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Sample GSM3587919 Query DataSets for GSM3587919
Status Public on Jan 20, 2022
Title STO_RNA_Rep1
Sample type SRA
 
Source name SIM embryonic fibroblasts cells
Organism Mus musculus
Characteristics passages: >30
strain: C57BL/6
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).
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Feb 01, 2019
Last update date Jan 20, 2022
Contact name Ji Wu
E-mail(s) jiwu@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Street address No.800, Dongchuan Road, Minhang District
City Shanghai
ZIP/Postal code 200240
Country China
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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