|
Status |
Public on Oct 01, 2018 |
Title |
MG1363 B |
Sample type |
SRA |
|
|
Source name |
Cell culture
|
Organism |
Lactococcus cremoris |
Characteristics |
strain: MG1363 accession: ASM942v1 genotype: Wild type growth stage: Exponential
|
Treatment protocol |
delta ArgX strain were compared to that of the wildtype L. lactis NZ9000 strain
|
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 |
MG1363 B B2
|
Data processing |
For the analysis, all reads were mapped on MG1363. 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 MG1363 (firmicutes) | 2007/02/06 | RefSeq assembly accession: GCF_000009425.1 | plus addition of ncRNAs Supplementary_files_format_and_content: [00.normalized.rpkm.txt] final data of all samples and is used and described in the manuscript [.rpkm] supplementary files containing the raw counts, raw RPKM and normalized RPKM per sample
|
|
|
Submission date |
Oct 02, 2017 |
Last update date |
May 15, 2019 |
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) |
GSE104515 |
The 3’UTR of ArgR regulates the arc operon |
|
Relations |
BioSample |
SAMN07731309 |
SRA |
SRX3238477 |