Microglia and Fn14 regulate transcription and chromatin accessibility in developing neurons
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 2 × Fn14 KO ATACseq vs 2 × Fn14 WT ATACseq vs 2 × PLX ATACseq vs 2 × PLX Control ATACseqGroups 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 GSE186632_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 PRJNA774832 and SRA study SRP343286. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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.
- GSM5658019 dLGN - Fn14 WT and KO multiplexed
- GSM5658020 dLGN - TWEAK WT and KO multiplexed
- GSM5658021 Fn14 KO ATACseq rep1 Fn14 KO ATACseq
- GSM5658022 Fn14 KO ATACseq rep2 Fn14 KO ATACseq
- GSM5658023 Fn14 WT ATACseq rep1 Fn14 WT ATACseq
- GSM5658024 Fn14 WT ATACseq rep2 Fn14 WT ATACseq
- GSM5658025 PLX ATACseq rep1 PLX ATACseq
- GSM5658026 PLX ATACseq rep2 PLX ATACseq
- GSM5658027 PLX Control ATACseq rep1 PLX Control ATACseq
- GSM5658028 PLX Control ATACseq rep2 PLX Control ATACseq
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares transcription, chromatin, regulate
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares transcription, chromatin, regulate
- GSE274040 Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer 16 samples shares transcription, accessibility, chromatin
- GSE281122 INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (TT-seq) 16 samples shares transcription, chromatin, regulate
- GSE263530 Chromatin site specific accessibility: a microtopography regulated door into the stem cell fate [Hi-C] 3 samples shares accessibility, chromatin, regulate
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares accessibility, chromatin
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription, chromatin
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares transcription, 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.