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Sample GSM1290213 Query DataSets for GSM1290213
Status Public on Feb 20, 2014
Title MDA-468-MeRIP rep2
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 SAMN02444965
SRA SRX392823

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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