|
| Status |
Public on Aug 18, 2022 |
| Title |
Skin containing hair follicle , H2 |
| Sample type |
SRA |
| |
|
| Source name |
Skin containing hair follicle , H
|
| Organism |
Capra hircus |
| Characteristics |
breed: Boer and Macheng Black crossbred goat with black head and white body
tissue: skin containing hair follicle
region: black-coated region
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 5 μg RNA per sample was isolated from each individual sample using TRIzol reagent (Invitrogen, USA). Purity and quantity of total RNA were measured by using Nanodrop equipment. Ribosomal RNAs were depleted using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using Hisat2
Cufflinks was used to estimate the gene expression levels for each sample using the gene annotation data obtained from ARS1
The read counts that mapped on each gene and the FPKM (fragments per kilobase of transcript per million mapped reads) values were calculated using featureConuts by mapping clean data back onto the transcripts.
Genome_build: ARS1 (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Capra_hircus/latest_assembly_versions/GCA_001704415.1_ARS1)
Supplementary_files_format_and_content: Microsoft excel format file including readscounts and FPKM values of all gene for each Sample
|
| |
|
| Submission date |
Aug 19, 2019 |
| Last update date |
Aug 18, 2022 |
| Contact name |
Qi Xiong |
| E-mail(s) |
raul_love@126.com
|
| Organization name |
Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences
|
| Street address |
No.1 Nanhu Yaoyuan, Shizisanjie, Hongsan D
|
| City |
Wuhan |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL27106 |
| Series (1) |
| GSE135963 |
Skin transcriptome profiles associated with black- and white-coated region in a crossbred goat |
|
| Relations |
| BioSample |
SAMN12600148 |
| SRA |
SRX6734121 |
