|
| Status |
Public on Nov 08, 2017 |
| Title |
E.coli_WT pH 5.6 C |
| Sample type |
RNA |
| |
|
| Source name |
WT pH 5.6 C
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: MG1655
ph: 5.6
sucrose status: no sucrose
genotype: Wildtype
|
| Growth protocol |
E. coli strains was grown in MgM media at pH 5.6, 7.2 and 7.2 with 15% (w/v) sucrose to O.D ~0.6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using an RNeasy mini kit (Qiagen).
|
| Label |
cyanine 3-CTP
|
| Label protocol |
100 ng of total RNA was labeled with Low Input Quick Amp WT Labeling Kit, One-Color (Agilent p/n 5190-2943) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp WT Labeling, version 2.0). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.
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| |
|
| Hybridization protocol |
600ng of labeled cRNA was hybridized onto Agilent SurePrint HD E.coli GE 8x15K Microarray for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37oC
|
| Scan protocol |
Scanning was performed on Agilent High Resolution Microarray Scanner (C-model).
|
| Data processing |
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The data analysis is done using a microarray specialized analysis software, Genespring GX. In this experiment, the microarray type used is a slide having 8 arrays with 60 thousand features per array. The exact number of features in the each array, inclusive of control probes, is 10,751 features. The microarray has a specific Agilent identifier called an AMADID which is used to identify what kind of array is being used; in this experiment the AMADID used is the design ID 020097.
Supplementary files contain the following: Raw Signal Values: The term “raw” signal values refer to the linear data after thresholding and summarization Summarization is performed by computing the geometric mean. Raw data filtered on Expression (20.0 - 343943.344)• Normalized Signal Values: ``Normalized'' value is the value generated after log transformation and normalization (Shift to 75 percentile) and baseline transformation.
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| |
|
| Submission date |
Nov 07, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
smarajit chakraborty |
| E-mail(s) |
chakrabortysmarajit@gmail.com
|
| Phone |
83682977
|
| Organization name |
Mechanobiology Institute
|
| Street address |
T-Lab, 5A Engineering Drive 1, NUS
|
| City |
singapore |
| ZIP/Postal code |
117411 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL13359 |
| Series (2) |
| GSE106628 |
To compare the transcriptome of ompR null strains with wild-type strain of E. coli during acid or osmotic stress |
| GSE106630 |
To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress |
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