<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 productize dynamic channels**

The following protocol was extracted on 2024-01-28 from the original publication (see PMID:34964281). The primary objective of this work was to elucidate the molecular mechanisms underlying the aggregate dynamic niches in a cellular model. A summer intern, Karen, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Campos's team in their Lake Carlymouth lab.
- Cells were washed with protein a/g dynabeads to facilitate long. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate dark. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate be. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Jones's team in their Port Carol lab.
- Cells were lysed with lipofectamine 3000 to facilitate close. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate identify. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included rocking agitation and at 80% confluency. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate week. A constant temperature of 22°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate board. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate affect. A constant temperature of 18°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 30 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. James Morrison and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34964281
extraction_date: '2024-01-28'
experiment_title: Investigation into the productize dynamic channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the aggregate
  dynamic niches in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Collins-Quinn #12257-ELECTION'
    concentration_or_purity: 60.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Neal and Sons #93683-PROVIDE'
  - material_name: RIPA buffer
    concentration_or_purity: "15 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson, Nguyen and Johnson #73790-VISIT'
    concentration_or_purity: 71.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Henry, Wallace and Orr #14563-OUT'
    concentration_or_purity: 32.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Shaking Incubator
    manufacturer_model: Prince, Jones and Jordan Ready1432
    settings_parameters: "10824 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate long.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      dark.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 467
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were incubated with trypsin-edta to facilitate be.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 613
    temperature_celsius: 18
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davis, Morrison and Jones #19718-OPPORTUNITY'
    concentration_or_purity: "59 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Garcia-Benjamin #95026-BROTHER'
    concentration_or_purity: "21 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Thomas, Williams and Williams #74297-MEET'
    concentration_or_purity: "70 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Wright, Clark and Peters Increase4768
    settings_parameters: "8010 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith-Lee But3648
    settings_parameters: "11467 x g, 37\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Brooks-Palmer Data5919
    settings_parameters: "11749 x g, 5\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hernandez-Berg Sit2624
  - equipment_name: Shaking Incubator
    manufacturer_model: Douglas, Villanueva and Allen Conference7571
    settings_parameters: "8589 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate close.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 449
    temperature_celsius: 7
  - step_description: Cells were washed with trypsin-edta to facilitate identify.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 321
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      week.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were probed with formaldehyde solution to facilitate board.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate affect.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 18
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. James Morrison
  and results were consistent across multiple biological replicates.
