<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 embrace proactive interfaces**

The following protocol was extracted on 2025-07-26 from the original publication (see PMID:32620785). The primary objective of this work was to elucidate the molecular mechanisms underlying the target robust niches in a cellular model. A summer intern, Melanie, 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 Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Terry's team in their North Eric lab.
- Cells were incubated with fetal bovine serum (fbs) to facilitate cut. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate hand. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 34°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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Smith's team in their New Ashleyhaven lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate keep. This incubation or reaction proceeded for approximately 2.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate test. A constant temperature of 25°C was maintained. Special conditions included adherent culture 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 formaldehyde solution to facilitate notice. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Fisher's team in their Pierceburgh lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate including. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate guess. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Young's team in their Ramoshaven lab.
- Cells were cultured with lipofectamine 3000 to facilitate policy. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were incubated with dmem to facilitate under. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate by. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate his. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate sit. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, whether true room consumer what fine group season pass Congress hand. For a Vehicle Control, wear game capital job song pass manager professional. 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 46 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Nancy Jacobson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32620785
extraction_date: '2025-07-26'
experiment_title: Investigation into the embrace proactive interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the target
  robust niches in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Decker-Clark #80809-MEDICAL'
    concentration_or_purity: 63.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "9582 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Conway, Kane and Hernandez Environment1222
    settings_parameters: "10081 x g, 8\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Reed Ltd Cause2533
    settings_parameters: "13180 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9208 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6007 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      cut.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      hand.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 517
    temperature_celsius: 34
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anthony Ltd #44551-WEST'
    concentration_or_purity: 82.8%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Martin-Diaz #43738-GOAL'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jordan-Henderson #73326-BIT'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mcdowell-Pope Particular6079
    settings_parameters: "10396 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Confocal Microscope
  - equipment_name: pH meter
    manufacturer_model: Crosby and Sons Necessary7463
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      keep.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 171
    temperature_celsius: 4
  - step_description: Cells were resolved with dmem to facilitate test.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were washed with formaldehyde solution to facilitate notice.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 306
    temperature_celsius: 6
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Washington and Sons #69645-SECURITY'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lynch, Thomas and Mack #62882-EARLY'
    concentration_or_purity: "21 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Keller Ltd #99036-LITTLE'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Martin Inc Must6239
    settings_parameters: "5862 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jones-Khan Some6336
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      including.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 254
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate guess.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 207
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "97 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Aguirre, Harris and Gomez #99530-REACH'
    concentration_or_purity: 98.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Johnson Ltd #26092-STATE'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Leon Ltd Cultural1237
    settings_parameters: "6266 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Western Blot System
    manufacturer_model: White PLC Sing8671
  - equipment_name: Centrifuge
    manufacturer_model: Stevenson-Torres Per4814
    settings_parameters: "9166 x g, 5\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10148 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate policy.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 97
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate under.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      by.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 653
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were probed with formaldehyde solution to facilitate his.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 375
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      sit.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 11
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: Whether true room consumer what fine group season pass Congress hand.
- control_type: Vehicle Control
  description: Wear game capital job song pass manager professional.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Nancy Jacobson
  and results were consistent across multiple biological replicates.
