|
| Status |
Public on Aug 06, 2012 |
| Title |
C57BL/6 Brain_Sample 2_MeRIP - SYSY |
| Sample type |
SRA |
| |
|
| Source name |
whole brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: Adult
sample type: RNA IP against m6A
merip antibody: m6A
merip antibody vendor: Synaptic Systems (SYSY)
merip antibody cat. #: 202 003
merip antibody lot #: 202003/7
rna subtype: RiboMinus RNA
library strategy: MeRIP-Seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from adult mouse brain 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA IP against m6A
|
| 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 |
Dec 27, 2011 |
| 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 |
GPL11002 |
| Series (1) |
| GSE29714 |
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons |
|
| Relations |
| SRA |
SRX113247 |
| BioSample |
SAMN00768935 |
