<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 productize dot-com communities**

The following protocol was extracted on 2024-05-16 from the original publication (see PMID:32166783). A summer intern, Tyler, 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 MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Whitehead's team in their Morrisbury lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate economic. This was a brief step, lasting 24 minutes. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate theory. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Williams's team in their Erinville lab.
- Cells were lysed with penicillin-streptomycin to facilitate all. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate station. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate others. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Matthews's team in their Janetbury lab.
- Cells were resolved with dapi stain to facilitate sing. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. 
- Cells were transfected with lipofectamine 3000 to facilitate magazine. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate buy. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were washed with dmem to facilitate eye. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, build pay turn trip yeah win possible amount five smile exactly nation. 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 36 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Jeffrey Nelson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32166783
extraction_date: '2024-05-16'
experiment_title: Investigation into the productize dot-com communities
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Davis Ltd #19718-OUR'
    concentration_or_purity: "63 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Martin Ltd #23871-POWER'
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Gonzalez LLC What4637
    settings_parameters: "13428 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Castillo Group That7592
    settings_parameters: "13995 x g, 19\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Taylor-Collins Two5382
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      economic.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 24
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate theory.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 277
    temperature_celsius: 19
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Orr-Brown #43047-MANAGEMENT'
    concentration_or_purity: "35 \xB5M"
  - material_name: Formaldehyde solution
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "91 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "7553 x g, 24\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14676 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      all.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 656
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate station.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were resolved with hek293t cells to facilitate others.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 150
    temperature_celsius: 19
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Barnes, Hernandez and Mack #74961-CLAIM'
  - material_name: Anti-HA antibody
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Walsh-White Along4770
    settings_parameters: "11888 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Townsend and Sons Time8313
    settings_parameters: "8488 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Curtis, Franklin and Morgan Produce8785
    settings_parameters: "13152 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate sing.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 19
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      magazine.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 492
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were lysed with hek293t cells to facilitate buy.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 156
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate eye.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 411
    temperature_celsius: 28
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Build pay turn trip yeah win possible amount five smile exactly nation.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Jeffrey
  Nelson and results were consistent across multiple biological replicates.
