ISWI chromatin remodeler SMARCA5 is essential for meiotic gene expression and male fertility in mammals
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: 5 conditions, mostly in duplicateGroups 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
- ISWI chromatin remodeler SMARCA5 is essential for meiotic gene expression and male fertility in mammalsbioRxiv : the preprint server for biology · 2024
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 GSE279216_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 PRJNA1171409 and SRA study SRP537744. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8564755 smarca5_scRNAseq smarca5_scRNAseq
- GSM8564756 atac_wt1 atac_wt
- GSM8564757 atac_wt2 atac_wt
- GSM8564758 atac_smarca5_ko1 atac_smarca5_ko
- GSM8564759 atac_smarca5_ko2 atac_smarca5_ko
- GSM8971034 smarca5_scRNAseq rep 2 smarca5_scRNAseq
- GSM8971035 atac_pachy_wt1 atac_pachy_wt
- GSM8971036 atac_pachy_wt2 atac_pachy_wt
- GSM8971037 atac_pachy_smarca5_ko1 atac_pachy_smarca5_ko
- GSM8971038 atac_pachy_smarca5_ko2 atac_pachy_smarca5_ko
- GSE273309 Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival 30 samples shares chromatin, remodeler
- GSE279810 Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8 18 samples shares chromatin, remodeler
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares chromatin, remodeler
- GSE274492 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Valid RNA-Seq] 200 samples shares chromatin, essential
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares chromatin, meiotic
- GSE280663 Targeting the chromatin remodeler BAZ2B mitigates liver aging and fibrosis 46 samples shares chromatin, remodeler
- GSE274493 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag] 46 samples shares chromatin, essential
- GSE295991 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice 32 samples shares chromatin, meiotic
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.