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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 10, 2015 |
| Title |
MC1-ZE7 cells (Em+ high fraction) rep1 |
| Sample type |
SRA |
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| Source name |
MC1-ZE7 ES cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: FACS sorted Emerald+ ES cells
strain: MC1 (129S6/SvEvTac)
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Whole RNA-seq Em-
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| 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
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| Submission date |
Jun 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
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| Phone |
410-558-8359
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| Organization name |
NIH
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| Department |
National Institute on Aging
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| Lab |
Lab of Genetics
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| Street address |
251 Bayview Blvd, Suite 100, 10C
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02866186 |
| SRA |
SRX610434 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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