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Status |
Public on Mar 17, 2016 |
Title |
PiAgo1-input_rep1 |
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 |
SAMN04216135 |
SRA |
SRX1384658 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1919039_NH.all.matches.mapped.clean.Ago1_Input_1.raw.sorted.bam.antisense.counts.tsv.gz |
521.6 Kb |
(ftp)(http) |
TSV |
GSM1919039_NH.all.matches.mapped.clean.Ago1_Input_1.raw.sorted.bam.antisense.repeat.counts.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
GSM1919039_NH.all.matches.mapped.clean.Ago1_Input_1.raw.sorted.bam.sense.counts.tsv.gz |
524.8 Kb |
(ftp)(http) |
TSV |
GSM1919039_NH.all.matches.mapped.clean.Ago1_Input_1.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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