|
| Status |
Public on Dec 22, 2012 |
| Title |
TW30 LP |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Photobacterium profundum |
| Characteristics |
strain: TW30
treatment: hydrostatic pressure Mpa 0.1
genotype: toxR
|
| Treatment protocol |
Samples DB110_HP and TW30_HP were grown in ~2 cm of stainless steel pressure vessels at 28 MPa (280 Atm), samples DB110_LP and TW30_LP were grown at 0.1 MPa (atmospheric pressure)
|
| Growth protocol |
Bacterial cultures were growth at 0.1 MPa and 28 MPa in Difco Marine 2216 Broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis bacterial cultures were grown as explained above at two different conditions (0.1 MPa; 16°C and 28 MPa; 16°C); for each growth condition total RNA was extracted from three independent cultures using trizol (Gibco) and RNeasy columns (Qiagen). Genomic DNA was removed using DNAsi (Ambion). RNA quality was determined using the 2100 Bioanalyzer (Agilent). Equal RNA quantities obtained from the three cultures grown in the same condition were pooled to reduce biological differences between replicates and to obtain a more robust sample and representative of each condition examined. Starting from 10 μgs of total RNA, 16S and 23S rRNAs were removed using the MICROBExpressTM kit (Ambion), after rRNA depletion, RNA was fragmented incubating the sample at 82°C for 6 mins in a fragmentation buffer (40 mM Tris Acetate pH 8.1, 100mM KOAc, 30 mM MgOAc-4H20). Fragments obtained were checked by gel electrophoresis, had an average length of 200 bases and range in quantity from 1 to 2 μgs (estimated using NanoDrop 1000 Spectrophotometer - Thermo Scientific). All the RNA obtained from each sample was retrotranscribed using One-Cycle cDNA Kit (Invitrogen), second strand synthesis was performed using the same kit. Protocol was modified because first strand synthesis was performed using random hexamers. DNA obtained was purified using AMPureR kit (Agencourt) and quantified using NanoDrop 3300 Fluorospectrometer (Thermo Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
TW30 is a toxR mutant strain
|
| Data processing |
SOLiD reads were aligned using PASS software; only those uniquely aligned on genome were considered
Using self-written perl script number of reads aliged on each gene was determined for each sample and an input file for DEGseq was generated
Differentially expressed genes were determined using DEGseq software 2.11.1
Genome_build: Photobacterium_profundum_SS9_uid62923
Supplementary_files_format_and_content: tab-delimited text files include number of reads for each Sample normalized respect to DB110_HP sample and considering the total number of reads aligned on the genome
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefano Campanaro |
| E-mail(s) |
[email protected]
|
| Phone |
+39 049 827 6306
|
| Organization name |
University of Padua
|
| Department |
Biology
|
| Street address |
Via Ugo Bassi 58/b
|
| City |
Padova |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15618 |
| Series (1) |
| GSE38259 |
Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa |
|
| Relations |
| SRA |
SRX149657 |
| BioSample |
SAMN00998562 |
