KDM2A and KDM2B cooperatively protect a subset of CpG Islands from DNA methylation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
- 15 samples: 6 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.
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 GSE180560_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 PRJNA748700. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 15 sample titles; they account for 12 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.
- GSM5464762 E14_RRBS_WT
- GSM5464763 E14_RRBS_KDM2A_KO_rep1 E14_RRBS_KDM2A_KO
- GSM5464764 E14_RRBS_KDM2A_KO_rep2 E14_RRBS_KDM2A_KO
- GSM5464765 E14_RRBS_KDM2B_KO_rep1 E14_RRBS_KDM2B_KO
- GSM5464766 E14_RRBS_KDM2B_KO_rep2 E14_RRBS_KDM2B_KO
- GSM5464767 E14_RRBS_KDM2A_2B_DKO_rep1 E14_RRBS_KDM2A_2B_DKO
- GSM5464768 E14_RRBS_KDM2A_2B_DKO_rep2 E14_RRBS_KDM2A_2B_DKO
- GSM5464769 E14_RRBS_KDM2A_2B_jmjcMUT_rep1 E14_RRBS_KDM2A_2B_jmjcM…
- GSM5464770 E14_RRBS_KDM2A_2B_jmjcMUT_rep2 E14_RRBS_KDM2A_2B_jmjcM…
- GSM5464771 E14_H3K36me2_input_ChIP_seq
- GSM5464772 E14_H3K36me2_WT_ChIP_seq
- GSM5464773 E14_H3K36me2_KDM2A_2B_DKO_rep1 E14_H3K36me2_KDM2A_2B_D…
- GSM5464774 E14_H3K36me2_KDM2A_2B_DKO_rep2 E14_H3K36me2_KDM2A_2B_D…
- GSM5464775 E14_H3K36me2_KDM2A_2B_jmjcMUT_rep1 E14_H3K36me2_KDM2A_2B_j…
- GSM5464776 E14_H3K36me2_KDM2A_2B_jmjcMUT_rep2 E14_H3K36me2_KDM2A_2B_j…
- GSE287032 H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation [ChIP-seq] 20 samples shares cooperatively, methylation
- GSE214682 The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice 56 samples shares kdm2a
- GSE230527 Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq] 18 samples shares kdm2a
- GSE242201 DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency 39 samples shares methylation
- GSE255961 Global Chromatin Remodeling and Widespread Differential Methylation Changes Underlie Brown Adipose Dysfunction and Dysregulated Metabolism in Response to Chronic Air Pollution Exposure: A Key Role for Reciprocal Regulation by HDAC9 and KDN2b 12 samples shares methylation
- GSE166226 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates 615 samples shares methylation
- 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 methylation
- GSE225173 Predicting age in single cells and low coverage DNA methylation data 250 samples shares methylation
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.