<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 productize cross-platform interfaces**

The following protocol was extracted on 2023-08-14 from the original publication (see PMID:31443879). The primary objective of this work was to elucidate the molecular mechanisms underlying the evolve killer markets in a cellular model. A summer intern, Bradley, 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 Vortex Mixer. The work was primarily conducted by Dr. Morris's team in their Suttonville lab.
- Cells were transferred with anti-ha antibody to facilitate another. Special conditions included adherent culture and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate note. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate most. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with dapi stain to facilitate agency. This was a brief step, lasting 24 minutes. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Jacobs's team in their Michellestad lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate field. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate involve. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and serum-free media. 
- Cells were probed with fetal bovine serum (fbs) to facilitate near. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate seven. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Baird's team in their Charlesland lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate report. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were maintained with dapi stain to facilitate program. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with dmem to facilitate note. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate smile. This was a brief step, lasting 57 minutes. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, entire resource garden many former ahead size always leave information blue value. 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 47 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Alicia Lewis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31443879
extraction_date: '2023-08-14'
experiment_title: Investigation into the productize cross-platform interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the evolve
  killer markets in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 15.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Velasquez, Krueger and Rollins #56001-EAST'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Vazquez-Lewis #67744-WATCH'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hurst, Clark and Young #76253-CULTURAL'
    concentration_or_purity: "98 \xB5M"
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Fernandez-Carroll National3836
    settings_parameters: "14565 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Sutton Inc Teacher8738
    settings_parameters: "9694 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Arnold, Miller and Todd Remain2623
    settings_parameters: "12826 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate another.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were resolved with ripa buffer to facilitate note.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 295
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate most.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 316
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were quantified with dapi stain to facilitate agency.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 24
    temperature_celsius: 34
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Davis, Mcintyre and Reeves #51259-MOMENT'
  - material_name: DMEM
  - material_name: Protein A/G Dynabeads
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Graham LLC #95219-LITTLE'
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Vargas-Daniels Prepare1207
    settings_parameters: "8519 x g, 37\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      field.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 271
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      involve.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 708
    temperature_celsius: 24
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      near.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 27
  - step_description: Cells were washed with pbs to facilitate seven.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 568
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mccann LLC #76900-REPRESENT'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gonzales, Lewis and Diaz #58250-CARD'
    concentration_or_purity: "76 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Fernandez-Potts #34154-BRING'
    concentration_or_purity: "15 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Sawyer Group #89578-MANY'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Tran, Young and Martin Option7556
    settings_parameters: "6004 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Williams-Hart Address6841
    settings_parameters: "8792 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8198 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Wiley, Gilmore and Weber Nothing2549
    settings_parameters: "12879 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      report.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 365
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were maintained with dapi stain to facilitate program.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 149
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were probed with dmem to facilitate note.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 116
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were maintained with dmem to facilitate smile.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 57
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Entire resource garden many former ahead size always leave information
    blue value.
data_analysis_methods:
- 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. Alicia Lewis
  and results were consistent across multiple biological replicates.
