GEO series

In Fanconi Anemia, impaired accumulation of bone marrow neutrophils during emergency granulopoiesis induces hematopoietic stem cell stress

GSE267161 Mus musculus (mouse) RNA-seq (gene expression) 38 samples Submitted 2024/08/28 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 38 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: 38 samples: 15 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.
Paper: In Fanconi anemia, impaired accumulation of bone marrow neutrophils during emergency granulopoiesis induces hematopoietic stem cell stressThe Journal of biological chemistry · 2024

Summary (written by the submitters)

Fanconi Anemia (FA) is an inherited disorder of DNA-repair caused by mutation in one of 20+ interrelated genes that repair intra-strand DNA crosslinks and rescue collapsed or stalled replication forks. The most common hematologic abnormality in FA is anemia, but progression to bone marrow failure (BMF), clonal hematopoiesis, or acute myeloid leukemia (AML) may also occur.

Read the full summary ↓

In prior studies, we found that Fanconi DNA-repair is required for successful emergency granulopoiesis; the process for rapid neutrophil production during the innate immune response. Specifically, Fancc-/- mice did not develop neutrophilia in response to emergency granulopoiesis stimuli, but instead exhibited apoptosis of bone marrow hematopoietic stem cells (HSCs) and differentiating neutrophils. Repeated emergency granulopoiesis challenges induced BMF in most Fancc-/- mice, with AML in survivors. In contrast, we found equivalent emergency granulopoiesis-induced neutrophilia in Fancc-/-Tp53+/- mice and wild type (WT) mice, without BMF in either. Since bone marrow neutrophil accumulation triggers termination of emergency granulopoiesis, we hypothesize neutrophilia protects Fancc-/-Tp53+/- bone marrow from the stress of sustained inflammatory physiology, as experienced by Fancc-/- mice.

Published in

In Fanconi anemia, impaired accumulation of bone marrow neutrophils during emergency granulopoiesis induces hematopoietic stem cell stress

Hu L, Huang W, Liu B et al. · The Journal of biological chemistry 2024 · PMID 38992437 · doi:10.1016/j.jbc.2024.107548

This dataset

Open GSE267161 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 GSE267161_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 PRJNA1109928 and SRA study SRP506893. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38992437) ↗

Study design

15 conditions, mostly in duplicate

Wt 2, 4 wks saline ×6 Wt 2 wks Alum ×3 FATp53 2, 4 wks saline ×3 Wt 2 wks Ly6G Alum ×3 FATp53 4 wks Ly6G Alum ×3 Wt 4 wks Alum ×2 FA 2, 4 wks saline ×2 FA 2 wks Alum ×2 +7 more

Supports a between-group comparison across 38 samples.

How we read this: 15 replicated groups read from 38 sample titles; they account for 38 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

GSM8261234 Wt 2, 4 wks saline rep 1 Wt 2, 4 wks saline
GSM8261235 Wt 2, 4 wks saline rep 2 Wt 2, 4 wks saline
GSM8261236 Wt 2, 4 wks saline rep 3 Wt 2, 4 wks saline
GSM8261237 Wt 2, 4 wks saline rep 4 Wt 2, 4 wks saline
GSM8261238 Wt 2, 4 wks saline rep 5 Wt 2, 4 wks saline
GSM8261239 Wt 2, 4 wks saline rep 6 Wt 2, 4 wks saline
GSM8261240 Wt 2 wks Alum rep 1 Wt 2 wks Alum
GSM8261241 Wt 2 wks Alum rep 2 Wt 2 wks Alum
GSM8261242 Wt 2 wks Alum rep 3 Wt 2 wks Alum
GSM8261243 Wt 4 wks Alum rep 1 Wt 4 wks Alum
GSM8261244 Wt 4 wks Alum rep 2 Wt 4 wks Alum
GSM8261245 FA 2, 4 wks saline rep 1 FA 2, 4 wks saline
GSM8261246 FA 2, 4 wks saline rep 2 FA 2, 4 wks saline
GSM8261247 FA 2 wks Alum rep 1 FA 2 wks Alum
GSM8261248 FA 2 wks Alum rep 2 FA 2 wks Alum
GSM8261249 FA 4 wks Alum rep 1 FA 4 wks Alum
GSM8261250 FA 4 wks Alum rep 2 FA 4 wks Alum
GSM8261251 FATp53 2, 4 wks saline rep 1 FATp53 2, 4 wks saline
GSM8261252 FATp53 2, 4 wks saline rep 2 FATp53 2, 4 wks saline
GSM8261253 FATp53 2, 4 wks saline rep 3 FATp53 2, 4 wks saline
GSM8261254 FATp53 2 wks Alum rep 1 FATp53 2 wks Alum
GSM8261255 FATp53 2 wks Alum rep 2 FATp53 2 wks Alum
GSM8261256 FATp53 4 wks Alum rep 1 FATp53 4 wks Alum
GSM8261257 FATp53 4 wks Alum rep 2 FATp53 4 wks Alum
GSM8261258 Wt 2 wks Ly6G Alum rep 1 Wt 2 wks Ly6G Alum
GSM8261259 Wt 2 wks Ly6G Alum rep 2 Wt 2 wks Ly6G Alum
GSM8261260 Wt 2 wks Ly6G Alum rep 3 Wt 2 wks Ly6G Alum
GSM8261261 Wt 4wks Ly6G Alum rep 1 Wt 4wks Ly6G Alum
GSM8261262 Wt 4wks Ly6G Alum rep 2 Wt 4wks Ly6G Alum
GSM8261263 FA 2 wks Ly6G Alum rep 1 FA 2 wks Ly6G Alum
GSM8261264 FA 2 wks Ly6G Alum rep 2 FA 2 wks Ly6G Alum
GSM8261265 FA 4 wks Ly6G Alum rep 1 FA 4 wks Ly6G Alum
GSM8261266 FA 4 wks Ly6G Alum rep 2 FA 4 wks Ly6G Alum
GSM8261267 FATp53 2 wks Ly6G Alum rep 1 FATp53 2 wks Ly6G Alum
GSM8261268 FATp53 2 wks Ly6G Alum rep 2 FATp53 2 wks Ly6G Alum
GSM8261269 FATp53 4 wks Ly6G Alum rep 1 FATp53 4 wks Ly6G Alum
GSM8261270 FATp53 4 wks Ly6G Alum rep 2 FATp53 4 wks Ly6G Alum
GSM8261271 FATp53 4 wks Ly6G Alum rep 3 FATp53 4 wks Ly6G Alum

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