|
| Status |
Public on Dec 03, 2014 |
| Title |
ALE4 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA isolated from E. coli
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: Evolved
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
Cells were grown to mid-log phase aerobically at 37°C on M9 Supplemented with 4g/L D-Glucose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
K-12 MG1655
|
| Data processing |
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v0.12.8 with parameters -X 1000 -n 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.1.1 with the option --library-type fr-firststrand
Genome_build: ASM584v2
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Sep 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bernhard Palsson |
| E-mail(s) |
[email protected]
|
| Phone |
858-534-5668
|
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE61327 |
Expression Profiling E. Coli Evolved on Glucose Minimal Media |
|
| Relations |
| BioSample |
SAMN03031684 |
| SRA |
SRX699438 |
