|
| Status |
Public on Nov 21, 2015 |
| Title |
Biopsy412 |
| 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 |
| 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) |
| GSE75236 |
Haemophilus ducreyi transcriptome during human infection |
|
| Relations |
| BioSample |
SAMN04283706 |
| SRA |
SRX1440226 |
