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| Status |
Public on Aug 22, 2018 |
| Title |
FOL_10dcast_rep4 |
| Sample type |
SRA |
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| Source name |
ventral prostates
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue type: ventral prostates
experimental groups: Folate diet-10d post castration
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Jun 26, 2018 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Chad Michael Vezina |
| Organization name |
University of Wisconsin-Madison
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| Department |
Comparative Biosciences
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| Street address |
1656 Linden Drive
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE116299 |
A folic acid-enriched diet attenuates prostate involution in response to androgen deprivation |
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| Relations |
| BioSample |
SAMN09498073 |
| SRA |
SRX4301941 |
| 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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