|
| Status |
Public on Jun 01, 2024 |
| Title |
HEK-293T, HS2-HBG_treated_by_ABA |
| Sample type |
SRA |
| |
|
| Source name |
HEK-293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293T
cell type: Human embryonic kidney
genotype: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS
treatment: Transfected by HS2 and HBG gRNAs and treated by ABA
|
| Growth protocol |
HEK-293T cells were cultured in DMEM medium with addition of 10% FBS and 1% PS at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells was fixed by 1% Formaldehyde and chromatin was sonicated after cell lysis, nuclei permeabilization, is situ digestion & ligation.
Sequencing libraries were constructed following the established in situ ChIA-PET protocol using 10 million input HEK 293 cells co-expressing both ABI1-mCherry-dCas9-VP64-FUS with gHS2 and PYL1-BFP-dCpf1-VP64-FUS with crRNAs before and after ABA treatment, employing an antibody specifically targeting mCherry
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
*library strategy: ChIA-PET
The obtained sequencing data from the in situ ChIA-PET experiment were subjected to data processing using the ChIA-PIPE software. Visualization of the data was performed using the BASIC Browser. Chromatin Contacts within the regions of interest were plotted as violin plots, with the corresponding pet counts being aggregated on the top. Statistical analysis was conducted using a binomial test to determine the significance, and the resulting p-value was shown.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes track loop for each sample
Supplementary files format and content: tab-delimited text file includes peak for each sample
|
| |
|
| Submission date |
Nov 23, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Rui Chen |
| E-mail(s) |
12131298@mail.sustech.edu.cn
|
| Phone |
13149905923
|
| Organization name |
Southern University of Science and Technology
|
| Lab |
Chenwei lab
|
| Street address |
Southern University of Science and Technology
|
| City |
ShenZhen |
| State/province |
GuangDong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248522 |
Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [ChIA-PET] |
| GSE249351 |
Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping. |
|
| Relations |
| BioSample |
SAMN38391735 |
| SRA |
SRX22629186 |
