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Sample GSM999244 Query DataSets for GSM999244
Status Public on Sep 08, 2012
Title Mouse P6 Sertoli Cells
Sample type SRA
 
Source name Sertoli Cells
Organism Mus musculus
Characteristics strain: C57Bl/6
age: post-natal day 6
cell type: pooled Sertoli cells
cell purity: >85%
molecule subtype: small RNA
Extracted molecule total RNA
Extraction protocol Ro S, Yan W. Small RNA Cloning. In: Sioud M (ed.) RNA Therapeutics: Function, Design, and Delivery: Humana Press Inc; 2010: 271-283
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 Two nucleotide barcode tag for Sertoli sequences is NA
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
Novel endo-siRNA detection was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html
Novel miRNA detection was performed using MIREAP - http://sourceforge.net/projects/MIREAP
Novel snoRNA detection was performed using snoREPORT - http://www.bioinf.uni-leipzig.de/Software/snoReport
Novel piRNA-like detection was determined by remaining unannotated sequence lengths (24-32 nts).
Genome_build: mm9
Supplementary_files_format_and_content: gff file contains novel small RNAs and their genomic locations
 
Submission date Sep 07, 2012
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)
GSE40692 P6 Mouse Sertoli Cell Small RNA seq
Relations
SRA SRX184872
BioSample SAMN01163379

Supplementary file Size Download File type/resource
GSM999244_Sertoli_P6_mm9.gff.gz 573.6 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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