|
| Status |
Public on Jun 18, 2019 |
| Title |
Oct6WTday3rep2 |
| Sample type |
SRA |
| |
|
| Source name |
OG2MEF
|
| Organism |
Mus musculus |
| Characteristics |
transduction: Oct6WT
cell type: reprogramming cells
day of reprogramming: Day3
|
| Treatment protocol |
NA
|
| Growth protocol |
OG2MEF cells were transduced twice by pMX-Sox2, Klf4 along with Oct4 or Oc6 or engineered Oct4 (YR or Oct4defSox2) or GFP retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to highly efficient chemically defined (iCD1) reprogramming medium. The iCD media switch day was defined as day 0 and cells were cultured with daily media change.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastqc
The mouse transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 15,130 genes
DESeq2 for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file; see RNAseqprocesseddata_description.txt for a description of the file contents.
|
| |
|
| Submission date |
Sep 18, 2017 |
| Last update date |
Jun 18, 2019 |
| Contact name |
Veeramohan Veerapandian |
| E-mail(s) |
veeramohan.v@mpi-muenster.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Biomedicine
|
| Department |
Department Tissue Morphogenesis
|
| Street address |
Röntgenstr. 20
|
| City |
Munster |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE103979 |
Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 [RNA-Seq] |
| GSE103980 |
Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 |
|
| Relations |
| BioSample |
SAMN07664967 |
| SRA |
SRX3196534 |
