Comment[ArrayExpressAccession]	E-GEOD-50858
MAGE-TAB Version	1.1				
Public Release Date	2015-01-20
Investigation Title	Towards a reference human platelet transcriptome: evaluation of inter-individual correlations and of its relationship with a platelet proteome				
Comment[Submitted Name]	Towards a reference human platelet transcriptome: evaluation of inter-individual correlations and of its relationship with a platelet proteome
Experiment Description	For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among  different  donors  or  across  different  RNA  profiling  platforms,  and  what  the transcriptomes’  relationship  is  with  the  platelet  proteome.  We  generated  RNA-seq  pro-files  of  the  long  RNA  transcriptomes  from  the  platelets  of  10  healthy  young  males  (5 white and 5 black) with median age of 24.5 years, no notable clinical history, and no pre-vious history of thrombosis or bleeding. We also profiled the subjects’ messenger RNAs using the Affymetrix microarray gene expression system. We found that the abundance of  platelet  mRNA  transcripts  was  highly  correlated  across  the  10  individuals,  inde-pendently of race and of the employed technology. Our RNA-seq data also showed that these  high  inter-individual  correlations  extend  beyond  mRNAs  to  several  categories  of non-coding RNAs. Pseudogenes represented a notable exception to this by exhibiting a clear difference in expression by race. Comparison of our mRNA signatures with the only publicly available quantitative platelet proteome data showed that most (87.5%) identified platelet  proteins  had  a  detectable  corresponding  mRNA.  However,  a  high  number  of mRNAs that were present in the transcriptomes of all 10 individuals had no representa-tion  in  the  proteome.  The  Spearman  correlation  of  the  relative  abundances  for  those platelet  genes  that  were  represented  by  both  an  mRNA  and  a  protein  showed  a  weak (~0.3) yet statistically significant (P=5.0E-16) connection. Further analysis of the overlap-ping  and  non-overlapping  platelet  mRNAs  and  proteins  identified  gene  groups  corre-sponding to distinct cellular processes, a finding that provides novel insights for platelet biology. This represents the Affymetrix GeneChip component of the study only 10 Resting Human Platelet samples				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Edelstein	Bray	Rigoutsos		
Person First Name	Leonard	Paul	Isidore		
Person Mid Initials	C.	F			
Person Email	geo@ncbi.nlm.nih.gov				
Person Affiliation	Thomas Jefferson University				
Person Address	Medicine/Hematology, Thomas Jefferson University, 1015 Walnut St., Philadelphia, PA, USA				
Person Roles	submitter				
Protocol Name	P-GSE50858-1	P-GSE50858-3	P-GSE50858-4	P-GSE50858-2	P-GSE50858-5
Protocol Description	data were analyzed in R using the GCRMA R package with defaults ID_REF =  VALUE = gcrma normalized data, log2 scale	standard Affymetrix protocol	standard Affymetrix protocol	Trizol	standard Affymetrix protocol
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Publication Title	The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.				
Publication Author List	Londin ER, Hatzimichael E, Loher P, Edelstein L, Shaw C, Delgrosso K, Fortina P, Bray PF, McKenzie SE, Rigoutsos I				
PubMed ID	24524654				
Publication DOI	10.1186/1745-6150-9-3				
Comment[SecondaryAccession]	GSE50858				
Comment[GEOReleaseDate]	2015-01-20				
Comment[ArrayExpressSubmissionDate]	2013-09-13				
Comment[GEOLastUpdateDate]	2015-01-20				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-50858.sdrf.txt