|
| Status |
Public on Jul 22, 2020 |
| Title |
OSKM Day 4 Jmjd3 overexpression rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse MEFs, OSKM day 4
|
| Organism |
Mus musculus |
| Characteristics |
day: 4
overexpression transfection: Jmjd3
shRNA transfection: None
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 |
SAMN04267360 |
| SRA |
SRX1431851 |
