Acute multi-level response to defective de novo chromatin assembly in S-phase
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 72 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
- Homo sapiens (human)
- Samples
- 72 samples: 50 distinct titles, 12 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
- Acute multi-level response to defective de novo chromatin assembly in S-phasebioRxiv : the preprint server for biology · 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 GSE262518_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 PRJNA1092098 and SRA study SRP497950. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 24 samples read as cases, 29 as controls.
How we read this: Read from 72 sample titles: 50 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.
- GSM8170823 repli-ATAC replicate 1 Nascent chromatin DMSO
- GSM8170824 repli-ATAC replicate 1 Nascent chromatin dTAG
- GSM8170825 repli-ATAC replicate 1 Mature 2h chromatin DMSO
- GSM8170826 repli-ATAC replicate 1 Mature 2h chromatin dTAG
- GSM8170827 repli-ATAC replicate 2 Nascent chromatin DMSO
- GSM8170828 repli-ATAC replicate 2 Nascent chromatin dTAG
- GSM8170829 repli-ATAC replicate 2 Mature 2h chromatin DMSO
- GSM8170830 repli-ATAC replicate 2 Mature 2h chromatin dTAG
- GSM8170831 repli-ATAC replicate 3 Nascent chromatin DMSO
- GSM8170832 repli-ATAC replicate 3 Nascent chromatin dTAG
- GSM8170833 repli-ATAC replicate 3 Mature 2h chromatin DMSO
- GSM8170834 repli-ATAC replicate 3 Mature 2h chromatin dTAG
- GSM8170835 repli-ATAC replicate 3 Mature 15h chromatin DMSO
- GSM8170836 repli-ATAC replicate 3 Mature 15h chromatin dTAG
- GSM8170837 repli-ATAC replicate 3 Post-replication chromatin DMSO 1
- GSM8170838 repli-ATAC replicate 3 Post-replication chromatin dTAG 1
- GSM8170839 repli-ATAC replicate 3 Post-replication chromatin DMSO 2
- GSM8170840 repli-ATAC replicate 3 Post-replication chromatin dTAG 2
- GSM8170841 repli-ATAC replicate 3 Nascent chromatin Unbound DMSO
- GSM8170842 repli-ATAC replicate 3 Nascent chromatin Unbound dTAG
- GSM8170843 repli-ATAC EdU Input CTRL replicate 1 Nascent chromatin DMSO
- GSM8170844 repli-ATAC EdU Input CTRL replicate 1 Nascent chromatin dTAG
- GSM8170845 repli-ATAC EdU Input CTRL replicate 1 Mature chromatin DMSO
- GSM8170846 repli-ATAC EdU Input CTRL replicate 1 Mature chromatin dTAG
- GSM8170847 repli-ATAC EdU Input CTRL replicate 2 Nascent chromatin DMSO
- GSM8170848 repli-ATAC EdU Input CTRL replicate 2 Nascent chromatin dTAG
- GSM8170849 repli-ATAC EdU Input CTRL replicate 2 Mature chromatin DMSO
- GSM8170850 repli-ATAC EdU Input CTRL replicate 2 Mature chromatin dTAG
- GSM8170851 repli-ATAC EdU Input CTRL replicate 3 Nascent chromatin DMSO
- GSM8170852 repli-ATAC EdU Input CTRL replicate 3 Nascent chromatin dTAG
- GSM8170853 repli-ATAC EdU Input CTRL replicate 3 Mature chromatin DMSO
- GSM8170854 repli-ATAC EdU Input CTRL replicate 3 Mature chromatin dTAG
- GSM8170855 ATAC-seq DMSO
- GSM8170856 ATAC-seq dTAG
- GSM8170857 10min dTAG treated RPE1 double pulse scEdU-seq plate 1
- GSM8170858 10min dTAG treated RPE1 double pulse scEdU-seq plate 2
- GSM8170859 10min dTAG treated RPE1 double pulse scEdU-seq plate 3
- GSM8170860 10min dTAG treated RPE1 double pulse scEdU-seq plate 4
- GSM8170861 2hr dTAG treated RPE1 double pulse scEdU-seq plate 1
- GSM8170862 2hr dTAG treated RPE1 double pulse scEdU-seq plate 2
+ 32 more — browse all 72 samples with per-sample file links →
- GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares chromatin, acute
- GSE342612 Transcriptomic and H3K27ac chromatin responses of human microglia to acute PFOS exposure and recovery 36 samples shares chromatin, acute
- GSE243299 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia 112 samples shares chromatin, acute
- GSE243298 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C] 35 samples shares chromatin, acute
- GSE301370 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [Micro-C human] 12 samples shares chromatin, acute
- GSE249492 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response 280 samples shares chromatin
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
- GSE280618 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment 34 samples shares chromatin
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.