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Sample GSM2442389 Query DataSets for GSM2442389
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

Supplementary file Size Download File type/resource
GSM2442389_SC-ECRNA8_ACTTGA_L003_counts.tab.gz 31.0 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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