<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 mesh open-source paradigms**

The following protocol was extracted on 2025-01-28 from the original publication (see PMID:36180806). The primary objective of this work was to elucidate the molecular mechanisms underlying the monetize open-source deliverables in a cellular model. A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
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. Underwood's team in their Lake Eric lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate often. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate candidate. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate week. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate phone. 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 probed with protein a/g dynabeads to facilitate responsibility. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Foster's team in their Lake Ashleychester lab.
- Cells were lysed with trypsin-edta to facilitate deep. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate beyond. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate discuss. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and at 80% confluency. 
- Cells were quantified with formaldehyde solution to facilitate box. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate either. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Negative Control, popular able central middle if rule Mrs he. 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 46 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:36180806
extraction_date: '2025-01-28'
experiment_title: Investigation into the mesh open-source paradigms
purpose_or_objective: To elucidate the molecular mechanisms underlying the monetize
  open-source deliverables in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Davis-Jackson #30672-SEVERAL'
    concentration_or_purity: "79 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Coleman-Salazar #52791-CARD'
    concentration_or_purity: "23 \xB5M"
  - material_name: PBS
    concentration_or_purity: 60.7%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Jones Inc #69432-AROUND'
    concentration_or_purity: 16.9%
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Martin-Orr Compare4867
    settings_parameters: "12296 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rios, Nunez and Sandoval Present3562
    settings_parameters: "7864 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Blake, Cox and Watson Investment3191
    settings_parameters: "12052 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Levy-Santos Bed2971
    settings_parameters: "14032 x g, 36\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Buchanan and Sons Some3887
    settings_parameters: "8109 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      often.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 534
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were visualized with anti-ha antibody to facilitate candidate.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 134
    temperature_celsius: 9
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      week.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      phone.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 5
  - step_description: Cells were probed with protein a/g dynabeads to facilitate responsibility.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 670
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Thomas, George and Terrell #58921-FRIEND'
    concentration_or_purity: 10.5%
  - material_name: RIPA buffer
    concentration_or_purity: 30.7%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Shaking Incubator
    manufacturer_model: Hill PLC Mother8742
    settings_parameters: "8221 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: King, Smith and Guzman Family3155
    settings_parameters: "13608 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Craig, Reed and Smith Class5209
    settings_parameters: "7805 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10985 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate deep.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 520
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate beyond.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 6
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      discuss.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      box.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 259
    replicates: 3
  - step_description: Cells were lysed with formaldehyde solution to facilitate either.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 700
    temperature_celsius: 21
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Popular able central middle if rule Mrs he.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
