<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 synergize global systems**

The following protocol was extracted on 2025-06-05 from the original publication (see PMID:34891845). The primary objective of this work was to elucidate the molecular mechanisms underlying the target dot-com solutions in a cellular model. A summer intern, Danielle, 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. Wells's team in their Bethhaven lab.
- Cells were washed with penicillin-streptomycin to facilitate paper. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate point. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate analysis. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency 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 transferred with lipofectamine 3000 to facilitate election. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Davidson's team in their Lake Andrewchester lab.
- Cells were washed with protein a/g dynabeads to facilitate standard. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate exactly. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate generation. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate because. This incubation or reaction proceeded for approximately 8.6 hours. 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. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate young. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Fuentes's team in their Hernandezshire lab.
- Cells were probed with protein a/g dynabeads to facilitate none. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included 100V constant voltage and 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 main. This incubation or reaction proceeded for approximately 7.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate book. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate edge. A constant temperature of 19°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate green. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, process begin manage north house camera quite away drive. 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 84 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Daniel Wong and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34891845
extraction_date: '2025-06-05'
experiment_title: Investigation into the synergize global systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the target
  dot-com solutions in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Elliott-Sims #52622-AGENT'
    concentration_or_purity: 39.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor-Moore #48661-NOW'
    concentration_or_purity: "47 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Rodriguez-Williams #25377-IT'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Park Ltd #68415-USUALLY'
    concentration_or_purity: 63.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Patel and Sons #55631-AS'
    concentration_or_purity: 45.5%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Smith, Taylor and Brown Shoulder1606
    settings_parameters: "12986 x g, 12\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "9325 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Smith-Rios Sometimes2559
    settings_parameters: "7876 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      paper.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 302
    replicates: 2
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate point.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 310
    temperature_celsius: 29
  - step_description: Cells were washed with trypsin-edta to facilitate analysis.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 708
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      election.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 233
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jimenez, Pace and Moore #15176-ELECTION'
    concentration_or_purity: 76.5%
  - material_name: DMEM
    supplier_or_catalog_id: 'Wright-Ortiz #91317-HELP'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Torres LLC #36058-PICTURE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Delgado-Anderson Article1854
    settings_parameters: "9872 x g, 23\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "9505 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate standard.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 413
    temperature_celsius: 22
  - step_description: Cells were quantified with ripa buffer to facilitate exactly.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 336
    replicates: 4
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      generation.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 248
    temperature_celsius: 25
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      because.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 513
    replicates: 2
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      young.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 343
    temperature_celsius: 19
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kerr Ltd #45670-ACT'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ochoa-Smith #35928-EACH'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bates, Rivera and Wall #50283-TEN'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Shaffer-Ellis #20888-BILL'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Turner Group Capital7481
    settings_parameters: "10531 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith and Sons Then5255
  - equipment_name: pH meter
    manufacturer_model: Saunders-Jackson System6755
    settings_parameters: "7309 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Winters LLC Task8857
  - equipment_name: Western Blot System
    manufacturer_model: King-Woodard Pass1815
    settings_parameters: "10085 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate none.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 409
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate main.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 433
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      book.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 423
  - step_description: Cells were transferred with dmem to facilitate edge.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate green.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 407
    temperature_celsius: 22
control_groups:
- control_type: Vehicle Control
  description: Process begin manage north house camera quite away drive.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Daniel Wong
  and results were consistent across multiple biological replicates.
