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Dataset View [GSE66053]

Series	GSE66053
Title	Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
Year	2015
Country	USA
Article	Raj A,Singh A,Churchman LS,Wu AR,Foley SW,Scarfone S,Mayer A,Biaesch AG,Nair GP,Padovan-Merhar O.Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.Molecular cell.2015 Apr 16
PMID	25866248
Bio Project	BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA275801
Sra	SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP055153
Overall Desgin	Single cell RNA sequencing of live and fixed cells, bulk RNA sequencing in two cell lines.
Summary	We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells.
Experimental Protocol	Cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.; First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual. Fixed cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.; First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual. RNA was harvested using Qiazol.; Used Ribo-Zero Gold and NEBNext Library Prep protocol.
Data processing	Aligned reads to genome using STAR; Assigned counts per gene using HTSeq; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text files include counts for all genes and samples. All single-cell data is compiled into a single .tsv file, and there is a separate .txt file for the bulk data from each cell line.
Platform	GPL16791;GPL18573
Public On	Public on Mar 01 2015

Cell Groups

Differential Expression Gene List

primary foreskin fibroblast cell CRL2097 (fixed cell)_VS_primary foreskin fibroblast cell CRL2097 (large live) primary foreskin fibroblast cell CRL2097 (fixed cell)_VS_primary foreskin fibroblast cell CRL2097 (med live) primary foreskin fibroblast cell CRL2097 (large live)_VS_primary foreskin fibroblast cell CRL2097 (med live)

KEGG GO Others  Gene List