|
| Status |
Public on Jul 30, 2018 |
| Title |
LP3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12 substr. MG1655
tissue: bacterial cells
stimulus: Control
|
| Treatment protocol |
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min
|
| Growth protocol |
E. coli K-12 MG 1655 was grown in LB-Miller broth at 37°C ,160rpm to an O.D.600 nm of 0. 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis.
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Biological 2, techinical 1
|
| Data processing |
MiSeq for base calling
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33).
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4)
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread'
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/).
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group.
Genome_build: U00096.3
Supplementary_files_format_and_content: Table of read counts with genes as rows and samples as columns.
|
| |
|
| Submission date |
May 25, 2018 |
| Last update date |
Jul 30, 2018 |
| Contact name |
Meng Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
01913409599
|
| Organization name |
Northumbria University
|
| Department |
Applied Sciences
|
| Lab |
EBA321
|
| Street address |
Ellison Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE1 8ST |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE114917 |
Genetic response of E.coli to mild elevated pressure |
|
| Relations |
| BioSample |
SAMN09259766 |
| SRA |
SRX4124776 |
