|
| Status |
Public on May 18, 2017 |
| Title |
HC1_RNA_seq |
| Sample type |
SRA |
| |
|
| Source name |
rumen epithelia cells, HC
|
| Organism |
Capra hircus |
| Characteristics |
tissue: rumen epithelium
age: 4 months
treatment: HC diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rumen epithelium were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2016_3
|
| 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 NCBI goat genome annotation release version 101 using bowtie v1.2.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks v2.2.1.The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI goat genome annotation release version 101
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values.
|
| |
|
| Submission date |
May 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong Shen |
| E-mail(s) |
hongshen@njau.edu.cn
|
| Phone |
15705181618
|
| Organization name |
Nanjing Agriculture University
|
| Street address |
Weigang No.1
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE99066 |
Next-Generation Sequencing Facilitates Quantitative Analysis of Rumen Epithelium Transcriptomes |
|
| Relations |
| BioSample |
SAMN06887682 |
| SRA |
SRX2782485 |
