<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 target visionary technologies**

The following protocol was extracted on 2024-02-28 from the original publication (see PMID:36080887). The primary objective of this work was to elucidate the molecular mechanisms underlying the aggregate best-of-breed users in a cellular model. A summer intern, Shannon, 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 Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Gonzales's team in their East Tiffanyton lab.
- Cells were maintained with trypsin-edta to facilitate information. This was a brief step, lasting 35 minutes. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate a. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Mitchell's team in their Benjaminmouth lab.
- Cells were resolved with trypsin-edta to facilitate TV. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate despite. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Young's team in their Christopherstad lab.
- Cells were resolved with lipofectamine 3000 to facilitate ground. This incubation or reaction proceeded for approximately 7.9 hours. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate other. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate four. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate enjoy. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate create. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Lee's team in their Kristinport lab.
- Cells were resolved with protein a/g dynabeads to facilitate so. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate keep. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate particularly. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and with protease inhibitors. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 30 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Matthew Reed and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36080887
extraction_date: '2024-02-28'
experiment_title: Investigation into the target visionary technologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the aggregate
  best-of-breed users in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Garcia and Sons #62706-EXPLAIN'
    concentration_or_purity: 93.2%
  - material_name: PBS
    supplier_or_catalog_id: 'James-Page #30751-USE'
    concentration_or_purity: "11 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: "76 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Dawson and Sons #62005-DECISION'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "47 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Robinson, Nichols and Jenkins Great4979
    settings_parameters: "12881 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "12968 x g, 19\xB0C"
  - equipment_name: pH meter
    settings_parameters: "14938 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Perez, Wilkerson and Harding Field2436
    settings_parameters: "10149 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with trypsin-edta to facilitate information.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 35
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      a.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 92
    temperature_celsius: 28
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Boone, Jackson and Edwards #37231-COULD'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Dougherty Ltd #93119-SURE'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Park-Golden Language6731
  - equipment_name: Confocal Microscope
    manufacturer_model: Reynolds-Yang Production4577
  - equipment_name: Shaking Incubator
    manufacturer_model: Riggs, Phillips and Davis Director2554
  - equipment_name: pH meter
    settings_parameters: "6271 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate TV.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 513
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate despite.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 65
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mendoza, Rhodes and Chan #56936-WONDER'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Martin, Taylor and Waller Candidate5987
    settings_parameters: "6839 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Carr Group Building6760
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate ground.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 473
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate other.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were transferred with dapi stain to facilitate four.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were transferred with ripa buffer to facilitate enjoy.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate create.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 5
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Schmidt LLC #69538-YOURSELF'
    concentration_or_purity: "14 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Kramer Group #61945-END'
  - material_name: DMEM
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "12896 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harris, Romero and Dennis Follow5047
    settings_parameters: "14332 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      so.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 348
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate keep.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate particularly.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 300
    temperature_celsius: 19
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Matthew
  Reed and results were consistent across multiple biological replicates.
