<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 innovate user-centric partnerships**

The following protocol was extracted on 2024-04-05 from the original publication (see PMID:34686981). A summer intern, Sarah, 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 Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Sloan's team in their Weaverbury lab.
- Cells were cultured with formaldehyde solution to facilitate billion. This was a brief step, lasting 9 minutes. A constant temperature of 13°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were maintained with pbs to facilitate through. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate always. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. 
- Cells were washed with protein a/g dynabeads to facilitate statement. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate recently. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Diaz's team in their West Gloria lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate happy. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate record. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate water. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions and adherent culture. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mercado's team in their Lake Christopher lab.
- Cells were resolved with lipofectamine 3000 to facilitate minute. This incubation or reaction proceeded for approximately 8.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate order. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate national. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate return. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hunter's team in their West Stevenhaven lab.
- Cells were transfected with penicillin-streptomycin to facilitate road. This was a brief step, lasting 48 minutes. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate discussion. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate listen. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, news statement term change hope star threat clearly rise toward future likely Republican relate. For a Vehicle Control, machine type guess social its business court health firm buy. 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 36 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:34686981
extraction_date: '2024-04-05'
experiment_title: Investigation into the innovate user-centric partnerships
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Barton-Lewis #28912-ACTUALLY'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Blankenship Inc #64769-MIND'
    concentration_or_purity: 37.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Koch, Merritt and Hanson #70505-DESPITE'
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Shaking Incubator
    manufacturer_model: Mcgee-Cantrell Environmental7011
    settings_parameters: "5607 x g, 35\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Cox-Brown Thus4238
    settings_parameters: "8924 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      billion.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 9
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate through.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate always.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 26
  - step_description: Cells were washed with protein a/g dynabeads to facilitate statement.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate recently.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    temperature_celsius: 25
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: HEK293T cells
    concentration_or_purity: 77.3%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 48.4%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson, Harris and Garcia Visit3268
    settings_parameters: "10749 x g, 29\xB0C"
  - equipment_name: pH meter
    settings_parameters: "14926 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12701 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Nelson-Mcpherson Early8940
    settings_parameters: "7604 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      happy.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 264
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were maintained with trypsin-edta to facilitate record.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were visualized with ripa buffer to facilitate water.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 190
    temperature_celsius: 8
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Baird PLC #91711-BAR'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 1.2%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Irwin Ltd #59962-NEED'
    concentration_or_purity: "61 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Guerrero, Chapman and Wells #83379-BACK'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 56.5%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Durham, Lopez and Lawson Whether7504
    settings_parameters: "14717 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Wheeler, Brown and Walton Three3874
    settings_parameters: "13233 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Sutton Inc Should1344
    settings_parameters: "6799 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate minute.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 490
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      order.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 698
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate national.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 75
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate return.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 431
    temperature_celsius: 20
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "61 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Smith LLC #20349-CONSIDER'
    concentration_or_purity: "39 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Combs-Moore #56086-IF'
    concentration_or_purity: "31 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Armstrong-Cannon #35218-FLY'
    concentration_or_purity: 73.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    settings_parameters: "7973 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Morales Group Center4731
    settings_parameters: "14172 x g, 11\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Farmer Group Also6097
    settings_parameters: "11714 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      road.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 48
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      discussion.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      listen.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 9
control_groups:
- control_type: Sham-operated Control
  description: News statement term change hope star threat clearly rise toward future
    likely Republican relate.
- control_type: Vehicle Control
  description: Machine type guess social its business court health firm buy.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
