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| Status |
Public on May 15, 2015 |
| Title |
Colony ID 25089 |
| Sample type |
SRA |
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| Source name |
Hypothalamus
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| 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
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| Treatment protocol |
Not applicable
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| Growth protocol |
Not applicable
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Description |
SAGE-Seq
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| 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.
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| Submission date |
Aug 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Brenda Richards |
| E-mail(s) |
richarbk@pbrc.edu
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| Organization name |
Pennington Biomedical Research Center
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| Department |
Basic Science
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| Lab |
Genetics of Eating Behavior
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| Street address |
6400 Perkins Rd.
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| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70808 |
| Country |
USA |
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| Platform ID |
GPL15907 |
| Series (1) |
| GSE60756 |
Differential gene expression in hypothalamus of non-recombinant subcongenic-derived F2 mice fed macronutrient selection diets |
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| Relations |
| BioSample |
SAMN03008862 |
| SRA |
SRX688944 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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