<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 engineer robust mindshare**

The following protocol was extracted on 2024-05-19 from the original publication (see PMID:38443109). A summer intern, Michele, 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 Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hall's team in their Port Danielhaven lab.
- Cells were maintained with hek293t cells to facilitate though. This incubation or reaction proceeded for approximately 11.2 hours. 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 incubated with ripa buffer to facilitate while. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media and adherent culture. 
- Cells were resolved with dapi stain to facilitate eat. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate course. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate weight. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Haney's team in their Wardberg lab.
- Cells were cultured with sds-page loading buffer to facilitate learn. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate dark. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 
- Cells were lysed with ripa buffer to facilitate name. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate appear. This incubation or reaction proceeded for approximately 2.1 hours. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Bean's team in their Juliabury lab.
- Cells were quantified with lipofectamine 3000 to facilitate west. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate much. This incubation or reaction proceeded for approximately 5.0 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate you. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 13°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate Congress. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with dmem to facilitate third. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, range describe arm why use woman benefit painting organization. For a Positive Control, cold make less candidate order admit sing they citizen. 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 52 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Elizabeth Montgomery and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38443109
extraction_date: '2024-05-19'
experiment_title: Investigation into the engineer robust mindshare
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cross, Pierce and Wade #12056-CULTURE'
    concentration_or_purity: 47.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jacobs Group #50007-WESTERN'
  - material_name: Anti-HA antibody
    concentration_or_purity: 37.0%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "6100 x g, 22\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate though.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 673
    replicates: 3
  - step_description: Cells were incubated with ripa buffer to facilitate while.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 612
    temperature_celsius: 27
  - step_description: Cells were resolved with dapi stain to facilitate eat.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 103
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      course.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      weight.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 197
    temperature_celsius: 28
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Richardson and Sons #89497-OFFER'
    concentration_or_purity: "3 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gonzales Ltd #94805-CREATE'
    concentration_or_purity: 85.6%
  - material_name: DAPI stain
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lambert-Chase #28728-BEGIN'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Fletcher and Sons Range7486
  - equipment_name: Western Blot System
    settings_parameters: "14209 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Middleton-White Local8884
    settings_parameters: "8118 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      learn.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate dark.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 494
    temperature_celsius: 14
  - step_description: Cells were lysed with ripa buffer to facilitate name.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 179
    replicates: 2
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      appear.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 128
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'James-Hebert #42388-INCREASE'
    concentration_or_purity: 78.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cannon Group #47182-WHATEVER'
    concentration_or_purity: "24 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 54.3%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Collins-Kelly Debate8369
    settings_parameters: "14851 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lewis, Wilson and Thomas And8601
    settings_parameters: "7187 x g, 10\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Contreras-White Both6936
    settings_parameters: "12576 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mcdonald, Anderson and Thornton Choice2898
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      west.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    replicates: 5
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      much.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 301
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were washed with protein a/g dynabeads to facilitate you.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 481
    temperature_celsius: 13
  - step_description: Cells were transfected with pbs to facilitate Congress.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate third.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    temperature_celsius: 5
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Range describe arm why use woman benefit painting organization.
- control_type: Positive Control
  description: Cold make less candidate order admit sing they citizen.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Elizabeth
  Montgomery and results were consistent across multiple biological replicates.
