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Sample GSM1058053

Query DataSets for GSM1058053

Status

Public on Feb 02, 2013

Title

Sample type

SRA

Source name

h99 wild type

Organism

Cryptococcus neoformans

Characteristics

genotype: wild type

Growth protocol

Strains were incubated in YPD to mid-log phase, washed twice, and then incubated in DMEM at 37°C with 5% CO2 or YPD for 3 h. Cells were then washed twice, frozen on dry ice, and lyophilized for 3 h.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted by using the Qiagen RNeasy Plant Minikit
Library preparation and RNA sequencing were performed by the Duke Sequencing Core Facility. Total RNA samples were purified and prepared according to the manufacturer’s protocols (Illumina, San Diego, CA)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer II

Data processing

All reads were mapped to the C. neoformans reference genome provided by the Broad Institute by using TopHat v1.3.0
The aligned reads were then analyzed for the number of fragments per kilobase of transcript per million mapped reads by using Cufflinks v.1.0.3. Statistically significant differences between strains was determined by CuffDiff
Genome_build: Broad Institute C. neoformans grubii h99
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample. Columns: test_id, locus, sample_1, sample_2, status, h99_fpkm, rim101_fpkm, ln(fold_change), test_stat, p_value, significant

Submission date

Dec 28, 2012

Last update date

May 15, 2019

Contact name

Teresa R O'Meara

Organization name

Duke University

Lab

J. Andrew Alspaugh

Street address

DUMC 3355