|
| Status |
Public on May 26, 2016 |
| Title |
Wildtype Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
D4 Embryoid Bodies
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Day 4 embryoid bodies
cell type: W9.5 mESCs
|
| Treatment protocol |
Cells were seeded at 2x104 cells/ml in embryonic stem cell media without LIF, as described previously (Bruce et al. 2007). Cells were then grown in this serum containing media for 4 days. Samples being compared were set up on the same day at the same time.
|
| Growth protocol |
W9.5 and Evx1Δfs mESCs were maintained in 1000U/ml LIF on gelatanized plates in standard embryonic stem cell media at 37 degrees C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the embryoid bodies using Trizol according to manufactors instructions.
Total RNA was analysed on the Bioanalyser (Agilent) to confirm high RNA quality (Rinn value > 8). mRNA selection of total RNA was performed using Ambion Dynabeads© mRNA DIRECT Micro Purification Kit (#61021, Life Technologies). Barcoded RNAseq libraries were generated from the mRNA using the Ion Total RNAseq Kit v3 (#4475936) and Ion Xpress RNAseq Barcode 1-16 Kit (#4475485, Life Technologies). RNAseq libraries were sequenced on the Ion Proton sequencing instrument using the Ion P1 Hi-Q Sequencing 200 Kit with the Ion P1 v2 chip. Each sample was sequenced to a depth of least 15 million reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Differentiation performed in serum
|
| Data processing |
RNAseq data was mapped to the Mus musculus reference genome (mm9) using TopHat2 and then TMAP (Kim et al. 2013). Tophat2 is required to map spliced junctions, while TMAP is designed for IonTorrent sequencing data and therefore performs better with IonTorrent data. Transcript counts were obtained by using HTSeq on the mapped data using the standard settings (Anders et al. 2013). Differential gene expression analysis was performed on the HTSeq output using DESeq2 using the standard settings (Love et al. 2014).
Genome_build: mm9
Supplementary_files_format_and_content: CSV file containing normalized counts for each replicate as calculated by DESeq2.
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Cameron Bell |
| E-mail(s) |
charles.bell@mater.uq.edu.au
|
| Phone |
0421483872
|
| Organization name |
Mater Research
|
| Lab |
Cancer Genomics
|
| Street address |
37 Kent Street
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4169 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE75737 |
Evx1 is required to regulate appropriate anterior-posterior patterning during murine gastrulation |
|
| Relations |
| BioSample |
SAMN04320957 |
| SRA |
SRX1466153 |
