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Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq]

GSE285077 Homo sapiens (human) RNA-seq (gene expression) 76 samples Submitted 2026/03/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 76 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
76 samples: 34 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
Hypoxia-induced alternative splicing (AS) controls tumor progression and metastasis. The underlying mechanism specifying hypoxia-responsive AS needs to be determined. We demonstrate the role of nuclear speckle (speckle) nuclear domain (ND) and the long noncoding RNA, MALAT1, in hypoxia-responsive AS. Hypoxia-responsive genes position near speckles, the NDs that enhance splicing efficiency, and their differentially spliced exons harbor features that are characteristic of inefficiently spliced transcripts.
Read the full summary ↓
Speckle-resident MALAT1, induced in response to hypoxia, boosts hypoxia-responsive AS by regulating the binding of SR-family splicing factor1 (SRSF1) to pre-mRNAs of speckle-associated genes. Mechanistically, MALAT1 facilitates the recruitment of SRSF1 to elongating RNA pol II (RNAP II) by promoting the formation of phase-separated SRSF1 condensates that are preferentially recognized and recruited to pre-mRNA by RNAP II. Our results reveal that MALAT1 boosts hypoxia-induced AS of speckle-associated genes by establishing the threshold concentration of SRSF1 as condensates, thereby promoting RNAP II-mediated recruitment of SRSF1 to pre-mRNAs.
This dataset
Open GSE285077 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE285077_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1201150 and SRA study SRP553000. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
34 conditions, mostly in duplicate
MCF7 MALAT1KO normoxia ×5 MCF7 MALAT1KO hypoxia ×5 MCF7 Wildtype normoxia ×3 MCF7 Wildtype hypoxia ×3 MCF7 Scramble ASO normoxia ×2 MCF7 Scramble ASO hypoxia ×2 MCF7 MALAT1 ASO normoxia ×2 MCF7 MALAT1 ASO hypoxia ×2 +26 more

Supports a between-group comparison across 76 samples.

How we read this: 34 replicated groups read from 76 sample titles; they account for 76 of them. 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.

Samples in this study

+ 36 more — browse all 76 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.