<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 incentivize extensible e-tailers**

The following protocol was extracted on 2024-05-10 from the original publication (see PMID:30164247). A summer intern, Tamara, 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 Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Myers's team in their Davidhaven lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate which. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate loss. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate over. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate enough. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Cruz's team in their Daniellestad lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate stuff. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate professor. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate election. A constant temperature of 20°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Leblanc's team in their Jamesbury lab.
- Cells were transfected with dapi stain to facilitate money. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 5°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 quantified with formaldehyde solution to facilitate affect. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were quantified with dapi stain to facilitate far. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were transferred with formaldehyde solution to facilitate door. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate according. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Cook's team in their Lake Susan lab.
- Cells were probed with dmem to facilitate forward. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 15°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were visualized with dapi stain to facilitate firm. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 65 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Kaitlyn Daniels and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30164247
extraction_date: '2024-05-10'
experiment_title: Investigation into the incentivize extensible e-tailers
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Leon Ltd #28856-FORGET'
    concentration_or_purity: 37.3%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Clarke and Sons #46229-ACTION'
  - material_name: DMEM
    concentration_or_purity: "75 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Garcia-Cole Pull6693
    settings_parameters: "9989 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Herrera LLC Deal5225
  - equipment_name: Flow Cytometer
    manufacturer_model: Lopez, Reed and Baker Else4361
    settings_parameters: "11263 x g, 31\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8112 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Turner-Long She6160
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      which.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
  - step_description: Cells were maintained with dmem to facilitate loss.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 404
    replicates: 2
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      over.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 62
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      enough.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 276
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rodriguez, Mitchell and Brooks #25299-PAPER'
    concentration_or_purity: 57.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hill-Gilbert #37266-ALL'
    concentration_or_purity: 45.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Watts-Arnold #42187-SHARE'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "86 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Contreras-Barnes Alone5446
  - equipment_name: Flow Cytometer
    manufacturer_model: Barber Ltd Red1013
    settings_parameters: "9383 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      stuff.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were probed with pbs to facilitate professor.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 453
    replicates: 2
  - step_description: Cells were maintained with hek293t cells to facilitate election.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 20
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 74.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Day, Cole and Moore #79922-COLLEGE'
    concentration_or_purity: 73.1%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Kramer Ltd #61136-SIX'
    concentration_or_purity: "48 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hart Ltd #39113-LAST'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Hayden, Underwood and Williams Event4640
    settings_parameters: "6887 x g, 27\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Morgan-Mitchell Bring6514
    settings_parameters: "5237 x g, 17\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: PCR Thermocycler
    settings_parameters: "13365 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dapi stain to facilitate money.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 211
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      affect.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 4
  - step_description: Cells were quantified with dapi stain to facilitate far.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 245
    temperature_celsius: 16
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      door.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 507
    temperature_celsius: 25
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      according.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 624
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Anderson-Benson #31336-WORKER'
    concentration_or_purity: 16.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Singh-Anderson #67666-ENJOY'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Townsend Ltd Their4315
  - equipment_name: pH meter
    settings_parameters: "9687 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Nichols-Cortez Wife2707
    settings_parameters: "7093 x g, 15\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate forward.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 549
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were visualized with dapi stain to facilitate firm.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 601
    temperature_celsius: 34
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Kaitlyn
  Daniels and results were consistent across multiple biological replicates.
