|
| Status |
Public on Feb 21, 2017 |
| Title |
Pycnoporus cinnabarinus, wheat straw rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Trametes cinnabarina |
| Characteristics |
strain: CIRM-BRFM137
agent: wheat straw
time: day 3
|
| Treatment protocol |
Mycelium and remaining solid substrate were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HighSeq-2500 JGI platform generating paired end reads of 150bp each.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137
|
| Data processing |
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the reference genome Pycnoporus coccineus BRFM 310 v1.0, Pycnoporus cinnabarinus BRFM 137, or Pycnoporus sanguineus BRFM 1264 v1.0,available via Mycocosm JGI portal, using TopHat2 (Galaxy Tool Version 0.7-INRA MIGALE bioinformatics platform) with only unique mapping allowed.
Read counts were determined by HTSeq (Galaxy Tool Version 0.3.2-INRA MIGALE bioinformatics platform)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5)
Supplementary_files_format_and_content: File "raw_counts_CIRM-BRFM310" includes read count values for each sample
Supplementary_files_format_and_content: File "rnorm_counts_CIRM-BRFM310" includes normalized read count values for each sample
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marie-Noëlle Rosso |
| E-mail(s) |
marie-noelle.rosso@inrae.fr
|
| Organization name |
INRAE - Aix Marseille University
|
| Department |
Biodiversity and Biotechnology of Fungi - BBF
|
| Street address |
163 avenue de Luminy
|
| City |
Marseille |
| ZIP/Postal code |
13288 Cedex 9 |
| Country |
France |
| |
|
| Platform ID |
GPL21988 |
| Series (2) |
| GSE82427 |
Early response of three Pycnoporus species to various carbon sources [Pycnoporus cinnabarinus] |
| GSE82486 |
Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus |
|
| Relations |
| BioSample |
SAMN03003259 |
| SRA |
SRX1755890 |
