|
| Status |
Public on Dec 08, 2023 |
| Title |
wildtype, glucose, 24hours, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wildtype
|
| Organism |
Mycosarcoma maydis |
| Characteristics |
strain: wildtype
genotype: FB2
treatment: glucose
|
| Treatment protocol |
grown in minimal media with 2% glucose for 24 hours
"moved to SAMPLES" section
|
| Growth protocol |
Samples were grown in PDB media overnight before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNA mini kit
The library construction was completed according to protocols from Genewiz.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were checked for quality using FastQC
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the ustilago_maydis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Differential gene expression was preformed using the DEseq2 package in R
Assembly: Ustilago maydis 521 v2.0
Supplementary files format and content: Processed files represent the differential gene expression information for all genes between specific comparisons. Files are in .csv format
|
| |
|
| Submission date |
Jul 26, 2023 |
| Last update date |
Dec 08, 2023 |
| Contact name |
James Kronstad |
| E-mail(s) |
[email protected]
|
| Phone |
6048224732
|
| Organization name |
University of British Columbia
|
| Department |
Mircobiology and Immunology
|
| Lab |
Kronstad Lab
|
| Street address |
2185 E Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL31263 |
| Series (1) |
| GSE239366 |
Gene expression of Grx4 regulated strains in the Ustilago maydis FB2 background |
|
| Relations |
| BioSample |
SAMN36718210 |
| SRA |
SRX21166586 |
