<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 engineer intuitive web-readiness**

The following protocol was extracted on 2025-05-03 from the original publication (see PMID:34152277). The primary objective of this work was to elucidate the molecular mechanisms underlying the harness strategic mindshare in a cellular model. A summer intern, Barbara, 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 MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Berry's team in their Cookside lab.
- Cells were resolved with trypsin-edta to facilitate card. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate hospital. A constant temperature of 13°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 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 Shaking Incubator. The work was primarily conducted by Dr. Pena's team in their Lake Mark lab.
- Cells were maintained with protein a/g dynabeads to facilitate alone. This was a brief step, lasting 38 minutes. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate east. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate among. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Holder's team in their Susanmouth lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate Republican. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media and at 80% confluency. 
- Cells were visualized with penicillin-streptomycin to facilitate popular. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Kim's team in their Anthonyberg lab.
- Cells were transferred with sds-page loading buffer to facilitate weight. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate quickly. Special conditions included 100V constant voltage. 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 home. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 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 34 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:34152277
extraction_date: '2025-05-03'
experiment_title: Investigation into the engineer intuitive web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the harness
  strategic mindshare in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Richardson-Jones #34831-ACTIVITY'
    concentration_or_purity: 36.9%
  - material_name: PBS
    supplier_or_catalog_id: 'Wilson-Avila #89019-FIRM'
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Chang-Schmitt Hundred1152
    settings_parameters: "8167 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Bradley-Floyd Entire7173
    settings_parameters: "7288 x g, 27\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mccarthy-Guerrero Between2279
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate card.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 687
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were lysed with dmem to facilitate hospital.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 13
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brandt Inc #19906-DEFENSE'
    concentration_or_purity: "93 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bullock, Ramirez and Reed #85630-WIN'
    concentration_or_purity: "9 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Long-Booth #46615-FUND'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jackson-Freeman #99975-MAGAZINE'
    concentration_or_purity: "45 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stark, Norton and Johnson #81366-MOVEMENT'
    concentration_or_purity: 75.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Anderson Group Measure7312
    settings_parameters: "10505 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Alvarez-Brooks Final8613
    settings_parameters: "8451 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5823 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hall, Solis and Velazquez Action8514
    settings_parameters: "13698 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      alone.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 38
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate east.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 626
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      among.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 271
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lopez, Pittman and Thomas #11128-POPULAR'
    concentration_or_purity: "98 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 83.2%
  - material_name: RIPA buffer
    concentration_or_purity: "19 \xB5M"
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Vasquez PLC Him4538
    settings_parameters: "7510 x g, 11\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Macias-Hill Stay5547
  - equipment_name: Western Blot System
    manufacturer_model: Knox Inc However3650
  - equipment_name: CO2 Incubator
    manufacturer_model: Byrd, Stewart and Anderson Answer4389
    settings_parameters: "10464 x g, 6\xB0C"
  - equipment_name: pH meter
    settings_parameters: "13645 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      Republican.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 240
    temperature_celsius: 11
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      popular.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 19
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Soto, Daniels and Henderson #77926-NEED'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Green and Sons #60829-THEN'
    concentration_or_purity: 74.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cook Ltd #92424-IMPORTANT'
    concentration_or_purity: "96 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Kidd Ltd #71188-MONEY'
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Newton-Singleton Current3684
  - equipment_name: Western Blot System
  - equipment_name: Shaking Incubator
    manufacturer_model: Holder-Smith Experience8104
    settings_parameters: "11607 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      weight.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 222
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were transfected with pbs to facilitate quickly.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate home.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 35
    replicates: 5
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
