|
| Status |
Public on Dec 26, 2022 |
| Title |
NC_2 [16s rRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
rumen digesta
|
| Organism |
Capra hircus |
| Characteristics |
breed: Guanzhong
disease state: healthy
tissue: rumen digesta
treatment: infusion of normal saline
time point: Day 13
individual: NC_2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Microbial DNA from different rumen digesta samples was extracted using TIANamp Stool DNA Kit.
SMRTbell libraries were prepared using the Pacific Biosciences SMRTbellTM Template Prep kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
Paired-end reads generated from Illumina platforms were processed and merged using FLASH software (v1.2.7).
Quality filtering on the raw reads was then performed under specific filtering conditions to obtain the high-quality clean tags according to the Fqtrim software (v0.9.4). Chimeric sequences were filtered using VSEARCH software (v2.3.4).
Finally, the feature table and feature sequence were obtained after dereplication using DADA2 software (v1.10.1).
The V3-V4 region of the prokaryotic small-subunit (16S) rRNA gene was amplified with primers 341 F (5′-CCTACGGGNGGCWGCAG-3′) and 805 R (5′-GACTACHVGGGTATCTAATCC-3′).
Supplementary files format and content: The_processed_data_for_16S_rRNA-seq.xlsx: Excel file
Library strategy: 16s rRNA-seq
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
Dec 26, 2022 |
| Contact name |
Yongkang Zhen |
| E-mail(s) |
dx120220164@stu.yzu.edu.cn
|
| Phone |
15062800765
|
| Organization name |
Yangzhou University
|
| Street address |
Yangzhou University
|
| City |
Yangzhou |
| State/province |
— Please Select — |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL32968 |
| Series (2) |
| GSE221508 |
RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids [16s rRNA-seq] |
| GSE221509 |
RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids |
|
| Relations |
| BioSample |
SAMN32348918 |
| SRA |
SRX18805127 |
