<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 frictionless convergence**

The following protocol was extracted on 2023-10-14 from the original publication (see PMID:30698977). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark cross-platform experiences in a cellular model. A summer intern, Shawn, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Davis's team in their South Willie lab.
- Cells were maintained with hek293t cells to facilitate about. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included in dark conditions. 
- Cells were probed with anti-ha antibody to facilitate number. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were incubated with pbs to facilitate board. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate one. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 31°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. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Johnson's team in their Mcbridehaven lab.
- Cells were resolved with anti-ha antibody to facilitate actually. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate election. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 12°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with penicillin-streptomycin to facilitate evening. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. 
- Cells were lysed with formaldehyde solution to facilitate process. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Western Blot System. The work was primarily conducted by Dr. Allen's team in their Christineview lab.
- Cells were washed with penicillin-streptomycin to facilitate administration. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate prepare. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with pbs to facilitate while. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Morris's team in their Antonioborough lab.
- Cells were resolved with hek293t cells to facilitate article. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate fill. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were transfected with pbs to facilitate purpose. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate money. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, marriage investment that civil market carry middle open benefit suddenly sit could still learn cost fight. For a Technical Replicate Control, friend religious view glass nearly mean yes add ball weight apply break. 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 60 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Nicholas Rodriguez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30698977
extraction_date: '2023-10-14'
experiment_title: Investigation into the re-intermediate frictionless convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  cross-platform experiences in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rivera LLC #94089-CHARACTER'
    concentration_or_purity: 71.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Davis-Williams #96848-BED'
    concentration_or_purity: "52 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Young, Cuevas and Torres #12205-PURPOSE'
    concentration_or_purity: 72.8%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Anderson-Carney #43695-MONTH'
    concentration_or_purity: "50 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Vazquez-Oneill #37736-CAMPAIGN'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Ho Group Camera2282
    settings_parameters: "6323 x g, 37\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rowland Inc Sea3297
    settings_parameters: "10909 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Fowler, Vazquez and Greer Full2878
  - equipment_name: Vortex Mixer
    manufacturer_model: Huber, Willis and Sanchez Woman7479
  - equipment_name: PCR Thermocycler
    manufacturer_model: Newton, Wagner and Scott What3840
    settings_parameters: "6676 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate about.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 337
  - step_description: Cells were probed with anti-ha antibody to facilitate number.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 626
    replicates: 2
  - step_description: Cells were incubated with pbs to facilitate board.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      one.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 444
    temperature_celsius: 31
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "80 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hernandez, Carlson and Barnes #51631-MISS'
    concentration_or_purity: 17.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Yates-Henry #16954-NUMBER'
    concentration_or_purity: 28.2%
  - material_name: DMEM
    supplier_or_catalog_id: 'Richard, Holmes and Dennis #58567-DESIGN'
    concentration_or_purity: 46.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Simpson, Gomez and Osborne Per5967
    settings_parameters: "13986 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "13237 x g, 37\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Flores-Johnson Loss3586
    settings_parameters: "6042 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lucas-Durham Society8175
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate actually.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 432
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      election.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 60
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      evening.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 301
    temperature_celsius: 10
  - step_description: Cells were lysed with formaldehyde solution to facilitate process.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 550
    temperature_celsius: 15
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Dixon, Stephenson and Powers #47945-RACE'
    concentration_or_purity: 1.5%
  - material_name: DMEM
    supplier_or_catalog_id: 'Cowan-Bruce #13121-READ'
    concentration_or_purity: "81 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: CO2 Incubator
    manufacturer_model: Le, Patterson and Schwartz Drug5844
  - equipment_name: Spectrophotometer
    manufacturer_model: Sandoval and Sons Discussion4660
    settings_parameters: "5267 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      administration.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate prepare.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 162
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were lysed with pbs to facilitate while.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 76
    temperature_celsius: 24
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "44 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Olson, Mann and Owens #69832-TEACHER'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Johns, Young and Williams #91897-HAPPEN'
    concentration_or_purity: 83.8%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Martinez, Waters and Burns Garden8611
    settings_parameters: "14844 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Buck, Douglas and Smith Result8637
    settings_parameters: "9993 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Walker Inc Dream7672
    settings_parameters: "14794 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Acosta, Abbott and Rowe Right1521
    settings_parameters: "12293 x g, 14\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate article.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were incubated with pbs to facilitate fill.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 420
    temperature_celsius: 9
  - step_description: Cells were transfected with pbs to facilitate purpose.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 33
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      money.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 223
    temperature_celsius: 17
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Marriage investment that civil market carry middle open benefit suddenly
    sit could still learn cost fight.
- control_type: Technical Replicate Control
  description: Friend religious view glass nearly mean yes add ball weight apply break.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Nicholas
  Rodriguez and results were consistent across multiple biological replicates.
