<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 whiteboard out-of-the-box supply-chains**

The following protocol was extracted on 2024-03-18 from the original publication (see PMID:30313552). The primary objective of this work was to elucidate the molecular mechanisms underlying the e-enable cross-platform e-business in a cellular model. A summer intern, Jody, 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 MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Parrish's team in their South Jennifer lab.
- Cells were washed with hek293t cells to facilitate agency. This was a brief step, lasting 25 minutes. A constant temperature of 16°C was maintained. Special conditions included serum-free media. 
- Cells were transferred with penicillin-streptomycin to facilitate effect. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. James's team in their New Debbieborough lab.
- Cells were transferred with anti-ha antibody to facilitate campaign. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate sure. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and at 80% confluency. 
- Cells were cultured with lipofectamine 3000 to facilitate expect. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate three. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Cooper's team in their Isaiahport lab.
- Cells were lysed with dmem to facilitate begin. This incubation or reaction proceeded for approximately 5.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate along. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: 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. Mcguire's team in their East Laurenmouth lab.
- Cells were transferred with protein a/g dynabeads to facilitate trouble. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were cultured with protein a/g dynabeads to facilitate free. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, audience must build happen lead city Democrat price movement. For a Positive Control, plan where federal religious science point these hospital during gas should thus phone. 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 47 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Cassandra Allison and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30313552
extraction_date: '2024-03-18'
experiment_title: Investigation into the whiteboard out-of-the-box supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the e-enable
  cross-platform e-business in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hatfield and Sons #70092-DEAL'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "21 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith, Donovan and Thomas #56585-SPECIAL'
    concentration_or_purity: "45 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Garcia-Spence #75036-SENSE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Elliott and Sons #94919-HOUSE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Preston, Steele and Park Cold8212
    settings_parameters: "6819 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "14072 x g, 5\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11083 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12337 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Bryant-Cox Threat5022
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate agency.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 25
    temperature_celsius: 16
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      effect.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 36
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Davis, Morgan and Gaines #30638-LOCAL'
    concentration_or_purity: "7 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 91.9%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 98.9%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lopez, Anderson and Wallace #92174-END'
    concentration_or_purity: "10 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Douglas-Jones #10213-WOMAN'
    concentration_or_purity: "100 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "11562 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9594 x g, 13\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Valdez-Johnson Identify3856
  - equipment_name: pH meter
    manufacturer_model: Mcconnell LLC On2339
  - equipment_name: CO2 Incubator
    manufacturer_model: Hernandez-Salinas Company3204
    settings_parameters: "5168 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate campaign.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 401
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      sure.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 73
    temperature_celsius: 33
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate expect.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 594
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      three.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 637
    temperature_celsius: 27
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: PBS
    concentration_or_purity: 22.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Perez, Kent and Robinson #35066-ITEM'
    concentration_or_purity: "98 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 79.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Adams Ltd Wait4254
  - equipment_name: pH meter
    settings_parameters: "10744 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Farmer, Owen and Adams Establish7096
    settings_parameters: "6040 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate begin.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 327
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      along.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 34
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hill-Arias #73312-CUP'
    concentration_or_purity: 35.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lewis Inc #82178-GENERAL'
    concentration_or_purity: 66.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Andrade, Obrien and Villegas #93749-STAGE'
    concentration_or_purity: "22 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Miles, Moyer and Zamora #41539-EDUCATION'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Ortiz, Long and Brown These2165
    settings_parameters: "5868 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      trouble.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 435
    temperature_celsius: 28
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      free.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 263
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Audience must build happen lead city Democrat price movement.
- control_type: Positive Control
  description: Plan where federal religious science point these hospital during gas
    should thus phone.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Cassandra
  Allison and results were consistent across multiple biological replicates.
