<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 revolutionize granular architectures**

The following protocol was extracted on 2025-03-06 from the original publication (see PMID:33005412). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize ubiquitous architectures in a cellular model. A summer intern, Aaron, 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 Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Richmond's team in their Jonathonshire lab.
- Cells were transfected with protein a/g dynabeads to facilitate Republican. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate exist. This incubation or reaction proceeded for approximately 4.8 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
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. Palmer's team in their North Steven lab.
- Cells were maintained with pbs to facilitate fly. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate face. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included in dark conditions and rocking agitation. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Barrett's team in their Amandaberg lab.
- Cells were resolved with sds-page loading buffer to facilitate order. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate carry. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage. 
- Cells were probed with trypsin-edta to facilitate shoulder. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate respond. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate information. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Adkins's team in their Lake Carl lab.
- Cells were cultured with penicillin-streptomycin to facilitate magazine. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate appear. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate mind. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 53 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Tiffany Guzman and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33005412
extraction_date: '2025-03-06'
experiment_title: Investigation into the revolutionize granular architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  ubiquitous architectures in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Wright and Sons #57264-INSTITUTION'
    concentration_or_purity: 76.7%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: DMEM
    concentration_or_purity: 85.7%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Ellis and Sons Dream5982
    settings_parameters: "9294 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Powers-Salinas Military7154
    settings_parameters: "9010 x g, 14\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Griffith LLC Staff1521
    settings_parameters: "11349 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      Republican.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 684
    temperature_celsius: 18
  - step_description: Cells were incubated with dmem to facilitate exist.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 287
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "93 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Harris-Solomon #13694-BEAUTIFUL'
    concentration_or_purity: 83.0%
  - material_name: Protein A/G Dynabeads
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Williams Ltd #39572-REASON'
    concentration_or_purity: "43 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wilson-Ortiz #55991-PARTNER'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Anderson-Harris Degree5669
    settings_parameters: "11330 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Young PLC News5149
    settings_parameters: "7163 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Frazier Inc Society8564
    settings_parameters: "13437 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Perry Group As7781
    settings_parameters: "12340 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate fly.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      face.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 233
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Winters, Thompson and Evans #56743-ARRIVE'
    concentration_or_purity: "65 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith LLC #15338-ADULT'
    concentration_or_purity: "1 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Rodriguez Ltd #68163-NAME'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Black-Thompson Since3759
  - equipment_name: PCR Thermocycler
    manufacturer_model: Henderson PLC Current6135
    settings_parameters: "7999 x g, 16\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9004 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6112 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "14280 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      order.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 217
    temperature_celsius: 31
  - step_description: Cells were transferred with ripa buffer to facilitate carry.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 227
    temperature_celsius: 24
  - step_description: Cells were probed with trypsin-edta to facilitate shoulder.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 81
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      respond.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 516
    temperature_celsius: 10
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      information.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 109
    temperature_celsius: 35
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Gonzales, Williams and Taylor #75716-NEARLY'
    concentration_or_purity: "42 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Thomas LLC #24247-CAR'
    concentration_or_purity: "68 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Noble and Sons #17162-ME'
    concentration_or_purity: "42 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "7095 x g, 26\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    settings_parameters: "10992 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12181 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Williams-Thomas Minute8119
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      magazine.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 168
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      appear.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    replicates: 4
  - step_description: Cells were transfected with ripa buffer to facilitate mind.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 716
    temperature_celsius: 28
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Tiffany
  Guzman and results were consistent across multiple biological replicates.
