NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1435024 Query DataSets for GSM1435024
Status Public on Aug 24, 2015
Title YJ1: pS6-IP from control 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 with acetophenone 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 No_litter2
pS6-IP from control olfactory epithelium
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 Jul 11, 2014
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 SAMN02909993
SRA SRX650932

Supplementary file Size Download File type/resource
GSM1435024_YJ1counts.txt.gz 200.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap