|
| Status |
Public on Dec 26, 2018 |
| Title |
ABPG1 |
| Sample type |
SRA |
| |
|
| Source name |
A. baumannii and P. gingivalis heterotypic community
|
| Organisms |
Acinetobacter baumannii; Porphyromonas gingivalis |
| Characteristics |
strain(s): P. gingivalis 33277 and A. baumannii AB0057
community: hetero-typic
|
| Treatment protocol |
1x10^9 cells of P. gingivalis and A. baumannii were washed two time in PBS and finally resuspended in 500 ul of PBS, pelleted by gentle centrifugation to force community development, and incubated aerobically for 3 hrs
|
| Growth protocol |
P. gingivalis was grown in TSB broth supplemented with hemin and menadione under anaerobic conditions. A. baumannii was grown in BHI under aerobic conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNAeasy kit according to manufacturers protocol
RNA libraries were prepared according to manufacturers protocols using the Ilumina Ribo-zero kit for rRNA depletion and the TruSeq kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ribo-depleted RNA
AB_vs_ABPG.txt
|
| Data processing |
Raw Fastq data was processed using the SPARTA (1.0) pipeline. (BMC Bioinformatics, 2016, Volume 17, Number 1, Page 1, Benjamin K. Johnson et al.)
Briefly, reads were trimmed to remove adaptors and low quality bases using Trimmomatic, and read quality was assessed by FastQC. Reads were mapped to the references genomes with Bowtie, transcript abundance was determined using HTSeq, and differential gene expression was determined using edgeR.
Reference genomes and gtf files were downloaded from ensemble.
Genome_build: Gene annotation from http://csbl.bmb.uga.edu/DOOR/. For Ab (NC_011585 and NC_011586) and Pg (NC_010729) were used for read alignment.
Supplementary_files_format_and_content: Tab-delimted text files, for PG_v_PGAB the RPKM adundance value for the 4 biological samples is shown along with the log2 fold change, p- and q- value. For AB_vs_ABPG the RPKM abundance values for each sample is shown along with the log2 fold change, the p-value and FDR.
|
| |
|
| Submission date |
Feb 23, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Daniel Miller |
| Organization name |
University of Louisville
|
| Street address |
570 South Preston Street, Baxter 1, Room 224
|
| City |
Louisville |
| State/province |
KY |
| ZIP/Postal code |
40202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24654 |
| Series (1) |
| GSE111038 |
Transcriptional analysis of P. gingivalis and A. baumannii |
|
| Relations |
| BioSample |
SAMN08583765 |
| SRA |
SRX3737108 |
