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Status |
Public on May 05, 2021 |
Title |
M_88_R2_L2 |
Sample type |
SRA |
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Source name |
Mycelia
|
Organisms |
Solanum tuberosum; Phytophthora infestans |
Characteristics |
p. infestans strain: NL-88069 dpi: 5 tissue: Mycelia
|
Treatment protocol |
To prepare mycelium samples for RNA isolation, P. infestans was grown in liquid pea medium (Whisson et al. 2005b) for 5 d at 20 °C. Mycelium was harvested by filtration, snap frozen in liquid nitrogen, and stored at −70 °C until required.
|
Growth protocol |
P. infestans were maintained at 20 °C on rye agar medium supplemented with 2 % sucrose (Caten & Jinks 1968), rifampicin (10 μg ml−1), and pimaricin (10 μg ml−1). Transgenic lines of P. infestans isolate 88069 were maintained as above, but with the addition of the antibiotic geneticin (G418; 10 μg ml−1) to the medium.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Mycelia were harvested and flash frozen in liquid nitrogen. Degradome library preparation was performed as earlier outlined (Sanz-Carbonell et al. 2020). 10 libraries were sequenced at SciLifeLab (Uppsala, Sweden) using HiSeq2500 rapid SR50 technologies.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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|
Data processing |
smallRNA processing: The function SamToFastq, included in the Picard tool package, was used to convert the original BAM format to FASTQ format (for the raw data which was not already in FASTQ format), on which a quality control was performed, using FastQC smallRNA processing: Cutadapt, quality trimming (20), read length filtration 18 - 38 nt smallRNA processing: 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 smallRNA processing: SamToFastq converted the files to fastq smallRNA processing: Seqtk was applied to convert the FASTQ files to FASTA. Degradome processing: Raw RNA reads from degradome libraries were adaptor- and quality trimmed with Cutadapt Degradome processing: Seqtk was applied to convert the FASTQ files to FASTA. The sRNA and degradome fasta files and were analyzed in PAREsnip2. PAREsnip output data was imported in R where PAREsnip2 replicates were merged and duplicated targets were discarded. Resulting datasets were analyzed in our machine learning script (https://github.com/kristianHoden/degradome). False positives were discarded The datsets were sorted in list according to their Normalized Fragment Abundance (NFA) and targeting transcriptome Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1) fasta format of small RNA and degradome libraries Genome_build: Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1) Supplementary_files_format_and_content: pinfDown - contain the datasets with targets in P. infestans with decreased NFA of the targets upon infection Supplementary_files_format_and_content: pinfUp - - contain the datasets with targets in P. infestans with increased NFA of the targets upon infection Supplementary_files_format_and_content: potDown - contain the datasets with targets in potato with decreased NFA of the targets upon infection Supplementary_files_format_and_content: potUp - - contain the datasets with targets in potato with increased NFA of the targets upon infection Supplementary_files_format_and_content: rDown - contain the datasets with targets in resistance (R) genes in potato with decreased NFA of the targets upon infection Supplementary_files_format_and_content: rUp - contain the datasets with targets in resistance (R) genes in potato with increased NFA of the targets upon infection
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Submission date |
Dec 16, 2020 |
Last update date |
May 05, 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 |
GPL29221 |
Series (1) |
GSE163382 |
Convolutional neural network modelling: advancing identification of true mRNA cleavage sites |
|
Relations |
BioSample |
SAMN17098856 |
SRA |
SRX9694842 |