|
| Status |
Public on Jul 22, 2020 |
| Title |
MEF Jmjd3+/+ FLAG overexpression P4 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse MEFs Passage 4
|
| Organism |
Mus musculus |
| Characteristics |
passage: 4
overexpression: FLAG
knockout: Wildtype
presumed cell type: mouse embryonic fibroblast
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 |
MEF WT P4 FLAG
genes_ntc_expression.tsv.gz
|
| 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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN14737632 |
| SRA |
SRX8181158 |
