Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [eCLIP-seq]
RNA-seq (gene expression) · human · 24 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
- 24 samples: 24 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.
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 GSE285088_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 PRJNA1201161 and SRA study SRP553051. 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 24 sample titles: 24 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.
- GSM8696282 MCF7 Scramble ASO normoxia rep1 [eCLIP-seq]
- GSM8696283 MCF7 Scramble ASO normoxia rep2 [eCLIP-seq]
- GSM8696284 MCF7 Scramble ASO hypoxia rep1 [eCLIP-seq]
- GSM8696285 MCF7 Scramble ASO hypoxia rep2 [eCLIP-seq]
- GSM8696286 MCF7 MALAT1 ASO normoxia rep1 [eCLIP-seq]
- GSM8696287 MCF7 MALAT1 ASO normoxia rep2 [eCLIP-seq]
- GSM8696288 MCF7 MALAT1 ASO hypoxia rep1 [eCLIP-seq]
- GSM8696289 MCF7 MALAT1 ASO hypoxia rep2 [eCLIP-seq]
- GSM8696290 MCF7 Scramble ASO normoxia input [eCLIP-seq]
- GSM8696291 MCF7 Scramble ASO hypoxia input [eCLIP-seq]
- GSM8696292 MCF7 MALAT1 ASO normoxia input [eCLIP-seq]
- GSM8696293 MCF7 MALAT1 ASO hypoxia input [eCLIP-seq]
- GSM8696294 HEK293T Scramble ASO normoxia rep1 [eCLIP-seq]
- GSM8696295 HEK293T Scramble ASO normoxia rep2 [eCLIP-seq]
- GSM8696296 HEK293T Scramble ASO hypoxia rep1 [eCLIP-seq]
- GSM8696297 HEK293T Scramble ASO hypoxia rep2 [eCLIP-seq]
- GSM8696298 HEK293T MALAT1 ASO normoxia rep1 [eCLIP-seq]
- GSM8696299 HEK293T MALAT1 ASO normoxia rep2 [eCLIP-seq]
- GSM8696300 HEK293T MALAT1 ASO hypoxia rep1 [eCLIP-seq]
- GSM8696301 HEK293T MALAT1 ASO hypoxia rep2 [eCLIP-seq]
- GSM8696302 HEK293T Scramble ASO normoxia input [eCLIP-seq]
- GSM8696303 HEK293T Scramble ASO hypoxia input [eCLIP-seq]
- GSM8696304 HEK293T MALAT1 ASO normoxia input [eCLIP-seq]
- GSM8696305 HEK293T MALAT1 ASO hypoxia input [eCLIP-seq]
- GSE285077 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq] 76 samples shares chromatin-associated, lncrna-splicing, pre-positioned, condensates, responsive, processing, regulate
- GSE276836 ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity 30 samples shares condensates, regulate
- GSE271854 AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (ChIP-Seq) 23 samples shares condensates, regulate
- GSE276835 ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity (ChIP) 18 samples shares condensates, regulate
- GSE300421 RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [ChIP-Seq] 14 samples shares chromatin-associated, condensates
- GSE276834 ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity (RNA) 12 samples shares condensates, regulate
- GSE263501 ZMAT2 condensates regulate the alternative splicing of TRIM28 to promote the proliferation of hepatocellular carcinoma cells 9 samples shares condensates, regulate
- GSE292850 Treacle’s ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair 3 samples shares condensates, processing
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.