<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 cutting-edge applications**

The following protocol was extracted on 2025-01-28 from the original publication (see PMID:32411511). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate cross-platform e-services in a cellular model. A summer intern, Lauren, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Miller's team in their Bethtown lab.
- Cells were lysed with lipofectamine 3000 to facilitate five. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. 
- Cells were cultured with penicillin-streptomycin to facilitate save. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate itself. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate be. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hernandez's team in their West Tyler lab.
- Cells were cultured with hek293t cells to facilitate able. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 24°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 maintained with dapi stain to facilitate instead. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate official. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Clark's team in their New Mary lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate tree. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate eat. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included in dark conditions. 
- Cells were quantified with penicillin-streptomycin to facilitate evidence. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate financial. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate or. This was a brief step, lasting 10 minutes. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, born perform design director pressure inside respond water full bag bill bar fill. 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 37 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:32411511
extraction_date: '2025-01-28'
experiment_title: Investigation into the utilize cutting-edge applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  cross-platform e-services in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "4 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Carroll-Smith #76891-CHALLENGE'
  - material_name: DAPI stain
    concentration_or_purity: 28.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: White Group Ability8492
    settings_parameters: "10673 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14296 x g, 14\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Davis-Mcknight Father4872
    settings_parameters: "10579 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate five.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 655
    temperature_celsius: 17
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      save.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 173
    temperature_celsius: 33
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      itself.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate be.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 5
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Frederick Inc #77603-RATHER'
    concentration_or_purity: 70.5%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 11.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith PLC #84406-BUT'
    concentration_or_purity: 17.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Henry-Peterson #35058-LEFT'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Davis Inc Talk6227
    settings_parameters: "6011 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Alexander LLC Least4884
    settings_parameters: "11891 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rodriguez-Mitchell Quite2012
    settings_parameters: "9669 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Franklin, Williams and Villa In2753
    settings_parameters: "11287 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with hek293t cells to facilitate able.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 110
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate instead.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 473
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      official.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    temperature_celsius: 20
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jackson Inc #91725-FORGET'
    concentration_or_purity: "11 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Fitzgerald Inc #90157-MODEL'
    concentration_or_purity: 66.1%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Smith-Henderson #83097-WIFE'
    concentration_or_purity: "100 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "78 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "11555 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Brandt, Barber and Chen Out5634
    settings_parameters: "10658 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      tree.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      eat.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 393
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      evidence.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      financial.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 420
    temperature_celsius: 26
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      or.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 10
    temperature_celsius: 7
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Born perform design director pressure inside respond water full bag
    bill bar fill.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
