|
| Status |
Public on Feb 09, 2018 |
| Title |
WT_CLIB214-YPD-2 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type YPD
|
| Organism |
Candida parapsilosis |
| Characteristics |
strain: CLIB214
growth phase: log phase
genotype: wild type
|
| Growth protocol |
Strains were grown overnight in YPD media at 30C, diluted to an OD600 of 0.2, grown to an OD600 of 1 in YPD media at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells filtered through a membrane and RNA was isolated using a Bioline ISOLATE II RNA Mini Kit
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Wild type YPD sample 2
|
| Data processing |
Raw Illumina reads for samples 1-12 were provided by BGI (http://www.genomics.cn/en/index)
Raw Illumina reads for samples 13-24 were obtained in-house using an Illumina NextSeq® sequencer with a NextSeq® 500/550 High Output v2 kit (75-cycles) (Illumina, FC-404- 2001)
Quality control of the data was verified using fastqc v0.11.2
Pair-end sequenced reads were trimmed for low-quality sequence or length using Skewer v0.1.120 with parameters -m pe -l 50 -q 15 -Q 15
Single-end sequenced reads were trimmed for low-quality sequence or length using Skewer v0.1.120 with parameters -m any -l 35 -q 15 -Q 15
Trimmed sequenced reads were mapped to the Candida parapsilosis CDC317 genome using Tophat v2.0.12 with parameters -g 1 --b2-very-sensitive --library-type fr-firststrand
Mapped reads were indexed and sorted for counting using Samtools v0.1.19
Raw number or mapped reads per gene was obtained using htseq-count from HTSeq (v0.6.1) with parameters -m union -s reverse -t exon -i Name
Differentially expressed genes from read count data were identified using the Bioconductor package DESeq2
Genome_build: Candida parapsilosis CDC 317
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads per gene for each SAMPLE
|
| |
|
| Submission date |
Jan 10, 2018 |
| Last update date |
Feb 09, 2018 |
| Contact name |
Geraldine Butler |
| E-mail(s) |
[email protected]
|
| Organization name |
UCD Conway Institute
|
| Department |
School of Biomolecular and Biomedical Science
|
| Lab |
Butler
|
| Street address |
Belfield, Dublin 4
|
| City |
Dublin |
| ZIP/Postal code |
D04 N2E5 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL24493 |
| Series (1) |
| GSE109034 |
Dal81 regulates expression of arginine biosynthesis genes in Candida parapsilosis |
|
| Relations |
| BioSample |
SAMN08347514 |
| SRA |
SRX3548948 |
