Expansion of peripheral T cell clonotypes predict response in patients with small cell neuroendocrine bladder and prostate cancers treated with chemo-immunotherapy in a phase I clinical trial [bulkRNA-Seq]
Single-cell RNA-seq · human · 10 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 10 samples: 5 × Tumor, Responder patient vs 4 × Tumor, Responder Progressed patientGroups 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
- PD-1 blockade plus cisplatin-based chemotherapy in patients with small cell/neuroendocrine bladder and prostate cancersCell reports. Medicine · 2024
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 GSE273798_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1143371 and SRA study SRP523822. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 9 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.
- GSM8437123 Tumor, Responder patient101 Tumor, Responder patient
- GSM8437124 Tumor, Progressor patient102
- GSM8437125 Tumor, Responder patient104 Tumor, Responder patient
- GSM8437126 Tumor, Responder patient105 Tumor, Responder patient
- GSM8437127 Tumor, Responder patient106 Tumor, Responder patient
- GSM8437128 Tumor, Responder patient107 Tumor, Responder patient
- GSM8437129 Tumor, Responder Progressed patient202 Tumor, Responder Progre…
- GSM8437130 Tumor, Responder Progressed patient203 Tumor, Responder Progre…
- GSM8437131 Tumor, Responder Progressed patient204 Tumor, Responder Progre…
- GSM8437132 Tumor, Responder Progressed patient208 Tumor, Responder Progre…
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- GSE244827 Immunologic changes are detectable in the peripheral blood transcriptome of clinically asymptomatic Chagas cardiomyopathy patients 33 samples shares peripheral, clinical
- GSE208111 Transcriptome of human peripheral blood regulatory T cells with distinct ex vivo expansion profile 19 samples shares peripheral, expansion
- GSE302864 DNMT3B drives neuroendocrine lineage plasticity and aggressive progression in prostate cancer 12 samples shares neuroendocrine, prostate
- GSE270387 Single cell profiling of peripheral blood mononuclear cells in diverse men with prostate cancer reveals lethal disease-associated immune signatures 165 samples shares peripheral, prostate
- GSE210848 Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer 32 samples shares neuroendocrine, prostate
- GSE139555 Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy 32 samples shares peripheral, expansion
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.