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Sample GSM1562395 Query DataSets for GSM1562395
Status Public on Jun 24, 2015
Title H1_Exp1.010
Sample type SRA
 
Source name single H1 hESC
Organism Homo sapiens
Characteristics cell type: human embryonic stem cells
passages: 30-35
treatment: not sorted
Treatment protocol FACS was performed on the FACSAria IIIu instrument and using FACSDiva software version 6.1.3 (Becton Dickinson). Unlabeled H1 cells or cells stained with single fluorochromes were served as controls for fluorescence gating.
Growth protocol Undifferentiated H1 or H1-Fucci hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance.
Extracted molecule total RNA
Extraction 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Dec 09, 2014
Last update date May 15, 2019
Contact name Ning Leng
E-mail(s) lengning1@gmail.com
Organization name Morgridge Institute for Research
Street address 330 N Orchard St
City Madison
State/province WI
ZIP/Postal code 53715
Country USA
 
Platform ID GPL16791
Series (1)
GSE64016 Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq
Relations
Reanalyzed by GSM1966544
BioSample SAMN03256879
SRA SRX802406

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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