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Sample GSM1946560 Query DataSets for GSM1946560
Status Public on Nov 21, 2015
Title Biopsy437
Sample type SRA
Source name H. ducreyi-infected pustules from humans
Organism [Haemophilus] ducreyi
Characteristics growth phase: Unknown
time point: end point pustules
strain: 35000HP
Growth protocol RNA was directly extracted from H. ducreyi-infected pustules and no growth conditions were involved for this study.
Extracted molecule total RNA
Extraction protocol RNA was harvested from pustules using Trizol reagent. The Ribo-Zero Gold rRNA Removal kit (Epidemiology) was used to remove rRNA and the Illumina TruSeq Stranded mRNA sample preparation kit (Cat# RS-122-2101) was used with 10 to 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Image analysis and base calling were performed with the HiSeq Control software and the Real Time Analysis software.
Demultiplexing was performed with the Illumina CASAVA software.
Sequenced reads were mapped with the Burrows-Wheeler Alignment tool
The total number of reads corresponding to the coding region of each gene was determined with the NGSUtils suite
Gene List was generated using an FDR cutoff of 0.1 and a fold change cutoff of 2 fold
Genome_build: AE017143
Supplementary_files_format_and_content: Excel Sheet includes RPKM values for each sample as well as calculated fold change, p-value, and FDR.
Submission date Nov 20, 2015
Last update date May 15, 2019
Contact name Dharanesh Gangaiah
Phone 317-278-1027
Organization name Indiana University School of Medicine
Department Department of Microbiology and Immunology
Lab Spinola lab
Street address 635 Barnhill drive, MS 420
City Indianapolis
State/province Indiana
ZIP/Postal code 46202
Country USA
Platform ID GPL21166
Series (1)
GSE75236 Haemophilus ducreyi transcriptome during human infection
BioSample SAMN04283708
SRA SRX1440228

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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