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Series GSE99866 Query DataSets for GSE99866
Status Public on Jul 20, 2017
Title Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in several of the reaction steps of Quartz-Seq2 allow us to effectively convert initial reads to UMI counts (at a rate of 30%–50%). To demonstrate the power of Quartz-Seq2, we analyzed transcriptomes from a cell population of in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of sequence reads.

Preprint: http://www.biorxiv.org/content/early/2017/07/21/159384
 
Overall design Technical validation of high-throughput single-cell RNA-seq methods using 10 pg total RNA. Demonstration of Quartz-Seq2 using 4,484 single-cells of embryonic stem cell and 1,052 single-cells of stromal vascular fraction (SVF).
Web link http://bit.riken.jp/
 
Contributor(s) Danno H, Sasagawa Y, Nikaido I
Citation(s) 29523163
Submission date Jun 09, 2017
Last update date May 15, 2019
Contact name Itoshi NIKAIDO
E-mail(s) itoshi.nikaido@riken.jp
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (74)
GSM2656447 v32ESPrE_S1
GSM2656448 T55ExoP_S2
GSM2656449 T55ExoM_S1
Relations
BioProject PRJNA389818
SRA SRP108899

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
GSE99866_RAW.tar 181.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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