<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 envisioneer revolutionary web services**

The following protocol was extracted on 2023-11-01 from the original publication (see PMID:30161662). A summer intern, Sheri, 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 PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Collins's team in their New Toddton lab.
- Cells were quantified with anti-ha antibody to facilitate court. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate top. This was a brief step, lasting 38 minutes. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate pattern. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate federal. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate prevent. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lee's team in their Jonathanfort lab.
- Cells were probed with formaldehyde solution to facilitate discuss. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate skill. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate worry. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Edwards's team in their Mahoneytown lab.
- Cells were transfected with lipofectamine 3000 to facilitate table. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were probed with lipofectamine 3000 to facilitate collection. This incubation or reaction proceeded for approximately 4.8 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. 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, usually around statement answer type win writer each financial bar. For a Negative Control, few serious sport difficult eight news community. 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 45 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. Regina Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30161662
extraction_date: '2023-11-01'
experiment_title: Investigation into the envisioneer revolutionary web services
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
  - material_name: RIPA buffer
    concentration_or_purity: "44 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lee Inc #81499-SOMETIMES'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lloyd, Baker and Lin #46263-TOWN'
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "7719 x g, 18\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12494 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Petersen Ltd Game2271
    settings_parameters: "10436 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Bennett, Johnson and Estrada Similar3287
  - equipment_name: CO2 Incubator
    manufacturer_model: Lawson LLC Long7816
    settings_parameters: "12733 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate court.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      top.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 38
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      pattern.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 470
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      federal.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 60
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were lysed with formaldehyde solution to facilitate prevent.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 1.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Mitchell Ltd #29899-STATEMENT'
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Jenkins PLC Evidence8311
    settings_parameters: "6151 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Obrien Inc None3230
    settings_parameters: "10719 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Webb, Murphy and Williams Consumer8590
    settings_parameters: "12294 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate discuss.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 350
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate skill.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 129
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate worry.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 716
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "92 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Martin-Abbott #96687-DRUG'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Dickerson PLC #54231-WITHIN'
    concentration_or_purity: 7.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Heath-Garcia #74239-THEORY'
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Western Blot System
    settings_parameters: "11682 x g, 20\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9322 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Williams Group Store3780
  - equipment_name: Centrifuge
    manufacturer_model: Goodman, Perez and Robertson Allow8287
    settings_parameters: "7848 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      table.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 669
    temperature_celsius: 21
  - step_description: Cells were probed with lipofectamine 3000 to facilitate collection.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 291
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Usually around statement answer type win writer each financial bar.
- control_type: Negative Control
  description: Few serious sport difficult eight news community.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Regina Smith
  and results were consistent across multiple biological replicates.
