|
| Status |
Public on Jan 01, 2013 |
| Title |
wt yeast Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type_yeast phase
|
| Organism |
Candida albicans |
| Characteristics |
genotype/variation: wild type
morphological phase: yeast phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by the hot phenol method after which RNA was further purified by the SV Total RNA isolation system (Promega) according to the manufacturer’s instructions. 5μg total RNA was depleted of rRNAs using the RiboMinus kit (Invitrogen) and cDNA was synthesized and amplified with the SMARTer cDNA synthesis kit (Clonetech) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Reads were mapped onto the Assembly 21 of the C. albicans genome containing only the coding sequences using TopHat (Trapnell C, Bioinfromatics, 2009) with default parameters, and allowing only for uniquely mapping reads.
Fragment Per Kilobase in a Million mapped reads (FPKM) values were calculated with Cufflinks (Trapnell C, Nat Biotechnology, 2010) including quartile normalization (removing top 25% of genes from the FPKM denominator) and bias correction. The transcript coordinates were fixed as in the annotation of the coding sequence assembly.
Genome_build: Assembly 21
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Jun 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Denes Hnisz |
| E-mail(s) |
dhnisz@yahoo.at, denes.hnisz@meduniwien.ac.at
|
| Organization name |
Max F Perutz Laboratories
|
| Department |
Medical Biochemistry
|
| Lab |
Kuchler
|
| Street address |
Dr Bohr-gasse
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL15645 |
| Series (2) |
| GSE38426 |
Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq] |
| GSE38427 |
Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis. |
|
| Relations |
| SRA |
SRX151327 |
| BioSample |
SAMN01036594 |
