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| Status |
Public on Jun 18, 2019 |
| Title |
stage 2 primordium, replicate 3 |
| Sample type |
SRA |
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| Source name |
NL-1724
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| Organism |
Auriculariopsis ampla |
| Characteristics |
strain: NL-1724
group: AUA_P2
flowcell_id: HKN5GBGXY
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| Treatment protocol |
Vegetative mycelium, stage 1 and 2 primordia, young and mature fruiting bodies were flash-frozen in liquid nitrogen and stored at -80°C.
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| Growth protocol |
Auriculariopsis ampla was grown on solid sterilized poplar (Populus alba) bark and solid wood pieces plugged into MEA in 250 ml glass beakers. Cultures were incubated for 14 days in the dark at 30°C, then transferred to room temperature 60 cm under a light panel of 6 Sylvania Activa 172 Daylight tubes, with a 12 hr light/dark cycle and >90% relative humidity. Primordia started to develop 7 days after the transfer to light.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the Quick-RNA Miniprep kit (Zymo Research), following the manufacturer’s protocol
Library generation was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. RNA quality and quantity were assessed using RNA ScreenTape and Reagents on TapeStation (all from Agilent); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified based on PolyA selection and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. Purification was done using AmPureXP Beads (Beackman Coulter). DNA concentration of each library was determined using the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)
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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 9.5.3). 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. 9.5.3). 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
Genome_build: Auriculariopsis ampla NL-1724 v1.0 (Auramp1)
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
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| Submission date |
Jun 17, 2019 |
| Last update date |
Jun 18, 2019 |
| Contact name |
Laszlo G. Nagy |
| E-mail(s) |
lnagy@fungenomelab.com
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| Phone |
003662599600
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| Organization name |
Biological Research Centre, Hungarian Academy of Sciences
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| Department |
Institute of Biochemistry, Synthetic and Systems Biology Unit
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| Lab |
Laboratory of Fungal Genomics and Evolution
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| Street address |
Temesvari krt 62
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| City |
Szeged |
| State/province |
Csongrad |
| ZIP/Postal code |
6726 |
| Country |
Hungary |
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| Platform ID |
GPL26790 |
| Series (1) |
| GSE132826 |
Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae |
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| Relations |
| BioSample |
SAMN12077197 |
| SRA |
SRX6077658 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3893159_AUA_P2_R3.RNASeq.csv.gz |
367.7 Kb |
(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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