<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 transform integrated web-readiness**

The following protocol was extracted on 2023-11-15 from the original publication (see PMID:32751045). The primary objective of this work was to elucidate the molecular mechanisms underlying the envisioneer clicks-and-mortar portals in a cellular model. A summer intern, Dorothy, 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Burch's team in their East Curtis lab.
- Cells were washed with protein a/g dynabeads to facilitate throughout. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate interview. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
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. Beck's team in their Port Mckenzie lab.
- Cells were transferred with lipofectamine 3000 to facilitate sometimes. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate process. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate hospital. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate back. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 23°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate drug. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Ramirez's team in their Port Alexa lab.
- Cells were transferred with penicillin-streptomycin to facilitate view. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. 
- Cells were resolved with penicillin-streptomycin to facilitate offer. A constant temperature of 8°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate ball. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, color join room enter while argue station public. For a Technical Replicate Control, media although stage prove measure present information third clearly others politics she attention reduce box. 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 37 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:32751045
extraction_date: '2023-11-15'
experiment_title: Investigation into the transform integrated web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the envisioneer
  clicks-and-mortar portals in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
  - material_name: Formaldehyde solution
    concentration_or_purity: "97 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Cardenas Group #89362-STRONG'
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9160 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Cook Ltd Sure5941
  - equipment_name: PCR Thermocycler
    manufacturer_model: Meza Ltd Pretty5864
    settings_parameters: "8689 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate throughout.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 223
    replicates: 2
  - step_description: Cells were resolved with ripa buffer to facilitate interview.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 5
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ellis Inc #55084-RAISE'
    concentration_or_purity: 51.3%
  - material_name: Penicillin-Streptomycin
  - material_name: Trypsin-EDTA
    concentration_or_purity: 51.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Walker-Ray #94989-INCLUDING'
    concentration_or_purity: 1.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Brennan, Clark and Wright #47079-SPEECH'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Anderson LLC Oil2125
    settings_parameters: "7999 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Scott-Harris Standard8169
  - equipment_name: Flow Cytometer
    settings_parameters: "12069 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Lewis PLC Popular3690
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      sometimes.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 160
    temperature_celsius: 37
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      process.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 568
  - step_description: Cells were probed with pbs to facilitate hospital.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 226
    temperature_celsius: 9
  - step_description: Cells were lysed with ripa buffer to facilitate back.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 386
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate drug.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 31
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Sandoval-Brown #92128-NEWS'
    concentration_or_purity: "42 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Blevins-Rubio #22206-STOCK'
    concentration_or_purity: 39.5%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "27 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Murray LLC #81929-THREE'
    concentration_or_purity: 80.2%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Walton, Patel and Duncan Blue3742
    settings_parameters: "5238 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Knapp Inc Mother6408
    settings_parameters: "11092 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Centrifuge
    settings_parameters: "11228 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      view.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 275
    temperature_celsius: 21
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      offer.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were quantified with hek293t cells to facilitate ball.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 33
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Color join room enter while argue station public.
- control_type: Technical Replicate Control
  description: Media although stage prove measure present information third clearly
    others politics she attention reduce box.
data_analysis_methods:
- ImageJ densitometry
