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Sample GSM5777342 Query DataSets for GSM5777342
Status Public on Mar 28, 2022
Title aero2_4h
Sample type SRA
 
Source name Haemophilus ducreyi
Organism [Haemophilus] ducreyi
Characteristics oxygen environment: aerobic
harvested: 4 hours
Treatment protocol Cells were grown either aerobically (buffer substrates) or anaerobically (with Oxyrase) for 4, 8, or 18 h.
Growth protocol Overnight Haemophilus ducreyi cultures in GC broth plus hemin, FBS, and IsoVitalex (complete GC broth) were subcultured into complete GC broth plus either the commercial product Oxyrase or the buffer substrates to generate anaerobic or aerobic environments, respectively. Cultures were evenly aliquoted into glass tubes with rubber lined screw caps (7.5 mL/ea). The cap was screwed shut on anerobic cultures and loosely shut on aerobic cultures. Cultures were shaken at ~200 rpm and 33 degrees for the duration of the experiment. Four independent experiments were performed.
Extracted molecule total RNA
Extraction protocol 5 mL of culture was pelleted, media was removed and the pellet was resuspended in 1 mL of Trizol. Samples were stored at -80 until all samples were collected. RNA was extracted using the Zymo Directzol kit with both on-column DNase digestion as well as a subsequent DNase digestion of the eluate with TurboDNase.
Ribosomal RNA was removed with Qiagen FastSelect for bacteria. Libraries were prepared with a Roche KAPA kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Basecalling was performed with Illumina RTA v3.4.4 and bcl2fastq v2.20.
Sequenced reads were aligned to the Haemophilus ducreyi 35000HP genome (AE017143.1) using Bowtie2 v2.3.2.
A single count matrix was derived using the featureCounts function in Rsubread run in R v3.6.0 for matched pairs with a min MQS of 30 or higher.
Library normalization and statistical analysis was performed in R v4.0.0 with the edgeR package.
Genome_build: AE017143.1
Supplementary_files_format_and_content: txt file for the count matrix of the 24 samples
 
Submission date Jan 07, 2022
Last update date Mar 28, 2022
Contact name Stanley M Spinola
E-mail(s) sspinola@iu.edu
Organization name Indiana University
Department Department of Microbiology & Immunology
Street address 635 Barnhill Dr., MS420
City Indianapolis
State/province Indiana
ZIP/Postal code 46202
Country USA
 
Platform ID GPL31188
Series (1)
GSE193250 Genes differentially expressed by Haemophilus ducreyi during anaerobic growth significantly overlap with those differentially expressed during experimental infection of human volunteers
Relations
BioSample SAMN24725792
SRA SRX13658741

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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