ChIP-SeqIlluminaSequencingTranscriptomeAnnotationTranscriptomicsEuropean Genome-Phenome ArchiveAligning to the human genomeGenomicsGENOMICNucleotideReadsDataReference genomesFull-length cDNAChromatinHigh-throughputAnalysisAssemblySequencesProfilingBiolAnalysesIsolatesAlignmentNCBIEpigeneticATCCQuantificationCladesMicroarrayDemonstrateContigsTranscriptionalAssaySangerHumanMethodsMethodCellsVivoChromosomeFibroblastsImportant for geneChenTranscriptsLibraries
ChIP-Seq16
- Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. (arxiv.org)
- ChIP-Seq generates large quantities of data which can be difficult to process and analyse, particularly for organisms with contig based genomes. (arxiv.org)
- Poorly annotated genomes make a comprehensive analysis of ChIP-Seq data difficult and as such standardized analysis pipelines are lacking. (arxiv.org)
- Methods: We report a computational pipeline that utilizes traditional High-Performance Computing techniques and open source tools for processing and analysing data obtained from ChIP-Seq. (arxiv.org)
- We applied our computational pipeline 'Rapid Analysis of ChIP-Seq data' (RACS) to ChIP-Seq data that was generated in the model organism Tetrahymena thermophila, an example of an organism with a genome that is available in contigs. (arxiv.org)
- Results: To test the performance and efficiency of RACs, we performed control ChIP-Seq experiments allowing us to rapidly eliminate false positives when analyzing our previously published data set. (arxiv.org)
- Conclusions: Altogether, the computational pipeline presented in this report is an efficient and highly reliable tool to analyze genome-wide ChIP-Seq data generated in model organisms with contig-based genomes. (arxiv.org)
- Combining this method with microarray (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows us to detect protein-binding sites scattered across the entire genome. (nig.ac.jp)
- Here, we describe a new method, “Genome Footprinting by high-throughput sequencing (GeF-seq)”, to attain high-resolution mapping of protein-binding sites by combining in vivo DNase I digestion and ChIP-seq. (nig.ac.jp)
- In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)
- Overall design: ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf. (nih.gov)
- Design description: ChIP-Seq Input from IMR90 Cells. (nih.gov)
- ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library LL-I1 were mapped to the human genome using Pash. (nih.gov)
- ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library LL-I1 were processed into density graphs of raw signal representing the aligned read density. (nih.gov)
- We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil line- ages. (lu.se)
- We performed chromatin immunoprecipitation sequencing (ChIP-seq) using a histone 3 lysine 9 acetylation (H3K9ac) mark in peripheral blood mononuclear cells from patients with atherosclerosis with T2D (n = 8) or without T2D (ND, n = 10). (lu.se)
Illumina7
- High-resolution CNV profile generated using SMURF-seq is highly concordant with the profile generated with Illumina WGS. (biomedcentral.com)
- Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. (nature.com)
- Dear all, Now I am assembling a plant genome using illumina 2*100 DNA and RNA-seq paired end reads. (seqanswers.com)
- The Ambion® RNA-Seq Library Construction Kit streamlines high-throughput sequencing of the whole transcriptome and small RNAs, while maintaining strand orientation, on the Illumina® GAII platform. (thermofisher.com)
- Do you currently perform RNA-Seq on the Illumina® platform, or plan to within the next two months? (thermofisher.com)
- Here, we applied Illumina RNA-Seq to study the gene expression patterns associated with resistance to three widely used insecticides (malathion, alphacypermethrin, and lambda-cyhalothrin) in Ae. (cdc.gov)
- Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)
Sequencing22
- Sequencing of restriction enzyme digested normal diploid genome without SMURF-seq. (biomedcentral.com)
- Sequencing normal diploid genome using SMURF-seq. (biomedcentral.com)
- Sequencing SK-BR-3 cancer genome using SMURF-seq. (biomedcentral.com)
- Replicate sequencing run of SK-BR-3 cancer genome using SMURF-seq. (biomedcentral.com)
- SMURF-seq generates fragments at a faster rate than sequencing short molecules directly. (biomedcentral.com)
- Multiplexed sequencing of normal diploid (barcode01) and SK-BR-3 cancer genome (barcode02) in a single sequencing run. (biomedcentral.com)
- In this Methods paper, we present AutoMeDIP-seq, a technique that combines an automated MeDIP protocol with library preparation steps for subsequent secondgeneration sequencing. (diagenode.com)
- Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. (authorea.com)
- A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. (authorea.com)
- 8 provided an update to the OryzaGenome database which includes short-read sequencing data for several non-AA genome Oryza species. (nature.com)
- TCR-Seq (T-cell Receptor Sequencing) is a method used to identify and track specific T cells and their clones. (wikipedia.org)
- Researchers from the University of Illinois at Urbana-Champaign have reported a new technique that can measure the position of every single gene in the nucleus to build a 3D picture of the genome's layout, called tyramide signal amplification sequencing (TSA-Seq). (drugtargetreview.com)
- NEW YORK (GenomeWeb News) - A team from the Chinese Academy of Agricultural Sciences and Gansu Agricultural University used genome sequencing as part of its effort to understand the traits and transmissibility of influenza A H7N9 viruses that are behind a spate of human infections in China. (genomeweb.com)
- From their genome sequencing data, investigators speculated that the increased virulence and transmissibility of the human H7N9 isolates may stem from subtle genetic changes that alter one or two amino acids encoded by H7N9's basic polymerase 2 gene, for instance, and/or shift hemagglutinin interactions with host cell receptors. (genomeweb.com)
- Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. (nih.gov)
- Here, we describe a simple, novel, high-throughput approach to Norovirus and Hepatitis C virus whole genome sequence determination based on RNA shotgun sequencing (also known as RNA-Seq). (ucl.ac.uk)
- Compared with Sanger sequencing, our method had no nucleotide differences in 14,019 nucleotides (nt) for Noroviruses (from a total of 2 Norovirus genomes obtained with Sanger sequencing), and 8 variants in 9,542 nt for Hepatitis C virus (1 variant per 1,193 nt). (ucl.ac.uk)
- We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. (biomedcentral.com)
- ex: Acknowledgement: "This work used the Genome Sequencing Service Center by Stanford Center for Genomics and Personalized Medicine Sequencing Center, supported by the grant award NIH S10OD025212, and NIH/NIDDK P30DK116074. (stanford.edu)
- Two samples were randomly selected for repeat extraction, library preparation and sequencing to evaluate reproducibility of whole genome analysis. (cdc.gov)
- The two populations were tested for differentiation similarities to iCAF and myCAF states through transcriptome-wide RNA-Sequencing (RNA-Seq) including comparison to an available iCAF-myCAF cell state atlas. (lu.se)
- Isolates are characterized using whole genome sequencing to determine serogroup and molecular typing information. (medscape.com)
Transcriptome5
- Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments.We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. (seqanswers.com)
- With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. (seqanswers.com)
- The authors discuss using transcriptome profiles for comprehensive referencing as an alternative to costly genome referencing. (sagescience.com)
- 80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. (nih.gov)
- cortex and hippocampus were dissociated, and the fluorescent cells FACS purified for transcriptome profiling by RNA-seq. (jneurosci.org)
Annotation3
- PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. (nature.com)
- The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. (biomedcentral.com)
- Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)
Transcriptomics2
- Dual-species transcriptomics or dual-RNA-seq studies use transcriptomics to assess the transcriptional profiles of multiple organisms originating from the same sample [ 15 ]. (biomedcentral.com)
- Lung tissue was collected 2 hrs post-overhaul and evaluated via whole genome transcriptomics by RNA-seq. (cdc.gov)
European Genome-Phenome Archive1
- The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure. (ega-archive.org)
Aligning to the human genome1
Genomics1
- BMC Genomics, 2013, 14, 604 Abstract: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. (seqanswers.com)
GENOMIC4
- The ideal whole genome methylation (methylome) assay should be accurate, affordable, high-throughput and agnostic with respect to genomic features. (diagenode.com)
- SPLICE-q uses aligned reads from RNA-Seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns' overlap with other genomic elements, such as exons from other genes. (fu-berlin.de)
- Moreover, as the first gapless genome assembly in the genus Saccharomycopsis including members with desirable traits for bioconversion, the unique genomic features of S. fibuligera and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation. (biomedcentral.com)
- To accomplish this, the Genome Analysis Core provides a broad range of genomic services with expert consultation, customized support, access to state-of-the-art technologies and the highest quality data. (mayo.edu)
Nucleotide3
- The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. (unboundmedicine.com)
- Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. (biomedcentral.com)
- Polyprotein gene regions were identified by nucleotide alignment to EVD68 reference genomes using blastn. (cdc.gov)
Reads7
- Mapping SMURF-seq reads. (biomedcentral.com)
- Because I have just one insert size library, so I got so many denovo assembled contigs using DNA reads , I wanted to improve the assembly using RNA-seq data, I just know that RNAPATH can do this from one genome research pepar publised on 2010. (seqanswers.com)
- But I am wondering if I can feed sspace with RNA-seq reads? (seqanswers.com)
- for RNA-seq, the reads contain many splice. (seqanswers.com)
- I am wondering if you have work out the way to incoporate RNAseq reads into genome assembly. (seqanswers.com)
- The reads are then polished using racon and are re-mapped onto the reference genome. (nanoporetech.com)
- Read Mapping: alignment of reads to a specified reference genome (human, mouse or rat). (lu.se)
Data8
- Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. (authorea.com)
- The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. (authorea.com)
- We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased.The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. (seqanswers.com)
- sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments. (nature.com)
- The RNA-seq and ATAC-seq are raw data in FASTQ format while the genotypes are in the VCF format which was filtered and imputed (more details are available in the main text of the study). (ega-archive.org)
- Furthermore, I provide an in-depth study of time course nascent BrU-Seq data to address questions concerning differences in the speed of splicing and the underlying biological features that might be associated with it. (fu-berlin.de)
- Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. (nih.gov)
- The cells' gene expression signatures were tested for association with clinical outcome of breast cancer patients using survival data from The Cancer Genome Atlas database. (lu.se)
Reference genomes2
Full-length cDNA1
- Researchers used PacBio's Iso-Seq method to sequence full-length cDNA transcripts from ripening Cabernet Savignon berries resulting in 1,5000 cultivar-specific genes. (sagescience.com)
Chromatin1
- alias" : "DRS002605", "center_name" : "MAEBASHI_TECH", "accession" : "DRS002605", "IDENTIFIERS" : { "PRIMARY_ID" : { "label" : "BioSample ID", "content" : "SAMD00010730" } }, "TITLE" : "Genome-wide analysis of in vivo AbrB binding sites in B. subtilis using GeF-seq", "SAMPLE_NAME" : { "TAXON_ID" : 1423, "SCIENTIFIC_NAME" : "Bacillus subtilis" }, "DESCRIPTION" : "Chromatin immunoprecipitation (ChIP) is a common method to map protein-binding sites in vivo. (nig.ac.jp)
High-throughput1
- AutoMeDIP-seq offers a competitive approach to high-throughput methylome analysis of medium to large cohorts. (diagenode.com)
Analysis8
- Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. (biomedcentral.com)
- Moreover, comparative genome analysis of S. fibuligera ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome. (biomedcentral.com)
- RNA-seq analysis of cortical neuron subpopulations. (jneurosci.org)
- The Genome Analysis Core, led by co-directors Eric D. Wieben, Ph.D. , and Julie M. Cunningham, Ph.D., provides consultations to help investigators achieve their research objectives. (mayo.edu)
- The Genome Analysis Core provides services to all Mayo Clinic faculty and staff engaged in research. (mayo.edu)
- Connect with the Genome Analysis Core to discuss your research needs. (mayo.edu)
- Learn about services offered by Mayo Clinic's Genome Analysis Core. (mayo.edu)
- After de-replication, 55 non-redundant representative EVD68 genomes were used for downstream analysis. (cdc.gov)
Assembly3
- Assembly of the O. australiensis genome has previously been challenging due to its high Long Terminal Repeat (LTR) retrotransposon (RT) content. (nature.com)
- Assembly of a high-quality genome for O. australiensis provides an important resource for the discovery of critical genes involved in development and stress tolerance. (nature.com)
- Libraries were pooled based upon estimated read counts needed for whole genome assembly. (cdc.gov)
Sequences3
- It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. (seqanswers.com)
- By comparing those sequences with the genomes of five H7N9 viruses involved in human infections, they found hints about the small genetic changes needed to make the H7N9 more virulent and transmissible in mammals. (genomeweb.com)
- When they compared the genomes to one another and to sequences from five human viruses - including an isolate called A/Anhui/1/2013 from the current outbreak in China - the researchers determined that much of the genome was similar across the isolates. (genomeweb.com)
Profiling1
- Genome-wide methylation profiling for 20 normal cervices, 6 ADC and 6 SCC using MethylCap-seq yielded 53 candidate regions hypermethylated in both ADC and SCC. (oncotarget.com)
Biol2
- Genome Biol. (biomedcentral.com)
- Genome Biol 21 , 214 (2020). (biomedcentral.com)
Analyses3
- These analyses illustrate that SPLICE-q can detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-Seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. (fu-berlin.de)
- analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)
- A number of RNA-Seq quality control analyses summarized in FastQC and MultiQC reports. (lu.se)
Isolates2
- As they reported today in the early, online edition of Science , the researchers sequenced the genomes of more than three-dozen H7N9 isolates collected from birds and poultry market sites. (genomeweb.com)
- To get at the genetics behind the newly emerged flu virus subtype, the team sequenced all eight genes that make up the influenza A genome in 37 of the new H7N9 isolates. (genomeweb.com)
Alignment1
- The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. (nature.com)
NCBI1
- As of August 10, 2000, draft sequence was available for 87% of the human genome (https://www.ncbi.nlm.nih.gov/genome/seq/), and at least 39 prokaryotic genomes, including those of more than a dozen human pathogens, had been completely sequenced https://www.tigr.org/tdb/mdb/mdbcomplete.html). (medscape.com)
Epigenetic2
- In this study, we mapped genome-wide epigenetic changes in patients with type 2 diabetes (T2D) and advanced atherosclerotic disease. (lu.se)
- Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)
ATCC1
- Ten peaks were obtained in the C. glutamicum ATCC 14067 genome including two new peaks related to three operons (RS_01910-RS_01915, RS_15995, and RS_16000). (frontiersin.org)
Quantification1
- In this thesis, I introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. (fu-berlin.de)
Clades2
- To date, the species and cultivars that make up the AA genome clade have provided most of the genetic variation and resources that have led to the success of domesticated rice 4 , while other genome clades have contributed relatively little to domestication. (nature.com)
- Notably, the lack of sulfate assimilation genes in the S. fibuligera genome reflects a unique phenotype for Saccharomycopsis clades as natural sulfur auxotrophs. (biomedcentral.com)
Microarray1
- The design and construction of a DNA microarray for any given microbial genome are straightforward. (medscape.com)
Demonstrate2
- Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment. (authorea.com)
- To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. (seqanswers.com)
Contigs1
- Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. (nature.com)
Transcriptional1
- Tiling a given promoter region with several sgRNAs can produce more robust transcriptional activation 9 - 11 , but this requirement presents enormous challenges for scalability, and in particular for establishing pooled, genome-wide GOF screens. (cdc.gov)
Assay1
Sanger1
- No discrepancies were observed across 118,757 nt compared between Sanger and our custom RNA-Seq method in 16 samples. (ucl.ac.uk)
Human2
- Distribution of length between restriction sites computed by measuring the distance between the recognition sites on the human reference genome. (biomedcentral.com)
- Despite the human genome being first sequenced almost 20 years ago, researchers know comparatively little about how the genome is organised within cells. (drugtargetreview.com)
Methods2
- We have four core methods for the preparation of RNA-seq libraries. (nanoporetech.com)
- To date, various genome-scale loss-of-function screening methods have been developed, including approaches employing RNA interference 1 , 2 and the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) adaptive immune system 3 , 4 . (cdc.gov)
Method3
- This method is among the most used in the generation of libraries for TCR-seq as it can capture a great deal of the diversity of the TCR through the primer pool. (wikipedia.org)
- The BluePippn was used to size select 1-2 kbp, 2-3 kbp, 3-6 kbp, and 5-10 kbp fractions for cDNA SMRTbell library construction for the Iso-Seq method. (sagescience.com)
- Strong correlations were obtained between observed and expected read counts in all cases, with no evidence of length bias, showing that each method of RNA-seq is low bias. (nanoporetech.com)
Cells2
- The selected T cells rapidly divide and differentiate into effector T-cells through a process called clonal expansion, which retains the TCR sequence (including the CDR3 sequence) that originally recognized the antigen TCR-Seq uses the unique nature of the TCR - in particular CDR3 - as a molecular barcode to track T cells through a variety of processes like differentiation and proliferation, which can be used for a wide variety of purposes. (wikipedia.org)
- The researchers say that the technique still needs to be improved, but they hope to use TSA-Seq to map the positions of genes in other cell types and examine how these positions change as cells develop or become diseased. (drugtargetreview.com)
Vivo1
- This study provides the first genome-wide captures of the dynamics of in vivo AmtR binding events and the regulatory network they define. (frontiersin.org)
Chromosome1
- Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. (frontiersin.org)
Fibroblasts1
- Inference of origin in interlobular and lobular fibroblasts relied on RNA-Seq profiles, immunocytochemistry and growth characteristics. (lu.se)
Important for gene1
- Contig-based genomes often have poor annotations for cis-elements, for example enhancers, that are important for gene expression. (arxiv.org)
Chen1
- Yu Chen, Andrew Belmont , and colleagues from the University of Illinois at Urbana-Champaign developed the TSA-Seq technique that allows the distance of every gene from specific nuclear landmarks to be measured simultaneously, in a collaborative study. (drugtargetreview.com)
Transcripts1
- Kuang, Y.-Y. & Sun, X.-W. L_RNA_scaffolder: scaffolding genomes with transcripts. (seqanswers.com)
Libraries2
- Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. (seqanswers.com)
- We evaluated all four RNA-seq approaches by making libraries from the ERCC spike-in panel (Fig. 2). (nanoporetech.com)