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Sample GSM1910817 Query DataSets for GSM1910817
Status Public on Oct 15, 2018
Title Mutant endolysin expressed in P. aeruginosa
Sample type SRA
 
Source name bacteria
Organism Pseudomonas aeruginosa
Characteristics strain background: PAO1
genotype/variation: expressing mutant endolysin
induced with: arabinose for 8-10hrs
Growth protocol Endolysin wild type and mutant were expressed in E. coli and P. aeruginosa after 8-10 hours of arabinose induction
Extracted molecule total RNA
Extraction protocol RNA was extracted by RNA extract kit,and MICROBExpress™ is designed to rapidly enrich bacterial mRNA from purified total RNA by removing the 16S and 23S ribosomal RNAs (rRNA).
Samples were barcoded and sequenced using the PE100 protocol on a HiSeq2000 sequencer, and RNA sequencing was performed by staff at Zhejiang Tianke (Hangzhou, China).Reads trimming and mapping were done using the CLC Genomics Workbench (QIAGEN, http://www.clcbio.com/). Default parameters were used if not specified. Reads of different samples were trimmed with maximal allowed ambiguous nucleotides of 2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file: Pa_exp.txt
Pa_E12 RPKM
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mo8 whole genome using CLC Genomics Workbench with default parameters
Reads Per Kilobase of exon per Million mapped reads (RPKM) for gene were calculated using CLC Genomics Workbench with default parameters
Genome_build: E. coli reference genome: DH10B, NC_010473.1
Genome_build: P. aeruginosa reference genome: PAO1, NC_002516.2
Supplementary_files_format_and_content: abundance measurements
 
Submission date Oct 19, 2015
Last update date May 15, 2019
Contact name Fei Xu
E-mail(s) fxu@zju.edu.cn
Organization name Zhejiang Academy of Agricultural Sciences
Street address 198 Shiqiao Road
City Hangzhou
ZIP/Postal code 310021
Country China
 
Platform ID GPL18644
Series (1)
GSE74121 Transcriptome analysis of E. coli and P. aeruginosa expressing endolysin wild type and mutant in vivo
Relations
BioSample SAMN04193709
SRA SRX1352982

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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