RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 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
- 34 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
- Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcriptionGenome research · 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 GSE156297_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 PRJNA657281 and SRA study SRP277563. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 10 replicated groups read from 34 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.
- GSM4728466 Control whole cell extract replicate 1 Control whole cell extr…
- GSM4728467 Control whole cell extract replicate 2 Control whole cell extr…
- GSM4728468 Control LaminB1 ChIP replicate 1 Control LaminB1 ChIP
- GSM4728469 Control LaminB1 ChIP replicate 2 Control LaminB1 ChIP
- GSM4728470 Suv39h1, Suv39h2 double knock-out whole cell extract replicate 1 Suv39h1, Suv39h2 double…
- GSM4728471 Suv39h1, Suv39h2 double knock-out whole cell extract replicate 2 Suv39h1, Suv39h2 double…
- GSM4728472 Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 1 Suv39h1, Suv39h2 double…
- GSM4728473 Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 2 Suv39h1, Suv39h2 double…
- GSM4728474 Control, replicate 1 Control,
- GSM4728475 Control, replicate 2 Control,
- GSM4728476 Suv39h1, Suv39h2 double knock-out, replicate 1 Suv39h1, Suv39h2 double…
- GSM4728477 Suv39h1, Suv39h2 double knock-out, replicate 2 Suv39h1, Suv39h2 double…
- GSM4728486 Control, RNA-Seq replicate 1 Control, RNA-Seq
- GSM4728487 Control, RNA-Seq replicate 2 Control, RNA-Seq
- GSM4728488 Control, RNA-Seq replicate 3 Control, RNA-Seq
- GSM4728489 Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 1 Suv39h1, Suv39h2 double…
- GSM4728490 Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 2 Suv39h1, Suv39h2 double…
- GSM4728491 Suv39h1, Suv39h2 double knock-out, RNA-Seq replicate 3 Suv39h1, Suv39h2 double…
- GSM8091847 CON ATAC-seq replicate 1 CON ATAC-seq
- GSM8091848 CON ATAC-seq replicate 2 CON ATAC-seq
- GSM8091849 DKO ATAC-seq replicate 1 DKO ATAC-seq
- GSM8091850 DKO ATAC-seq replicate 2 DKO ATAC-seq
- GSM8091851 CON H3K4me3 replicate
- GSM8091852 CON H3K27ac replicate
- GSM8091853 CON H3K27me3 replicate
- GSM8091854 CON whole cell extract replicate
- GSM8091855 CON IgG replicate
- GSM8091856 DKO H3K4me3 replicate
- GSM8091857 DKO H3K27ac replicate
- GSM8091858 DKO H3K27me3 replicate
- GSM8091859 DKO whole cell extract replicate
- GSM8091860 DKO IgG replicate
- GSM8091861 CON H3K9me3 replicate
- GSM8091862 CON H3K9me3 whole cell extract
- GSE156293 LaminB1 ChIP-seq of DP thymocytes from wildtype and Suv39h1 and Suv39h2 double knockout mice 8 samples shares laminb1, suv39h1, suv39h2, thymocytes, chip-seq, knockout
- GSE256245 ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice 12 samples shares suv39h1, suv39h2, thymocytes, chip-seq, knockout
- GSE156296 RNA-seq profiles of DP thymocytes from control and Suv39h1/Suv39h2 double knockout mice 6 samples shares suv39h1, suv39h2, thymocytes, knockout, rna-seq
- GSE256244 ATAC-seq of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice 4 samples shares suv39h1, suv39h2, thymocytes, knockout
- GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares laminb1, rna-seq
- GSE313769 SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming 122 samples shares thymocytes, positive
- GSE298292 RNA-seq of whole thymocytes and purified CD4+CD8+TCRlow DP thymocytes 8 samples shares thymocytes, rna-seq
- GSE300637 Bulk RNA-seq datasets supporting analysis of the MYC–USP10–SOX4 pathway in thymocytes and T-ALL 7 samples shares thymocytes, rna-seq
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.