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Sample GSM6659125 Query DataSets for GSM6659125
Status Public on May 03, 2023
Title PAO1 hfq-V SP total RNA replicate C
Sample type SRA
 
Source name Tagged Hfq
Organism Pseudomonas aeruginosa PAO1
Characteristics strain: PAO1
genotype: hfq-VSVG
treatment: Growth: OD approximately 2.0 in LB
Treatment protocol Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.
Growth protocol Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.5, samples 3&4 were collected at OD ≈ 2.0.
Extracted molecule total RNA
Extraction protocol Standard TRI Reagent protocol was used for RNA extraction
Libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015) for samples 5 - 8.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Sample 7C
Data processing fastq records trimming (cutadapt 2.10) (Samples 5 - 8)
Quality control and adapter trimming (bcl2fastq 2.20.0.445) (Samples 9-10)
short reads mapping (bowtie2 2.4.4) (Samples 5-10)
BED file conversion (bedtools 2.30.0) (Samples 5-10)
bigwig file conversion (bedGraphToBigWig 2.9) (Samples 5-10)
Read quantification (htseq-count 2.0.2) (Samples 9-10)
Assembly: Pseudomonas aeruginosa PAO1, NC_002516.2
Supplementary files format and content: Supplementary_files_format_and_content: bigwig format for samples 5 - 10.
 
Submission date Oct 19, 2022
Last update date May 03, 2023
Contact name Michael J Gebhardt
Organization name University of Iowa
Department Department of Microbiology and Microbiology
Lab Gebhardt
Street address 431 Newton Road, 200A EMRB
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL23999
Series (2)
GSE216134 PAO1 Hfq-V RNA-seq
GSE216135 PAO1 Hfq-V RIL-seq and RNA-seq
Relations
BioSample SAMN31369352
SRA SRX17958251

Supplementary file Size Download File type/resource
GSM6659125_Hfq-V_SP_tot_C_minus.bw 989.7 Kb (ftp)(http) BW
GSM6659125_Hfq-V_SP_tot_C_plus.bw 795.4 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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