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Sample GSM3495866 Query DataSets for GSM3495866
Status Public on Nov 30, 2018
Title CLJ1-RNA2
Sample type SRA
 
Source name P. aeruginosa CLJ1
Organism Pseudomonas aeruginosa
Characteristics clone: clinical isolate
clone id: CLJ1
culture: OD600 of 1.0
Growth protocol Bacteria were grown at 37°C in liquid Lysogeny Broth (LB) medium (10 g/L Bacto tryptone, 5 g/L yeast extract, 10 g/L NaCl) with agitation until the cultures reached an optical density at 600 nm (OD600) of 1.0.
Extracted molecule total RNA
Extraction protocol The total RNA for RNA-Seq was prepared as described in Han, K., Tjaden, B. and Lory, S. (2016) GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation. Nature microbiology, 2, 16239. Two bacterial cultures were treated independently.
The preparations of the Illumina libraries and sequencing were done by standard procedures at the Biopolymer Facility, Harvard Medical School, Boston, USA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description LIB013127_TRA00031091_CAGATC_L001_R1
Data processing For each replicate, raw RNA-Seq read trimmings to remove low quality sequences (limit = 0.05) and ambiguous nucleotides (maximum two nucleotides allowed) were done in CLC Genomics Workbench 9.0.
The trimmed reads were mapped to the CLJ1 genome using the RNA-Seq analysis tool in CLC Genomics Workbench 9.0.
Total number of reads mapped to each genes were exported to be used as the raw count data.
Genome_build: GCA_003032395.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.
 
Submission date Nov 29, 2018
Last update date Nov 30, 2018
Contact name Ina Attrée
E-mail(s) ina.attree-delic@cea.fr
Organization name Biosciences and Biotechnology Institute of Grenoble
Department Laboratory Biology of Cancer and Infection
Lab Bacterial Pathogenesis and Cellular Responses
Street address 17 avenue des Martyrs
City Grenoble
ZIP/Postal code 38054
Country France
 
Platform ID GPL18644
Series (1)
GSE123106 Pseudomonas aeruginosa CLJ1 genome sequencing, transcriptomics, and proteomics [transcriptomics]
Relations
BioSample SAMN07372049
SRA SRX5057739

Supplementary file Size Download File type/resource
GSM3495866_CountCLJ1-RNA2.txt.gz 26.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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