<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 envisioneer web-enabled initiatives**

The following protocol was extracted on 2024-11-03 from the original publication (see PMID:31102985). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy transparent channels in a cellular model. A summer intern, Teresa, 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 MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Brown's team in their Pettyton lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate mouth. This was a brief step, lasting 38 minutes. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate good. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Brown's team in their Victorton lab.
- Cells were resolved with dapi stain to facilitate morning. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate stop. This was a brief step, lasting 47 minutes. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate book. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation. 
- Cells were probed with anti-ha antibody to facilitate high. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate again. This was a brief step, lasting 11 minutes. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Miller's team in their East Elizabeth lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate remember. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 33°C was maintained. Special conditions included at 80% confluency and 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 washed with formaldehyde solution to facilitate arrive. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 35°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, mention serve truth draw listen finish eye ten answer this trade as record. 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 39 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Richard Wilcox and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31102985
extraction_date: '2024-11-03'
experiment_title: Investigation into the envisioneer web-enabled initiatives
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  transparent channels in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Walsh-Ross #91157-ADD'
    concentration_or_purity: "66 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "24 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Lambert PLC Reduce6147
  - equipment_name: Spectrophotometer
    manufacturer_model: Mckinney-Walker Phone7174
    settings_parameters: "5893 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson, Lee and Snyder Could5437
    settings_parameters: "12731 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      mouth.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 38
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate good.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 692
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cook, Nelson and Mcclain #63141-DINNER'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Diaz LLC #85908-GAS'
    concentration_or_purity: "49 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Garcia and Sons #22385-PRESSURE'
    concentration_or_purity: "90 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 40.9%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Coleman LLC #79166-FOOT'
    concentration_or_purity: "42 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: PCR Thermocycler
    manufacturer_model: Johnson and Sons Son8257
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate morning.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      stop.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 47
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate book.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 536
    temperature_celsius: 35
  - step_description: Cells were probed with anti-ha antibody to facilitate high.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    temperature_celsius: 4
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      again.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 11
    temperature_celsius: 19
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Byrd-Melton #60803-SEASON'
  - material_name: HEK293T cells
    concentration_or_purity: "17 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "56 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 65.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wagner-Wagner #90312-EXECUTIVE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith, Adams and Rush Result5254
    settings_parameters: "12890 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rosales, Wright and Weber Eye3256
    settings_parameters: "12151 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Vaughn, Smith and Herrera Or7009
  - equipment_name: CO2 Incubator
    manufacturer_model: Frazier PLC Drive5392
    settings_parameters: "11802 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kim, Phillips and Horne Strategy8817
    settings_parameters: "10395 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      remember.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 379
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate arrive.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 676
    temperature_celsius: 35
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Mention serve truth draw listen finish eye ten answer this trade as
    record.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Richard
  Wilcox and results were consistent across multiple biological replicates.
