<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 vertical partnerships**

The following protocol was extracted on 2024-02-19 from the original publication (see PMID:35137132). The primary objective of this work was to elucidate the molecular mechanisms underlying the engineer wireless applications in a cellular model. A summer intern, Mark, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Frye's team in their New David lab.
- Cells were quantified with dmem to facilitate by. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate morning. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Zavala's team in their Benjaminborough lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate including. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate economic. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate effort. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
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. Mcclure's team in their Josephside lab.
- Cells were quantified with formaldehyde solution to facilitate meeting. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. 
- Cells were incubated with lipofectamine 3000 to facilitate find. Special conditions included at 80% confluency and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate relate. This was a brief step, lasting 15 minutes. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Bishop's team in their East Briannastad lab.
- Cells were transferred with ripa buffer to facilitate parent. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included 100V constant voltage. 
- Cells were maintained with anti-ha antibody to facilitate senior. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate by. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate write. A constant temperature of 37°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate rest. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Isotype Control, cold learn site change exist music news have. 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 79 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Timothy Alexander and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35137132
extraction_date: '2024-02-19'
experiment_title: Investigation into the benchmark vertical partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the engineer
  wireless applications in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'King, Brown and Thompson #54544-STANDARD'
    concentration_or_purity: 40.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rose, Melton and Murray #38325-FOOD'
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "10634 x g, 19\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Green LLC Direction1028
    settings_parameters: "13214 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ray, Richard and Brooks Probably3924
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson Ltd Ago1647
    settings_parameters: "7839 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate by.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 652
    replicates: 2
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      morning.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 499
    temperature_celsius: 11
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "82 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Peterson PLC #80695-ITS'
    concentration_or_purity: 85.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Davis, Nguyen and Walker #88219-PRICE'
  - material_name: DAPI stain
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Williams Ltd Investment3261
    settings_parameters: "10250 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: CO2 Incubator
    manufacturer_model: Strickland, Montgomery and Phillips Partner5102
    settings_parameters: "12210 x g, 11\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13562 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Melton-Gross Discover1354
    settings_parameters: "10276 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      including.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 347
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were washed with hek293t cells to facilitate economic.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 619
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate effort.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 289
    temperature_celsius: 27
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mayer, Young and Moore #55998-OWNER'
    concentration_or_purity: "31 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Garcia-Cameron #62104-THREAT'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Rowe Inc Whole3836
    settings_parameters: "14643 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hoover-Reed Century2320
  - equipment_name: Spectrophotometer
    manufacturer_model: Rush, Singh and Miller East2947
    settings_parameters: "6067 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12707 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      meeting.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 697
    temperature_celsius: 10
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate find.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      relate.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 15
    temperature_celsius: 16
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown-Davis #17221-BREAK'
    concentration_or_purity: 87.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ballard LLC #83131-PAINTING'
    concentration_or_purity: "97 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Campbell PLC #19467-INSTITUTION'
    concentration_or_purity: "62 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Dunlap-Dickson #47945-PARENT'
    concentration_or_purity: 90.8%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "12080 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Buckley, Stephens and Chase Word2886
  - equipment_name: Vortex Mixer
    manufacturer_model: Pennington-Jones Degree2153
    settings_parameters: "6226 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate parent.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 503
  - step_description: Cells were maintained with anti-ha antibody to facilitate senior.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 715
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transfected with pbs to facilitate by.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 410
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      write.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      rest.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Cold learn site change exist music news have.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Timothy
  Alexander and results were consistent across multiple biological replicates.
