|
Status |
Public on Apr 07, 2017 |
Title |
KI_CRZ1__37C_rep1 |
Sample type |
SRA |
|
|
Source name |
liquid culture
|
Organism |
Cryptococcus neoformans var. grubii H99 |
Characteristics |
growth temperature: 37C genotype: KI_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 |
SCEC008
|
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 |
SAMN06190110 |
SRA |
SRX2450287 |