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Sample GSM1415501 Query DataSets for GSM1415501
Status Public on Sep 10, 2015
Title MC1-ZE7 cells (Em+ high fraction) rep1
Sample type SRA
 
Source name MC1-ZE7 ES cells
Organism Mus musculus
Characteristics cell type: FACS sorted Emerald+ ES cells
strain: MC1 (129S6/SvEvTac)
Treatment protocol The ES cells were FACS-sorted according to the fluorescent intensity of Emerald and centrifuged to collect. The cells were resolved in Trizol and stored in -80 C.
Growth protocol MC1-ZE7 ES cells were cultured on gelatin-coated feeder-free plates in complete ES medium, DMEM (Gibco), 15% FBS (Atlanta Biologicals), 1000 U/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids (NEAA), 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin (50 U/50 µg/ml). Medium was changed daily and cells were split every 2 to 3 days routinely.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol solution (Roche) from individual cell populations separately. The extraction followed the manufacture’s instruction. Briefly, 200 ul chroloform was mixed with 1ml Trizol containing 3x10^6 cells, centrifuged and its aqueous phase was precipitated by isopropanol alcohol. The RNA pellet was washed by 70% ethanol and resolved in nuclease free water. The quality of total RNA was checked by Nanodrop (260/280=1.9-2.1, 260/230>2) and BioAnalyzer 2000 (RIN>7).
500 ng total RNA was used to remove rRNA, mtrRNA using TruSeq Stranded Total RNA with Ribo-Zero Gold Sample Prep Kit (Illumina). The cDNA was fragmented with alkaline-denatured fragmentation with 2min at 94 C, which produced the fragments with size 130-290 bp. The library was quantified by KAPA quantification kit and sequenced by HiSeq 2500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Whole RNA-seq Em-
Data processing Paired-end RNA-seq reads were aligned to mouse genome mm10 using Bowtie-2. We used reads with quality score MAPQ >=6, maximum 2 mismatches, and maximum distance of 700 pb between 3' and 5' reads. Intersection of sequence reads with genes was evaluated using genomic coordinates of exons downloaded from the UCSC database (files refGene.txt, knownGene.txt, ensGene.txt, and wgEncodeGencodeCompVM2.txt). Finally we estimated FPKM based on gene length and total number of reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: text,fpkm
 
Submission date Jun 18, 2014
Last update date May 15, 2019
Contact name Minoru S.H. Ko
E-mail(s) kom@mail.nih.gov
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL17021
Series (2)
GSE51682 Zscan4 mediates transient remodeling and transcriptional burst of heterochromatin in mouse embryonic stem cells
GSE58619 Genome-wide transcriptome analyses by the RNA-seq method
Relations
BioSample SAMN02866186
SRA SRX610434

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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