Somatic mutations reveal the ontogeny of microglia in human aging
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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
- 36 samples: 20 × UW vs 2 × RA2_BMGroups 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 GSE338521_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 PRJNA1494616 and SRA study SRP717695. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 2 replicated groups read from 36 sample titles; they account for 22 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.
- GSM9875058 UW1 UW
- GSM9875060 UW2 UW
- GSM9875061 UW3 UW
- GSM9875062 UW4_v2
- GSM9875063 UW5 UW
- GSM9875064 UW6_v2
- GSM9875065 UW6_Ce
- GSM9875066 UW6_Pu
- GSM9875067 UW7 UW
- GSM9875068 UW8 UW
- GSM9875070 UW9 UW
- GSM9875071 UW9_Pu
- GSM9875072 UW10 UW
- GSM9875073 UW11 UW
- GSM9875074 UW12 UW
- GSM9875075 UW13 UW
- GSM9875076 UW14 UW
- GSM9875077 UW15 UW
- GSM9875078 UW15_Pu
- GSM9875080 UW16_v2
- GSM9875081 UW16_Ce
- GSM9875082 UW16_Pu
- GSM9875083 UW17 UW
- GSM9875084 UW18 UW
- GSM9875085 UW19 UW
- GSM9875086 UW20 UW
- GSM9875087 UW21 UW
- GSM9875088 UW22 UW
- GSM9875089 UW23 UW
- GSM9876299 RA1_Ce
- GSM9876300 RA1_Co
- GSM9876301 RA1_Pu
- GSM9876302 RA2_BM_1 RA2_BM
- GSM9876303 RA2_BM_2 RA2_BM
- GSM9876304 RA2_Ce
- GSM9876305 RA2_PFC
- GSE338484 Somatic mutations reveal the ontogeny of microglia in human aging [snATAC-seq] 29 samples shares mutations, microglia, ontogeny, somatic, aging
- GSE301458 Single-cell analysis of human fibrous dysplasia bone reveals a fibrotic transcriptome and somatic, mosaic GNAS R201H/C mutations in endothelial, perivascular, and stromal cells 12 samples shares mutations, somatic
- GSE254205 APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia 102 samples shares microglia, aging
- GSE292700 Molecular architecture of the tumor microenvironment caused by BRCA1 and BRCA2 somatic mutations in human lung adenocarcinoma 12 samples shares mutations, somatic
- GSE271384 The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [ATAC-seq] 20 samples shares microglia
- GSE314930 Cohesin mutations suppress HLA class II gene expression to promote immune evasion during the progression to acute leukemia in children with Down syndrome [CUT&Run] 72 samples shares mutations
- GSE278642 Growth signaling promotes H2A.Z deposition by SRCAP to sustain somatic tissue regeneration [ChIP-Seq] 30 samples shares somatic
- GSE226482 Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations 1415 samples shares mutations
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.