|
| Status |
Public on Nov 21, 2018 |
| Title |
2i rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Rex1GFPd2
strain: 129
passage number: p11
condition: 2i
|
| Treatment protocol |
Rex1GFPd2 cells were derived and expanded for 6 passages in 2i, then cells were expanded in the indicated conditions for 5 additional passages. Cells were splitted every 3 days at a density of 15,000 cells/cm^2 and fresh medium was provided daily.
|
| Growth protocol |
Murine ES cells were cultured on Gelatin-coated plates in N2B27 medium in the presence of different combinations of the cytokine LIF and the inhibitors CH (GSK3 inhibitor, CHIR99021, 3µM) and PD (Mek inhibitor, PD0325901, 1µM), as indicated in the title of each sample
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and total RNA was extracted with the RNAeasy kit from Qiagen according to manufactorer's instructions
Library were constructed from 1µg of polyA RNA using Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Tophat2 (with defaults parameters) was use to align reads to reference genome (mm10)
Cufflinks was used to assemble transcriptome and CuffDiff to quantify the levels of gene expression (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing aboundance of genes in FPKM, (genes.fpkm_tracking)
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Nov 21, 2018 |
| Contact name |
Graziano Martello |
| E-mail(s) |
graziano.martello@unipd.it
|
| Organization name |
University of Padua
|
| Department |
Department of Molecular Medicine
|
| Street address |
viale Colombo 3
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE111694 |
Trascriptome profiling of murine Embryonic Stem cells under different culture conditions |
|
| Relations |
| BioSample |
SAMN08687063 |
| SRA |
SRX3782063 |
