DOT1L shapes ncPRC1-target gene repression to maintain cell identity of DLBCL [CUT&Tag]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- Homo sapiens (human)
- Topic
- Diffuse large B-cell lymphomaThis series is part of our curated briefing on it.
- Samples
- 12 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 GSE327306_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 PRJNA1450391 and SRA study SRP690068. 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 12 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.
- GSM9653191 DMSO_H2AK119ub1_rep1 DMSO_H2AK119ub1
- GSM9653192 DMSO_H2AK119ub1_rep2 DMSO_H2AK119ub1
- GSM9653193 DMSO_H3K27me3_rep1 DMSO_H3K27me3
- GSM9653194 DMSO_H3K27me3_rep2 DMSO_H3K27me3
- GSM9653195 DOT1Li_H2AK119ub1_rep1 DOT1Li_H2AK119ub1
- GSM9653196 DOT1Li_H2AK119ub1_rep2 DOT1Li_H2AK119ub1
- GSM9653197 DOT1Li_H3K27me3_rep1 DOT1Li_H3K27me3
- GSM9653198 DOT1Li_H3K27me3_rep2 DOT1Li_H3K27me3
- GSM9653199 shUSP7_H2AK119ub1_rep1 shUSP7_H2AK119ub1
- GSM9653200 shUSP7_H2AK119ub1_rep2 shUSP7_H2AK119ub1
- GSM9653201 shUSP7_H3K27me3_rep1 shUSP7_H3K27me3
- GSM9653202 shUSP7_H3K27me3_rep2 shUSP7_H3K27me3
- GSE277665 DOT1L and EZH2 cooperatively repress PRC2 targets to maintain the GC B cell identity in DLBCL [RNA-seq] 48 samples same disease briefing · shares dot1l, dlbcl, maintain, identity
- GSE231623 Effect of DLBCL-associated NOTCH2 mutants on genomic RBP-J localization and H3K27 acetylation 7 samples same disease briefing · shares dlbcl
- GSE254715 Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [CUT&RUN] 6 samples same disease briefing · shares cut
- GSE262641 Discovery of golcadomide (CC-99282) as a promising drug candidate for diffuse large B-cell lymphoma (DLBCL) 6 samples same disease briefing · shares dlbcl
- GSE232330 Targeting AURKA to induce synthetic lethality in CREBBP-deficient DLBCL via attenuation of MYC expression 3 samples same disease briefing · shares dlbcl
- GSE11318 Molecular subtypes of DLBCL have distinct chromosomal aberrations 406 samples same disease briefing · shares dlbcl
- GSE231624 (1) Effect of KLHL6 loss on the transcriptome in DLBCL upon NOTCH ligand stimulation. (2) Effect of KLHL6 and NOTCH2 loss on the transcriptome in DLBCL. (3) Effect of DLBCL-associated NOTCH2 mutants on the transcriptome in DLBCL. 48 samples same disease briefing · shares dlbcl
- GSE224867 RNA-seq analysis of DLBCL cell lines in response to chemotherapy 36 samples same disease briefing · shares dlbcl
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.