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SRX802554: GSM1562543: H1_Exp3.234; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 9.3M spots, 476.8M bases, 303.6Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq
show Abstracthide Abstract
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. Overall design: 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
Sample: H1_Exp3.234
SAMN03256736 • SRS784714 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction 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.
Experiment attributes:
GEO Accession: GSM1562543
Links:
External link:
Runs: 1 run, 9.3M spots, 476.8M bases, 303.6Mb
Run# of Spots# of BasesSizePublished
SRR17000309,349,017476.8M303.6Mb2015-06-24

ID:
1146151

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