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| Status |
Public on Mar 17, 2016 |
| Title |
PiAgo1-input_rep2 |
| Sample type |
SRA |
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| Source name |
Total RNA
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| Organism |
Phytophthora infestans |
| Characteristics |
gfp-tagged protein: N/A
wild-type background: 88069
transformed construct: PiAgo1-GFP
tissue: Mycelium
ip antibody: N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium from the different strains were harvested and flash frozen in liquid nitrogen. PiAgo and control GFP immunoprecipitations were performed with anti-GFP antibody (Chromotek, gtm-100). PiAgo1_input RNA samples enriched for the low molecular weight fraction were prepared using the mirVana™ miRNA Isolation Kit (Ambion).
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 Sequencing 200 kit v3 (Life Technologies).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Read length filtration, 18-30 nt. Custom Perl script
tRNA/rRNA filtration (RFAM v10), bowtie v1.0.0 -v 0
Map to P. Infestans genome (http://www.broadinstitute.org) using bowtie v1.0.0, -v 0 -a
Count reads mapping to features (genes/repeats) using featureCount v1.4.6 (-M --fraction -s 1/2). Gene annotation was taken from http://www.broadinstitute.org, repeat annotation was made by mapping repeats from Haas et al. (2009) to the P. infestans genome (RepeatMasker v4.0.3)
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: For each sample, there are four data files, containing the number of sense|antisense reads mapping to genes|repeats. Each file consists of tab-separated values with the following columns:Geneid, Chr, Start, End, Strand, Length, Number of reads
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| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Åsman |
| E-mail(s) |
anna.asman@slu.se
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| Organization name |
Swedish University of Agricultural Sciences (SLU)
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| Department |
Molecular Sciences
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| Street address |
PO Box 7080
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| City |
Uppsala |
| ZIP/Postal code |
SE-750 07 |
| Country |
Sweden |
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| Platform ID |
GPL21069 |
| Series (2) |
| GSE74370 |
Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (small RNA-Seq) |
| GSE75282 |
Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements |
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| Relations |
| BioSample |
SAMN04216136 |
| SRA |
SRX1384659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1919040_NH.all.matches.mapped.clean.Ago1_Input_2.raw.sorted.bam.antisense.counts.tsv.gz |
522.7 Kb |
(ftp)(http) |
TSV |
| GSM1919040_NH.all.matches.mapped.clean.Ago1_Input_2.raw.sorted.bam.antisense.repeat.counts.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSM1919040_NH.all.matches.mapped.clean.Ago1_Input_2.raw.sorted.bam.sense.counts.tsv.gz |
526.8 Kb |
(ftp)(http) |
TSV |
| GSM1919040_NH.all.matches.mapped.clean.Ago1_Input_2.raw.sorted.bam.sense.repeat.counts.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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