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Sample GSM3105136 Query DataSets for GSM3105136
Status Public on Oct 09, 2018
Title MAT1_2_OE2
Sample type SRA
 
Source name case mating-type MAT1-2
Organism Aspergillus fumigatus
Characteristics strain: AfS147
mating-type: MAT1-2
genotype: pxylP::MAT1-2
tissue: mycelium
Treatment protocol mycelia were separated from culture broth by filtration, washed, and snap frozen in liquid nitrogen
Growth protocol liquid cultures were inoculated with fungal conidia and allowed to grow overnight before shifting the formed mycelia to inducing, xylose-containing culture media
Extracted molecule total RNA
Extraction protocol nucleic acids from frozen and ground mycelia were extraced with the TRIzole reagent, cleaned, and DNase I digested to be followed by RNA purification
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description replicate2

Data processing Sequencing in 50 bp single reads was performed on the Genome Sequencer Illumina HiSeq2000, and trimming to eliminate contaminating adapter sequences was carried out using Trimmomatic, version 0.36. The number of total raw and trimmed reads per sample ranged from 19.1 to 29.5 Mio and 18.0 to 28.1 Mio, respectively, with mapping percentages reaching at least 96% throughout all samples (minimum 96.0%, maximum 97.6%) upon alignment to the annotated reference genome sequences of the A. fumigatus A1163 [MAT1-1] and Af293 [MAT1-2] isolates using the most recent version 2.1.0 of HISAT2. The resulting read count data were then analysed for differential expression by comparison between sample and control (AfS146 and AfS147 compared to D141 and Af293, respectively) by means of the DESeq2 software package (v1.20.0).
 
Submission date Apr 19, 2018
Last update date Oct 09, 2018
Contact name Sven Krappmann
E-mail(s) [email protected]
Organization name FAU Erlangen-Nuernberg
Department Institute for Microbiology
Street address Wasserturmstr. 3/5
City Erlangen
ZIP/Postal code 91054
Country Germany
 
Platform ID GPL18295
Series (1)
GSE113404 Monitoring the mating-type-driven transcriptomes of Aspergillus fumigatus
Relations
BioSample SAMN08957069
SRA SRX3974088

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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