Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader [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 × MEF vs 3 × D4 vs 3 × D4_DUX vs 3 × iPSCGroups 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
- Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation readerNucleic acids research · 2024
Read the full summary ↓
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 GSE251640_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 PRJNA1055002 and SRA study SRP479154. 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.
- GSM7984493 MEF_1 MEF
- GSM7984494 MEF_2 MEF
- GSM7984495 MEF_3 MEF
- GSM7984496 D4_1 D4
- GSM7984497 D4_2 D4
- GSM7984498 D4_3 D4
- GSM7984499 D4_DUX_1 D4_DUX
- GSM7984500 D4_DUX_2 D4_DUX
- GSM7984501 D4_DUX_3 D4_DUX
- GSM7984502 iPSC_1 iPSC
- GSM7984503 iPSC_2 iPSC
- GSM7984504 iPSC_3 iPSC
- GSE306458 ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain {ChIP-seq] 12 samples shares reprogramming, lactylation, promotes, histone
- GSE307669 Succinate-GPR91 signaling promotes cardiomyocyte metabolic reprogramming and NAD⁺ production to alleviate HFpEF 16 samples shares reprogramming, promotes
- GSE291661 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_RNA-seq] 12 samples shares lactylation, histone
- GSE287483 Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic progenitor cells [RNA-Seq] 12 samples shares reprogramming, network
- GSE318448 Pharmacological elevation of lactate alleviates sepsis via histone lactylation-induced IL-10 production 10 samples shares lactylation, histone
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares reprogramming, promotes
- GSE291677 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina 38 samples shares lactylation, histone
- GSE115354 Metabolic regulation of gene expression by histone lactylation 38 samples shares lactylation, histone
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.