|
| Status |
Public on Aug 24, 2015 |
| Title |
YJG6: pS6-IP from 100% TMT stimulated olfactory epithelium |
| Sample type |
SRA |
| |
|
| Source name |
olfactory epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: c57BL/6
developmental stage: post natal day 21
ip antibody: pS6 antibody, Cell signaling, #2215
|
| Treatment protocol |
mice were stiumlated withTMT or control for 1 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
homogenates of olfactory epithelium were incubated with pS6 antibody to immunoprecipitate mRNAs associated with pS6
mRNAs were reverse-transcribed into cDNA, which was then amplified and constructed into sequencing biraries using Illumina Nextera library prep kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pS6-IP from 100% TMT stimulated olfactory epithelium
TMT_litter3
|
| Data processing |
we implemented a stepwise mapping scheme that allows reads aligned to multiple regions to be distributed proportionally to these regions based on the previous read counts from these regions (Mortazavi et al., 2008).
reads were aligned to mm10 by Bowtie with -m 20 -a, 100bp reads were trimmed to 50bp
the resulted mapping file was separated into 20 sub-files that includes reads only mapped to 1, 2, ... , 20 regions respectively. BEDTools was used to first count reads mapped to coding exons of genes using only uniquely mapped reads. Reads mapped to two regions were distributed based on read counts from uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: The first column contains gene names. The next 20 columns are read counts corresponding to the 20 iterations described above.
|
| |
|
| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hiroaki Matsunami |
| E-mail(s) |
hiroaki.matsunami@duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Department of Molecular Genetics and Microbiology
|
| Street address |
264 CARL Building Box 3509 DUMC
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE59324 |
Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo |
|
| Relations |
| BioSample |
SAMN03351781 |
| SRA |
SRX879195 |
