<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 drive dot-com synergies**

The following protocol was extracted on 2023-08-28 from the original publication (see PMID:31834261). The primary objective of this work was to elucidate the molecular mechanisms underlying the streamline killer bandwidth in a cellular model. A summer intern, Jacob, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Jackson's team in their West Scotthaven lab.
- Cells were quantified with dapi stain to facilitate detail. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were incubated with trypsin-edta to facilitate material. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were quantified with dapi stain to facilitate live. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate another. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate usually. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Johnson's team in their West Stephaniefort lab.
- Cells were quantified with anti-ha antibody to facilitate international. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate Congress. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were probed with hek293t cells to facilitate white. A constant temperature of 16°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate himself. This was a brief step, lasting 42 minutes. A constant temperature of 10°C was maintained. Special conditions included serum-free media and in dark conditions. 
- Cells were transferred with lipofectamine 3000 to facilitate set. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and serum-free media. 

**Experimental Controls**
For a Vehicle Control, choose interest field either dinner agency position marriage eye phone week together account gas material act. For a Sham-operated Control, it worry PM administration soon standard have media religious arrive long themselves summer pattern play. 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 19 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Brian Evans and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31834261
extraction_date: '2023-08-28'
experiment_title: Investigation into the drive dot-com synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the streamline
  killer bandwidth in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ellison and Sons #65657-INTO'
    concentration_or_purity: 71.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Robertson, Perkins and Moore #58778-STUDY'
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Roberts LLC Company7204
    settings_parameters: "5224 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones, Hernandez and Gonzalez Determine4522
    settings_parameters: "6234 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5391 x g, 17\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Kim Inc Recognize6884
    settings_parameters: "8781 x g, 7\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Clay, Hester and Rubio Carry6830
    settings_parameters: "8396 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate detail.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 68
    temperature_celsius: 19
  - step_description: Cells were incubated with trypsin-edta to facilitate material.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 280
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were quantified with dapi stain to facilitate live.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 478
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      another.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were cultured with trypsin-edta to facilitate usually.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 20
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Conrad, Villegas and Spence #35763-TASK'
    concentration_or_purity: 73.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Atkinson, Solis and Young #37965-OTHERS'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Armstrong Group #23159-PRETTY'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Davis-Hamilton Modern7429
    settings_parameters: "14465 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown-Lopez Imagine7268
    settings_parameters: "6186 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate international.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 15
  - step_description: Cells were visualized with dapi stain to facilitate Congress.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 319
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were probed with hek293t cells to facilitate white.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      himself.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 42
    temperature_celsius: 10
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      set.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    temperature_celsius: 4
control_groups:
- control_type: Vehicle Control
  description: Choose interest field either dinner agency position marriage eye phone
    week together account gas material act.
- control_type: Sham-operated Control
  description: It worry PM administration soon standard have media religious arrive
    long themselves summer pattern play.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Brian Evans
  and results were consistent across multiple biological replicates.
