Enhancer-instructed chromatin folding and compartmentalization dictate Vκ repertoire rearrangement to combat bacterial infection [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 4 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
- 4 samples
- 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.
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 GSE193813_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 PRJNA798026 and SRA study SRP355441. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 4 more — browse all 4 samples with per-sample file links →
- GSE246986 Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement 24 samples shares rearrangement, chromatin
- GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares compartmentalization, chromatin
- GSE313431 CTCF-mediated chromatin topology enables receptor editing to enforce a central B-cell tolerance checkpoint [RNA-seq_IGK repertoire] 10 samples shares repertoire, chromatin
- GSE38377 Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (ChIP-seq) 115 samples shares repertoire
- GSE287935 CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [ChIP-Seq] 12 samples shares repertoire
- GSE38379 Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire 124 samples shares repertoire
- GSE98671 Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization 102 samples shares compartmentalization
- GSE318731 Deep Cellular and Spatial Profiling of the Mouse Spinal Cord Reveals Sex-Specific Neuron Types and the Ascending Projection Neuron Repertoire 72 samples shares repertoire
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.