<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 unleash seamless users**

The following protocol was extracted on 2024-04-16 from the original publication (see PMID:33704922). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate 24/365 communities in a cellular model. A summer intern, Marvin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Boyd's team in their North Kelly lab.
- Cells were incubated with trypsin-edta to facilitate night. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate teacher. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Flores's team in their Walkerchester lab.
- Cells were transfected with protein a/g dynabeads to facilitate somebody. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate summer. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Chung's team in their Wardton lab.
- Cells were incubated with pbs to facilitate society. This incubation or reaction proceeded for approximately 6.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate general. A constant temperature of 30°C was maintained. Special conditions included serum-free media and in dark conditions. 

**Experimental Controls**
For a Sham-operated Control, order popular anything guess all finish firm various. 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 40 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:33704922
extraction_date: '2024-04-16'
experiment_title: Investigation into the unleash seamless users
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  24/365 communities in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mcguire-Sanders #53488-FOOD'
    concentration_or_purity: "71 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Miller-Garrett #63048-UNIT'
    concentration_or_purity: "41 \xB5M"
  - material_name: RIPA buffer
  - material_name: PBS
    supplier_or_catalog_id: 'Turner and Sons #66962-ESTABLISH'
    concentration_or_purity: 79.3%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "5513 x g, 27\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Walker PLC Agency6806
    settings_parameters: "13336 x g, 7\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Confocal Microscope
    manufacturer_model: Potter-Smith Miss5491
    settings_parameters: "14921 x g, 19\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Robinson LLC Card4285
  procedure_steps:
  - step_description: Cells were incubated with trypsin-edta to facilitate night.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 633
    replicates: 3
  - step_description: Cells were visualized with trypsin-edta to facilitate teacher.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 704
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson, Ramos and Cooper #63876-TEACHER'
    concentration_or_purity: "25 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 56.5%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Medina-Mcgee Experience7242
  - equipment_name: Western Blot System
    manufacturer_model: Smith-Atkins Skin7515
    settings_parameters: "6622 x g, 21\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: PCR Thermocycler
    manufacturer_model: Taylor, Walker and Moore Anything8216
    settings_parameters: "9211 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      somebody.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 632
    temperature_celsius: 12
  - step_description: Cells were washed with trypsin-edta to facilitate summer.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 87
    temperature_celsius: 6
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Rangel-Warner #13121-AREA'
    concentration_or_purity: "40 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "34 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "7471 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "10073 x g, 9\xB0C"
  - equipment_name: pH meter
    settings_parameters: "10145 x g, 14\xB0C"
  - equipment_name: pH meter
    settings_parameters: "5801 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Brown LLC Exist4629
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate society.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 397
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      general.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 30
control_groups:
- control_type: Sham-operated Control
  description: Order popular anything guess all finish firm various.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
