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| Status |
Public on Sep 30, 2020 |
| Title |
P4 - P74-3 |
| Sample type |
SRA |
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| Source name |
mycelium
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| Organism |
Cryphonectria parasitica |
| Characteristics |
strain: P74-3
tissue: mycelium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures for RNA extraction were grown in 8.5 cm Petri plates on potato dextrose agar (PDA, BD Difco Brand, NJ, USA) overlaid with sterile semi-permeable cellophane membranes. Total RNA was extracted using the Qiagen RNeasy Plant RNA extraction kit following manufacturer manual (Qiagen, Valencia, CA, USA) with DNAse treatment step.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NS.1339.004.NEBNext_dual_i7_159---NEBNext_dual_i5_159.P4
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| Data processing |
Sequenced reads were trimmed for adaptor sequence and low-quality sequence to about 100bp length. Then mapped to C.parasitica whole genome v.2 using STAR v2.7
Novel transcripts from regions of the genome that showed significant expression, but were not previously annotated as genes were identified using StringTie v.2.1.3
Raw Count table was created using SummarizedExperiment R package.
Genome_build: C.parasitica v.2, FASTA for novel transcripts is available on the series record.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Sep 29, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Myron Smith |
| E-mail(s) |
myronsmith@cunet.carleton.ca
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| Organization name |
Carleton University
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| Department |
Biology
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| Street address |
1125 Colonel By drive
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| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1S 5B6 |
| Country |
Canada |
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| Platform ID |
GPL29197 |
| Series (1) |
| GSE158756 |
Transcriptome analysis of programmed cell death during allorecognition in Cryphonectria parasitica |
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| Relations |
| BioSample |
SAMN16292994 |
| SRA |
SRX9215400 |
| 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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