|
| Status |
Public on Oct 01, 2018 |
| Title |
MG1363 A |
| 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 A
A1
|
| 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 |
SAMN07731310 |
| SRA |
SRX3238476 |
