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Status |
Public on Jan 20, 2022 |
Title |
STO_RNA_Rep1 |
Sample type |
SRA |
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Source name |
SIM embryonic fibroblasts cells
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Organism |
Mus musculus |
Characteristics |
passages: >30 strain: C57BL/6
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Growth protocol |
SSCs were cultured on mitomycin C (MMC)-treated mouse embryonic fibroblast (MEF) feeder cells with SSC culture medium. FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium. STOs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose (Life Technologies), 10% FBS (Life Technologies), 1% non-essential amino acids (Life Technologies), 2mM glutamine (Sigma) and Penicillin (100U/ml, Sigma)/streptomycin (0.1mg/ml, Sigma).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA were extracted from 2-6 million cells using Trizol Reagent (Invitrogen). The RNA quality was assessed using Agilent Bioanalyzer 2100 RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq kit following the manufacturer’s instructions
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized. Genome_build: mm9 Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample
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Submission date |
Feb 01, 2019 |
Last update date |
Jan 20, 2022 |
Contact name |
Ji Wu |
E-mail(s) |
jiwu@sjtu.edu.cn
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Organization name |
Shanghai Jiao Tong University
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Street address |
No.800, Dongchuan Road, Minhang District
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City |
Shanghai |
ZIP/Postal code |
200240 |
Country |
China |
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Platform ID |
GPL17021 |
Series (2) |
GSE126013 |
3D Chromosome Structure Can Reveal Stem Cell Signatures (RNA-Seq) |
GSE126014 |
3D Chromosome Structure Can Reveal Stem Cell Signatures |
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Relations |
BioSample |
SAMN10861549 |
SRA |
SRX5324073 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3587919_STO1_FPKM.txt.gz |
829.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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