Jay will have a talk at the 1ST Annual Junior Investigator Symposium held by New England Stem Cell Consortium. The title is ‘Single-cell Transcript Analysis of Human Embryonic Stem Cells’.

Jason Gibson et al. just submitted the final version of their paper “Single-cell Transcript Analysis of Human Embryonic Stem Cells” to the Integrative Biology Journal. Here is a abstract of the paper:

“We demonstrate the qualitative and quantitative power of single-cell transcript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC’s). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency.  Using single-cell analysis of H9 hESC’s differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers. Our single-cell profiles reveal mixed populations of cell types, with both transcriptional and temporal heterogeneity marking differentiation under all conditions. Interestingly, we also observe extensive and prolonged co-expression of markers regulating both pluripotency and lineage differentiation in all culture conditions, and we find that pluripotency marker transcripts remain detectable in the majority of cells for many days.  Finally, we show that cells derived from undifferentiated hESC colonies display consistent gene expression profiles characterized by three cohorts of transcripts: uniform, absent, and sporadically detected messages, and that a striking correlation exists between genes’ membership in these cohorts and their hESC promoter chromatin state, with bivalent promoters dominating the sporadic transcripts.”

SCLD (Stem Cell Lineage Database) has been released to the public (site link), along with the poster presentation at StemCONN’09.

“The SCLD provides user-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells. These lineage maps contain lineage relationships between individual cell types, gene expression profiles for cell type identification, and information on inductive stimuli that transition cells from one stage to another.” (from About page of SCLD)

No user registration is required to use the database. However, to add/update lineages/celltypes or just to leave comments, users can register through the database website by clicking ‘User’-'Create’ menu.

StemCONN 09 will be held at New Haven, Connecticut on March 23-24, 2009. From our lab, two posters will be presented: one from single cell analysis experiment and the other from SCLD (Stem Cell Lineage Database project). 

‘Comparative Genomics‘ is published as the proceedings of RECOMB-CG 2008 from Springer. Craig is one of the editors with S. Vialette of this lecture notes series: LNBI 5267. The 19 revised full papers including Paul and Jin’s papers were reviewed and selected from 48 submissions. You can access the papers here. Following is a part of book flyer.

… The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes….

I have just found an online video link of Craig’s talk about Paul and Jin’s research at RECOMB-CG’07, in SciVee (research related video sharing service) web site. I added this in Publications section.

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