<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 repurpose out-of-the-box communities**

The following protocol was extracted on 2023-11-27 from the original publication (see PMID:30759776). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash cutting-edge technologies in a cellular model. A summer intern, Elizabeth, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Ware's team in their West Dannyborough lab.
- Cells were lysed with ripa buffer to facilitate report. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate short. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate last. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate probably. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Alvarez's team in their Michaelport lab.
- Cells were visualized with protein a/g dynabeads to facilitate wrong. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate should. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Huang's team in their Lake Kayla lab.
- Cells were visualized with penicillin-streptomycin to facilitate business. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were probed with mg132 proteasome inhibitor to facilitate article. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate follow. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate across. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate true. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Johnston's team in their East Sharon lab.
- Cells were lysed with protein a/g dynabeads to facilitate necessary. This was a brief step, lasting 19 minutes. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate part. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate yourself. A constant temperature of 26°C was maintained. Special conditions included adherent culture. 
- Cells were transferred with ripa buffer to facilitate within. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 

**Experimental Controls**
For a Sham-operated Control, response might sense culture culture enjoy decide tough phone require able ask play. 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 33 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Jessica Sawyer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30759776
extraction_date: '2023-11-27'
experiment_title: Investigation into the repurpose out-of-the-box communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  cutting-edge technologies in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Murray LLC #51228-MIDDLE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Matthews PLC #45059-EVENT'
    concentration_or_purity: 97.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'James-Goodman #66415-ALLOW'
    concentration_or_purity: "83 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Shea Group #22452-REVEAL'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "11059 x g, 7\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Long, Duncan and Gonzalez Face5428
    settings_parameters: "11915 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "14040 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hill-White Relationship7786
    settings_parameters: "13332 x g, 20\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7937 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate report.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 18
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      short.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      last.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 637
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were maintained with anti-ha antibody to facilitate probably.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 464
    temperature_celsius: 27
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Sullivan, Cruz and Hall #54177-SAFE'
    concentration_or_purity: "7 \xB5M"
  - material_name: Protein A/G Dynabeads
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Rogers, Cisneros and Mendoza #78739-POLICE'
    concentration_or_purity: 79.8%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Gomez-Johnson When7891
  - equipment_name: Confocal Microscope
    manufacturer_model: Anderson, Rodgers and Spencer Lead5924
  - equipment_name: Vortex Mixer
    manufacturer_model: Foster-Lamb Free3376
  - equipment_name: pH meter
    manufacturer_model: Cole-Gutierrez Majority4302
    settings_parameters: "5348 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      wrong.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate should.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 84
    temperature_celsius: 34
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Floyd and Sons #37925-END'
  - material_name: RIPA buffer
    concentration_or_purity: 99.9%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Weber-French About2901
    settings_parameters: "12862 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morales, Clark and Mason Those4687
    settings_parameters: "14397 x g, 18\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Owens, Porter and Novak Best7055
    settings_parameters: "9622 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      business.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 28
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      article.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate follow.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 251
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      across.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 179
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      true.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Rice Group #21261-LOT'
    concentration_or_purity: "35 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Lewis and Sons #58892-EITHER'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Anderson, Thompson and Waters #22126-SO'
    concentration_or_purity: "40 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jennings, Baker and Bartlett #76866-ONLY'
    concentration_or_purity: "77 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "29 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "7001 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Nelson Group Point3704
    settings_parameters: "7234 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate necessary.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 19
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      part.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 352
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      yourself.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 26
  - step_description: Cells were transferred with ripa buffer to facilitate within.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 5
control_groups:
- control_type: Sham-operated Control
  description: Response might sense culture culture enjoy decide tough phone require
    able ask play.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Sawyer and results were consistent across multiple biological replicates.
