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GenomicsHEB and E2A function as SMAD/FOXH1 cofactors
Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We have identified a new motif, termed SMAD Complex Associated (SCA) that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. We de...
ORGANISM(S): Xenopus (Silurana) tropicalis 
2011-08-23 | E-GEOD-30146 | biostudies-arrayexpress
GenomicsChromatin and Transcriptional Signatures for Nodal Signaling During Endoderm Formation in hESCs
To elucidate the Nodal transcriptional network that governs endoderm formation, we used ChIP-Seq to identify genomic targets for SMAD2/3, SMAD3, SMAD4, FOXH1 and the active and repressive chromatin marks, H3K4me3 and H3K27me3, in human embryonic stem cells (hESCs) and derived endoderm. We demonstrat...
ORGANISM(S): Homo sapiens 
2011-05-21 | E-GEOD-29422 | biostudies-arrayexpress
GenomicsRodent trophoblast epigenome
We characterized the trophoblast stem cell epigenome and gene expression profiles in rat and mouse. We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast stem cells derived from rat and mouse. Furthermore, for mouse, we p...
ORGANISM(S): Mus musculus 
2012-12-04 | E-GEOD-42207 | biostudies-arrayexpress
TranscriptomicsTrophoblast giant cell underrepresentation (sequencing)
We characterized the mouse trophoblast giant cell epigenome and gene expression profiles. We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells. We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles ...
ORGANISM(S): Mus musculus 
2014-05-29 | E-GEOD-50561 | biostudies-arrayexpress
TranscriptomicsTrophoblast giant cell underrepresentation (CGH)
We characterized regions of underrepresentation that are specific to mouse polyploid trophoblast giant cells. We performed array Comparative Genomics Hybridization (aCGH) to examine copy number variation (CNV) in mouse polyploid trophoblast giant cells (TGCs). We performed the following experiments...
ORGANISM(S): Mus musculus 
2014-05-29 | E-GEOD-50543 | biostudies-arrayexpress
Transcriptomics3' RNA-Seq (3'SEQ) analysis gene expression profiling at G1-S transition in human embryonic stem cells (hESCs) and hESC-derived endoderm cells
In this report, we examine transcripts on a genome-wide level between the synchronized cell cycles of hESCs and hESC-derived endoderm cells. We found 10347, 10299 and 10362 genes expressed in the G1, G1/S, and S phase of hESCs, respectively; 10333, 10227 and 10215 genes expressed at the G1, G1/S and...
ORGANISM(S): Homo sapiens 
2014-05-14 | E-GEOD-47117 | biostudies-arrayexpress
TranscriptomicsTrophoblast giant cell underrepresentation (tiling)
We profiled trophoblast stem cell replication-timing in order to compare these data to our data on underrepresented (UR) domainss in trophoblast giant cells (polyploid cells derived from 2N trophoblast stem cells). We found that UR domains are formed from late-replicating regions in tropoblast stem...
ORGANISM(S): Mus musculus 
2014-05-29 | E-GEOD-50207 | biostudies-arrayexpress
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