yHSC AThi oHSC ATlo oHSC ATAC-Seq - Differences in Chromatin Accessibility in Autophagy engaging vs non-autophagy engaging old hematopoeitic stem cells (HSC) comapred to young HSC.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 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
- 11 samples: 7 distinct titles, 1 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
- Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cellsCell stem cell · 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 GSE230275_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 PRJNA958178 and SRA study SRP433759. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 11 sample titles: 7 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.
- GSM7211173 Young_1
- GSM7211174 Young_2
- GSM7211175 Young_3
- GSM7211176 Young_4
- GSM7211177 Young_5
- GSM7211178 O1 AThi
- GSM7211179 O1 ATlo
- GSM7211180 O2 AThi
- GSM7211181 O2 ATlo
- GSM7211182 O3 AThi
- GSM7211183 O3 ATlo
- GSE246700 Regulatory T cells in the Tumor Microenvironment Display a Unique Chromatin Accessibility Profile (ATAC-Seq) 140 samples shares accessibility, chromatin, atac-seq
- GSE242799 Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq] 40 samples shares accessibility, chromatin, atac-seq
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares accessibility, chromatin, atac-seq
- GSE289298 OTX2 controls chromatin accessibility to direct somatic versus germline differentiation [ATAC-Seq] 32 samples shares accessibility, chromatin, atac-seq
- GSE278048 KLF13 promotes SLE Pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes [ATAC-seq] 28 samples shares accessibility, chromatin, atac-seq
- GSE240782 Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner [ATAC-Seq] 25 samples shares accessibility, chromatin, atac-seq
- GSE249077 Mapping the female mouse chromatin accessibility landscape by UUATAC-seq 23 samples shares accessibility, chromatin, atac-seq
- GSE280169 Impact of Early Bisphenol A Exposure on Transcriptome and Chromatin Accessibility in Brain Oligodendrocytes of Juvenile Mice [ATAC-seq] 19 samples shares accessibility, chromatin, atac-seq
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.