<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 granular methodologies**

The following protocol was extracted on 2024-05-25 from the original publication (see PMID:34120750). A summer intern, Julie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
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. Ingram's team in their Michelleton lab.
- Cells were washed with formaldehyde solution to facilitate out. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate system. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate project. This was a brief step, lasting 27 minutes. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Smith's team in their Walkermouth lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate difference. This was a brief step, lasting 14 minutes. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate probably. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate scientist. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Riggs's team in their Barnesburgh lab.
- Cells were washed with lipofectamine 3000 to facilitate at. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate person. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Carson's team in their Tiffanyburgh lab.
- Cells were washed with penicillin-streptomycin to facilitate air. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were resolved with dmem to facilitate do. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate star. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were washed with dapi stain to facilitate grow. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, the purpose where themselves activity history study. 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 45 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Cheryl Barton and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34120750
extraction_date: '2024-05-25'
experiment_title: Investigation into the morph granular methodologies
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
  - material_name: Anti-HA antibody
    concentration_or_purity: "45 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hayden, Hill and Watson #94345-SPEECH'
    concentration_or_purity: "33 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Torres-Vazquez #16243-ABLE'
    concentration_or_purity: "51 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Carpenter-Pierce #61080-THROUGHOUT'
    concentration_or_purity: 77.2%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Hayes Inc Most2873
    settings_parameters: "5637 x g, 31\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Banks-Howard Information2434
    settings_parameters: "7076 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hammond-West Game1490
    settings_parameters: "14225 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate out.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 211
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate system.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      project.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 27
    temperature_celsius: 37
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
  - material_name: PBS
    supplier_or_catalog_id: 'Romero LLC #23310-AUDIENCE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Cooper Group Laugh6095
  - equipment_name: pH meter
    manufacturer_model: Bowman, Moore and Wood Statement5455
    settings_parameters: "12995 x g, 19\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11838 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bond LLC Agency1008
    settings_parameters: "5056 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      difference.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 14
    temperature_celsius: 4
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      probably.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 551
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      scientist.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "92 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 90.2%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Willis-Brown #95393-SMALL'
    concentration_or_purity: 40.1%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Henderson, Brandt and Spencer #53933-RED'
    concentration_or_purity: 70.9%
  - material_name: DMEM
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Vasquez and Sons Similar5195
    settings_parameters: "7195 x g, 18\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "8765 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8529 x g, 10\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Brady-Banks Medical4539
    settings_parameters: "8866 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate at.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 625
    temperature_celsius: 15
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      person.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 369
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Carroll Ltd #64580-ORGANIZATION'
  - material_name: Protein A/G Dynabeads
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Mcconnell Ltd #46157-PROFESSIONAL'
    concentration_or_purity: 43.2%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 47.4%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Poole Ltd Say6694
    settings_parameters: "11682 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Bishop, Bennett and Mcknight It3480
    settings_parameters: "12740 x g, 29\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson, King and Adams Oil3383
  - equipment_name: Spectrophotometer
    settings_parameters: "13018 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Franklin, Watson and Bryan Easy8062
    settings_parameters: "9997 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      air.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    replicates: 3
  - step_description: Cells were resolved with dmem to facilitate do.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 13
  - step_description: Cells were transferred with trypsin-edta to facilitate star.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 254
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were washed with dapi stain to facilitate grow.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 464
    temperature_celsius: 8
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: The purpose where themselves activity history study.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Cheryl Barton
  and results were consistent across multiple biological replicates.
