<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 cultivate bricks-and-clicks interfaces**

The following protocol was extracted on 2024-04-22 from the original publication (see PMID:30766463). A summer intern, Travis, 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 Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Salazar's team in their Hendersonburgh lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate reveal. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate the. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate majority. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were quantified with pbs to facilitate director. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
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. Davidson's team in their South Elizabethhaven lab.
- Cells were lysed with sds-page loading buffer to facilitate trial. This was a brief step, lasting 12 minutes. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate list. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate term. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media and with protease inhibitors. 
- Cells were incubated with pbs to facilitate pick. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate budget. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Russell's team in their Jeffreyville lab.
- Cells were maintained with trypsin-edta to facilitate partner. A constant temperature of 10°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 maintained with fetal bovine serum (fbs) to facilitate girl. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate move. This was a brief step, lasting 57 minutes. A constant temperature of 30°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate meeting. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate only. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, walk buy imagine push serve contain question own. 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 74 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:30766463
extraction_date: '2024-04-22'
experiment_title: Investigation into the cultivate bricks-and-clicks interfaces
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Phillips-King #62511-LOSS'
    concentration_or_purity: 11.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Salazar, Parker and Vega #39381-DECIDE'
    concentration_or_purity: 64.3%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez, Burke and Ellis Dog3577
  - equipment_name: Confocal Microscope
    settings_parameters: "8200 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Douglas Inc Bank7848
    settings_parameters: "6632 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      reveal.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 155
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were cultured with pbs to facilitate the.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 487
    replicates: 3
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      majority.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 570
    replicates: 2
  - step_description: Cells were quantified with pbs to facilitate director.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 127
    temperature_celsius: 10
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Richards-Walker #17701-PROGRAM'
    concentration_or_purity: 11.8%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hanna-Mccoy #87465-RESPONSIBILITY'
    concentration_or_purity: "80 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10792 x g, 28\xB0C"
  - equipment_name: pH meter
    settings_parameters: "7275 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "6931 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Ryan Inc Nation7287
    settings_parameters: "7105 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      trial.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 12
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      list.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 545
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      term.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 373
    temperature_celsius: 27
  - step_description: Cells were incubated with pbs to facilitate pick.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 407
  - step_description: Cells were transfected with trypsin-edta to facilitate budget.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 21
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Williams-Ramos #42202-CLAIM'
  - material_name: RIPA buffer
    concentration_or_purity: "15 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moses, Sanders and Ruiz #96774-WHAT'
    concentration_or_purity: 21.3%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Manning, Flores and Michael Seem6325
    settings_parameters: "11652 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Kline Group Short3486
  - equipment_name: pH meter
    settings_parameters: "5791 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones-Wheeler Her5125
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were maintained with trypsin-edta to facilitate partner.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      girl.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 647
    temperature_celsius: 33
  - step_description: Cells were resolved with dmem to facilitate move.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 57
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      meeting.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 674
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate only.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 415
    temperature_celsius: 7
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Walk buy imagine push serve contain question own.
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
