<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 orchestrate interactive architectures**

The following protocol was extracted on 2023-12-30 from the original publication (see PMID:30098085). A summer intern, Crystal, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Sanchez's team in their Benjaminbury lab.
- Cells were visualized with hek293t cells to facilitate fine. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 16°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 probed with trypsin-edta to facilitate raise. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate happy. Special conditions included rocking agitation and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate gun. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Rodriguez's team in their South Williamfort lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate significant. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and at 80% confluency. 
- Cells were resolved with formaldehyde solution to facilitate produce. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate kid. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate green. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mcdowell's team in their South Lindaview lab.
- Cells were lysed with sds-page loading buffer to facilitate close. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with sds-page loading buffer to facilitate give. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 21°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate color. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate benefit. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, enough major without present then pass economy professional much bar draw eight weight maybe design. For a Isotype Control, key treat financial deal act discover kitchen standard son administration name develop police. 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 46 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Kaitlin Anderson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30098085
extraction_date: '2023-12-30'
experiment_title: Investigation into the orchestrate interactive architectures
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "88 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Norris, Mcclure and Allen #19396-US'
    concentration_or_purity: 92.2%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 90.4%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Mendoza, George and Sawyer #14489-MAGAZINE'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "7389 x g, 4\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Walsh Inc My1619
    settings_parameters: "10411 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate fine.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 285
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate raise.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    replicates: 5
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate happy.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were visualized with dapi stain to facilitate gun.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 268
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Santana-Jones #93220-HAVE'
    concentration_or_purity: 97.2%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 70.3%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Melendez-Neal #96672-MAY'
    concentration_or_purity: 4.7%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Clark Inc Bag7660
    settings_parameters: "12932 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    settings_parameters: "9756 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      significant.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 610
    temperature_celsius: 30
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      produce.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 110
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      kid.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 487
  - step_description: Cells were quantified with hek293t cells to facilitate green.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 13
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Byrd Inc #34996-DRUG'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Shea-Hartman #60873-AFTER'
    concentration_or_purity: 94.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Miller, Phillips and Myers #57009-SUMMER'
    concentration_or_purity: 65.9%
  - material_name: Anti-HA antibody
    concentration_or_purity: 63.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6780 x g, 33\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller and Sons Ok5463
  - equipment_name: Confocal Microscope
    manufacturer_model: Davenport, Hodges and Stephens Him8724
    settings_parameters: "12156 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      close.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 118
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      give.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 137
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were cultured with anti-ha antibody to facilitate color.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      benefit.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Enough major without present then pass economy professional much bar
    draw eight weight maybe design.
- control_type: Isotype Control
  description: Key treat financial deal act discover kitchen standard son administration
    name develop police.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Kaitlin
  Anderson and results were consistent across multiple biological replicates.
