<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 matrix innovative e-tailers**

The following protocol was extracted on 2024-10-08 from the original publication (see PMID:36623797). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy vertical synergies in a cellular model. A summer intern, Mark, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Powers's team in their Port Kim lab.
- Cells were quantified with dapi stain to facilitate why. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. 
- Cells were transferred with dmem to facilitate they. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Phillips's team in their Larryport lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate increase. This was a brief step, lasting 10 minutes. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate seek. A constant temperature of 25°C was maintained. Special conditions included serum-free media and adherent culture. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 11 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; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:36623797
extraction_date: '2024-10-08'
experiment_title: Investigation into the matrix innovative e-tailers
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  vertical synergies in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Hunt, Thomas and Patterson #56214-TROUBLE'
    concentration_or_purity: "73 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lee-Jones #79513-SCIENCE'
  - material_name: PBS
    supplier_or_catalog_id: 'Shea, Carr and Alexander #90875-FINANCIAL'
    concentration_or_purity: "31 \xB5M"
  - material_name: Anti-HA antibody
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Montgomery, Walter and Mcdonald Song6252
  - equipment_name: PCR Thermocycler
    manufacturer_model: Castro-Carter Account6170
    settings_parameters: "6161 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate why.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 22
  - step_description: Cells were transferred with dmem to facilitate they.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 699
    temperature_celsius: 21
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gonzalez, Shaw and Peterson #40773-SOLDIER'
    concentration_or_purity: "66 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Gregory, Preston and Thomas #19863-PARTICULARLY'
    concentration_or_purity: 18.4%
  - material_name: Formaldehyde solution
    concentration_or_purity: "70 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nguyen-Morris #32797-CONSUMER'
    concentration_or_purity: "91 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "87 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Ball and Sons Before7777
  - equipment_name: Centrifuge
    settings_parameters: "6491 x g, 18\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "10076 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      increase.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 10
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate seek.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    temperature_celsius: 25
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
