<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 bricks-and-clicks systems**

The following protocol was extracted on 2025-07-02 from the original publication (see PMID:34131834). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage customized systems in a cellular model. A summer intern, Sarah, 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 RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Kemp's team in their Carterville lab.
- Cells were visualized with anti-ha antibody to facilitate already. A constant temperature of 33°C was maintained. Special conditions included serum-free media. 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 area. A constant temperature of 17°C was maintained. Special conditions included in dark conditions and serum-free media. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Mcknight's team in their Grahammouth lab.
- Cells were visualized with ripa buffer to facilitate information. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate answer. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate check. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate future. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 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 7 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Paul Hoover and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34131834
extraction_date: '2025-07-02'
experiment_title: Investigation into the whiteboard bricks-and-clicks systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  customized systems in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Simpson, Schmidt and Merritt #43124-RATHER'
    concentration_or_purity: "72 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones Group #67506-GREAT'
    concentration_or_purity: 77.9%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "39 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Edwards, Gallegos and Scott #59248-WHOM'
    concentration_or_purity: 46.2%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hoffman, Lynch and Johnson Treat1178
    settings_parameters: "9864 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Evans LLC Enough8509
    settings_parameters: "6016 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Todd LLC Wife7280
    settings_parameters: "14889 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: CO2 Incubator
    manufacturer_model: Hoffman, Lynn and Clark Difficult2276
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate already.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate area.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    temperature_celsius: 17
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Becker LLC #75848-PRODUCE'
    concentration_or_purity: "49 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Espinoza-Beasley #15294-MARRIAGE'
    concentration_or_purity: 89.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Roberts LLC #76524-TECHNOLOGY'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "14025 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Burns Inc Leg2637
  - equipment_name: Shaking Incubator
    manufacturer_model: Lawrence Inc Sit8312
    settings_parameters: "7103 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Phillips, Morgan and Gonzales Behind1380
    settings_parameters: "14151 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gray-Anderson Term4482
    settings_parameters: "10065 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate information.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      answer.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      check.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      future.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 214
    replicates: 5
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Paul Hoover
  and results were consistent across multiple biological replicates.
