AID Orchestrates MYC/E2F Target Gene Activation and Cell-of-Origin Transcriptional Programs in Diffuse Large B-cell Lymphoma [GCB_AID-ER_RNA-seq]
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Diffuse large B-cell lymphomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × SUDHL6_AID-E vs 3 × SUDHL6_NGF vs 3 × LY18_AID-E vs 3 × LY18_NGFGroups 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 GSE308039_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1328630 and SRA study SRP620424. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 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.
- GSM9236252 SUDHL6_AID-ER_1 SUDHL6_AID-E
- GSM9236253 SUDHL6_AID-ER_2 SUDHL6_AID-E
- GSM9236254 SUDHL6_AID-ER_3 SUDHL6_AID-E
- GSM9236255 SUDHL6_NGFR_1 SUDHL6_NGF
- GSM9236256 SUDHL6_NGFR_2 SUDHL6_NGF
- GSM9236257 SUDHL6_NGFR_3 SUDHL6_NGF
- GSM9236258 LY18_AID-ER_1 LY18_AID-E
- GSM9236259 LY18_AID-ER_2 LY18_AID-E
- GSM9236260 LY18_AID-ER_3 LY18_AID-E
- GSM9236261 LY18_NGFR_1 LY18_NGF
- GSM9236262 LY18_NGFR_2 LY18_NGF
- GSM9236263 LY18_NGFR_3 LY18_NGF
- GSE252690 Increased CCL2/CCR2 axis in MYC/BCL2 double-expressor DLBCL promotes tumor progression by increasing M2 macrophages 28 samples same disease briefing · shares myc
- GSE211451 Targeting AURKA to induce synthetic lethality in CREBBP-deficient DLBCL via attenuation of MYC expression 8 samples same disease briefing · shares myc
- GSE230396 Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma 132 samples same disease briefing · shares myc
- GSE232330 Targeting AURKA to induce synthetic lethality in CREBBP-deficient DLBCL via attenuation of MYC expression 3 samples same disease briefing · shares myc
- GSE253910 PriOmics: integration of high_throughput proteomic data with complementary omics layers using mixed graphical modeling with group priors 360 samples same disease briefing
- GSE193566 Longitudinal gene expression profiling identifies a poor risk subset of patients with ABC-type Diffuse Large B Cell Lymphoma 76 samples same disease briefing
- GSE262621 Gene expression profiling of HIV-associated diffuse large B-cell lymphomas from Malawi 70 samples same disease briefing
- GSE277575 Large B-cell lymphoma imprints a dysfunctional immune phenotype that persists years after treatment 62 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.