Gene expression profiling of HIV and EBV-associated classic Hodgkin lymphomas from Malawi
RNA-seq (gene expression) · human · 19 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
- Hodgkin lymphomaThis series is part of our curated briefing on it.
- Samples
- 19 samples: 19 samples, each with a distinct title — no replicated groupsGroups 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
- Immunogenomic profiles of HIV-associated classic Hodgkin lymphoma from MalawiBlood global hematology · 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 GSE289903_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 PRJNA1225276. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 19 sample titles: 19 distinct titles with little repetition. 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.
- GSM8801166 YF02, NS, CHL, EBV+/HIV+, Female
- GSM8801167 YF03, MC, CHL, EBV+/HIV-, Male
- GSM8801168 YF05, NS, CHL, EBV+/HIV-, Male
- GSM8801169 YF06, MC, CHL, EBV+/HIV+, Female
- GSM8801170 YF07, MC, CHL, EBV+/HIV-, Male
- GSM8801171 YF08, LD, CHL, EBV-/HIV-, Female
- GSM8801172 YF09, LR, CHL, EBV+/HIV-, Male
- GSM8801173 YF10, NS, CHL, EBV+/HIV+, Male
- GSM8801174 YF11, MC, CHL, EBV+/HIV-, Male
- GSM8801175 YF12, NS, CHL, EBV+/HIV-, Male
- GSM8801176 YF13, NS, CHL, EBV-/HIV-, Male
- GSM8801177 YF14, NS, CHL, EBV+/HIV-, Female
- GSM8801178 YF15, NS, CHL, EBV+/HIV+, Female
- GSM8801179 YF17, NA, CHL, EBV-/HIV-, Female
- GSM8801180 YF18, NS, CHL, EBV+/HIV-, Female
- GSM8801181 YF19, NS, CHL, EBV+/HIV-, Male
- GSM8801182 YF21, MC, CHL, EBV+/HIV-, Male
- GSM8801183 YF22, NS, CHL, EBV-/HIV-, Female
- GSM8801184 YF23, NS, CHL, EBV-/HIV-, Female
- GSE290026 scRNA and TCR-Seq of peripheral blood mononuclear cells (PBMC) from r/r classical Hodgkin Lymphoma patients under anti-PD1 therapy. 23 samples same disease briefing · shares classic, hodgkin
- GSE14879 Gene expression study of anaplastic large cell lymphomas: cellular origin, pathogenesis and relation to Hodgkin lymphoma 64 samples same disease briefing · shares lymphomas, hodgkin
- GSE305165 Redefining the Spectrum of EBV-Positive Diffuse Large B-Cell Lymphoma and EBV-Positive Classic Hodgkin Lymphoma 47 samples same disease briefing · shares classic, hodgkin
- GSE40160 Analyzing primary Hodgkin and Reed-Sternberg cells to capture the molecular and cellular pathogenesis of classical Hodgkin lymphoma 10 samples same disease briefing · shares classic, hodgkin
- GSE232761 5' gene expression (GEX) single-cell RNA sequencing of four (4) Hodgkin Lymphoma patient tumor biopsies 5 samples same disease briefing · shares hodgkin
- GSE301492 Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response 41 samples same disease briefing · shares hodgkin
- GSE288623 Transcriptional profiles of the Hodgkin lymphoma tumor-associated macrophage in vitro models 24 samples same disease briefing · shares hodgkin
- GSE17920 Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients 130 samples same disease briefing · shares hodgkin
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.