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Dataset View [GSE64016]

Series	GSE64016
Title	Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq
Year	2015
Country	USA
Article	Kendziorski C,Thomson JA,Stewart RM,Jiang P,Li X,Choi J,Li Y,Barry C,Chu LF,Leng N.Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments.Nature methods.2015 Oct
PMID	26301841
Bio Project	BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA269761
Sra	SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP050992
Overall Desgin	Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs. Normalized expected counts are provided in GSE64016_H1andFUCCI_normalized_EC.csv.gz
Summary	Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform.
Experimental Protocol	Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.; Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system.
Data processing	Basecalls performed using CASAVA version 1.8.2; Sequencing reads were mapped to hg19 using bowtie 0.12.8; Gene expected counts were calculated using RSEM 1.2.3; Normalized expected counts were calculated using EBSeq 1.5.4; Genome_build: hg19
Platform	GPL16791
Public On	Public on Jun 24 2015

Cell Groups

Differential Expression Gene List

single H1 hESC_VS_single H1-Fucci cell sorted from G1 phase of the cell cycle only single H1 hESC_VS_single H1-Fucci cell sorted from G2-M phase of the cell cycle only single H1 hESC_VS_single H1-Fucci cell sorted from S phase of the cell cycle only single H1-Fucci cell sorted from G1 phase of the cell cycle only_VS_single H1-Fucci cell sorted from G2-M phase of the cell cycle only single H1-Fucci cell sorted from G1 phase of the cell cycle only_VS_single H1-Fucci cell sorted from S phase of the cell cycle only single H1-Fucci cell sorted from G2-M phase of the cell cycle only_VS_single H1-Fucci cell sorted from S phase of the cell cycle only

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