|
| Status |
Public on Feb 20, 2014 |
| Title |
MDA-468-MeRIP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-468-MeRIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-468
cell type: Human breast cancer 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 |
SAMN02444962 |
| SRA |
SRX392821 |
