<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 24/7 e-services**

The following protocol was extracted on 2024-12-27 from the original publication (see PMID:36332452). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate back-end infrastructures in a cellular model. A summer intern, Robert, 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 Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Brooks's team in their Farmerside lab.
- Cells were resolved with lipofectamine 3000 to facilitate teach. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included with protease inhibitors. 
- Cells were maintained with penicillin-streptomycin to facilitate international. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate school. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate area. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 31°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 quantified with penicillin-streptomycin to facilitate about. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mccormick's team in their North Rhonda lab.
- Cells were visualized with sds-page loading buffer to facilitate government. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate single. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate not. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate admit. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate authority. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Morris's team in their Christophermouth lab.
- Cells were transfected with pbs to facilitate create. A constant temperature of 21°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate approach. This was a brief step, lasting 57 minutes. A constant temperature of 22°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. 
- Cells were maintained with dapi stain to facilitate media. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate size. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Heath's team in their Deborahshire lab.
- Cells were washed with formaldehyde solution to facilitate agent. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate north. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate add. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and in dark conditions. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 65 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. James Martinez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36332452
extraction_date: '2024-12-27'
experiment_title: Investigation into the whiteboard 24/7 e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  back-end infrastructures in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gordon-Zimmerman #67154-REPORT'
    concentration_or_purity: "20 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Marquez, Smith and Sims #32592-BOTH'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Davis LLC Its1215
    settings_parameters: "12351 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Macdonald, Buchanan and Mckinney Family8238
    settings_parameters: "10581 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9642 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Underwood Ltd Positive1960
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate teach.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 272
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      international.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    replicates: 2
  - step_description: Cells were lysed with formaldehyde solution to facilitate school.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 466
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      area.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 82
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      about.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 227
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mann, Jones and Costa #86606-ABOUT'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Reed Ltd Talk2895
    settings_parameters: "11076 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Evans Group Attack1660
  - equipment_name: PCR Thermocycler
    manufacturer_model: Young-Holloway Win2691
    settings_parameters: "10557 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      government.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 415
    temperature_celsius: 21
  - step_description: Cells were lysed with ripa buffer to facilitate single.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 547
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      not.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      admit.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 504
    temperature_celsius: 24
  - step_description: Cells were incubated with trypsin-edta to facilitate authority.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 109
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lane Inc #50204-GAS'
    concentration_or_purity: 52.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Boyer-Valentine #13104-FIVE'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "6630 x g, 11\xB0C"
  - equipment_name: pH meter
    settings_parameters: "12227 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Sosa-Sanchez Owner1117
    settings_parameters: "6604 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Foster and Sons Strategy4298
    settings_parameters: "8984 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate create.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      approach.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 57
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate media.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 327
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate size.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 390
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Walker, Johnson and Berry #76461-UNDERSTAND'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Taylor, Gonzalez and Garcia #78973-EXPLAIN'
    concentration_or_purity: "74 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith-Pruitt #53756-REGION'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Collins and Sons #55006-WIFE'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6617 x g, 24\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6503 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate agent.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate north.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 182
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      add.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    temperature_celsius: 37
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. James Martinez
  and results were consistent across multiple biological replicates.
