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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 30, 2020 |
| Title |
Terc-/-ESC PDL450times |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse Embryonic Stem Cell
strain: DKO741
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| Treatment protocol |
Cells were longitudinally harvested at 100, 350, 450 and 800 passage
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN)
DNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: WGS
WGS reads were mapped to the mm10 reference genome using Burrows-Wheeler Aligner (BWA) MEM algorithm (version 0.7.17)
Duplicated reads were marked with Picard-Tools (version 1.96) and Samtools (version 1.9)
For visualizing mTALT reads on the UCSC genome browser (Kent et al., 2002), chr13: 119,891,001-120,300,000 region on the mm10 reference genome was masked with Ns and then all the reads were re-mapped onto the masked genome. Coverage of mapped reads was computed by bedtools genomecov (version v2.25.0)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format of genome coverage
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| Submission date |
Apr 01, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
DAEUN KIM |
| Organization name |
Ajou university
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| Street address |
World cup-ro
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| City |
suwon |
| ZIP/Postal code |
KS002 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE147914 |
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (WGS) |
| GSE147916 |
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN14518725 |
| SRA |
SRX8042371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4448851_PD450_741_chr13N.bw |
5.1 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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