NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2802752 Query DataSets for GSM2802752
Status Public on Oct 01, 2018
Title NZ9000 exp B
Sample type SRA
 
Source name Cell culture
Organism Lactococcus cremoris
Characteristics strain: NZ9000
accession: ASM14320v1
genotype: NZ9000 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 NZ9000 exp B
X24
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 SAMN07731320
SRA SRX3238485

Supplementary file Size Download File type/resource
GSM2802752_X24.rpkm.gz 89.1 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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap