Spleen and brain T cells in Toxoplasma gondii infection- scRNA-seq, CITE-seq and TCRab
Single-cell RNA-seq · mouse · 30 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
- 30 samples: 30 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 GSE330911_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 PRJNA1465895 and SRA study SRP700375. 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 30 sample titles: 30 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.
- GSM9735551 I59H1_spleen_FBC
- GSM9735552 I59H1_spleen_GEX
- GSM9735553 I59H1_spleen_TCR
- GSM9735554 I59H10_spleen_Toxo_D23_FBC
- GSM9735555 I59H10_spleen_Toxo_D23_GEX
- GSM9735556 I59H10_spleen_Toxo_D23_TCR
- GSM9735557 I59H11_spleen_Toxo_D23_FBC
- GSM9735558 I59H11_spleen_Toxo_D23_GEX
- GSM9735559 I59H11_spleen_Toxo_D23_TCR
- GSM9735560 I59H2_spleen_Toxo_D9_FBC
- GSM9735561 I59H2_spleen_Toxo_D9_GEX
- GSM9735562 I59H2_spleen_Toxo_D9_TCR
- GSM9735563 I59H3_spleen_Toxo_D9_FBC
- GSM9735564 I59H3_spleen_Toxo_D9_GEX
- GSM9735565 I59H3_spleen_Toxo_D9_TCR
- GSM9735566 I59H4_spleen_Toxo_D9_FBC
- GSM9735567 I59H4_spleen_Toxo_D9_GEX
- GSM9735568 I59H4_spleen_Toxo_D9_TCR
- GSM9735569 I59H5_brain_Toxo_D23_FBC
- GSM9735570 I59H5_brain_Toxo_D23_GEX
- GSM9735571 I59H5_brain_Toxo_D23_TCR
- GSM9735572 I59H6_brain_Toxo_D23_FBC
- GSM9735573 I59H6_brain_Toxo_D23_GEX
- GSM9735574 I59H6_brain_Toxo_D23_TCR
- GSM9735575 I59H7_brain_Toxo_D23_FBC
- GSM9735576 I59H7_brain_Toxo_D23_GEX
- GSM9735577 I59H7_brain_Toxo_D23_TCR
- GSM9735578 I59H8_spleen_Toxo_D23_FBC
- GSM9735579 I59H8_spleen_Toxo_D23_GEX
- GSM9735580 I59H8_spleen_Toxo_D23_TCR
- GSE337460 Chlamydia serovars in uterus- scRNA-seq, CITE-seq and TCRab 30 samples shares scrna-seq, cite-seq, tcrab
- GSE330985 Positive and Negative Selection of abT cells (OT-I and OT-II) in the thymus 2 - scRNA-seq, CITE-seq and TCRab 21 samples shares scrna-seq, cite-seq, tcrab
- 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, tcrab
- GSE266145 Macrophage-mediated myelin recycling fuels brain cancer malignancy (scRNA-Seq) 22 samples shares scrna-seq, brain
- GSE228455 Gene expression profile at single cell level of monocytes sorted from C57BL/6J mouse ear tissue at 3 weeks post Leishmania major infection [scRNA-seq] 218 samples shares scrna-seq
- GSE270050 Expansion of Tumor-Infiltrating CD8+ T Cell Clonotypes Occurs in the Spleen in Response to Immune Checkpoint Blockade 29 samples shares spleen
- GSE274125 Timestamp tracing delineates thymic regulatory T cell ontogeny in native conditions [scRNA-seq] 20 samples shares scrna-seq
- GSE306035 scRNA-Seq of immune populations from nasal mucosa and lungs of C57BL/6 mice and BLT1 receptor deficient mice infected intranasally with MCMV K181 strain 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.