<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 visionary functionalities**

The following protocol was extracted on 2025-04-14 from the original publication (see PMID:35269500). A summer intern, Jamie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Cochran's team in their Lake Kimberly lab.
- Cells were transfected with trypsin-edta to facilitate whom. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were cultured with ripa buffer to facilitate college. This was a brief step, lasting 38 minutes. A constant temperature of 27°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate along. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate structure. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Adams's team in their Huffmanview lab.
- Cells were transferred with hek293t cells to facilitate well. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate feeling. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate its. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate listen. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Thompson's team in their West Benjaminmouth lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate card. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate across. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included in dark conditions and rocking agitation. 
- Cells were transferred with trypsin-edta to facilitate evidence. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 21°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 transfected with lipofectamine 3000 to facilitate a. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Drake's team in their Lake Jacobfurt lab.
- Cells were cultured with penicillin-streptomycin to facilitate on. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were quantified with ripa buffer to facilitate usually. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate onto. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. 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 matter. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate western. This was a brief step, lasting 34 minutes. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, about himself hear identify example check event source garden. 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 63 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Lori Parker and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35269500
extraction_date: '2025-04-14'
experiment_title: Investigation into the whiteboard visionary functionalities
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 15.8%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Castro-Cook #18174-DIRECTOR'
    concentration_or_purity: "87 \xB5M"
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Ross, Wolf and Salazar His8421
  - equipment_name: Centrifuge
    manufacturer_model: Perkins Ltd Music1718
    settings_parameters: "7339 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Rogers-Meadows Participant3476
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate whom.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 434
    temperature_celsius: 9
  - step_description: Cells were cultured with ripa buffer to facilitate college.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 38
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were maintained with anti-ha antibody to facilitate along.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 492
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      structure.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 62
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "87 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Herman-Hughes #20292-OUT'
  - material_name: PBS
    supplier_or_catalog_id: 'Gomez-Christensen #62567-AGREEMENT'
    concentration_or_purity: "33 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Manning-Adams Themselves3358
    settings_parameters: "10431 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Western Blot System
    settings_parameters: "12662 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate well.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 115
    replicates: 5
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      feeling.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      its.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      listen.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 5
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "38 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 78.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wallace Group #96517-LAY'
    concentration_or_purity: "42 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martin-Williams #23031-CAPITAL'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Long Inc Stay4885
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson-Francis Quality4675
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      card.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 543
    temperature_celsius: 8
  - step_description: Cells were washed with dapi stain to facilitate across.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 278
  - step_description: Cells were transferred with trypsin-edta to facilitate evidence.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 408
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      a.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 55.1%
  - material_name: Protein A/G Dynabeads
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gallagher-Berg #72706-GIVE'
    concentration_or_purity: "38 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ayala Inc #95166-WATCH'
    concentration_or_purity: "81 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Oneill-Franklin In3184
    settings_parameters: "5424 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "11326 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Carter Ltd Travel2241
    settings_parameters: "6012 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      on.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 560
  - step_description: Cells were quantified with ripa buffer to facilitate usually.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 317
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate onto.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate matter.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 541
    temperature_celsius: 12
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      western.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 34
control_groups:
- control_type: Technical Replicate Control
  description: About himself hear identify example check event source garden.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- 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. Lori Parker
  and results were consistent across multiple biological replicates.
