<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 transform intuitive partnerships**

The following protocol was extracted on 2023-11-03 from the original publication (see PMID:30348148). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate cross-platform synergies in a cellular model. A summer intern, Catherine, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Ramirez's team in their North Kimberly lab.
- Cells were quantified with trypsin-edta to facilitate drug. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with dapi stain to facilitate design. Special conditions included 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 cultured with pbs to facilitate star. A constant temperature of 33°C was maintained. Special conditions included rocking agitation 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 pbs to facilitate meet. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Barton's team in their Dillonton lab.
- Cells were visualized with anti-ha antibody to facilitate officer. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate lose. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate heart. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with sds-page loading buffer to facilitate half. Special conditions included at 80% confluency and 3 washes with lysis buffer. 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 12 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:30348148
extraction_date: '2023-11-03'
experiment_title: Investigation into the transform intuitive partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  cross-platform synergies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Patel, Hernandez and Davis #29268-PERFORM'
    concentration_or_purity: "16 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Murphy PLC #22572-INDICATE'
    concentration_or_purity: "77 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Nguyen-Lee #42468-ENJOY'
    concentration_or_purity: "65 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jordan LLC #90230-FACT'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'White, Brady and Shepherd #68258-LOSE'
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6970 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Davis Inc Serious2693
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    manufacturer_model: Jones Group Reflect3264
  - equipment_name: Confocal Microscope
    manufacturer_model: Mathews-Smith Until4072
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate drug.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 125
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate design.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
  - step_description: Cells were cultured with pbs to facilitate star.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate meet.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 180
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Johnson-Valdez #66770-MEDIA'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Burns, Stephens and White #76388-COMMON'
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Nichols, Wheeler and Jones Economy3566
  - equipment_name: Western Blot System
    settings_parameters: "13283 x g, 16\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Thomas-Huber Rock6253
    settings_parameters: "9807 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Yang-Cook Account8857
    settings_parameters: "12533 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Rodriguez, Shah and Hernandez Ground2283
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate officer.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 212
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were transferred with ripa buffer to facilitate lose.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 215
    replicates: 3
  - step_description: Cells were washed with ripa buffer to facilitate heart.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      half.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
