Chez Charles/ tags/ pages tagged sequence_tags
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NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.
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Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler
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Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers.
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Unamplified cap analysis of gene expression on a single-molecule sequencer.
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Genome annotation by high-throughput 5' RNA end determination.
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Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
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Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
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5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
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Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation.
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Identification and prevention of a GC content bias in SAGE libraries.
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The significance of digital gene expression profiles.
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The comparison of gene expression from multiple cDNA libraries.
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aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells.
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Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite.
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Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements.
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Analysis of human transcriptomes.
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5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation.
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The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
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Serial analysis of gene expression in a single cell.
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A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design.
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Disruption of promoter memory by synthesis of a long noncoding RNA.
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Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
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Efficient and quantitative high-throughput tRNA sequencing.
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ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.
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NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
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Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.
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CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors.
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Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells.
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Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
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Counting absolute numbers of molecules using unique molecular identifiers.
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Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.
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Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE.
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Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
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Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy.
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Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.
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Accurate whole human genome sequencing using reversible terminator chemistry.
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Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
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Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling.
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Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two Sites in the DNA Target.
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High-throughput verification of transcriptional starting sites by Deep-RACE.
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The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection.
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Transcriptome analysis by strand-specific sequencing of complementary DNA.
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FRT-seq: amplification-free, strand-specific transcriptome sequencing.
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The primary transcriptome of the major human pathogen Helicobacter pylori.
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Optimized design and data analysis of tag-based cytosine methylation assays.
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Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer.
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A paired-end sequencing strategy to map the complex landscape of transcription initiation.
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Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
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Mammalian microRNAs predominantly act to decrease target mRNA levels.
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Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.
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Genome-wide measurement of RNA secondary structure in yeast.
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Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.
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