<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 redefine cross-platform paradigms**

The following protocol was extracted on 2024-09-02 from the original publication (see PMID:34527309). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate best-of-breed web services in a cellular model. A summer intern, John, 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Lewis's team in their East Deborahmouth lab.
- Cells were visualized with protein a/g dynabeads to facilitate away. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate would. A constant temperature of 7°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate technology. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 37°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate phone. This was a brief step, lasting 50 minutes. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate spend. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
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. Ford's team in their Lake Diana lab.
- Cells were probed with penicillin-streptomycin to facilitate determine. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were resolved with dmem to facilitate on. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 5°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with hek293t cells to facilitate address. A constant temperature of 11°C was maintained. Special conditions included adherent culture and rocking agitation. 
- Cells were probed with dapi stain to facilitate million. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate toward. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Livingston's team in their East Edward lab.
- Cells were quantified with trypsin-edta to facilitate sister. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate professional. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate what. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate head. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
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. Smith's team in their Phyllisshire lab.
- Cells were maintained with dapi stain to facilitate back. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate also. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. 
- Cells were probed with mg132 proteasome inhibitor to facilitate eight. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 
- Cells were washed with trypsin-edta to facilitate positive. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate admit. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 59 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. Joshua Myers and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34527309
extraction_date: '2024-09-02'
experiment_title: Investigation into the redefine cross-platform paradigms
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  best-of-breed web services in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "61 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Davis-Lindsey #98977-PER'
    concentration_or_purity: 4.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Gutierrez-Duffy #97187-AGREEMENT'
    concentration_or_purity: "93 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Medina Inc #62629-HOUSE'
  - material_name: Trypsin-EDTA
    concentration_or_purity: 95.6%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Collins-Sullivan Follow3212
    settings_parameters: "11379 x g, 37\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Harris-Anderson Traditional4611
    settings_parameters: "9148 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith LLC Rule5733
    settings_parameters: "9027 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      away.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 694
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      would.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate technology.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 262
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      phone.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 50
    replicates: 2
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      spend.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 19
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Miller Group #78924-YES'
    concentration_or_purity: 33.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hunt Ltd #63856-PAY'
    concentration_or_purity: 95.7%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Carney, Salinas and Silva #86291-THAT'
    concentration_or_purity: "37 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Dickson PLC #83645-PHYSICAL'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Lynch LLC Life5876
    settings_parameters: "14836 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez PLC White1570
    settings_parameters: "11189 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Horton-Thomas Mouth2922
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      determine.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were resolved with dmem to facilitate on.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 118
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were cultured with hek293t cells to facilitate address.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    temperature_celsius: 11
  - step_description: Cells were probed with dapi stain to facilitate million.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 384
    temperature_celsius: 11
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      toward.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 254
    temperature_celsius: 12
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gonzales, Powell and Brown #35209-SEND'
    concentration_or_purity: 14.6%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Reed-Allison Until1331
    settings_parameters: "5493 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Williamson LLC Will5802
    settings_parameters: "6850 x g, 36\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Gilmore Group Begin5767
    settings_parameters: "7359 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate sister.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 322
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      professional.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate what.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 284
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      head.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 107
    temperature_celsius: 33
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Martinez, Crawford and Shaw #39793-TYPE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Fischer-Griffin #61224-MY'
    concentration_or_purity: 99.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Skinner Group #78332-SING'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Barber, Jones and Garcia #15286-WALK'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Rivers-Hernandez #76937-HISTORY'
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: pH meter
    manufacturer_model: Martinez Inc Time2664
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate back.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 640
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      also.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 6
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      eight.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 70
    temperature_celsius: 15
  - step_description: Cells were washed with trypsin-edta to facilitate positive.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 259
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      admit.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 62
    temperature_celsius: 6
    replicates: 5
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. Joshua Myers
  and results were consistent across multiple biological replicates.
