|
| Status |
Public on Aug 06, 2012 |
| Title |
HEK293T_Sample 3_Non-IP Control |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: embryonic kidney cells
tissue source: kidney
sample type: no IP (input RNA)
rna subtype: RiboMinus RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from adult mouse brain and HEK293T cells and subjected to RiboMinus treatment to remove rRNAs. RNA was then subjected to 2 rounds of m6A RNA immunoprecipitation (MeRIP) using an antibody that recognizes m6A
library strategy: MeRIP-Seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads aligned to genome using BWA with default settings, converted to BAM files using SamTools, converted to sorted BAM files using SamTools, converted to bedgraphs using genomeCoverageBed and converted to bigwigs using bedGraphToBigWig
Peaks were found using MeRIPPeR software, inputting BWA-aligned reads, processed across 3 replicates for each organism.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bigwigs show number of reads mapping to the genome
|
| |
|
| Submission date |
May 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher E Mason |
| E-mail(s) |
chm2042@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Physiology and Biophysics
|
| Lab |
Christopher Mason Lab
|
| Street address |
1305 York Ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE29714 |
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons |
|
| Relations |
| SRA |
SRX146456 |
| BioSample |
SAMN00991412 |
