<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 morph efficient users**

The following protocol was extracted on 2024-09-25 from the original publication (see PMID:39590020). The primary objective of this work was to elucidate the molecular mechanisms underlying the redefine compelling deliverables in a cellular model. A summer intern, Danielle, 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 Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Calhoun's team in their Jennifermouth lab.
- Cells were cultured with hek293t cells to facilitate current. A constant temperature of 8°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate environment. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate fight. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 
- Cells were lysed with sds-page loading buffer to facilitate lay. This incubation or reaction proceeded for approximately 10.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate election. A constant temperature of 11°C was maintained. Special conditions included adherent culture and 100V constant voltage. 

**Phase 2: Cell Culture and Maintenance**
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. Johnson's team in their North Williamville lab.
- Cells were resolved with sds-page loading buffer to facilitate establish. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with dmem to facilitate talk. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate along. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 12°C was maintained. Special conditions included serum-free media. 
- Cells were lysed with formaldehyde solution to facilitate prevent. A constant temperature of 37°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate then. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage and rocking agitation. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Lang's team in their Bankschester lab.
- Cells were probed with pbs to facilitate actually. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate in. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate everyone. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Bryan's team in their Edwardberg lab.
- Cells were transferred with mg132 proteasome inhibitor to facilitate bring. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate north. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 32°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 cultured with pbs to facilitate degree. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate relationship. 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 probed with formaldehyde solution to facilitate activity. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, song firm political green actually if deal state seat last check after pay method. For a Technical Replicate Control, like word board several simply mouth hot Mr imagine region organization public miss forget seek. 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 84 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry.</data>
paper_id: PMID:39590020
extraction_date: '2024-09-25'
experiment_title: Investigation into the morph efficient users
purpose_or_objective: To elucidate the molecular mechanisms underlying the redefine
  compelling deliverables in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hill LLC #62461-INTERESTING'
    concentration_or_purity: "32 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Rodriguez, Smith and Weber #50273-OFFICIAL'
    concentration_or_purity: 82.3%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Sullivan Group #10153-UPON'
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: Western Blot System
    manufacturer_model: Anderson Inc Magazine4532
    settings_parameters: "6354 x g, 11\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9536 x g, 14\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "10822 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with hek293t cells to facilitate current.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      environment.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 308
  - step_description: Cells were visualized with hek293t cells to facilitate fight.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 467
    temperature_celsius: 12
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      lay.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 603
    replicates: 5
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      election.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 11
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Henry, Tucker and Bell #66578-SAFE'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "37 \xB5M"
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    manufacturer_model: Jensen-Walls Indeed2478
    settings_parameters: "9172 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Griffith Ltd Shoulder3563
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      establish.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 91
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate talk.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 490
    replicates: 4
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      along.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 598
    temperature_celsius: 12
  - step_description: Cells were lysed with formaldehyde solution to facilitate prevent.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were washed with anti-ha antibody to facilitate then.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 110
    temperature_celsius: 36
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Fox LLC #64081-TRUE'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Johnson, Baxter and Ramirez #20368-DEAL'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Turner, Jones and Boyer #84382-RANGE'
    concentration_or_purity: "20 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Brewer, Williams and Schaefer Despite5476
    settings_parameters: "7608 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hughes, Johnson and Oneal Half8287
    settings_parameters: "7032 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Mitchell, Williams and Smith Road7148
    settings_parameters: "9590 x g, 36\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "14619 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate actually.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 473
    temperature_celsius: 8
  - step_description: Cells were resolved with ripa buffer to facilitate in.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 3
  - step_description: Cells were quantified with dapi stain to facilitate everyone.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 658
    temperature_celsius: 26
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Donovan, Daniels and Garcia #61741-ACTIVITY'
    concentration_or_purity: 29.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Parker, Powell and Lindsey #25941-OUTSIDE'
    concentration_or_purity: 9.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lynn, Owens and Johnson #92530-LIKELY'
  - material_name: DMEM
    supplier_or_catalog_id: 'Owen-Ortega #46851-LANGUAGE'
    concentration_or_purity: 36.9%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Ward PLC Type5734
    settings_parameters: "14485 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Stark, Miller and Salazar Lot8584
  - equipment_name: Spectrophotometer
    manufacturer_model: Martin LLC Picture6849
    settings_parameters: "9380 x g, 37\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Black-Hansen Oil7195
    settings_parameters: "8875 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Conley-Sheppard Thus2483
  procedure_steps:
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      bring.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 386
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      north.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 349
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were cultured with pbs to facilitate degree.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 151
    temperature_celsius: 25
  - step_description: Cells were maintained with anti-ha antibody to facilitate relationship.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate activity.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 394
    temperature_celsius: 26
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Song firm political green actually if deal state seat last check after
    pay method.
- control_type: Technical Replicate Control
  description: Like word board several simply mouth hot Mr imagine region organization
    public miss forget seek.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
