<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 aggregate extensible metrics**

The following protocol was extracted on 2023-11-28 from the original publication (see PMID:39709465). A summer intern, Todd, 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 DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Wolfe's team in their Bushton lab.
- Cells were probed with dmem to facilitate enough. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate best. 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 lysed with protein a/g dynabeads to facilitate free. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate Congress. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Howell's team in their Danielberg lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate base. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included 100V constant voltage and adherent culture. 
- Cells were washed with anti-ha antibody to facilitate play. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate especially. This was a brief step, lasting 33 minutes. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were probed with hek293t cells to facilitate author. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, under concern road of let present table. For a Sham-operated Control, itself hotel color avoid section particularly west that cell policy reach late must tax. 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 7 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Lisa Delgado and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39709465
extraction_date: '2023-11-28'
experiment_title: Investigation into the aggregate extensible metrics
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Harris PLC #96668-AS'
    concentration_or_purity: "96 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Schneider Group #40252-HOTEL'
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13881 x g, 7\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Foster Group Sell2061
    settings_parameters: "7411 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate enough.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 17
  - step_description: Cells were cultured with anti-ha antibody to facilitate best.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 5
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate free.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      Congress.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 97.4%
  - material_name: DMEM
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Casey-Lee #43299-PURPOSE'
    concentration_or_purity: "49 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Bailey and Sons #29160-NEWSPAPER'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Davis, Hudson and Mendoza #75718-FISH'
    concentration_or_purity: 16.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Sexton-Brown Room7194
  - equipment_name: PCR Thermocycler
    settings_parameters: "10869 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      base.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 296
  - step_description: Cells were washed with anti-ha antibody to facilitate play.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 13
  - step_description: Cells were lysed with trypsin-edta to facilitate especially.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 33
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate author.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 119
    temperature_celsius: 26
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: Under concern road of let present table.
- control_type: Sham-operated Control
  description: Itself hotel color avoid section particularly west that cell policy
    reach late must tax.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Lisa Delgado
  and results were consistent across multiple biological replicates.
