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Bone marrow derived macrophage response to CSF1R stimulation or starvation after deletion of Ptpn6 or Rraga

GSE312715 Mus musculus (mouse) RNA-seq (gene expression) 27 samples Submitted 2026/03/26 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 27 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
27 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)
A genome-wide CRISPR screen in primary mouse bone marrow derived macrophages identified Rraga and Ptpn6 as important regulators of cell death upon CSF-1 starvation. To explore how Rraga and Ptpn6 deletion influence cellular state after CSF-1 stimulation or during growth factor starvation, CRISPR-edited BMDMs were harvested at different timepoints after addition of CSF-1, which is required to maintain cellular survival in these cultures.
Read the full summary ↓
RNA-seq and differential expression analyses were conducted to illuminate differential pro-survival mechanisms in cultures lacking Ptpn6 or Rraga, respectively.
This dataset
Open GSE312715 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 GSE312715_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 PRJNA1375773 and SRA study SRP651805. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
Control 24 hrs ×3 Rraga KO 24 hrs ×3 Ptpn6 KO 24 hrs ×3 Control 4 hrs ×3 Rraga KO 4 hrs ×3 Ptpn6 KO 4 hrs ×3 Control 48 hrs ×3 Rraga KO 48 hrs ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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

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