|
| Status |
Public on Mar 26, 2019 |
| Title |
WT + CP Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
WT A. baumannii strain ATCC 17978
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: ATCC 17978
genotype/variation: wild type
treatment: 250 ug/ml calprotectin (CP) added for 7 hrs
|
| Growth protocol |
Bacterial cultures were grown in 60% LB, 40% CP buffer (20 mM Tris-HCL pH 7.5, 100 mM NaCl, 5 mM 2-mercaptoethanol, 3 mM CaCl2) with 250 ug/ml CP added for 7 hours at 37 C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cultures were frozen in 1:1 ice cold acetone:ethanol. They were later thawed and RNA was extracted with TRIzol reagent and Qiagen Rneasy kit. Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug 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 |
Illumina CASAVA-1.8.2 for FASTQ conversion and demultiplexing
Sequences were processed using Bayesian adapter trimmer Scythe v0.992 to trim 3 = adapter contaminants from reads.
EDGE-pro v1.3 was used to align reads with Bowtie2 v2.1.0
FASTA of the reference genome sequence, protein translation table with coordinates of protein coding genes, and a table with coordinates of tRNA and rRNA genes were downloaded from NCBI.
EDGE-pro was run with default parameters, except for defining read length as 50 bp and using 16 threads on a 64-core Linux server.
Genome_build: NCBI Acinetobacter baumannii ATCC 17978 uid17477
Supplementary_files_format_and_content: Excel file with base mean expression in each condition, fold change, p value, and adjusted p value
|
| |
|
| Submission date |
Jan 23, 2019 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Eric Skaar |
| E-mail(s) |
eric.skaar@vumc.org
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Pathology, Microbiology, and Immunology
|
| Street address |
1161 21 Ave S
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24655 |
| Series (1) |
| GSE125491 |
Acinetobacter baumannii gene expression in the presence of calprotectin |
|
| Relations |
| BioSample |
SAMN10791431 |
| SRA |
SRX5281859 |
