NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1176872 Query DataSets for GSM1176872
Status Public on Jul 15, 2013
Title Mouse Adult Small Intestine
Sample type SRA
 
Source name Small Intestine
Organism Mus musculus
Characteristics strain/background: C57BL/6
developmental stage: adult
tissue: small intestine
tissue/cell preparation: homogenized tissue
sample type: pooled
Extracted molecule total RNA
Extraction protocol ICC were FACS sorted by c-kit antibodies, frozen and lysed. Sm Int was collected, flash frozen, and whole tissue homogenized and lysed. sncRNA were collected with the mirVana isolation kit.
Barcoded and prepared per 454 library preparation protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model 454 GS 20
 
Description Small RNA
Data processing 454 instrument data processing to fastA files.
Filtering and adaptor trimming were performed on Sequery - www.medicine.nevada.edu/yan/sequery.html.
Mapping to known small RNA sequences was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Alignment to mm9 Mus musculus genome was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Removal of novel endo-siRNA detection was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Removal of novel miRNA detection was performed using MIREAP - http://sourceforge.net/projects/MIREAP.
Novel piRNA-like detection was determined by remaining unannotated sequence lengths (24-32 nts).
Genome_build: MGSCv37
Supplementary_files_format_and_content: .GFF file contains novel pilRNAs and their genomic locations.
 
Submission date Jun 27, 2013
Last update date May 15, 2019
Contact name Nicole Ortogero
Organization name University of Nevada, Reno
Department Physiology and Cell Biology
Lab Dr. Wei Yan
Street address 1664 N. Virginia St
City Reno
State/province Nevada
ZIP/Postal code 89557
Country USA
 
Platform ID GPL9522
Series (1)
GSE48388 Adult Murine Interstitial Cells of Cajal (ICC) and Small Intestine (Sm Int) Somatic piRNA-like RNA (pilRNA)
Relations
BioSample SAMN02215333
SRA SRX316586

Supplementary file Size Download File type/resource
GSM1176872_SmInt_novel_pilRNA.gff.gz 2.4 Kb (ftp)(http) GFF
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