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| Status |
Public on May 01, 2020 |
| Title |
SC5 |
| Sample type |
SRA |
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| Source name |
PC iPS-5
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| Organism |
Mus musculus |
| Characteristics |
tissue: palmitoylcarnitine induced pluripotent stem cell
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| Growth protocol |
MEF were maintained in 90% DMEM + 10% FBS. Mouse ES and iPSCs were maintained in M15 medium, which is composed of Dulbecco’s modified Eagle’s medium (DMEM; Gibco Invitrogen, Carlsbad, CA)supplemented with 15% FBS (Gibco), 100 μM -mercaptoethanol (Sigma-Aldrich, St. Louis, MO), 2 mM non-essential amino acids(Gibco), 2 mM L-glutamine(Gibco), 1 mM sodium pyruvate (Gibco),and 10 ng/ml leukemia inhibitory factor (LIF; Chemicon, Temecula, CA) on feeder cells composed of mitomycin C-treated primary mouse embryonic fibroblast (MEF) cells.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells by RNAiso Plus (Takara, Dalian, China).
Libraries were prepared from 100-1000ng total RNA using the VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s protocol. Libraries were validated by the 2100 BioAnalyzer (Agilent, Beijing, China), normalized, and pooled for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
base calling were performed with Illumina CASAVA-1.8.2
This yielded about 10M usable reads per sample. Short read sequences were mapped to a UCSC mm10 reference sequences
Differential gene expression analysis, statistical testing and annotation were performed using the number of uniquely mapped reads per kilobase transcriptome per million mapppable reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include RPKM values and Coverage for each Sample
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| Submission date |
May 09, 2017 |
| Last update date |
May 01, 2020 |
| Contact name |
Zhaoyu lin |
| E-mail(s) |
linzy@nju.edu.cn
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| Organization name |
Nanjing University
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| Street address |
12 Xuefu Road
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210061 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE85272 |
Comparison of the transcription of palmitoylcarnitine induced pluripotent stem cells, normal induced pluripotent stem cells and embryonic stem cells through RNA-seq |
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| Relations |
| BioSample |
SAMN06920733 |
| SRA |
SRX2792695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2610270_SC5.Gene.rpkm.txt.gz |
312.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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