Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 20 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.
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 GSE251642_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1054996 and SRA study SRP479145. 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 20 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
- GSM7984505 D4_NC_1 Cut & Tag
- GSM7984506 D4_NC_3 Cut & Tag
- GSM7984507 D4_oeDUX_1 Cut & Tag
- GSM7984508 D4_oeDUX_3 Cut & Tag
- GSM7984509 ipsc_1 Cut & Tag
- GSM7984510 ipsc_3 Cut & Tag
- GSM7984511 MEF_1 Cut & Tag
- GSM7984512 MEF_3 Cut & Tag
- GSE251640 Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader [RNA-Seq] 12 samples shares brg1, metabolism-lactylation-met, reprogramming, lactylation, promotes, cascaded, network, histone
- GSE306458 ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain {ChIP-seq] 12 samples shares reprogramming, lactylation, promotes, histone
- GSE291677 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina 38 samples shares lactylation, histone
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares reprogramming, promotes
- GSE115354 Metabolic regulation of gene expression by histone lactylation 38 samples shares lactylation, histone
- GSE279042 Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [CUT&Tag] 30 samples shares reprogramming, promotes
- GSE296797 CD38+CD93+ microglia and macrophages drive neuroinflammation through glycolysis-histone lactylation axis in multiple sclerosis model mice 17 samples shares lactylation, histone
- GSE307669 Succinate-GPR91 signaling promotes cardiomyocyte metabolic reprogramming and NAD⁺ production to alleviate HFpEF 16 samples shares reprogramming, promotes
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.