|
| Status |
Public on May 14, 2018 |
| Title |
D-lyxose Exp. 2 Flask 90 - Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
cell cultures
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
carbon source: D-lyxose
genotype/variation: Evolved - endpoint/optimization
|
| Treatment protocol |
The cell cultures were treated with RNAprotect reagent (Qiagen).
|
| Growth protocol |
All evolved populations were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with either 0.2% D-lyxose, D-2-deoxyribose, D-arabinose, or m-tartrate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using Qiagen’s RNeasy minikit column according to the manufacturer’s specifications. Ribosomal RNA (rRNA) was removed utilizing Ribo-Zero rRNA removal kit (Epicentre) for Gram-negative bacteria.
The KAPA Stranded RNA-seq kit (Kapa Biosystems) was used for generation of paired-end, strand-specific RNA sequencing libraries.
RNA sequencing libraries were then run on an Illumina HiSeq 2500 using the ‘rapid-run mode’ with 2 x 35 paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were mapped onto NC_000913.2 reference genome sequence using bowtie v.1.1.2 with parameters -X 1000 -n 2 -p 2 -3 3 -S.
Expression levels of each gene in units per kilobase per million fragments mapped (FPKM) were calculated using cufflinks v.2.2.1.
FPKM data was then utilized to run cuffdiff to calculate gene expression fold changes between endpoint and initial growth populations using a geomentric normalization and a false discovery rate of 0.05.
Gene expression fold changes was considered significant if the calculated q-value was smaller that 0.05.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: FPKM tracking files (cufflinks output files) include FPKM values for each sample.
|
| |
|
| Submission date |
May 11, 2018 |
| Last update date |
May 14, 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 |
GPL18956 |
| Series (1) |
| GSE114358 |
Enzyme promiscuity shapes evolutionary innovation and optimization |
|
| Relations |
| BioSample |
SAMN09198480 |
| SRA |
SRX4073858 |
