B-cell depletion improves therapeutic index of combination checkpoint blockade in patients with advanced melanoma
RNA-seq (gene expression) · human · 44 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
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 44 samples: 44 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.
Read the full summary ↓
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 GSE335494_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 PRJNA1478643 and SRA study SRP709746. 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 44 sample titles: 44 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.
- GSM9814597 PBMC CITE-seq, S002-A, gene expression (GEX)
- GSM9814598 PBMC CITE-seq, S002-A, antibody-derived tags (ADT)
- GSM9814599 PBMC CITE-seq, S002-B, gene expression (GEX)
- GSM9814600 PBMC CITE-seq, S002-B, antibody-derived tags (ADT)
- GSM9814601 PBMC CITE-seq, S003-A, gene expression (GEX)
- GSM9814602 PBMC CITE-seq, S003-A, antibody-derived tags (ADT)
- GSM9814603 PBMC CITE-seq, S003-C, gene expression (GEX)
- GSM9814604 PBMC CITE-seq, S003-C, antibody-derived tags (ADT)
- GSM9814605 PBMC CITE-seq, S004-A, gene expression (GEX)
- GSM9814606 PBMC CITE-seq, S004-A, antibody-derived tags (ADT)
- GSM9814607 PBMC CITE-seq, S004-B, gene expression (GEX)
- GSM9814608 PBMC CITE-seq, S004-B, antibody-derived tags (ADT)
- GSM9814609 PBMC CITE-seq, S006-A, gene expression (GEX)
- GSM9814610 PBMC CITE-seq, S006-A, antibody-derived tags (ADT)
- GSM9814611 PBMC CITE-seq, S006-C, gene expression (GEX)
- GSM9814612 PBMC CITE-seq, S006-C, antibody-derived tags (ADT)
- GSM9814613 PBMC CITE-seq, S008-A, gene expression (GEX)
- GSM9814614 PBMC CITE-seq, S008-A, antibody-derived tags (ADT)
- GSM9814615 PBMC CITE-seq, S008-C, gene expression (GEX)
- GSM9814616 PBMC CITE-seq, S008-C, antibody-derived tags (ADT)
- GSM9814617 PBMC CITE-seq, S009-A, gene expression (GEX)
- GSM9814618 PBMC CITE-seq, S009-A, antibody-derived tags (ADT)
- GSM9814619 PBMC CITE-seq, S009-B, gene expression (GEX)
- GSM9814620 PBMC CITE-seq, S009-B, antibody-derived tags (ADT)
- GSM9814621 PBMC CITE-seq, S010-A, gene expression (GEX)
- GSM9814622 PBMC CITE-seq, S010-A, antibody-derived tags (ADT)
- GSM9814623 PBMC CITE-seq, S010-BC, gene expression (GEX)
- GSM9814624 PBMC CITE-seq, S010-BC, antibody-derived tags (ADT)
- GSM9814625 PBMC CITE-seq, S012-A, gene expression (GEX)
- GSM9814626 PBMC CITE-seq, S012-A, antibody-derived tags (ADT)
- GSM9814627 PBMC CITE-seq, S012-C, gene expression (GEX)
- GSM9814628 PBMC CITE-seq, S012-C, antibody-derived tags (ADT)
- GSM9814629 PBMC CITE-seq, S013-A, gene expression (GEX)
- GSM9814630 PBMC CITE-seq, S013-A, antibody-derived tags (ADT)
- GSM9814631 PBMC CITE-seq, S013-B, gene expression (GEX)
- GSM9814632 PBMC CITE-seq, S013-B, antibody-derived tags (ADT)
- GSM9814633 PBMC CITE-seq, S014-A, gene expression (GEX)
- GSM9814634 PBMC CITE-seq, S014-A, antibody-derived tags (ADT)
- GSM9814635 PBMC CITE-seq, S014-C, gene expression (GEX)
- GSM9814636 PBMC CITE-seq, S014-C, antibody-derived tags (ADT)
+ 4 more — browse all 44 samples with per-sample file links →
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing · shares checkpoint, blockade
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares blockade, melanoma
- GSE317605 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq] 168 samples same disease briefing · shares advanced
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
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.