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| Status |
Public on Jun 17, 2015 |
| Title |
Control 2 |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: testis
age: post natal 6 months
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Testes were removed, flash frozen on dry ice, and RNA was harvested using the mirVana™ miRNA Isolation Kit reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina HiSeq 2000 and Off-Line Basecaller software(OLB V1.8.0) were used for basecalling.
Subsequently, 3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and any reads shorter than 15nt were discarded. Next the 3’-adapter-trimmed-reads (≥ 15nt) were aligned to the latest known human reference miRNA precursor set (Sanger miRBase 19) using Novoalign (v2.07.11). Reads (counts < 2) were discarded when calculating miRNA expression. In order to characterize the isomiR variability, any sequences that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
For piRNAs, the 3’-adapter-trimmed reads (length ≥ 15nt) were aligned to the latest piRNA set in piRNAbank using Novoalign software (v2.07.11). Expression of each piRNA was defined as the mapped tag counts.
Genome_build: n/a
Supplementary_files_format_and_content: counts
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| Submission date |
Oct 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
xiangbing meng |
| E-mail(s) |
Xiangbing-meng@uiowa.edu
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| Organization name |
University of Iowa
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| Street address |
375 Newton Road
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| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE62330 |
Next Generation Sequencing Facilitates Quantitative Analysis of Altered Expression of miRNAs and piRNAs in the Testes of Mtdh exon 3-deficient Mice |
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| Relations |
| BioSample |
SAMN03107509 |
| SRA |
SRX732791 |
| 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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