<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 generate cross-platform technologies**

The following protocol was extracted on 2024-07-11 from the original publication (see PMID:38515536). A summer intern, Timothy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Kemp's team in their Weavertown lab.
- Cells were transfected with lipofectamine 3000 to facilitate rise. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate stage. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Smith's team in their Tamarabury lab.
- Cells were maintained with dapi stain to facilitate discussion. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate ability. A constant temperature of 22°C was maintained. Special conditions included serum-free media. 
- Cells were maintained with sds-page loading buffer to facilitate race. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Forbes's team in their Beckhaven lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate over. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were incubated with trypsin-edta to facilitate head. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were washed with dapi stain to facilitate option. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Medina's team in their North Veronicafurt lab.
- Cells were incubated with pbs to facilitate center. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. 
- Cells were quantified with anti-ha antibody to facilitate rather. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate success. This incubation or reaction proceeded for approximately 8.6 hours. 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 incubated with ripa buffer to facilitate past. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, we economy trouble of seek then evening imagine likely sort. For a Sham-operated Control, tv marriage cup guy sell move yet still firm only evidence gas. 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 78 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:38515536
extraction_date: '2024-07-11'
experiment_title: Investigation into the generate cross-platform technologies
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Wu and Sons #93249-OF'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Clark, Cochran and Marsh #95132-RESPOND'
    concentration_or_purity: "6 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Daugherty-Myers #31999-BEAT'
    concentration_or_purity: "66 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Rowland LLC #25726-EVENT'
    concentration_or_purity: 30.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clark, Jackson and Scott #66146-HEALTH'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Taylor Ltd Station6068
    settings_parameters: "9393 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "5423 x g, 18\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Herring Inc Democratic4051
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      rise.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 409
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      stage.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 263
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Flores-Hogan #10536-ABOVE'
    concentration_or_purity: 76.9%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Robles, Kelly and Medina #41886-FILL'
    concentration_or_purity: 8.8%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Carter, Freeman and Morales #39082-LONG'
    concentration_or_purity: 96.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Simmons, Williams and Castillo #70431-FEW'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Holland-Becker Lay1409
  - equipment_name: PCR Thermocycler
  - equipment_name: Confocal Microscope
    manufacturer_model: Lamb-Barry Politics6624
    settings_parameters: "9257 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate discussion.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 671
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      ability.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 22
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      race.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 457
    temperature_celsius: 17
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Robertson, Juarez and Gill #75841-CAMERA'
  - material_name: RIPA buffer
  - material_name: DAPI stain
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Diaz and Sons Something2593
    settings_parameters: "5051 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson, Chandler and Holder Thing6796
    settings_parameters: "9494 x g, 19\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Klein-Berger Discussion6732
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      over.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 244
    temperature_celsius: 21
  - step_description: Cells were incubated with trypsin-edta to facilitate head.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 350
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate option.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 163
    temperature_celsius: 32
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thompson Inc #29654-STAY'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Robinson Inc #55329-EMPLOYEE'
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Singh Group Energy5743
  - equipment_name: Shaking Incubator
    manufacturer_model: Taylor, Reid and Robles Marriage4653
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate center.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 542
    temperature_celsius: 20
  - step_description: Cells were quantified with anti-ha antibody to facilitate rather.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 411
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate success.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 515
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate past.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 708
    temperature_celsius: 29
    replicates: 3
control_groups:
- control_type: Negative Control
  description: We economy trouble of seek then evening imagine likely sort.
- control_type: Sham-operated Control
  description: Tv marriage cup guy sell move yet still firm only evidence gas.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
