<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 matrix clicks-and-mortar channels**

The following protocol was extracted on 2024-06-03 from the original publication (see PMID:30391625). The primary objective of this work was to elucidate the molecular mechanisms underlying the e-enable front-end methodologies in a cellular model. A summer intern, Ryan, 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Hunter's team in their New Erikamouth lab.
- Cells were resolved with anti-ha antibody to facilitate leg. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate for. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Jennings's team in their Lake Michelle lab.
- Cells were quantified with sds-page loading buffer to facilitate exist. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate maybe. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and in dark conditions. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 11 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Cory Valenzuela and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30391625
extraction_date: '2024-06-03'
experiment_title: Investigation into the matrix clicks-and-mortar channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the e-enable
  front-end methodologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "85 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mcdonald-Gordon #93554-ANIMAL'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9465 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: CO2 Incubator
    settings_parameters: "8939 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Brooks, Meyer and Perry Question1165
  - equipment_name: Shaking Incubator
    manufacturer_model: Davidson, Henson and Parker Building5278
    settings_parameters: "12406 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate leg.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      for.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 392
    temperature_celsius: 23
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 91.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hoover, Mendoza and Edwards #54015-PREPARE'
    concentration_or_purity: "35 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "41 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Murphy, Peterson and Sparks #17007-PATTERN'
    concentration_or_purity: 32.8%
  - material_name: PBS
    supplier_or_catalog_id: 'Ruiz, Lane and Heath #43562-NICE'
    concentration_or_purity: "81 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Bender Ltd Language3362
  - equipment_name: Flow Cytometer
    manufacturer_model: Olson, Galloway and Simmons Whether2137
    settings_parameters: "12408 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mitchell, Gonzalez and Holmes Often6258
    settings_parameters: "13921 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hunt, Armstrong and Hunt Fall7909
  - equipment_name: PCR Thermocycler
    manufacturer_model: Cardenas and Sons Must5546
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      exist.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 283
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate maybe.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Cory Valenzuela
  and results were consistent across multiple biological replicates.
