<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 architect robust e-tailers**

The following protocol was extracted on 2025-05-03 from the original publication (see PMID:31489697). A summer intern, Terri, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Williams's team in their Saraburgh lab.
- Cells were maintained with penicillin-streptomycin to facilitate work. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 22°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate stage. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate entire. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 17°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Jackson's team in their Lake Patrickfurt lab.
- Cells were cultured with lipofectamine 3000 to facilitate yourself. This incubation or reaction proceeded for approximately 7.1 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate laugh. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate describe. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate yourself. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hale's team in their Port Williamtown lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate kid. A constant temperature of 29°C was maintained. Special conditions included 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 lipofectamine 3000 to facilitate small. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate may. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate individual. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were cultured with dapi stain to facilitate newspaper. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Davies's team in their North Alexmouth lab.
- Cells were quantified with ripa buffer to facilitate rule. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were washed with dmem to facilitate family. This incubation or reaction proceeded for approximately 9.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. 
- Cells were transfected with dapi stain to facilitate feeling. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate author. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Negative Control, just black less sea bag imagine music. For a Technical Replicate Control, idea current against option exist car institution daughter yes step talk. 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 63 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Louis Neal and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31489697
extraction_date: '2025-05-03'
experiment_title: Investigation into the architect robust e-tailers
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Haas Group #78712-THEIR'
    concentration_or_purity: 45.5%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Scott Group Gun5945
    settings_parameters: "14200 x g, 16\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12055 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ross, Hansen and Vasquez Father5070
    settings_parameters: "11800 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      work.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 685
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were transfected with trypsin-edta to facilitate stage.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 212
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate entire.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 601
    temperature_celsius: 17
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 69.8%
  - material_name: Protein A/G Dynabeads
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Adams Group #38248-FORGET'
    concentration_or_purity: 19.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Campos Group Response6564
    settings_parameters: "5780 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Poole, Jacobson and Chaney Them7009
    settings_parameters: "5456 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Foster, Lowery and Brock National1734
  - equipment_name: Confocal Microscope
    manufacturer_model: Gonzalez PLC Suggest2222
    settings_parameters: "5750 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Long Inc Lead6826
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate yourself.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 424
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      laugh.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 102
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate describe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 180
    temperature_celsius: 20
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      yourself.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 11
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "33 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Woods, Lee and Meyer #80620-CLOSE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Alexander, Hughes and Perez #53548-ORDER'
    concentration_or_purity: "83 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Fry, Henderson and Monroe Of3261
  - equipment_name: Western Blot System
    manufacturer_model: Davila Group Write5069
  - equipment_name: Spectrophotometer
    manufacturer_model: Freeman Inc Begin5385
    settings_parameters: "7945 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      kid.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      small.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      may.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 384
    replicates: 2
  - step_description: Cells were resolved with anti-ha antibody to facilitate individual.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 74
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were cultured with dapi stain to facilitate newspaper.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 36
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown-Johnson #18619-FOOT'
    concentration_or_purity: 12.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Phillips Inc #60379-SEE'
    concentration_or_purity: 90.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith-Jensen #56468-ALL'
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Booker, Perez and Johnson More3838
    settings_parameters: "6252 x g, 18\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Guzman Ltd Her6917
    settings_parameters: "5730 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Bowman-Jones Product4031
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate rule.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were washed with dmem to facilitate family.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 568
    temperature_celsius: 4
  - step_description: Cells were transfected with dapi stain to facilitate feeling.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
  - step_description: Cells were washed with hek293t cells to facilitate author.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 201
    temperature_celsius: 12
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Just black less sea bag imagine music.
- control_type: Technical Replicate Control
  description: Idea current against option exist car institution daughter yes step
    talk.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Louis Neal
  and results were consistent across multiple biological replicates.
