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Sample GSM4500873 Query DataSets for GSM4500873
Status Public on Jul 22, 2020
Title iPSCs (RNA-seq)
Sample type SRA
Source name OSK-induced pluripotent stem cells
Organism Mus musculus
Characteristics passage: 13
overexpression: None
knockout: Wildtype
presumed cell type: embryonic stem cell
strain: C57BL/6J-OG2
Treatment protocol Plat-E cells were transfected with pMXs vectors for FLAG/JMJD3 to produce virus. Plat-E cells were maintained in DMEM/high glucose containing 10% FBS. MEFs in P2 or P4 were plated at 20,000 per square centimetre and infected with retrovirus for 24 hours once.
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 iPSCs were cultured on feeder layer (MEF treated with mitomycin-C) in ESC medium ( DMEM/high glucose (Hyclone) supplemented with 15% FBS (GIBCO), Glutamax, nonessential amino acids, sodium pyruvate, penicillin/streptomycin, beta-mercaptoethanol and leukaemia inhibitory factor (LIF))supplemented with 3 μM CHIR99021 and 1 μM PD0325901.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using TRIzol following the manufacture’s instruction.
Standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description iPSCs
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 Apr 27, 2020
Last update date Jul 22, 2020
Contact name Andrew P Hutchins
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 GPL17021
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
BioSample SAMN14737636
SRA SRX8181156

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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