|
| Status |
Public on Oct 08, 2015 |
| Title |
sperm wt rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Sperm
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Sperm
age: Adult
genotype: wild type
|
| Treatment protocol |
Sperm were collected in HTF medium at 37 degree from adult WT and Dicer cKO / Drosha cKO mouse cadua epididymis. Sperm suspension was then centrifuged by 700g to pellet the sperm. Oocytes were collected from WT oivducts after superovulation. 2PN stage embryos were collected after ICSI using WT spermatozoa, Dicer cKO/Drosha cKO spermatozoa.
|
| Growth protocol |
All mice were housed and maintained under specific pathogen-free conditions with a temperature- and humidity-controlled animal facility in the University of Nevada, Reno. All flox and Cre lines used in this study were purchased from the Jackson Laboratory. All mouse lines were backcrossed for five generations to get onto the C57B6/6J background. The Cre-loxp strategy was used to generate the germ line conditional knockout mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using the mirVana miRNA Isolation Kit (Life Technologies) following the manufacturer’s instructions with modifications at the lysis stage. In brief, after addition of lysis buffer, the frozen sperm pellets were homogenized at low settings for 90 seconds, followed by a five minute incubation at 65 °C. Complete lysis of sperm heads was verified by microscopic examination. Once a total lysis of sperm heads was achieved, the samples were then placed on ice, and the default protocol was resumed. Samples were then placed on ice, and the default protocol was resumed.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
AAwt-FF-TTsperm-SS2_L001_R1
|
| Data processing |
Ion Torrent suite software was used for basecalling.
Sequenced reads were matched to known murine small noncoding RNA using Sequery software
Unmatched sequenced reads were mapped to mm10 whole genome using Bowtie (n = 2)
Aligned reads were matched to genomic coordinates of known murine small noncoding RNA using in-house Python scripts
Reads Per Million aligned reads (RPM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain the unnormalized or normalized (RPM) endo-siRNA and miRNA read counts .txt tab-delimited format
|
| |
|
| Submission date |
Oct 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Yan |
| E-mail(s) |
wyan@medicine.nevada.edu
|
| Phone |
(775) 784-7765
|
| Organization name |
University of Nevada
|
| Department |
Physiology
|
| Lab |
Wei Yan Lab
|
| Street address |
1664 N. Virginia Street
|
| City |
reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE73824 |
Next Generation Sequencing Facilitates Quantitative Analysis of oocyte, sperm, 2PN embryos derived from WT, Dicer cKO and Drosha cKO small non-coding RNAs |
|
| Relations |
| BioSample |
SAMN04155318 |
| SRA |
SRX1310980 |
