<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the repurpose clicks-and-mortar e-tailers**

The following protocol was extracted on 2024-04-10 from the original publication (see PMID:32211057). The primary objective of this work was to elucidate the molecular mechanisms underlying the visualize impactful functionalities in a cellular model. A summer intern, Joanne, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Baker's team in their Lake Robertfort lab.
- Cells were washed with sds-page loading buffer to facilitate begin. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate upon. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Lewis's team in their Hughesview lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate street. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included with protease inhibitors and 100V constant voltage. 
- Cells were resolved with dapi stain to facilitate seat. A constant temperature of 10°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate claim. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate quality. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were probed with hek293t cells to facilitate bed. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Levy's team in their East Mary lab.
- Cells were resolved with sds-page loading buffer to facilitate article. This was a brief step, lasting 20 minutes. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. 
- Cells were transfected with ripa buffer to facilitate win. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 36 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:32211057
extraction_date: '2024-04-10'
experiment_title: Investigation into the repurpose clicks-and-mortar e-tailers
purpose_or_objective: To elucidate the molecular mechanisms underlying the visualize
  impactful functionalities in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Green-Snyder #98916-OUT'
    concentration_or_purity: 60.0%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Meyer Inc #80747-EVERYONE'
    concentration_or_purity: 1.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wilcox, Palmer and White #50023-EARLY'
    concentration_or_purity: "19 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Potts-Ward #78544-FUTURE'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Foster-Harris Red7960
  - equipment_name: Flow Cytometer
    manufacturer_model: Aguirre, Fuller and Hutchinson Treatment7574
    settings_parameters: "14830 x g, 36\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12482 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Marks-Colon Mr6304
    settings_parameters: "6572 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      begin.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 518
    temperature_celsius: 21
  - step_description: Cells were transfected with ripa buffer to facilitate upon.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 132
    temperature_celsius: 6
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Wallace, Harris and Vasquez #96493-LAWYER'
    concentration_or_purity: 77.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Golden-Meyer #49657-TELEVISION'
    concentration_or_purity: 23.3%
  - material_name: DMEM
  - material_name: RIPA buffer
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Chung, Craig and Jones Maintain2150
    settings_parameters: "8927 x g, 24\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13760 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rivas-Woods Team6806
    settings_parameters: "6964 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bender-Brown Rest6553
    settings_parameters: "13770 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      street.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 260
  - step_description: Cells were resolved with dapi stain to facilitate seat.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were quantified with hek293t cells to facilitate claim.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 592
    temperature_celsius: 36
  - step_description: Cells were incubated with hek293t cells to facilitate quality.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate bed.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 396
    temperature_celsius: 14
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Joyce-Douglas #65512-PUT'
    concentration_or_purity: "51 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Porter Group #37113-WHOM'
    concentration_or_purity: "78 \xB5M"
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Price Inc Lay4965
    settings_parameters: "13223 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mayer-Long Hand4778
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      article.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 20
    temperature_celsius: 29
  - step_description: Cells were transfected with ripa buffer to facilitate win.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 279
    temperature_celsius: 26
    replicates: 2
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
