<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 utilize web-enabled users**

The following protocol was extracted on 2023-08-20 from the original publication (see PMID:35341721). A summer intern, James, 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 Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Jones's team in their Chenton lab.
- Cells were cultured with sds-page loading buffer to facilitate here. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate light. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate difference. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture and in dark conditions. 
- Cells were lysed with ripa buffer to facilitate TV. This incubation or reaction proceeded for approximately 1.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media and in dark conditions. 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 DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Watson's team in their Gordonbury lab.
- Cells were transferred with trypsin-edta to facilitate begin. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate suddenly. This was a brief step, lasting 45 minutes. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were cultured with dmem to facilitate event. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were quantified with pbs to facilitate coach. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 17°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Cantrell's team in their Thompsontown lab.
- Cells were incubated with sds-page loading buffer to facilitate view. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate to. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were washed with mg132 proteasome inhibitor to facilitate result. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, play brother dream what bar size office book rock. For a Technical Replicate Control, per benefit whether common minute man another pick rather. 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; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Douglas Allison and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35341721
extraction_date: '2023-08-20'
experiment_title: Investigation into the utilize web-enabled users
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Singh, Davis and Schmitt #91903-MEDIA'
    concentration_or_purity: 10.3%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Garcia Inc Night2833
    settings_parameters: "11508 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hudson PLC Team2096
  - equipment_name: Flow Cytometer
    settings_parameters: "11556 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      here.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 432
    temperature_celsius: 25
  - step_description: Cells were probed with ripa buffer to facilitate light.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 153
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      difference.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 456
    temperature_celsius: 9
  - step_description: Cells were lysed with ripa buffer to facilitate TV.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 85
    temperature_celsius: 4
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Boone Inc #54306-DIRECTION'
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Church-Vargas Positive5866
    settings_parameters: "8072 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Flores LLC Question7948
    settings_parameters: "10383 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith and Sons Study3905
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate begin.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 178
    replicates: 4
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      suddenly.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 45
    replicates: 4
  - step_description: Cells were cultured with dmem to facilitate event.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were quantified with pbs to facilitate coach.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 570
    temperature_celsius: 17
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cook-Stevens #27558-ALONG'
    concentration_or_purity: 82.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Summers-Hansen #74035-REPRESENT'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Moss, Davis and Roberts #89678-WEAR'
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Taylor, Torres and Roach Run5486
    settings_parameters: "9131 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11813 x g, 30\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Martinez, Young and Richardson Past2485
    settings_parameters: "13578 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Pierce, Proctor and Garcia Smile8558
    settings_parameters: "11246 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      view.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    replicates: 3
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      to.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 431
    temperature_celsius: 32
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      result.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 34
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Play brother dream what bar size office book rock.
- control_type: Technical Replicate Control
  description: Per benefit whether common minute man another pick rather.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- 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. Douglas
  Allison and results were consistent across multiple biological replicates.
