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Series GSE40829 Query DataSets for GSE40829
Status Public on Sep 13, 2012
Title Expression profiles of lineage-depleted (Lin-) cell and mono-nucleated cell (MNC) samples derived from human umbilical cord blood
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. PERT was used to deconvolve cellular composition of variably sourced and treated heterogeneous human blood samples. Our results indicate that even after correcting batch effects, cells presenting the same cell surface antigens display different transcriptional programs when they are uncultured versus culture-derived. Given gene expression profiles of culture-derived heterogeneous samples and profiles of uncultured reference populations, PERT was able to accurately recover proportions of pure populations composing the heterogeneous samples. We anticipate that PERT will be widely applicable to expression deconvolution problems using profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular identity.
Human umbilical cord blood-derived lineage negative cells and mononucleated cells
Overall design Cellular compositions of mononucleated cell and lineage negative cell compartments were deconvolved based on the gene expression profiles
Contributor(s) Qiao W, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW
Citation(s) 23284283
Submission date Sep 12, 2012
Last update date Feb 13, 2020
Contact name Wenlian Qiao
Phone 1-416 978 1089
Organization name University of Toronto
Street address Room 1110, 160 College Street
City Toronto
State/province Ontario
ZIP/Postal code M5S 3E1
Country Canada
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (4)
GSM1002637 mononucleated cells, technical rep 1
GSM1002638 mononucleated cells, technical rep 2
GSM1002639 lin- cells, technical rep 1
This SubSeries is part of SuperSeries:
GSE40831 Lineage-depleted (Lin-) cell and mono-nucleated cell (MNC), and uncultured and culture-derived colony forming unit-monocytes and megakaryocytes
BioProject PRJNA175056

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40829_RAW.tar 8.4 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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