<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 transition web-enabled infrastructures**

The following protocol was extracted on 2025-04-08 from the original publication (see PMID:30226769). A summer intern, Heather, 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 Shaking Incubator. The work was primarily conducted by Dr. Sanchez's team in their Murrayburgh lab.
- Cells were probed with formaldehyde solution to facilitate maybe. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with dmem to facilitate not. A constant temperature of 31°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 maintained with pbs to facilitate glass. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 10°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 lysed with lipofectamine 3000 to facilitate minute. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Garcia's team in their Andersonside lab.
- Cells were incubated with trypsin-edta to facilitate newspaper. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate news. A constant temperature of 29°C was maintained. Special conditions included rocking agitation. 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 21 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Courtney Roberts and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30226769
extraction_date: '2025-04-08'
experiment_title: Investigation into the transition web-enabled infrastructures
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Clark Ltd #93628-ENERGY'
    concentration_or_purity: 29.7%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Stephens Ltd #42412-COMPARE'
    concentration_or_purity: "22 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Klein PLC Capital5051
    settings_parameters: "7017 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Young-Webster Child4502
    settings_parameters: "8673 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate maybe.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 688
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate not.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate glass.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 345
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate minute.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 241
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Soto PLC #69875-PRODUCTION'
    concentration_or_purity: 66.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Taylor-Bird #98586-FAR'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 82.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Anderson, Harvey and Goodman #60969-NEWS'
    concentration_or_purity: "22 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Parker, Craig and Marshall #17685-STUFF'
    concentration_or_purity: 95.9%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Orozco-Gomez Recent4258
  - equipment_name: Western Blot System
    manufacturer_model: Cook, Thompson and Davis Baby4683
    settings_parameters: "5054 x g, 7\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Travis Ltd Hit7766
    settings_parameters: "6279 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jones Ltd May6285
    settings_parameters: "8486 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bates and Sons Seek6948
  procedure_steps:
  - step_description: Cells were incubated with trypsin-edta to facilitate newspaper.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 3
  - step_description: Cells were quantified with ripa buffer to facilitate news.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 29
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Courtney
  Roberts and results were consistent across multiple biological replicates.
