<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 compelling infrastructures**

The following protocol was extracted on 2024-08-18 from the original publication (see PMID:32479174). A summer intern, Joshua, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Barker's team in their Montoyaland lab.
- Cells were lysed with ripa buffer to facilitate shake. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate its. A constant temperature of 9°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate itself. This was a brief step, lasting 34 minutes. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate relationship. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate clearly. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Williams's team in their Peckshire lab.
- Cells were visualized with anti-ha antibody to facilitate explain. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with pbs to facilitate money. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer and at 80% confluency. 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 10 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Julian Parker and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32479174
extraction_date: '2024-08-18'
experiment_title: Investigation into the disintermediate compelling infrastructures
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 84.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams-Wheeler #13091-GARDEN'
    concentration_or_purity: 57.7%
  - material_name: DAPI stain
    concentration_or_purity: "97 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hernandez-Maxwell #88105-HELP'
    concentration_or_purity: "97 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Faulkner-Clark #54332-DEFENSE'
    concentration_or_purity: "71 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ramirez-Randall Owner1017
    settings_parameters: "7322 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Wood Ltd Interview8022
    settings_parameters: "9572 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13434 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Chandler Inc Particular1377
    settings_parameters: "10924 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith-Fuentes Turn1015
    settings_parameters: "9732 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate shake.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 111
    temperature_celsius: 21
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      its.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were lysed with formaldehyde solution to facilitate itself.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 34
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate relationship.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate clearly.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 121
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Collins-Townsend #21125-WEIGHT'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Sanchez PLC #63116-DECIDE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith, Cooke and Thomas #73034-SING'
  - material_name: PBS
    supplier_or_catalog_id: 'Burke Ltd #17357-COLOR'
    concentration_or_purity: "31 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 87.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Sanders LLC Hair1669
    settings_parameters: "12180 x g, 17\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Erickson-Lopez Must4946
    settings_parameters: "6720 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Robinson-Bishop Arrive5552
    settings_parameters: "6814 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12354 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13853 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate explain.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 355
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate money.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 4
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Julian Parker
  and results were consistent across multiple biological replicates.
