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Sample GSM1622724 Query DataSets for GSM1622724
Status Public on Jan 01, 2017
Title Stomach_Sox2-CreER, p53fl/+, Kras
Sample type SRA
 
Source name primary forestomach
Organism Mus musculus
Characteristics genotype/variation: Sox2-CreER, p53fl/+, Kras
strain: Mixed
tissue: primary forestomach
age: 1-2 month
Extracted molecule total RNA
Extraction protocol Primary tissues were isolated from 1-2 month old mice. Isolated tissues were homogenized with a polytrone in Trizol. The extracted RNA was purified with RNeasy Micro Kit from the homogenates.
RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). strand specific total RNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava v1.8.2 software used for basecalling.
Reads were aligned to the mouse (mm9) genome with STAR (v2.2.0c) with default parameters. Only uniquely alignable reads were used for downstream analysis
Fragments Per Kilobase of exon per milion mapped reads (FPKM) were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq)
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) annotation (8 to the end) FPKM
 
Submission date Mar 03, 2015
Last update date May 15, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platform ID GPL17021
Series (1)
GSE66457 Mutational blows to Sox2+ cells induce epithelial squamous tumor initiation
Relations
BioSample SAMN03383159
SRA SRX895474

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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