|
| Status |
Public on Apr 07, 2017 |
| Title |
KO_crz1__37C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
growth temperature: 37C
genotype: KO_crz1
replicate: 1
|
| Growth protocol |
grown at 37C
Strains were grown overnight at 24°C with shaking, until an OD600 = 0.5 was reached. Cell cultures were divided in two. One half was incubated at 24°C while the other half was transferred to 37°C, for a further 2 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected by centrifugation, frozen at -80°C, and then lyophilized overnight. Total RNA was isolated from lyophilized cells using Trizol solution (Invitrogen Life Technologies, Carlsbad, CA) and the Qiagen RNeasy® Mini kit (Qiagen, Valencia, CA).
cDNA libraries were prepared for sequencing using the Illumina RNA TruSeq kit, following the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SCEC007
|
| Data processing |
Illumina CASAVA v.1.8.2 was used for base calling. A one-base mismatch was allowed in barcodes during demultiplexing.
Quality filtering was performed using fastq-mcf to remove sequencing adapters and trim low quality bases
Tophat2 was used to map the processed reads; parameters used were "--transcriptome-max-hits 1 --max-multihits 1 --max-intron-length 4000 --library-type fr-unstranded --no-coverage-search"
htseq-count was used to determine read counts per gene; parameters used were "--stranded=no --type=exon --idattr=gene_id"
Genome_build: H99 genome version 2, downloaded from the Broad Institute
Supplementary_files_format_and_content: .tab files were generated using htseq-count, for each row, column 1 is gene name, and column 2 is the raw (not normalized) read count for that gene
|
| |
|
| Submission date |
Dec 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua Aaron Granek |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University School of Medicine
|
| Department |
Department of Biostatistics and Bioinformatics
|
| Street address |
Box 3568, 213 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21548 |
| Series (1) |
| GSE93005 |
Extensive rewiring of the Calcineurin-Crz1 stress response network in the human fungal pathogen Cryptococcus neoformans |
|
| Relations |
| BioSample |
SAMN06190111 |
| SRA |
SRX2450286 |
