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Series GSE99330 Query DataSets for GSE99330
Status Public on May 26, 2017
Title A comparison between single cell RNA sequencing and single molecule RNA FISH for rare cell analysis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ~2000 genes detected. A similar complexity threshold also allows for robust assignment of multi-genic cell states such as cell cycle phase.
 
Overall design Comparison of gene expression estimates obtained through 3 different platforms (RNA FISH, DropSeq, and Fluidigm's C1 HT IFC) using the same cell line.
 
Contributor(s) Torre EA, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A
Citation(s) 29454938
Submission date May 25, 2017
Last update date May 21, 2019
Contact name Eduardo A Torre
E-mail(s) edatorre@gmail.com
Organization name University of Pennsylvania
Department Bioengineering
Lab Raj
Street address 210 S. 33rd St.
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (801)
GSM2641350 WM989-A6G3_DropSeq
GSM2641351 WM989-A6G3_Fluidigm COL01_ROW01_sample1
GSM2641352 WM989-A6G3_Fluidigm COL01_ROW02_sample1
Relations
BioProject PRJNA388108
SRA SRP108076

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
GSE99330_dropseqHumanDge.txt.gz 13.5 Mb (ftp)(http) TXT
GSE99330_dropseqRPM.txt.gz 87.2 Mb (ftp)(http) TXT
GSE99330_fluidigmRPM.txt.gz 10.2 Mb (ftp)(http) TXT
GSE99330_fluidigm_counts.txt.gz 2.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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