|
| Status |
Public on Nov 15, 2022 |
| Title |
ΔBcFRQ1, LP, without nitrogen, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole fungus
|
| Organism |
Botrytis cinerea |
| Characteristics |
tissue: whole fungus
strain: {delta}BcFRQ1
treatment: Light pulse, without nitrogen
|
| Treatment protocol |
Plates were exposed to different ligth conditions during 48 hours. Constant Light (LL), Constant Darkness (DD) or Light Pulse (LP). For LP treatment plates were grown at DD during 44 hours and were exposed to light for 4 hours.
|
| Growth protocol |
B05.10 and ΔBcFRQ1 strains of Botrytis cinerea were grown by 48 hours in CM media plates covered with celofan and depleted of nitrogen sources or complemented with glutamine 0.1M as nitrogen source.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol and cleaned up with Qiagen RNAeasy Plant Minikit. 500 uL at 600ng/uL were send to Macrogen for the construction of sequencing libraries and sequencing.
RNA libraries for RNA-seq were prepared by TruSeq stranded mRNA library in Macrogen.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
A17
|
| Data processing |
Sequenced reads were pseudo-aligned to the publicly available Botrytis cinerea B05.10 transcriptome obtained from Ensembl Fungi using kallisto (v0.46.2)
RNA-seq data was normalized using the R package DESeq2 package version 1.36.0
Assembly: ASM83294v1
Supplementary files format and content: Excel xlsx-file include raw-counts values for each sample and gene
Supplementary files format and content: Excel xlsx-file include normalized-counts values for each sample and gene
|
| |
|
| Submission date |
Oct 27, 2022 |
| Last update date |
Nov 15, 2022 |
| Contact name |
Javier Canales |
| E-mail(s) |
javier.canales@uach.cl
|
| Phone |
+56967660831
|
| Organization name |
Universidad Austral de Chile
|
| Department |
Instituto de Bioquimica y Microbiologia
|
| Lab |
Plant Nutrition and Genomics Lab
|
| Street address |
Campus Isla Teja s/n
|
| City |
Valdivia |
| State/province |
Los Ríos |
| ZIP/Postal code |
5090000 |
| Country |
Chile |
| |
|
| Platform ID |
GPL32786 |
| Series (1) |
| GSE216747 |
The clock protein FREQUENCY (BcFRQ1) in Botrytis cinerea is required for normal mitochondrial function and has an extra-circadian role in nitrogen metabolism |
|
| Relations |
| BioSample |
SAMN31493660 |
| SRA |
SRX18050994 |
