|
| Status |
Public on Oct 10, 2017 |
| Title |
WT Day 0 ESCs [3wtd0] |
| Sample type |
SRA |
| |
|
| Source name |
WT Day 0 ESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
cell type: Mouse Embryonic Stem Cells
cell subtype: Pluripotent ESCs
|
| Treatment protocol |
Cardiac differentiation of ES cells was induced by aggregating aliquots containing ~1000 cells in hanging drop of 25µl of differentiation medium: IMDM (Life Technologies #21980-032) medium supplemented with 200mM L-glutamine (Life Technologies #25030-024), 20% FBS, 6.5µl of 1-thioglycerol (Sigma #M6145), 1M L-ascorbic acid (Sigma #A4544) and Gentamicin (1:500) to form embryoid bodies.
|
| Growth protocol |
Mouse embryonic EomesEGFP reporter stem cells (WT and KO) were cultured on mouse embryonic fibroblast feeders in standard ES cell medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy isolation kit (Qiagen).
Sequencing libraries were prepared according to Illumina TruSeq Stranded mRNA protocol instructions with PolyA selection. Libraries were sequenced with the Illumina HiSeq2500 (1x100 bp).
RNAseq. Sequencing data was generated and analyzed at the Lausanne Genomic Technologies Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3wtd0
|
| Data processing |
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus genome (v. GRCm38) using STAR (v. 2.4.2a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using M. musculus gene annotation (Ensembl v.82).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Maric |
| E-mail(s) |
daniel.maric@chuv.ch
|
| Phone |
+41213140743
|
| Organization name |
CHUV
|
| Department |
Coeur-vaisseaux
|
| Lab |
215
|
| Street address |
Rue du Bugnon 27
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE103583 |
RNAseq on WT and Meteor KO Embryonic Stem Cells and day3 differentiated cells |
|
| Relations |
| BioSample |
SAMN07614241 |
| SRA |
SRX3166604 |
