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Sample GSM1487457 Query DataSets for GSM1487457
Status Public on May 15, 2015
Title Colony ID 25089
Sample type SRA
 
Source name Hypothalamus
Organism Mus musculus
Characteristics study id: 93
colony id: 25089
genotype across subcongenic segment: cast/cast
10 sum total kcal: 133.1
10 sum carbohydrate/protein kcal: 85.7
Treatment protocol Not applicable
Growth protocol Not applicable
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated using the AllPrep RNA/Protein kit (Qiagen, Valencia, CA) and re-suspended in Nanopure water.
Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE kit (Life Technologies) according to manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Description SAGE-Seq
Data processing XSQ files generated from 5500XL SOLiD sequencer were converted into CSFASTA and QUAL files using XSQ Tools.
Sequenced reads were aligned to the NCBI RefSeq reference sequence and
SAGE tags were counted using SOLiD SAGE Analysis Software v1.10
SAGE tag counts were normalized to reads per million (RPM) using R.
Values of RPM were expressed as binary logarithm values (log2 RPM).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file; tag hits, i.e., successfully aligned reads, were normalized according to DESeq by estimating the size factor for each sample and dividing the sample counts by the corresponding size factor. File contains: symbol, id, geneID, chr, strand, transcStart, transEnd, baseMean, baseMeanA, baseMeanB, foldChange,log2FoldChange, pval, padj; and one column per individual mouse sample/ID.
 
Submission date Aug 26, 2014
Last update date May 15, 2019
Contact name Brenda Richards
E-mail(s) richarbk@pbrc.edu
Organization name Pennington Biomedical Research Center
Department Basic Science
Lab Genetics of Eating Behavior
Street address 6400 Perkins Rd.
City Baton Rouge
State/province LA
ZIP/Postal code 70808
Country USA
 
Platform ID GPL15907
Series (1)
GSE60756 Differential gene expression in hypothalamus of non-recombinant subcongenic-derived F2 mice fed macronutrient selection diets
Relations
BioSample SAMN03008862
SRA SRX688944

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

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