Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival [RNA-seq]
RNA-seq (gene expression) · mouse · 20 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 20 samples: 10 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
- Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survivalbioRxiv : 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 GSE273306_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1141405 and SRA study SRP522808. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM8425937 RNA-seq_P1_NGO_Dctrl_rep1 RNA-seq_P1_NGO_Dctrl
- GSM8425938 RNA-seq_P1_NGO_Dctrl_rep2 RNA-seq_P1_NGO_Dctrl
- GSM8425939 RNA-seq_P1_NGO_DcKO_rep1 RNA-seq_P1_NGO_DcKO
- GSM8425940 RNA-seq_P1_NGO_DcKO_rep2 RNA-seq_P1_NGO_DcKO
- GSM8425941 RNA-seq_P5_NGO_Dctrl_rep1 RNA-seq_P5_NGO_Dctrl
- GSM8425942 RNA-seq_P5_NGO_Dctrl_rep2 RNA-seq_P5_NGO_Dctrl
- GSM8425943 RNA-seq_P5_NGO_DcKO_rep1 RNA-seq_P5_NGO_DcKO
- GSM8425944 RNA-seq_P5_NGO_DcKO_rep2 RNA-seq_P5_NGO_DcKO
- GSM8425945 RNA-seq_P10_NGO_Gctrl_rep1 RNA-seq_P10_NGO_Gctrl
- GSM8425946 RNA-seq_P10_NGO_Gctrl_rep2 RNA-seq_P10_NGO_Gctrl
- GSM8425947 RNA-seq_P10_NGO_GcKO_rep1 RNA-seq_P10_NGO_GcKO
- GSM8425948 RNA-seq_P10_NGO_GcKO_rep2 RNA-seq_P10_NGO_GcKO
- GSM8425949 RNA-seq_P10_GO_Gctrl_rep1 RNA-seq_P10_GO_Gctrl
- GSM8425950 RNA-seq_P10_GO_Gctrl_rep2 RNA-seq_P10_GO_Gctrl
- GSM8425951 RNA-seq_P10_GO_GcKO_rep1 RNA-seq_P10_GO_GcKO
- GSM8425952 RNA-seq_P10_GO_GcKO_rep2 RNA-seq_P10_GO_GcKO
- GSM8425953 RNA-seq_P3_male_Dctrl_rep1 RNA-seq_P3_male_Dctrl
- GSM8425954 RNA-seq_P3_male_Dctrl_rep2 RNA-seq_P3_male_Dctrl
- GSM8425955 RNA-seq_P3_male_DcKO_rep1 RNA-seq_P3_male_DcKO
- GSM8425956 RNA-seq_P3_male_DcKO_rep2 RNA-seq_P3_male_DcKO
- GSE273309 Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival 30 samples shares chd4, establishes, maintenance, chromatin, remodeler, formation, required, survival
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares chromatin, remodeler
- GSE280663 Targeting the chromatin remodeler BAZ2B mitigates liver aging and fibrosis 46 samples shares chromatin, remodeler
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares maintenance, chromatin
- GSE241262 Histone marks enable formation of immiscible phase-separated chromatin compartments 35 samples shares chromatin, formation
- GSE279810 Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8 18 samples shares chromatin, remodeler
- GSE281122 INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (TT-seq) 16 samples shares chromatin, remodeler
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares 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.