GEO series

TATA-binding Associated Factors have distinct roles during early mammalian development

GSE264153 Mus musculus (mouse) RNA-seq (gene expression) 57 samples Submitted 2025/04/05 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 57 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: 57 samples: 14 conditions, mostly with about 4 replicates eachGroups 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)

Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes.

Read the full summary ↓

Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.

This dataset

Open GSE264153 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 GSE264153_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 PRJNA1101065 and SRA study SRP502100. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 conditions, mostly with about 4 replicates each

Taf13 HET, E6.5, ×9 Taf12 WT, E3.5, ×5 Taf12 HET, E3.5, ×5 Taf5 MUT, E3.5, ×4 Taf12 WT, OG, ×4 Taf12 MUT, OG, ×4 Taf13 WT, E3.5, ×4 Taf13 HET, E3.5, ×4 +6 more

Supports a between-group comparison across 57 samples.

How we read this: 14 replicated groups read from 57 sample titles; they account for 57 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

GSM8212988 Taf5 WT, E3.5, 1 Taf5 WT, E3.5,
GSM8212989 Taf5 WT, E3.5, 2 Taf5 WT, E3.5,
GSM8212990 Taf5 WT, E3.5, 3 Taf5 WT, E3.5,
GSM8212991 Taf5 MUT, E3.5, 1 Taf5 MUT, E3.5,
GSM8212992 Taf5 MUT, E3.5, 2 Taf5 MUT, E3.5,
GSM8212993 Taf5 MUT, E3.5, 3 Taf5 MUT, E3.5,
GSM8212994 Taf5 MUT, E3.5, 4 Taf5 MUT, E3.5,
GSM8212995 Taf12 WT, E3.5, 1 Taf12 WT, E3.5,
GSM8212996 Taf12 WT, E3.5, 2 Taf12 WT, E3.5,
GSM8212997 Taf12 WT, E3.5, 3 Taf12 WT, E3.5,
GSM8212998 Taf12 WT, E3.5, 4 Taf12 WT, E3.5,
GSM8212999 Taf12 WT, E3.5, 5 Taf12 WT, E3.5,
GSM8213000 Taf12 HET, E3.5, 1 Taf12 HET, E3.5,
GSM8213001 Taf12 HET, E3.5, 2 Taf12 HET, E3.5,
GSM8213002 Taf12 HET, E3.5, 3 Taf12 HET, E3.5,
GSM8213003 Taf12 HET, E3.5, 4 Taf12 HET, E3.5,
GSM8213004 Taf12 HET, E3.5, 5 Taf12 HET, E3.5,
GSM8213005 Taf12 MUT, E3.5, 1 Taf12 MUT, E3.5,
GSM8213006 Taf12 MUT, E3.5, 2 Taf12 MUT, E3.5,
GSM8213007 Taf12 MUT, E3.5, 3 Taf12 MUT, E3.5,
GSM8213008 Taf12 WT, OG, 1 Taf12 WT, OG,
GSM8213009 Taf12 WT, OG, 2 Taf12 WT, OG,
GSM8213010 Taf12 WT, OG, 3 Taf12 WT, OG,
GSM8213011 Taf12 WT, OG, 4 Taf12 WT, OG,
GSM8213012 Taf12 HET, OG, 1 Taf12 HET, OG,
GSM8213013 Taf12 HET, OG, 2 Taf12 HET, OG,
GSM8213014 Taf12 HET, OG, 3 Taf12 HET, OG,
GSM8213015 Taf12 MUT, OG, 1 Taf12 MUT, OG,
GSM8213016 Taf12 MUT, OG, 2 Taf12 MUT, OG,
GSM8213017 Taf12 MUT, OG, 3 Taf12 MUT, OG,
GSM8213018 Taf12 MUT, OG, 4 Taf12 MUT, OG,
GSM8213019 Taf13 WT, E3.5, 1 Taf13 WT, E3.5,
GSM8213020 Taf13 WT, E3.5, 2 Taf13 WT, E3.5,
GSM8213021 Taf13 WT, E3.5, 3 Taf13 WT, E3.5,
GSM8213022 Taf13 WT, E3.5, 4 Taf13 WT, E3.5,
GSM8213023 Taf13 HET, E3.5, 1 Taf13 HET, E3.5,
GSM8213024 Taf13 HET, E3.5, 2 Taf13 HET, E3.5,
GSM8213025 Taf13 HET, E3.5, 3 Taf13 HET, E3.5,
GSM8213026 Taf13 HET, E3.5, 4 Taf13 HET, E3.5,
GSM8213027 Taf13 MUT, E3.5, 1 Taf13 MUT, E3.5,

+ 17 more — browse all 57 samples with per-sample file links →

Datasets on a similar topic

GSE277835 TUT1 and USB1, the biogenesis enzymes for 2′,3′-cyclic phosphate modification at U6 snRNA 3’ end, have distinct roles in mammalian development [RNA-seq] 17 samples shares mammalian, distinct
GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares factors
GSE300734 Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis [RNA-seq] 25 samples shares factors
GSE292224 Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk RNA-seq] 190 samples shares distinct
GSE296365 Prenatal stress induces transient developmental alterations in distinct GABAergic populations and leads to long-lasting behavioral abnormalities 16 samples shares distinct
GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares distinct
GSE283086 Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis [RNA-seq] 15 samples shares distinct
GSE273440 A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies [scRNA-seq] 13 samples shares distinct

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.