 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 22, 2023 |
| Title |
MEF (ICR) WT Passage 6 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MEF (ICR)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MEF (ICR)
transgenes: None
genotype: wildtype
treatment: None
|
| Treatment protocol |
WT (ICR) MEF and transformed MEFs in an OG2 reporter background were reprogrammed as described in Zhuang, 2018. Briefly, OKSM in lentivirus was transfected into 15,000 MEFs in one well of a 12-well plate. One day after transfection the medium was changed to reprogramming medium: DMEM high-glucose media containing 15% FBS (GIBCO), 1× GlutaMAX (GIBCO), 1x non-essential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone), 1mM sodium pyruvate (GIBCO), 0.1 mM 2-mercaptoethanol (GIBCO), 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) and vitamin C, as indicated in the figures. Medium was changed daily. Inhibitors were added at the change to reprogramming medium: PD0325901, CHIR99021, Y23637, BIX-01294, and TSA.
|
| Growth protocol |
MEFs were derived from E13.5 embryos from wildtype ICR genetic background, an OG2 or Oct4-GFP knock in mice. MEF cells were cultured in DMEM high-glucose media containing 10% FBS (GIBCO), 1 × GlutaMAX (GIBCO), and 1x nonessential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone). We generated immortalized MEF cell lines and used the oncogenic genes: P53DD, SV40T, Hdac7SA, Mef2d, Bcl2, Myc, Ras, E1A.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocols. cDNA synesis by using a PrimeScript RT Master Mix (Takara, RR036A).
RNA-seq NEB Next Ultra RNA Library Prep Kit cat.7530
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage6 rp2
|
| Data processing |
Aligned to genome/transcriptome using STAR (2.7.10a)
Genes and TEs counted using te_counts (https://github.com/oaxiom/te_counter)
Normalised using EDASeq (v2.30.0)
Differential expression using DESeq2 (v1.36.0) q-value <0.01 fold-change >2
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalised tag counts for each sample
Supplementary files format and content: tab-delimited text files include normalised tag counts for the mean of all replicates (where avaiable)
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Jun 22, 2023 |
| 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 |
GPL24247 |
| Series (2) |
| GSE213224 |
Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells [RNA-Seq] |
| GSE213225 |
Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells |
|
| Relations |
| BioSample |
SAMN30815768 |
| SRA |
SRX17539600 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
