In order to help you get proficient in using the OneOmics suite workflows, we have provided some demo datasets along with numerous other valuable files and supporting information to help you get started.
Once you get access to your SCIEX Cloud account and can view your SCIEX Data Store, you will notice that there is a SHARED folder, in addition to the folders that you have already created. In this folder, you will see folders that have been shared with you by other SCIEX Data Store users. There is also a folder called Shared by SCIEX with a sub-folder called Getting Started. This sub-folder contains all the files you need to get started. These files are the same files used in the Cloud Talks and in the SCIEX Now Learning Hub, so you can always follow along.
There are three sections for each of the general workflows. Let’s explore each one.
Proteomics
In this folder you will find sub-folders that contain commonly used FASTA files and ion libraries. You can use these in your ProteinPilot App searches and your SWATH acquisition data processing. The three folders labeled CDK4 contain the data files you can use for data processing. Finally, in Supplementary files, you will find *.csv files that contain the meta data information for the iTRAQ reagent study and the SWATH acquisition study. These can be uploaded in Experiment manager to correctly set the metadata when building your experiments. The paper that describes the CDK4 study and the SWATH Acquisition data set is called Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition (Lambert et al. 2013).
Metabolomics
In this folder you will find sub-folders that contain SWATH acquisition data for a small metabolomics study, including both positive ion mode data and negative ion mode data. This data can be processed using the SCIEX Accurate Mass Metabolomics Spectral Library that is accessible during Extractor processing. In Supplementary files, you will find *.csv files that contain the metadata information for processing. These can be uploaded in Experiment manager to correctly set the metadata when building your experiments.
Multi-omics
In this folder you will find sub-folders that contain SWATH acquisition data and RNA-Seq data for exploring the multi-omics workflow within OneOmics suite. The library required for SWATH acquisition processing is also provided in the Libraries folder. In Supplementary files, you will find *.csv files that contain the metadata information for processing. These can be uploaded in Experiment manager to correctly set the metadata when building your experiments.
The paper that describes this dataset is Multi-omic profiling of tyrosine kinase inhibitor-resistant K562 cells suggests metabolic reprogramming to promote cell survival (Noel BM et al. 2019).
These same Demo Data Files are also available in BaseSpace via the following share links:
RUO-MKT-18-12200-B
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