|
| Status |
Public on Mar 15, 2024 |
| Title |
RG0095 control seed 20 h biol rep 2 [A_2] |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Aspergillus niger |
| Characteristics |
tissue: mycelium
cell line: ATCC 1015
cell type: GR0095
genotype: {delta}oahA, pyc, mdhC, Pgpd-C4T318
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using mirVana™ miRNA ISOlation Kit, Ambion-1561. 4 μg of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit and other kits following manufacture’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample A_2
|
| Data processing |
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic. The readscontaining ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each genewere obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq (2012) functions estimate Size Factors and nbinomTest. P value < 0.05 and fold Change >2 or fold Change < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using StringTie . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofil. SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: Aspergillus niger 513.88
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample
|
| |
|
| Submission date |
Jun 21, 2023 |
| Last update date |
Mar 15, 2024 |
| Contact name |
Chi Zhang |
| E-mail(s) |
zhangchi@njnu.edu.cn
|
| Phone |
8618795955583
|
| Organization name |
Nanjing Normal University
|
| Department |
School of Food Science and Pharmaceutical Engineering
|
| Lab |
Chi Zhang
|
| Street address |
1 WenYuan Road
|
| City |
NanJing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210023 |
| Country |
China |
| |
|
| Platform ID |
GPL32288 |
| Series (1) |
| GSE235528 |
Differential expression analysis of Aspergillus niger genes in mRMA level between in seed medium and fermentation media for L-malic acid production |
|
| Relations |
| BioSample |
SAMN35822987 |
| SRA |
SRX20742140 |
