|
| Status |
Public on Jan 25, 2016 |
| Title |
para-carcinoma nasal tissues from goat 2 |
| 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 |
SAMN03295021 |
| SRA |
SRX852849 |
