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Sample GSM1946572 Query DataSets for GSM1946572
Status Public on Nov 21, 2015
Title deltacpxR_midlog_rep3
Sample type SRA
 
Source name bacteria
Organism [Haemophilus] ducreyi
Characteristics growth phase: Mid-log
od600: 0.2
strain: 35000HPdelta-cpxR
Growth protocol Bacteria were grown in gonococcal broth supplemented with 5% fetal bovine serum, 1% IsoVitalex and 50 μg/ml hemin (Aldrich Chemical Co.) in a 33°C waterbath.
Extracted molecule total RNA
Extraction protocol Bacteria was collected and RNA was harvested using Trizol reagent. The Ribo-Zero Magnetic kit 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
E-mail(s) dgangaia@iupui.edu
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)
GSE75237 Transcriptomes of 35000HP, ΔcpxA, ΔcpxR mutant strains of Haemophilus ducreyi in mid-log, transition, and stationary phase
Relations
BioSample SAMN04283720
SRA SRX1440241

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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