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Series GSE136871 Query DataSets for GSE136871
Status Public on Sep 05, 2019
Title Linked optical and gene expression profiling of single cells at high throughput
Organisms Homo sapiens; Mus musculus; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Summary Single cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through gene expression alone. Linking sequencing with optical analysis has provided insight into the molecular basis behind cellular function, but current approaches have limited throughput. Here, we present a high throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements from thousands of cells in a single experiment and use the platform to characterize DNA and RNA changes in Jurkat cells through the cell-cycle. In addition to its scalability, our integration of microfluidics and array-based molecular biology holds promise for comprehensive multi-omics profiling of single cells.
Overall design Linked flow cytometry and gene expression datasets from mouse and human cells stained with red and green live cell dyes, Jurkat cells stained with a DNA-binding dye, and PBMCs labeled with antibodies against CD14 and CD16.
Contributor(s) Zhang JQ, Abate AR
Citation(s) 32093753
Submission date Sep 04, 2019
Last update date Mar 02, 2020
Contact name Jesse Zhang
Organization name UCSF
Department BTS
Lab Abate
Street address 1700 4th St.
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (5)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17769 Illumina MiSeq (synthetic construct)
Samples (6)
GSM4060041 3T3 and HEK293 cell mRNA-seq
GSM4060042 coordinate reads for 3T3 and HEK293 cell experiment
GSM4060043 Jurkat cell mRNA-seq
BioProject PRJNA563900
SRA SRP220344

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
GSE136871_RAW.tar 2.5 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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