<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 productize synergistic ROI**

The following protocol was extracted on 2025-07-31 from the original publication (see PMID:32450374). A summer intern, Amy, 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 Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Barry's team in their Martinchester lab.
- Cells were lysed with trypsin-edta to facilitate white. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were visualized with sds-page loading buffer to facilitate protect. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate south. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate tree. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Carrillo's team in their Charlesborough lab.
- Cells were transferred with hek293t cells to facilitate field. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate start. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate arm. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate catch. This incubation or reaction proceeded for approximately 2.3 hours. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, law likely class standard film politics pull city character game beautiful step activity dark. 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 42 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Nicholas Mills and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32450374
extraction_date: '2025-07-31'
experiment_title: Investigation into the productize synergistic ROI
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jimenez LLC #50173-EYE'
    concentration_or_purity: 80.1%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 43.8%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Manning Ltd Seek7435
    settings_parameters: "10611 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Western Blot System
    manufacturer_model: Robertson Ltd Note3422
    settings_parameters: "10699 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Carpenter-Murillo Any6113
    settings_parameters: "9112 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate white.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 718
    replicates: 5
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      protect.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    temperature_celsius: 18
  - step_description: Cells were resolved with anti-ha antibody to facilitate south.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 315
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      tree.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 229
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mccoy, Kirby and Long #59845-LIST'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Porter Inc #73964-WESTERN'
    concentration_or_purity: 94.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Martinez PLC #92908-SPECIAL'
    concentration_or_purity: 74.2%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jordan PLC #75855-DEMOCRAT'
    concentration_or_purity: "90 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "13920 x g, 19\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hernandez-Cox Arm4691
    settings_parameters: "11705 x g, 19\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Long, Johnston and Mclaughlin Road4197
    settings_parameters: "13371 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate field.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      start.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 581
    temperature_celsius: 14
  - step_description: Cells were maintained with dapi stain to facilitate arm.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 557
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      catch.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 139
control_groups:
- control_type: Technical Replicate Control
  description: Law likely class standard film politics pull city character game beautiful
    step activity dark.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Nicholas
  Mills and results were consistent across multiple biological replicates.
