|
| Status |
Public on Jul 19, 2018 |
| Title |
FPS1: wt_R1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
carbon source: D-glucose
genotype/variation: wild type
|
| Treatment protocol |
The cell cultures were treated with RNAprotect reagent (Qiagen).
|
| Growth protocol |
All samples were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 2 g/L D-glucose and 50 mg/L Kanamycin A (with the exception of wild type which was grown in the absence of antibiotics) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using Qiagen’s RNeasy minikit column according to the manufacturer’s specifications. The total RNA quality was checked with the Agilent Bioanalyzer RNA 600 nano kit. Ribosomal RNA (rRNA) was removed utilizing Ribo-Zero rRNA removal kit (Epicentre) for Gram-negative bacteria.
The KAPA RNA HyperPrep kit (Kapa Biosystems) was used for generation of paired-end, strand-specific RNA sequencing libraries. The final pool of libraries was subjected to a 1x SPRI bead size selection to further remove unincorporated PCR primers.
RNAsequencing libraries were run on an Illumina NextSeq 550 machine using a NextSeq 500/550 Mid Output v2 kit (150 cycles).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequenced reads were mapped onto CP009273.1 reference genome sequence using bowtie2 v.2.3.4.1 with parameters -X 1000 -N 1 -p 20 -3 3 -1 <R1_files> -2 <R2_files> -x <index>.
The SAM output file of bowtie2 was converted to BAM and sorted using samtools version 1.8
Expression levels of each gene in units transcripts per million (TPM) were computed from fragment counts normalized per kilobase of feature length per million mapped fragments (FPKM) using the R (v.3.5.0) package DESeq2 in Bioconductor.
Differentially expressed genes were identified using the R package DESeq2 in Bioconductor. Gene expression fold changes were considered significant if the log2(fold change) was greater than 1 and the calculated p-value was smaller that 0.05.
Genome_build: CP009273.1
Supplementary_files_format_and_content: A single .csv file containing all TPM values in a matrix table for all genes in each sample is provided.
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Jul 20, 2018 |
| Contact name |
Adam M Feist |
| E-mail(s) |
afeist@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Lab |
Palsson Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25344 |
| Series (1) |
| GSE117303 |
Reframing gene essentiality in terms of adaptive flexibility |
|
| Relations |
| BioSample |
SAMN09689227 |
| SRA |
SRX4403859 |
