19 Result(s)
within
Fatih Ozsolak
English
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Protocol
Quantitative Polyadenylation Site Map** with Single-Molecule Direct RNA Sequencing
The known regulatory role of 3′ untranslated regions (3′UTRs) and poly(A) tails in RNA localization, stability, and translation, and polyadenylation regulation defects leading to human diseases such as oculoph...
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Article
Correction: Corrigendum: RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis
Nature 487, 510–513 (2012); doi:10.1038/nature11217 In this Letter, we omitted the following accession information. The digital gene expression matrix and the Helicos single-molecule sequence data from which i...
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Article
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
RNA 3′-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3′ ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogen...
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Article
RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis
A new method allows the collection of circulating tumour cells (CTCs) despite their rarity; transcriptome sequencing of CTCs could allow identification of pathways involved in metastasis.
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Protocol
Profiling of Short RNAs Using Helicos Single-Molecule Sequencing
The importance of short (<200 nt) RNAs in cell biogenesis has been well documented. These short RNAs include crucial classes of molecules such as transfer RNAs, small nuclear RNA, microRNAs, and many others (r...
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Chapter
Recent Advances in Sequencing Technology
As we celebrate the tenth anniversary of the sequencing of the first human genome, we recognize the remarkable technological innovation that now provides the ability to resequence thousands of human genomes a ...
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Article
Open AccessErratum to: The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
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Article
Erratum: The Lkb1 metabolic sensor maintains haematopoietic stem cell survival
Nature 468, 659–663 (2010) In this Article, Figs 1f and 2e appeared incorrectly (the corrected figure parts are shown below). In Fig. 1f, the y-axis of the CLP graph should read “Cells (×102)” and the y-axis o...
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Article
RNA sequencing: advances, challenges and opportunities
Powered by improving next-generation sequencing capabilities, RNA-seq studies continue to provide knowledge about the quantitative and qualitative aspects of t...
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Protocol
Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing
Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to...
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Article
Open AccessThe majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
Discovery that the transcriptional output of the human genome is far more complex than predicted by the current set of protein-coding annotations and that most RNAs produced do not appear to encode proteins ha...
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Article
The Lkb1 metabolic sensor maintains haematopoietic stem cell survival
Haematopoietic stem cells (HSCs) can convert between growth states that have marked differences in bioenergetic needs. Although often quiescent in adults, these cells become proliferative upon physiological de...
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Article
Amplification-free digital gene expression profiling from minute cell quantities
On-flowcell capture and reverse transcription followed by single-molecule cDNA sequencing provides reproducible digital gene expression results from as few as 1,000 cells.
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Article
New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism
An analysis of short RNAs (with fewer than 200 nucleotides) from human cells using single molecule high-throughput sequencing has uncovered a previously unknown short RNA species with a difference. They all ha...
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Article
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
Single-molecule sequencing of poly(A)-tailed chromatin immunoprecipitated DNA proves equal in sensitivity and accuracy to amplification-based sequencing technologies and allows analysis of samples sizes as sma...
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Article
Direct RNA sequencing
Understanding the functional output of the genome — the sum total of messenger RNAs in a cell or cell population, known as the transcriptome — is an essential step on the way to understanding biology. Current ...
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Article
High-throughput map** of the chromatin structure of human promoters
Our understanding of how chromatin structure influences cellular processes such as transcription and replication has been limited by a lack of nucleosome-positioning data in human cells. We describe a high-res...
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Article
Open AccessComparison of dot chromosome sequences from D. melanogaster and D. virilisreveals an enrichment of DNA transposon sequences in heterochromatic domains
Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. I...
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Chapter
mRNA Applications
