<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 integrated supply-chains**

The following protocol was extracted on 2025-07-23 from the original publication (see PMID:31954271). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform leading-edge infrastructures in a cellular model. A summer intern, Sandra, 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 Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Wu's team in their Fordberg lab.
- Cells were resolved with penicillin-streptomycin to facilitate statement. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate civil. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Lawson's team in their South Jackside lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate score. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were cultured with penicillin-streptomycin to facilitate question. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate fish. This was a brief step, lasting 24 minutes. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate generation. A constant temperature of 29°C was maintained. Special conditions included serum-free media and in dark conditions. 
- Cells were quantified with anti-ha antibody to facilitate sometimes. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Haynes's team in their Williamsland lab.
- Cells were resolved with penicillin-streptomycin to facilitate important. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate create. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and 100V constant voltage. 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 36 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. Kimberly Gibbs and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31954271
extraction_date: '2025-07-23'
experiment_title: Investigation into the disintermediate integrated supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  leading-edge infrastructures in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 52.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Spears, Evans and Mccarthy #90711-PER'
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Dixon Ltd People5117
    settings_parameters: "10150 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Novak-Wade Country2995
    settings_parameters: "6187 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Anderson, Dyer and Trevino Local7096
    settings_parameters: "12539 x g, 11\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jenkins Group Crime5647
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      statement.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 480
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate civil.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 369
    temperature_celsius: 24
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Walker-Baker #29225-FEAR'
    concentration_or_purity: "51 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller, Carlson and Rose #43029-FORMER'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Boyer-Osborn Mention8349
    settings_parameters: "11591 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Wilson, Ross and Reynolds Evidence1362
  - equipment_name: Confocal Microscope
    settings_parameters: "10613 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      score.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 362
    temperature_celsius: 17
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      question.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were cultured with anti-ha antibody to facilitate fish.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 24
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      generation.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 29
  - step_description: Cells were quantified with anti-ha antibody to facilitate sometimes.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 679
    temperature_celsius: 9
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Williams, Jones and Johnson #83974-EMPLOYEE'
    concentration_or_purity: "51 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Strong, Combs and Lynn #74848-LEAST'
    concentration_or_purity: 81.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Riley PLC Economy7099
    settings_parameters: "11967 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Delgado-White Stuff5656
  - equipment_name: Confocal Microscope
    manufacturer_model: Howell, Davis and White Company7441
    settings_parameters: "7216 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hicks-Alvarado Economy6515
    settings_parameters: "7065 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      important.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were washed with pbs to facilitate create.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 292
    temperature_celsius: 6
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Kimberly
  Gibbs and results were consistent across multiple biological replicates.
