Positive and Negative Selection of abT cells (OT-I and OT-II) in the thymus 2 - scRNA-seq, CITE-seq and TCRab
Single-cell RNA-seq · mouse · 21 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 21 samples: 21 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.
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 GSE330985_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 PRJNA1466367 and SRA study SRP700632. 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 21 sample titles: 21 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.
- GSM9736793 I60H1_spleen_FBC
- GSM9736794 I60H1_spleen_GEX
- GSM9736795 I60H1_spleen_TCR
- GSM9736796 I60H13_thymus_NegSelected_FBC
- GSM9736797 I60H13_thymus_NegSelected_GEX
- GSM9736798 I60H13_thymus_NegSelected_TCR
- GSM9736799 I60H2_thymus_PosSelected_FBC
- GSM9736800 I60H2_thymus_PosSelected_GEX
- GSM9736801 I60H2_thymus_PosSelected_TCR
- GSM9736802 I60H3_thymus_PreSelection_FBC
- GSM9736803 I60H3_thymus_PreSelection_GEX
- GSM9736804 I60H3_thymus_PreSelection_TCR
- GSM9736805 I60H5_thymus_PosSelected_FBC
- GSM9736806 I60H5_thymus_PosSelected_GEX
- GSM9736807 I60H5_thymus_PosSelected_TCR
- GSM9736808 I60H6_thymus_PreSelection_FBC
- GSM9736809 I60H6_thymus_PreSelection_GEX
- GSM9736810 I60H6_thymus_PreSelection_TCR
- GSM9736811 I60H7_thymus_NegSelected_FBC
- GSM9736812 I60H7_thymus_NegSelected_GEX
- GSM9736813 I60H7_thymus_NegSelected_TCR
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares scrna-seq, positive, negative
- GSE337460 Chlamydia serovars in uterus- scRNA-seq, CITE-seq and TCRab 30 samples shares scrna-seq, cite-seq
- GSE330911 Spleen and brain T cells in Toxoplasma gondii infection- scRNA-seq, CITE-seq and TCRab 30 samples shares scrna-seq, cite-seq
- GSE313769 SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming 122 samples shares selection, positive
- GSE311488 Chemotherapeutic Induction of Single-Stranded DNA Accumulation Sensitizes Triple-Negative Breast Cancer to Immunotherapy [scRNA-seq] 32 samples shares scrna-seq, negative
- GSE294999 Obesity-driven inflammation enables triple-negative breast cancer progression through immunosuppression [scRNA-Seq] 16 samples shares scrna-seq, negative
- GSE311344 T cells in B16 tumor model with ACT and checkpoint blockade - scRNA-seq, CITE-seq and TCRab [i35] 15 samples shares scrna-seq, cite-seq
- GSE274125 Timestamp tracing delineates thymic regulatory T cell ontogeny in native conditions [scRNA-seq] 20 samples shares scrna-seq
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.