Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Epi-microRNA mediated metabolic reprogramming counteracts hypoxia to preserve affinity maturationNature communications · 2024
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 GSE230527_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 PRJNA961712 and SRA study SRP434407. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM7226214 WT_H3K36me2_replicate 1_Male
- GSM7226215 WT_H3K36me2_replicate 2_Female
- GSM7226216 WT_H3K36me2_replicate 3_Female
- GSM7226217 KO_H3K36me2_replicate 1_Male
- GSM7226218 KO_H3K36me2_replicate 2_Female
- GSM7226219 KO_H3K36me2_replicate 3_Female
- GSM7226220 WT_Kdm2a_replicate 1_Male
- GSM7226221 WT_Kdm2a_replicate 2_Female
- GSM7226222 WT_Kdm2a_replicate 3_Female
- GSM7226223 KO_Kdm2a_replicate 1_Male
- GSM7226224 KO_Kdm2a_replicate 2_Female
- GSM7226225 KO_Kdm2a_replicate 3_Female
- GSM7226226 WT_input_replicate 1_Male
- GSM7226227 WT_input_replicate 2_Female
- GSM7226228 WT_input_replicate 3_Female
- GSM7226229 KO_input_replicate 1_Male
- GSM7226230 KO_input_replicate 2_Female
- GSM7226231 KO_input_replicate 3_Female
- GSE273314 Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [ChIP-Seq] 159 samples shares h3k36me2, chip-seq
- GSE214679 The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice [ChIP-Seq] 24 samples shares kdm2a, chip-seq
- GSE180559 KDM2A and KDM2B cooperatively protect a subset of CpG Islands from DNA methylation [ChIP-seq] 6 samples shares kdm2a, chip-seq
- GSE231649 Analysis of transcriptomes of germinal center (GC) B cells derived from miR-155-sufficient and -deficient mice 10 samples shares mir-155-sufficient, deficient
- GSE230528 Analysis of transcriptomes of germinal center (GC) B cells derived from miR-155-sufficient and -deficient mice at the single-cell level [scRNA-seq] 6 samples shares mir-155-sufficient, deficient
- GSE333948 Genomic H3K36me2 enrichment profile for Vehicle or dimethyl fumarate-treated mouse bone marrow-derived neutrophil 8 samples shares h3k36me2
- GSE273316 Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [RNA-Seq] 68 samples shares h3k36me2
- GSE214682 The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice 56 samples shares kdm2a
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.