|
| Status |
Public on Jul 31, 2022 |
| Title |
Established Trophoblast Stem Cells, clone 2, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Trophoblast Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BDF2
|
| Treatment protocol |
Doxycycline treatment for different time points decribed in each sample. Some samples were treated with LPA as indicated.
|
| Growth protocol |
Cell were cultured on MEFs in humdified 5%Co2 , 21% O2 incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy mini RNA kit
Bulk MARS-seq
3 primed library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Established Trophoblast Stem Cells, clone 2, replicate 1
|
| Data processing |
Samples were analyzed using UTAP software (Kohen et al. 2019). Reads were trimmed using CutAdapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic - alignSoftClipAtReferenceEnds No).
Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes. Further analysis was done for genes having a minimum of five reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters betaPrior = true, cooksCutoff = false, and independentFiltering = false.
Assembly: mm10
|
| |
|
| Submission date |
Jun 07, 2022 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
[email protected]
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Street address |
Weizmann Institute
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE205634 |
Ex Utero Development of Post-Gastrulation Synthetic Mouse Embryos Generated Solely from Naïve Pluripotent Stem Cells [RNA-seq] |
| GSE208681 |
Ex Utero Development of Post-Gastrulation Synthetic Embryos Generated Solely from Naïve Pluripotent Stem Cells |
|
| Relations |
| BioSample |
SAMN28901956 |
| SRA |
SRX15625536 |
