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Sample GSM1359361 Query DataSets for GSM1359361
Status Public on Apr 01, 2014
Title Sample 13a
Sample type SRA
 
Source name Ehrlichia (Jax) in Ixodes tick cell line ISE6
Organism Ehrlichia chaffeensis str. Jax
Characteristics ehrlichia strain: Jax
host cell: Ixodes scapularis
infectivity: 10%, 5 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 Jax strain-infected Ixodes tick 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 GPL18490
Series (1)
GSE56339 Comparison of Transcriptome Profiles of Human Ehrlichiosis Agents
Relations
BioSample SAMN02688285
SRA SRX486669

Supplementary file Size Download File type/resource
GSM1359361_ISE6_Jax_totalRNA1.accepted_hits.sorted_by_position.genic.coverage.stats.rpkm.txt.gz 583.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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