lifted.bed.gz processed_file_md5 b092169eb4fb0766f1ebd6df526a7726 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_PU1_superEnhancer_L1_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/formatted_output_PU1_superEnhancer_L1_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Super-enhancer/bed6-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/Super_enhancers/PU1_superEnhancer_L1.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/Super_enhancers/PU1_superEnhancer_L1.gz raw_file_md5 b7f0d422ddeea5e5a8b5df151d9f4e21 data_category Enhancer Genomic feature type H3K27ac super-enhancer peaks track_description version=2019;Original_cell_type=microglia;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;notes=Active enhancers were identified by H3K27ac peaks that were outside of H3K4me3 peaks;ages=14yo, 4yo, 18yo;sexes=M;ethnicities=His, Caucasian;brain_regions=Parietal Cortex, Temporal Cortex;p system_category Nervous life_stage Adult, Child track_name Nott_2019 PU.1+ Microglia Super-enhancer H3K27ac-histone-mark super-enhancer peaks (bed6-lifted) [Life stage: Adult, Child] [Enhancer]
H3K4me3 • Astrocyte NGBEPELUAKDKDCNE • Nott 2019 Histone ChIP-seq Astrocyte Histone Show metadata identifier NGBEPELUAKDKDCNE data_source Nott_2019 Download track Download number_of_intervals 19,254 bp_covered 24,973,448 output_type peaks genome_build hg38 cell_type Astrocyte biosample_type Tissue biosample_term_id CL:0000127 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody H3K4me3 assay Histone ChIP-seq file_format bed bed3-lifted file_size 337,937 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz processed_file_md5 72fcc04c69b24db1f1ccc0e5133334d5 wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/formatted_output_LHX2_optimal_peak_IDR_ENCODE.H3K4me3_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/Histone_ChIP-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/H3K4me3/LHX2_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/H3K4me3/LHX2_optimal_peak_IDR_ENCODE.H3K4me3.sorted.bigBed.gz raw_file_md5 79032d90285ecdf5b80ae979b50f42cb data_category Histone ChIP-seq peaks Genomic feature type Histone ChIP-seq H3K4me3 peaks track_description version=2019;Original_cell_type=LHX2_optimal_peak_IDR_ENCODE.H3K4me3;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology;dataSource_pubmed_id system_category Nervous life_stage Child track_name Nott_2019 Astrocyte Histone ChIP-seq H3K4me3 peaks (bed3-lifted) [Life stage: Child] [Histone ChIP-seq peaks]
PU.1+ Microglia NGBEPELVGBAZPWVJ • Nott 2019 ATAC-seq PU.1+ Microglia Accessible chromatin Show metadata identifier NGBEPELVGBAZPWVJ data_source Nott_2019 Download track Download number_of_intervals 50,199 bp_covered 26,339,987 output_type accessible chromatin region genome_build hg38 cell_type PU.1+ Microglia biosample_type Tissue biosample_term_id CL:0000129 tissue_category Brain encode_experiment_id Not applicable biological_replicate Not reported technical_replicate Not applicable antibody Not applicable assay ATAC-seq file_format bed bed3-lifted file_size 841,467 downloaded_date 10/02/2020 release_date 02/04/2020 date_added_to_filer 12/03/2024 processed_file_download_url https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz processed_file_md5 9fc7767d501a938f90c44caa25a2d68f wget_command wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ tabix_index_download wget https://filer2.niagads.org/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/formatted_output_PU1_optimal_peak_IDR_ENCODE.ATAC_lifted.bed.gz.tbi -P FILER2/Annotationtracks/hg38_lifted/Nott_2019/ATAC-seq/bed3-lifted/hg38/ link_out_url https://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ raw_file_url Not applicable raw_file_download wget https://filer2.niagads.org/Annotationtracks/Downloads/Nott_2019/ATAC/PU1_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz -P FILER2/Annotationtracks/Downloads/Nott_2019/ATAC/PU1_optimal_peak_IDR_ENCODE.ATAC.sorted.bigBed.gz raw_file_md5 3a37870a7e3568ebd976057707371bd2 data_category Accessible chromatin Genomic feature type ATAC-seq accessible chromatin region track_description version=2019;Original_cell_type=PU1_optimal_peak_IDR_ENCODE.ATAC;doi=https://doi.org/10.1126/science.aay0793;pubmed_id=31727856;ages=14yo, 4yo;sexes=M;ethnicities=Caucasian, His;brain_regions=Temporal Cortex;pathologies_dx=Focal cortical dysplasia type Ic, Negative pathology;dataSource_pubmed_id=317 system_category Nervous life_stage Child track_name Nott_2019 PU.1+ Microglia ATAC-seq accessible chromatin region (bed3-lifted) [Life stage: Child] [Accessible chromatin]