|
| Status |
Public on Jan 30, 2020 |
| Title |
HC3 |
| Sample type |
SRA |
| |
|
| Source name |
Aspergillus niger
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: DS03043
growth phase: oxygen limited middle phase
|
| Treatment protocol |
oxygen limitation fermentation
|
| Growth protocol |
A 5 L fermenter with an electronic balance was used for the fed-batch cultivations with the agitation rate at 375 rpm and the aeration at 1 vvm. During the cultivation, the overpressure was maintained at 0.05 MPa and the temperature was at 34 ºC .The broth pH was maintained at 4.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After sampling at 18h,24h,42h and 66h, the broth was immediately frozen in liquid nitrogen and stored at -80 ºC for RNA extraction.
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 |
HC_FPKM.xls
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The clean reads were produced after the raw reads were filtered to the following criteria: remove reads with sequence adaptors; remove reads with more than 10% ‘N’ bases; and remove low-quality reads, which have more than 50% QA ≤ 10 bases.
Clean reads were then aligned to the reference genome and no more than three mismatches were allowed in the alignment for each read. Reads that could be uniquely mapped to a gene were used to calculate the expression level. The gene expression level was quantified using RSEM (Li and Dewey 2011).
The formula to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) value is as follows:FPKM = 106C/(NL/103), in which FPKM (A) is the expression level of gene A. C is counts of fragments that uniquely mapped to the gene A. N is total counts of fragments that uniquely mapped to the reference genes. L is the base counts of the coding region of gene A.
Genome_build: A. niger strain CBS 513.88 (Genbank ID:GCA_000002855.2)
Supplementary_files_format_and_content: excel files including FPKM values for each Sample
|
| |
|
| Submission date |
Jan 23, 2018 |
| Last update date |
Jan 30, 2020 |
| Contact name |
Weiqiang Cao |
| E-mail(s) |
362988935@qq.com
|
| Organization name |
East China University of Science and Technology
|
| Street address |
130 Meilong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200237 |
| Country |
China |
| |
|
| Platform ID |
GPL21721 |
| Series (1) |
| GSE109525 |
Omics analysis with modeling reveals global adaptation of Aspergillus niger to hypoxic condition |
|
| Relations |
| BioSample |
SAMN08386883 |
| SRA |
SRX3593067 |
