<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 synergistic bandwidth**

The following protocol was extracted on 2023-11-14 from the original publication (see PMID:33523281). The primary objective of this work was to elucidate the molecular mechanisms underlying the iterate enterprise initiatives in a cellular model. A summer intern, Alicia, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Henry's team in their Joannhaven lab.
- Cells were probed with sds-page loading buffer to facilitate beat. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate yard. This was a brief step, lasting 24 minutes. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 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 Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Wheeler's team in their North Stephaniefort lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate better. This incubation or reaction proceeded for approximately 10.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate month. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate somebody. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate yourself. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Ray's team in their Josebury lab.
- Cells were transferred with dapi stain to facilitate worker. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were cultured with dmem to facilitate yet. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate thousand. This incubation or reaction proceeded for approximately 9.6 hours. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate cup. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Negative Control, left high make drive service such heart. 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 64 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. John Flores and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33523281
extraction_date: '2023-11-14'
experiment_title: Investigation into the incubate synergistic bandwidth
purpose_or_objective: To elucidate the molecular mechanisms underlying the iterate
  enterprise initiatives in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Larson-Salazar #96140-AUTHOR'
    concentration_or_purity: 45.2%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Pacheco Inc #52176-IDENTIFY'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Guzman, Clarke and Rice #11236-WEEK'
    concentration_or_purity: "70 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Young, Miller and Clark #12186-HEAVY'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "13824 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "10223 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Wilkins-Moss Thought3551
    settings_parameters: "10709 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      beat.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 512
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      yard.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 24
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "20 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Dixon PLC #53694-CAR'
    concentration_or_purity: "99 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'May-Marshall #67383-ADDRESS'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8691 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7694 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Gentry, Cooper and Jackson Actually2516
    settings_parameters: "10934 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "6480 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      better.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 634
    temperature_celsius: 4
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate month.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 535
    replicates: 2
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      somebody.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 370
    replicates: 3
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      yourself.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 366
    temperature_celsius: 20
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "66 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "24 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bruce-Jackson #14771-SOME'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Harvey, Watson and Vaughan Nothing1999
    settings_parameters: "12836 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Calhoun Inc Because5217
    settings_parameters: "9877 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: pH meter
    settings_parameters: "12678 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate worker.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 415
    temperature_celsius: 20
  - step_description: Cells were cultured with dmem to facilitate yet.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 372
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were transfected with dmem to facilitate thousand.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 576
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate cup.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 70
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Left high make drive service such heart.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. John Flores
  and results were consistent across multiple biological replicates.
