|
| Status |
Public on Dec 10, 2022 |
| Title |
Cat.Dec.M |
| Sample type |
SRA |
| |
|
| Source name |
Secondary hair follicle
|
| Organism |
Capra hircus |
| Characteristics |
strain: Liaoning cashmere goat
tissue: Secondary hair follicle
age: 1.5 years
time point: Dec
gender: male
|
| Treatment protocol |
Temporarily stored in normal saline at 4 ° C for collected secondary hair follicles and than rapidly frozen in liquid nitrogen.
|
| Growth protocol |
Skin samples were taken from middle of the scapula , and the secondary hair follicles were separated from the skin with scalpel under dissecting microscope.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the secondary follicles using the RNAiso plus as the manufacturer’s instructions (Takara Biotechnology Dalian, Co. Ltd., China).
Total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
A total of 3 µg RNA per sample were used as the basis for small RNA library construction by sequencing company (Novogene, Beijing, China). The sRNA library was sequenced at Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Clean reads were mapped to the reference genome CHIR_2.0. The abundances of the miRNA sequencing reads were reported in TPM using the Bowtie (v.0.12.9) pipeline without mismatch.
mirdeep2(v.2.0.0.5) and srna-tools-cli softwares were used to predict the potential miRNA candidates.
The available software miREvo (v1.1) and mirdeep2 (v.2.0.0.5) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
Assembly: Capra hircus CHIR_2.0
Supplementary files format and content: tab-delimited text files include TPM values for each miRNA in each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 06, 2022 |
| Last update date |
Dec 11, 2022 |
| Contact name |
Wang Ming Lin |
| E-mail(s) |
amazinglin@126.com
|
| Organization name |
shenyang agricultural university
|
| Street address |
120 Dongling Road
|
| City |
Shenyang |
| ZIP/Postal code |
110866 |
| Country |
China |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE220211 |
Discovery and Functional Analysis of Secondary Hair Follicle miRNAs during Annual Cashmere Growth |
|
| Relations |
| BioSample |
SAMN32073311 |
| SRA |
SRX18512169 |
