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| Status |
Public on Jun 03, 2015 |
| Title |
Duo_normal diet_1,25_5 |
| Sample type |
SRA |
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| Source name |
Duodenum
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| Organism |
Mus musculus |
| Characteristics |
strain: Cyp27b1 null mice
age: 8 weeks old
gender: male
diet: normal
tissue: Duodenum
treatment: 1,25(OH)2D3 (2 ng/g body weight (bw))
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| Treatment protocol |
Cyp27b1 null mice at 8 weeks of age were treated with vehicle or 2 ng/g body weight of 1,25(OH)2D3 for 6 hours prior to RNA harvesting.
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| Growth protocol |
Cyp27b1 null mice were fed on highly purified vitamin D-deficient diet containing 0.47% Ca, 0.3% P and vitamins A, E, and K (normal diet) or on the same diet containing 20% lactose, 2% Ca, 1.25% P (rescue diet) at weaning and until 8 weeks of age.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH). Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions. Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings. Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample
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| Submission date |
May 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark B Meyer |
| E-mail(s) |
markmeyer@wisc.edu
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| Phone |
608-890-0857
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| Organization name |
University of Wisconsin-Madison
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| Department |
Nutritional Sciences
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| Lab |
Meyer Lab
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| Street address |
1415 Linden Dr.
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE69170 |
1,25-Dihydroxyvitamin D3 Controls a Cohort of Vitamin D Receptor Target Genes in the Proximal Intestine That Is Enriched for Calcium Regulating Components (RNA-seq) |
| GSE69180 |
1,25-Dihydroxyvitamin D3 Controls a Cohort of Vitamin D Receptor Target Genes in the Proximal Intestine That Is Enriched for Calcium Regulating Components |
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| Relations |
| BioSample |
SAMN03732300 |
| SRA |
SRX1036962 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1694284_Duo_normal_diet_125_5_RPKM.txt.gz |
183.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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