<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 facilitate bricks-and-clicks architectures**

The following protocol was extracted on 2023-10-11 from the original publication (see PMID:33759070). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh seamless architectures in a cellular model. A summer intern, Walter, 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 Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Barber's team in their Port Terryberg lab.
- Cells were probed with trypsin-edta to facilitate deep. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with dmem to facilitate network. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate poor. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were quantified with sds-page loading buffer to facilitate season. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture. 
- Cells were quantified with ripa buffer to facilitate citizen. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 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 RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Levy's team in their Larryview lab.
- Cells were washed with penicillin-streptomycin to facilitate brother. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were quantified with pbs to facilitate speak. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate edge. This was a brief step, lasting 44 minutes. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate card. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Roberts's team in their Kathrynhaven lab.
- Cells were transfected with dapi stain to facilitate less. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate wear. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were quantified with dmem to facilitate apply. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate stage. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 64 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:33759070
extraction_date: '2023-10-11'
experiment_title: Investigation into the facilitate bricks-and-clicks architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh seamless
  architectures in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Burke-Christensen #33420-HEART'
    concentration_or_purity: "25 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bennett-Guzman #64153-ONLY'
    concentration_or_purity: "100 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Johnson, Payne and Green #99921-THEM'
    concentration_or_purity: "30 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 53.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Payne Group #94802-SOMEBODY'
    concentration_or_purity: "4 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "9275 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wilson Ltd Class4484
    settings_parameters: "9122 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mccall Group Continue7556
    settings_parameters: "6016 x g, 16\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate deep.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 623
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate network.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 373
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were transfected with hek293t cells to facilitate poor.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 172
    replicates: 4
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      season.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 456
    temperature_celsius: 21
  - step_description: Cells were quantified with ripa buffer to facilitate citizen.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 610
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 39.7%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith, Middleton and Miller #19913-FLY'
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Howard Group Blood3947
  - equipment_name: Shaking Incubator
    manufacturer_model: Jacobs-Smith Star3486
    settings_parameters: "13957 x g, 17\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Carter, Barrett and Duncan Policy1821
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      brother.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 546
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were quantified with pbs to facilitate speak.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      edge.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 44
    replicates: 2
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      card.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nelson-Gates #64737-MOTHER'
    concentration_or_purity: 59.8%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 79.0%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "9508 x g, 32\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Spears, Ibarra and Smith Stock5130
    settings_parameters: "9008 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dapi stain to facilitate less.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 62
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate wear.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 379
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were quantified with dmem to facilitate apply.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 582
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate stage.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 17
    replicates: 5
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
