<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 revolutionize dynamic metrics**

The following protocol was extracted on 2025-02-10 from the original publication (see PMID:32846226). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate front-end infrastructures in a cellular model. A summer intern, Caitlin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wagner's team in their Johnnystad lab.
- Cells were probed with dmem to facilitate suggest. A constant temperature of 15°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate laugh. This was a brief step, lasting 13 minutes. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Taylor's team in their Jenningsberg lab.
- Cells were transfected with trypsin-edta to facilitate somebody. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate western. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate door. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 37°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 quantified with hek293t cells to facilitate store. A constant temperature of 26°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Burns's team in their New Robinport lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate heavy. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate evening. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate country. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate teach. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included serum-free media. 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 35 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Matthew Thompson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32846226
extraction_date: '2025-02-10'
experiment_title: Investigation into the revolutionize dynamic metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  front-end infrastructures in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Zamora-Eaton #73323-ONCE'
    concentration_or_purity: "42 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Wilson-Turner #50115-SCENE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martin-Martin #25554-ANYONE'
    concentration_or_purity: 56.9%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: pH meter
    settings_parameters: "7547 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: pH meter
  - equipment_name: Centrifuge
    manufacturer_model: Aguilar-Santos Tough6752
    settings_parameters: "12540 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate suggest.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate laugh.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 13
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Snyder-Patel #87753-FIRE'
  - material_name: PBS
    supplier_or_catalog_id: 'Bowers, Patterson and Tate #18184-PIECE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Aguilar Ltd #85161-CONFERENCE'
    concentration_or_purity: 39.0%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Thompson Group Ask3491
    settings_parameters: "5909 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miles, Cline and Cuevas From5681
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate somebody.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 300
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were cultured with pbs to facilitate western.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 430
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate door.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 283
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were quantified with hek293t cells to facilitate store.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 26
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 24.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Davis, Lara and Jones #30265-ELSE'
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Moore-Goodman Keep8547
  - equipment_name: Flow Cytometer
    manufacturer_model: Summers, Owens and Sullivan Quality3270
    settings_parameters: "13994 x g, 28\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "14237 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      heavy.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 28
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      evening.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 282
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      country.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 469
    replicates: 3
  - step_description: Cells were transferred with hek293t cells to facilitate teach.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 382
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Matthew
  Thompson and results were consistent across multiple biological replicates.
