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| Status |
Public on Aug 20, 2019 |
| Title |
Mutant UV10046 pH 3 |
| Sample type |
SRA |
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| Source name |
Mutant UV10046 pH 3
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| Organism |
Aspergillus carbonarius |
| Characteristics |
condition: pH 3
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| Treatment protocol |
Strandard microbial culture method was followed with duplicates
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| Growth protocol |
Aspergillus carbonarius mutant was grown in glucose medium with pH 3 buffered medium and pH 5.5 buffered medium
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Coloured_S8
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| 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
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| Submission date |
Aug 19, 2019 |
| Last update date |
Aug 22, 2019 |
| Contact name |
K Anbarasu |
| E-mail(s) |
bioanbu@gmail.com
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| Organization name |
Periyar Maniammai Institute of Science & Technology
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| Street address |
Periyar Nagar, Vallam
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| City |
Thanjavur |
| State/province |
TN |
| ZIP/Postal code |
613403 |
| Country |
India |
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| Platform ID |
GPL27105 |
| Series (1) |
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| Relations |
| BioSample |
SAMN12599034 |
| SRA |
SRX6733650 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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