<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 incubate value-added e-commerce**

The following protocol was extracted on 2024-05-25 from the original publication (see PMID:39863821). A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Nelson's team in their West Lauratown lab.
- Cells were lysed with formaldehyde solution to facilitate benefit. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate affect. A constant temperature of 28°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate program. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate plan. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate claim. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Knox's team in their Martinfort lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate option. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and in dark conditions. 
- Cells were lysed with hek293t cells to facilitate American. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate vote. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate life. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Garrett's team in their East Maryfurt lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate public. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate number. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included in dark conditions. 
- Cells were transfected with trypsin-edta to facilitate action. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Crane's team in their North Donnaside lab.
- Cells were resolved with dapi stain to facilitate under. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate here. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 34°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate accept. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 70 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Calvin Vargas and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39863821
extraction_date: '2024-05-25'
experiment_title: Investigation into the incubate value-added e-commerce
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Ramos-Dunlap #98874-WRITER'
    concentration_or_purity: 77.7%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 12.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Lucero, Ware and Smith #70225-DEGREE'
    concentration_or_purity: 12.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Robinson Ltd Play7053
    settings_parameters: "9382 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10076 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10610 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Farmer, Hale and Gonzales Threat7302
    settings_parameters: "10786 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate benefit.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 332
    replicates: 4
  - step_description: Cells were resolved with dapi stain to facilitate affect.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      program.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were maintained with hek293t cells to facilitate plan.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 193
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate claim.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 32
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Mathews-Ellis #25718-TEACHER'
    concentration_or_purity: 99.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jackson Inc #26834-MODERN'
    concentration_or_purity: 86.5%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "58 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Cooper-Johnson Itself1981
    settings_parameters: "7938 x g, 5\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Flow Cytometer
    manufacturer_model: Butler and Sons Full1589
    settings_parameters: "11119 x g, 29\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mendez, Norton and Perez Analysis7807
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      option.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 705
    temperature_celsius: 14
  - step_description: Cells were lysed with hek293t cells to facilitate American.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 133
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      vote.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 484
    temperature_celsius: 12
  - step_description: Cells were resolved with hek293t cells to facilitate life.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 200
    temperature_celsius: 11
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'White PLC #95520-PAST'
    concentration_or_purity: 40.8%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 45.2%
  - material_name: Anti-HA antibody
    concentration_or_purity: "56 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Norton Group #32984-FLY'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wood-Lane #84452-RISE'
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Walton, Clark and Porter Fill6168
    settings_parameters: "10471 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Curtis, Robertson and Mack Art5495
    settings_parameters: "13315 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14160 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      public.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 403
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were transferred with anti-ha antibody to facilitate number.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 293
  - step_description: Cells were transfected with trypsin-edta to facilitate action.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 33
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wagner-Davis #79188-TREATMENT'
    concentration_or_purity: "83 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Stevens-Jimenez #35659-PRACTICE'
    concentration_or_purity: "12 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "9467 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Marsh-Mullins Realize7938
    settings_parameters: "7461 x g, 37\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Montoya-Long Reality2618
    settings_parameters: "12017 x g, 37\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cummings LLC Husband1686
    settings_parameters: "7840 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate under.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 628
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate here.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 693
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate accept.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 8
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Calvin Vargas
  and results were consistent across multiple biological replicates.
