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Sample GSM5399996 Query DataSets for GSM5399996
Status Public on Dec 10, 2022
Title ECH2
Sample type SRA
 
Source name Bacterial
Organism Escherichia coli
Characteristics strain: ATCC_25922
sample groupd: ECH
Growth protocol Cell were grown and treated as described in the attached article
Extracted molecule total RNA
Extraction protocol RNA was isolated as describe in attached article
Standard library preparation protocol as describe in attached article
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 4B_S12
Data processing mapping of reads was done using: bowtie2 --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Escherichia coli ASM74325v1, NCBI_Assembly:GCA_000743255.1
Genome_build: Staphylococcus aureus ASM75620v1, NCBI_Assembly:GCA_000756205.1
Supplementary_files_format_and_content: Tab delimited text file
 
Submission date Jun 25, 2021
Last update date Dec 10, 2022
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 GPL14548
Series (1)
GSE178890 G-quadruplex DNA as a target for pathogenic bacteria: efficacy of an extended naphthalene diimide ligand and mode of action
Relations
BioSample SAMN19871896
SRA SRX11229403

Supplementary file Size Download File type/resource
GSM5399996_ECH2.rpkm.gz 107.3 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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