|
| Status |
Public on Mar 26, 2017 |
| Title |
dog_piRNA_fraction |
| Sample type |
SRA |
| |
|
| Source name |
Testes
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Testes
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Testes were snap frozen from dog, horse, and a bat (Eptesicus fuscus). Total RNA was extracted from ground tissue using standard TRIzol protocols.
The small RNA fraction was isolated and prepped for Illumina sequencing (50 bp, single-end).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNA
|
| Data processing |
Adapters were trimmed and reads quality filtered using the FastX toolkit
Idenical small RNA reads were collapsed into one sequence and counted
Small RNA equences were mapped to the genome using Bowtie allowing zero mismatches
RNA-seq reads were mapped to TE consensus libraries using Bowtie and RSEM
Expression levels measured at transcripts per million (TPM) were estimated from RSEM
Genome_build: equCab2 (GCA_000002305.1)
Genome_build: canFam3.1 (GCF_000002285.3)
Genome_build: Ept.fus.01 (GCA_000308155.1)
Supplementary_files_format_and_content: abundance
|
| |
|
| Submission date |
Mar 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael W Vandewege |
| E-mail(s) |
mike.vandewege@gmail.com
|
| Organization name |
Mississippi State University
|
| Street address |
32 Creelman St
|
| City |
Mississippi State |
| State/province |
Mississippi |
| ZIP/Postal code |
39762 |
| Country |
USA |
| |
|
| Platform ID |
GPL16540 |
| Series (1) |
| GSE56336 |
Transposable element targeting by piRNAs in Laurasiatherians with distinct TE activities |
|
| Relations |
| BioSample |
SAMN02711378 |
| SRA |
SRX502869 |
