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TranscriptomicsMapping translocation breakpoints by next-generation sequencing
Balanced chromosome rearrangements (BCRs) can cause genetic diseases by disrupting or inactivating specific genes, and the characterisation of breakpoints in disease-associated BCRs has been instrumental in the molecular elucidation of a wide variety of genetic disorders. However, mapping chromosome...
ORGANISM(S): Homo sapiens 
2010-05-22 | E-GEOD-10115 | biostudies-arrayexpress
GenomicsDNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that ...
ORGANISM(S): Homo sapiens 
2010-04-02 | E-GEOD-21159 | biostudies-arrayexpress
TranscriptomicsDeepCAGE and DeepSAGE with proliferating and differentiated C2C12 mouse myoblasts
We use tag-based next generation sequencing analysis to quantify gene expression levels during myogenic differentiation and focused on the identifcation of novel 3' ends with DeepSAGE and novel 5' ends with DeepCAGE. Illumina DeepCAGE and DeepSAGE with C2C12 cells at time points T0 (proliferating) a...
ORGANISM(S): Mus musculus 
2010-07-06 | E-GEOD-21580 | biostudies-arrayexpress
TranscriptomicsSequencing random oligonucleotides using standard GA II protocol
Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina...
ORGANISM(S): synthetic construct 
2012-07-23 | E-GEOD-36540 | biostudies-arrayexpress
TranscriptomicsNext Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Small RNA, after 1 week pressure overload
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies. 5 female mice were subjected to a sham operation, and 5 female mice were subjected to transv...
ORGANISM(S): Mus musculus 
2014-04-18 | E-GEOD-56891 | biostudies-arrayexpress
TranscriptomicsHigh-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing
We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index...
ORGANISM(S): Danio rerio 
2010-09-30 | E-GEOD-20682 | biostudies-arrayexpress
TranscriptomicsNext Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Small RNA
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies. We have made widespread use of Illumina sequencing technologies for RNA quantitation in seve...
ORGANISM(S): Mus musculus 
2014-03-12 | E-GEOD-55791 | biostudies-arrayexpress
TranscriptomicsRNA-Seq anlalysis of prostate cancer cell lines using Next Generation Sequencing
Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generatio...
ORGANISM(S): Homo sapiens 
2011-05-09 | E-GEOD-29155 | biostudies-arrayexpress
TranscriptomicsChimeraScan: A tool for identifying chimeric transcription in sequencing data
Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts. Thre...
ORGANISM(S): Homo sapiens 
2011-09-01 | E-GEOD-29098 | biostudies-arrayexpress
TranscriptomicsNext Generation Sequencing of Wild-Type C57BL/6J Mouse Cardiac Small RNA
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison of RNA abundances within tissues and cells in a manner not possible with previous microarray technologies. We have made widespread use of Illumina sequencing technologies for RNA quantitation in seve...
ORGANISM(S): Mus musculus 
2014-03-12 | E-GEOD-55789 | biostudies-arrayexpress
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