|
| Status |
Public on Aug 16, 2024 |
| Title |
HEK293T_LTR12C-target_VP64_WGBS |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human Embryonic Kidney
genotype: WT
treatment: LTR12C-target CRISPRa (VP64)
|
| Treatment protocol |
Transfections were performed by Lipofectamine LTX Reagent (Termo Fisher Scientific) with 500ng plasmid constructs into HEK293T cells. The cells were harvested at 3 days after treatment.
|
| Growth protocol |
HEK293T cells were mainteined in DMEM with 10%FBS and antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from HEK293T after CRISPRa was purified using a DNAzol (Invitrogen)
Bisulfite conversion, library preparation, and sequencing were performed by the Van Andel Research Institute Genomics Core.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BSMAP_LTR12C-target_result.txt
|
| Data processing |
Sequencing reads were aligned against the human GRCh37/hg19 reference genomeb by BSMAP.
The DNA methylation levels at each CpG site were calculated as the ratio of methylated CpG and all CpG in uniquely mapped reads.
The definitions of ERV elements were based on RepeatMasker.
Assembly: hg19
Supplementary files format and content: BSMAP_Non-target_result.txt
Supplementary files format and content: BSMAP_LTR12C-target_result.txt
|
| |
|
| Submission date |
Sep 19, 2023 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Hitoshi Ohtani |
| E-mail(s) |
otani@agr.nagoya-u.ac.jp
|
| Organization name |
Nagoya University
|
| Department |
Graduate School of Bioagricultural Sciences
|
| Lab |
Laboratory of Genome and Epigenome Dynamics
|
| Street address |
Furo-cho
|
| City |
Chikusa-ku |
| State/province |
Nagoya |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE243548 |
Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq] |
| GSE243551 |
Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer |
|
| Relations |
| BioSample |
SAMN37458850 |
| SRA |
SRX21827800 |
