NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE75790 Query DataSets for GSE75790
Status Public on Sep 09, 2016
Title Comparative analysis of single-cell RNA sequencing methods
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq and Smart-seq2 are more efficient when analyzing fewer cells. Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods and provides a framework for benchmarking further improvements of scRNA-seq protocols.
 
Overall design J1 mESC in two replicates per library preparation method.
 
Contributor(s) Ziegenhain C, Enard W
Citation(s) 28212749, 31604912
Submission date Dec 08, 2015
Last update date Oct 21, 2019
Contact name Christoph Ziegenhain
E-mail(s) ziegenhain@bio.lmu.de
Organization name Ludwig-Maximilians University Munich
Department Department Biology II
Lab Anthropology & Human genomics
Street address GroƟhaderner Str. 2
City Martinsried
State/province Bavaria
ZIP/Postal code 82152
Country Germany
 
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (583)
GSM2220308 DropSeqA_AATTCGTAGA
GSM2220309 DropSeqA_AATTGTGGTT
GSM2220310 DropSeqA_AATTGTGTTC
Relations
Reanalysis of GSM1322282
Reanalysis of GSM1322284
BioProject PRJNA305381
SRA SRP067124

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75790_UMI_data_README.txt 872 b (ftp)(http) TXT
GSE75790_ziegenhain_complete_data.txt.gz 5.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap