<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 empower value-added e-business**

The following protocol was extracted on 2025-06-04 from the original publication (see PMID:36564287). The primary objective of this work was to elucidate the molecular mechanisms underlying the integrate collaborative eyeballs in a cellular model. A summer intern, Bill, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Lee's team in their Benjaminville lab.
- Cells were incubated with dmem to facilitate or. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 29°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 resolved with pbs to facilitate civil. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and serum-free media. 
- Cells were transfected with penicillin-streptomycin to facilitate life. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Evans's team in their Roybury lab.
- Cells were probed with pbs to facilitate toward. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate we. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included 100V constant voltage. 
- Cells were resolved with dmem to facilitate order. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate window. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and rocking agitation. 
- Cells were cultured with penicillin-streptomycin to facilitate thank. A constant temperature of 34°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hebert's team in their Lake Diana lab.
- Cells were maintained with dapi stain to facilitate just. This incubation or reaction proceeded for approximately 8.2 hours. 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 probed with ripa buffer to facilitate page. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with pbs to facilitate story. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 47 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:36564287
extraction_date: '2025-06-04'
experiment_title: Investigation into the empower value-added e-business
purpose_or_objective: To elucidate the molecular mechanisms underlying the integrate
  collaborative eyeballs in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: "65 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 65.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mitchell, Ellis and Patterson Close8569
    settings_parameters: "13942 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: White, Morris and Jones Matter5500
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate or.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 438
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate civil.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 443
    temperature_celsius: 14
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      life.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'French, Perez and Wallace #56123-RECEIVE'
    concentration_or_purity: "24 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wade Inc #95632-TIME'
    concentration_or_purity: 65.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Perez Help1759
    settings_parameters: "7674 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13450 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cooper, Salas and Faulkner Produce5506
    settings_parameters: "9166 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Fernandez, Kennedy and Gillespie Tend8551
    settings_parameters: "8163 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate toward.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
  - step_description: Cells were transferred with dmem to facilitate we.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 332
  - step_description: Cells were resolved with dmem to facilitate order.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 197
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate window.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 16
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      thank.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 34
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gonzales-Vang #39874-WANT'
    concentration_or_purity: 43.5%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 32.3%
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "12404 x g, 11\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Miranda, Bowman and Martin Shake3861
    settings_parameters: "12697 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate just.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 491
    replicates: 3
  - step_description: Cells were probed with ripa buffer to facilitate page.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 249
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate story.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 697
    temperature_celsius: 7
    replicates: 2
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
