GEO series

Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis [RNA-Seq]

GSE341753 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/07/31 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 6 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)

During erythropoiesis, differentiating cells silence much of the genome while maintaining high expression of select genes. It remains unclear whether this transcriptional specialization is linked to specific changes in 3D genome organization. We generated deep Micro-C maps across human erythropoiesis to understand the relationship between cis-regulatory elements and cohesin-mediated loop extrusion during erythroid differentiation.

Read the full summary ↓

Shifts in erythroid 3D genome structure during differentiation and under perturbations of transcription factors and cohesin subunits/cofactors indicates that a subset of CREs concentrate loop extrusion near key genes during erythroid differentiation.

This dataset

Open GSE341753 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 GSE341753_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 PRJNA1503805 and SRA study SRP722300. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

AAVS1, RNA-Seq, Dono ×2 NFE2-KO, RNA-Seq, Dono ×2 STAG1-KO, RNA-Seq, Donor 3, Condition ×2 STAG2-KO, RNA-Seq, Donor 3, Condition ×2 NIPBL-KO, RNA-Seq, Donor 3, Condition ×2 AAVS1, RNA-Seq, Donor 3, Condition ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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

GSM9916473 AAVS1, RNA-Seq, Donor 1 AAVS1, RNA-Seq, Dono
GSM9916474 AAVS1, RNA-Seq, Donor 2 AAVS1, RNA-Seq, Dono
GSM9916475 NFE2-KO, RNA-Seq, Donor 1 NFE2-KO, RNA-Seq, Dono
GSM9916476 NFE2-KO, RNA-Seq, Donor 2 NFE2-KO, RNA-Seq, Dono
GSM9916477 STAG1-KO, RNA-Seq, Donor 3, Condition 1 STAG1-KO, RNA-Seq, Dono…
GSM9916478 STAG1-KO, RNA-Seq, Donor 3, Condition 2 STAG1-KO, RNA-Seq, Dono…
GSM9916479 STAG2-KO, RNA-Seq, Donor 3, Condition 1 STAG2-KO, RNA-Seq, Dono…
GSM9916480 STAG2-KO, RNA-Seq, Donor 3, Condition 2 STAG2-KO, RNA-Seq, Dono…
GSM9916481 NIPBL-KO, RNA-Seq, Donor 3, Condition 1 NIPBL-KO, RNA-Seq, Dono…
GSM9916482 NIPBL-KO, RNA-Seq, Donor 3, Condition 2 NIPBL-KO, RNA-Seq, Dono…
GSM9916483 AAVS1, RNA-Seq, Donor 3, Condition 1 AAVS1, RNA-Seq, Donor 3…
GSM9916484 AAVS1, RNA-Seq, Donor 3, Condition 2 AAVS1, RNA-Seq, Donor 3…

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