Burkitt lymphoma cells (Ramos cell line), wild type and SP140 knockout
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- Topic
- Burkitt lymphomaThis series is part of our curated briefing on it.
- Samples
- 15 samples: 2 × H3K27ME3, wt, vs 2 × H3K27ME3, SP140 ko, vs 2 × Sp140, Daudi, vs 2 × Sp140, wt,Groups 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
- SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complexNucleic acids research · 2025
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 GSE229802_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 PRJNA956073 and SRA study SRP432796. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 15 sample titles; they account for 8 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.
- GSM6337919 Ramos cells wild type, MBD3
- GSM6337920 Ramos cells Sp140 KO, MBD3
- GSM6337921 Ramos cells wild type, input
- GSM6337922 Ramos cells Sp140 KO, input
- GSM6745537 H3K27ME3, wt, replicate 1 H3K27ME3, wt,
- GSM6745538 H3K27ME3, wt, replicate 2 H3K27ME3, wt,
- GSM6745539 H3K27ME3, SP140 ko, replicate 1 H3K27ME3, SP140 ko,
- GSM6745540 H3K27ME3, SP140 ko, replicate 2 H3K27ME3, SP140 ko,
- GSM7178079 Sp140, Daudi, replicate 1 Sp140, Daudi,
- GSM7178080 Sp140, Daudi, replicate 2 Sp140, Daudi,
- GSM7178081 Daudi, Input, WT
- GSM7178082 Sp140, wt, replicate 1 Sp140, wt,
- GSM7178083 Sp140, wt, replicate 2 Sp140, wt,
- GSM7178084 Ramos, Input, WT
- GSM7178085 Ramos, Input, KO
- GSE303569 RNA-seq of Burkitt lymphoma cell lines Ramos and ST14 knockout Ramos 4 samples same disease briefing · shares lymphoma, knockout, burkitt, ramos, line
- GSE4732 Expression Data from Burkitt Lymphoma Patients 303 samples same disease briefing · shares lymphoma, burkitt
- GSE4475 A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling 221 samples same disease briefing · shares lymphoma, burkitt
- GSE35163 Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics 32 samples same disease briefing · shares lymphoma, burkitt
- GSE240252 Single-cell transcriptomics of pediatric Burkitt lymphoma 30 samples same disease briefing · shares lymphoma, burkitt
- GSE294862 Inhibiting the RNA helicase DDX3X in Burkitt lymphoma induces oxydative stress and impedes tumor progression in xenografts 30 samples same disease briefing · shares lymphoma, burkitt
- GSE26673 Expression data from Burkitt lymphoma cases 16 samples same disease briefing · shares lymphoma, burkitt
- GSE289711 Regulation of Epstein–Barr Virus latency by histone variant H2A.Z [ChIP-seq] 10 samples same disease briefing
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.