|
| 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 |
