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TranscriptomicsRNA Subcellular Localization by Paired End diTag Sequencing from ENCODE/GIS
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yijun Ruan mailto:ruanyj@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track i...
ORGANISM(S): Homo sapiens 
2011-11-10 | E-GEOD-33600 | biostudies-arrayexpress
GenomicsAn Estrogen Receptor α-bound Human Chromatin Interactome
We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing an...
ORGANISM(S): Homo sapiens 
2009-09-11 | E-GEOD-18046 | biostudies-arrayexpress
GenomicsComprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes
Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long span paired-end-tag (PET) sequencing approach using 10 Kb genomic DNA inserts to study human genome structural variations (SVs). The use of 10 Kb insert size allows the identification of brea...
ORGANISM(S): Homo sapiens 
2011-04-06 | E-GEOD-26954 | biostudies-arrayexpress
GenomicsLong Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. Genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs. The current application of PET sequencing with...
ORGANISM(S): Homo sapiens 
2012-10-04 | E-GEOD-32674 | biostudies-arrayexpress
GenomicsAn East-Asian polymorphism underlies BCR-ABL mutation-independent resistance to tyrosine kinase inhibitors in chronic myelogenous leukemia
We used massively parallel DNA sequencing of paired-end ditags (DNA-PET) to identify structural genetic factors associated with disease progression and drug-resistance in representative samples from four CML patients and one CML cell line. The functional consequences of our genetic findings were ev...
ORGANISM(S): Homo sapiens 
2012-02-27 | E-GEOD-28303 | biostudies-arrayexpress
TranscriptomicsPPARg dependent expression changes during differentiation of 3T3L1 cell into adipocytes
We profiled PPARg dependent gene expression changes during differntiation of 3T3L1 cell using PPARg siRNA 3T3-L1 (Pre-adipocyte) cell line was induced to differentiate using standard adipocyte differentiation media (IBMX, Dex and Insulin) 48hrs post-confluency. RNA was harvested at day -2 (confluent...
ORGANISM(S): Mus musculus 
2010-04-08 | E-GEOD-12929 | biostudies-arrayexpress
TranscriptomicsTranscriptional profiles of bovine in vivo pre-implantation development
During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology. Here we report the first transcriptome dynamics...
ORGANISM(S): Bos taurus 
2014-09-10 | E-GEOD-59186 | biostudies-arrayexpress
Transcriptomicscomprehensive chromatin interaction in TNF alpha stimulated HUVECs
HUVECs were stimulated and samples were prepared after 0 and 30 min. Chromatin interaction mediated by active RNA polymerase II was detected by ChIA-PET. Samples were made afrer 0 and 30 min after TNF alpha stimulation.
ORGANISM(S): Homo sapiens 
2012-10-13 | E-GEOD-41553 | biostudies-arrayexpress
ProteomicsIdentification of pharmacokinetic markers for safflower injection using a combination of system pharmacology, multicomponent pharmacokinetics, and quantitative proteomics study
Safflower injection (SI), a water-extract preparation from safflower (Carthamus tinctorius L.), has been widely used for the treatment of cardio-cerebrovascular diseases. This work aims to develop an approach for identifying PK markers of cardiovascular herbal medicines using SI as a case study. Fir...
ORGANISM(S): Rattus Norvegicus 
2022-11-15 | PXD038145 |
TranscriptomicsB cell super-enhancers and regulatory clusters recruit AID tumorigenic activity
The antibody gene mutator AID promiscuously damages oncogenes and B cell identity genes leading to chromosomal translocations and tumorigenesis. Why non-immunoglobulin loci are susceptible to AID activity is unknown. Here we study AID-mediated lesions in the context of nuclear architecture and the B...
ORGANISM(S): Mus musculus 
2014-12-04 | E-GEOD-62063 | biostudies-arrayexpress
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