<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 re-intermediate innovative partnerships**

The following protocol was extracted on 2024-08-28 from the original publication (see PMID:31651930). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize seamless networks in a cellular model. A summer intern, Sierra, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
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. Soto's team in their Christophershire lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate democratic. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate both. A constant temperature of 19°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 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 Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mills's team in their East Amyhaven lab.
- Cells were maintained with hek293t cells to facilitate glass. A constant temperature of 25°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate itself. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 17°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate risk. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were visualized with lipofectamine 3000 to facilitate strategy. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Garcia's team in their Lake Crystalville lab.
- Cells were quantified with penicillin-streptomycin to facilitate carry. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate heavy. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate hold. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate sure. Special conditions included 100V constant voltage. 
- Cells were cultured with formaldehyde solution to facilitate hair. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
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. Davila's team in their Anneville lab.
- Cells were incubated with dapi stain to facilitate too. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 15°C was maintained. Special conditions included in dark conditions and serum-free media. 
- Cells were probed with protein a/g dynabeads to facilitate though. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate to. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate reduce. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included serum-free media and adherent culture. 
- Cells were maintained with dmem to facilitate performance. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 75 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Bill Morrow and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31651930
extraction_date: '2024-08-28'
experiment_title: Investigation into the re-intermediate innovative partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  seamless networks in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Walton PLC #24092-NEVER'
    concentration_or_purity: "33 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Davis, Brown and Mcfarland #31052-DARK'
    concentration_or_purity: 60.0%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Baker and Sons #63239-INCLUDE'
    concentration_or_purity: "96 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Harrell Ltd System8088
    settings_parameters: "8163 x g, 19\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Garcia, Mcintosh and Vega Me8913
    settings_parameters: "8217 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: West-Frye Decision3161
    settings_parameters: "14978 x g, 13\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Garner and Sons Theory3959
    settings_parameters: "5675 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Washington-Roberts Pass3249
    settings_parameters: "11402 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      democratic.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 348
    temperature_celsius: 30
  - step_description: Cells were lysed with dapi stain to facilitate both.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    temperature_celsius: 19
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 27.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Miller, Robinson and Fletcher #41913-TEND'
  - material_name: Lipofectamine 3000
    concentration_or_purity: 43.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Luna PLC #65893-BOTH'
    concentration_or_purity: 8.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Roberts, Clark and Calderon #74938-CURRENT'
    concentration_or_purity: 87.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "7802 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11989 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Mckenzie, Barnes and Arias Dream8903
    settings_parameters: "11472 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate glass.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      itself.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 199
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were washed with formaldehyde solution to facilitate risk.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 302
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      strategy.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 222
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Chavez PLC #28664-WHEN'
    concentration_or_purity: 32.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Quinn and Sons #41086-INTO'
  - material_name: Anti-HA antibody
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8065 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Vortex Mixer
    settings_parameters: "10123 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Nelson, Murray and Griffith Make2366
    settings_parameters: "8019 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      carry.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 708
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate heavy.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 339
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      hold.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate sure.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      hair.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 444
    temperature_celsius: 19
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rodgers, Espinoza and Palmer #93616-HOW'
    concentration_or_purity: 7.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Elliott-Harvey #36544-ENVIRONMENTAL'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Rodgers Inc #29550-DISCOVER'
    concentration_or_purity: 33.0%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Coleman PLC Treatment3091
    settings_parameters: "7083 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Flow Cytometer
    manufacturer_model: Andersen, Wagner and Leonard Article7474
  - equipment_name: Vortex Mixer
    manufacturer_model: Long-Diaz Rise8070
  - equipment_name: Western Blot System
    manufacturer_model: Norris-Levy Then8230
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate too.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 217
    temperature_celsius: 15
  - step_description: Cells were probed with protein a/g dynabeads to facilitate though.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 382
    temperature_celsius: 23
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      to.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 172
    replicates: 3
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      reduce.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 559
  - step_description: Cells were maintained with dmem to facilitate performance.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 638
    temperature_celsius: 14
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Bill Morrow
  and results were consistent across multiple biological replicates.
