Altering metabolism to program cell identity via NAD+ dependent deacetylation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 141 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
- 141 samples: 101 distinct titles, 27 of them repeatedGroups 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
- Altering metabolism programs cell identity via NAD(+)-dependent deacetylationThe EMBO journal · 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 GSE173543_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 PRJNA726042 and SRA study SRP316790. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 141 sample titles: 101 distinct titles with little repetition. 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.
- GSM5269362 Serum_LIF_rep1 (RNA-seq)
- GSM5269363 Serum_LIF_rep2 (RNA-seq)
- GSM5269364 Serum_LIF_rep3 (RNA-seq)
- GSM5269365 EMM_3h_rep1 (RNA-seq)
- GSM5269366 EMM_3h_rep2 (RNA-seq)
- GSM5269367 EMM_3h_rep3 (RNA-seq)
- GSM5269368 EMM_9h_rep1 (RNA-seq)
- GSM5269369 EMM_9h_rep2 (RNA-seq)
- GSM5269370 EMM_9h_rep3 (RNA-seq)
- GSM5269371 EMM_24h_rep1 (RNA-seq)
- GSM5269372 EMM_24h_rep2 (RNA-seq)
- GSM5269373 EMM_24h_rep3 (RNA-seq)
- GSM5269467 Serum_LIF_rep1 (ATAC-seq)
- GSM5269468 Serum_LIF_rep2 (ATAC-seq)
- GSM5269469 EMM_3h_rep1 (ATAC-seq)
- GSM5269470 EMM_3h_rep2 (ATAC-seq)
- GSM5269471 EMM_9h_rep1 (ATAC-seq)
- GSM5269472 EMM_9h_rep2 (ATAC-seq)
- GSM5269473 EMM_24h_rep1 (ATAC-seq)
- GSM5269474 EMM_24h_rep2 (ATAC-seq)
- GSM7999712 Sox2_EMM_GLCp18
- GSM7999713 Sox2_SL_GLCp18
- GSM7999714 Sox2_EMMplusNAM_GLCp18
- GSM7999715 Sox2_SL_Jup20
- GSM7999716 Sox2_EMM_Jup20
- GSM7999717 Sox2_EMMplusNAM_Jup20
- GSM7999718 Sox2_SL_Jup24
- GSM7999719 Sox2_EMM_Jup24
- GSM7999720 Sox2_EMMplusNAM_Jup24
- GSM7999721 Klf4_SL_GLCp18
- GSM7999722 Klf4_EMM_GLCp18
- GSM7999723 Klf4_EMMplusNAM_GLCp18
- GSM7999724 Klf4_SL_Jup20
- GSM7999725 Klf4_EMM_Jup20
- GSM7999726 Klf4_EMMplusNAM_Jup20
- GSM7999727 Klf4_SL_Jup24
- GSM7999728 Klf4_EMM_Jup24
- GSM7999729 Klf4_EMMplusNAM_Jup24
- GSM7999730 IgG_SL_GLCp18_Sox2Klf4
- GSM7999731 IgG_EMMplusNAM_GLCp18_Sox2Klf4
+ 101 more — browse all 141 samples with per-sample file links →
- GSE307669 Succinate-GPR91 signaling promotes cardiomyocyte metabolic reprogramming and NAD⁺ production to alleviate HFpEF 16 samples shares nad, program
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares dependent, program
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares dependent, program
- GSE337304 Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming 64 samples shares dependent, program
- GSE255061 Phosphatase-independent activity of smooth-muscle calcineurin orchestrates a gene expression program leading to arterial hypertension 40 samples shares dependent, program
- GSE247845 FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [RNA-Seq] 20 samples shares dependent, program
- GSE318707 ST8Sia6-dependent glycosylation restrains gut inflammation and pathogenic Th1 and Th17 programs 18 samples shares dependent, program
- GSE330309 Impact of Sex Chromosomes and Gonad Type in Stress Susceptibility in Corticostriatal Brain Regions 96 samples shares nad
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.