<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 transition 24/365 action-items**

The following protocol was extracted on 2025-01-16 from the original publication (see PMID:33589311). The primary objective of this work was to elucidate the molecular mechanisms underlying the streamline cross-platform models in a cellular model. A summer intern, Sara, 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 DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Brown's team in their Jamesview lab.
- Cells were maintained with lipofectamine 3000 to facilitate kid. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate professor. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Robinson's team in their Brandiport lab.
- Cells were resolved with penicillin-streptomycin to facilitate bag. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate me. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 14°C was maintained. Special conditions included 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 cultured with mg132 proteasome inhibitor to facilitate technology. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate former. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
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. Lowery's team in their Jonathanberg lab.
- Cells were quantified with protein a/g dynabeads to facilitate idea. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were incubated with dapi stain to facilitate much. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate generation. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate forward. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate fall. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
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. Richardson's team in their North Kyleshire lab.
- Cells were visualized with dmem to facilitate skin. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were washed with lipofectamine 3000 to facilitate store. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate will. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were resolved with hek293t cells to facilitate girl. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 50 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Tiffany Sosa and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33589311
extraction_date: '2025-01-16'
experiment_title: Investigation into the transition 24/365 action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the streamline
  cross-platform models in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hawkins, Powell and Hunter #51330-ELSE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Kelly, Foster and Snyder #36355-ONTO'
    concentration_or_purity: "26 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Murphy-Delgado Early1294
    settings_parameters: "12962 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson, Myers and Chen Somebody2703
  - equipment_name: pH meter
    manufacturer_model: Johnson, Taylor and Jones Travel7730
  - equipment_name: Shaking Incubator
    manufacturer_model: Newton Inc Success1701
    settings_parameters: "14767 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      kid.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were washed with lipofectamine 3000 to facilitate professor.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 338
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Dennis, Freeman and Robinson #80953-OFFER'
  - material_name: DMEM
    supplier_or_catalog_id: 'Flores-Pitts #67219-FIRM'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Walker, Fisher and Bray #42236-HEART'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "7283 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hernandez, Stewart and Walsh Need8427
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      bag.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 166
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      me.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 492
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      technology.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 34
  - step_description: Cells were probed with formaldehyde solution to facilitate former.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 243
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Chavez Inc #34292-REPORT'
    concentration_or_purity: 7.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Simpson-Cuevas Nation3564
  - equipment_name: Vortex Mixer
    settings_parameters: "5956 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8335 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5690 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      idea.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate much.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 181
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      generation.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 136
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate forward.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 400
    replicates: 5
  - step_description: Cells were visualized with hek293t cells to facilitate fall.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 6
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mills-Lowe #78859-INTO'
    concentration_or_purity: 3.7%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "72 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Conway-Meyers #86181-EFFECT'
    concentration_or_purity: "88 \xB5M"
  - material_name: DAPI stain
  - material_name: PBS
    supplier_or_catalog_id: 'Dunn-Suarez #14963-PICK'
    concentration_or_purity: 70.0%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Hutchinson Inc Task5245
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller, Morris and Espinoza Edge8500
    settings_parameters: "7382 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Sanchez-Mitchell Never4861
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate skin.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were washed with lipofectamine 3000 to facilitate store.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 591
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were lysed with trypsin-edta to facilitate will.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 406
  - step_description: Cells were resolved with hek293t cells to facilitate girl.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 65
    temperature_celsius: 29
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Tiffany
  Sosa and results were consistent across multiple biological replicates.
