|
| Status |
Public on Mar 31, 2022 |
| Title |
si-N6AMT1 6mA-IP-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-453
6ma-ip-seq antibody: 6mA antibodies (Synaptic Systems)
|
| Treatment protocol |
siRNA (10 nM) targeting human N6AMT1 and scramble siRNA (Control) were transfected into MDA-MB-453 cells using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) for 48 hours.
|
| Growth protocol |
MDA-MB-453 cells were cultured in DMEM growth medium supplemented with 10% FBS, 1% 100x penicillin-streptomycin-amphotericin B, and 1% 100x nonessential amino acid solution in a humidified incubator at 37°C with 5% carbon dioxide.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cultured cells via a TIANamp Genomic DNA Kit (Tiangen Biotech, China). To exclude contaminating RNA, the genomic DNA was treated with 0.1 mg/ml RNase A.
Six libraries (two biological replicates each for immune-precipitated DNA and their input) were prepared using a NovaSeq 6000 S4 Reagent Kit (300 cycles) according to the manufacturer’s instructions
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The high quality of reads was aligned to the human reference genome (hg19) by bowtie2 (v2.3.5) (PMID: 22388286).
Duplicated reads were removed by samtools (v1.9).
6mA methylated regions were identified with MACS2 with parameters -p 1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Feb 10, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Ping Wang |
| E-mail(s) |
pingwangwp@gmail.com
|
| Organization name |
Tianjin Medical University
|
| Street address |
No22.Qixiangtai Rd.,Heping Dist
|
| City |
Tianjin |
| ZIP/Postal code |
300000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE166580 |
Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression [MeDIP-seq] |
| GSE166582 |
Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression |
|
| Relations |
| BioSample |
SAMN17861046 |
| SRA |
SRX10070654 |
