Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing
Single-cell RNA-seq · mouse · 10 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
- 10 samples: 9 distinct titles, 1 of them repeatedGroups 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 GSE98561_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 PRJNA385514 and SRA study SRP106481. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 9 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.
- GSM2599699 HEK293T, HeLa S3 and NIH/3T3 cell mixture (384 x 384 sci-RNA-seq)
- GSM2599700 HEK293T, HeLa S3 and NIH/3T3 cell and nuclei mixture (96 x 96 sci-RNA-seq)
- GSM2599701 c.elegans cells (L2 stage)
- GSM2599702 bulk 293T
- GSM2599703 HEK293T and NIH/3T3 cell mixture (16 x 84 sci-RNA-seq)
- GSM2599704 frozen fixed HEK293T and NIH/3T3 cell mixture (16 x 80 sci-RNA-seq)
- GSM2599705 HEK293T and NIH/3T3 cell mixture (sciRNA-seq with three levels indexing)
- GSM2599706 c.elegans cells (L2 stage) 2
- GSM2611059 c.elegans cells (L2 stage) and HEK293T cell mixture (experiment 1)
- GSM2611060 c.elegans cells (L2 stage) and HEK293T cell mixture (experiment 2)
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.