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Spatial Transcriptomic Profiling of Male Germ Cells from Control and Cbfb cKO mice

GSE244586 Mus musculus (mouse) RNA-seq (gene expression) 54 samples Submitted 2024/12/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 54 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
54 samples: 17 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.
Paper
Core binding factor subunit β plays diverse and essential roles in the male germlineFrontiers in cell and developmental biology · 2023
Summary (written by the submitters)
Much of the framework for spermatogenesis is established postnatally before sexual maturation. To evaluate the role of core-binding factor subunit β (CBFβ) in prepubertal male germline development, we generated male mice with conditional knockout of Cbfb using Blimp1-Cre (denoted Blimp1-Cbfb cKO). Outcomes from phenotype analysis revealed that Blimp1-Cbfb cKO males were completely infertile and experienced rapid germline degeneration prior to puberty.
Read the full summary ↓
To evaluate the pathways downstream of Cbfb that coincide with this degeneration, we conducted spatial transcriptomics of heterozygous control and Blimp1-Cbfb cKO testes at postnatal days 6 (P6) and 21 (P21) and used fluorescence immunostaining to identify and capture cell-type specific transcriptomic signatures. Collectively, our analysis revealed central roles of CBFβ in maintenance, differentiation, and cell cycle checkpoint regulation within the prepubertal male germline.
Published in
Core binding factor subunit β plays diverse and essential roles in the male germline
Rahmawati M, Stadler KM, Lopez-Biladeau B et al. · Frontiers in cell and developmental biology 2023 · PMID 38020932 · doi:10.3389/fcell.2023.1284184
This dataset
Open GSE244586 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 GSE244586_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 PRJNA1023629 and SRA study SRP464408. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38020932) ↗
Study design
17 conditions, mostly in triplicate
P21_LIN28A.negative_Diff Pheno ×4 P21_LIN28A.positive_Diff Pheno ×4 P6_LIN28A.positive_cko1 ×3 P6_LIN28A.positive_Het2 ×3 P6_LIN28A.positive_cko2 ×3 P6_LIN28A.positive_Het3 ×3 P6_LIN28A.positive_cko3 ×3 P6_LIN28A.positive_Het1 ×3 +10 more

Supports a between-group comparison across 53 samples.

How we read this: 17 replicated groups read from 54 sample titles; they account for 53 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

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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