|
| Status |
Public on Apr 14, 2018 |
| Title |
250 mM NaCl |
| Sample type |
SRA |
| |
|
| Source name |
T. elongatus BP1 and M. ruber strain A cells
|
| Organisms |
Meiothermus ruber; Thermosynechococcus vestitus BP-1 |
| Characteristics |
meiothermus ruber strain: A
culture type: Planktonic
condition type: Batch
treatment: 250 mM NaCl
|
| Treatment protocol |
Each treatment was carried out for 4 hours.
|
| Growth protocol |
T. elongatus BP1 and M. ruber strain A cells cultured under batch conditions in BG-11 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SV Total RNA Isolation System (Promega, Madison, WI).
Libraries were prepared for Illumina sequencing using the Ovation Universal RNA seq system (NuGEN, San Carlos, CA).
cDNA sequencing took place on an Illumina NextSeq 500 using 75-bp single end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Na250_sequence
processed data file: All_Normalized_Expression_Levels.csv
|
| Data processing |
Fastq files were examined with FastQC to confirm high quality as well as the lack of sequences from the adaptor present in the reads.
Reads from all samples were aligned to the genomes of Thermosynechococcus elongatus BP-1 (NCBI: NC_004113) and Meiothermus ruber strain A (NCBI: NZ_JXOP01000000.1) using the Burrows Wheeler Aligner (BWA) with the default settings.
Gene counts were determined using HT-seq.
Raw counts were normalized using DESeq2.
Genome_build: Thermosynechococcus elongatus BP-1 (NC_004113.1), Meiothermus ruber strain A (NZ_JXOP01000000.1).
Supplementary_files_format_and_content: All_Normalized_Expression_Levels.csv: Comma-separated text file contains normalized log2 gene expression values for all genes of T. elongatus and M. ruber that were expressed in at least one of 20 conditions.
|
| |
|
| Submission date |
Apr 13, 2018 |
| Last update date |
Apr 16, 2018 |
| Contact name |
Ryan McClure |
| E-mail(s) |
[email protected]
|
| Phone |
5093753746
|
| Organization name |
Pacific Northwest National Laboratory
|
| Department |
Microbiology
|
| Street address |
11829272 Battelle for the US DOE, 790 6th Street
|
| City |
Richland |
| State/province |
Washington |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
|
| Platform ID |
GPL22951 |
| Series (1) |
| GSE113134 |
Species-specific transcriptomic network inference of interspecies interactions |
|
| Relations |
| BioSample |
SAMN08930178 |
| SRA |
SRX3934132 |
