|
| Status |
Public on Mar 28, 2022 |
| Title |
aero3_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 |
SAMN24725791 |
| SRA |
SRX13658742 |
