READ ME File For 'Dataset for in support of the thesis 'Characterising a 3D culture model of triple-negative breast cancer through systems-based molecular phenotyping'

Dataset DOI: 10.5258/SOTON/D3234

Date that the file was created: September, 2024

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GENERAL INFORMATION
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ReadMe Author: Luis Coy, University of Southampton, ORCID ID 0000-0001-6466-6408

Date of data collection: 2019 to 2024

Information about geographic location of data collection: 

Related projects:
ABC Discover Programme Grant

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SHARING/ACCESS INFORMATION
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Licenses/restrictions placed on the data, or limitations of reuse: Creative Commons Attribution CC-BY 

Recommended citation for the data:

This dataset supports the publication:
AUTHORS:
TITLE:
JOURNAL:
PAPER DOI IF KNOWN:

Links to other publicly accessible locations of the data:

Links/relationships to ancillary or related data sets: 
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers
10.6019/PXD055504 and 10.6019/PXD055519.

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DATA & FILE OVERVIEW
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This dataset contains:
ULA_2D_differential_expression - Differential expression analysis of ULA vs 2D cultures of HCC1143, HCC1806, HCC1937 and MDA-MB-231 TNBC cell lines
ULA_2D_pathway_analysis - Pathway analysis (KEGG and GO) of ULA vs 2D cultures of HCC1143, HCC1806, HCC1937 and MDA-MB-231 TNBC cell lines
ULA_2D_unique_proteins - Proteins identified in one condition only for ULA vs 2D cultures of HCC1143, HCC1806, HCC1937 and MDA-MB-231 TNBC cell lines
HCC1143_chemotherapy_treated_differential_expression - Differential expression analysis of doxorubicin-treated vs vehicle control and paclitaxel-treated vs vehicle control of HCC1143 cultured in ULA or 2D  
HCC1143_chemotherapy_treated_pathway_analysis - Pathway analysis (KEGG and GO) of doxorubicin-treated vs vehicle control and paclitaxel-treated vs vehicle control of HCC1143 cultured in ULA or 2D 
HCC1143_chemotherapy_treated_unique_proteins - Proteins identified in one condition only for doxorubicin-treated vs vehicle control and paclitaxel-treated vs vehicle control of HCC1143 cultured in ULA or 2D

Relationship between files, if important for context:  

Additional related data collected that was not included in the current data package:

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If there are there multiple versions of the dataset, list the file updated, when and why update was made:



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METHODOLOGICAL INFORMATION
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Description of methods used for collection/generation of data: <Include links or references to publications or other documentation containing experimental design or protocols used in data collection>

Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>

Software- or Instrument-specific information needed to interpret the data, including software and hardware version numbers:

Standards and calibration information, if appropriate:

Environmental/experimental conditions:

Describe any quality-assurance procedures performed on the data:

People involved with sample collection, processing, analysis and/or submission:


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DATA-SPECIFIC INFORMATION <Create sections for each datafile or set, as appropriate>
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Number of variables:

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Variable list, defining any abbreviations, units of measure, codes or symbols used:
   
Missing data codes:

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