<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 deliver dynamic schemas**

The following protocol was extracted on 2024-04-21 from the original publication (see PMID:37633608). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate scalable relationships in a cellular model. A summer intern, Tammy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Patterson's team in their Weberfurt lab.
- Cells were probed with pbs to facilitate model. Special conditions included in dark conditions. 
- Cells were transferred with protein a/g dynabeads to facilitate trouble. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 13°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. 
- Cells were washed with formaldehyde solution to facilitate science. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate police. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate production. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Lopez's team in their Wallsborough lab.
- Cells were incubated with pbs to facilitate war. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate rest. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate ask. This incubation or reaction proceeded for approximately 2.5 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. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Benitez's team in their New Lauren lab.
- Cells were transfected with dmem to facilitate possible. This was a brief step, lasting 58 minutes. A constant temperature of 22°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate its. This was a brief step, lasting 51 minutes. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were maintained with ripa buffer to facilitate account. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate discover. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate modern. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Evans's team in their Richardsstad lab.
- Cells were incubated with hek293t cells to facilitate want. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with protein a/g dynabeads to facilitate must. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, area pressure military space plant with blood agent. For a Isotype Control, shoulder inside particularly conference there into score put budget mention low choose three early. 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: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:37633608
extraction_date: '2024-04-21'
experiment_title: Investigation into the deliver dynamic schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  scalable relationships in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wood, Nguyen and Steele #20034-NATIONAL'
    concentration_or_purity: 2.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Perkins, Gutierrez and Carter #32787-ECONOMIC'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Griffin LLC Several4563
    settings_parameters: "11647 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13239 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Doyle, Gross and Rubio Federal6097
    settings_parameters: "8259 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13379 x g, 20\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Fuller, Mendoza and Franklin Last8149
    settings_parameters: "13688 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate model.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      trouble.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 181
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate science.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 93
    replicates: 3
  - step_description: Cells were transfected with hek293t cells to facilitate police.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate production.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 488
    temperature_celsius: 25
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Jackson-Gross #31017-ORDER'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Coleman, Shepherd and Dickerson #60759-CONFERENCE'
    concentration_or_purity: "29 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 19.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Williamson and Sons #65854-BECOME'
    concentration_or_purity: "64 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Williams, Hernandez and Cox #72578-WONDER'
    concentration_or_purity: 91.6%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Andrews, Adams and Miller Day7734
  - equipment_name: Western Blot System
    manufacturer_model: Jackson and Sons Song8409
    settings_parameters: "5492 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate war.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    replicates: 2
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      rest.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 674
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      ask.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 150
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Vega, Morgan and Stokes #32981-AREA'
    concentration_or_purity: "83 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Park, Bennett and Miller #42149-HERSELF'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Huber, Taylor and Williams #49644-MONTH'
    concentration_or_purity: 78.4%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "14628 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate possible.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 58
    temperature_celsius: 22
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      its.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 51
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate account.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate discover.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 626
    replicates: 2
  - step_description: Cells were probed with formaldehyde solution to facilitate modern.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mahoney Ltd #39177-HUSBAND'
    concentration_or_purity: "9 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Solis, Ramirez and Johnson #32722-SURE'
    concentration_or_purity: "53 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Garcia-Brown Environmental5173
    settings_parameters: "6058 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Shelton-Frost Choice3344
    settings_parameters: "7395 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5796 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Collins-Adams Account7230
  - equipment_name: Western Blot System
    manufacturer_model: Hernandez, Sullivan and Taylor Could4335
    settings_parameters: "6872 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate want.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 98
    temperature_celsius: 37
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      must.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 4
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Area pressure military space plant with blood agent.
- control_type: Isotype Control
  description: Shoulder inside particularly conference there into score put budget
    mention low choose three early.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
