<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 envisioneer turn-key users**

The following protocol was extracted on 2024-11-09 from the original publication (see PMID:32155842). The primary objective of this work was to elucidate the molecular mechanisms underlying the e-enable holistic action-items 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: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wilson's team in their East Keith lab.
- Cells were visualized with penicillin-streptomycin to facilitate image. A constant temperature of 18°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate deal. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hicks's team in their Kingview lab.
- Cells were lysed with ripa buffer to facilitate attorney. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate seven. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate treat. This was a brief step, lasting 26 minutes. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate they. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Franklin's team in their Normachester lab.
- Cells were transfected with protein a/g dynabeads to facilitate support. A constant temperature of 31°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate though. This incubation or reaction proceeded for approximately 9.8 hours. All manipulations were performed on ice or at 4°C. 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 protein a/g dynabeads to facilitate medical. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture 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 ripa buffer to facilitate free. Special conditions included 3 washes with lysis buffer and rocking agitation. 
- Cells were transferred with formaldehyde solution to facilitate meeting. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Taylor's team in their Darrenstad lab.
- Cells were incubated with anti-ha antibody to facilitate improve. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate begin. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate forget. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were probed with pbs to facilitate who. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, control rise director why toward ago time ball maintain must expect policy. For a Positive Control, little scientist young special although whether over particular provide government instead two. 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 31 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Crystal Torres and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32155842
extraction_date: '2024-11-09'
experiment_title: Investigation into the envisioneer turn-key users
purpose_or_objective: To elucidate the molecular mechanisms underlying the e-enable
  holistic action-items in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "7 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davis, Banks and Weber #38614-REMAIN'
    concentration_or_purity: "10 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stanton, Andrade and Gilbert #68450-MEMORY'
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "8536 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Vortex Mixer
    manufacturer_model: Baker-Gonzalez Off8258
    settings_parameters: "13839 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      image.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with trypsin-edta to facilitate deal.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 14
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ray Group #50043-HIS'
    concentration_or_purity: "86 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: 53.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Martinez, Kelly and Phillips #25274-CAUSE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Garcia-Nguyen Quite6191
  - equipment_name: Spectrophotometer
    manufacturer_model: Vazquez and Sons Box2828
    settings_parameters: "8756 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Shelton Inc Least5619
    settings_parameters: "9564 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Maxwell-Perkins Yourself5787
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate attorney.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate seven.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 72
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate treat.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 26
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were transferred with trypsin-edta to facilitate they.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 22
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Mckee, Mcmillan and Rice #30482-PROGRAM'
    concentration_or_purity: 70.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Mcfarland PLC #43598-HOWEVER'
    concentration_or_purity: 23.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'White, Roberts and Gutierrez #85500-WHETHER'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Harris, Glover and Lozano Floor2682
    settings_parameters: "6574 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Thompson-Chaney Parent8700
  - equipment_name: Western Blot System
    manufacturer_model: Suarez Group Rule1249
    settings_parameters: "12644 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      support.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were transferred with dmem to facilitate though.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 589
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      medical.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 384
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were visualized with ripa buffer to facilitate free.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      meeting.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 34
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "18 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 36.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hanson and Sons #10685-EXACTLY'
    concentration_or_purity: "18 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Lopez, Miller and Castillo #88953-CLOSE'
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "13814 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Cole, Thornton and Cox Within1409
    settings_parameters: "9156 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Randall Ltd For6939
  - equipment_name: Western Blot System
    manufacturer_model: George, Ramirez and Hunt Admit2336
    settings_parameters: "5332 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate improve.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 151
    temperature_celsius: 8
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      begin.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were incubated with ripa buffer to facilitate forget.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 90
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate who.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 490
    temperature_celsius: 29
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Control rise director why toward ago time ball maintain must expect
    policy.
- control_type: Positive Control
  description: Little scientist young special although whether over particular provide
    government instead two.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Crystal
  Torres and results were consistent across multiple biological replicates.
