|
| Status |
Public on Jun 30, 2014 |
| Title |
Total RNA from Candida albicans wild-type strain (SC5314) yeast cells Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells, wild-type
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
cell type: Yeast
growth stage: OD (600 nm) = 1
|
| Treatment protocol |
Overnight YPD broth culture of Candida albicans SC5314 diluted to OD600 nm = 0.25 in 10 ml fresh YPD broth and incubated at 30 °C with shaking (200 rpm) until OD600 nm = 1.0
|
| Growth protocol |
Cells grown in rich broth medium (YPD) until OD (600 nm) = 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5 x 107 cells were disrupted with glass beads using a FASTPREP-24 bead beater (3 x 20 s at 6 m/s). Total RNA was then extracted from each sample using a Qiagen RNeasy mini kit following the manufacturers instructions. RNA was quantified (nanodrop) and purity assessed using an Agilent Bioanalyser. Double stranded cDNA was generated using reverse transcription with random hexamers. Double-stranded cDNA was then fragmented using a Bioruptor sonication device and libraries prepared for Illumina GA2 sequencing using the standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
CLCBio software was used to align each set of replicate sequences to the 14217 Assembly 19 diploid reference ORFs detailed by Jones et al (2004). Standard parameters were set to allow up to 2 mismatches per read. For diploid alignments, non-unique matches to the ORFs were discarded. This ensured that only reads which were able to distinguish between alternative alleles were considered. For haploid alignments, all matches were counted.
Genome Build:
ypd3.txt: C. albicans SC5314 Assembly 19
Ca19-orfs-haploid_3_RNA-Seq.txt: C. albicans SC5314 Assembly 19
|
| |
|
| Submission date |
Jan 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sophie Shaw |
| E-mail(s) |
s.shaw@abdn.ac.uk
|
| Organization name |
University of Aberdeen
|
| Department |
Centre for Genome Enabled Biology and Medicine
|
| Street address |
23 St. Machar Drive
|
| City |
Aberdeen |
| State/province |
Aberdeen City |
| ZIP/Postal code |
AB24 3RY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15149 |
| Series (1) |
| GSE35233 |
RNA-sequencing reveals allelic expression imbalance in the diploid pathogen Candida albicans |
|
| Relations |
| SRA |
SRX116684 |
| BioSample |
SAMN00777111 |
