|
| Status |
Public on Oct 23, 2023 |
| Title |
ASFV-ASFV PPI network |
| Sample type |
SRA |
| |
|
| Source name |
Y2HGold, Y188
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: Y2HGold, Y187
cell type: MATa, MAT&alpha
treatment: RLL-Y2H screening and library construction
sample type: recombined bait and prey fragments
|
| Treatment protocol |
Yeast plasmids were extracted using the Yeast Plasmid Kit
|
| Growth protocol |
Clontech Yeast Protocols Handbook
|
| Extracted molecule |
other |
| Extraction protocol |
All the colonies on SD/-AHLT selective plates were pooled for plasmid extraction, according to Clontech yeast plasmid extraction protocol
The plasmid were amplified, and then harvested for MmeI digestion.These digested products were ligated with Illumina P5 and P7 adaptors to generate a high throughput sequencing library.
The libraries were constructed into the pmAD/pmBD vector in yeast Y187 and Y2HGoldstrain strain by recombilation.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Data filtering: The semi-global alignment algorithm and unique alignment algorithm were used to obtain the protein interaction information between Prey library and Bait library in RLL-Y2H sequencing data.The raw sequencing reads without complete MmeI-ATTL-MmeI site “gttggaTAGCGTGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGGCGTTGACtccgac” were excluded by the tool RLLNP (https://github.com/thxie/RLLNP). Reads with adapters sequences was also excluded.
Trimming: retained the reads containing about 13 bp DNA flanking both sides of MmeI-ATTL-MmeI
Aligning: The two subreads libraries were aligned to bait library and prey library respectively using RLLNP. Only unambiguously aligned reads without mismatch were retained.
Frequency counting: Interaction frequency of a protein pair was calculated by counting the sequencing pairs that could be aligned to them.
Supplementary files format and content: text files include PPI for each Sample
|
| |
|
| Submission date |
Dec 09, 2022 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Yingying Lei |
| Organization name |
Huazhong Agricultural University
|
| Street address |
NO. 1 shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
China |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL30266 |
| Series (1) |
| GSE220585 |
Interactome between ASFV and host immune pathway proteins |
|
| Relations |
| BioSample |
SAMN32123965 |
| SRA |
SRX18549417 |
