|
| Status |
Public on Nov 02, 2022 |
| Title |
ΔsrmB1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: <delta>srmB
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 |
ΔsrmB
|
| 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 |
SAMN17369859 |
| SRA |
SRX9864165 |
