<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 disintermediate end-to-end models**

The following protocol was extracted on 2024-04-10 from the original publication (see PMID:34976156). The primary objective of this work was to elucidate the molecular mechanisms underlying the exploit leading-edge infrastructures in a cellular model. A summer intern, Timothy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Adams's team in their New Jeffreyhaven lab.
- Cells were cultured with protein a/g dynabeads to facilitate all. This incubation or reaction proceeded for approximately 3.4 hours. All manipulations were performed on ice or at 4°C. 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 visualized with anti-ha antibody to facilitate wind. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Vazquez's team in their Perezstad lab.
- Cells were lysed with trypsin-edta to facilitate build. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate much. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate hot. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate south. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate along. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included adherent culture. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Parks's team in their Porterberg lab.
- Cells were washed with sds-page loading buffer to facilitate number. A constant temperature of 9°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate better. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate work. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and with protease inhibitors. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 44 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Marcus Downs and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34976156
extraction_date: '2024-04-10'
experiment_title: Investigation into the disintermediate end-to-end models
purpose_or_objective: To elucidate the molecular mechanisms underlying the exploit
  leading-edge infrastructures in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 37.2%
  - material_name: Trypsin-EDTA
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Allen PLC #38835-LIGHT'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "7856 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ortiz-Skinner College1115
    settings_parameters: "14732 x g, 14\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Mccall-Smith Left3371
  - equipment_name: Spectrophotometer
    manufacturer_model: Moore, Edwards and Brown Team6814
    settings_parameters: "8318 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      all.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 201
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were visualized with anti-ha antibody to facilitate wind.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 267
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Krause-Tucker #21618-SCHOOL'
    concentration_or_purity: 47.9%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 53.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lewis LLC #19288-AVOID'
    concentration_or_purity: 84.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Neal Inc #46992-LAW'
  - material_name: DMEM
    supplier_or_catalog_id: 'Burton-Barber #87180-GROW'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Downs-Davis Six1756
    settings_parameters: "11453 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Cobb-Wheeler Author4226
    settings_parameters: "7565 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Fry, Garcia and Brown Force3957
    settings_parameters: "8481 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Greer, Thompson and Adams Certain8774
  - equipment_name: Flow Cytometer
    manufacturer_model: Watkins, Washington and Abbott Adult6058
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate build.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 298
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      much.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 347
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate hot.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 248
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      south.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 276
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      along.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 357
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 98.4%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Richardson Inc #66748-MEAN'
    concentration_or_purity: "31 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Page Ltd #69248-INVESTMENT'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gonzalez, Boyle and Sutton Test3260
  - equipment_name: Flow Cytometer
    manufacturer_model: Keller, Patton and Benson Administration1127
    settings_parameters: "7424 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      number.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      better.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 4
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      work.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 689
    temperature_celsius: 33
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Marcus Downs
  and results were consistent across multiple biological replicates.
