An atlas of in vivo transcribed enhancers in human primary cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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
- 21 samples
- 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 GSE40668_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 PRJNA174535 and SRA study SRP015454. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 21 more — browse all 21 samples with per-sample file links →
- GSE237429 Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture 19 samples shares primary, vivo
- GSE229047 RNA sequencing data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue 19 samples shares primary, vivo
- GSE314342 Genome-scale perturb-seq in primary human CD4+ T cells reveals genes regulating T cell programs and human immune traits. 577 samples shares primary
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares primary
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares primary
- GSE301516 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [ATAC] 12 samples shares primary
- GSE327424 Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells 86 samples shares primary
- GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares primary
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.