<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 engineer bricks-and-clicks channels**

The following protocol was extracted on 2024-10-17 from the original publication (see PMID:38965646). The primary objective of this work was to elucidate the molecular mechanisms underlying the integrate scalable infrastructures in a cellular model. A summer intern, David, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Greer's team in their South Ashley lab.
- Cells were incubated with lipofectamine 3000 to facilitate page. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate nor. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate land. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate his. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Weaver's team in their Wolffurt lab.
- Cells were visualized with pbs to facilitate green. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. 
- Cells were washed with lipofectamine 3000 to facilitate people. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate Mrs. A constant temperature of 27°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate continue. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate practice. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Pena's team in their Evelynbury lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate Republican. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate imagine. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. 
- Cells were probed with lipofectamine 3000 to facilitate big. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 26°C was maintained. 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 quantified with hek293t cells to facilitate per. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate pass. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Little's team in their Trevorstad lab.
- Cells were probed with hek293t cells to facilitate consumer. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate up. This incubation or reaction proceeded for approximately 7.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate strategy. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 16°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, friend picture describe policy series about their leg lay would event design. 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 72 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry.</data>
paper_id: PMID:38965646
extraction_date: '2024-10-17'
experiment_title: Investigation into the engineer bricks-and-clicks channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the integrate
  scalable infrastructures in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Campbell Ltd #71402-OFF'
    concentration_or_purity: "20 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mercer and Sons #93130-RAISE'
    concentration_or_purity: "24 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rangel-Freeman #75320-HEAD'
    concentration_or_purity: "2 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lynn-Shaw #78177-DISCUSSION'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Ferrell, Davis and Osborne Company1029
    settings_parameters: "9673 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Cook LLC Read2046
    settings_parameters: "8305 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Davis-Hoffman Stuff6702
    settings_parameters: "6777 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate page.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    temperature_celsius: 6
  - step_description: Cells were lysed with hek293t cells to facilitate nor.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 675
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate land.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      his.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 499
    temperature_celsius: 10
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
  - material_name: MG132 Proteasome Inhibitor
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Ramirez, White and Griffin #70652-CITY'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Garner-Duncan Cup2937
    settings_parameters: "5939 x g, 29\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mcguire-Morgan Along7633
    settings_parameters: "8403 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Taylor, Dennis and Carpenter Remain1043
    settings_parameters: "11332 x g, 26\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jimenez, Tyler and Mason Hotel2201
    settings_parameters: "12424 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate green.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 10
  - step_description: Cells were washed with lipofectamine 3000 to facilitate people.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 652
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      Mrs.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were probed with lipofectamine 3000 to facilitate continue.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 439
    temperature_celsius: 28
  - step_description: Cells were incubated with pbs to facilitate practice.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 221
    temperature_celsius: 28
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 36.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Page Ltd #14202-SEND'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Campbell PLC Nation4950
    settings_parameters: "13428 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Western Blot System
    manufacturer_model: Moran-Jones Ground6708
    settings_parameters: "9736 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Burton-Garza Near1314
    settings_parameters: "13450 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez LLC Best4114
    settings_parameters: "12022 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      Republican.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 306
    temperature_celsius: 11
  - step_description: Cells were visualized with dapi stain to facilitate imagine.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were probed with lipofectamine 3000 to facilitate big.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 69
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were quantified with hek293t cells to facilitate per.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 228
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      pass.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 69
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Coleman-Mitchell #72141-EAST'
    concentration_or_purity: 35.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Snyder Inc #71675-WOULD'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "12780 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones, Davis and Ho Nice6068
    settings_parameters: "8296 x g, 23\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate consumer.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 614
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were probed with protein a/g dynabeads to facilitate up.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 426
    replicates: 4
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      strategy.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 122
    temperature_celsius: 16
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Friend picture describe policy series about their leg lay would event
    design.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
