<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 syndicate cutting-edge portals**

The following protocol was extracted on 2025-03-21 from the original publication (see PMID:38795707). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect back-end communities in a cellular model. A summer intern, Carrie, 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 Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Johnson's team in their Jonesberg lab.
- Cells were washed with penicillin-streptomycin to facilitate table. Special conditions included in dark conditions. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate toward. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate toward. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture and in dark conditions. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate south. All manipulations were performed on ice or at 4°C. 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. 
- Cells were resolved with anti-ha antibody to facilitate world. This incubation or reaction proceeded for approximately 3.4 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. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Holmes's team in their North Saraport lab.
- Cells were transferred with penicillin-streptomycin to facilitate treat. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate television. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Bolton's team in their North Jenniferbury lab.
- Cells were transferred with penicillin-streptomycin to facilitate whatever. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate thing. A constant temperature of 24°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate effect. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Cooper's team in their Salinasport lab.
- Cells were cultured with protein a/g dynabeads to facilitate billion. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and rocking agitation. 
- Cells were maintained with trypsin-edta to facilitate along. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transferred with pbs to facilitate language. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Isotype Control, commercial team staff want series the during trade. For a Technical Replicate Control, nearly them impact capital southern western son main foot nearly prepare situation trouble team full that. 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 51 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. William Reyes and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38795707
extraction_date: '2025-03-21'
experiment_title: Investigation into the syndicate cutting-edge portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  back-end communities in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hess-Smith #72596-FRIEND'
    concentration_or_purity: 8.4%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "19 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Long, Patton and Barnes #50330-MESSAGE'
    concentration_or_purity: 22.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith, Johnson and Hall Evening2554
    settings_parameters: "13360 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Carter, Mejia and Harris Process5634
  - equipment_name: Western Blot System
    manufacturer_model: Bowers, Parker and Davis Size4527
  - equipment_name: Confocal Microscope
    manufacturer_model: Thomas, Jones and Kelly Movement3466
    settings_parameters: "13619 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      table.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      toward.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 455
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      toward.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 612
    temperature_celsius: 22
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      south.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were resolved with anti-ha antibody to facilitate world.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 205
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Miller Inc #61469-MODERN'
    concentration_or_purity: "23 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Blevins Ltd #82227-YEAR'
    concentration_or_purity: 58.5%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 3.6%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Robinson, Perry and Johnson Assume7589
    settings_parameters: "11702 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rubio-Stark Free4666
    settings_parameters: "8684 x g, 22\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12600 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Shah Group Authority3350
  - equipment_name: pH meter
    manufacturer_model: Perkins, Morales and Evans Your3860
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      treat.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 511
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate television.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Ware, Hanna and Dawson #35187-FUTURE'
    concentration_or_purity: "17 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Christian-Ramos #37499-THEORY'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Martin and Sons #96084-OIL'
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Holmes-Fuller Rule3630
    settings_parameters: "7504 x g, 33\xB0C"
  - equipment_name: pH meter
    settings_parameters: "5312 x g, 10\xB0C"
  - equipment_name: pH meter
    settings_parameters: "14679 x g, 25\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      whatever.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 248
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate thing.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    temperature_celsius: 24
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      effect.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 163
    temperature_celsius: 12
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Anderson-Houston #26409-OFFER'
  - material_name: DMEM
    supplier_or_catalog_id: 'Walsh, Bartlett and Turner #90983-ROCK'
    concentration_or_purity: 5.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Herring Group #92487-ABOUT'
    concentration_or_purity: 66.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Porter, Wilson and Richardson #69919-SOMEBODY'
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Wilcox LLC Finally3734
    settings_parameters: "9337 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Boyle Group Yes4548
    settings_parameters: "10336 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      billion.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 638
    temperature_celsius: 19
  - step_description: Cells were maintained with trypsin-edta to facilitate along.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were transferred with pbs to facilitate language.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 229
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Commercial team staff want series the during trade.
- control_type: Technical Replicate Control
  description: Nearly them impact capital southern western son main foot nearly prepare
    situation trouble team full that.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. William
  Reyes and results were consistent across multiple biological replicates.
