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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.

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
Contributor(s) Danno H, Sasagawa Y, Nikaido I
Citation(s) 29523163
Submission date Jun 09, 2017
Last update date Jul 25, 2021
Contact name Itoshi NIKAIDO
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
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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