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GenomicsIn vivo live imaging of RNA polymerase II transcription factories in primary cells
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thou...
ORGANISM(S): Mus musculus 
2013-05-13 | E-GEOD-46849 | biostudies-arrayexpress
GenomicsThe inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.
3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps...
ORGANISM(S): Mus musculus 
2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress
TranscriptomicsThe role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis (Affymetrix)
The first site exhibiting hematopoietic activity in mammalian development is the yolk sac blood island, which originates from the hemangioblast. Here we performed differentiation assays, as well as genome-wide molecular and functional studies in BL-CFCs to gain insight into the function of the essen...
ORGANISM(S): Mus musculus 
2013-02-09 | E-GEOD-43042 | biostudies-arrayexpress
TranscriptomicsThe role of Ldb1 in hemangioblast development: genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis (sequencing)
The first site exhibiting hematopoietic activity in mammalian development is the yolk sac blood island, which originates from the hemangioblast. Here we performed differentiation assays, as well as genome-wide molecular and functional studies in BL-CFCs to gain insight into the function of the essen...
ORGANISM(S): Mus musculus 
2013-02-09 | E-GEOD-43041 | biostudies-arrayexpress
TranscriptomicsRNAi knock down of SWI-SNF subunits BRM, MOR, SNR1, OSA, PB, BAP170 and ISWI in Drosophila
RNAi knockdown of SWI-SNF subunits BRM, MOR, SNR1, OSA, PB, BAP170 and ISWI
ORGANISM(S): Drosophila melanogaster 
2007-03-01 | E-TABM-169 | biostudies-arrayexpress
TranscriptomicsEarly divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes
Helper T cells can adopt a number of different phenotypes. We performed microarray-assisted mRNA profiling on antigen-stimulated, TCR transgenic murine splenocytes that were cultured in the presence of cytokines. Transcriptome snapshots of Th cells differentiating into Th1 and Th2 phenotypes were o...
ORGANISM(S): Mus musculus 
2013-03-01 | E-MTAB-1475 | biostudies-arrayexpress
GenomicsGenome-wide DNA methylation profiles of non-small cell lung carcinomas and control lung tissues
Purpose: Generate genome-wide methylation profiles of non-small cell lung carcinomas (NSCLC) and their matching lung tissues for detection of hypermethylated and hypomethylated regions present in the tumors. Methods: MethylCapture followed by next-generation sequencing (Illumina GAIIx) of 7 nsclc tu...
ORGANISM(S): Homo sapiens 
2012-10-05 | E-GEOD-41343 | biostudies-arrayexpress
TranscriptomicsExpression profiling of peripheral blood of chronic HCV infection
In the present study, we studied chronic HCV patients who responded to IFN-based therapy as evidenced by absence of HCV RNA at the end of treatment, and focused on two issues that have not received much attention. Firstly, we evaluated whether specific genes or gene expression patterns in blood were...
ORGANISM(S): Homo sapiens 
2014-09-02 | E-GEOD-59312 | biostudies-arrayexpress
GenomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq]
CTCF and CTCFL DNA binding profile in CTCFL induced and non-induced ES cells.CTCF is a highly conserved and essential zinc finger protein that in conjunction with cohesin organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the tes...
ORGANISM(S): Mus musculus 
2012-07-25 | E-GEOD-34094 | biostudies-arrayexpress
TranscriptomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression]
CTCFL binding to DNA and the effect of CTCFL expression in ES cells RNA extracted from CTCFL induced and non-induced ES cells was hybridized on Affymetrix Mouse Gene 1.0ST arrays
ORGANISM(S): Mus musculus 
2012-07-24 | E-GEOD-34092 | biostudies-arrayexpress
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