ASCL1 phospho-regulation during lineage restrictions of embryonic stem cells (RNA-Seq)
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × RNA, ESC, d3 NE, vs 3 × RNA, WT ASCL1 05, d3 NE, vs 3 × RNA, SA ASCL1 01, d3 NE, vs 3 × RNA, SA ASCL1 05, d3 NE,Groups 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
- Phospho-regulation of ASCL1-mediated chromatin opening during cellular reprogrammingDevelopment (Cambridge, England) · 2024
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 GSE267619_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 PRJNA1111941 and SRA study SRP507988. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8270259 RNA, ESC, d3 NE, rep1 RNA, ESC, d3 NE,
- GSM8270260 RNA, ESC, d3 NE, rep2 RNA, ESC, d3 NE,
- GSM8270261 RNA, ESC, d3 NE, rep3 RNA, ESC, d3 NE,
- GSM8270262 RNA, WT ASCL1 05, d3 NE, rep1 RNA, WT ASCL1 05, d3 NE,
- GSM8270263 RNA, WT ASCL1 05, d3 NE, rep2 RNA, WT ASCL1 05, d3 NE,
- GSM8270264 RNA, WT ASCL1 05, d3 NE, rep3 RNA, WT ASCL1 05, d3 NE,
- GSM8270265 RNA, SA ASCL1 01, d3 NE, rep1 RNA, SA ASCL1 01, d3 NE,
- GSM8270266 RNA, SA ASCL1 01, d3 NE, rep2 RNA, SA ASCL1 01, d3 NE,
- GSM8270267 RNA, SA ASCL1 01, d3 NE, rep3 RNA, SA ASCL1 01, d3 NE,
- GSM8270268 RNA, SA ASCL1 05, d3 NE, rep1 RNA, SA ASCL1 05, d3 NE,
- GSM8270269 RNA, SA ASCL1 05, d3 NE, rep2 RNA, SA ASCL1 05, d3 NE,
- GSM8270270 RNA, SA ASCL1 05, d3 NE, rep3 RNA, SA ASCL1 05, d3 NE,
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- GSE267432 Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells (RNA-Seq) 20 samples shares embryonic, rna-seq, stem
- GSE193082 Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [bulk RNA-Seq] 16 samples shares embryonic, rna-seq, stem
- GSE259215 Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [RNA-Seq] 12 samples shares embryonic, rna-seq, stem
- GSE232844 Effect of conditional triple-knockout of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c or overexpression of KDM4C/JMJD2C mutants with different phase separation ability on gene expression in mouse embryonic stem cells. [RNA-Seq] 10 samples shares embryonic, rna-seq, stem
- GSE202079 Short term perturbation of mouse embryonic stem cells with morphogens and small molecule compounds 208 samples shares embryonic, stem
- GSE285231 Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells 186 samples shares embryonic, stem
- GSE252199 Quantification of subcellular mRNA kinetics in mouse embryonic stem cells 100 samples shares embryonic, stem
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.