|
Status |
Public on Oct 14, 2016 |
Title |
R3_IP |
Sample type |
SRA |
|
|
Source name |
LCL
|
Organism |
Macaca mulatta |
Characteristics |
cell line: lymphoblastoid cell line (LCL) ip antibody: m6A specific antibody (SYSY, CAT#202003, LOT#42)
|
Treatment protocol |
mRNA was fragmented to ~100nt, and enriched by m6A specific antibody
|
Growth protocol |
LCLs were cultured in RPMI1640 media with 15% FBS and Penicillin-Streptomycin
|
Extracted molecule |
total RNA |
Extraction protocol |
Regular RNA isolation Illumina TruSeq stranded total RNA protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
library strategy: m6A-seq Base calling was performed using CASAVA 1.3 Alignment was done by TopHat v2.0.14 Peak calling was done by customized algorithm Genome_build: hg38; panTro4; rheMac2(Mmul_051212) Supplementary_files_format_and_content: Peaks were generated by customized algorithm, enrichment score of each peak file represented the ratio of reads between m6A-enriched mRNA and intact mRNA.
|
|
|
Submission date |
Jun 26, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Kevin P. White |
E-mail(s) |
kpwhite@uchicago.edu
|
Organization name |
University of Chicago
|
Department |
Institute for Genomics and Systems Biology
|
Street address |
900 E. 57th STR. 10th FL.
|
City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60615 |
Country |
USA |
|
|
Platform ID |
GPL19129 |
Series (1) |
GSE70299 |
The evolution of N6-methyladenosine in primates |
|
Relations |
BioSample |
SAMN03797555 |
SRA |
SRX1074170 |