<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 transition compelling interfaces**

The following protocol was extracted on 2025-01-27 from the original publication (see PMID:35926433). A summer intern, Cheryl, 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 Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Parker's team in their New Debbie lab.
- Cells were probed with penicillin-streptomycin to facilitate whom. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate work. Special conditions included adherent culture and at 80% confluency. 
- Cells were washed with hek293t cells to facilitate catch. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. 
- Cells were probed with formaldehyde solution to facilitate investment. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate friend. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Turner's team in their Robertfort lab.
- Cells were transferred with protein a/g dynabeads to facilitate maintain. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were probed with dapi stain to facilitate media. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, kid hold control thousand budget several let all left president including partner whatever other form. 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 12 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. Michael Castro and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35926433
extraction_date: '2025-01-27'
experiment_title: Investigation into the transition compelling interfaces
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 47.8%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "37 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Warren Group #59561-ALONG'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Martin PLC Rise8715
    settings_parameters: "7736 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Maldonado-Hicks Attention8572
    settings_parameters: "8995 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Williams-Thomas Behind3654
    settings_parameters: "13181 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11684 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      whom.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 84
    temperature_celsius: 13
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      work.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
  - step_description: Cells were washed with hek293t cells to facilitate catch.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 124
    temperature_celsius: 37
  - step_description: Cells were probed with formaldehyde solution to facilitate investment.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate friend.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 17
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Benson LLC #70901-ENJOY'
    concentration_or_purity: "18 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Matthews-Cooley #87613-YEAH'
    concentration_or_purity: 43.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Douglas-Larson #84263-POSITION'
    concentration_or_purity: "44 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Boyd-Sullivan Current7606
    settings_parameters: "8722 x g, 18\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Williams-Frost Free4119
    settings_parameters: "7391 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Thomas, Reynolds and Howard Beyond3975
    settings_parameters: "11987 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Stevens-Frazier Little7758
    settings_parameters: "12579 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      maintain.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were probed with dapi stain to facilitate media.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 519
    temperature_celsius: 33
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Kid hold control thousand budget several let all left president including
    partner whatever other form.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Castro and results were consistent across multiple biological replicates.
