|
| Status |
Public on Jan 10, 2022 |
| Title |
TP53BP1 KD |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T (stable cell line; CGGBP1-targetting shRNA)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293T
transduction: CGGBP1-targetting shRNA
antibody: NB100-304 (Novus Biologicals)
|
| Treatment protocol |
HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) [Origene Lentiviral system TL313955V]. For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin. Human primary fibroblast (GM02639) cells were cultured at 37°C, heat stressed at 40°C for 24h with 1°C increment per day and recovered at 37°C post-heat stress for 24 h. The CT and KD cells were cultured at 37°C, heat stressed at 42°C for 24h and recovered at 37°C post-heat stress for 24h.
|
| Growth protocol |
Human primary fibroblasts [Coriell Cell Repository GM02639] and HEK293T CT and KD [lentivirally transduced shRNA system as described in PMID 31547883] were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Human primary fibroblasts [Coriell Cell Repository GM02639] were harvested from two T25 flasks for each sample. HEK293T CT and KD cells were harvested from two 10cm dishes for each sample. Genomic DNA was extracted using standard phenol:chloroform:isoamyl alcohol extraction method followed by ethanol precipitation and dissolution in nuclease-free water. For TP53BP1 ChIP-seq was performed as described elsewhere [PMID 31547883] except for the following modifications: The antibody used was NB100-304 (Novus Biologicals) against TP53BP1.
Ion Express Plus Fragment Library kit (Cat. No. 4471269) from ThermoFisher Scientific
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
The ChIP DNA libraries were sequenced on Ion Torrent S5 platform. The quality attribution for base call was done as per the IonTorrent suite default of Q20 or more.
TP53BP1 signals exclusive to CT or KD with a minimum read coverage of 5 reads in genomic bins of 0.2kb were generated and used to compare TP53BP1 occupancy difference between the two samples using frequency plots for read densities and pileups across the 0.2kb bins genome-wide.
Genome_build: hg38
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Umashankar Singh |
| Organization name |
IIT Gandhinagar
|
| Department |
Biological Sciences and Engineering
|
| Lab |
HoMeCell Lab
|
| Street address |
Acad Block 4 Room 317 IIT Gandhinagar Palaj
|
| City |
Gandhinagar |
| State/province |
Gujarat |
| ZIP/Postal code |
382055 |
| Country |
India |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE169435 |
The homeotherm-conserved protein CGGBP1 connects heat stress to chromosomal fusions |
|
| Relations |
| BioSample |
SAMN18439503 |
| SRA |
SRX10421016 |
