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| Status |
Public on Dec 12, 2014 |
| Title |
3928A_s |
| Sample type |
SRA |
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| Source name |
Isolate 3928A sporangium
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| Organism |
Phytophthora infestans |
| Characteristics |
isolate: 3928A
tissue: Sporangium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Material from the four life cycle stages were harvested and flash frozen in liquid nitrogen. Total RNA was prepared with the mirVana™ miRNA Isolation Kit (Ambion), according to the manufacturer’s protocol.
RNA library preparation was done with the sRNA library protocol provided with the SOLiD Total RNASeq kit (Applied Biosystems). RNA sequencing wad done using the SOLiD (version 2) platform (Applied Biosystems).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 2.0 |
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| Data processing |
Sequenced reads were filtered for adaptor sequences using cutadapt v1.2.1, requiring at least 5 bases overlap. Only forward reads were used in the subsequent anaysis.
Consensus reference sequences for P. Infestans tRNA were constructued. Briefly, tRNA sequences for each codon were clustered using cd-hit, and a consensus sequence was obtained from the aligned sequences.
The data was mapped to the tRNA consensus sequences using SHRIMP2 (v2.2.2, -s). 001111110011111111,001111111100111111,001111111111001111,001111111111110011,001111111111111100 -n 1 -Q --strata -v 80% -o 10)
The number of reads mapping tRNA was asessed using samtools (v 0.1.19).
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: Tab-delimited file showing the number of reads mapping to each tRNA.
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| Submission date |
Oct 24, 2014 |
| 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 |
GPL19354 |
| Series (2) |
| GSE62674 |
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [life cycle] |
| GSE63293 |
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection |
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| Relations |
| BioSample |
SAMN03142506 |
| SRA |
SRX740651 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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