 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 04, 2019 |
| Title |
Cyclo Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
with cycloheximide
|
| Organism |
Plenodomus lingam |
| Characteristics |
strain: v23.1.2
tissue: mycelia
treatment: with cycloheximide
|
| Growth protocol |
Liquid MMII medium supplemented or not with cycloheximide was inoculated with 10^8 conidia of the v23.1.2 isolate of L. maculans. Incubation lasted for 3-4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol reagent (Invitrogen,Cergy Pontoise, France) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs, Ipswich, MA, U.S.A.).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sofwtware CLC worckbench v8.5.1 (Qiagen, Venlo, Netherlands) was used for data processing.
Sequenced reads were trimmed with the following parameters: ambiguous limit: 2, quality limit: 0.05, maximum number of nucleotides in reads: 50, minimum number of nucleotides in reads: 15. Short reads were discarded.
Reads were mapped on the genomes of L. maculans and B. napus with the following parameters: maximum number of mismatches allowed: 2, minimum lenght fraction: 0.80, Minim fraction of similarity: 0.8, unspecific match limit: 30
Gene expression was normalized using the DESeq2 package (Love et al., 2014)
Genome_build: Leptosphaeria maculans JN3 (Rouxel et al., 2011)
Supplementary_files_format_and_content: Text files include raw and normalized (with DESeq2) values for each fungal gene.
|
| |
|
| Submission date |
Nov 04, 2016 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Julie Gervais |
| E-mail(s) |
julie.gerv@gmail.com
|
| Phone |
0033130814573
|
| Organization name |
INRA
|
| Department |
BIOGER
|
| Street address |
Avenue Lucien Brétignières
|
| City |
Thiverval Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
| |
|
| Platform ID |
GPL21935 |
| Series (1) |
| GSE89558 |
Impact of biotic and abiotic factors on the expression of fungal effector-encoding genes in axenic growth conditions |
|
| Relations |
| BioSample |
SAMN05982132 |
| SRA |
SRX2328615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2375929_cyclo_R1.txt.gz |
101.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
