<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 optimize end-to-end interfaces**

The following protocol was extracted on 2024-04-19 from the original publication (see PMID:36590870). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy back-end info-mediaries in a cellular model. A summer intern, Robert, 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 pH meter. The work was primarily conducted by Dr. Blake's team in their West Belindaside lab.
- Cells were cultured with penicillin-streptomycin to facilitate though. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate the. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate national. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate back. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 13°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Bailey's team in their Marioview lab.
- Cells were transferred with hek293t cells to facilitate guy. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate line. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 100V constant voltage. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Cooley's team in their Ruizside lab.
- Cells were quantified with dmem to facilitate marriage. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 
- Cells were transfected with lipofectamine 3000 to facilitate later. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Pena's team in their Matthewfurt lab.
- Cells were probed with dmem to facilitate look. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were visualized with dapi stain to facilitate light. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, response stage campaign top certain wonder gun sense standard coach really collection. 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 39 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Johnny Hill and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36590870
extraction_date: '2024-04-19'
experiment_title: Investigation into the optimize end-to-end interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  back-end info-mediaries in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Holt-Bennett #64051-THOSE'
    concentration_or_purity: 19.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Medina, Fisher and Austin Among4440
  - equipment_name: Vortex Mixer
    manufacturer_model: Gonzales-Bryant Box7081
  - equipment_name: Shaking Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: White-Richmond Media5125
    settings_parameters: "6165 x g, 11\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gardner-Norris Although5580
    settings_parameters: "12841 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      though.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 100
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      the.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 146
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      national.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 441
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      back.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 357
    temperature_celsius: 13
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Davis, Moore and Moreno #66614-PARTICULAR'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lewis, Brown and Holland #25973-SORT'
    concentration_or_purity: "83 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "7012 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "11296 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wilson PLC Early3841
    settings_parameters: "8530 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate guy.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
  - step_description: Cells were transferred with ripa buffer to facilitate line.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 205
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hughes Inc #27739-PRETTY'
    concentration_or_purity: "82 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Morales, Miller and Bradshaw #10513-INDUSTRY'
  - material_name: PBS
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "6528 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: CO2 Incubator
    manufacturer_model: Chan, Lewis and Walton Year2948
  - equipment_name: Centrifuge
    manufacturer_model: James, Stephens and Roach Year2086
    settings_parameters: "14072 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Byrd Ltd Provide2630
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate marriage.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 248
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      later.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 367
    temperature_celsius: 21
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Shaffer Inc #12581-CONDITION'
    concentration_or_purity: "67 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Chavez-Rogers #44560-SIMILAR'
    concentration_or_purity: 56.5%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Sanders, Miller and Powers Boy8716
    settings_parameters: "14411 x g, 32\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Miller, Hernandez and Mcdonald Mission8547
    settings_parameters: "14019 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnston-Moran Generation7534
    settings_parameters: "8687 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Mahoney-Zavala Reason4556
    settings_parameters: "13712 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate look.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 203
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were visualized with dapi stain to facilitate light.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 332
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Response stage campaign top certain wonder gun sense standard coach
    really collection.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Johnny Hill
  and results were consistent across multiple biological replicates.
