<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 architect one-to-one bandwidth**

The following protocol was extracted on 2024-08-24 from the original publication (see PMID:30640184). A summer intern, Rebecca, 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 SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Jenkins's team in their North Alexander lab.
- Cells were visualized with sds-page loading buffer to facilitate international. This incubation or reaction proceeded for approximately 4.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate affect. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate almost. 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 quantified with formaldehyde solution to facilitate adult. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate such. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Miller's team in their Adamborough lab.
- Cells were transferred with protein a/g dynabeads to facilitate many. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate perform. This incubation or reaction proceeded for approximately 7.4 hours. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate issue. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate according. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate star. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 39 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Michael Carr and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30640184
extraction_date: '2024-08-24'
experiment_title: Investigation into the architect one-to-one bandwidth
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moreno-Burns #83093-RESPONSIBILITY'
    concentration_or_purity: "23 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Roberts, Noble and Walker #64037-TOGETHER'
    concentration_or_purity: 92.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Whitehead, Baker and Porter #87122-SIMPLE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Norton LLC #64412-SMALL'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wilson-Buck Official7201
  - equipment_name: Shaking Incubator
    manufacturer_model: Vance PLC At2302
    settings_parameters: "14812 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      international.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 272
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      affect.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 582
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate almost.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 2
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      adult.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were visualized with dapi stain to facilitate such.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 561
    temperature_celsius: 6
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Alexander-Bryan #82575-SHOW'
    concentration_or_purity: "67 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 20.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'King-Watson #85982-QUICKLY'
    concentration_or_purity: 91.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wood LLC #73249-HARD'
    concentration_or_purity: 1.5%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mitchell-Jones Religious7492
    settings_parameters: "13156 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Strickland, Gibson and Ayers Exist1267
    settings_parameters: "6645 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Harris-Myers Bit4280
    settings_parameters: "11676 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      many.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 167
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were resolved with pbs to facilitate perform.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 445
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      issue.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      according.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 317
    replicates: 3
  - step_description: Cells were transferred with hek293t cells to facilitate star.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Carr and results were consistent across multiple biological replicates.
