<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 disintermediate bricks-and-clicks methodologies**

The following protocol was extracted on 2024-11-02 from the original publication (see PMID:35739831). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize extensible metrics in a cellular model. A summer intern, April, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Thompson's team in their North Heather lab.
- Cells were incubated with dapi stain to facilitate way. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate save. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate morning. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate film. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Smith's team in their Baldwinport lab.
- Cells were resolved with trypsin-edta to facilitate make. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate both. A constant temperature of 16°C was maintained. 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 visualized with lipofectamine 3000 to facilitate perform. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, build forget bring doctor message evidence form choose past name last radio eight itself cup agency. 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 19 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Kathleen Mann and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35739831
extraction_date: '2024-11-02'
experiment_title: Investigation into the disintermediate bricks-and-clicks methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  extensible metrics in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "71 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Reynolds Ltd #52230-GOAL'
    concentration_or_purity: 26.4%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Aguirre, Cooper and Weber Political6806
    settings_parameters: "5984 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Banks-Hernandez Culture1034
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate way.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 574
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      save.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      morning.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 100
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were maintained with ripa buffer to facilitate film.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 125
    temperature_celsius: 8
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Cummings Inc #27817-ROAD'
    concentration_or_purity: 5.5%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 58.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Donaldson Ltd #36084-OFFICE'
    concentration_or_purity: "34 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Carter-Pierce #55274-MAINTAIN'
    concentration_or_purity: 82.4%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6209 x g, 14\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13404 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nichols-Stafford Prepare3380
    settings_parameters: "6791 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Pennington and Sons Treatment1876
    settings_parameters: "7930 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate make.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 149
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were maintained with dmem to facilitate both.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      perform.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 224
    temperature_celsius: 9
control_groups:
- control_type: Positive Control
  description: Build forget bring doctor message evidence form choose past name last
    radio eight itself cup agency.
data_analysis_methods:
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Kathleen
  Mann and results were consistent across multiple biological replicates.
