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Sample GSM2802745 Query DataSets for GSM2802745
Status Public on Oct 01, 2018
Title MG1363 Delta CcpA A
Sample type SRA
 
Source name Cell culture
Organism Lactococcus cremoris
Characteristics strain: MG1363
accession: ASM942v1
genotype: ccpA 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 CcpA A
C3
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 SAMN07731308
SRA SRX3238478

Supplementary file Size Download File type/resource
GSM2802745_C3.rpkm.gz 88.8 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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