|
| Status |
Public on Jul 26, 2019 |
| Title |
d0.homo.r1 |
| Sample type |
SRA |
| |
|
| Source name |
ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Foxa2 knock-in/knock-out (Foxa2-Venus) KO mouse ES cell line
genotype/variation: Foxa2-Venus-KO/Foxa2-Venus-KO
facs sorting markers: Cherry-negative
time point: d0
|
| Growth protocol |
ES cells were split on red-fluorescent mitomycin-treated MEFs in ESC medium without LIF. The following day were collected for FACS isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol and RNA clean and concentrator kit (Zymo research).
Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
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 |
GPL18480 |
| Series (2) |
| GSE116260 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq low input] |
| GSE116262 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 |
|
| Relations |
| BioSample |
SAMN09486960 |
| SRA |
SRX4298485 |
