Cohesin loss eliminates all loop domains [PRO-Seq]
RNA-seq (gene expression) · human · 16 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 16 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.
Read the full summary ↓
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 GSE106886_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA418323 and SRA study SRP124968. 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.
+ 16 more — browse all 16 samples with per-sample file links →
- GSE104334 Cohesin loss eliminates all loop domains 132 samples shares eliminates, cohesin, domains, loss, loop
- GSE104888 Cohesin loss eliminates all loop domains [ChIP-Seq] 39 samples shares eliminates, cohesin, domains, loss, loop
- GSE102884 Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL and PDS5 proteins 30 samples shares cohesin, domains, loop
- GSE315529 RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [ChIP-seq] 10 samples shares cohesin, loss, loop
- GSE246944 RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [RNA-Seq] 12 samples shares cohesin, loop
- GSE319745 DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (RNA-seq) 10 samples shares domains, loss
- GSE288172 Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages 263 samples shares cohesin, loop
- GSE218803 Characterization of induced cohesin loop extrusion trajectories in living cells 179 samples shares cohesin, loop
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.