Identification of Chromatin proteins involved in gene repression in lamina-associated domains
RNA-seq (gene expression) · human · 22 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
- 22 samples: 17 distinct titles, 3 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.
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 GSE261955_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 PRJNA1089617 and SRA study SRP496223. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 22 sample titles: 17 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.
- GSM8153279 LB2 pA-DamID, clone SC9, parental, replicate 1, dam only
- GSM8153280 LB2 pA-DamID, clone SC9, parental, replicate 1, dam-LB2
- GSM8153281 LB2 pA-DamID, clone SC9, parental, replicate 2, dam only
- GSM8153282 LB2 pA-DamID, clone SC9, parental, replicate 2, dam-LB2
- GSM8155087 RNASEQ, clone SC9, pLB187, replicate 1
- GSM8155088 RNASEQ, clone SC9, pLB187, replicate 2
- GSM8155089 RNASEQ, clone SC9, pLB187, replicate 3
- GSM8155090 RNASEQ, clone SC9, NELFE, replicate 1
- GSM8155091 RNASEQ, clone SC9, NELFE, replicate 2
- GSM8155092 RNASEQ, clone SC9, NELFE, replicate 3
- GSM8155093 RNASEQ, clone SC9, NELFB, replicate 1
- GSM8155094 RNASEQ, clone SC9, NELFB, replicate 2
- GSM8378907 LB2 pA-DamID,HCT116, replicate 1, dam-LB2
- GSM8378908 LB2 pA-DamID,HCT116, replicate 1, dam-only
- GSM8378909 LB2 pA-DamID,HCT116, replicate 2, dam-LB2
- GSM8378910 LB2 pA-DamID,HCT116, replicate 2, dam-only
- GSM8378911 LB2 pA-DamID,HCT116, replicate 3, dam-LB2
- GSM8378912 LB2 pA-DamID,HCT116, replicate 3, dam-only
- GSM8378913 LB2 pA-DamID,HeLa, replicate 1, dam only
- GSM8378914 LB2 pA-DamID,HeLa, replicate 1, dam-LB2
- GSM8378915 LB2 pA-DamID,HeLa, replicate 2, dam only
- GSM8378916 LB2 pA-DamID,HeLa, replicate 2, dam-LB2
- GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares lamina-associated, chromatin
- GSE254244 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes 112 samples shares repression, chromatin
- GSE291751 Profling of breast cancer cells using single-cell triomics analysis of DNA, RNA, and proteins with Tapestri chemistry 24 samples shares proteins
- GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares chromatin
- GSE328578 CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL 156 samples shares chromatin
- GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares chromatin
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
- GSE296192 Hypoxic regulation of chromatin and gene transcription 98 samples shares 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.