Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 60 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
- 60 samples: 16 conditions, mostly in triplicateGroups 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 GSE286968_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 PRJNA1210608. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 52 samples.
How we read this: 16 replicated groups read from 60 sample titles; they account for 52 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.
- GSM8734808 ATAC-seq of Mus musculus : young fresh HSCs, rep1 young fresh HSCs,
- GSM8734809 ATAC-seq of Mus musculus : young fresh HSCs, rep2 young fresh HSCs,
- GSM8734810 ATAC-seq of Mus musculus : young cultured HSCs, rep1 young cultured HSCs,
- GSM8734811 ATAC-seq of Mus musculus : young cultured HSCs, rep2 young cultured HSCs,
- GSM8734812 ATAC-seq of Mus musculus : old fresh HSCs, rep1 old fresh HSCs,
- GSM8734813 ATAC-seq of Mus musculus : old fresh HSCs, rep2 old fresh HSCs,
- GSM8734814 ATAC-seq of Mus musculus : old cultured HSCs, rep1 old cultured HSCs,
- GSM8734815 ATAC-seq of Mus musculus : old cultured HSCs, rep2 old cultured HSCs,
- GSM8734824 RNA-seq of Mus musculus : young fresh HSCs, rep1 young fresh HSCs,
- GSM8734825 RNA-seq of Mus musculus : young fresh HSCs, rep2 young fresh HSCs,
- GSM8734826 RNA-seq of Mus musculus : young cultured HSCs, rep1 young cultured HSCs,
- GSM8734827 RNA-seq of Mus musculus : young cultured HSCs, rep2 young cultured HSCs,
- GSM8734828 RNA-seq of Mus musculus : old fresh HSCs, rep1 old fresh HSCs,
- GSM8734829 RNA-seq of Mus musculus : old fresh HSCs, rep2 old fresh HSCs,
- GSM8734830 RNA-seq of Mus musculus : old cultured HSCs, rep1 old cultured HSCs,
- GSM8734831 RNA-seq of Mus musculus : old cultured HSCs, rep2 old cultured HSCs,
- GSM8734838 Young_Mock_ATAC-seq_rep1 Young_Mock_ATAC-seq
- GSM8734839 Young_Mock_ATAC-seq_rep2 Young_Mock_ATAC-seq
- GSM8734840 Young_Mock_ATAC-seq_rep3 Young_Mock_ATAC-seq
- GSM8734841 Young_Pbx1_ATAC-seq_rep1 Young_Pbx1_ATAC-seq
- GSM8734842 Young_Pbx1_ATAC-seq_rep2 Young_Pbx1_ATAC-seq
- GSM8734843 Young_Pbx1_ATAC-seq_rep3 Young_Pbx1_ATAC-seq
- GSM8734844 Old_Mock_ATAC-seq_rep1 Old_Mock_ATAC-seq
- GSM8734845 Old_Mock_ATAC-seq_rep2 Old_Mock_ATAC-seq
- GSM8734846 Old_Mock_ATAC-seq_rep3 Old_Mock_ATAC-seq
- GSM8734847 Old_Pbx1_ATAC-seq_rep1 Old_Pbx1_ATAC-seq
- GSM8734848 Old_Pbx1_ATAC-seq_rep2 Old_Pbx1_ATAC-seq
- GSM8734849 Old_Pbx1_ATAC-seq_rep3 Old_Pbx1_ATAC-seq
- GSM8734850 Young_Mock_CutTag_rep1 Young_Mock_CutTag
- GSM8734851 Young_Mock_CutTag_rep2 Young_Mock_CutTag
- GSM8734852 Young_Mock_CutTag_rep3 Young_Mock_CutTag
- GSM8734853 Young_Pbx1_CutTag_rep1 Young_Pbx1_CutTag
- GSM8734854 Young_Pbx1_CutTag_rep2 Young_Pbx1_CutTag
- GSM8734855 Young_Pbx1_CutTag_rep3 Young_Pbx1_CutTag
- GSM8734856 Old_Mock_CutTag_rep1 Old_Mock_CutTag
- GSM8734857 Old_Mock_CutTag_rep2 Old_Mock_CutTag
- GSM8734858 Old_Mock_CutTag_rep3 Old_Mock_CutTag
- GSM8734859 Old_Pbx1_CutTag_rep1 Old_Pbx1_CutTag
- GSM8734860 Old_Pbx1_CutTag_rep2 Old_Pbx1_CutTag
- GSM8734861 Old_Pbx1_CutTag_rep3 Old_Pbx1_CutTag
+ 20 more — browse all 60 samples with per-sample file links →
- GSE286957 Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [26hr RNA-seq] 8 samples shares pbx1, hematopoietic, identifies, learning, network, aging, deep, stem
- GSE284988 Epigenetic profiling of hematopoietic stem cells identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response 58 samples shares hematopoietic, identifies, aging, stem
- GSE229137 Autophagy engaging and non-engaging hematopoietic stem cells 607 samples shares hematopoietic, aging, stem
- GSE266509 A Bcl11a-driven mechanism maintaining hematopoietic stem cell functionality gives rise to dysfunction during aging [RNA-Seq] 52 samples shares hematopoietic, aging, stem
- GSE285109 Non-necroptotic MLKL function damages mitochondria and promotes hematopoietic stem cell aging [ATAC-seq] 12 samples shares hematopoietic, aging, stem
- GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic, stem
- GSE233879 Increased molecular and functional heterogeneity of hematopoietic stem cells contributes to age-related decline of tissue and body function 80 samples shares hematopoietic, stem
- GSE272913 Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres 66 samples shares hematopoietic, stem
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.