Investigate the functions of core pluripotency transcription factors in embryonic stem cells
RNA-seq (gene expression) · mouse · 30 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
- 30 samples: 10 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
- Loss of sex-determining region Y-box 2 (Sox2) captures embryonic stem cells in a primed pluripotent stateThe Journal of biological chemistry · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE270036_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1124896 and SRA study SRP514324. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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.
- GSM8333116 SXFF_1 SXFF
- GSM8333117 SXFF_2 SXFF
- GSM8333118 SXFF_3 SXFF
- GSM8333119 SXKO_1 SXKO
- GSM8333120 SXKO_2 SXKO
- GSM8333121 SXKO_3 SXKO
- GSM8333122 SX2FF_1 SX2FF
- GSM8333123 SX2FF_2 SX2FF
- GSM8333124 SX2FF_3 SX2FF
- GSM8333125 SX2FFCRE_1 SX2FFCRE
- GSM8333126 SX2FFCRE_2 SX2FFCRE
- GSM8333127 SX2FFCRE_3 SX2FFCRE
- GSM8333128 SX13KO_1 SX13KO
- GSM8333129 SX13KO_2 SX13KO
- GSM8333130 SX13KO_3 SX13KO
- GSM8333131 SX123_1 SX123
- GSM8333132 SX123_2 SX123
- GSM8333133 SX123_3 SX123
- GSM8333134 OtFF_1 OtFF
- GSM8333135 OtFF_2 OtFF
- GSM8333136 OtFF_3 OtFF
- GSM8333137 OtKO_1 OtKO
- GSM8333138 OtKO_2 OtKO
- GSM8333139 OtKO_3 OtKO
- GSM8333140 NGFF_1 NGFF
- GSM8333141 NGFF_2 NGFF
- GSM8333142 NGFF_3 NGFF
- GSM8333143 NGKO_1 NGKO
- GSM8333144 NGKO_2 NGKO
- GSM8333145 NGKO_3 NGKO
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription, embryonic, stem
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factors
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, factors
- GSE243165 Signal-responsive transcription factors cooperate to establish alveolar macrophage identity 42 samples shares transcription, factors
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription, factors
- GSE281941 Klf5 functions as a multi-lineage reprogramming transcription factor 30 samples shares transcription, functions
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.