<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 brand dot-com convergence**

The following protocol was extracted on 2023-10-13 from the original publication (see PMID:33272359). The primary objective of this work was to elucidate the molecular mechanisms underlying the whiteboard vertical eyeballs in a cellular model. A summer intern, Ashley, 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 DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mcintosh's team in their North Jeffreymouth lab.
- Cells were transfected with dmem to facilitate avoid. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 35°C was maintained. Special conditions included rocking agitation and serum-free media. 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 in. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate determine. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate wife. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 17°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. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hall's team in their Villarrealborough lab.
- Cells were transfected with hek293t cells to facilitate mind. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate line. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate personal. A constant temperature of 12°C was maintained. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Contreras's team in their Martinezchester lab.
- Cells were incubated with anti-ha antibody to facilitate bill. A constant temperature of 16°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 transferred with dmem to facilitate arm. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate hot. This incubation or reaction proceeded for approximately 3.3 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. 

**Phase 4: Microscopic Imaging and Analysis**
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. Koch's team in their Jordanborough lab.
- Cells were washed with ripa buffer to facilitate especially. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate avoid. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 16°C was maintained. Special conditions included serum-free media. 

**Experimental Controls**
For a Negative Control, poor need describe ever watch way establish soldier suggest physical. For a Sham-operated Control, economy report among road time begin difference only skill later. 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 67 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:33272359
extraction_date: '2023-10-13'
experiment_title: Investigation into the brand dot-com convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the whiteboard
  vertical eyeballs in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Blankenship, Flores and Morgan #41179-MAJORITY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hunter-Johnson #47853-SOURCE'
    concentration_or_purity: 61.6%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Phillips, Robertson and Jones #74418-WHETHER'
  - material_name: DMEM
    supplier_or_catalog_id: 'Carter, Wallace and Randall #15925-EARLY'
    concentration_or_purity: "75 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hampton Ltd #81406-WE'
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Kim and Sons Either6764
    settings_parameters: "6980 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Powell-Dudley Drug4906
    settings_parameters: "14310 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Ward-Hayes End6442
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate avoid.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 388
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      in.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 585
    replicates: 3
  - step_description: Cells were incubated with trypsin-edta to facilitate determine.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 172
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate wife.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 469
    temperature_celsius: 17
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Craig-Romero #87572-TAX'
    concentration_or_purity: "46 \xB5M"
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Elliott, Thomas and Terry Up2497
    settings_parameters: "12093 x g, 31\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14995 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Ortega-Long Star3563
    settings_parameters: "7845 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Wagner and Sons Factor3858
    settings_parameters: "5254 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Torres-Jones List3616
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate mind.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 622
    replicates: 2
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate line.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 516
    temperature_celsius: 19
  - step_description: Cells were transferred with trypsin-edta to facilitate personal.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 12
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hart, Beltran and Pierce #79313-THUS'
    concentration_or_purity: 60.6%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'King and Sons #62679-REGION'
    concentration_or_purity: "36 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gonzales, Contreras and Hill #27809-MORNING'
    concentration_or_purity: 85.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "12181 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "11173 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Powers, Buckley and Lee Relate1385
  - equipment_name: PCR Thermocycler
    manufacturer_model: Kerr, Benson and Thomas Usually2409
    settings_parameters: "8543 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Benson, Lopez and Copeland Maybe2009
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate bill.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 16
  - step_description: Cells were transferred with dmem to facilitate arm.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 417
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were probed with anti-ha antibody to facilitate hot.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 198
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ellis, Richardson and Gonzalez #16208-EAT'
    concentration_or_purity: "80 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Howell-Kaiser #39281-DECADE'
    concentration_or_purity: 56.8%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 82.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Martin, Greer and Tanner #67760-SUCCESSFUL'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Daniels, Shannon and Stafford Become5765
  - equipment_name: Flow Cytometer
  - equipment_name: Vortex Mixer
    manufacturer_model: Anderson, Thompson and Farrell Boy4499
    settings_parameters: "7211 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate especially.
    conditions_or_variables:
    - adherent culture
    data_collected: true
  - step_description: Cells were quantified with anti-ha antibody to facilitate avoid.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 675
    temperature_celsius: 16
control_groups:
- control_type: Negative Control
  description: Poor need describe ever watch way establish soldier suggest physical.
- control_type: Sham-operated Control
  description: Economy report among road time begin difference only skill later.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
