|
| Status |
Public on Apr 30, 2021 |
| Title |
Wt_exp_1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: KUE100
genotype: Wild type
condition: planktonic condition
|
| Growth protocol |
Cells were grown in SDB (pH 5.6) medium. Planktonic cells were cultured at 30ºC with orbital agitation (250rpm), while biofilm cells were cultured at 30ºC, in square Petri dishes, with orbital agitation (30rpm). Cells were pelleted and frozen at -80ºC until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)
|
| |
|
| Submission date |
Nov 14, 2019 |
| Last update date |
Apr 30, 2021 |
| Contact name |
Miguel Cacho Teixeira |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Bioengineering and Biosciences, Instituto Superior Técnico
|
| Street address |
Av. Robisco Pais
|
| City |
Lisbon |
| ZIP/Postal code |
1049-001 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL26394 |
| Series (1) |
| GSE140427 |
CgEfg1 and CgTec1 transcription factors controlling biofilm formation in Candida glabrata |
|
| Relations |
| BioSample |
SAMN13287692 |
| SRA |
SRX7141997 |
