Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

rawData

Escherichia coli culture was subjected to two different types of nutritional scenarios, abundant carbon/ nitrogen sources and scarce carbon/nitrogen medium. Study revealed that scarce medium adapted culture were more tolerant to hydrogen peroxide than abundant medium.

GROWTH CONDITION

Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress

Nutritional condition dependant differential tolerance to hydrogen peroxide stress in Escherichia coli

Escherichia coli culture was subjected to two different types of nutritional scenarios, abundant carbon/ nitrogen sources and scarce carbon/nitrogen medium. Study revealed that scarce medium adapted culture were more tolerant to hydrogen peroxide than abundant medium.


P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MTAB-30393

Preparation of Poly-A controls – Requires the Poly- A RNA control kit (Affymetrix p/n 900433) cDNA Synthesis Purification and Quantitation of cDNA[Use MinElute PCR purification columns (Qiagen)] cDNA Fragmentation Terminal Labeling Prokaryotic Target Hybridization Array Washing and Staining Mini_prok2v1_450 Fluidics Profile  Post Hyb Wash #1  10 cycles of 2 mixes/cycle with Wash Buffer A at 30C Post Hyb Wash #2  4 cycles of 15 mixes/cycle with Wash Buffer B at 50C 1st Stain   Stain the probe array for 300 sec. in Streptavidin solution (vial 1) at 35C Post Stain Wash  10 cycles of 4 mixes/cycle with Wash Buffer A at 30C 2nd Stain   Stain the probe array for 300 sec. in Antibody Solution (vial 2) at 35C 3rd Stain   Stain the probe array for 300 sec. in SAPE solution (vial 1) at 35C Final Wash  15 cycles of 4 mixes/cycle with Wash Buffer A at 35C. The holding      Temperature is 25C. Wash Buffer A = non-stringent wash buffer. Wash Buffer B = stringent wash buffer. (Parameters: Chamber type = OTHER: Affymetrix GeneChip Hybridization Oven 645, Quantity of label target used = 10, Mass unit = Micro gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 45)

P-MTAB-30394

Escherichia coli ATCC 25922 culture was grown in media differing in carbon and nitrogen source (2.5g glucose/lit and 5mM ammonium chloride represented rich medium whereas 0.25g glucose/lit and 0.25mM amminium chloride represented starvation medium). Cells were given adaptation in respective media for two cycles, first cycle for 4 hours and second cycle overnight(22 hrs). These cultures were then tested for their ability to combat hydrogen peroxide stress. Cultures were named starvation derived seed culture (SDSC) and rich derived seed culture (RDSC). The goal was to highlight the differences in SDSC and RDSC. All experiments were performed in 500ml flasks with 100ml medium. From RDSC, 0.1OD/ml culture was transferred to Control-R (Rich medium), Sample-RM1 (Rich medium with 1ul H2O2 harvested at 9th hour) and Sample-RM2 (Rich medium with 1ul H2O2 harvested at 24th hour). From SDSC, 0.1OD/ml culture was transferred to Control-SR (Rich medium), Control-S (Starvation medium), Sample-SM1 (Rich medium with 1ul H2O2 harvested at 3rd hour), Sample-SM2(Rich medium with 1ul H2O2 harvested at 6th hour),Sample-SM3 (Rich medium with 2.5ul H2O2 harvested at 3rd hour) and Sample-SM4(Rich medium with 2.5ul H2O2 harvested at 6th  hour). (Parameters: start time = 4, stop time = 22, time unit = hours, min temperature = 37, temperature unit = C, media = Minimal media)

P-MTAB-30395

RNA extraction was done as per Qiagen RNeasy mini-kit protocol. (Parameters: Extracted product = total_RNA, Amplification = none)

Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress

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