|
| Status |
Public on Jul 25, 2022 |
| Title |
MCF-7 AP2C siTRIM37 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer cell line
genotype/variation: siTRIM37
chip antibody: AP-2γ (Santa Cruz, sc12762x)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and interested protein-DNA complexes were isolated with antibody.
library preparations were constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie v0.12.9 with default parameters
SAM to BAM conversion and sorting was performed using samtools v1.9.0
The duplicated reads were marked using Picard MarkDuplicates v2.20.0 utility
Peak calling was performed using MACS1.4 with pvalue < 1e-4
The alignment coverage was calculated and converted into bigwig format using deeptools v3.4.3 bamCoverage utility and visualized into IGV v2.7.2 (Genome Build: hg19)
Genome_build: hg19
Supplementary_files_format_and_content: .bed files representing the peaks in text formate
Supplementary_files_format_and_content: .bw files store alignment coverage in binary foramte
|
| |
|
| Submission date |
Aug 22, 2021 |
| Last update date |
Jul 27, 2022 |
| Contact name |
Edwin Chong Wing CHEUNG |
| E-mail(s) |
ECheung@um.edu.mo
|
| Organization name |
University of Macau
|
| Department |
Faculty of Health Sciences
|
| Lab |
Edwin CHEUNG's lab
|
| Street address |
Avenida da Universidade, Taipa
|
| City |
Macau |
| State/province |
Macau |
| ZIP/Postal code |
999078 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE182546 |
TRIM37 augments AP-2γ transcriptional activity and cellular localization via K63-linked polyubiquitination to drive breast cancer progression [ChIP-seq] |
| GSE182547 |
TRIM37 augments AP-2γ transcriptional activity and cellular localization via K63-linked polyubiquitination to drive breast cancer progression. |
|
| Relations |
| BioSample |
SAMN20924821 |
| SRA |
SRX11858168 |
