KDM4A/KDM4C lysine demethylases sustain an oncogenic transcriptional program in diffuse large B-cell lymphoma [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 31 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
- 31 samples: 15 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 GSE139022_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 PRJNA578104 and SRA study SRP226062. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 31 samples.
How we read this: 15 replicated groups read from 31 sample titles; they account for 31 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.
- GSM4126931 DMSO_H3K9me2_1 DMSO_H3K9me2
- GSM4126932 DMSO_H3K9me2_2 DMSO_H3K9me2
- GSM4126933 H3K9me2_150_1 H3K9me2_150
- GSM4126934 H3K9me2_150_2 H3K9me2_150
- GSM4126935 H3K9me2_500_1 H3K9me2_500
- GSM4126936 H3K9me2_500_2 H3K9me2_500
- GSM4126937 H3K9me3_150_1 H3K9me3_150
- GSM4126938 H3K9me3_150_2 H3K9me3_150
- GSM4126939 H3K9me3_500_1 H3K9me3_500
- GSM4126940 H3K9me3_500_2 H3K9me3_500
- GSM4126941 H3K9me3_DMSO_1 H3K9me3_DMSO
- GSM4126942 H3K9me3_DMSO_2 H3K9me3_DMSO
- GSM4126943 Input_150_1 Input_150
- GSM4126944 Input_150_2 Input_150
- GSM4126945 Input_500_1 Input_500
- GSM4126946 Input_500_2 Input_500
- GSM4126947 Input_DMSO_1 Input_DMSO
- GSM4126948 Input_DMSO_2 Input_DMSO
- GSM4126949 Input_DMSO_3 Input_DMSO
- GSM4126950 H3K27Ac_150_1 H3K27Ac_150
- GSM4126951 H3K27Ac_150_2 H3K27Ac_150
- GSM4126952 H3K27Ac_500_1 H3K27Ac_500
- GSM4126953 H3K27Ac_500_2 H3K27Ac_500
- GSM4126954 H3K27Ac_DMSO_1 H3K27Ac_DMSO
- GSM4126955 H3K27Ac_DMSO_2 H3K27Ac_DMSO
- GSM4126956 H3K4me3_150_1 H3K4me3_150
- GSM4126957 H3K4me3_150_2 H3K4me3_150
- GSM4126958 H3K4me3_500_1 H3K4me3_500
- GSM4126959 H3K4me3_500_2 H3K4me3_500
- GSM4126960 H3K4me3_DMSO_1 H3K4me3_DMSO
- GSM4126961 H3K4me3_DMSO_2 H3K4me3_DMSO
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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.