|
| 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 |
