|
| Status |
Public on Jan 10, 2022 |
| Title |
HEK293T KD - recovery |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T (stable cell line; CGGBP1-targetting shRNA)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293T
transduction: CGGBP1-targetting shRNA
|
| 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.
As per the Ligation Sequencing Kit SQK-LSK109 from Oxford Nanopore Technologies
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Data processing |
Library strategy: Oxford Nanopore Long-read sequencing
The library were sequencd using MinKNOW v20.10.3 with real-time basecalling using Guppy v4.2.2.
Sequencing adapters were trimmed using Porechop v0.2.4 from quality filtered reads and the reads were mapped using minimap2. For fusion analysis, the reads were splitted into 0.2kb bins followed by aligning to hg38 using bowtie2 v2.3.5.1.
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 |
GPL24106 |
| Series (1) |
| GSE169435 |
The homeotherm-conserved protein CGGBP1 connects heat stress to chromosomal fusions |
|
| Relations |
| BioSample |
SAMN18439505 |
| SRA |
SRX10421014 |
