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Sample GSM1552686 Query DataSets for GSM1552686
Status Public on May 06, 2015
Title EpiSCs Rep #2
Sample type SRA
 
Source name Epiblast stem cells
Organism Mus musculus
Characteristics cell type: E5.75 derived EpiSCs
passages: 20-25
strain: OCT4-deltaPE-GFP x C57BL/6
Growth protocol EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A supplemented with 20% KSR; rsEpiSCs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM; Human ESCs (H1 & H9) were grown on matrigel-coated dishes in mTeSR1 media; Human rsESCs (H1 & H9) and Chimp rsiPSCs were grown on Matrigel-coated plates in modified mTeSR1 media containing 20ng/ml FGF2 and 2.5uM IWR1; Rhesus ORMES23 rsESCs were grown on MEFs in modified N2B27 media containing 20ng/ml FGF2 and 2.5uM IWR1, MEFs were removed before RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA of all samples was extracted using RNeasy Mini Kit (Qiagen) per manufacturer's instructions.
RNA libraries were prepared for sequencing using strand-specific Illumina TruSeq kits per the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Epblast stem cells RNA-seq
PolyA+ RNA
Strand-specific polyA+ RNA-Seq
Processed data file: fpkm.mouse-EpiSC.txt.gz
Data processing Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) or human (hg19) genomes with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis.
Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text file. Columns: (1) RefSeq acc, (2) chr, (3) start, (4) end, (5) strand, (6) length, (7) copies, (8) annotation, (9 to the end) FPKM.
 
Submission date Nov 21, 2014
Last update date May 15, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platform ID GPL17021
Series (2)
GSE60603 An alternative pluripotent state confers interspecies chimaeric competency [RNA-Seq]
GSE60605 An alternative pluripotent state confers interspecies chimaeric competency
Relations
BioSample SAMN03216779
SRA SRX765896

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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