|
| Status |
Public on Jun 04, 2017 |
| Title |
WT_RNA-seq-1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_conidia
|
| Organism |
Aspergillus flavus |
| Characteristics |
strain: NRRL3357
genotype/variation: WT
tissue: conidia
|
| Growth protocol |
The fungal strains were grown on minimal medium with appropriate supplements and incubated at 30C for 2 days.The conidia were collected in ddH2O from the entire colony.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by adding silica/zirconium beads (Biospec, Bartlesville, OK) and Trizol (Invitriogen, San Diego) and homogenizing in a Mini Bead Beater (Biospec), and then subsequently following manufacturere's instructions (Invitrogen)
Strand-specific library was prepared from total RNA using Illumina TruSeq Strand specific RNA sample preparation system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
WT-1
|
| Data processing |
Reads were mapped to the A. flavus genome using Tophat version 2.1.1 with the default parameters except for --max-intron-length 4000
The number of reads that mapped to each gene were counted with HTSeq-count version 0.6.1p1 with the parameters -f bam -r pos -s no -i Note
Differential gene expression analysis was carried out with version 1.14.1 of DeSeq2 using the DESeqDataSetFromHTSeqCount function and an adjusted p-value cutoff of 0.05
After carrying out multiple quality control analyses, sample dwetA_1 was excluded from further study
Genome_build: GCF_000006275.2_JCVI-afl1-v2.0_genomic
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each gene in each sample
|
| |
|
| Submission date |
Mar 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ming-Yueh Wu |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Bacteriology
|
| Street address |
1550 Linden Dr
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL23153 |
| Series (1) |
| GSE95711 |
Genome-wide analyses for the cellular and chemical development regulator WetA in Aspergillus flavus |
|
| Relations |
| BioSample |
SAMN06480829 |
| SRA |
SRX2613926 |
