hiseq 2500 platform  (Illumina Inc)

 
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    Name:
    HiSeq 2500 Installation and Operational Qualification
    Description:
    Comprehensive Qualification Services from Illumina Illumina Installation and Operational Qualification IQ OQ services carry out numerous experiments for each system to ensure critical components are tested and validated have cut off metrics and to confirm these metrics show the system is operating in accordance with specifications Our IQ service provides documented verification that instrument is installed according to our specifications and safety regulations During the IQ a trained engineer verifies latest supported firmware and software versions were installed verifies instrument setup and accessory logistics checks physical and environmental safety conditions are met and provides a signed audit ready report Our OQ service follows a comprehensive well defined protocol to verify the system functions according to pre set and validated operational specifications We update the OQ protocol following each instrument hardware and software release ensuring your laboratory receives the most up to date service Critical aspects of the OQ include motion qualification optics qualification fluidics qualification and thermal qualification As regulatory guidelines continue to evolve and increase in stringency laboratories need well documented system qualification protocols for compliance Performed by Illumina trained and certified engineers IQ OQ helps research and diagnostic genomic laboratories meet regulatory guidelines Provides an audit ready signed IQ OQ report Accelerates use by ensuring the Illumina instrument is installed operational and ready to use after initial delivery Verifies Illumina sequencers perform according to manufacturer specifications after major repairs relocation or system software upgrades Helps establish instrument log files for change control Provides engineer training and tool calibration certificates upon customer request
    Catalog Number:
    sp-102-2506
    Price:
    None
    Category:
    Service Products
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    Structured Review

    Illumina Inc hiseq 2500 platform
    HiSeq 2500 Installation and Operational Qualification
    Comprehensive Qualification Services from Illumina Illumina Installation and Operational Qualification IQ OQ services carry out numerous experiments for each system to ensure critical components are tested and validated have cut off metrics and to confirm these metrics show the system is operating in accordance with specifications Our IQ service provides documented verification that instrument is installed according to our specifications and safety regulations During the IQ a trained engineer verifies latest supported firmware and software versions were installed verifies instrument setup and accessory logistics checks physical and environmental safety conditions are met and provides a signed audit ready report Our OQ service follows a comprehensive well defined protocol to verify the system functions according to pre set and validated operational specifications We update the OQ protocol following each instrument hardware and software release ensuring your laboratory receives the most up to date service Critical aspects of the OQ include motion qualification optics qualification fluidics qualification and thermal qualification As regulatory guidelines continue to evolve and increase in stringency laboratories need well documented system qualification protocols for compliance Performed by Illumina trained and certified engineers IQ OQ helps research and diagnostic genomic laboratories meet regulatory guidelines Provides an audit ready signed IQ OQ report Accelerates use by ensuring the Illumina instrument is installed operational and ready to use after initial delivery Verifies Illumina sequencers perform according to manufacturer specifications after major repairs relocation or system software upgrades Helps establish instrument log files for change control Provides engineer training and tool calibration certificates upon customer request
    https://www.bioz.com/result/hiseq 2500 platform/product/Illumina Inc
    Average 99 stars, based on 3341 article reviews
    Price from $9.99 to $1999.99
    hiseq 2500 platform - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery"

    Article Title: Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

    Journal: Genes

    doi: 10.3390/genes7070035

    Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.
    Figure Legend Snippet: Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.

    Techniques Used: Flow Cytometry, Sequencing, Software, Functional Assay

    2) Product Images from "Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization"

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.1613294113

    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Figure Legend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Techniques Used: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    3) Product Images from "Avian Leukosis Virus Subgroup J Attenuates Type I Interferon Production Through Blocking IκB Phosphorylation"

    Article Title: Avian Leukosis Virus Subgroup J Attenuates Type I Interferon Production Through Blocking IκB Phosphorylation

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.01089

    mRNA-Seq data. HD11 cells were infected with ALV-J or medium as a control. Twelve hours later, total RNA were isolated from the mock- and ALV-J-infected cells for mRNA sequencing on an Illumina Hiseq 2500 platform. (A) Distribution of the differentially expressed genes in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells. (B) KEGG classification analysis in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells.
    Figure Legend Snippet: mRNA-Seq data. HD11 cells were infected with ALV-J or medium as a control. Twelve hours later, total RNA were isolated from the mock- and ALV-J-infected cells for mRNA sequencing on an Illumina Hiseq 2500 platform. (A) Distribution of the differentially expressed genes in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells. (B) KEGG classification analysis in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells.

    Techniques Used: Infection, Isolation, Sequencing

    4) Product Images from "Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations"

    Article Title: Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

    Journal: Scientific Reports

    doi: 10.1038/srep31602

    Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.
    Figure Legend Snippet: Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.

    Techniques Used: Expressing, Sequencing, Flow Cytometry, Derivative Assay, Standard Deviation

    Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.
    Figure Legend Snippet: Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.

    Techniques Used: Derivative Assay, Transformation Assay

    Detection of different cDNA species for the RPL41 gene from either the Illumina HiSeq 2500 platform, the ONT MinION platform or the PacBio RS II platform. ONT MinION reads that were sequenced as full length, as defined by the presence of both the 5′ and 3′ RT adaptors, are presented. For the PacBio RS II example the corresponding “Circular Consensus Sequencing” reads are presented. These reads correspond to fully sequenced molecules. mRNA molecules from GenBank for the RPL41 gene are also shown. For the Illumina data a pileup of the sequenced paired-end fragments is presented.
    Figure Legend Snippet: Detection of different cDNA species for the RPL41 gene from either the Illumina HiSeq 2500 platform, the ONT MinION platform or the PacBio RS II platform. ONT MinION reads that were sequenced as full length, as defined by the presence of both the 5′ and 3′ RT adaptors, are presented. For the PacBio RS II example the corresponding “Circular Consensus Sequencing” reads are presented. These reads correspond to fully sequenced molecules. mRNA molecules from GenBank for the RPL41 gene are also shown. For the Illumina data a pileup of the sequenced paired-end fragments is presented.

    Techniques Used: Sequencing

    Estimation of the HEK-293 cDNA isoform abundance with three sequencing platforms. The comparison between the cDNA isoform abundance estimated from the Illumina HiSeq 2500 platform and from the PacBio RS II platform is presented in ( A ). The expression level of the HEK-293 isoforms estimated with the ONT MinION platform is compared with the one calculated from either the PacBio RS II ( B ) or the Illumina HiSeq 2500 platform ( C ). For the Illumina HiSeq 2500 platform the expression level, presented as TPM, was estimated with the Sailfish 21 software. For the PacBio RS II or the ONT MinION platform the counts of sequenced molecules per isoform are presented.
    Figure Legend Snippet: Estimation of the HEK-293 cDNA isoform abundance with three sequencing platforms. The comparison between the cDNA isoform abundance estimated from the Illumina HiSeq 2500 platform and from the PacBio RS II platform is presented in ( A ). The expression level of the HEK-293 isoforms estimated with the ONT MinION platform is compared with the one calculated from either the PacBio RS II ( B ) or the Illumina HiSeq 2500 platform ( C ). For the Illumina HiSeq 2500 platform the expression level, presented as TPM, was estimated with the Sailfish 21 software. For the PacBio RS II or the ONT MinION platform the counts of sequenced molecules per isoform are presented.

    Techniques Used: Sequencing, Expressing, Software

    5) Product Images from "TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration"

    Article Title: TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36669-6

    Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.
    Figure Legend Snippet: Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.

    Techniques Used: Variant Assay

    6) Product Images from "Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization"

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.1613294113

    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Figure Legend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Techniques Used: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    7) Product Images from "TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration"

    Article Title: TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36669-6

    Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.
    Figure Legend Snippet: Number of variable sites in SiHa replicates. SiHa-1 (red dots) and SiHa-2 (blue dots) served as technical replicates to assess the variant calling performance. In SiHa libraries, sequenced on MiSeq and HiSeq 2500 platforms, increasing number of variable sites were detected with higher mean coverage.

    Techniques Used: Variant Assay

    8) Product Images from "Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4+ T Cells in Early Human Pregnancy"

    Article Title: Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4+ T Cells in Early Human Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2017.00682

    Human dCD4 T cells show a distinct transcriptional signature and upregulate genes related to immune system process as compared with autologous pCD4 T cells. Three healthy women at the first trimester of normal pregnancy were recruited and their dCD4 and pCD4 T cells were isolated by fluorescence-activated cell sorting (FACS). (A) Summary of mRNA-Seq data for the purified dCD4 and pCD4 T cells. RNA samples of paired dCD4 and pCD4 T cells from three individuals were sequenced on the Illumina Hiseq 2500 platform, yielding approximately 30–40 million 2 × 125-bp paired-end reads per sample, which were then mapped to the human reference genome (hg19 version). (B) Number and percentage of the differentially expressed genes ( P
    Figure Legend Snippet: Human dCD4 T cells show a distinct transcriptional signature and upregulate genes related to immune system process as compared with autologous pCD4 T cells. Three healthy women at the first trimester of normal pregnancy were recruited and their dCD4 and pCD4 T cells were isolated by fluorescence-activated cell sorting (FACS). (A) Summary of mRNA-Seq data for the purified dCD4 and pCD4 T cells. RNA samples of paired dCD4 and pCD4 T cells from three individuals were sequenced on the Illumina Hiseq 2500 platform, yielding approximately 30–40 million 2 × 125-bp paired-end reads per sample, which were then mapped to the human reference genome (hg19 version). (B) Number and percentage of the differentially expressed genes ( P

    Techniques Used: Isolation, Fluorescence, FACS, Purification

    9) Product Images from "Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy"

    Article Title: Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2018.00937

    The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P
    Figure Legend Snippet: The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P

    Techniques Used: Fluorescence, FACS, Sequencing, Isolation, Software

    10) Product Images from "Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy"

    Article Title: Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2018.00937

    The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P
    Figure Legend Snippet: The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P

    Techniques Used: Fluorescence, FACS, Sequencing, Isolation, Software

    11) Product Images from "Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten"

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-018-0194-0

    Coverage comparison between HiSeq 2500 and HiSeq X Ten. a Plot shows the fraction of genome covered at different depths for four samples sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. The coverage plot for the HiSeq 2500 HO mode is the merged coverage obtained from multiplexing the four samples. b Plot shows the fraction of CpG sites covered at different depths when four clinical samples are sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. c , d Box plot showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a sample sequenced on one lane of HiSeq X Ten ( c ) and HiSeq 2500 ( d )
    Figure Legend Snippet: Coverage comparison between HiSeq 2500 and HiSeq X Ten. a Plot shows the fraction of genome covered at different depths for four samples sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. The coverage plot for the HiSeq 2500 HO mode is the merged coverage obtained from multiplexing the four samples. b Plot shows the fraction of CpG sites covered at different depths when four clinical samples are sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. c , d Box plot showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a sample sequenced on one lane of HiSeq X Ten ( c ) and HiSeq 2500 ( d )

    Techniques Used: Multiplexing

    Comparison of methylation correlation between HiSeq 2500 and HiSeq X Ten. a Correlation plots of methylation levels obtained from a cell line, a clinical sample and a FFPET sample sequenced on the Hiseq 2500 versus HiSeq X Ten (Pearson r > 0.94). b Correlation of methylation values obtained from HiSeq 2500 and HiSeq X Ten for a cell line, clinical sample and a FFPET sample after grouping them into four bins of methylation percentages. c Average kappa values for six sample pairs, including two cell lines, two clinical samples and two FFPE samples compared between the HiSeq 2500 and HiSeq X Ten platform. d Bar plot showing the distribution of percentage of discordant sites across the genome for a cell line, clinical sample and a FFPET sample
    Figure Legend Snippet: Comparison of methylation correlation between HiSeq 2500 and HiSeq X Ten. a Correlation plots of methylation levels obtained from a cell line, a clinical sample and a FFPET sample sequenced on the Hiseq 2500 versus HiSeq X Ten (Pearson r > 0.94). b Correlation of methylation values obtained from HiSeq 2500 and HiSeq X Ten for a cell line, clinical sample and a FFPET sample after grouping them into four bins of methylation percentages. c Average kappa values for six sample pairs, including two cell lines, two clinical samples and two FFPE samples compared between the HiSeq 2500 and HiSeq X Ten platform. d Bar plot showing the distribution of percentage of discordant sites across the genome for a cell line, clinical sample and a FFPET sample

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded

    Comparing different library preparation methods using genomic DNA on the HiSeq 2500.  a  Cluster plot of sequencing output metrics obtained from different library preparation methods from intact genomic DNA.  b  Bar graph showing fragment size distribution for different bead size selection for each library preparation method.  c  Plot with  x -axis indicating coverage and  y -axis indicating fragment size illustrating how increase in fragment size leads to improved coverage
    Figure Legend Snippet: Comparing different library preparation methods using genomic DNA on the HiSeq 2500. a Cluster plot of sequencing output metrics obtained from different library preparation methods from intact genomic DNA. b Bar graph showing fragment size distribution for different bead size selection for each library preparation method. c Plot with x -axis indicating coverage and y -axis indicating fragment size illustrating how increase in fragment size leads to improved coverage

    Techniques Used: Sequencing, Selection

    Correlation between duplicate reads, spike-ins and the sequencing platforms.  a ,  b  Plots showing the frequency of distribution of duplicate reads for two cell line DNA samples during down sampling of the raw reads from HiSeq X Ten to the number of raw reads obtained from HiSeq 2500.  c  Box plot showing the difference in duplicate percentage when the same set of ten bisulphite libraries were spiked with 25% of 250 pM genomic library and 25% of 300 pM PhiX library
    Figure Legend Snippet: Correlation between duplicate reads, spike-ins and the sequencing platforms. a , b Plots showing the frequency of distribution of duplicate reads for two cell line DNA samples during down sampling of the raw reads from HiSeq X Ten to the number of raw reads obtained from HiSeq 2500. c Box plot showing the difference in duplicate percentage when the same set of ten bisulphite libraries were spiked with 25% of 250 pM genomic library and 25% of 300 pM PhiX library

    Techniques Used: Sequencing, Sampling

    12) Product Images from "Mechanical stimulation of Schwann cells promote peripheral nerve regeneration via extracellular vesicle-mediated transfer of microRNA 23b-3p"

    Article Title: Mechanical stimulation of Schwann cells promote peripheral nerve regeneration via extracellular vesicle-mediated transfer of microRNA 23b-3p

    Journal: Theranostics

    doi: 10.7150/thno.44912

    miRNA expression profile of MS-SCs-EVs is significantly altered compared with SCs-EVs. ( A ) Percentage of small RNA categories in all reads mapped to noncoding RNA databases. ( B ) Heatmap diagram of differential miRNA expression between MS-SCs-EVs and SCs-EVs. Gene expression data were obtained using next-generation sequencing on the Illumina HiSeq 2500 platform. Expression values shown are mean centered. Red, increased expression; blue, decreased expression, and white, mean value. ( C ) Differentially expressed miRNAs between MS-SCs-EVs and SCs-EVs. Red, increased expression; green, decreased expression; gray, no difference. P
    Figure Legend Snippet: miRNA expression profile of MS-SCs-EVs is significantly altered compared with SCs-EVs. ( A ) Percentage of small RNA categories in all reads mapped to noncoding RNA databases. ( B ) Heatmap diagram of differential miRNA expression between MS-SCs-EVs and SCs-EVs. Gene expression data were obtained using next-generation sequencing on the Illumina HiSeq 2500 platform. Expression values shown are mean centered. Red, increased expression; blue, decreased expression, and white, mean value. ( C ) Differentially expressed miRNAs between MS-SCs-EVs and SCs-EVs. Red, increased expression; green, decreased expression; gray, no difference. P

    Techniques Used: Expressing, Next-Generation Sequencing

    13) Product Images from "Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis"

    Article Title: Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2020.01327

    Analytical methods. (A) Schematic workflow describing experimental procedure and transcriptomic analysis. Primary airway epithelial cells (AECs) from non-CF children ( n = 5) and children with CF ( n = 7) were obtained from bronchial brushings. AECs were established for infection with human rhinovirus 1B (RV1B) at MOI 12.5. At 24 h post-infection, RNA was isolated and processed for library preparation. Sample libraries were sequenced on the Illumina HiSeq 2500 platform as described in the methods section (B) Principal component analysis (PCA). Components 1 (PC1) and 2 (PC2) highlight distinct clustering of samples. PC1 shows the highest percentage of variance (69%) for all samples and completely separates the control and RV-infected samples. PC2 shows the second highest variance (8%) and separates non-CF and CF samples. Data points represent individual samples for non-CF controls (turquoise), non-CF infected (purple), CF control (coral), and CF infected (green).
    Figure Legend Snippet: Analytical methods. (A) Schematic workflow describing experimental procedure and transcriptomic analysis. Primary airway epithelial cells (AECs) from non-CF children ( n = 5) and children with CF ( n = 7) were obtained from bronchial brushings. AECs were established for infection with human rhinovirus 1B (RV1B) at MOI 12.5. At 24 h post-infection, RNA was isolated and processed for library preparation. Sample libraries were sequenced on the Illumina HiSeq 2500 platform as described in the methods section (B) Principal component analysis (PCA). Components 1 (PC1) and 2 (PC2) highlight distinct clustering of samples. PC1 shows the highest percentage of variance (69%) for all samples and completely separates the control and RV-infected samples. PC2 shows the second highest variance (8%) and separates non-CF and CF samples. Data points represent individual samples for non-CF controls (turquoise), non-CF infected (purple), CF control (coral), and CF infected (green).

    Techniques Used: Infection, Isolation

    14) Product Images from "Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization"

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.1613294113

    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Figure Legend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Techniques Used: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    15) Product Images from "Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L."

    Article Title: Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

    Journal: Scientific Data

    doi: 10.1038/s41597-020-0352-7

    Overview of experimental design and analysis pipeline. RNA from pepper leaves subjected to each abiotic stress (heat, cold, salinity, and osmotic stress) and the 0-h sample from the mock control was harvested. Marker gene expression was confirmed for each stress condition, and the values were normalized to C. annuum actin expression and were calculated relative to control group as mean values with standard deviation. The validated RNAs were sequenced by the Illumina HiSeq 2500 system. All RNA-seq reads were preprocessed for a quality assessment. The filtered transcriptome reads were aligned to the CM334 genome, and the expression profile was analyzed.
    Figure Legend Snippet: Overview of experimental design and analysis pipeline. RNA from pepper leaves subjected to each abiotic stress (heat, cold, salinity, and osmotic stress) and the 0-h sample from the mock control was harvested. Marker gene expression was confirmed for each stress condition, and the values were normalized to C. annuum actin expression and were calculated relative to control group as mean values with standard deviation. The validated RNAs were sequenced by the Illumina HiSeq 2500 system. All RNA-seq reads were preprocessed for a quality assessment. The filtered transcriptome reads were aligned to the CM334 genome, and the expression profile was analyzed.

    Techniques Used: Marker, Expressing, Standard Deviation, RNA Sequencing Assay

    16) Product Images from "Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer"

    Article Title: Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer

    Journal: Scientific Reports

    doi: 10.1038/srep28446

    RNA sequencing and validation of select genes. ( A ) Total RNA was isolated from control (MiaPaCa-NTScr) and MYB-silenced (MiaPaCa-ShMYB) MiaPaCa cells, cDNA synthesized and further subjected to sequencing using Illumina HiSeq 2500 platform. Bioinformatics analysis revealed 774 differentially expressed genes (*p value ≤ 0.05, fold change ≥± 1.5) in the sample set. ( B ) The expression of a few select genes from the resulting MiaPaCa (shMYB Vs. NTScr) RNA-Seq data was also validated using qPCR. In a converse approach, we also compared the ( C ) relative expression of these genes in ectopic MYB-expressing (BxPC3-MYB) vs. control BxPC3 (BxPC3-Neo) cell lines. ( D,E ) The expression at protein level of these genes was also analyzed by immunoblotting. PUMA and GLUT1 represent the proteins encoded by BBC3 and SLC2A1 genes, respectively.
    Figure Legend Snippet: RNA sequencing and validation of select genes. ( A ) Total RNA was isolated from control (MiaPaCa-NTScr) and MYB-silenced (MiaPaCa-ShMYB) MiaPaCa cells, cDNA synthesized and further subjected to sequencing using Illumina HiSeq 2500 platform. Bioinformatics analysis revealed 774 differentially expressed genes (*p value ≤ 0.05, fold change ≥± 1.5) in the sample set. ( B ) The expression of a few select genes from the resulting MiaPaCa (shMYB Vs. NTScr) RNA-Seq data was also validated using qPCR. In a converse approach, we also compared the ( C ) relative expression of these genes in ectopic MYB-expressing (BxPC3-MYB) vs. control BxPC3 (BxPC3-Neo) cell lines. ( D,E ) The expression at protein level of these genes was also analyzed by immunoblotting. PUMA and GLUT1 represent the proteins encoded by BBC3 and SLC2A1 genes, respectively.

    Techniques Used: RNA Sequencing Assay, Isolation, Synthesized, Sequencing, Expressing, Real-time Polymerase Chain Reaction

    17) Product Images from "Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy"

    Article Title: Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2018.00937

    The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P
    Figure Legend Snippet: The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P

    Techniques Used: Fluorescence, FACS, Sequencing, Isolation, Software

    18) Product Images from "Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population"

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-15-673

    Box plots of read depths at concordant/discordant SNP loci among the NGSs and Omni 2.5-8. A) Box plots of the NGS read depth at the SNP loci showing concordance/discordance between the NGSs and Omni 2.5-8. The box indicates the first and third quartiles and the lines indicate the highest and lowest value that is within 1.5 x inter-quartile range. Outliers were omitted. The graph on the left indicates the distribution of read depths at HiSeq2500 SNP loci and the graph on the right indicates the distribution of read depths at Ion Proton and Omni 2.5-8 SNP loci. B) Box plots of the NGS read depths at the SNP loci showing concordance/discordance among the three platforms. The box indicates the first and third quartiles and the lines indicate the highest and lowest value that is within 1.5 x inter-quartile range. Outliers were omitted. The three columns (shaded gray rectangle) from right indicate the distribution of read depths of the discordant SNPs between the NGSs and Omni 2.5-8. The read depth at SNP loci that showed Ion Proton discordance against HiSeq 2500 and Omni 2.5-8 was significantly different. The read depths at SNP loci for SNPs that both HiSeq 2500 and Ion Proton failed to call are shown in the gray box.
    Figure Legend Snippet: Box plots of read depths at concordant/discordant SNP loci among the NGSs and Omni 2.5-8. A) Box plots of the NGS read depth at the SNP loci showing concordance/discordance between the NGSs and Omni 2.5-8. The box indicates the first and third quartiles and the lines indicate the highest and lowest value that is within 1.5 x inter-quartile range. Outliers were omitted. The graph on the left indicates the distribution of read depths at HiSeq2500 SNP loci and the graph on the right indicates the distribution of read depths at Ion Proton and Omni 2.5-8 SNP loci. B) Box plots of the NGS read depths at the SNP loci showing concordance/discordance among the three platforms. The box indicates the first and third quartiles and the lines indicate the highest and lowest value that is within 1.5 x inter-quartile range. Outliers were omitted. The three columns (shaded gray rectangle) from right indicate the distribution of read depths of the discordant SNPs between the NGSs and Omni 2.5-8. The read depth at SNP loci that showed Ion Proton discordance against HiSeq 2500 and Omni 2.5-8 was significantly different. The read depths at SNP loci for SNPs that both HiSeq 2500 and Ion Proton failed to call are shown in the gray box.

    Techniques Used: Next-Generation Sequencing

    19) Product Images from "Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations"

    Article Title: Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

    Journal: Scientific Reports

    doi: 10.1038/srep31602

    Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.
    Figure Legend Snippet: Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.

    Techniques Used: Expressing, Sequencing, Flow Cytometry, Derivative Assay, Standard Deviation

    Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.
    Figure Legend Snippet: Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.

    Techniques Used: Derivative Assay, Transformation Assay

    Detection of different cDNA species for the RPL41 gene from either the Illumina HiSeq 2500 platform, the ONT MinION platform or the PacBio RS II platform. ONT MinION reads that were sequenced as full length, as defined by the presence of both the 5′ and 3′ RT adaptors, are presented. For the PacBio RS II example the corresponding “Circular Consensus Sequencing” reads are presented. These reads correspond to fully sequenced molecules. mRNA molecules from GenBank for the RPL41 gene are also shown. For the Illumina data a pileup of the sequenced paired-end fragments is presented.
    Figure Legend Snippet: Detection of different cDNA species for the RPL41 gene from either the Illumina HiSeq 2500 platform, the ONT MinION platform or the PacBio RS II platform. ONT MinION reads that were sequenced as full length, as defined by the presence of both the 5′ and 3′ RT adaptors, are presented. For the PacBio RS II example the corresponding “Circular Consensus Sequencing” reads are presented. These reads correspond to fully sequenced molecules. mRNA molecules from GenBank for the RPL41 gene are also shown. For the Illumina data a pileup of the sequenced paired-end fragments is presented.

    Techniques Used: Sequencing

    Estimation of the HEK-293 cDNA isoform abundance with three sequencing platforms. The comparison between the cDNA isoform abundance estimated from the Illumina HiSeq 2500 platform and from the PacBio RS II platform is presented in ( A ). The expression level of the HEK-293 isoforms estimated with the ONT MinION platform is compared with the one calculated from either the PacBio RS II ( B ) or the Illumina HiSeq 2500 platform ( C ). For the Illumina HiSeq 2500 platform the expression level, presented as TPM, was estimated with the Sailfish 21 software. For the PacBio RS II or the ONT MinION platform the counts of sequenced molecules per isoform are presented.
    Figure Legend Snippet: Estimation of the HEK-293 cDNA isoform abundance with three sequencing platforms. The comparison between the cDNA isoform abundance estimated from the Illumina HiSeq 2500 platform and from the PacBio RS II platform is presented in ( A ). The expression level of the HEK-293 isoforms estimated with the ONT MinION platform is compared with the one calculated from either the PacBio RS II ( B ) or the Illumina HiSeq 2500 platform ( C ). For the Illumina HiSeq 2500 platform the expression level, presented as TPM, was estimated with the Sailfish 21 software. For the PacBio RS II or the ONT MinION platform the counts of sequenced molecules per isoform are presented.

    Techniques Used: Sequencing, Expressing, Software

    20) Product Images from "Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4+ T Cells in Early Human Pregnancy"

    Article Title: Distinct Transcriptional and Alternative Splicing Signatures of Decidual CD4+ T Cells in Early Human Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2017.00682

    Human dCD4 T cells show a distinct transcriptional signature and upregulate genes related to immune system process as compared with autologous pCD4 T cells. Three healthy women at the first trimester of normal pregnancy were recruited and their dCD4 and pCD4 T cells were isolated by fluorescence-activated cell sorting (FACS). (A) Summary of mRNA-Seq data for the purified dCD4 and pCD4 T cells. RNA samples of paired dCD4 and pCD4 T cells from three individuals were sequenced on the Illumina Hiseq 2500 platform, yielding approximately 30–40 million 2 × 125-bp paired-end reads per sample, which were then mapped to the human reference genome (hg19 version). (B) Number and percentage of the differentially expressed genes ( P
    Figure Legend Snippet: Human dCD4 T cells show a distinct transcriptional signature and upregulate genes related to immune system process as compared with autologous pCD4 T cells. Three healthy women at the first trimester of normal pregnancy were recruited and their dCD4 and pCD4 T cells were isolated by fluorescence-activated cell sorting (FACS). (A) Summary of mRNA-Seq data for the purified dCD4 and pCD4 T cells. RNA samples of paired dCD4 and pCD4 T cells from three individuals were sequenced on the Illumina Hiseq 2500 platform, yielding approximately 30–40 million 2 × 125-bp paired-end reads per sample, which were then mapped to the human reference genome (hg19 version). (B) Number and percentage of the differentially expressed genes ( P

    Techniques Used: Isolation, Fluorescence, FACS, Purification

    21) Product Images from "Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization"

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.1613294113

    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Figure Legend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Techniques Used: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    22) Product Images from "Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery"

    Article Title: Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

    Journal: Genes

    doi: 10.3390/genes7070035

    Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.
    Figure Legend Snippet: Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.

    Techniques Used: Flow Cytometry, Sequencing, Software, Functional Assay

    23) Product Images from "Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy"

    Article Title: Deep Surveying of the Transcriptional and Alternative Splicing Signatures for Decidual CD8+ T Cells at the First Trimester of Human Healthy Pregnancy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2018.00937

    The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P
    Figure Legend Snippet: The numbers of DEGs are comparable in human dCD8 versus pCD8 T cells. (A) Fluorescence-activated cell sorting was performed to purify the CD8 + T cells, based on the phenotype of CD3 + CD8 + CD4 − , in paired decidual and peripheral blood samples from three healthy women at the first trimester of normal pregnancy (mean gestational day 50, range 44–58). (B) Summary of mRNA sequencing data of the isolated human pCD8 and autologous dCD8 T cells. 2 × 125-bp paired-end cDNA fragments were acquired after sequencing the polyadenylated [poly(A)+] enriched mRNAs on an Illumina Hiseq 2500 platform, and the sequenced reads was aligned to human reference genome (hg19 version) by STAR software. (C) The number and proportion of DEGs that were upregulated or downregulated in human dCD8 versus pCD8 T cells ( P

    Techniques Used: Fluorescence, FACS, Sequencing, Isolation, Software

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    RNA Sequencing Assay:

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    Isolation:

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    Illumina Inc hiseq 2500 platform
    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina <t>HiSeq</t> 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.
    Hiseq 2500 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 3341 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc hiseq 2500 miseq platforms
    Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq <t>2500/MiSeq</t> estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.
    Hiseq 2500 Miseq Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

    doi: 10.1073/pnas.1613294113

    Figure Lengend Snippet: Diagram of the validation procedure of the noninvasive chromosome screening (NICS) assay. Briefly, D3 embryos achieved via intracytoplasmic sperm injection (ICSI) were placed in blastocyst culture medium. Both the D3–D5 culture medium and the corresponding whole embryos were collected and used for WGA by multiple annealing and looping-based amplification cycles (MALBAC). Whole-genome–amplified products from both the D3–D5 culture medium and the embryo were sequenced using an Illumina HiSeq 2500 platform. The chromosome ploidy information was obtained from both the culture medium and the corresponding embryo.

    Article Snippet: The MALBAC single-cell WGA method was used to amplify DNA from the culture medium, as well as from the embryos, following the manufacturer’s protocol (catalog no. YK001B; Yikon Genomics), and used to construct the sequencing libraries (NEBNext Ultra DNA Kit; New England Biolabs) for sequencing on an Illumina HiSeq 2500 platform, yielding ∼2 million sequencing reads on each sample.

    Techniques: Injection, Whole Genome Amplification, Multiple Annealing and Looping–Based Amplification Cycles, Amplification

    Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.

    Journal: Genes

    Article Title: Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

    doi: 10.3390/genes7070035

    Figure Lengend Snippet: Schematic work-flow of C. retropictus transcriptome using Illumina sequencing, de novo analysis, and annotation. The visceral mass transcriptome of C. retropictus was obtained using an Illumina HiSeq 2500 platform. The raw reads were pre-processed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Using Trinity (K-mer: 25; minimum contig length: 200) de novo assembler and TGICL clustering, the clean reads were processed to unigene sequences. Subsequently, the unigene sequences were blasted against public databases including PANM, Unigene, COG, GO, and KEGG for functional annotation. The SSRs were detected within the unigene sequences using MISA software.

    Article Snippet: Finally, the library preparations were sequenced on an Illumina HiSeq 2500 platform at the sequencing facility of GnC Company (Daejeon, South Korea) with the generation of 100-base pair (bp) PE-reads.

    Techniques: Flow Cytometry, Sequencing, Software, Functional Assay

    mRNA-Seq data. HD11 cells were infected with ALV-J or medium as a control. Twelve hours later, total RNA were isolated from the mock- and ALV-J-infected cells for mRNA sequencing on an Illumina Hiseq 2500 platform. (A) Distribution of the differentially expressed genes in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells. (B) KEGG classification analysis in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells.

    Journal: Frontiers in Microbiology

    Article Title: Avian Leukosis Virus Subgroup J Attenuates Type I Interferon Production Through Blocking IκB Phosphorylation

    doi: 10.3389/fmicb.2018.01089

    Figure Lengend Snippet: mRNA-Seq data. HD11 cells were infected with ALV-J or medium as a control. Twelve hours later, total RNA were isolated from the mock- and ALV-J-infected cells for mRNA sequencing on an Illumina Hiseq 2500 platform. (A) Distribution of the differentially expressed genes in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells. (B) KEGG classification analysis in ALV-J-infected HD11 cells compared to that in mock-infected HD11 cells.

    Article Snippet: Sequencing was performed on an Illumina Hiseq 2500 platform.

    Techniques: Infection, Isolation, Sequencing

    Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.

    Journal: Scientific Reports

    Article Title: Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

    doi: 10.1038/srep31602

    Figure Lengend Snippet: Effect of the GC content and ERCC length on the estimation of the ERCC cDNA abundance with the ONT MinION platform. The figures present deviations of the ERCC expression level estimates with the ONT MinION platform from the Ambion RNA molecular counts ( A,C ) or from the Illumina HiSeq 2500/MiSeq estimated cDNA abundance ( B,D ) as a function of the GC content ( A,B ) and the ERCC length ( C,D ). We plot the log2 ratio of observed (ONT MinION) to expected (Ambion, Illumina) read counts for the ERCC spike-ins (y-axis, log) for each of the samples relative to their length or GC content (x-axis). Due to the variable sequencing depth from each ERCC MinION experiment, each point is the average value from different MinION flow cell runs if at least 5 reads have been detected for this point in the corresponding MinION runs. The points are colored differently based on the number of flow cell runs in which they were detected (red, green, cyan, purple correspond to values derived from one, two, three or four flow cell runs respectively). The standard deviation is also presented for points with values from two or more MinION runs.

    Article Snippet: The abundance of the different ERCC cDNA molecules sequenced from either the Illumina HiSeq 2500/MiSeq platforms, the PacBio RS II platform or the ONT MinION is comparable To test whether the ONT MinION performs equally well as the Illumina platforms in estimating the ERCC cDNA abundance, the same full length ERCC cDNA population used in the ONT MinION experiments, was sequenced on an Illumina HiSeq 2500 or MiSeq instruments.

    Techniques: Expressing, Sequencing, Flow Cytometry, Derivative Assay, Standard Deviation

    Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.

    Journal: Scientific Reports

    Article Title: Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

    doi: 10.1038/srep31602

    Figure Lengend Snippet: Estimation of the ERCC cDNA abundance with the ONT MinION platform. We compared the ERCC cDNA abundance estimated from the ONT MinION ( A ) and the Illumina HiSeq 2500 or MiSeq platforms ( B ) against the expected number of RNA molecules as provided from the manufacturer (Ambion). The template reads from the ERCC MinION experiments number 1, 2, 3, 4 were pooled together and used for ( A ). Similarly, the corresponding Illumina data were pooled together for ( B ). The Illumina molecular counts data were derived using 5′ molecular tags at the RT step as described in material and methods. The total number of molecules presented on the x-axis corresponds to 3.5 pgs of ERCC RNA. In both axes the log10 transformation of the original count number is used.

    Article Snippet: The abundance of the different ERCC cDNA molecules sequenced from either the Illumina HiSeq 2500/MiSeq platforms, the PacBio RS II platform or the ONT MinION is comparable To test whether the ONT MinION performs equally well as the Illumina platforms in estimating the ERCC cDNA abundance, the same full length ERCC cDNA population used in the ONT MinION experiments, was sequenced on an Illumina HiSeq 2500 or MiSeq instruments.

    Techniques: Derivative Assay, Transformation Assay