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Sample GSM2802750 Query DataSets for GSM2802750
Status Public on Oct 01, 2018
Title MG1363 Delta ArgR C
Sample type SRA
Source name Cell culture
Organism Lactococcus cremoris
Characteristics strain: MG1363
accession: ASM942v1
genotype: argR mutant
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 Delta ArgR C
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
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
BioSample SAMN07731305
SRA SRX3238483

Supplementary file Size Download File type/resource
GSM2802750_H8.rpkm.gz 89.4 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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