|
| Status |
Public on Jun 23, 2021 |
| Title |
M0624H1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: ATCC2001
treatment: 0.06 µg/ml micafungin 24h
|
| Treatment protocol |
0.06 µg/ml micafungin 24h
|
| Growth protocol |
YPD 37°C (C. glabrata)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy kit according to manufacturer instructions
The libraries were made using NEBNext Ultra RNA Library Preparation Kit for rRNA depletion according to manufacturer instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data was trimmed with fastp version 0.20.0 with the following params: -w 8 --detect_adapter_for_pe-W 4 -M 10 --cut_by_quality3 --length_required 15
Reads were aligned to the transcriptome derived from NCBI reference GCF_000002545.3_ASM254v2 using STAR version 2.5.1b with default parameters
Read counts for each transcript was measured using featureCounts from subread-1.6.2 package
Differentially expressed genes were determined using DESeq2 and a cut-off of 0.05 on adjusted p-value (corrected for multiple hypotheses testing)
GSEA was performed on normalized gene expression counts, using gene permutations for calculating p-value
Genome_build: GCF_000002545.3_ASM254v2
Supplementary_files_format_and_content: Tab-delimited text files with raw expression counts for each sample
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Erika Shor |
| E-mail(s) |
erika.shor@hmh-cdi.org
|
| Phone |
6098655143
|
| Organization name |
Hackensack Meridian Health
|
| Department |
Center for Discovery and Innovation
|
| Street address |
111 Ideation Way
|
| City |
Nutley |
| State/province |
New Jersey |
| ZIP/Postal code |
07110-1150 |
| Country |
USA |
| |
|
| Platform ID |
GPL28968 |
| Series (1) |
| GSE178656 |
Multifactorial role of mitochondria in echinocandin tolerance revealed by transcriptome analysis of drug-tolerant cells |
|
| Relations |
| BioSample |
SAMN19812751 |
| SRA |
SRX11195970 |
