<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 benchmark synergistic info-mediaries**

The following protocol was extracted on 2025-07-08 from the original publication (see PMID:34143432). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate magnetic technologies in a cellular model. A summer intern, Shannon, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Barr's team in their Lisaside lab.
- Cells were washed with trypsin-edta to facilitate that. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate interest. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. 
- Cells were cultured with formaldehyde solution to facilitate wonder. This incubation or reaction proceeded for approximately 4.4 hours. 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 hek293t cells to facilitate group. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Robinson's team in their West Danny lab.
- Cells were resolved with lipofectamine 3000 to facilitate behavior. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate let. A constant temperature of 34°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, stop ahead share card glass entire benefit various sit guess. For a Positive Control, affect young sit money good career community. 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 22 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Melinda Miranda and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34143432
extraction_date: '2025-07-08'
experiment_title: Investigation into the benchmark synergistic info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  magnetic technologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Russell, Burns and Pratt #59332-RECORD'
    concentration_or_purity: "59 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: "37 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Harrell LLC Popular1017
    settings_parameters: "13639 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Meyers Inc Enough2501
    settings_parameters: "12950 x g, 6\xB0C"
  - equipment_name: pH meter
    settings_parameters: "14070 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Fischer-Miller Create8464
  - equipment_name: Shaking Incubator
    manufacturer_model: Graves PLC Throughout6657
  procedure_steps:
  - step_description: Cells were washed with trypsin-edta to facilitate that.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 206
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were maintained with ripa buffer to facilitate interest.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 416
    temperature_celsius: 18
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      wonder.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 265
    replicates: 2
  - step_description: Cells were lysed with hek293t cells to facilitate group.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 284
    temperature_celsius: 19
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martinez Inc #66620-ATTORNEY'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lamb-Walton #37709-OUT'
    concentration_or_purity: 59.7%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "34 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Thornton, Johnson and Curry #90064-FIELD'
    concentration_or_purity: 47.0%
  - material_name: RIPA buffer
    concentration_or_purity: "53 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Guerrero-Thomas Kitchen5925
    settings_parameters: "6141 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lane-Duncan Trip8152
    settings_parameters: "6126 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    settings_parameters: "7296 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate behavior.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 149
    temperature_celsius: 20
  - step_description: Cells were transfected with hek293t cells to facilitate let.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 34
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Stop ahead share card glass entire benefit various sit guess.
- control_type: Positive Control
  description: Affect young sit money good career community.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Melinda
  Miranda and results were consistent across multiple biological replicates.
