|
| Status |
Public on Jun 07, 2019 |
| Title |
Deletion-control rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
deletion control cultivated in wheat bran solid culture
|
| Organism |
Aspergillus oryzae |
| Characteristics |
strain/background: RIB40
genotype/variation: del-pyrG[pyrG+ ligD+]
growth media: wheat bran solid medium
incubation temperature: 30ºC
incubation time: 72 h
|
| Growth protocol |
A. oryzae mutant strains and control strain conidia of 3.8 x 10^7 were inoculated into 76.5 g of wheat bran solid medium (70 mL of water per 100 g wheat bran) in a 1 L Fernbach flask (giving 5.0 x 10^5 conidia/g wheat bran) and cultured at 30ºC for 72 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Wheat bran solid culture was immediately frozen with liquid N2, pulverized using a pestle and mortar, and then RNA was harvested using Sepasol®-RNA I Super G (Nacalai Tesque Inc., Kyoto, Japan).
TruSeq® RNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA) was used with 4 µg of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
The single-end sequencing reads were demultiplexed and the indexed adaptor sequences were trimmed using Illumina CASAVA v1.8.2 software.
The raw FASTQ format data sets generated from the above software were assessed for quality using FASTQC v0.10.1.
Poor-quality reads (Phred score <3) were trimmed from the tail end of each single-end read and only reads with lengths ≥35 bp were subjected to further analysis.
These data sets were aligned to reference genome and transcriptome sequences of Aspergillus oryzae RIB40 with TopHat v2.0.9.
Reads per kilobase of transcript per million mapped reads (RPKMs) for each experiment were calculated with Cufflinks v 2.1.1.
Genome_build: ASM18445v3 (Aspergillus oryzae RIB40 genomic DNA sequenced in "Genome sequencing and analysis of Aspergillus oryzae", Nature 438, 1157-1161, 2005 [PMID 16372010]).
Supplementary_files_format_and_content: Tab-delimited text files include gene IDs and RPKM values for each Sample.
|
| |
|
| Submission date |
Jun 09, 2016 |
| Last update date |
Jun 07, 2019 |
| Contact name |
Takuji Kobayashi |
| E-mail(s) |
s143821z@st.go.tuat.ac.jp
|
| Organization name |
Tokyo Univ. of Agriculture and Technology
|
| Street address |
3-5-8 Saiwai-cho
|
| City |
Fuchu-shi |
| State/province |
Tokyo |
| ZIP/Postal code |
183-8509 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22000 |
| Series (1) |
| GSE83207 |
RNA-Seq analysis of Aspergillus oryzae admA and admB gene deletion strains |
|
| Relations |
| BioSample |
SAMN05224540 |
| SRA |
SRX1836732 |
