|
Status |
Public on Feb 20, 2014 |
Title |
MCF-10A-MeRIP rep1 |
Sample type |
SRA |
|
|
Source name |
MCF-10A-MeRIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF-10A cell type: Mammary Epithelial cells m5c antibody: Anti-5-Methlycytosine m5c antibody vendor: Zymo Research m5c antibody cat.#: A3001-50
|
Treatment protocol |
No additional treatment was performed to cell cultures
|
Growth protocol |
Human breast cancer cells MDA-MB-468 were grown in (150 mm X 16 cell culture plates) in RPMI medium (Invitrogen) supplemented with 10% fetal bovine serum, anti-anti (Invitrogen). Cells were allowed to grown until reaches 80% confluent were harvested using 0.25% trypsin (Invitrogen).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated and quantified from the cell culture using QIAZoL(Qiagen Inc.). Next, total RNA was enriched for polyadenylated RNA (polyA mRNA). Poly A+RNA was chemically fragmented into ~100-nucleotide long fragments. A portion of the fragmented RNA was subjected to RNA-seq that served as input (control). The remaining RNA was subjected to immunoprecipitation (IP) with anti-methyl cytosine antibody. The isolated, fragmented, and enriched m5C mRNAs were submitted for sequencing library preparation by using standard Illumina TruSeq Sample Preparation Kits, without poly-A purification step RNA-Seq, 50bp SR by Hiseq 2000
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
library strategy: MeRIP-Seq llumina Casava1.8 software used for basecalling. Sequenced reads were first aligned to TopHat. Peak calling was performed by ExomePeak at FDR < 0.05 with IP/Input Ratio set to 1. Differential analysis was performd by ExomePeak at FDR < 0.05. Genome_build: hg19 Supplementary_files_format_and_content: bed and xls files
|
|
|
Submission date |
Dec 16, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Xiaodong Cui |
E-mail(s) |
xdchoi@gmail.com
|
Organization name |
Univ of Texas SA
|
Department |
Electrical engineering
|
Street address |
126 Arrow Oaks
|
City |
San Antonio |
State/province |
Texas |
ZIP/Postal code |
78249 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE53370 |
RNA m5C Methylation in breast cancer using MeRIP-Seq |
|
Relations |
BioSample |
SAMN02444968 |
SRA |
SRX392825 |