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Transcriptomics454 Life Sciences/Roche and Illumina sequencing of small RNAs from planarian samples
Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians....
ORGANISM(S): Schmidtea mediterranea 
2009-06-30 | E-GEOD-16159 | biostudies-arrayexpress
TranscriptomicsHigh-resolution mapping of copy-number alterations with massively parallel sequencing
In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numb...
ORGANISM(S): Homo sapiens 
2008-11-13 | E-GEOD-13372 | biostudies-arrayexpress
TranscriptomicsFine-scale mapping of copy-number alterations with massively parallel sequencing
In order to benchmark the reproducibility of Affymetrix 238K Sty arrays for detecting copy-number alterations. We performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP...
ORGANISM(S): Homo sapiens 
2008-11-13 | E-GEOD-12019 | biostudies-arrayexpress
TranscriptomicsA high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals (RNA-Seq)
Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription...
ORGANISM(S): Mus musculus 
2012-09-11 | E-GEOD-36103 | biostudies-arrayexpress
TranscriptomicsMammalian microRNAs: Experimental evaluation of novel and previously annotated genes
MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences ...
ORGANISM(S): Homo sapiens 
2010-04-26 | E-GEOD-20384 | biostudies-arrayexpress
TranscriptomicsRNA sequencing of mouse DCs
RNA-Seq data were targeted for de novo assembly and reconstruction of full-length mouse transcripts. Sequencing of RNA taken from unstimulated DCs.
ORGANISM(S): Mus musculus 
2011-05-12 | E-GEOD-29209 | biostudies-arrayexpress
GenomicsMapping polycomb complexes in human and mouse embryonic stem cells
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we m...
ORGANISM(S): Mus musculus 
2008-11-01 | E-GEOD-13084 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse ES cells, neural precursor cells and embryonic fibroblasts
Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5. Experiment Overall Design: 3 replicates of wt ES cells, 3 replicates of wt...
ORGANISM(S): Mus musculus 
2008-06-15 | E-GEOD-8024 | biostudies-arrayexpress
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