GEO series

RNA-seq analysis of WT, SREBP knockout and SREBP2 knockout HeLa cells and liver samples of WT and SREBP2 (F167A) knockin mice

GSE267018 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2025/03/16 Platform GPL24676Platform GPL24247

At a glance

RNA-seq (gene expression) · human · 30 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: 30 samples: 10 conditions, mostly in triplicateGroups 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)

The transcription factor SREBP2, plays a specific and non-redundant role in cholesterol metabolism, autophagy of lipid droplets and apoptosis regulation. Under cholesterol-depletion condition, nuclear SREBP2 (nSREBP2) is released after proteolytic cleavage, enters nucleus and activates cholesterogenic genes expression.

Read the full summary ↓

Here, we report that the nSREBP2 forms discrete nuclear condensates through its N-terminal intrinsically disordered region (IDR) and works together with transcription coactivators BRD4 and p300, partly on super-enhancers, for the transcriptional activation of SREBP2 target genes. The substitution of a critical and conserved phenylalanine (F) to alanine (A) within the IDR abolished the formation of nSREBP2 condensates. Conversely, the condensate formation and efficient transcription activation were rescued by fusion with a phase separation driving FUS-IDR. Knock-in of the F to A substitution in mice compromised the feeding-induced nSREBP2 activity and lowered the cholesterol levels. Furthermore, a SNP of SREBF2 in humans leading to single amino acid change, P183S, showed less nuclear condensate formation and lower transcriptional activity, underscoring the physiological relevance of nSREBP2 condensates. Together, this study reveals that nuclear condensates driven by the N terminal IDR of nSREBP2 facilitate the efficient activation of lipogenic genes and play an important role in cholesterol homeostasis.

This dataset

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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 GSE267018_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 PRJNA1109350 and SRA study SRP506497. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 conditions, mostly in triplicate

Hela WT-FBS ×3 Hela WT-Chol-Dep ×3 Hela SREBP2 KO-FBS ×3 Hela SREBP2 KO-Chol-Dep ×3 Hela SREBP1 KO-FBS ×3 Hela SREBP1 KO-Chol-Dep ×3 WT-F ×3 WT-R ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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

GSM8258543 Hela WT-FBS-rep 1 Hela WT-FBS
GSM8258544 Hela WT-FBS-rep 2 Hela WT-FBS
GSM8258545 Hela WT-FBS-rep 3 Hela WT-FBS
GSM8258546 Hela WT-Chol-Dep-rep 1 Hela WT-Chol-Dep
GSM8258547 Hela WT-Chol-Dep-rep 2 Hela WT-Chol-Dep
GSM8258548 Hela WT-Chol-Dep-rep 3 Hela WT-Chol-Dep
GSM8258549 Hela SREBP2 KO-FBS-rep 1 Hela SREBP2 KO-FBS
GSM8258550 Hela SREBP2 KO-FBS-rep 2 Hela SREBP2 KO-FBS
GSM8258551 Hela SREBP2 KO-FBS-rep 3 Hela SREBP2 KO-FBS
GSM8258552 Hela SREBP2 KO-Chol-Dep-rep 1 Hela SREBP2 KO-Chol-Dep
GSM8258553 Hela SREBP2 KO-Chol-Dep-rep 2 Hela SREBP2 KO-Chol-Dep
GSM8258554 Hela SREBP2 KO-Chol-Dep-rep 3 Hela SREBP2 KO-Chol-Dep
GSM8258555 Hela SREBP1 KO-FBS-rep 1 Hela SREBP1 KO-FBS
GSM8258556 Hela SREBP1 KO-FBS-rep 2 Hela SREBP1 KO-FBS
GSM8258557 Hela SREBP1 KO-FBS-rep 3 Hela SREBP1 KO-FBS
GSM8258558 Hela SREBP1 KO-Chol-Dep-rep 1 Hela SREBP1 KO-Chol-Dep
GSM8258559 Hela SREBP1 KO-Chol-Dep-rep 2 Hela SREBP1 KO-Chol-Dep
GSM8258560 Hela SREBP1 KO-Chol-Dep-rep 3 Hela SREBP1 KO-Chol-Dep
GSM8258561 WT-F-rep 1 WT-F
GSM8258562 WT-F-rep 2 WT-F
GSM8258563 WT-F-rep 3 WT-F
GSM8258564 WT-R-rep 1 WT-R
GSM8258565 WT-R-rep 2 WT-R
GSM8258566 WT-R-rep 3 WT-R
GSM8258567 F167A-F-rep 1 F167A-F
GSM8258568 F167A-F-rep 2 F167A-F
GSM8258569 F167A-F-rep 3 F167A-F
GSM8258570 F167A-R-rep 1 F167A-R
GSM8258571 F167A-R-rep 2 F167A-R
GSM8258572 F167A-R-rep 3 F167A-R

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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.