|
Status |
Public on Nov 02, 2022 |
Title |
Δgor2 |
Sample type |
SRA |
|
|
Source name |
bacteria
|
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
genotype: <delta>gor age: 24 h
|
Treatment protocol |
N/A
|
Growth protocol |
24 h at 37oC under shaking.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. Ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Δgor
|
Data processing |
Filtering using Trimmomatic ILLUMINACLIP:"adapters.fa":2:30:10 SLIDINGWINDOW:5:20 MINLEN:50. Alignment using Bowtie2. Generation of count table using HTSeq-count -m union -s yes -t exon -i Parent. Genome_build: Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.chromosome.Chromosome.fa Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw reads per transcript.
|
|
|
Submission date |
Jan 17, 2021 |
Last update date |
Nov 02, 2022 |
Contact name |
Ioly Kotta-Loizou |
E-mail(s) |
i.kotta-loizou13@imperial.ac.uk
|
Organization name |
Imperial College London
|
Department |
Life Sciences
|
Street address |
South Kensington Campus
|
City |
London |
ZIP/Postal code |
SW7 2AZ |
Country |
United Kingdom |
|
|
Platform ID |
GPL21117 |
Series (2) |
GSE165008 |
Transcriptome profile of Escherichia coli K12 MG1655 cells lacking selected genes |
GSE165118 |
Transcriptome profile of Escherichia coli K12 MG1655 under Rtc-inducing conditions |
|
Relations |
BioSample |
SAMN17369862 |
SRA |
SRX9864162 |