|
| Status |
Public on Feb 08, 2023 |
| Title |
menF/ubiC KO adapted 1, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
GMOS menF/ubiC KO adapted
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: GMOS menF/ubiC KO adapted
culture type: batch
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
quinone__menFubiC_ale1__1
quinone_log_tpm.csv
quinone_counts.csv
|
| Data processing |
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: quinone_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: quinone_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.
|
| |
|
| Submission date |
Feb 08, 2023 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Cameron Lamoureux |
| E-mail(s) |
clamoure@eng.ucsd.edu
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24659 |
| Series (1) |
| GSE224889 |
Adaptive laboratory evolution of chorismate synthase knockouts |
|
| Relations |
| BioSample |
SAMN33214564 |
| SRA |
SRX19316097 |
