Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 30 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
- 30 samples: 15 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
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 GSE273309_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 PRJNA1141395 and SRA study SRP522801. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 15 replicated groups read from 30 sample titles; they account for 30 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
- GSM8425957 CUTTag_CHD4_P1_NGO_Chd4f/f_rep1 CUTTag_CHD4_P1_NGO_Chd4…
- GSM8425958 CUTTag_CHD4_P1_NGO_Chd4f/f_rep2 CUTTag_CHD4_P1_NGO_Chd4…
- GSM8425959 ATAC-seq_P1_NGO_Dctrl_rep1 ATAC-seq_P1_NGO_Dctrl
- GSM8425960 ATAC-seq_P1_NGO_Dctrl_rep2 ATAC-seq_P1_NGO_Dctrl
- GSM8425961 ATAC-seq_P1_NGO_DcKO_rep1 ATAC-seq_P1_NGO_DcKO
- GSM8425962 ATAC-seq_P1_NGO_DcKO_rep2 ATAC-seq_P1_NGO_DcKO
- GSM8425963 ATAC-seq_P3_male_Dctrl_rep1 ATAC-seq_P3_male_Dctrl
- GSM8425964 ATAC-seq_P3_male_Dctrl_rep2 ATAC-seq_P3_male_Dctrl
- GSM8425965 ATAC-seq_P3_male_DcKO_rep1 ATAC-seq_P3_male_DcKO
- GSM8425966 ATAC-seq_P3_male_DcKO_rep2 ATAC-seq_P3_male_DcKO
- 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
- 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
- GSE281122 INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (TT-seq) 16 samples shares chromatin, remodeler
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares maintenance
- GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares maintenance
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.