Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
- 22 samples: 8 conditions, mostly in triplicateGroups 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
- SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cellsGenome 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 GSE247620_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 PRJNA1039825 and SRA study SRP471598. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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.
- GSM7898067 WT_NPC_Hi-C_Rep1 WT_NPC_Hi-C
- GSM7898068 WT_NPC_Hi-C_Rep2 WT_NPC_Hi-C
- GSM7898069 WT_NPC_Hi-C_Rep3 WT_NPC_Hi-C
- GSM7898070 KO_NPC_Hi-C_Rep1 KO_NPC_Hi-C
- GSM7898071 KO_NPC_Hi-C_Rep2 KO_NPC_Hi-C
- GSM7898072 KO_NPC_Hi-C_Rep3 KO_NPC_Hi-C
- GSM7898073 WT_NPC_H3K9me3_Rep1 WT_NPC_H3K9me3
- GSM7898074 WT_NPC_H3K9me3_Rep2 WT_NPC_H3K9me3
- GSM7898075 WT_NPC_H3K9me3_Rep3 WT_NPC_H3K9me3
- GSM7898076 KO_NPC_H3K9me3_Rep1 KO_NPC_H3K9me3
- GSM7898077 KO_NPC_H3K9me3_Rep2 KO_NPC_H3K9me3
- GSM7898078 KO_NPC_H3K9me3_Rep3 KO_NPC_H3K9me3
- GSM7898079 WT_NPC_CTCF_Rep1 WT_NPC_CTCF
- GSM7898080 WT_NPC_CTCF_Rep2 WT_NPC_CTCF
- GSM7898081 WT_NPC_CTCF_Rep3 WT_NPC_CTCF
- GSM7898082 KO_NPC_CTCF_Rep1 KO_NPC_CTCF
- GSM7898083 KO_NPC_CTCF_Rep2 KO_NPC_CTCF
- GSM7898084 KO_NPC_CTCF_Rep3 KO_NPC_CTCF
- GSM7898085 WT_NPC_WGBS_Rep1 WT_NPC_WGBS
- GSM7898086 WT_NPC_WGBS_Rep2 WT_NPC_WGBS
- GSM7898087 KO_NPC_WGBS_Rep1 KO_NPC_WGBS
- GSM7898088 KO_NPC_WGBS_Rep2 KO_NPC_WGBS
- GSE297837 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment. 126 samples shares sine, retrotransposons
- GSE183403 METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity 98 samples shares sine, methyltransferase
- GSE297834 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [ChIP-seq] 72 samples shares sine, retrotransposons
- GSE214682 The histone H3 lysine 36 demethylase KDM2A/FBXL11 is essential for germ cell development in male mice 56 samples shares sine, histone
- GSE297833 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq] 54 samples shares sine, retrotransposons
- GSE341379 Distinct histone 3 lysine methylation states underlie tumor immune surveillance 50 samples shares sine, histone
- GSE242179 Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification 40 samples shares sine, histone
- GSE268687 The nBAF complex subunit CREST/SS18L1 regulates hippocampal memory processes via tyrosine 397 and histone acetyltransferase CBP 30 samples shares sine, histone
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.