|
| Status |
Public on Nov 20, 2018 |
| Title |
FIL_1_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
Candida in Spider media (DMSO)
|
| Organism |
Candida albicans |
| Characteristics |
background strain: DSY1050
genotype/variation: drug pump mutant
agent: Filimenation 2 hours
|
| Treatment protocol |
100 μΜ MDIVI-1 was added after 2h of growth in Spider media. Sampels were taken after 15min, 30min, 45min, 1h, 2h, 3h, and 4h,
|
| Growth protocol |
Candida albicans (DSY1050) was grown in either rich media (YPD) or in filimentation media (SPIDER). The drug MDIVI-1 was added after 2 hours and monitored over a time course of treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total Candida RNA was extracted by the hot phenol method. One microgram of total RNA was used for library preparation by the PAT-seq method (Harrison et al., 2015).
Library construction was by the PAT-seq approach (Harrison et al 2015)
9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Illumina index 3
Filimenation 2 hours
|
| Data processing |
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using bowtie2 (v2.2.5 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: C albicans SC5314 assembly 21 plus AF167163 downloaded from NCBI
Supplementary_files_format_and_content: read_count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.
|
| |
|
| Submission date |
Oct 19, 2017 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Traude Beilharz |
| E-mail(s) |
traude.beilharz@monash.edu
|
| Organization name |
Monash University
|
| Department |
Biomedicine Discovery Institute
|
| Lab |
RNA Systems Biology Laboratory
|
| Street address |
Wellington Rd
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23573 |
| Series (1) |
| GSE105148 |
A metabolic checkpoint controls hyphal development in Candida albicans via nitric oxide signaling |
|
| Relations |
| BioSample |
SAMN07814699 |
| SRA |
SRX3299717 |
