GEO series

A gene regulatory network of the endothelial-to-hematopoietic transition [RNA-seq]

GSE233056 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/06/30 Platform GPL13112

At a glance

RNA-seq (gene expression) · mouse · 28 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: Mus musculus (mouse)
Samples: 28 samples: 9 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)

In vertebrate embryos, hematopoietic stem cells (HSCs) are generated from a subset of the aortic endothelium, the hemogenic endothelium (HE), via a process called endothelial-to-hematopoietic transition (EHT). The transcriptional mechanisms by which EHT is controlled, and how HE initiates hematopoietic differentiation, are not fully understood. In this study, we generated mini-bulk RNA-seq and ATAC-seq datasets from EHT populations in the E8.5 to E10.5 mouse embryonic dorsal aorta, and integrated these data to construct a predictive gene regulatory network underlying EHT.

This dataset

Open GSE233056 in finder → Find more mouse 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 GSE233056_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 PRJNA974841 and SRA study SRP438835. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 conditions, mostly in triplicate

RNA, E8.5 HE, ×4 RNA, E10.5 EC, ×3 RNA, E10.5 HE, ×3 RNA, E10.5 pre-HSC I, ×3 RNA, E10.5 pre-HSC II, ×3 RNA, E8.5 EC, ×3 RNA, E9.5 EC, ×3 RNA, E9.5 HE, ×3 +1 more

Supports a between-group comparison across 28 samples.

How we read this: 9 replicated groups read from 28 sample titles; they account for 28 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

GSM7401026 RNA, E10.5 EC, rep 1 RNA, E10.5 EC,
GSM7401027 RNA, E10.5 EC, rep 2 RNA, E10.5 EC,
GSM7401028 RNA, E10.5 EC, rep 3 RNA, E10.5 EC,
GSM7401029 RNA, E10.5 HE, rep 1 RNA, E10.5 HE,
GSM7401030 RNA, E10.5 HE, rep 2 RNA, E10.5 HE,
GSM7401031 RNA, E10.5 HE, rep 3 RNA, E10.5 HE,
GSM7401032 RNA, E10.5 pre-HSC I, rep 1 RNA, E10.5 pre-HSC I,
GSM7401033 RNA, E10.5 pre-HSC I, rep 2 RNA, E10.5 pre-HSC I,
GSM7401034 RNA, E10.5 pre-HSC I, rep 3 RNA, E10.5 pre-HSC I,
GSM7401035 RNA, E10.5 pre-HSC II, rep 1 RNA, E10.5 pre-HSC II,
GSM7401036 RNA, E10.5 pre-HSC II, rep 2 RNA, E10.5 pre-HSC II,
GSM7401037 RNA, E10.5 pre-HSC II, rep 3 RNA, E10.5 pre-HSC II,
GSM7401038 RNA, E8.5 EC, rep 1 RNA, E8.5 EC,
GSM7401039 RNA, E8.5 EC, rep 2 RNA, E8.5 EC,
GSM7401040 RNA, E8.5 EC, rep 3 RNA, E8.5 EC,
GSM7401041 RNA, E8.5 HE, rep 1 RNA, E8.5 HE,
GSM7401042 RNA, E8.5 HE, rep 2 RNA, E8.5 HE,
GSM7401043 RNA, E8.5 HE, rep 3 RNA, E8.5 HE,
GSM7401044 RNA, E8.5 HE, rep 4 RNA, E8.5 HE,
GSM7401045 RNA, E9.5 EC, rep 1 RNA, E9.5 EC,
GSM7401046 RNA, E9.5 EC, rep 2 RNA, E9.5 EC,
GSM7401047 RNA, E9.5 EC, rep 3 RNA, E9.5 EC,
GSM7401048 RNA, E9.5 HE, rep 1 RNA, E9.5 HE,
GSM7401049 RNA, E9.5 HE, rep 2 RNA, E9.5 HE,
GSM7401050 RNA, E9.5 HE, rep 3 RNA, E9.5 HE,
GSM7401051 RNA, E9.5 pro-HSC/HPC, rep 1 RNA, E9.5 pro-HSC/HPC,
GSM7401052 RNA, E9.5 pro-HSC/HPC, rep 2 RNA, E9.5 pro-HSC/HPC,
GSM7401053 RNA, E9.5 pro-HSC/HPC, rep 3 RNA, E9.5 pro-HSC/HPC,

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