Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 84 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
- 84 samples: 84 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE244594_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 PRJNA1023837 and SRA study SRP464402. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 84 sample titles: 84 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.
- GSM7821164 KTBset_1_AAF
- GSM7821165 KTBset_2_AAF
- GSM7821166 KTBset4_nulliparous
- GSM7821167 KTBset5_Parous
- GSM7821192 Ashkenazi_NormalBreastSample_multiome_Pool1, scATAC-seq
- GSM7821193 KTB_pool-3-Ashkenazi_jew, scATAC-seq
- GSM7821194 KTB_pool-4-Ashkenazi_jew, scATAC-seq
- GSM7821195 KTBpool5_Ashkenazi_jew, scATAC-seq
- GSM7821196 KTBpool6_Ashkenazi_jew, scATAC-seq
- GSM7821197 Pool7_BRCA2Positive, scATAC-seq
- GSM7821198 Pool8_BRCA1Positive, scATAC-seq
- GSM7821199 KTBpool9-White American, scATAC-seq
- GSM7821200 KTBpool11-White American, scATAC-seq
- GSM7821201 KTBpool12-White American, scATAC-seq
- GSM7821202 KTBpool_13-Indigenous American, scATAC-seq
- GSM7821203 KTBpool_14-Indigenous American, scATAC-seq
- GSM7821204 KTBpool15_Asian, scATAC-seq
- GSM7821205 KTBpool17_Asian, scATAC-seq
- GSM7821206 C23_KTBpool-23_Hispanic, scATAC-seq
- GSM7821207 C25_KTBpool-25_Hispanic, scATAC-seq
- GSM7821208 Ashkenazi_NormalBreastSample_multiome_Pool1, scRNA-seq
- GSM7821209 KTB_pool-3-Ashkenazi_jew, scRNA-seq
- GSM7821210 KTB_pool-4-Ashkenazi_jew, scRNA-seq
- GSM7821211 KTBpool5_Ashkenazi_jew, scRNA-seq
- GSM7821212 KTBpool6_Ashkenazi_jew, scRNA-seq
- GSM7821213 Pool7_BRCA2Positive, scRNA-seq
- GSM7821214 Pool8_BRCA1Positive, scRNA-seq
- GSM7821215 KTBpool9-White American, scRNA-seq
- GSM7821216 KTBpool11-White American, scRNA-seq
- GSM7821217 KTBpool12-White American, scRNA-seq
- GSM7821218 KTBpool_13-Indigenous American, scRNA-seq
- GSM7821219 KTBpool_14-Indigenous American, scRNA-seq
- GSM7821220 KTBpool15_Asian, scRNA-seq
- GSM7821221 KTBpool17_Asian, scRNA-seq
- GSM7821222 C23_KTBpool-23_Hispanic, scRNA-seq
- GSM7821223 C25_KTBpool-25_Hispanic, scRNA-seq
- GSM7821465 K104334/K104973_ROI_1_well_A02
- GSM7821466 K104334/K104973_ROI_2_well_A03
- GSM7821467 K104334/K104973_ROI_3_well_A04
- GSM7821468 K104334/K104973_ROI_4_well_A05
+ 44 more — browse all 84 samples with per-sample file links →
- GSE244585 Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome] 32 samples shares accessibility, chromatin, ancestry, diverse, genetic, breast, women
- GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares accessibility, chromatin, genetic
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares accessibility, chromatin, breast
- GSE316391 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq] 32 samples shares accessibility, chromatin, breast
- GSE281526 Single-nuclei RNA-seq and ATAC-seq for Human Retina from Diverse Ancestry Backgrounds 185 samples shares ancestry, diverse
- GSE204912 Mapping genotypes to chromatin accessibility profiles in single cells 55 samples shares accessibility, chromatin
- GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares chromatin, genetic
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares accessibility, chromatin
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.