|
| Status |
Public on Jun 30, 2021 |
| Title |
Pot_PiAgo1-GFP_IP_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Ago-RNA co-immunoprecipitation
|
| Organisms |
Solanum tuberosum; Phytophthora infestans |
| Characteristics |
gfp-tagged protein: PiAgo1
wild-type background: 88069
transformed construct: PiAgo1-GFP
tissue: Mycelium, Leaves
potato line: Bintje
ip antibody: GFP (Chromotek, gtm-100)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia and infected leaves were harvested and flash frozen in liquid nitrogen. PiAgo1-GFP and control Pi-GFP immunoprecipitations were performed with anti-GFP antibody (Chromotek, gtm-100).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Phytophthora infestans, Solanum tuberosum (Bintje)
|
| Data processing |
Cutadapt, quality trimming (20), read length filtration 18 - 38 nt
Bowtie2 in combination with SAMtools view were used for tRNA and rRNA trimming and potato and P. infestans sRNA filtering to exclude the reads from the other genome for the different datasets, using 0 mismatches allowed per seed against each Fasta filter
SamToFastq converted the files to fastq
Fastx_collapser in the FASTX-toolkit counted the number of St- and Pi-sRNA
ShortStack was used to predict miRNA and summarize sRNA, using strand cutoff 0.5, fold size 1000, dicermin 18 and dicermax 38
Genome_build: Solanom tuberosum genome v4.04
Genome_build: Phytophthora infestans genome (ASM14294v1)
Supplementary_files_format_and_content: Results.txt files from the output of Shortstack including predicted sRNA
|
| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Kristian Erik Persson Hodén |
| E-mail(s) |
kristian.hoden@gmail.com
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Department |
Plant Biology
|
| Lab |
Christina Dixelius
|
| Street address |
Almas allé 5
|
| City |
Uppsala |
| ZIP/Postal code |
75651 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL25509 |
| Series (1) |
| GSE119230 |
Phytophthora infestans miRNA translocation facilitates infection in potato |
|
| Relations |
| BioSample |
SAMN09935754 |
| SRA |
SRX4624244 |
