|
| Status |
Public on Jul 26, 2019 |
| Title |
RNA_d3F_r2 |
| Sample type |
SRA |
| |
|
| Source name |
mesendoderm cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: double knock-in (DKI) mouse ES cell line carrying Foxa2-Venus and Sox17-Cherry gene fusions
genotype/variation: Foxa2-Venus heterozygous;Sox17-Cherry homozygous
facs sorting markers: Foxa2-Venus-pos/Sox17-Cherry-neg
time point: d3
antibody: none
|
| Growth protocol |
The cells were cultured for few consecutive passages on gelatine and ES medium. On the day of differentiation, mESCs were seeded on 10 cm gelatine coated dishes directly in endoderm differentiation medium (EDM) supplemented with 1 ng/ml of murine Wnt3a and 10 ng/ml of Activin A. Freshly prepared EDM supplemented with Wnt3a and Activin A was added every day. Cells were collected on day0, day3 and day5 for FACS isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol and RNA clean and concentrator kit (Zymo research), including the on-column DNase step. Ribo-depletion with Ribozero goldkit (Illumina MRZG126).
Illumina TruSeq V2 RNA prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired-end RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013). Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_rsem.genes.results.txt: Tab-delimited text files were generated with RSEM.
|
| |
|
| Submission date |
Jun 25, 2018 |
| Last update date |
Aug 12, 2019 |
| Contact name |
Filippo M. Cernilogar |
| E-mail(s) |
filippo.cernilogar@med.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center
|
| Street address |
Grosshaderner Strasse 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE116259 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq] |
| GSE116262 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 |
|
| Relations |
| BioSample |
SAMN09486935 |
| SRA |
SRX4298479 |
