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| Status |
Public on Dec 03, 2018 |
| Title |
Sperm Donor2 smRNA-seq |
| Sample type |
SRA |
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| Source name |
Sperm Donor 2, smRNA
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| Organism |
Homo sapiens |
| Characteristics |
cell type: sperm
library prep method: smRNA directional
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| Growth protocol |
The two sperm donor samples were obtained from men of known fertility attending the University of Utah Andrology laboratory, consented for research. Samples were collected after 2-5 days abstinence and subjected to a density gradient to purify viable, motile, mature sperm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fertile donors (Donor1 and Donor2) using Trizol. The RNA was treated with DNase and submitted for long and small RNA-seq directional library preparation using the standard Illumina protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
7397X2
Directional RNA-Seq.
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| Data processing |
Basecalls were performed using CASAVA version 1.7.
Reads were aligned to hg18 using Novoalign V2.07.09 allowing up to 10 alignments per read, using these parameters for mRNA-seq alignments: -FILMFQ -o SAM -m -l17 -t60 -rA 10 -a and these settings for smRNA-seq alignments: -FILMFQ -o SAM -m -l17 -h90 -t30 -rA 10 -a. The novoalign index was made by combining hg18 fasta files (UCSC), Illumina adapter sequences, and splice junction fasta files made using MakeSpliceJunctionFasta (USeq version 6.0) with -s 34 as input radius and merged ensGene and knownGene table (from genome.ucsc.edu) as annotation.
Alignment (SAM format) files were fixed using SamFixer (USeq 8.3.3). For each donor sample, smRNA and mRNA alignment files were merged and sorted with SortSam (picard 1.40), then converted to binary PointData with SamParser (USeq 8.3.3) using parameters -m 0 -a 1000 to retain all reads. Counts for Refseq genes, piRNAs, and miRNAs were determined with DefinedRegionScanSeqs (USeq 8.3.3) using parameters -p 0 -o.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files contain RPKM expression values for RefSeq genes, piRNAs, and miRNAs. Files are linked to the Series record as supplementary files.
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| Submission date |
Aug 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Oler |
| E-mail(s) |
andrew.oler@nih.gov
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| Organization name |
NIAID/NIH
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| Department |
Bioinformatics and Computational Biosciences Branch (BCBB)
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| Lab |
Computational Biology Section
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| Street address |
31 Center Drive, Room 3B62E
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE40181 |
Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (RNA-Seq) |
| GSE40196 |
Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs |
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| Relations |
| SRA |
SRX178613 |
| BioSample |
SAMN01120629 |
| 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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