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Sample GSM1694282 Query DataSets for GSM1694282
Status Public on Jun 03, 2015
Title Duo_normal diet_1,25_3
Sample type SRA
 
Source name Duodenum
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))
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.
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
 
Submission date May 22, 2015
Last update date May 15, 2019
Contact name Mark B Meyer
E-mail(s) markmeyer@wisc.edu
Phone 608-890-0857
Organization name University of Wisconsin-Madison
Department Nutritional Sciences
Lab Meyer Lab
Street address 1415 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
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
Relations
BioSample SAMN03732327
SRA SRX1036960

Supplementary file Size Download File type/resource
GSM1694282_Duo_normal_diet_125_3_RPKM.txt.gz 181.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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