|
| Status |
Public on Mar 06, 2018 |
| Title |
Pseudomonas aeruginosa FMN Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas aeruginosa
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
protocol: FMN
strain: PAO1
chip antibody: none
|
| Growth protocol |
Candida S5314 strain was grown in GMM and YPD media to log phase (OD=0.6-0.8) and to saturated phases (OD>2). Pseudomonas aeruginosa PAO1 and bacillus subtilis 168 strain are grown in minimal media and LB to log (OD-0.6) and saturated phases (OD>2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from candida albicans using hot acid phenol protocol. Poly(A)+ selected mRNAs were obtained using Poly(A)purist kit from Ambion. Total RNA was extracted from pseudomonas aeruginosa using Trizol. Total RNA was extracted from bacillus subtilis using 1%SDS and lysozyme, followed by Trizol. Ribosomal depletion on total bacillus and pseudomonas RNA was carried out using RiboZero kit for bacteria (Epicenter)
Poly(A) enriched or ribosomal RNA depleted RNA were structured probed in the presence and absence of ligands using RNase V1. The structure probed RNA was then fragmented, ligated to adapters, reverse transcribed and PCR amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Short reads from PARCEL libraries (Illumina NextSeq 500, 50 bp, single-end) in P. aeruginosa PAO1 and B. subtilis 168 were aligned to their corresponding reference genomes downloaded from NCBI using the short-read aligner bowtie2 (parameters: -k 1 --local)23. In the case of C. albicans SC5314, we extracted the UTR annotation from Bruno et al and integrated them into their corresponding transcriptomes before alignment by bowtie2. In both cases, only uniquely mapped reads were used for subsequent analysis.
Genome_build: Candida albicans SC5314 (v21)
Genome_build: Bacillus subtilis subsp. subtilis 168. (NC_000964)
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516)
Supplementary_files_format_and_content: bedgraph file generated using Bedtools
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
YANG SHEN |
| Organization name |
Genome Institute of Singapore
|
| Street address |
Genome Institute of Singapore (A*STAR) 60 Biopolis Street, #02-01 Genome
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE106133 |
Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes |
|
| Relations |
| BioSample |
SAMN07832850 |
| SRA |
SRX3324117 |
