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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 07, 2016 |
| Title |
mouse total sperm sncRNA-Seq rep2 |
| Sample type |
SRA |
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| Source name |
mouse total sperm sncRNA-Seq
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: adult
genotype: wild type
tissue: total sperm
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sperm samples using the mirVana total RNA extraction protocol. Human and rabbit sperm samples were pipeted up and down during lysis; mouse sperm samples were homogenized for one minute during lysis; rat samples were homogenized for 90 seconds and subsequently incubated at 65C for five minutes during lysis.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Torrent suite
RNA-Seq: Sequenced reads were mapped to (mm10, mouse; rn5, rat; oryCun2, rabbit; hg19, human) whole genome using TOPHAT; sncRNA-Seq: Sequenced reads were matched to sncRNA sequences via Sequery and then mapped to (mm10, mouse; rn5, rat; oryCun2, rabbit; hg19, human) via Bowtie.
RNA-Seq: Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated and isoforms were assembled by using a protocol from Cufflinks; sncRNA-Seq: reads per 100,000 aligned reads (RPK) were calculated
Genome_build: mm10, mouse; hg19, human; oryCun2, rabbit; rn5, rat
Supplementary_files_format_and_content: Averaged, normalized expression values are provided for the RNA-Seq (RPKM) and sncRNA-Seq (RPK) samples. The processed data table is organized by gene name ("Gene"), species of origin ("Species"), sample type, i.e., total sperm or sperm head ("Sample"), class of RNA ("Class"), normalized average expression ("Expression")
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| Submission date |
May 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Yan |
| E-mail(s) |
wyan@medicine.nevada.edu
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| Phone |
(775) 784-7765
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| Organization name |
University of Nevada
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| Department |
Physiology
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| Lab |
Wei Yan Lab
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| Street address |
1664 N. Virginia Street
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| City |
reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE81216 |
SpermBase - A database for sperm-borne RNA contents |
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| Relations |
| BioSample |
SAMN04958933 |
| SRA |
SRX1745752 |
| 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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