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Transcriptome data of hematopoietic stem cells of mice under ionizing radiation

GSE244971 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/06/05 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × Ctrl_HSC vs 3 × IR_HSC vs 3 × Ab_IR_HSC vs 3 × L_IR_HSCGroups 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.
Paper
Megakaryocytic IGF1 coordinates activation and ferroptosis to safeguard hematopoietic stem cell regeneration after radiation injuryCell communication and signaling : CCS · 2024
Summary (written by the submitters)
Analysis of hematopoietic stem cells (HSC, Lineage-Sca-1+c-Kit+Flt3–CD34–). In order to better experiment, we treated mice with total body irradiation and local irradiation respectively. Next, the HSC were purified from the bone marrow of 8 weeks WT mice (Ctrl), total body radiation mice (IR), irradiated legs of locally irradiated mice (L_IR) and the other leg which unirradiated of locally irradiated mice (Ab_IR). Results provide the injury effect of IR on HSC under different conditions.
Published in
Megakaryocytic IGF1 coordinates activation and ferroptosis to safeguard hematopoietic stem cell regeneration after radiation injury
Liao W, Chen X, Zhang S et al. · Cell communication and signaling : CCS 2024 · PMID 38802843 · doi:10.1186/s12964-024-01651-5
This dataset
Open GSE244971 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 GSE244971_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 PRJNA1026541 and SRA study SRP465454. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38802843) ↗
Study design
3 × Ctrl_HSC vs 3 × IR_HSC vs 3 × Ab_IR_HSC vs 3 × L_IR_HSC

Supports a between-group comparison across 12 samples.

How we read this: 4 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
Datasets on a similar topic

Search all mouse 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.