|
| Status |
Public on Apr 01, 2014 |
| Title |
Sample 9a |
| Sample type |
SRA |
| |
|
| Source name |
Ehrlichia (West Paces) in canine cell line DH82
|
| Organism |
Ehrlichia chaffeensis str. West Paces |
| Characteristics |
ehrlichia strain: West Paces
host cell: Canis lupus familiaris
infectivity: 90%, 2 d pi
assayed molecule: total RNA
|
| Growth protocol |
All Ehrlichia strains were cultured in DH82 canine cells (37°C 5%CO2 in DMEM medium supplemented with 2% L-Glutamine and 10% FBS), or ISE6 tick cells (34°C in L15C300 medium). No antibiotics were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from E. chaffeensis-infected DH82 or ISE6 cells using RNeasy (Qiagen) with on-column DNase and bacterial mRNA were enriched by removing host and bacterial rRNA with Ribozero kits and subtracting polyA-RNA with Dynabeads.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ehrlichia chaffeensis West Paces strain-infected DH82 cells
|
| Data processing |
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Canis lupus familiaris and Ixodes scapularis genomes using TopHat v. 1.4 and to the Ehrlichia chaffeensis genomes using Bowtie v. 0.12.9
RPKM values were calculated for the genes present in the Canis lupus familiaris, Ixodes scapularis and Ehrlicha chaffeensis genomes.
Genome_build: Canis lupus familiaris v. 3.1.71, Ixodes scapularius v. 1.20
Supplementary_files_format_and_content: Tab-delimted files report RPKM values.
|
| |
|
| Submission date |
Mar 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sean Daugherty |
| E-mail(s) |
sdaugherty@som.umaryland.edu
|
| Phone |
410-706-8012
|
| Organization name |
University of Maryland School of Medicine
|
| Department |
Institute for Genome Sciences
|
| Street address |
801 W. Baltimore St.
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL18495 |
| Series (1) |
| GSE56339 |
Comparison of Transcriptome Profiles of Human Ehrlichiosis Agents |
|
| Relations |
| BioSample |
SAMN02688727 |
| SRA |
SRX487147 |
