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Sample GSM4038312 Query DataSets for GSM4038312
Status Public on Aug 20, 2019
Title Mutant UV10046 pH 3
Sample type SRA
Source name Mutant UV10046 pH 3
Organism Aspergillus carbonarius
Characteristics condition: pH 3
Treatment protocol Strandard microbial culture method was followed with duplicates
Growth protocol Aspergillus carbonarius mutant was grown in glucose medium with pH 3 buffered medium and pH 5.5 buffered medium
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from fungal samples as per the manufacturer protocol of Qiagen Rneasy Plant Mini Kit (#74903)
paired-end sequencing library preparation using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7770S) and NEBNext Singleplex (NEB #E7350) Oligos for Illumina as per the protocol described by the manufacturer
The library preparation was initiated with the capture of mRNA from Total RNA using Oligo dT beads, fragmentation, first Strand cDNA synthesis, second strand synthesis, end-repairof the double-stranded cDNA and Adaptor ligation, indexing and final library amplification. The libraries were purified using SPRISelect beads. The amplified libraries were analyzed in 4200 TapeStation (Agilent Technologies) using kit as per manufacturer's instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Coloured_S8
Data processing Sequencing
The library was loaded onto illumina NextSeq500 sequencing kit and flow-cell for cluster generation and sequencing. During the sequencing run, the library molecules bind to complementary adapter oligos on paired-end flow cell. In paired-end (PE) sequencing, the DNA library fragments are sequenced in both the forward and reverse directions. The sequencing was performed using the 2 x 75 bp run cycles to generate about 3GB raw data per sample.
Alignment Stats
All processed reads were aligned with reference using Tophat-2 .0.13. TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.
We have used Aspergillus carbonarius ITEM 5010, as reference genome for this study.
Assembly:GCA_001990825.1 Aspca3
Submission date Aug 19, 2019
Last update date Aug 22, 2019
Contact name K Anbarasu
Organization name Periyar Maniammai Institute of Science & Technology
Street address Periyar Nagar, Vallam
City Thanjavur
State/province TN
ZIP/Postal code 613403
Country India
Platform ID GPL27105
Series (1)
GSE135950 Next generation sequence analysis
BioSample SAMN12599034
SRA SRX6733650

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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