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| Status |
Public on Sep 17, 2013 |
| Title |
Wt Ribo-Seq 2.0 ppm Se |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
age: 3 weeks
treatment: 6 week diet 2.0 ppm selenium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were excised, flash frozen in liquid nitrogen, and homogenized in the presence of cycloheximide using a bead mill. Ribo-Seq samples were treated with Rnase 1 and monosomes isolated by ultracentrifugation. Ribosome protected fragments and total mRNA were isolated using Trizol reagent.
TruSeq small RNA Sample Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ribosome protected mRNA
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| Data processing |
base calling was done with the standard Illumina pipeline
Sequence reads were trimmed for adaptor sequences, and aligned using bowtie (alignment parameters -m1 -v2 -a --best --strata) to a mm9 RefSeq mRNA database in which each transcript with multiple isoforms was reduced to a single entry corresponding to the longest isoform. For Selenoprotein analysis, a data base of selenoprotein mRNAs was created from RefSeq entries and ribosome protected or mRNA sequences were aligned individually using the same bowtie parameters.
Reads per kilobase per million mapped reads (RPKM for total RNA RPFKM for ribosome protected fragments) in each experiment were determined for entire mRNAs, for coding sequences (excluding the first 15 and last 3 codons). For selenoproteins, coding sequences upstream of the UGA-Sec codon and downstream of the UGA-Sec codon were also examined and assigned RPKM values.
Genome_build: RefSeq July 2008 release
Supplementary_files_format_and_content: RPKM
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| Submission date |
Apr 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael T Howard |
| E-mail(s) |
[email protected]
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| Phone |
801-585-1927
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| Organization name |
University of Utah
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| Department |
Human Genetics
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| Lab |
Howard
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| Street address |
15 N 2030 E
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE46038 |
The effects of dietary selenium on selenocysteine incorporation and selenoprotein expression |
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| Relations |
| SRA |
SRX265140 |
| BioSample |
SAMN02045515 |
| 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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