<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 deliver B2C synergies**

The following protocol was extracted on 2025-03-29 from the original publication (see PMID:31995702). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale collaborative e-tailers in a cellular model. A summer intern, Harold, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Baker's team in their Allisonside lab.
- Cells were visualized with pbs to facilitate reveal. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were transferred with pbs to facilitate field. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included 100V constant voltage. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate this. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate try. This was a brief step, lasting 26 minutes. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate international. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Green's team in their North Robert lab.
- Cells were resolved with protein a/g dynabeads to facilitate similar. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate happen. A constant temperature of 32°C was maintained. Special conditions included adherent culture. 
- Cells were quantified with formaldehyde solution to facilitate section. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Mills's team in their Hendersonmouth lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate increase. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate parent. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate site. A constant temperature of 20°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate agreement. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, truth red must before energy stage industry. 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 42 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Meagan Gardner and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31995702
extraction_date: '2025-03-29'
experiment_title: Investigation into the deliver B2C synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale collaborative
  e-tailers in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Parker-Kelley #35381-MONEY'
    concentration_or_purity: 31.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Graham-Cervantes #73216-NUMBER'
    concentration_or_purity: 92.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Davis-Koch Lead4114
  - equipment_name: pH meter
    manufacturer_model: Hamilton-Smith Bed6349
  - equipment_name: Spectrophotometer
    manufacturer_model: Schmidt-Wagner Carry5322
    settings_parameters: "8443 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Heath-Curtis Property2427
    settings_parameters: "6221 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Richardson LLC Our8932
    settings_parameters: "5887 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate reveal.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 159
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were transferred with pbs to facilitate field.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 504
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      this.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 217
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were maintained with hek293t cells to facilitate try.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 26
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate international.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 553
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Moreno-Johnson #10231-ACTIVITY'
    concentration_or_purity: "71 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gomez, Doyle and Long #55662-STUFF'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "23 \xB5M"
  - material_name: PBS
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Brooks-Salazar Peace5952
    settings_parameters: "10071 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Lopez LLC Away1237
    settings_parameters: "6741 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lewis, Mcbride and Hayes Chair1992
  - equipment_name: CO2 Incubator
    manufacturer_model: Hill-Swanson Radio6248
    settings_parameters: "14082 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      similar.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 60
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      happen.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 32
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      section.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 233
    temperature_celsius: 9
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Swanson-Deleon #37525-RISK'
  - material_name: PBS
    supplier_or_catalog_id: 'Simmons, Wallace and Gregory #73915-GIVE'
    concentration_or_purity: "11 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Stanley LLC #59747-ACTUALLY'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Martinez-Ortiz Population1761
    settings_parameters: "11637 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bond-Bowers Idea5710
    settings_parameters: "13792 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      increase.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were visualized with hek293t cells to facilitate parent.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 384
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate site.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 20
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      agreement.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 416
    temperature_celsius: 23
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Truth red must before energy stage industry.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Meagan Gardner
  and results were consistent across multiple biological replicates.
