|
| Status |
Public on Nov 04, 2014 |
| Title |
MG-1655_Urine_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MG-1655_Urine_rep3
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
condition: urine
growth phase: OD600 0.2
|
| Growth protocol |
For RNA preparation, both strains were grown with shaking at 37°C in 12ml MOPS media supplemented with 0.2% tryptone and 0.2% glucose until the OD600 reached 0.2. Five ml of the bacterial media were then passed through a 0.2m pore size filter and re-suspended with either urine or MOPS. The re-suspended bacteria were grown for 15 additional minutes with shaking at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To stop bacterial growth, ice was added to the MOPS and urine-grown samples and the cultures were harvested by centrifugation (10 min, 8,000g, 4°C). The supernatant was discarded and 500µl of saline (0.9% NaCl) was added to each sample. Samples were then treated with RNA Protect Bacterial Reagent (QIAGEN) to stabilize RNA according to the manufacturer’s instructions
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kits (Illumina). High RNA quality was confirmed prior to library construction using Agillent’s TapeStation 2200. 50 bp-long single end reads were then sequenced on an Illumina Hi-Seq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MG_urine_6
|
| Data processing |
Base-calling, alignment, filtering and of normalized abundance measurements were all done using the program "Rockhopper" version 1.3.0 with default parameters. The two reference E. coli used for this study were: NC_000913.2 for E. coli K12 1655 and NC_004431.1 for E. coli CFT073.
genome build: E. coli K12 1655: ASM584v1 and E. coli CFT073: ASM744v1
Supplementary_files_format_and_content: A matrix listing features of the called genes and normalized abundance measurements (upper quartile normalization)
|
| |
|
| Submission date |
Jul 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaara Oren |
| E-mail(s) |
[email protected]
|
| Organization name |
Broad institute
|
| Lab |
Yaara Oren
|
| Street address |
415 Main street cambridge
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE59468 |
Transfer of Non-coding DNA Drives Regulatory Rewiring in Bacteria |
|
| Relations |
| BioSample |
SAMN02918317 |
| SRA |
SRX652892 |
