|
| Status |
Public on Dec 30, 2020 |
| Title |
Terc-/-ESC PDL800times-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse Embryonic Stem Cell
strain: DKO741
|
| Treatment protocol |
Cells were longitudinally harvested at 100 and 800 passage
|
| Growth protocol |
The Terc targeting construct (TR-10) was transfected into E14 mESC by electroporation to exchange the first Terc allele. The targeting plasmid included PGK-neo gene flanked by loxP sites. The transfected cells were selected with G418 (200 mg/ml) and Ganciclovir (1 mM). The resistant Terc+/- cells were picked after eight days. The neo gene was removed by infection with the adenovirus of Cre recombinase. The Terc+/- cells were re-targeted with TR-10. Two lines of Terc-/- ESC, DKO301 and DKO741 were recovered. Both of DKO301 and DKO741 produced survivors with rare frequencies. We got those ALT survivor cells at each PDL timing (PD100, PD350, PD400, PD450) with control (Terc+/+) cells. For mESC maintenance and stock preparation, mouse embryonic fibroblast (MEF) cells were used as feeder cells. Feeder-free mESCs were used for all experiments including nucleic acids extraction, protein extraction, immunostaining, and fluorescent in situ hybridization.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using chloroform and isopropanol precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The reads were aligned to the mm10 reference genome using the STAR aligner (version 2.5.3a)
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TMP for each sample from the corresponding bam files.
The read counts were processed using DESeq2 (v1.18.1) to identify differentailly expressed genes.
Genome_build: mm10
|
| |
|
| Submission date |
Apr 01, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
DAEUN KIM |
| Organization name |
Ajou university
|
| Street address |
World cup-ro
|
| City |
suwon |
| ZIP/Postal code |
KS002 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE147913 |
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (RNA-seq) |
| GSE147916 |
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN14518730 |
| SRA |
SRX8042367 |
