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Series GSE100501 Query DataSets for GSE100501
Status Public on Aug 28, 2017
Title The dynamics of cellular response to therapeutic perturbation using multiplexed quantification of the proteome and transcriptome at single-cell resolution
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We developed a scalable assay permitting the simultaneous quantification of hundreds of proteins and the full transcriptome in thousands of individual cells from samples where cell number is limiting. The RNA Expression and Protein Sequencing assay (REAP-seq) uses DNA-labeled antibodies to permit DNA sequencing of both mRNA and antibodies in a single workflow using droplet microfluidics. We describe the development and validation of REAP-seq in human PBMCs, and use the assay to assess the costimulatory effects of an anti-CD27 agonist antibody in naïve CD8+ lymphocytes. Protein quantification using REAP-seq was more sensitive than parallel mRNA measurements and differentiated cell states with fewer analytes. Unbiased profiling of single cells without prior selection enabled identification and characterization of an unexpected cell type that would have been missed with population-averaged profiling methodologies.
Overall design The RNA Expression and Protein Sequencing assay (REAP-seq) which uses DNA-labeled antibodies to permit DNA sequencing of both mRNA and antibodies in a single workflow using droplet microfluidics was developed and validated in human PBMCs and naïve CD8+ T cells that were costimulated with either 1) aCD3 and aCD28 or 2) aCD3, aCD28 and aCD27.
Contributor(s) Peterson V, Zhang K
Citation(s) 28854175
Submission date Jun 26, 2017
Last update date Jul 25, 2021
Contact name Kelvin Zhang
Organization name Codiak Biosciences
Street address 35 CambridgePark Drive, Suite 500
City Cambridge
State/province Massachusetts
ZIP/Postal code 02140
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (31)
GSM2685237 mRNA_1_PBMCs
GSM2685238 mRNA_2_PBMCs
GSM2685239 mRNA_3_PBMCs
BioProject PRJNA391958
SRA SRP110537

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
GSE100501_RAW.tar 50.1 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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