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Sample GSM3227747 Query DataSets for GSM3227747
Status Public on Aug 22, 2018
Title CNTRL_10dcast_rep1
Sample type SRA
 
Source name ventral prostates
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue type: ventral prostates
experimental groups: Control diet-10d post castration
Treatment protocol Mice were exposed to a control (4mg/kg folic acid) or folic acid enriched diet (24mg/kg folic acid) from in utero and throughout lifetime. At 7weeks of age,intact mice were sacrificed to collected ventral prostates or castrated and the ventral prostate collected after 3 or 10 days.
Extracted molecule total RNA
Extraction protocol RNA was isolated from the ventral prostates of four mice per group from each of six groups: Control diet-Intact, FA diet-Intact, Control diet-3d post-castration, FA diet-3d post-castration, Control diet-10d post-castration and FA diet-10d post-castration using the Illustra RNAspin Mini kit (#25-0500-72, GE Healthcare, Chicago, Illinois, USA).
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls/demuxxing performed using Illumina bcl2fastq, v2.17.1.14
Reads were filtered and trimmed for adapters and quality.
Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with a table of Expected Counts expression estimates from the RSEM application
 
Submission date Jun 26, 2018
Last update date Aug 22, 2018
Contact name Chad Michael Vezina
Organization name University of Wisconsin-Madison
Department Comparative Biosciences
Street address 1656 Linden Drive
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL21493
Series (1)
GSE116299 A folic acid-enriched diet attenuates prostate involution in response to androgen deprivation
Relations
BioSample SAMN09498080

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

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