Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 284 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
- 284 samples: 69 conditions, mostly in duplicateGroups 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
- Nucleotide depletion promotes cell fate transitions by inducing DNA replication stressDevelopmental cell · 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 GSE172335_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 PRJNA722984 and SRA study SRP391122. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 198 samples.
How we read this: 69 replicated groups read from 284 sample titles; they account for 198 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.
- GSM5252045 63.3_DMSO_H3K4me1 63.3_DMSO_H3K4me
- GSM5252046 63.3_DMSO_H3K4me3 63.3_DMSO_H3K4me
- GSM5252048 63.3_DMSO_IgG
- GSM5252049 63.3_BRQ_H3K4me1 63.3_BRQ_H3K4me
- GSM5252050 63.3_BRQ_H3K4me3 63.3_BRQ_H3K4me
- GSM5252052 63.3_BRQ_IgG
- GSM5252053 THP_DMSO_PU1
- GSM5252054 THP_BRQ_24h_PU1
- GSM5252055 THP_BRQ_48h_PU1
- GSM5252056 THP_PMA_24h_PU1
- GSM5252057 THP_PMA_48h_PU1
- GSM5252058 THP_DMSO_H3K27ac
- GSM5252059 THP_BRQ_24h_H3K27ac
- GSM5252060 THP_BRQ_48h_H3K27ac
- GSM5252061 THP_PMA_24h_H3K27ac
- GSM5252062 THP_PMA_48h_H3K27ac
- GSM5252068 THP_DMSO_IgG
- GSM5252080 THP1_DMSO_rep1_ATACseq
- GSM5252081 THP1_DMSO_rep2_ATACseq
- GSM5252082 THP1_BRQ24_rep1_ATACseq
- GSM5252083 THP1_BRQ24_rep2_ATACseq
- GSM5252084 THP1_BRQ48_rep1_ATACseq
- GSM5252085 THP1_BRQ48_rep2_ATACseq
- GSM5252086 THP1_PMA24_rep1_ATACseq
- GSM5252087 THP1_PMA24_rep2_ATACseq
- GSM5252088 THP1_PMA48_rep1_ATACseq
- GSM5252089 THP1_PMA48_rep2_ATACseq
- GSM5252090 633_BRQ0_rep1_ATACseq
- GSM5252091 633_BRQ0_rep2_ATACseq
- GSM5252092 633_BRQ4_rep1_ATACseq
- GSM5252093 633_BRQ4_rep2_ATACseq
- GSM5252094 633_BRQ8_rep1_ATACseq
- GSM5252095 633_BRQ8_rep2_ATACseq
- GSM5252096 633_BRQ12_rep1_ATACseq
- GSM5252097 633_BRQ12_rep2_ATACseq
- GSM5252098 633_BRQ24_rep1_ATACseq
- GSM5252099 633_BRQ24_rep2_ATACseq
- GSM5252100 633_BRQ36_rep1_ATACseq
- GSM5252101 633_BRQ36_rep2_ATACseq
- GSM5252102 633_BRQ48_rep1_ATACseq
+ 244 more — browse all 284 samples with per-sample file links →
- GSE172296 A myeloid maturation program initiated by nucleotide depletion during S phase [Cut & Run] 47 samples shares nucleotide, depletion
- GSE287896 G-quadruplex DNA suppresses transcription during DNA replication 80 samples shares replication
- GSE55486 Defective Mitophagy in XPA via PARP1 activation and NAD+/SIRT1-depletion: Implications for neurodegeneration 28 samples shares depletion
- GSE219284 Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia 24 samples shares nucleotide
- GSE287972 BRAF/MEK Inhibition Induces Cell State Transitions Boosting Immune Checkpoint Sensitivity in BRAFV600E-mutant Glioma 15 samples shares transitions
- GSE273027 Germline TET2 variants contribute to the pathogenesis of kidney disease through impaired DNA damage repair and the activation of cytosolic nucleotide sensors 6 samples shares nucleotide
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.