"MAGE-TAB Version"	"1.1"
"Investigation Title"	"Mapping embryonic stem cell surface interactions to transcriptional phenotypes"

"Experimental Design"	
"Experimental Design Term Source REF"	
"Experimental Design Term Accession Number"	

"Experimental Factor Name"	"sample description"	"Treatment"	
"Experimental Factor Type"	"sample description"	"Treatment"	
"Experimental Factor Term Source REF"	""	""	
"Experimental Factor Term Accession Number"	""	""	

"Person Last Name"	"The Wellcome Trust Sanger Institute"	
"Person First Name"	""	
"Person Mid Initials"	""	
"Person Email"	"datahose@sanger.ac.uk"	
"Person Phone"	""	
"Person Fax"	""	
"Person Affiliation"	"Wellcome Trust Sanger Institute"	
"Person Address"	"Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"	
"Person Roles"	"submitter"	
"Person Roles Term Source REF"	""	
"Person Roles Term Accession Number"	""	

"Quality Control Type"	
"Quality Control Term Source REF"	
"Quality Control Term Accession Number"	

"Replicate Type"	
"Replicate Term Source REF"	
"Replicate Term Accession Number"	

"Normalization Type"	
"Normalization Term Source REF"	
"Normalization Term Accession Number"	

"Date of Experiment"	
"Public Release Date"	"2015-04-21"

"PubMed ID"	
"Publication DOI"	
"Publication Author List"	
"Publication Title"	
"Publication Status"	
"Publication Status Term Source REF"	
"Publication Status Term Accession Number"	

"Experiment Description"	"The activation of receptors displayed on the surface of cells typically initiates cytoplasmic signalling cascades that lead to changes in cellular transcriptional responses so that a cell expresses proteins that enable it to behave appropriately as a function of their position within an organism. Understanding these signals and learning how to either prevent or ectopically activate them could have many therapeutic benefits and applications. In some cases these signals are highly localised, being delivered by directly neighbouring cells that express ligands which specifically bind to and activate receptors; for example, stem cells display receptors for ligands provided by cells within their niche to both ensure continual production of cells, and that their cellular progeny are directed towards appropriate fates. While for some cell types we know something of these signals enabling the in vitro differentiation of stem cells towards certain cellular fates, the differentiation processes is often not complete and so immature cell types which are not fully functional are produced, implying that some important signals are missing. Here, we propose to systematically identify receptor-triggered signalling pathways by stimulating receptors on the surface of human stem cells by using a library of soluble recombinant oligomerised protein ligands and measuring the consequent transcriptional perturbations using RNA-seq. We propose to screen an existing library of ~50 oligomerised human ligands previously used in receptor protein interaction screens and first test them for their ability to bind to human stem cells to identify those ligands for which the stem cells express a cell surface receptor. For those ligands which interact with the stem cells (we estimate between 2 and 5), they will be added to stem cell cultures and their effects on transcription quantified. The budget requested is sufficient for us to include controls and test important parameters such different time points after addition of the proteins. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/"

"Protocol Name"	"SEQUENCING_PROTOCOL_1"	"LIBRARY_CONSTRUCTION_PROTOCOL_1"	
"Protocol Type"	"nucleic acid sequencing protocol"	"nucleic acid library construction protocol"	
"Protocol Term Source REF"	"EFO"	"EFO"	
"Protocol Term Accession Number"	"EFO_0004170"	"EFO_0004184"	
"Protocol Description"	"Illumina HiSeq 2000 software. Illumina HiSeq2000 flow cell preparation: PE-401-3001: TruSeq PE Cluster Kit v3 - cBot - HS; GD-401-3001: TruSeq SR Cluster Kit v3 - cBot - HS; FC-401-3001: TruSeq SBS Kit v3 - HS (200-cycles). http://www.illumina.com/technology/sequencing_technology.ilmn"	"RNA-seq dUTP"	
"Protocol Parameters"	""	""	
"Protocol Hardware"	"Illumina HiSeq 2000"	""	
"Protocol Software"	""	""	
"Protocol Contact"	""	""	

"Term Source Name"	"EFO"	"NCBI Taxonomy"
"Term Source File"	"http://www.ebi.ac.uk/efo"	"http://www.ncbi.nlm.nih.gov/Taxonomy/"
"Term Source Version"	"2.38"	"2.31"

"SDRF File"	"E-ERAD-351.sdrf.txt"	
"Comment [Submitted Name]"	"Mapping embryonic stem cell surface interactions to transcriptional phenotypes"
"Comment [SecondaryAccession]"	"ERP008967"
"Comment [SequenceDataURI]"	"http://www.ebi.ac.uk/ena/data/view/ERP008967"
"Comment [AEExperimentType]"	"RNA-seq of coding RNA"
"Comment[ArrayExpressAccession]"	"E-ERAD-351"
"Comment [SRASubmissionDate]"	"2014-12-09"
"Comment [AEMINSEQEScore]"	"2"
"Comment [AEExperimentDisplayName]"	"Mapping embryonic stem cell surface interactions to transcriptional phenotypes"