|
Status |
Public on Sep 26, 2016 |
Title |
WT rep2 T8h |
Sample type |
SRA |
|
|
Source name |
Glucose (3%) + Yeast Extract (1%) medium
|
Organism |
Aspergillus fumigatus |
Characteristics |
strain: A1163 age: Germinated conidia T8h genotype: CEA17_delta_akuBKU80
|
Treatment protocol |
Dormant (0h), swollen (4h) and germinated (8h) conidia thus obtained were disrupted with 0.5 mm diameter glass beads in a volume of 500 µl and then RNA was isolated using the QIAGEN RNA/DNA kit.
|
Growth protocol |
Parental strain conidia (10^8) were inoculated in Glucose (3%) + Yeast Extract (1%) at 37°C for 4 or 8 h at 150 rpm.
|
Extracted molecule |
total RNA |
Extraction protocol |
For RNAseq analysis, we used 2 to 5 μg of total RNA to purify polyadenylated mRNAs and construct the sequencing libraries using the TruSeq RNA Sample Prep Kit v2 Non-directional libraries were prepared using the TruSeq RNA Sample preparation kit v2 following the manufacturer’s instructions (Illumina). The nondirectional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies). 50-bp Single Read sequences were generated on the Hiseq2000 sequencer according to manufacturer’s instructions (Illumina). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
cleaning with clean_ngs (v 0.7) alignment with tophat (v 1.4.1) counting with htseq-count (v 0.1) Genome_build: Aspergillus fumigatus A1163 Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting
|
|
|
Submission date |
May 26, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Rachel Legendre |
E-mail(s) |
rachel.legendre@pasteur.fr
|
Organization name |
Institut Pasteur
|
Department |
Research and Resource Center for Scientific Informatics
|
Lab |
Hub of Bioinformatics and Biostatistics
|
Street address |
28, rue du docteur Roux
|
City |
Paris |
ZIP/Postal code |
75724 |
Country |
France |
|
|
Platform ID |
GPL18295 |
Series (1) |
GSE81956 |
Gene expression level of Aspergillus fumigatus CEA17_ΔakuBKU80 at three different stages |
|
Relations |
BioSample |
SAMN05180056 |
SRA |
SRX1802077 |