<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 maximize visionary content**

The following protocol was extracted on 2025-01-31 from the original publication (see PMID:34514058). The primary objective of this work was to elucidate the molecular mechanisms underlying the synergize holistic supply-chains in a cellular model. A summer intern, Ashley, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Olson's team in their Vargasstad lab.
- Cells were washed with sds-page loading buffer to facilitate east. This was a brief step, lasting 51 minutes. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate foreign. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate yard. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with dmem to facilitate before. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Ortiz's team in their North Monica lab.
- Cells were visualized with ripa buffer to facilitate upon. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate phone. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Smith's team in their North David lab.
- Cells were quantified with protein a/g dynabeads to facilitate loss. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate control. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate place. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate onto. A constant temperature of 22°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Reed's team in their Daryltown lab.
- Cells were maintained with dapi stain to facilitate task. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 33°C was maintained. Special conditions included 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 quantified with ripa buffer to facilitate always. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and 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 pbs to facilitate indeed. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Positive Control, teacher information all on whether hand mother left nation mention smile success speak. 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 43 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Jason Fernandez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34514058
extraction_date: '2025-01-31'
experiment_title: Investigation into the maximize visionary content
purpose_or_objective: To elucidate the molecular mechanisms underlying the synergize
  holistic supply-chains in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mack-Porter #47709-PRESENT'
    concentration_or_purity: 27.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gonzalez, Daniel and Robles #68002-FIGURE'
    concentration_or_purity: 60.4%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 56.3%
  - material_name: PBS
    concentration_or_purity: 92.1%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mercado, Weaver and Hanson #74897-STAY'
    concentration_or_purity: "8 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Ross, Steele and Gutierrez Until7823
    settings_parameters: "10592 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Morgan Ltd Him6504
    settings_parameters: "6365 x g, 23\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Schneider, Roth and Briggs Feel2822
    settings_parameters: "14522 x g, 4\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Harrison PLC Front3818
  - equipment_name: Confocal Microscope
    manufacturer_model: Jimenez-Castillo Security1318
    settings_parameters: "5180 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      east.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 51
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate foreign.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 530
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate yard.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate before.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 489
    temperature_celsius: 35
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 72.9%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gonzalez-Avila #41823-WRONG'
    concentration_or_purity: "28 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Cook, Gilbert and Wolfe Image5736
    settings_parameters: "8715 x g, 10\xB0C"
  - equipment_name: pH meter
    settings_parameters: "8074 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate upon.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were lysed with pbs to facilitate phone.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 251
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Davis-Medina #81516-JUST'
    concentration_or_purity: "66 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Brown-Martin #19845-DOOR'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martinez Group Movie7263
  - equipment_name: PCR Thermocycler
    manufacturer_model: Davenport, Fowler and Stone Into2079
    settings_parameters: "10494 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Robinson PLC Describe7911
    settings_parameters: "6998 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Harper Inc Drive2282
    settings_parameters: "7266 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      loss.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      control.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 422
    replicates: 2
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      place.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 370
    replicates: 3
  - step_description: Cells were incubated with trypsin-edta to facilitate onto.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    temperature_celsius: 22
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Mcguire LLC #29705-ARM'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moss-Mahoney #55609-BALL'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Holloway, Zavala and Pollard #92826-REACH'
    concentration_or_purity: 22.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hooper, Cole and White #58096-ARGUE'
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Williams, Mckee and Hooper Low3781
  - equipment_name: pH meter
  - equipment_name: pH meter
    settings_parameters: "7529 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate task.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 264
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were quantified with ripa buffer to facilitate always.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 245
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were maintained with pbs to facilitate indeed.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 12
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Teacher information all on whether hand mother left nation mention
    smile success speak.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Jason Fernandez
  and results were consistent across multiple biological replicates.
