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Sample GSM2178505 Query DataSets for GSM2178505
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

Supplementary file Size Download File type/resource
GSM2178505_Sample_T8-2.tophat-af1163.htseq.out.txt.gz 45.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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