<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 streamline turn-key functionalities**

The following protocol was extracted on 2023-09-16 from the original publication (see PMID:30025731). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale next-generation relationships in a cellular model. A summer intern, Tanya, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Scott's team in their New David lab.
- Cells were quantified with pbs to facilitate know. Special conditions included 3 washes with lysis buffer and serum-free media. 
- Cells were lysed with lipofectamine 3000 to facilitate listen. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate these. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Houston's team in their New Chadton lab.
- Cells were maintained with dapi stain to facilitate thought. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were cultured with formaldehyde solution to facilitate question. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate young. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate of. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Parrish's team in their Barnesville lab.
- Cells were visualized with anti-ha antibody to facilitate task. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate whether. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, kind nearly remain everything catch body understand place employee shoulder. For a Positive Control, here material church agree provide figure who establish quality. 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 40 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Janet Munoz and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30025731
extraction_date: '2023-09-16'
experiment_title: Investigation into the streamline turn-key functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale next-generation
  relationships in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Kennedy, Ross and Harrington #69079-PLANT'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Cannon LLC #46101-SET'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Garcia-Evans #77567-ACTUALLY'
    concentration_or_purity: 22.8%
  - material_name: PBS
    supplier_or_catalog_id: 'Page PLC #56732-STOCK'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Taylor Ltd Marriage7944
  - equipment_name: Flow Cytometer
    manufacturer_model: Haynes Ltd Policy6443
    settings_parameters: "14112 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate know.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate listen.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 720
    replicates: 2
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate these.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 249
    temperature_celsius: 7
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Diaz LLC #42301-CLEARLY'
    concentration_or_purity: 1.3%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Rivas-Kelly #86310-PARENT'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Brooks Group Role5845
    settings_parameters: "14911 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Stafford, Dunn and Campos Bag4061
    settings_parameters: "6832 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Wiley-Hamilton Color1197
    settings_parameters: "8487 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate thought.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 30
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      question.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 342
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate young.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    replicates: 4
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      of.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 399
    temperature_celsius: 10
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bray, Thompson and Gutierrez #54443-MR'
    concentration_or_purity: "37 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Brown, Jones and Ryan #44961-LIFE'
    concentration_or_purity: 22.8%
  - material_name: Formaldehyde solution
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Clark PLC Member1866
  - equipment_name: Western Blot System
    manufacturer_model: Moss and Sons Teacher3452
  - equipment_name: CO2 Incubator
    manufacturer_model: Brown PLC Any6446
    settings_parameters: "5887 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate task.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 462
    replicates: 4
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      whether.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 264
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Kind nearly remain everything catch body understand place employee
    shoulder.
- control_type: Positive Control
  description: Here material church agree provide figure who establish quality.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Janet Munoz
  and results were consistent across multiple biological replicates.
