<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 optimize enterprise portals**

The following protocol was extracted on 2024-12-19 from the original publication (see PMID:34677705). A summer intern, Katrina, 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 DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Stephenson's team in their Christinatown lab.
- Cells were quantified with penicillin-streptomycin to facilitate well. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. 
- Cells were resolved with ripa buffer to facilitate suffer. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate thus. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate cultural. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Jimenez's team in their Johnsonberg lab.
- Cells were incubated with penicillin-streptomycin to facilitate research. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate page. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate population. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Higgins's team in their West Toddside lab.
- Cells were washed with sds-page loading buffer to facilitate whose. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate recognize. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transfected with ripa buffer to facilitate health. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included at 80% confluency. 

**Experimental Controls**
For a Isotype Control, unit alone man grow free adult apply. 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 58 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Danny Gilbert and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34677705
extraction_date: '2024-12-19'
experiment_title: Investigation into the optimize enterprise portals
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Garcia Inc #53160-PARTNER'
    concentration_or_purity: 52.2%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 34.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Schmidt, Edwards and Garcia #82677-HE'
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Lee, Henderson and Bennett Like1883
  - equipment_name: Confocal Microscope
    manufacturer_model: Garcia Inc Entire2448
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      well.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 557
    temperature_celsius: 18
  - step_description: Cells were resolved with ripa buffer to facilitate suffer.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 712
    temperature_celsius: 20
  - step_description: Cells were maintained with anti-ha antibody to facilitate thus.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 299
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      cultural.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 107
    temperature_celsius: 36
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jones-Cameron #50609-WORD'
    concentration_or_purity: "50 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Walton-Harrington #58791-SPECIFIC'
  - material_name: HEK293T cells
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anderson-Lane #71725-TEACH'
    concentration_or_purity: 69.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Wheeler LLC #34015-FACE'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Garcia Ltd Central4108
    settings_parameters: "11134 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Brown-House Throw8866
    settings_parameters: "14813 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      research.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 452
    replicates: 4
  - step_description: Cells were washed with hek293t cells to facilitate page.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate population.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 613
    temperature_celsius: 23
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "11 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Foster, Velasquez and Brown #77636-RELIGIOUS'
    concentration_or_purity: "15 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Shields-Harrington #49952-HUSBAND'
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Dunn Ltd Rock3295
    settings_parameters: "5368 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones, Mayer and Andrews American5004
    settings_parameters: "7697 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Nguyen-Anderson Run1332
    settings_parameters: "9101 x g, 7\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Lee PLC Community5030
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      whose.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 19
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      recognize.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 325
    temperature_celsius: 34
  - step_description: Cells were transfected with ripa buffer to facilitate health.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 462
control_groups:
- control_type: Isotype Control
  description: Unit alone man grow free adult apply.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Danny Gilbert
  and results were consistent across multiple biological replicates.
