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TranscriptomicsHOXA3 expression in wound tissue
To investigate how HOXA3 expression in wound tissue alters gene expression to control selective recruitment of bone marrow-derived cell populations, we utilized murine whole genome expression arrays (MEEBO arrays) to identify differentially expressed genes in cutaneous wounds from db/db (diabetic) m...
ORGANISM(S): Mus musculus 
2009-10-12 | E-GEOD-13324 | biostudies-arrayexpress
TranscriptomicsRNA Capture-Seq resolves the deep complexity of the human transcriptome (454)
Transcriptomic analyses have revealed an unexpected complexity of the human transcriptome, whose breadth and depth exceeds current RNA sequencing capacity 1-3. Here we combine tiling arrays and RNA sequencing technologies, in an approach we term RNA Capture-Seq, to enable the assembly and characteri...
ORGANISM(S): Homo sapiens 
2011-09-12 | E-GEOD-29040 | biostudies-arrayexpress
TranscriptomicsMany Human Large Intergenic Non-coding RNAs Associate with Chromatin Modifying Complexes and Affect Gene Expression
We recently showed that the mammalian genome encodes more than a thousand large intergenic non-coding RNAs (lincRNAs) that are clearly conserved across mammals and thus functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes including cell cycle regulatio...
ORGANISM(S): Homo sapiens 
2009-07-09 | E-GEOD-16226 | biostudies-arrayexpress
GenomicsIntegrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
The tumor suppressor p53 has been studied extensively as a direct transcriptional activator of protein-coding genes. Recent studies, however, have shed light on novel regulatory functions of p53 within noncoding regions of the genome. Here, we use a systematic approach that integrates transcriptom...
ORGANISM(S): Homo sapiens 
2015-04-18 | E-GEOD-55727 | biostudies-arrayexpress
TranscriptomicsThe transposable element composition of human lincRNAs reveals a role for HERVH elements to promote stem cell specific expression of lincRNAs
Numerous studies over the past decade have elucidated a substantial set of long intergenic noncoding RNAs (lincRNAs). It has since become clear that lincRNAs constitute an important layer of genome regulation across a wide spectrum of species. Yet, the factors governing their evolution and origins r...
ORGANISM(S): Homo sapiens 
2013-01-22 | E-GEOD-38993 | biostudies-arrayexpress
TranscriptomicsHOXA13 Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set
HOXA13 Binding sites were located genome wide in primary human foreskin fibroblasts Tiled promoters with a probe per 100bp of refseq known genes 3kb upstream and 700 bp downstream of transcriptional start
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-9922 | biostudies-arrayexpress
TranscriptomicsA large intergenic non-coding RNA induced by p53 mediates global gene repression in the p53 transcriptional response
Recently, more than a thousand large intergenic non-coding RNAs (lincRNAs) have been reported. These RNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Here, we report the identification of lincRNAs that are regulated by p53. One of ...
ORGANISM(S): Mus musculus 
2010-08-09 | E-GEOD-21761 | biostudies-arrayexpress
TranscriptomicsLarge intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells (LincRNA expression)
Expression profiling of non coding RNAs using tilling arrays from ES, Fibroblasts and Fibroblasts derived iPSC LincRNA profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derive...
ORGANISM(S): Homo sapiens 
2010-11-10 | E-GEOD-24181 | biostudies-arrayexpress
TranscriptomicsLarge intergenic non-coding RNAs as novel modulators of reprogramming: ESCs, fibroblast, and fibroblast-derived iPSC (gene expression)
Gene expression profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derived iPSC lines, then hybridized to Affymetrix arrays Affymetrix Human Genome U133 Plus 2.0 Array [Affy_HG...
ORGANISM(S): Homo sapiens 
2010-11-10 | E-GEOD-23968 | biostudies-arrayexpress
TranscriptomicsLarge intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells (LincRNA expression)
LincRNA expression profiles of human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells Total RNA was extracted from human ESCs, CD34+ cells, and CD34+ derived iPSC lines, then hybridized to Nimblegen tiling array GPL8792; Human lincRNA 391k Tiling Array V2
ORGANISM(S): Homo sapiens 
2010-11-10 | E-GEOD-23970 | biostudies-arrayexpress
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