GEO series

Quantitative assessment of single-cell RNA sequencing methods

GSE51254 Homo sapiens (human) Single-cell RNA-seq 113 samples Submitted 2013/10/20 Platform GPL11154

At a glance

Single-cell RNA-seq · human · 113 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 113 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.

Summary (written by the submitters)

We generated single-cell transcriptomes from a large number of single cells using several commercially available platforms, in both microliter and nanoliter volumes, and compared performance between them. We benchmarked each method to conventional RNA-seq of the same sample using bulk total RNA, as well as to multiplexed qPCR, which is the current gold standard for quantitative single-cell gene expression analysis.

Read the full summary ↓

In doing so, we were able to systematically evaluate the sensitivity, precision, and accuracy of various approaches to single-cell RNA-seq. Our results show that it is possible to use single-cell RNA-seq to perform quantitative transcriptome measurements of individual cells, that it is possible to obtain quantitative and accurate gene expression measurements with a relatively small number of sequencing reads, and that when such measurements are performed on large numbers of cells, one can recapitulate the bulk transcriptome complexity, and the distributions of gene expression levels found by single-cell qPCR.

This dataset

Open GSE51254 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE51254_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA222225 and SRA study SRP030617. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24141493) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 113 more — browse all 113 samples with per-sample file links →

Datasets on a similar topic

GSE305971 Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma 2105 samples shares single-cell
GSE287301 Single-cell RNA-sequencing of HNSCC-infiltrating T cells 48 samples shares single-cell
GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares single-cell
GSE291890 Single-Cell RNA Sequencing Unveils Macrophage Involvement in Aortic Valve Stenosis Progression 33 samples shares single-cell
GSE243013 A single-cell atlas of immune heterogeneity in anti-PD1-treated non-small cell lung cancer 243 samples shares single-cell
GSE305078 Single-cell RNA sequencing of ICB samples from FUSCC 32 samples shares single-cell
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 single-cell
GSE282122 A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease 216 samples shares single-cell

Search all human RNA-seq datasets in GEO →

Share this dataset

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.