|
Status |
Public on Jan 25, 2016 |
Title |
para-carcinoma nasal tissuesfrom goat 3 |
Sample type |
SRA |
|
|
Source name |
nose
|
Organism |
Capra hircus |
Characteristics |
breed: Nanjiang yellow goat tissues: nose tissues status: para-carcinoma tissues
|
Extracted molecule |
total RNA |
Extraction protocol |
tumor tissue or para-carcinoma tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.The 18-30nt fraction of total RNA was excised and purified following 155 Tris-Borate-EDTA denaturing polyacrylamide gel electrophoresis.Before RT-PCR, 5'adaptor and 3'adptor were respectively ligated using T4 RNAligase.Finally, Illumina TruSeq SmallRNA Sample Prep Kit Set D(Cat#RS-200-0048) was used for the construction of sequencing libraries. SmallRNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to capra hircus whole genome using bowtie v0.12.2 with parameters -q -p 4 -n 1-e 100--best --strata Number of reads mapping to each kown and novel predicted miRNA was counted and TPM (numbers of each miRNA matched to total reads)/number total reads(M)) was calculated.
|
|
|
Submission date |
Jan 26, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Yan Qi gui |
Organization name |
Sichuan Agricultural University
|
Department |
College of Veterinary Medicine
|
Street address |
Xin kang road no.48
|
City |
Yaan |
ZIP/Postal code |
625000 |
Country |
China |
|
|
Platform ID |
GPL19149 |
Series (1) |
GSE65305 |
Identification of Novel and Differentially Expressed MicroRNAs in Goat Enzootic Nasal Adenocarcinoma |
|
Relations |
BioSample |
SAMN03295023 |
SRA |
SRX852851 |