|
| Status |
Public on Jul 15, 2019 |
| Title |
TS cells treated with DES replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
TS cells treated with DES
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F4
cell type: Trophoblast stem cells (TSCs)
treatment: 20 μM diethylstilbestrol (DES, Esrrb inhibitor)
|
| Treatment protocol |
1.6 x 10^5 TS cells were grown in 6-well plates for 2 days in 70CM + F4H medium in the presence of DES (20 μM) or the vehicle (ethanol)
|
| Growth protocol |
TS cells were maintained in RPMI1640 (Sigma) supplemented with 20% FBS (Life Technologies), 1mM sodium pyruvate (Life Technologies), 50U/ml penicillin, 50μg/ml streptomycin, 100mM 2-mercaptoethanol (Sigma), 2mM Glutamax (Life Technologies), 25ng/ml FGF4 (R & D Systems), and 1μg/ml heparin (Sigma), with 70% of the media preconditioned by mitotically inactivated E12.5 embryonic fibroblasts (70CM + F4H medium)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from TS cells treated with DES or vehicle (ethanol) for 2 days using TRIzol reagent with PureLink RNA Micro Kit
Single-end 100bp RNA-sequencing libraries were prepared using TruSeq Stranded Sample Prep Kit with human/mouse/rat Ribo Zero Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DES_rep3
|
| Data processing |
FASTQ sequences were aligned to the mm9 genome using STAR v2.3.1z12 with default parameters
Gene expression was quantified using HTSeq v0.6.1, using genic GTF from mm9 refGene
Genome_build: mm9
Supplementary_files_format_and_content: Individual count tables generated as output from HTSeq
|
| |
|
| Submission date |
Dec 05, 2018 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Eiichi Okamura |
| E-mail(s) |
eiokamu@gmail.com
|
| Organization name |
Shiga University of Medical Science
|
| Department |
Research Center for Animal Life Science
|
| Lab |
Department of Stem Cells and Human Disease Models
|
| Street address |
Seta, Tsukinowa-cho
|
| City |
Otsu |
| State/province |
Shiga |
| ZIP/Postal code |
520-2192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE123362 |
Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [RNA-seq] |
| GSE123363 |
Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos |
|
| Relations |
| BioSample |
SAMN10523694 |
| SRA |
SRX5097638 |
