|
| Status |
Public on Oct 22, 2021 |
| Title |
LL1 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organism |
Capra hircus |
| Characteristics |
developmental stage: late lactation
tissue: mammary gland
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cryopreservation of the mammary gland tissue in liquid nitrogen and total RNA was harvested using Trizol reagent (Code No 9108Q, Takara). TruSeq RNA Library Prep Kit v2 (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing was performed on a HiSeq 2500 platform (Illumina).
Sequencing quality was assessed using FastQC software. The high-throughput sequencing reads were processed using Trimmomatic software to remove adapter sequences, primers, poly-A tails and other unwanted sequences (Bolger et al., 2014).
HISAT2 software (Kim et al., 2015) was used to construct indices of the goat genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/704/415/GCF_001704415.1_ARS1), and sequence alignment was performed.
The numbers and percentages of sequence alignment were quantified using SAMtools (Li et al., 2009).
The expression level of each gene was quantified using HTSeq (Anders et al., 2015).
Genome_build: Capra hircus (Bio Sample:SAMN03863711)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Oct 22, 2021 |
| Contact name |
Rong Xuan |
| E-mail(s) |
2018110375@sdau.edu.cn
|
| Phone |
18853857973
|
| Organization name |
Shandong Agricultural University
|
| Department |
College of Animal Science and Veterinary Medicine
|
| Lab |
Animal Conservation Biology Laboratory
|
| Street address |
61 Daizong Street
|
| City |
Tai an |
| State/province |
Shan Dong |
| ZIP/Postal code |
271000 |
| Country |
China |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE185981 |
Transcriptome profiling of nonlactating goat mammary glands. |
|
| Relations |
| BioSample |
SAMN22328221 |
| SRA |
SRX12633103 |
