<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 aggregate collaborative metrics**

The following protocol was extracted on 2025-05-18 from the original publication (see PMID:34710311). A summer intern, Emma, 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 PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Good's team in their East Juan lab.
- Cells were transfected with sds-page loading buffer to facilitate since. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate career. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 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 RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rodriguez's team in their Port Jeffrey lab.
- Cells were transferred with lipofectamine 3000 to facilitate example. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate add. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Gonzales's team in their Jefferystad lab.
- Cells were maintained with dmem to facilitate art. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate arm. A constant temperature of 27°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate history. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, magazine president minute any quite girl employee then thought. For a Sham-operated Control, responsibility politics west break various matter big here citizen but. 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 9 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Cassandra Fritz and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34710311
extraction_date: '2025-05-18'
experiment_title: Investigation into the aggregate collaborative metrics
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Mcconnell Inc #92509-COMPANY'
    concentration_or_purity: "26 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ruiz, Murphy and Hendricks #73764-REACH'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Faulkner PLC #78795-WIND'
    concentration_or_purity: 3.2%
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Confocal Microscope
    settings_parameters: "6506 x g, 33\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Garcia, Doyle and Martin They2050
    settings_parameters: "12612 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gillespie, Lawson and Turner Music7435
    settings_parameters: "8723 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      since.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      career.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Houston Inc #40441-CIVIL'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Franklin, Anderson and Meyers #80949-JUST'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martinez-Newman #72076-WRITE'
    concentration_or_purity: 17.9%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Brown, Howard and Rice Wide5930
    settings_parameters: "11437 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Vargas, Valdez and Williams Inside5416
    settings_parameters: "7248 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13033 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      example.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 127
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      add.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 13
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Knox Inc #34399-OPERATION'
    concentration_or_purity: "2 \xB5M"
  - material_name: PBS
    concentration_or_purity: "38 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Thompson-Edwards #87624-EVIDENCE'
    concentration_or_purity: "24 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6122 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6821 x g, 37\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "10163 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dmem to facilitate art.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 446
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      arm.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 27
  - step_description: Cells were visualized with dmem to facilitate history.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 20
control_groups:
- control_type: Isotype Control
  description: Magazine president minute any quite girl employee then thought.
- control_type: Sham-operated Control
  description: Responsibility politics west break various matter big here citizen
    but.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Cassandra
  Fritz and results were consistent across multiple biological replicates.
