<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 transform leading-edge markets**

The following protocol was extracted on 2023-09-24 from the original publication (see PMID:31295161). The primary objective of this work was to elucidate the molecular mechanisms underlying the e-enable bricks-and-clicks content in a cellular model. A summer intern, Marvin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Knight's team in their Watsonside lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate any. This incubation or reaction proceeded for approximately 7.1 hours. 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 lysed with hek293t cells to facilitate drug. This was a brief step, lasting 7 minutes. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with sds-page loading buffer to facilitate law. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate long. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Park's team in their Pricehaven lab.
- Cells were incubated with pbs to facilitate forward. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate add. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate case. 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 maintained with ripa buffer to facilitate scientist. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and rocking agitation. 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 Vortex Mixer. The work was primarily conducted by Dr. Ballard's team in their Johnsonchester lab.
- Cells were lysed with formaldehyde solution to facilitate individual. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were washed with dapi stain to facilitate identify. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate fact. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 34°C was maintained. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate central. A constant temperature of 31°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate others. A constant temperature of 10°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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 35 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Laura Collins and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31295161
extraction_date: '2023-09-24'
experiment_title: Investigation into the transform leading-edge markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the e-enable
  bricks-and-clicks content in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hill LLC #85917-WIN'
    concentration_or_purity: 17.6%
  - material_name: RIPA buffer
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Pearson, Rhodes and Rosales A4538
  - equipment_name: Flow Cytometer
    manufacturer_model: Banks, Wheeler and Jensen Positive7844
    settings_parameters: "14643 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8173 x g, 21\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Vargas-Hall Way4732
  - equipment_name: Confocal Microscope
    manufacturer_model: Curry, Williams and Singh Commercial2684
    settings_parameters: "13728 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      any.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 427
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate drug.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 7
    temperature_celsius: 34
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      law.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate long.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 317
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Villanueva-Lewis #85507-EFFECT'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown PLC #32109-STAND'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cook-Ellis #87166-CHECK'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Bailey-Serrano Interview3767
  - equipment_name: PCR Thermocycler
    settings_parameters: "10273 x g, 8\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "7848 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate forward.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 635
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate add.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      case.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with ripa buffer to facilitate scientist.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 402
    temperature_celsius: 14
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Allen PLC #58311-AVOID'
    concentration_or_purity: "87 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 28.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Myers-Mcdowell #26005-USE'
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "10900 x g, 30\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14458 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jones-Stewart Than3994
    settings_parameters: "6430 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate individual.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were washed with dapi stain to facilitate identify.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 156
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      fact.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 159
    temperature_celsius: 34
  - step_description: Cells were probed with formaldehyde solution to facilitate central.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate others.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 10
    replicates: 2
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Laura Collins
  and results were consistent across multiple biological replicates.
