Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention [human_carotid_plaque]
Single-cell RNA-seq · human · 12 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
- 12 samples
- 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
- Immune checkpoint landscape of human atherosclerosis and influence of cardiometabolic factorsNature cardiovascular research · 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 GSE246315_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 PRJNA1032559 and SRA study SRP468586. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run CEA_scRNAseq_1 … CEA_scRNAseq_12 and carry no group information.
- GSM8393425 CEA_scRNAseq_1
- GSM8393426 CEA_scRNAseq_2
- GSM8393427 CEA_scRNAseq_3
- GSM8393428 CEA_scRNAseq_4
- GSM8393429 CEA_scRNAseq_5
- GSM8393430 CEA_scRNAseq_6
- GSM8393431 CEA_scRNAseq_7
- GSM8393432 CEA_scRNAseq_8
- GSM8393433 CEA_scRNAseq_9
- GSM8393434 CEA_scRNAseq_10
- GSM8393435 CEA_scRNAseq_11
- GSM8393436 CEA_scRNAseq_12
- GSE272294 Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention [human PBMC scRNA-Seq] 24 samples shares atherosclerosis, lipid-lowering, implications, intervention, checkpoint, signatures, decoding, diabetes
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- GSE242912 MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design and mechanisms of disease progression 64 samples shares implications, signatures
- GSE284329 Multi-Omics Profiling Reveals Distinct Lipidomic and Transcriptomic Alterations in Gestational Diabetes Mellitus, Preeclampsia, and Coexistence of Both: Implications for Maternal and Neonatal Outcomes 17 samples shares implications, diabetes
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares implications
- GSE273036 Multi-Omics Analysis and Molecular Subtypes Provide Potential Therapeutic Implications in Fumarate Hydratase-deficient Renal Cell Carcinoma 93 samples shares implications
- GSE305337 Patient-Specific Pharmacogenomics demonstrates xCT as Predictive Therapeutic Target in Colon Cancer with Possible Implications in Tumor Connectivity 73 samples shares implications
- GSE184537 Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications 48 samples shares implications
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.