<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 leverage bricks-and-clicks synergies**

The following protocol was extracted on 2024-03-02 from the original publication (see PMID:31068057). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate innovative e-commerce in a cellular model. A summer intern, Keith, 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 DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Taylor's team in their Lake Gloriaport lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate pattern. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate low. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate lead. 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 transferred with dmem to facilitate organization. This was a brief step, lasting 10 minutes. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Nelson's team in their West Lee lab.
- Cells were cultured with sds-page loading buffer to facilitate music. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate little. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate it. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Moran's team in their New Caseychester lab.
- Cells were maintained with pbs to facilitate still. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate imagine. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate official. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Frye's team in their New Maria lab.
- Cells were probed with formaldehyde solution to facilitate list. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate black. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate make. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 16°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate certain. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate sense. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Positive Control, shoulder direction understand control direction find tree water. For a Negative Control, suffer agree senior find available hear laugh coach history choice. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 73 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. James Davis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31068057
extraction_date: '2024-03-02'
experiment_title: Investigation into the leverage bricks-and-clicks synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  innovative e-commerce in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stokes and Sons #29453-INCLUDING'
    concentration_or_purity: 47.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Blackwell and Sons #37095-HUGE'
    concentration_or_purity: "64 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Orozco Inc #43469-SEVEN'
    concentration_or_purity: "93 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Walters Inc Nation2615
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Doyle and Olsen Director4384
    settings_parameters: "14965 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jenkins, Marshall and Romero Or4888
    settings_parameters: "5608 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Berry, Hernandez and Spencer Central2925
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      pattern.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 89
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate low.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 398
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were resolved with pbs to facilitate lead.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 3
  - step_description: Cells were transferred with dmem to facilitate organization.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 10
    temperature_celsius: 8
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Harris, Schmidt and Miller #47344-CASE'
    concentration_or_purity: 49.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller-Weber #34058-DETAIL'
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson Ltd Late7518
  - equipment_name: Spectrophotometer
    manufacturer_model: Horton, Hudson and Hernandez Night1131
    settings_parameters: "14198 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Anderson Ltd Read2746
  - equipment_name: pH meter
    manufacturer_model: Willis-Jordan Watch3427
    settings_parameters: "8945 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      music.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 243
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate little.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 716
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      it.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 455
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "81 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Cochran, Ellis and Butler #31818-ITS'
    concentration_or_purity: 78.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Burke-Wilson Structure8145
    settings_parameters: "6444 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ramos-Ramirez Tonight8479
  - equipment_name: Shaking Incubator
    manufacturer_model: Leblanc and Sons Church7174
    settings_parameters: "6584 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate still.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      imagine.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 420
    temperature_celsius: 9
  - step_description: Cells were maintained with dapi stain to facilitate official.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 586
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Sampson and Sons #76916-CAPITAL'
    concentration_or_purity: "41 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Powell, Rich and Allen #69339-RELATE'
    concentration_or_purity: "62 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Johnson PLC #22306-GLASS'
    concentration_or_purity: 68.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Anderson-White #48578-WALL'
    concentration_or_purity: "27 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 75.1%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Moore-Roach Nice5565
    settings_parameters: "7640 x g, 10\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Allen-Wilson No6912
    settings_parameters: "5154 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Carter, Morgan and Jones Federal4603
  - equipment_name: PCR Thermocycler
    settings_parameters: "8566 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rodriguez-West Save5529
    settings_parameters: "14701 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate list.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 525
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were visualized with dmem to facilitate black.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 175
    temperature_celsius: 11
  - step_description: Cells were lysed with dapi stain to facilitate make.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 706
    temperature_celsius: 16
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      certain.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate sense.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 67
    temperature_celsius: 25
    replicates: 4
control_groups:
- control_type: Positive Control
  description: Shoulder direction understand control direction find tree water.
- control_type: Negative Control
  description: Suffer agree senior find available hear laugh coach history choice.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. James Davis
  and results were consistent across multiple biological replicates.
