Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 59 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 59 samples: 40 distinct titles, 10 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic lociCell genomics · 2025
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE286226_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1208702 and SRA study SRP554139. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 59 sample titles: 40 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8702781 HAP1,wild-type,ATAC
- GSM8702782 HAP1-KRAB, non-targeting control (NTC) sgRNA, ATAC-seq
- GSM8702783 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, ATAC-seq
- GSM8702784 HAP1-delta64, ATAC-seq
- GSM8702785 HAP1-delta17, ATAC-seq
- GSM8702816 CRISPRi, transcriptomes scRNA-seq, rep1
- GSM8702817 CRISPRko, transcriptomes scRNA-seq, rep1
- GSM8702818 CRISPRa, transcriptomes scRNA-seq, rep1
- GSM8702819 CRISPRi, transcriptomes scRNA-seq, rep2
- GSM8702820 CRISPRko, transcriptomes scRNA-seq, rep2
- GSM8702821 CRISPRa, transcriptomes scRNA-seq, rep2
- GSM8702822 CRISPRi, transcriptomes scRNA-seq,rep3
- GSM8702823 CRISPRko, transcriptomes scRNA-seq, rep3
- GSM8702824 CRISPRa, transcriptomes scRNA-seq, rep3
- GSM8702825 CRISPRi, sgRNA enrichment scRNA-seq, rep1
- GSM8702826 CRISPRa, sgRNA enrichment scRNA-seq, rep1
- GSM8702827 CRISPRko, sgRNA enrichment scRNA-seq, rep1
- GSM8702828 CRISPRi, sgRNA enrichment scRNA-seq, rep2
- GSM8702829 CRISPRa, sgRNA enrichment scRNA-seq, rep2
- GSM8702830 CRISPRko, sgRNA enrichment scRNA-seq, rep2
- GSM8702831 CRISPRi, sgRNA enrichment scRNA-seq, rep3
- GSM8702832 CRISPRa, sgRNA enrichment scRNA-seq, rep3
- GSM8702833 CRISPRko, sgRNA enrichment scRNA-seq, rep3
- GSM8707255 HAP1,wild-type, H3K27ac
- GSM8707256 HAP1,wild-type, H3K27me3
- GSM8707257 HAP1,wild-type, H3K4me1
- GSM8707258 HAP1,wild-type, H3K4me3
- GSM8707259 HAP1,wild-type, H3K9me3
- GSM8707260 HAP1,wild-type, H2AK119ub
- GSM8707261 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K27ac
- GSM8707262 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K27me3
- GSM8707263 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K4me1
- GSM8707264 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K4me3
- GSM8707265 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K9me3
- GSM8707266 HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H2AK119ub
- GSM8707267 HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K27ac
- GSM8707268 HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K27me3
- GSM8707269 HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K4me1
- GSM8707270 HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K4me3
- GSM8707271 HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K9me3
+ 19 more — browse all 59 samples with per-sample file links →
- GSE325670 Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects 140 samples shares regulatory, elements, genetic
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares regulatory, elements, genetic
- GSE236022 Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci 53 samples shares regulatory, loci
- GSE243526 Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling 40 samples shares regulatory, genetic
- GSE290054 H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq] 35 samples shares regulatory, elements
- GSE319266 Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition [hFOB BMD STING-seq] 24 samples shares regulatory, loci
- GSE295449 Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (non-diseased controls, bulkRNAseq) 22 samples shares regulatory, genetic
- GSE278245 Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers 21 samples shares regulatory, elements
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.