Single cell view of tumor microenvironment gradients in pleural mesothelioma
Single-cell RNA-seq · human · 34 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- MesotheliomaThis series is part of our curated briefing on it.
- Samples
- 34 samples: 8 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.
- Paper
- Single-Cell View of Tumor Microenvironment Gradients in Pleural MesotheliomaCancer discovery · 2024
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 GSE190597_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 PRJNA787622 and SRA study SRP350142. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 8 replicated groups read from 34 sample titles; they account for 20 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.
- GSM7114948 Patient P1 Primary Tumor, gene expression, CD45neg
- GSM7114949 Patient P1 Primary Tumor, gene expression, CD45pos
- GSM7114950 Patient P4 Primary Tumor, gene expression
- GSM7114951 Patient P8 Primary Tumor, gene expression
- GSM7114952 Patient P3 Primary Tumor, gene expression
- GSM7114953 Patient P5 Primary Tumor, gene expression
- GSM7114954 Blood, gene expression_1 Blood, gene expression
- GSM7114955 Blood, gene expression_2 Blood, gene expression
- GSM7114956 Blood, protein features_1 Blood, protein features
- GSM7114957 Blood, protein features_2 Blood, protein features
- GSM7114958 Blood, T cell receptors_1 Blood, T cell receptors
- GSM7114959 Blood, T cell receptors_2 Blood, T cell receptors
- GSM7114960 Patient P7 Primary Tumor, gene expression, Biopsy
- GSM7114961 Patient P6 Primary Tumor, gene expression, Biopsy
- GSM7114962 Patient P2 Primary Tumor, gene expression, Biopsy, neg
- GSM7114963 Patient P2 Primary Tumor, gene expression, Biopsy, pos
- GSM7114964 Patient P9 Primary Tumor, gene expression, Biopsy
- GSM7114965 Patient P6 Primary Tumor, T cell receptors, Biopsy
- GSM7114966 Patient P2 Primary Tumor, T cell receptors, Biopsy, pos
- GSM7114967 Patient P9 Primary Tumor, T cell receptors, Biopsy
- GSM8138122 Tumor_Raw_GEX_P10 Tumor_Raw_GEX_P
- GSM8138123 Tumor_Raw_GEX_P11 Tumor_Raw_GEX_P
- GSM8138124 Tumor_Raw_GEX_P12 Tumor_Raw_GEX_P
- GSM8138125 Tumor_Raw_GEX_P13 Tumor_Raw_GEX_P
- GSM8138126 PBMC_P2_P7_P9_Raw_GEX-2-1 PBMC_P2_P7_P9_Raw_GEX-2
- GSM8138127 PBMC_P2_P7_P9_Raw_GEX-2-2 PBMC_P2_P7_P9_Raw_GEX-2
- GSM8138128 PBMC_P2_P7_P9_Raw_CITE-2-1 PBMC_P2_P7_P9_Raw_CITE-2
- GSM8138129 PBMC_P2_P7_P9_Raw_CITE-2-2 PBMC_P2_P7_P9_Raw_CITE-2
- GSM8138130 PBMC_P2_P7_P9_Raw_TCR-2-1 PBMC_P2_P7_P9_Raw_TCR-2
- GSM8138131 PBMC_P2_P7_P9_Raw_TCR-2-2 PBMC_P2_P7_P9_Raw_TCR-2
- GSM8138132 Tumor_raw_TCR_P11 Tumor_raw_TCR_P
- GSM8138133 Tumor_raw_TCR_P12 Tumor_raw_TCR_P
- GSM8138134 Tumor_raw_TCR_P13 Tumor_raw_TCR_P
- GSM8368632 Tumor_raw_TCR_P7 Tumor_raw_TCR_P
- GSE282870 microRNA-497-5p-based Screening Identifies a Novel Synthetic Lethal-type Interaction via PKMYT1 and WEE1 in Pleural Mesothelioma 24 samples same disease briefing · shares mesothelioma, pleural
- GSE51024 Gene Expression of Malignant Pleural Mesothelioma Tumor and paired Normal Lung tissue 96 samples same disease briefing · shares mesothelioma, pleural
- GSE327167 Single-cell RNA-seq profiling of pleural mesothelioma and comparator pleural specimens 113 samples same disease briefing · shares mesothelioma, pleural
- GSE272176 PD-1 blockade mitigates surgery-induced immunosuppression and increases the efficacy of photodynamic therapy for malignant pleural mesothelioma 82 samples same disease briefing · shares mesothelioma, pleural
- GSE2549 Malignant pleural mesothelioma 54 samples same disease briefing · shares mesothelioma, pleural
- GSE274983 Soluble Mesothelin-Related Peptide as a Prognosticator in Pleural Mesothelioma Patients Receiving Checkpoint Immunotherapy 18 samples same disease briefing · shares mesothelioma, pleural
- GSE305915 Generating Revitalized Stem Cell-Engineered CAR-NKT Cells for the Treatment of Malignant Pleural Mesothelioma 1 samples same disease briefing · shares mesothelioma, pleural
- GSE292620 Genome-wide CRISPR Screen Identifies BUB1 Kinase as a Druggable Vulnerability in Malignant Pleural Mesothelioma 12 samples same disease briefing · shares mesothelioma, pleural
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.