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| Status |
Public on Sep 15, 2017 |
| Title |
ARO_YFB_S_R3 |
| Sample type |
SRA |
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| Source name |
young fruiting body, stipe
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| Organism |
Armillaria ostoyae |
| Characteristics |
strain: C18
developmental stage (group): YFB_S
flowcell_id: HKY2VBGXY
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| Growth protocol |
RSTO medium was prepared in 720 ml jars and inoculated with A. ostoyae C18, incubated for 28 days at 24 °C in the dark, then placed in a growth chamber at 15 °C with a 10/14 hour light/dark cycle. Light intensity: 11 µE / (m2*s).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Vegetative mycelia, rhizomorphs, stage I and II primordia, young and mature fruiting bodies were harvested. RNA was extracted by using the RNEasy Midi kit (QIAGEN, Cat.Num.: 75144) following the manufacturer’s instructions
PolyA RNA-Seq library was generated using TrueSeq RNA Library Preparation Kit v2 (Illumina, Cat.Num.: RS-122-2001 according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.1 of CLC Genomics Workbench Tool (v. 9.5.2) allowing intergenic mapping. Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Reference sequence file: p3_i2_t47428_Arm_ostoy_v2.scaf (fasta file containing assembled reference genome for Armillaria ostoyae). GFF3 annotation file: p3_i2_t47428_Arm_ostoy_v2.gff (gff3 annotation file containing genome annotation data for Armillaria ostoyae).
Supplementary_files_format_and_content: [*.CLC.RNA_Seq.csv.gz] Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
Supplementary_files_format_and_content: [ARO_RPKM_22Nov2016.csv.gz] Supplementary file containing RPKM gene expression data matrix for all samples
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| Submission date |
Jun 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Balazs Balint |
| E-mail(s) |
balintb@seqomics.hu
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| Phone |
0036304276152
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| Organization name |
Seqomics Ltd
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| Street address |
Vallalkozok street
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| City |
7 |
| State/province |
Csongrad |
| ZIP/Postal code |
6782 |
| Country |
Hungary |
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| Platform ID |
GPL23605 |
| Series (1) |
| GSE100213 |
Lineage-specific genetic innovations streamline the genomes of Armillaria species to pathogenesis |
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| Relations |
| BioSample |
SAMN07256032 |
| SRA |
SRX2933049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2674740_ARO_YFB_S_R3.CLC.RNA_Seq.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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