|
| Status |
Public on Mar 31, 2019 |
| Title |
EpiSC-IwAF_REP2 |
| Sample type |
SRA |
| |
|
| Source name |
Epiblast Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Epiblast Stem Cell
genotype/variation: IWP2 removed after derivation
growth factor: Activin A + FGF2
inhibitor: --
|
| Treatment protocol |
Media were supplemented with recombinant human Fgf2 (10ng/mL) and recombinant Human/Mouse/Rat Activin A (20ng/mL), IWP2 (5µM) and SB431542 (2 µM).
|
| Growth protocol |
Dissected epiblast were maintained on gelatin 0.1% inactivated mouse embryonic fibroblasts (MEF) in EpiSC culture medium consisting of Knockout-DMEM , Knockout Serum Replacement (20%), Non-Essential Amino Acid , GlutaMAX-TM , Penicillin-Streptomycinand β-Mercaptoethanol .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cell samples with the ISOLATE II RNA Mini Kit (Bioline, Cat# BIO-52075)
TruSeq Stranded mRNA Sample preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Extraction and alignment: Raw reads from published dataset and from newly generated data were extracted and aligned using Salmon program (Patro et al 2017) using reference transcriptome M17 (05/04/2018) from Gencode (Website) which converts the raw reads into Transcripts Per Million (TPM).
Filtering: Transcripts which had a count value of 0 across all conditions were removed from the analysis.
Normalisation: We performed normalisation of the TPM across the different samples by using DESEq2 and negative binomial transformation of the data per sample was performed by using the EdgeR package.
Genome_build: Gencode M17
|
| |
|
| Submission date |
Jul 27, 2018 |
| Last update date |
Mar 31, 2019 |
| Contact name |
PIERRE OSTEIL |
| E-mail(s) |
posteil@cmri.org.au
|
| Phone |
412012956
|
| Organization name |
CMRI
|
| Department |
Embryology
|
| Lab |
Tam's lab
|
| Street address |
214 Hawkesbury Road
|
| City |
WESTMEAD |
| State/province |
NSW |
| ZIP/Postal code |
2145 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE117756 |
WNT signalling activity on epiblast cells (RNA-seq analysis) |
|
| Relations |
| BioSample |
SAMN09726399 |
| SRA |
SRX4474713 |
