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Sample GSM6796789 Query DataSets for GSM6796789
Status Public on Dec 10, 2022
Title Ana.May.F
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: May
gender: female
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 SAMN32073318
SRA SRX18512162

Supplementary file Size Download File type/resource
GSM6796789_Ana.May.F_TPM.txt.gz 2.4 Kb (ftp)(http) TXT
GSM6796789_Ana.May.F_counts.txt.gz 2.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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