RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing
Single-cell RNA-seq · mouse · 13 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
- 13 samples: 13 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.
- Paper
- [Estimation of ocular perfusion: a practical oriented comparison of different methods]Klinische Monatsblatter fur Augenheilkunde · 2003
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 GSE266161_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 PRJNA1106029 and SRA study SRP504310. 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 13 sample titles: 13 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.
- GSM8238055 unmod, first mixing experiment
- GSM8238056 unmod_T, first mixing experiment
- GSM8240933 unmod, second mixing experiment
- GSM8240934 unmod_roi, second mixing experiment
- GSM8240935 rock, second mixing experiment
- GSM8240936 rockroi, second mixing experiment
- GSM8241647 Colon, rockroi multimodal
- GSM8241648 Colon, unmod unimodal
- GSM8241649 Colon, rockroi unimodal
- GSM8752429 leukemia cell lines, rockroi
- GSM8752430 leukemia patient sample, rockroi
- GSM9186646 hela cell lines, unmodified
- GSM9186647 hela cell lines, rockroi
- GSE265962 RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I 2 samples shares roi, region-specific, rna-sequencing, single-cell, information, transcripts, preselected, enrichment
- GSE327497 Localized PD-1 CAR T therapy reprograms neuroinflammation. 390 samples shares roi
- GSE305442 MBNL loss of function in smooth muscle as a model for myotonic dystrophy gastrointestinal dysmotility 44 samples shares roi
- GSE219284 Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia 24 samples shares roi
- GSE255495 Perturbing local steroidogenesis to improve breast cancer immunity 20 samples shares roi
- GSE269121 CD22 modulation regulates neuroinflammation in microglia 20 samples shares roi
- GSE275233 Circadian Gene BMAL1 Regulation of Cell Senescence in Thyroid aging [scRNA-Seq] 10 samples shares roi
- GSE253852 Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover 31 samples shares roi
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.