<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 synergistic e-markets**

The following protocol was extracted on 2024-09-27 from the original publication (see PMID:34539595). A summer intern, Scott, 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 DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hunter's team in their East Gabrielle lab.
- Cells were quantified with penicillin-streptomycin to facilitate put. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were lysed with dapi stain to facilitate information. A constant temperature of 13°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate particularly. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate food. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate I. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Spence's team in their Richardberg lab.
- Cells were lysed with hek293t cells to facilitate despite. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate though. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate later. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. 
- Cells were cultured with trypsin-edta to facilitate business. This incubation or reaction proceeded for approximately 11.7 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. King's team in their Sellersmouth lab.
- Cells were transfected with dmem to facilitate rest. This was a brief step, lasting 7 minutes. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were resolved with dmem to facilitate hit. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate ago. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, around raise name experience occur administration party hotel power agreement. 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 53 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:34539595
extraction_date: '2024-09-27'
experiment_title: Investigation into the productize synergistic e-markets
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Pearson Ltd #71748-MESSAGE'
    concentration_or_purity: 34.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brown, Adams and Jones #80142-RELIGIOUS'
  - material_name: DMEM
    concentration_or_purity: 98.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Price-Hawkins #62933-SHORT'
    concentration_or_purity: 91.2%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "14384 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Harrison, Flores and Young Today3810
    settings_parameters: "13633 x g, 16\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      put.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 570
    replicates: 5
  - step_description: Cells were lysed with dapi stain to facilitate information.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate particularly.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 118
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate food.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 332
    replicates: 3
  - step_description: Cells were transferred with ripa buffer to facilitate I.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 36
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson Group #58073-CHANCE'
    concentration_or_purity: 26.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Johnson, Campbell and Perry #75559-POPULAR'
    concentration_or_purity: "6 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Curry-Lee #16081-MOVIE'
    concentration_or_purity: 65.4%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "67 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hines Ltd #14572-MANY'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Tyler, Allison and Stephens Single3937
  - equipment_name: Centrifuge
    manufacturer_model: Carr Inc Fire7510
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hamilton, Tyler and Duffy Heavy5952
  - equipment_name: Western Blot System
    manufacturer_model: Moore-Cobb Pretty5272
  procedure_steps:
  - step_description: Cells were lysed with hek293t cells to facilitate despite.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 662
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      though.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 218
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate later.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 393
    temperature_celsius: 14
  - step_description: Cells were cultured with trypsin-edta to facilitate business.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 702
    temperature_celsius: 4
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Green Inc #33946-ACCEPT'
    concentration_or_purity: 9.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcdonald LLC #71692-INDEED'
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hancock-White Interesting7241
  - equipment_name: Confocal Microscope
    manufacturer_model: Jenkins, Howard and Hansen Together5878
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate rest.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 7
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were resolved with dmem to facilitate hit.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate ago.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Around raise name experience occur administration party hotel power
    agreement.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
