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| Status |
Public on Apr 01, 2014 |
| Title |
Comparison of Transcriptome Profiles of Human Ehrlichiosis Agents |
| Organisms |
Ixodes scapularis; Canis lupus familiaris; Ehrlichia chaffeensis str. Arkansas; Ehrlichia japonica; Ehrlichia chaffeensis str. West Paces; Ehrlichia chaffeensis str. Heartland; Ehrlichia chaffeensis str. Jax; Ehrlichia chaffeensis str. Liberty; Ehrlichia chaffeensis str. Osceola; Ehrlichia chaffeensis str. Saint Vincent; Ehrlichia chaffeensis str. Wakulla |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
This study is to determine and compare the transcriptomes in two eukaryotic hosts (mammalian host - DH82 canine cell line and tick vector - ISE6 Ixodes scapularis cell line) of eight Ehrlichia chaffeensis strains in three divergent genetic groups, including Arkansas, Heartland, Jax, Liberty, Osceola, St. Vincent, Wakulla, and West Paces, and one Ehrlichia sp. HF strain.
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| Overall design |
RNA samples for the Arkansas (reference), Heartland, Jax, Liberty, Osceola, St. Vincent, Wakulla, and West Paces strains in both tick and canine cell lines, including two uninfected controls, will be isolated in triplicate. As such 108 libraries will be constructed and sequenced corresponding to (8 strains + 1 control) x 2 conditions (tick cells + dog cells) x 3 biological triplicates x 2 molecules sequenced (eukaryotic RNA + prokaryotic RNA).
The transcriptomes are obtained with Illumina HiSeq reads obtained from paired end libraries. The bacterial reads will be mapped against the reference genome and compared through a differential expression analysis. The eukaryotic reads from the same cell types (i.e. tick or canine) will be assembled with Trinity. The reads will then be mapped back to this assembly for the differential expression analysis.
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| Contributor(s) |
Lin M, Daugherty SC, Parankush S, Kumar N, Cheng Z, Xiong Q, Dunning Hotopp JC, Rikihisa Y |
| Citation(s) |
30181274 |
| Submission date |
Mar 28, 2014 |
| Last update date |
May 20, 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 |
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| Platforms (11)
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| GPL16540 |
Illumina HiSeq 2000 (Canis lupus familiaris) |
| GPL18488 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Arkansas) |
| GPL18489 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Heartland) |
| GPL18490 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Jax) |
| GPL18491 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Liberty) |
| GPL18492 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Osceola) |
| GPL18494 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Wakulla) |
| GPL18495 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. West Paces) |
| GPL18496 |
Illumina HiSeq 2000 (Ixodes scapularis) |
| GPL18497 |
Illumina HiSeq 2000 (Ehrlichia sp. HF) |
| GPL18512 |
Illumina HiSeq 2000 (Ehrlichia chaffeensis str. Saint Vincent) |
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| Samples (120)
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| Relations |
| BioProject |
PRJNA243269 |
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