|
| Status |
Public on Jun 15, 2022 |
| Title |
BT-549 (TQ- / control) |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Triple negative breast cancer
chip antibody: anti- MBD1 (#ab2846, Abcam, USA)
treatment: thymoquinone untreated (DMSO treated)
|
| Treatment protocol |
BT-549 cells were treated with thymoquinone for 6 h and chromatin immune-precipitation (ChIP) was performed using anti- MBD1 antibody (Abcam, USA).
|
| Growth protocol |
BT-549 cells were cultured in DMEM media (Gibco, Thermo Fisher ScientificTM) supplemented with 10-15% fetal bovine serum (FBS) in cell culture dishes or flasks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA Lysates were clarified from sonicated nuclei and Anti-MBD1 could precipitate specific genomic region, which are methylated.
Libraries were prepared according to Life's instructions accompanying the DNA Sample Kit (Ion AmpliSeq Library Kit 2.0). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Life primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Ion Torrent S5 following the manufacturer's protocols.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
raw data QC with FastQC
reads filtered and mapped to the mm9 genome assembly using Bowtie2 which default parameters.
peaks were called using MACS2 version 2.2.4 with default parameters.
call genes with 2K bandwidth at two side of each peak with R codes.
genes annotation was performed using ANNOVAR (June 8 2017)
Genome_build: mm9
Supplementary_files_format_and_content: fastq
Supplementary_files_format_and_content: peak
|
| |
|
| Submission date |
Jun 16, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Md. Asaduzzaman Khan |
| E-mail(s) |
asadkhanbmj@yahoo.com
|
| Organization name |
Southwest Medical University
|
| Department |
The research center for preclinical medicine
|
| Lab |
Key laboratory of epigenetics and oncology
|
| Street address |
3-319, Zhongshan road
|
| City |
Luzhou |
| State/province |
Sichuan |
| ZIP/Postal code |
646000 |
| Country |
China |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE178334 |
Identification of methylated sites in BT-549 cells affected by thymoquinone treatment |
|
| Relations |
| BioSample |
SAMN19731406 |
| SRA |
SRX11169306 |
