|
| Status |
Public on Jun 19, 2018 |
| Title |
MS2-082B |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Lactococcus cremoris |
| Characteristics |
strain: NZ9000
accession: ASM14320v1
genotype: CisR-MS2 overexpression
growth stage: Exponential
|
| Treatment protocol |
cells were induced with nisin to overexpress (MS2-)LLMGnc_082 (CisR)
|
| Growth protocol |
Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
CisR-MS2 overexpression
01.RPKM_normalized.txt
|
| Data processing |
mapping of reads was done using: bowtie2 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Lactococcus lactis subsp. cremoris NZ9000, NC_017949.1, GI:389853198, Assembly: GCF_000143205.1, 12-AUG-2015
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Jun 18, 2018 |
| Last update date |
Jun 19, 2018 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24073 |
| Series (1) |
| GSE115974 |
Target identification of the cold stress induced sRNA CisR in Lactococcus lactis |
|
| Relations |
| BioSample |
SAMN09445545 |
| SRA |
SRX4232783 |
