|
| Status |
Public on Dec 12, 2014 |
| Title |
PiDcl1_m |
| Sample type |
SRA |
| |
|
| Source name |
P. Infestans line PiDcl1 mycelium
|
| Organism |
Phytophthora infestans |
| Characteristics |
p. infestans strain: PiDcl1 knockdown (background 88069)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Material from P. infestans mycelium and infected potato leaves were harvested and flash frozen in liquid nitrogen. Total RNA extraction was done with the mirVana™ miRNA Isolation Kit (Ambion), according to the manufacturer’s protocol.
RNA library preparation was done according to the Illumina small RNA sample preparation kit. RNA sequencing was done using the Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Demultiplexing and conversion using CASAVA v1.8.2.
Adaptor trimming using cutadapt v2.2, only saving reads with adaptor match of at least 5 bp
Consensus reference sequences for P. infestans tRNA were constructed. Briefly, tRNA sequences for each codon were clustered using cd-hit, and a consensus sequence was obtained from the aligned sequences (tRNA_clusters.fa).
Reads were mapped to the tRNA reference sequence (bowtie v2.1.0, one mismatch in seed, seed length 18bp, report up to 10 matches)
The number of reads mapping to tRNA was asessed using bedtools v2.21.0.
Genome_build: P. infestans strain T30-4, http://www.broadinstitute.org
Supplementary_files_format_and_content: tRNA_read_counts.txt file shows the number of reads mapping to each tRNA.
|
| |
|
| Submission date |
Nov 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Åsman |
| E-mail(s) |
anna.asman@slu.se
|
| Organization name |
Swedish University of Agricultural Sciences (SLU)
|
| Department |
Molecular Sciences
|
| Street address |
PO Box 7080
|
| City |
Uppsala |
| ZIP/Postal code |
SE-750 07 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19416 |
| Series (2) |
| GSE63292 |
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [host plant infection] |
| GSE63293 |
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection |
|
| Relations |
| BioSample |
SAMN03195645 |
| SRA |
SRX759743 |
