|
| Status |
Public on Mar 03, 2021 |
| Title |
FB2 11.1: Wild type (rev) |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells from Basidiomycota
|
| Organism |
Mycosarcoma maydis |
| Characteristics |
strain: genetic background a2b2
genotype/variation: wild type
tissue: Yeast cells from Basidiomycota
|
| Treatment protocol |
The pH was modified to acidic conditions
|
| Growth protocol |
Cells cultures were grown on minimum media at pH 4, and recovered after 14 h of growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from frozen and ground fungal tissue using the PureLink RNA Mini Kit (Invitrogen)
1 µg of total RNA was subjeted to library synthesis using the TruSeq RNA sample prep LT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ust_EA1UM1SS01_S9_L001_R2
|
| Data processing |
Quality-control checkpoints (Bioconductor QuasR v1.09.0 utility "preprocessReads"): Raw reads were processed by fitering Quality <Q20, minimum lengths of 130nt (after adapter removal), trimmed read lengths of 130nt (to remove low quality sequences). Other parameters that were taken in consideration for filtration were GC content, overrepresented k-mers and duplicated reads.
Read alignment (Bioconductor QuasR v1.09.0 utility "qAlign"): The reads were mapped to the reference genome of Ustilago maydis 521, GenBank assembly accession: GCA_000328475.2
Differential gene expression (DEG) (Blas2GO v 5.0): BAM files were employed to generate the count tables, All differentially expressed genes were classified into the categories of molecular function, cellular component, and biological process in the Gene Ontology (GO) database (http://www.geneontology.org/). FB2 samples were consider to be basal and FMA luminal
GSEA analysis (Blas2GO v 5.0): Default BLAST2GO parameters were used and only GO terms with P<0.005 were included in the present study. GSEA Enrichment analysis was used to find enriched GO terms, p-value P<0.005.
The read files are paired end but the mapping was made like single end, and in the differential expression analysis the samples were concatenated.
|
| |
|
| Submission date |
Jul 04, 2019 |
| Last update date |
Mar 03, 2021 |
| Contact name |
Jose Alejandro Sánchez-Arreguin |
| E-mail(s) |
alejandro.sanchez@cinvestav.mx
|
| Phone |
+52 462 6239600
|
| Organization name |
Universidad Autónoma de Nuevo León
|
| Department |
Facultad de ciencias Biológicas
|
| Lab |
Micología y Fitopatología Unidad de Manipulación Genética
|
| Street address |
Pedro de Alba S/N
|
| City |
Monterrey |
| State/province |
Nuevo León |
| ZIP/Postal code |
66455 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL19655 |
| Series (1) |
| GSE133840 |
NRG1 as a regulator of pH adaptation in the Basidiomycota Ustilago maydis |
|
| Relations |
| BioSample |
SAMN12216788 |
| SRA |
SRX6406522 |
