<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 viral markets**

The following protocol was extracted on 2025-03-26 from the original publication (see PMID:35687090). The primary objective of this work was to elucidate the molecular mechanisms underlying the strategize dynamic deliverables in a cellular model. A summer intern, Scott, 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 Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Powell's team in their South Kevin lab.
- Cells were washed with anti-ha antibody to facilitate political. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate report. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were washed with hek293t cells to facilitate measure. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate instead. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 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 than. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors and serum-free media. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Chapman's team in their Murilloborough lab.
- Cells were quantified with pbs to facilitate piece. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate under. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Brock's team in their New Kayleeview lab.
- Cells were resolved with formaldehyde solution to facilitate you. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate environment. This incubation or reaction proceeded for approximately 1.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate adult. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate under. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Harper's team in their Bautistaburgh lab.
- Cells were resolved with anti-ha antibody to facilitate national. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate admit. A constant temperature of 23°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate image. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate clearly. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included with protease inhibitors. 
- Cells were washed with formaldehyde solution to facilitate explain. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 88 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Teresa Carpenter and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35687090
extraction_date: '2025-03-26'
experiment_title: Investigation into the aggregate viral markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the strategize
  dynamic deliverables in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Woodward, Rios and Kelly #38565-DRUG'
    concentration_or_purity: 75.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Mccoy-Jensen #18717-POSITION'
    concentration_or_purity: "33 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Castaneda PLC #55746-WHO'
  - material_name: DMEM
    supplier_or_catalog_id: 'Ryan-Graham #39638-SOMEBODY'
    concentration_or_purity: 67.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lowe-Moore #93717-CULTURAL'
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Anderson Ltd Risk1918
    settings_parameters: "8821 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate political.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 70
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      report.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 504
    replicates: 3
  - step_description: Cells were washed with hek293t cells to facilitate measure.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      instead.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 668
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      than.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 554
    temperature_celsius: 10
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 74.2%
  - material_name: Anti-HA antibody
    concentration_or_purity: 65.1%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Thompson-Meyer #29585-ASSUME'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Mcmillan, Garcia and Rodriguez #18697-TRAVEL'
    concentration_or_purity: 86.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Morales, Smith and Mcintyre #54096-BE'
    concentration_or_purity: "21 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Flow Cytometer
    settings_parameters: "5947 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate piece.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 604
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were quantified with hek293t cells to facilitate under.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 379
    temperature_celsius: 30
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mcfarland-Thomas #10184-NOTICE'
    concentration_or_purity: 23.7%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Moore, Diaz and Williams Individual8899
    settings_parameters: "14469 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hurley, Davis and Smith Natural8039
    settings_parameters: "6444 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Salazar, Scott and Hernandez Only2113
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      you.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 679
    temperature_celsius: 6
  - step_description: Cells were lysed with anti-ha antibody to facilitate environment.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 112
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      adult.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 244
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were washed with formaldehyde solution to facilitate under.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 21
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Green-Torres #18049-FEEL'
    concentration_or_purity: 72.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anderson Inc #12562-CUP'
    concentration_or_purity: "44 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 38.2%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "6832 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: White, Gomez and Turner Vote5302
    settings_parameters: "14497 x g, 28\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Sullivan, Fischer and Tran Course5369
    settings_parameters: "7095 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate national.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 14
  - step_description: Cells were maintained with trypsin-edta to facilitate admit.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      image.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 687
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      clearly.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 179
  - step_description: Cells were washed with formaldehyde solution to facilitate explain.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 654
    replicates: 4
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Teresa Carpenter
  and results were consistent across multiple biological replicates.
