Structured Review

Illumina Inc illumina hiseq instrument
Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an <t>Illumina</t> <t>HiSeq</t> 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).
Illumina Hiseq Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 176 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina hiseq instrument/product/Illumina Inc
Average 99 stars, based on 176 article reviews
Price from $9.99 to $1999.99
illumina hiseq instrument - by Bioz Stars, 2020-09
99/100 stars

Images

1) Product Images from "Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology"

Article Title: Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2013.10.002

Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).
Figure Legend Snippet: Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).

Techniques Used: Derivative Assay, Formalin-fixed Paraffin-Embedded, Sonication, Amplification, Polymerase Chain Reaction, Hybridization, Variant Assay

2) Product Images from "Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma"

Article Title: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

Journal: Genome Research

doi: 10.1101/gr.126516.111

Hive plots showing alignment of three Fusobacterium genomes. Approximately 32 million high-quality WGS Illumina HiSeq reads (≥99 consecutive Q30 bases) from Fusobacterium tumor isolate CC53 were assembled with SSAKE (v3.7, default options) into
Figure Legend Snippet: Hive plots showing alignment of three Fusobacterium genomes. Approximately 32 million high-quality WGS Illumina HiSeq reads (≥99 consecutive Q30 bases) from Fusobacterium tumor isolate CC53 were assembled with SSAKE (v3.7, default options) into

Techniques Used:

3) Product Images from "Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology"

Article Title: Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2013.10.002

Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).
Figure Legend Snippet: Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).

Techniques Used: Derivative Assay, Formalin-fixed Paraffin-Embedded, Sonication, Amplification, Polymerase Chain Reaction, Hybridization, Variant Assay

Related Articles

Sequencing:

Article Title: Direct determination of diploid genome sequences
Article Snippet: .. Sequencing was conducted with an Illumina HiSeq X with 2x150 paired-end reads based on manufacturer's protocols. .. Internal representation of Supernova assembliesAn assembly is first represented as a directed graph in which each edge represents a single strand of DNA sequence.

Article Title: SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples
Article Snippet: .. Paired-End 150 sequencing was performed using the HiSeq X Ten platform (Illumina, San Diego, CA) supporting dual indexing with raw sequencing depths over 20,000×. .. Duplex consensus sequence generation The complete computational workflow of the SinoDuplex approach is illustrated in .

Article Title: First de novo whole genome sequencing and assembly of the bar-headed goose
Article Snippet: .. De novo sequencing was conducted with an Illumina HiSeq X Ten platform. ..

Construct:

Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

Purification:

Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

cDNA Library Assay:

Article Title: Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L
Article Snippet: .. The cDNA library was sequenced with a 100-bp paired-end format using the Illumina HiSeq X Ten, and each sample yielded more than 6 Gb of clean data. ..

Polymerase Chain Reaction:

Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

ChIP-sequencing:

Article Title: Tandem Directional CTCF Sites Balance Protocadherin Promoter Usage
Article Snippet: .. ChIP-seq libraries were sequenced on a HiSeq X Ten Platform (Illumina). .. Quantitative High-resolution Chromatin Conformation Capture Copy (QHR-4C)The QHR-4C protocol was modified from previously published method [ ].

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  • 90
    Illumina Inc hiseq 4000 instrument
    Single cell RNA sequencing of ex vivo human bone marrow HSCs a. Experimental design. Sternal bone marrow was harvested from 5 individuals undergoing sternotomy for heart valve replacement. It was stained with antibodies for surface markers that define the human HSC population and sorted as single cells using index FACS into cell lysis buffer. Single cell RNA sequencing libraries were then prepared, sequenced on a <t>HiSeq</t> 4000 instrument and analysis was performed as described in Methods; b. Cell filtering. Performed using a SVM machine learning method (modified from a previously described model 37 ) trained on cDNA from HSCs selected by expression of the housekeeping gene GAPDH. High and low quality cells shown by mitochondrial mapping (ChrM), ERCC ratio (ERCC), exonic ratio (Exon), number of called genes (Genes). Green denotes high quality, red denotes low quality. Out of 884 cells, 119 were taken forward for further analysis based on high quality; c. Filtered cells are larger. Flow cytometric plot FSC/SSC showing cells filtered as high quality by the SVM machine learning method. Green denotes high quality, red denotes low quality; d. Gene filtering. Variance of normalized log-expression values for each gene in the HSC dataset, plotted against the mean log-expression. Variance estimates for ERCC spike-in transcripts and curve fit are highlighted in red. Blue dots represent highly varying genes (n=2000).
    Hiseq 4000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc hiseq 2000 instrument
    Sampling and major sources of variation . Strains CT43 and ATCC10792 grown in two medium lots #1091744 and 7220443 in water taken from building 1520 and 1610. Bacteria were cultured on four different dates and four biological replicates were grown to mid-log phase for each date, harvested and then RNA-seq data were generated using an Illumina <t>Hiseq</t> 2000 instrument.
    Hiseq 2000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 1056 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc hiseq 2000 sequencing instrument
    Comparison of expression profiles of selected genes as determined by Illumina <t>HiSeq</t> 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.
    Hiseq 2000 Sequencing Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Price from $9.99 to $1999.99
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    85
    Illumina Inc hiseq sequencing reads gpar clip
    <t>gPAR-CLIP</t> captures known RBP crosslinking signatures . (a) Overlap of crosslinking sites identified in Puf3p PAR-CLIP and wild-type (WT) gPAR-CLIP. Puf3p PAR-CLIP crosslinking sites with > 1% T-to-C conversion rate (Additional file 8 ) were considered captured by gPAR-CLIP if at least 50% of their nucleotides overlapped with a WT gPAR-CLIP crosslinking site with FDR
    Hiseq Sequencing Reads Gpar Clip, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Single cell RNA sequencing of ex vivo human bone marrow HSCs a. Experimental design. Sternal bone marrow was harvested from 5 individuals undergoing sternotomy for heart valve replacement. It was stained with antibodies for surface markers that define the human HSC population and sorted as single cells using index FACS into cell lysis buffer. Single cell RNA sequencing libraries were then prepared, sequenced on a HiSeq 4000 instrument and analysis was performed as described in Methods; b. Cell filtering. Performed using a SVM machine learning method (modified from a previously described model 37 ) trained on cDNA from HSCs selected by expression of the housekeeping gene GAPDH. High and low quality cells shown by mitochondrial mapping (ChrM), ERCC ratio (ERCC), exonic ratio (Exon), number of called genes (Genes). Green denotes high quality, red denotes low quality. Out of 884 cells, 119 were taken forward for further analysis based on high quality; c. Filtered cells are larger. Flow cytometric plot FSC/SSC showing cells filtered as high quality by the SVM machine learning method. Green denotes high quality, red denotes low quality; d. Gene filtering. Variance of normalized log-expression values for each gene in the HSC dataset, plotted against the mean log-expression. Variance estimates for ERCC spike-in transcripts and curve fit are highlighted in red. Blue dots represent highly varying genes (n=2000).

    Journal: bioRxiv

    Article Title: Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation

    doi: 10.1101/2020.02.20.957936

    Figure Lengend Snippet: Single cell RNA sequencing of ex vivo human bone marrow HSCs a. Experimental design. Sternal bone marrow was harvested from 5 individuals undergoing sternotomy for heart valve replacement. It was stained with antibodies for surface markers that define the human HSC population and sorted as single cells using index FACS into cell lysis buffer. Single cell RNA sequencing libraries were then prepared, sequenced on a HiSeq 4000 instrument and analysis was performed as described in Methods; b. Cell filtering. Performed using a SVM machine learning method (modified from a previously described model 37 ) trained on cDNA from HSCs selected by expression of the housekeeping gene GAPDH. High and low quality cells shown by mitochondrial mapping (ChrM), ERCC ratio (ERCC), exonic ratio (Exon), number of called genes (Genes). Green denotes high quality, red denotes low quality. Out of 884 cells, 119 were taken forward for further analysis based on high quality; c. Filtered cells are larger. Flow cytometric plot FSC/SSC showing cells filtered as high quality by the SVM machine learning method. Green denotes high quality, red denotes low quality; d. Gene filtering. Variance of normalized log-expression values for each gene in the HSC dataset, plotted against the mean log-expression. Variance estimates for ERCC spike-in transcripts and curve fit are highlighted in red. Blue dots represent highly varying genes (n=2000).

    Article Snippet: 150 base pair (bp) paired-end sequencing was performed on the Illumina HiSeq 4000 instrument using TruSeq reagents (Illumina), according to manufacturer’s instructions.

    Techniques: RNA Sequencing Assay, Ex Vivo, Staining, FACS, Lysis, Modification, Expressing

    Sampling and major sources of variation . Strains CT43 and ATCC10792 grown in two medium lots #1091744 and 7220443 in water taken from building 1520 and 1610. Bacteria were cultured on four different dates and four biological replicates were grown to mid-log phase for each date, harvested and then RNA-seq data were generated using an Illumina Hiseq 2000 instrument.

    Journal: Frontiers in Microbiology

    Article Title: Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets

    doi: 10.3389/fmicb.2016.00794

    Figure Lengend Snippet: Sampling and major sources of variation . Strains CT43 and ATCC10792 grown in two medium lots #1091744 and 7220443 in water taken from building 1520 and 1610. Bacteria were cultured on four different dates and four biological replicates were grown to mid-log phase for each date, harvested and then RNA-seq data were generated using an Illumina Hiseq 2000 instrument.

    Article Snippet: Samples were diluted according to manufacturer's recommendations using the Illumina dilution calculator, and sequence data was generated via two runs using an Illumina HiSeq 2000 instrument with SR50 sequencing kits (50 bp single end reads) and using phiX control DNA (Illumina, Inc., San Diego, CA, USA), as previously described (Wilson et al., ).

    Techniques: Sampling, Cell Culture, RNA Sequencing Assay, Generated

    Comparison of expression profiles of selected genes as determined by Illumina HiSeq 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.

    Journal: PeerJ

    Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon

    doi: 10.7717/peerj.8107

    Figure Lengend Snippet: Comparison of expression profiles of selected genes as determined by Illumina HiSeq 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.

    Article Snippet: Sequencing and de novo assembly cDNA libraries from mRNAs extracted from the hepatopancreas, haemolymph and muscle tissue of surviving WSSV-challenged shrimp and control shrimp were subjected to a run on the Illumina HiSeq 2000 sequencing instrument, resulting in 55,692,118 and 56,206,168 raw reads respectively.

    Techniques: Expressing, Sequencing, Quantitative RT-PCR

    gPAR-CLIP captures known RBP crosslinking signatures . (a) Overlap of crosslinking sites identified in Puf3p PAR-CLIP and wild-type (WT) gPAR-CLIP. Puf3p PAR-CLIP crosslinking sites with > 1% T-to-C conversion rate (Additional file 8 ) were considered captured by gPAR-CLIP if at least 50% of their nucleotides overlapped with a WT gPAR-CLIP crosslinking site with FDR

    Journal: Genome Biology

    Article Title: Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

    doi: 10.1186/gb-2013-14-2-r13

    Figure Lengend Snippet: gPAR-CLIP captures known RBP crosslinking signatures . (a) Overlap of crosslinking sites identified in Puf3p PAR-CLIP and wild-type (WT) gPAR-CLIP. Puf3p PAR-CLIP crosslinking sites with > 1% T-to-C conversion rate (Additional file 8 ) were considered captured by gPAR-CLIP if at least 50% of their nucleotides overlapped with a WT gPAR-CLIP crosslinking site with FDR

    Article Snippet: Data processing of Illumina HiSeq sequencing reads gPAR-CLIP, PAR-CLIP, and mRNA-seq reads were processed to remove linkers, sorted into libraries based on six-nucleotide barcodes (underlined residues above), and removed if they were low quality (Additional file ).

    Techniques: Cross-linking Immunoprecipitation

    RBP crosslinking sites exhibit global sequence conservation . (a) Average ribosome depleted mRNA-seq and gPAR-CLIP read distributions across 5' UTR, CDS, and 3' UTR regions for all libraries. Error bar: 1 standard deviation. RPKM: reads per million mapped reads per kilobase. (b) Cumulative distribution of CLS values from wild-type (WT) libraries. (c) Proportion of Ts in crosslinking site binned by crosslinking site coverage (reads per million mapped reads (RPM)). The dashed red line indicates average T content of all crosslinking sites. (d) Number of conserved blocks in 3' and 5' UTRs overlapping 100% with WT gPAR-CLIP crosslinking sites (χ 2 P -values indicated). Control blocks were randomly generated within 3' and 5' UTRs to match the number and size of conserved blocks. (e) Two major gPAR-CLIP crosslinking sites in ATG8 3' UTR (top) and TOM40 3' UTR (bottom) overlapping conserved blocks. (f) Mean phastCons scores for Ts ranked and binned by CLS. Control lines represent mean phastCons scores of randomly ranked and binned Ts with no CLS, repeated ten times.

    Journal: Genome Biology

    Article Title: Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

    doi: 10.1186/gb-2013-14-2-r13

    Figure Lengend Snippet: RBP crosslinking sites exhibit global sequence conservation . (a) Average ribosome depleted mRNA-seq and gPAR-CLIP read distributions across 5' UTR, CDS, and 3' UTR regions for all libraries. Error bar: 1 standard deviation. RPKM: reads per million mapped reads per kilobase. (b) Cumulative distribution of CLS values from wild-type (WT) libraries. (c) Proportion of Ts in crosslinking site binned by crosslinking site coverage (reads per million mapped reads (RPM)). The dashed red line indicates average T content of all crosslinking sites. (d) Number of conserved blocks in 3' and 5' UTRs overlapping 100% with WT gPAR-CLIP crosslinking sites (χ 2 P -values indicated). Control blocks were randomly generated within 3' and 5' UTRs to match the number and size of conserved blocks. (e) Two major gPAR-CLIP crosslinking sites in ATG8 3' UTR (top) and TOM40 3' UTR (bottom) overlapping conserved blocks. (f) Mean phastCons scores for Ts ranked and binned by CLS. Control lines represent mean phastCons scores of randomly ranked and binned Ts with no CLS, repeated ten times.

    Article Snippet: Data processing of Illumina HiSeq sequencing reads gPAR-CLIP, PAR-CLIP, and mRNA-seq reads were processed to remove linkers, sorted into libraries based on six-nucleotide barcodes (underlined residues above), and removed if they were low quality (Additional file ).

    Techniques: Sequencing, Cross-linking Immunoprecipitation, Standard Deviation, Generated

    gPAR-CLIP identifies transcriptome-wide RBP crosslinking sites . (a) Schematic of the gPAR-CLIP protocol. (b) Reproducibility of crosslinking sites generated from replicate gPAR-CLIP libraries prepared from yeast grown in synthetic defined media (abbreviated as WT gPAR-CLIP hereafter). Pearson correlation coefficient is indicated. Inset: distribution of log 2 crosslinking site RPM ratios between replicates. Replicate error σ = 1.3-fold. (c) Length distribution of crosslinking sites in WT gPAR-CLIP libraries. Dotted line: average crosslinking site length of 23 nucleotides. (d) Pearson correlation coefficients of total mRNA-seq and gPAR-CLIP read coverage between 5' UTR, CDS, and 3' UTR regions as well as correlation coefficients of ribosome depleted (-ribosome) mRNA-seq and gPAR-CLIP read coverage between replicate WT libraries.

    Journal: Genome Biology

    Article Title: Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

    doi: 10.1186/gb-2013-14-2-r13

    Figure Lengend Snippet: gPAR-CLIP identifies transcriptome-wide RBP crosslinking sites . (a) Schematic of the gPAR-CLIP protocol. (b) Reproducibility of crosslinking sites generated from replicate gPAR-CLIP libraries prepared from yeast grown in synthetic defined media (abbreviated as WT gPAR-CLIP hereafter). Pearson correlation coefficient is indicated. Inset: distribution of log 2 crosslinking site RPM ratios between replicates. Replicate error σ = 1.3-fold. (c) Length distribution of crosslinking sites in WT gPAR-CLIP libraries. Dotted line: average crosslinking site length of 23 nucleotides. (d) Pearson correlation coefficients of total mRNA-seq and gPAR-CLIP read coverage between 5' UTR, CDS, and 3' UTR regions as well as correlation coefficients of ribosome depleted (-ribosome) mRNA-seq and gPAR-CLIP read coverage between replicate WT libraries.

    Article Snippet: Data processing of Illumina HiSeq sequencing reads gPAR-CLIP, PAR-CLIP, and mRNA-seq reads were processed to remove linkers, sorted into libraries based on six-nucleotide barcodes (underlined residues above), and removed if they were low quality (Additional file ).

    Techniques: Cross-linking Immunoprecipitation, Generated