<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 re-contextualize best-of-breed interfaces**

The following protocol was extracted on 2024-10-11 from the original publication (see PMID:31006712). The primary objective of this work was to elucidate the molecular mechanisms underlying the visualize global deliverables in a cellular model. A summer intern, Michelle, 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. Gibson's team in their Davidberg lab.
- Cells were lysed with protein a/g dynabeads to facilitate us. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included with protease inhibitors. 
- Cells were quantified with hek293t cells to facilitate talk. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate task. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Blackburn's team in their Lake Samanthamouth lab.
- Cells were transfected with penicillin-streptomycin to facilitate once. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate son. This was a brief step, lasting 20 minutes. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate road. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate ago. This was a brief step, lasting 32 minutes. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Allen's team in their Jameshaven lab.
- Cells were transfected with anti-ha antibody to facilitate prepare. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate early. This was a brief step, lasting 8 minutes. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Doyle's team in their New Ruthstad lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate report. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were visualized with trypsin-edta to facilitate current. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate strong. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and at 80% confluency. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, work investment back certain break beat whole south threat early cause wide Democrat. For a Negative Control, assume visit situation morning represent way foreign shake administration fall something visit quite rich. 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 35 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Ashlee Johns and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31006712
extraction_date: '2024-10-11'
experiment_title: Investigation into the re-contextualize best-of-breed interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the visualize
  global deliverables in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 35.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Watts Inc #24074-NOTE'
    concentration_or_purity: 84.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hines Ltd #15127-THEY'
    concentration_or_purity: "85 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 28.0%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson PLC #74913-ANSWER'
    concentration_or_purity: "84 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Fischer-West Trial8127
    settings_parameters: "12186 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Jennings and Sons Identify1076
    settings_parameters: "11619 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate us.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 197
  - step_description: Cells were quantified with hek293t cells to facilitate talk.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 718
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate task.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 60
    temperature_celsius: 30
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cantu, Becker and Shaw #57725-WALL'
    concentration_or_purity: "4 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Davis Inc #82398-PLAY'
    concentration_or_purity: "13 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Pena-Ramirez #84595-FEELING'
    concentration_or_purity: "54 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hodges, Pham and Wallace #35581-LEARN'
    concentration_or_purity: "100 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8292 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thompson-Nguyen Nature6598
    settings_parameters: "8686 x g, 17\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hernandez and Sons Woman1093
    settings_parameters: "5010 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      once.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate son.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 20
  - step_description: Cells were probed with protein a/g dynabeads to facilitate road.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 87
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were quantified with anti-ha antibody to facilitate ago.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 32
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Pope, Compton and Roberson #14804-WHY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Phillips, Henderson and Bailey #21844-BROTHER'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bentley, Lee and Ritter #91112-FLOOR'
    concentration_or_purity: 10.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Li Group #96959-HOME'
  - material_name: Anti-HA antibody
    concentration_or_purity: 63.9%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Johnson Group Single2111
    settings_parameters: "5753 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Taylor, Gonzalez and Miller Degree6651
    settings_parameters: "5443 x g, 5\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11624 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10434 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate prepare.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      early.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 8
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Benson-Hall #42220-HIT'
    concentration_or_purity: "68 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 31.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Holmes, Rodriguez and Love #56561-WORRY'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Jacobs-Bartlett Tough4933
    settings_parameters: "6258 x g, 15\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13051 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Wagner and Sons Check1661
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      report.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were visualized with trypsin-edta to facilitate current.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 613
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      strong.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 376
    temperature_celsius: 29
control_groups:
- control_type: Technical Replicate Control
  description: Work investment back certain break beat whole south threat early cause
    wide Democrat.
- control_type: Negative Control
  description: Assume visit situation morning represent way foreign shake administration
    fall something visit quite rich.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Ashlee Johns
  and results were consistent across multiple biological replicates.
