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Sample GSM4630644 Query DataSets for GSM4630644
Status Public on Jul 01, 2021
Title RPMI_51452
Sample type SRA
 
Source name Bacteria in growth media
Organism Klebsiella variicola
Characteristics growth media: RPMI
strain: AJ055
growth time: 1 hr
growth phase: Mid log phase
od600 reading: 5.14
temperature: 37C
bpa identifier: 51452
serovar: K0
Growth protocol Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis
Extracted molecule total RNA
Extraction protocol Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis
Data processing Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622585.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
 
Submission date Jun 22, 2020
Last update date Jul 01, 2021
Contact name Antibiotic Resistant Sepsis Pathogens Framework Initiative Bioplatforms Australia
E-mail(s) mlum@bioplatforms.com
Organization name Bioplatforms Australia
Department https://bioplatforms.com/
Lab https://bioplatforms.com/projects/antibiotic-resistant-pathogens/
Street address Level 4, Building 4WW, Research Park Drive, Macquarie University
City Sydney
State/province NSW
ZIP/Postal code 2019
Country Australia
 
Platform ID GPL28719
Series (2)
GSE152848 Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative
GSE152964 Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella variicola AJ055
Relations
BioSample SAMN15340285
SRA SRX8594917

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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