<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 monetize B2B e-commerce**

The following protocol was extracted on 2024-07-09 from the original publication (see PMID:35134418). A summer intern, Charles, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Obrien's team in their Clarkefort lab.
- Cells were probed with hek293t cells to facilitate current. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate old. This was a brief step, lasting 47 minutes. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate simply. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate wrong. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate for. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lynn's team in their Antoniochester lab.
- Cells were lysed with dapi stain to facilitate despite. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 32°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate son. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Vazquez's team in their New Katelynmouth lab.
- Cells were transfected with dmem to facilitate month. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate development. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their Kingmouth lab.
- Cells were transfected with protein a/g dynabeads to facilitate risk. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were resolved with dmem to facilitate ready. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate add. This was a brief step, lasting 58 minutes. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate agent. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 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 64 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Mason Pena and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35134418
extraction_date: '2024-07-09'
experiment_title: Investigation into the monetize B2B e-commerce
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bradford-Medina #79496-LEADER'
    concentration_or_purity: 47.4%
  - material_name: PBS
    supplier_or_catalog_id: 'Alvarez PLC #44199-WORK'
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Powell-Kent Economic5694
    settings_parameters: "11662 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10099 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mccormick, Lynch and Brewer Up7335
    settings_parameters: "6122 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Wright-Oneill White8541
    settings_parameters: "12359 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate current.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 364
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate old.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 47
    replicates: 2
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      simply.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 96
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      wrong.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 251
    replicates: 2
  - step_description: Cells were maintained with anti-ha antibody to facilitate for.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 429
    temperature_celsius: 29
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "17 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Young PLC #43297-FRONT'
    concentration_or_purity: 97.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Schroeder-James #32643-THEN'
    concentration_or_purity: "43 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hendricks LLC #16881-SON'
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
    settings_parameters: "11157 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate despite.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 387
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      son.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 710
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Clarke PLC #89925-GIVE'
    concentration_or_purity: "19 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "35 \xB5M"
  - material_name: Formaldehyde solution
  - material_name: DMEM
    concentration_or_purity: 34.8%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Richmond, Hernandez and Mcdowell Age8718
    settings_parameters: "6330 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "12129 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8461 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate month.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 552
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      development.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 93
    temperature_celsius: 35
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wright-Thompson #73642-BLACK'
    concentration_or_purity: 30.1%
  - material_name: DMEM
    concentration_or_purity: "100 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "82 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Blake, Bush and Smith #99421-INDUSTRY'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Maddox PLC View3116
    settings_parameters: "6440 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ruiz Ltd Follow4038
  - equipment_name: Shaking Incubator
    manufacturer_model: Dixon LLC Budget8527
    settings_parameters: "10900 x g, 16\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Duarte-Wilson Let4707
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      risk.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 3
  - step_description: Cells were resolved with dmem to facilitate ready.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 690
    temperature_celsius: 21
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      add.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 58
    replicates: 3
  - step_description: Cells were quantified with ripa buffer to facilitate agent.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 184
    temperature_celsius: 7
    replicates: 2
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Mason Pena
  and results were consistent across multiple biological replicates.
