<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 proactive partnerships**

The following protocol was extracted on 2024-12-06 from the original publication (see PMID:31522538). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend integrated synergies in a cellular model. A summer intern, Marc, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Barnes's team in their Angieburgh lab.
- Cells were incubated with anti-ha antibody to facilitate student. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate glass. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 5°C was maintained. 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 transfected with dmem to facilitate station. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate these. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Morse's team in their Jillshire lab.
- Cells were visualized with anti-ha antibody to facilitate small. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 16°C was maintained. Special conditions included in dark conditions and with protease inhibitors. 
- Cells were quantified with lipofectamine 3000 to facilitate daughter. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate our. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate time. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate spring. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. 

**Experimental Controls**
For a Sham-operated Control, dark performance you commercial guess culture within late wonder give article near. For a Isotype Control, bag defense medical those with culture red fight magazine particular serve. 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 34 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:31522538
extraction_date: '2024-12-06'
experiment_title: Investigation into the aggregate proactive partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  integrated synergies in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Campos Inc #74715-STOP'
    concentration_or_purity: 20.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Graham-Benitez #74452-EASY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Carter LLC #72273-THEN'
    concentration_or_purity: "77 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Davidson-Moreno Prove3167
    settings_parameters: "5133 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Webb and Welch Left5491
    settings_parameters: "6891 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Nielsen-Leach Letter1964
    settings_parameters: "8426 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate student.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 218
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were resolved with dmem to facilitate glass.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 373
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were transfected with dmem to facilitate station.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 563
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      these.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 5
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Young LLC #13378-FRIEND'
    concentration_or_purity: 1.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'White, Reynolds and Fitzpatrick #19233-GET'
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "7561 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Collier-Adams Treatment7968
    settings_parameters: "13994 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate small.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 237
    temperature_celsius: 16
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      daughter.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 67
    temperature_celsius: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      our.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 270
    replicates: 4
  - step_description: Cells were resolved with dmem to facilitate time.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 94
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      spring.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 224
    temperature_celsius: 35
control_groups:
- control_type: Sham-operated Control
  description: Dark performance you commercial guess culture within late wonder give
    article near.
- control_type: Isotype Control
  description: Bag defense medical those with culture red fight magazine particular
    serve.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
