|
Status |
Public on Nov 26, 2020 |
Title |
WBN4-1a |
Sample type |
SRA |
|
|
Source name |
RNA derived from liquid culture in LB (OD600=0.4-0.6)
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
strain: PA14 mutS::Tn media: LB culture number: 4 clone number: 1 replica: Replica 1
|
Treatment protocol |
Directly after cultivation, the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C.
|
Growth protocol |
Cells were grown in LB to an OD600 =0.4-0.6.
|
Extracted molecule |
total RNA |
Extraction protocol |
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Single-colony-derived clone isolated from the 45th passage of WBN4 culture. processed data file: ProcessedDataMatrix.xlsx
|
Data processing |
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters. Genome_build: NC_008463.1 (PA14) Supplementary_files_format_and_content: ProcessedDataMatrix.xlsx file is a data matrix that contains raw unique gene reads.
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|
|
Submission date |
Mar 12, 2020 |
Last update date |
Nov 26, 2020 |
Contact name |
Susanne Häußler |
E-mail(s) |
Susanne.Haeussler@helmholtz-hzi.de
|
Organization name |
Twincore
|
Department |
Molecular Bacteriology
|
Street address |
Feodor-Lynen-Str. 7
|
City |
Hanover |
ZIP/Postal code |
30625 |
Country |
Germany |
|
|
Platform ID |
GPL18287 |
Series (1) |
GSE146906 |
Adaptation of Pseudomonas aeruginosa to cultivation in standard laboratory conditions |
|
Relations |
BioSample |
SAMN14369343 |
SRA |
SRX7904307 |