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Sample GSM1940114 Query DataSets for GSM1940114
Status Public on Jul 22, 2020
Title OSKM Day 4 shRNA-Utx overexpression rep 1
Sample type SRA
 
Source name Mouse MEFs, OSKM day 4
Organism Mus musculus
Characteristics day: 4
overexpression transfection: None
shRNA transfection: shRNA-Utx
transfection: OSKM lentiviral transfection
presumed cell type: Intermediate pluripotent reprogrammed cells
strain: C57BL/6J-OG2
Treatment protocol Plat-E cells were transfected with pMXs vectors for OSKM to produce virus. Plat-E cells were maintained in DMEM/high glucose containing 10% FBS. MEFs within 3 passages were plated at 4000-5000 per square centimetre and infected with retrovirus. We marked the first infection time point as day0, after 2 rounds of 24h infection, the medium was changed to ESC medium, including Vitamin C.
Growth protocol MEFs were maintained in DMEM/high glucose (Hyclone) containing 10% fetal bovine serum (FBS, PAA), Glutamax (Invitrogen), nonessential amino acids (Invitrogen), and penicillin/streptomycin (Hyclone). Mouse ESCs and iPSCs were cultured on feeder layer (MEF treated with mitomycin-C) in ESC medium containing DMEM/high glucose (Hyclone) supplemented with 15% FBS (GIBCO), Glutamax, nonessential amino acids, sodium pyruvate, penicillin/streptomycin, beta-mercaptoethanol and leukaemia inhibitory factor (LIF). Reprogramming of MEFs was performed either in mES medium or iSF1 medium (DMEM/high glucose supplemented with 10% Knockout Serum Replacement, nonessential amino acids, basic fibroblast growth factor (bFGF) and LIF). Vitamin C was purchased from Sigma and used at concentration of 50 µg/ml. Drosophila S2 cells were obtained from Dr. Jianguo He’s lab and cultured in Schneider’s Drosophila medium (Life technologies, 21720-024) supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using TRIzol following the manufacture’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing rsem v1.2.22/bowtie2 v2.2.5 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 63 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript
 
Submission date Nov 13, 2015
Last update date Jul 22, 2020
Contact name Andrew P Hutchins
E-mail(s) andrewh@sustech.edu.cn
Organization name Southern University of Science and Technology
Department Bioinformatics
Lab Bioinformatics and Genomics
Street address 1088 Xueyuan Rd
City Shenzhen
ZIP/Postal code 518055
Country China
 
Platform ID GPL13112
Series (2)
GSE74998 Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [RNA-Seq]
GSE75005 Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming
Relations
BioSample SAMN04267366
SRA SRX1431857

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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