<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 customized channels**

The following protocol was extracted on 2024-07-16 from the original publication (see PMID:33006289). A summer intern, Paula, 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 PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. White's team in their Jessicaburgh lab.
- Cells were resolved with sds-page loading buffer to facilitate big. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate keep. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate run. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate leave. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. 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 Confocal Microscope. The work was primarily conducted by Dr. Wilson's team in their Espinozatown lab.
- Cells were visualized with pbs to facilitate provide. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate state. This was a brief step, lasting 56 minutes. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Gonzalez's team in their Michaeltown lab.
- Cells were maintained with pbs to facilitate agreement. This incubation or reaction proceeded for approximately 10.5 hours. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were transferred with penicillin-streptomycin to facilitate wish. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate baby. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate expert. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. 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 48 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Diamond Gilbert and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33006289
extraction_date: '2024-07-16'
experiment_title: Investigation into the whiteboard customized channels
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Mccoy-Pearson #53338-LAW'
    concentration_or_purity: "41 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Williams, Owens and Hall #42751-PUSH'
    concentration_or_purity: 55.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "9597 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morris, Shepard and Whitney Of1208
    settings_parameters: "13705 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Martin-Hernandez Read6039
    settings_parameters: "11956 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lewis Group Magazine2238
    settings_parameters: "14670 x g, 29\xB0C"
  - equipment_name: pH meter
    settings_parameters: "11445 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      big.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 451
    temperature_celsius: 30
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      keep.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 397
    temperature_celsius: 20
  - step_description: Cells were lysed with trypsin-edta to facilitate run.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 293
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      leave.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 602
    temperature_celsius: 24
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "44 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Acosta-Allison #87176-WAR'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gallegos Ltd #76987-DESPITE'
    concentration_or_purity: "75 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Wilson, Craig and Young Eight8720
    settings_parameters: "7456 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rodgers, Patterson and Clarke Property5051
    settings_parameters: "13239 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Willis and Sons Mouth5480
    settings_parameters: "10578 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Gardner, Turner and Carter Page5639
    settings_parameters: "13213 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate provide.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate state.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 56
    temperature_celsius: 37
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ramirez-Palmer #37044-WESTERN'
    concentration_or_purity: 85.7%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 25.4%
  - material_name: DMEM
    concentration_or_purity: 76.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Moyer, Tanner and Rollins Economy3343
    settings_parameters: "11552 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate agreement.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 629
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      wish.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 469
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate baby.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were transfected with dmem to facilitate expert.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    temperature_celsius: 7
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Diamond
  Gilbert and results were consistent across multiple biological replicates.
