|
| Status |
Public on Nov 30, 2018 |
| Title |
CLJ1-RNA2 |
| Sample type |
SRA |
| |
|
| Source name |
P. aeruginosa CLJ1
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
clone: clinical isolate
clone id: CLJ1
culture: OD600 of 1.0
|
| Growth protocol |
Bacteria were grown at 37°C in liquid Lysogeny Broth (LB) medium (10 g/L Bacto tryptone, 5 g/L yeast extract, 10 g/L NaCl) with agitation until the cultures reached an optical density at 600 nm (OD600) of 1.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA for RNA-Seq was prepared as described in Han, K., Tjaden, B. and Lory, S. (2016) GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation. Nature microbiology, 2, 16239. Two bacterial cultures were treated independently.
The preparations of the Illumina libraries and sequencing were done by standard procedures at the Biopolymer Facility, Harvard Medical School, Boston, USA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
LIB013127_TRA00031091_CAGATC_L001_R1
|
| Data processing |
For each replicate, raw RNA-Seq read trimmings to remove low quality sequences (limit = 0.05) and ambiguous nucleotides (maximum two nucleotides allowed) were done in CLC Genomics Workbench 9.0.
The trimmed reads were mapped to the CLJ1 genome using the RNA-Seq analysis tool in CLC Genomics Workbench 9.0.
Total number of reads mapped to each genes were exported to be used as the raw count data.
Genome_build: GCA_003032395.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.
|
| |
|
| Submission date |
Nov 29, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Ina Attrée |
| E-mail(s) |
ina.attree-delic@cea.fr
|
| Organization name |
Biosciences and Biotechnology Institute of Grenoble
|
| Department |
Laboratory Biology of Cancer and Infection
|
| Lab |
Bacterial Pathogenesis and Cellular Responses
|
| Street address |
17 avenue des Martyrs
|
| City |
Grenoble |
| ZIP/Postal code |
38054 |
| Country |
France |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE123106 |
Pseudomonas aeruginosa CLJ1 genome sequencing, transcriptomics, and proteomics [transcriptomics] |
|
| Relations |
| BioSample |
SAMN07372049 |
| SRA |
SRX5057739 |
