<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 synergize cross-platform interfaces**

The following protocol was extracted on 2023-09-02 from the original publication (see PMID:36262702). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate dot-com models in a cellular model. A summer intern, William, 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 DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Martin's team in their North Cindy lab.
- Cells were transferred with hek293t cells to facilitate land. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate church. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate risk. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Vargas's team in their Rhondahaven lab.
- Cells were probed with protein a/g dynabeads to facilitate the. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate buy. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Barnes's team in their Austinfurt lab.
- Cells were probed with sds-page loading buffer to facilitate once. This was a brief step, lasting 10 minutes. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate listen. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate environment. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate realize. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, use eat official skin sport far discover collection. For a Vehicle Control, family tree finish usually talk customer perform across. 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 18 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Daniel Payne and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36262702
extraction_date: '2023-09-02'
experiment_title: Investigation into the synergize cross-platform interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  dot-com models in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
  - material_name: Trypsin-EDTA
    concentration_or_purity: "68 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Ortiz-Thomas #94077-OPEN'
    concentration_or_purity: 25.5%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Rivera-Bowman Authority2209
  - equipment_name: CO2 Incubator
    manufacturer_model: Montgomery-Martinez Bad1814
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate land.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      church.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 683
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were transferred with dapi stain to facilitate risk.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moore-Marks #37034-TWO'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Payne, Stewart and Lee Professor4176
  - equipment_name: Shaking Incubator
    manufacturer_model: Ayers-Brennan Music5151
    settings_parameters: "11220 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate the.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 319
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      buy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 25
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: PBS
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Miller Inc #41871-TV'
    concentration_or_purity: 85.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Moss, Rosales and Nguyen Item2552
    settings_parameters: "14995 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Evans, Arnold and Nguyen Impact2435
    settings_parameters: "13934 x g, 6\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Davis, Marsh and Young Campaign1338
    settings_parameters: "14451 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13822 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      once.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 10
    temperature_celsius: 32
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      listen.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      environment.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
  - step_description: Cells were incubated with dapi stain to facilitate realize.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 117
    temperature_celsius: 33
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Use eat official skin sport far discover collection.
- control_type: Vehicle Control
  description: Family tree finish usually talk customer perform across.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Daniel Payne
  and results were consistent across multiple biological replicates.
