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  • 99
    Illumina Inc rna library
    Modulation of MIR157c processing efficiency. ( A–C ) Small <t>RNA</t> gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P
    Rna Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 4612 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq rna library
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Truseq Rna Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 475 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc truseq rna library prep kit v2
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Truseq Rna Library Prep Kit V2, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1104 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc rna sequencing library preparation
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Rna Sequencing Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc short rna library preparation
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Short Rna Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc rna library preparation protocol
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Rna Library Preparation Protocol, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc rna seq library kits
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Rna Seq Library Kits, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc rna library generation
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Rna Library Generation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 29 article reviews
    Price from $9.99 to $1999.99
    rna library generation - by Bioz Stars, 2020-04
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    99
    Illumina Inc truseq rna preparation kit
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: <t>TruSeq</t> using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Truseq Rna Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 306 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq rna preparation kit/product/Illumina Inc
    Average 99 stars, based on 306 article reviews
    Price from $9.99 to $1999.99
    truseq rna preparation kit - by Bioz Stars, 2020-04
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    Image Search Results


    Modulation of MIR157c processing efficiency. ( A–C ) Small RNA gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P

    Journal: Nucleic Acids Research

    Article Title: Efficiency and precision of microRNA biogenesis modes in plants

    doi: 10.1093/nar/gky853

    Figure Lengend Snippet: Modulation of MIR157c processing efficiency. ( A–C ) Small RNA gel blots of transgenic lines expressing different precursors from the 35S promoter. Each sample represents a pool of 25 independent transgenic lines. Top panels show a schematic representation of the precursors analyzed. See Supplementary Table S2 for the expressed sequences of each vector. Supplementary Figure S1 shows the original image of the blot autoradiography. ( D ) Combined box/violin plots representing the distribution of rosette leaves number at the flowering time for primary transgenic plants over-expressing each construct grown in short days. Different letters indicate significant difference, as determined by Kruskal Wallis test, P

    Article Snippet: The small RNA library was constructed using the Illumina TruSeq sRNA kit, and sequenced on the Illumina HiSeq platform at the University of Delaware.

    Techniques: Transgenic Assay, Expressing, Plasmid Preparation, Autoradiography, Construct

    Small RNA sequence variation caused by variability in the position of the first cut. (A–P) miRNAs for which the biogenesis is base-to-loop are displayed on the left panels (turquoise bars) (A–H), while loop-to-base miRNAs are displayed on the right panels (blue bars) (I–P). ( A ) miR165a, ( B ) miR168ab, ( C ) miR390ab, ( D ) miR396a ( E ) miR398bc ( F ) miR173, ( G ) miR824, and ( H ) average base-to-loop miRNA; ( I ) miR156a-f, ( J ) miR157ab, ( K ) miR157c, ( L ) miR160a-c, ( M ) miR408, ( N ) miR400, ( O ) miR825, ( P ) average loop-to-base miRNA. The miRNA sequence is indicated below each graph. The bar shows the frequency of the small RNAs ending at that position. For the average miRNA ( H and P ) the bases are depicted as squares.

    Journal: Nucleic Acids Research

    Article Title: Efficiency and precision of microRNA biogenesis modes in plants

    doi: 10.1093/nar/gky853

    Figure Lengend Snippet: Small RNA sequence variation caused by variability in the position of the first cut. (A–P) miRNAs for which the biogenesis is base-to-loop are displayed on the left panels (turquoise bars) (A–H), while loop-to-base miRNAs are displayed on the right panels (blue bars) (I–P). ( A ) miR165a, ( B ) miR168ab, ( C ) miR390ab, ( D ) miR396a ( E ) miR398bc ( F ) miR173, ( G ) miR824, and ( H ) average base-to-loop miRNA; ( I ) miR156a-f, ( J ) miR157ab, ( K ) miR157c, ( L ) miR160a-c, ( M ) miR408, ( N ) miR400, ( O ) miR825, ( P ) average loop-to-base miRNA. The miRNA sequence is indicated below each graph. The bar shows the frequency of the small RNAs ending at that position. For the average miRNA ( H and P ) the bases are depicted as squares.

    Article Snippet: The small RNA library was constructed using the Illumina TruSeq sRNA kit, and sequenced on the Illumina HiSeq platform at the University of Delaware.

    Techniques: Sequencing

    Impact of biological replication on mRNA editing discovery. Distribution (in %) of unbiased mRNA editing events across the 12 classes of substitution according to the number of replicates they are detected in, ranging from N = 1 to N = 3, in white adipose tissue (WAT) and liver. The first two classes (AtoG and TtoC) are associated to ADAR-mediated RNA editing, and the next two (CtoT and GtoA) to APOBEC-meditated RNA editing. At the top-right of each graph, the total number of RNA editing events detected for a given number of replicates is shown. ADAR: Adenosine deaminases acting on RNA. APOBEC: Apolipoprotein B mRNA editing enzyme, catalytic polypetide-like.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

    doi: 10.1534/g3.115.022251

    Figure Lengend Snippet: Impact of biological replication on mRNA editing discovery. Distribution (in %) of unbiased mRNA editing events across the 12 classes of substitution according to the number of replicates they are detected in, ranging from N = 1 to N = 3, in white adipose tissue (WAT) and liver. The first two classes (AtoG and TtoC) are associated to ADAR-mediated RNA editing, and the next two (CtoT and GtoA) to APOBEC-meditated RNA editing. At the top-right of each graph, the total number of RNA editing events detected for a given number of replicates is shown. ADAR: Adenosine deaminases acting on RNA. APOBEC: Apolipoprotein B mRNA editing enzyme, catalytic polypetide-like.

    Article Snippet: RNA sequencing: Libraries with a mean insert size of 200 bp were prepared according to the manufacturer’s instructions for RNA-seq library preparation, selecting polyadenylated mRNA using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) from each sample.

    Techniques:

    Study design, sample validation and data analysis. (A) Undifferentiated myoblasts (MB) and differentiated myotubes (MT) from two unaffected and two FSHD2 individuals were used to identify small RNAs differentially expressed in FSHD2 during muscle differentiation. (B) Control and FSHD2 muscle cells used in this study were characterized in terms of D4Z4 DNA methylation (Bsa A1/Fse1), D4Z4 repeat size and presence of SMCHD1 mutations. (C) qRT-PCR analysis of the control and FSHD2 MB and MT samples used for small RNA seq showed that the muscle differentiation marker, Actin alpha1, was induced in both control and FSHD2 MT samples and that DUX4 was expressed in FSHD2 samples but not in controls. Error bars in the graph show the SD of the mean for technical triplicates. (D) The flowchart depicting main steps of our small RNA sequencing data analysis. (E) Small RNA libraries were validated by comparing normalized log2 read counts for myogenic and ubiquitous miRNAs between MT and MB samples. Levels of expression of myogenic miRNAs (myomiRs), miR1–1 and miR133A were induced both in control and FSHD2 MT compared to MB, but expression of miR16–1, a ubiquitous miRNA, was not changed during muscle differentiation as expected.

    Journal: Human Molecular Genetics

    Article Title: Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures

    doi: 10.1093/hmg/ddy173

    Figure Lengend Snippet: Study design, sample validation and data analysis. (A) Undifferentiated myoblasts (MB) and differentiated myotubes (MT) from two unaffected and two FSHD2 individuals were used to identify small RNAs differentially expressed in FSHD2 during muscle differentiation. (B) Control and FSHD2 muscle cells used in this study were characterized in terms of D4Z4 DNA methylation (Bsa A1/Fse1), D4Z4 repeat size and presence of SMCHD1 mutations. (C) qRT-PCR analysis of the control and FSHD2 MB and MT samples used for small RNA seq showed that the muscle differentiation marker, Actin alpha1, was induced in both control and FSHD2 MT samples and that DUX4 was expressed in FSHD2 samples but not in controls. Error bars in the graph show the SD of the mean for technical triplicates. (D) The flowchart depicting main steps of our small RNA sequencing data analysis. (E) Small RNA libraries were validated by comparing normalized log2 read counts for myogenic and ubiquitous miRNAs between MT and MB samples. Levels of expression of myogenic miRNAs (myomiRs), miR1–1 and miR133A were induced both in control and FSHD2 MT compared to MB, but expression of miR16–1, a ubiquitous miRNA, was not changed during muscle differentiation as expected.

    Article Snippet: To ensure high standard and consistency in small RNA libraries preparation, the eight total RNA preps from FSHD2 and control MB and MT samples were further processed at the FHCRC Genomics Core for quality control (QC) analysis and small RNA libraries preparation using Illumina TruSeq small RNA protocol.

    Techniques: DNA Methylation Assay, Quantitative RT-PCR, RNA Sequencing Assay, Marker, Expressing

    A treatment/control experimental design. Ten mice were treated with IL-1β ( n = 5), or saline ( n = 5; referred to as untreated). Four hours after treatment, the mice were sacrificed, liver samples were collected, and total RNA was extracted from the tissue. At this point, aliquots of the same RNA sample were sequenced on both an Illumina HiSeq 2500 and an Ion Torrent Proton. Next, RNA-Seq reads from each platform were aligned using three alignment algorithms: 1) GSNAP, 2) STAR, and 3) STAR, followed by Bowtie2 to align reads not mapped by STAR (STAR + Bowtie2). Lastly, all aligned data were normalized using the P ipeline O f R NA-Seq T ransformations (PORT)

    Journal: BMC Genomics

    Article Title: A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

    doi: 10.1186/s12864-017-4011-0

    Figure Lengend Snippet: A treatment/control experimental design. Ten mice were treated with IL-1β ( n = 5), or saline ( n = 5; referred to as untreated). Four hours after treatment, the mice were sacrificed, liver samples were collected, and total RNA was extracted from the tissue. At this point, aliquots of the same RNA sample were sequenced on both an Illumina HiSeq 2500 and an Ion Torrent Proton. Next, RNA-Seq reads from each platform were aligned using three alignment algorithms: 1) GSNAP, 2) STAR, and 3) STAR, followed by Bowtie2 to align reads not mapped by STAR (STAR + Bowtie2). Lastly, all aligned data were normalized using the P ipeline O f R NA-Seq T ransformations (PORT)

    Article Snippet: Illumina library preparation and sequencing 200 ng of total RNA from each liver sample was prepared for Illumina sequencing according to the manufacturer’s protocol using the TruSeq stranded mRNA Sample Preparation Kit (Illumina, catalog no. RS-122-2103).

    Techniques: Mouse Assay, RNA Sequencing Assay

    Recurrent LACTB2 - NCOA2 fusion in colorectal cancer (CRC). ( a ) Structural variations (SVs) in the tumor tissue of a CRC case were illustrated as a Circos plot with red and blue lines indicating inter-chromosomal and intra-chromosomal SVs, respectively. ( b ) The DNA and RNA structures of the LACTB2 - NCOA2 fusion were illustrated. RT–PCR (M: size marker; N: normal cDNA; T: CRC cDNA) and Sanger sequencing confirmed the tumor-specific occurrence of LACTB2 - NCOA2 fusion. ( c ) The LACTB2 - NCOA2 fusion transcript with the same breakpoints was present in 6 out of 99 (6.1%) CRC cDNA samples as confirmed by RT–PCR and Sanger sequencing (chromatogram).

    Journal: Oncogene

    Article Title: Disruption of NCOA2 by recurrent fusion with LACTB2 in colorectal cancer

    doi: 10.1038/onc.2015.72

    Figure Lengend Snippet: Recurrent LACTB2 - NCOA2 fusion in colorectal cancer (CRC). ( a ) Structural variations (SVs) in the tumor tissue of a CRC case were illustrated as a Circos plot with red and blue lines indicating inter-chromosomal and intra-chromosomal SVs, respectively. ( b ) The DNA and RNA structures of the LACTB2 - NCOA2 fusion were illustrated. RT–PCR (M: size marker; N: normal cDNA; T: CRC cDNA) and Sanger sequencing confirmed the tumor-specific occurrence of LACTB2 - NCOA2 fusion. ( c ) The LACTB2 - NCOA2 fusion transcript with the same breakpoints was present in 6 out of 99 (6.1%) CRC cDNA samples as confirmed by RT–PCR and Sanger sequencing (chromatogram).

    Article Snippet: Poly-A-containing mRNA purification, double-stranded cDNA synthesis, end repair, 3' end adenylation, adapter ligation and enrichment of DNA fragments for RNA-Seq library construction were performed using the reagents provided in the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Marker, Sequencing

    Integrative analysis revealed IL8 as a target of increased FOXA1 in ER transcriptional reprogramming. ( A ) Integrated RNA-seq and FOXA1 ChIP-seq data in MCF7L-P and TamR cells. Genes aligned in RNA-seq were calculated for their expression log 2 ratio of fragments per kilobase of transcript per million mapped reads (FPKM) in TamR vs. P cells, by which the genes were sorted in a descending order. FOXA1 binding events (tags) within ± 20 kb of each gene’s TSS were counted and represented by average normalized RPM for every 300 consecutive genes along the order of sorted genes from RNA-seq. These FOXA1 tags were plotted separately for P (in blue) and TamR (in red) cells. ( B ) Heat maps of genes with high expression [log 2 (FPKM)] and with enriched FOXA1 binding (log 2 ratio of RPM) in TamR vs. P cells. Heat maps of the expression in these genes (log 2 ratio of FPKM) in MCF7L/FOXA1 +Dox vs. −Dox cells and in TamR cells with si-ER vs. si-N.S. knockdown are also shown. ( C ) Venn diagram showing the overlap genes, including IL8 , CTGF , and LOX , between the FOXA1-overexpression (O.E.) up-regulated genes and the MCF7L-TamR signature genes. P value was calculated by Fisher’s exact test. ( D ) IL-8 gene expression measured by qRT-PCR in four Endo-R cell models. Data represent means ± SEM, * P

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

    Article Title: FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer

    doi: 10.1073/pnas.1612835113

    Figure Lengend Snippet: Integrative analysis revealed IL8 as a target of increased FOXA1 in ER transcriptional reprogramming. ( A ) Integrated RNA-seq and FOXA1 ChIP-seq data in MCF7L-P and TamR cells. Genes aligned in RNA-seq were calculated for their expression log 2 ratio of fragments per kilobase of transcript per million mapped reads (FPKM) in TamR vs. P cells, by which the genes were sorted in a descending order. FOXA1 binding events (tags) within ± 20 kb of each gene’s TSS were counted and represented by average normalized RPM for every 300 consecutive genes along the order of sorted genes from RNA-seq. These FOXA1 tags were plotted separately for P (in blue) and TamR (in red) cells. ( B ) Heat maps of genes with high expression [log 2 (FPKM)] and with enriched FOXA1 binding (log 2 ratio of RPM) in TamR vs. P cells. Heat maps of the expression in these genes (log 2 ratio of FPKM) in MCF7L/FOXA1 +Dox vs. −Dox cells and in TamR cells with si-ER vs. si-N.S. knockdown are also shown. ( C ) Venn diagram showing the overlap genes, including IL8 , CTGF , and LOX , between the FOXA1-overexpression (O.E.) up-regulated genes and the MCF7L-TamR signature genes. P value was calculated by Fisher’s exact test. ( D ) IL-8 gene expression measured by qRT-PCR in four Endo-R cell models. Data represent means ± SEM, * P

    Article Snippet: For samples from the MCF7L-P and MCF7L-TamR cells, the RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and the Agilent Automation NGS system according to manufacturers’ instructions.

    Techniques: RNA Sequencing Assay, Chromatin Immunoprecipitation, Expressing, Binding Assay, Over Expression, Quantitative RT-PCR

    Experimental pipeline of SUPeR-seq, and its sensitivity at the whole-transcriptome scale. a The schematic of SUPeR-seq analysis. A single cell is lysed to release RNAs. RNAs are then reverse transcribed into first-strand cDNAs using random primers with a fixed anchor sequence (AnchorX-T 15 N 6 ). Unreacted primers are then digested using ExoSAP-IT, followed by adding poly(A) tails to the 3′ ends of the first-strand cDNAs using dATP doped with 1 % ddATP to restrict the length of poly(A) tails. Second-strand cDNAs are synthesized using poly(T) primers with a different anchor sequence (AnchorY-T 24 ). Then the double-stranded cDNAs are evenly amplified by PCR using AnchorX-T 15 and AnchorY-T 24 primers. Finally the purified single cell cDNAs are used to prepare sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. b Detection sensitivity of SUPeR-seq on poly(A)- genes in individual cells. We identified 696 poly(A)- genes by bulk RNA sequencing, of which around 30 % could be recovered in a single cell by SUPeR-seq (for details, see Additional file 3 ). When merged the SUPeR-seq data of the seven single cell samples together, over 50 % of these 696 genes could be successfully recovered by SUPeR-seq in at least one cell. c The number of genes detected from individual and bulk HEK293T cells using different protocols. SUPeR-seq detected 10,911 genes on average from an individual cell with FPKM ≥1(Fragments Per Kilobase of exon model per Million mapped reads), 19.3 % more than the Tang2009 protocol did (9148 genes on average). For comparison, 14,931 genes were detected with FPKM ≥1 in the four rRNA-depleted total RNA samples from bulk HEK293T cells, and 15,535 genes were detected in the four oligo(dT)-enriched total RNA samples from bulk HEK293T cells

    Journal: Genome Biology

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

    doi: 10.1186/s13059-015-0706-1

    Figure Lengend Snippet: Experimental pipeline of SUPeR-seq, and its sensitivity at the whole-transcriptome scale. a The schematic of SUPeR-seq analysis. A single cell is lysed to release RNAs. RNAs are then reverse transcribed into first-strand cDNAs using random primers with a fixed anchor sequence (AnchorX-T 15 N 6 ). Unreacted primers are then digested using ExoSAP-IT, followed by adding poly(A) tails to the 3′ ends of the first-strand cDNAs using dATP doped with 1 % ddATP to restrict the length of poly(A) tails. Second-strand cDNAs are synthesized using poly(T) primers with a different anchor sequence (AnchorY-T 24 ). Then the double-stranded cDNAs are evenly amplified by PCR using AnchorX-T 15 and AnchorY-T 24 primers. Finally the purified single cell cDNAs are used to prepare sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. b Detection sensitivity of SUPeR-seq on poly(A)- genes in individual cells. We identified 696 poly(A)- genes by bulk RNA sequencing, of which around 30 % could be recovered in a single cell by SUPeR-seq (for details, see Additional file 3 ). When merged the SUPeR-seq data of the seven single cell samples together, over 50 % of these 696 genes could be successfully recovered by SUPeR-seq in at least one cell. c The number of genes detected from individual and bulk HEK293T cells using different protocols. SUPeR-seq detected 10,911 genes on average from an individual cell with FPKM ≥1(Fragments Per Kilobase of exon model per Million mapped reads), 19.3 % more than the Tang2009 protocol did (9148 genes on average). For comparison, 14,931 genes were detected with FPKM ≥1 in the four rRNA-depleted total RNA samples from bulk HEK293T cells, and 15,535 genes were detected in the four oligo(dT)-enriched total RNA samples from bulk HEK293T cells

    Article Snippet: Sequencing library generation for bulk amount of mouse ES cell RNA and HEK293T cell RNA Total RNA (1 μg) was used for deep-sequencing library construction following the instructions of the TruSeq RNA sample preparation kit (Illumina).

    Techniques: Sequencing, Synthesized, Amplification, Polymerase Chain Reaction, Purification, Sample Prep, RNA Sequencing Assay

    Transcription and splicing of the HIV 89.6 RNA. a Junctions between HIV splice donors and acceptors observed in the RNA-Seq data. Acceptors are shown as the columns and donors as the rows with the coloring indicating the frequency of each pairing. b The relative abundance of 78 HIV 89.6 transcripts as determined by a combination of PacBio sequencing [ 6 ] and Illumina sequencing. Message structures were generated by targeted long read single molecule sequencing, which allowed association of multiple splice junctions in single sequence reads. The Illumina short read sequencing allowed normalization of message abundances between size classes. The inferred HIV message population is shown colored by relative abundance

    Journal: Retrovirology

    Article Title: Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

    doi: 10.1186/s12977-015-0205-1

    Figure Lengend Snippet: Transcription and splicing of the HIV 89.6 RNA. a Junctions between HIV splice donors and acceptors observed in the RNA-Seq data. Acceptors are shown as the columns and donors as the rows with the coloring indicating the frequency of each pairing. b The relative abundance of 78 HIV 89.6 transcripts as determined by a combination of PacBio sequencing [ 6 ] and Illumina sequencing. Message structures were generated by targeted long read single molecule sequencing, which allowed association of multiple splice junctions in single sequence reads. The Illumina short read sequencing allowed normalization of message abundances between size classes. The inferred HIV message population is shown colored by relative abundance

    Article Snippet: mRNA sequencing Messenger RNA was isolated and amplified from purified total cellular RNA (3 µL or approximately 9 µg from each uninfected sample, 25 µL or approximately 3 µg from each infected sample) using the Illumina TruSeq RNA sample preparation kit according to manufacturer’s protocol.

    Techniques: RNA Sequencing Assay, Sequencing, Generated

    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques: Expressing

    Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques:

    Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques: Generated

    Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques:

    Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques:

    Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques: Expressing

    Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: Following the manufacturer protocol, the library was prepared from the sheared cDNA using the Illumina TruSeq RNA Library Prep Kit with 8 cycles of PCR.

    Techniques:

    NEERV transcription is globally increased in C57BL/6N, but not C57BL/6J, lymphocytes and bone marrow-derived macrophages (A) Representative histogram and calculated MFI of ERV envelope protein expression detected via FACS on the surface of peripheral blood B cells, CD4 + T, and CD8 + T lymphocytes from adult C57BL/6N (B6N) and C57BL/6J (B6J) mice. Each histogram or point represents an individual mouse and mean and standard deviation are plotted. (B) RT-qPCR of RNA from total splenocytes from B6N (n=8) and B6J (n=8) mice. Primers amplify respective envelope regions of all Xmv, Pmv, Mpmv, and Emv transcripts, the gag or polymerase regions of IAP, MusD, and ETn elements (Maksakova et al., 2009), or LINE1 ORFp1. Values were normalized to GAPDH expression. Mean and standard deviation are plotted. (C) Volcano plot of differentially expressed cellular genes all 47 uniquely mappable ERV loci from mRNA sequencing of B6N and B6J naïve CD4 + T cells. (D) Normalized read counts mapping to NEERV LTR families using the RepEnrich alignment strategy from mRNA sequencing of naïve CD4+ T cells. (E) Volcano plot of differentially expressed cellular genes all 47 uniquely mappable ERV loci from mRNA sequencing of B6N and B6J bone marrow-derived macrophages (F) .

    Journal: Immunity

    Article Title: The lupus susceptibility locus Sgp3 encodes the suppressor of endogenous retrovirus expression SNERV

    doi: 10.1016/j.immuni.2018.12.022

    Figure Lengend Snippet: NEERV transcription is globally increased in C57BL/6N, but not C57BL/6J, lymphocytes and bone marrow-derived macrophages (A) Representative histogram and calculated MFI of ERV envelope protein expression detected via FACS on the surface of peripheral blood B cells, CD4 + T, and CD8 + T lymphocytes from adult C57BL/6N (B6N) and C57BL/6J (B6J) mice. Each histogram or point represents an individual mouse and mean and standard deviation are plotted. (B) RT-qPCR of RNA from total splenocytes from B6N (n=8) and B6J (n=8) mice. Primers amplify respective envelope regions of all Xmv, Pmv, Mpmv, and Emv transcripts, the gag or polymerase regions of IAP, MusD, and ETn elements (Maksakova et al., 2009), or LINE1 ORFp1. Values were normalized to GAPDH expression. Mean and standard deviation are plotted. (C) Volcano plot of differentially expressed cellular genes all 47 uniquely mappable ERV loci from mRNA sequencing of B6N and B6J naïve CD4 + T cells. (D) Normalized read counts mapping to NEERV LTR families using the RepEnrich alignment strategy from mRNA sequencing of naïve CD4+ T cells. (E) Volcano plot of differentially expressed cellular genes all 47 uniquely mappable ERV loci from mRNA sequencing of B6N and B6J bone marrow-derived macrophages (F) .

    Article Snippet: RNA was isolated from naïve and bulk CD4 T cells using the RNeasy Kit and 500ng was used for paired-end library generation with the Illumina TruSeq RNA Library Prep Kit (naïve) or the NEB Ultra RNA Library Prep Kit (bulk).

    Techniques: Derivative Assay, Expressing, FACS, Mouse Assay, Standard Deviation, Quantitative RT-PCR, Sequencing

    Boxplot of the coefficients of determination ( R 2 values) of the RNA-seq log fold change values vs TaqMan qPCR measurements. The boxes are coloured by protocol: red for RNA Access, green for Ribo-Zero, and blue for TruSeq. Darker shades indicate boxes for samples to which a more severe degradation protocol was applied

    Journal: BMC Genomics

    Article Title: A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples

    doi: 10.1186/s12864-017-3827-y

    Figure Lengend Snippet: Boxplot of the coefficients of determination ( R 2 values) of the RNA-seq log fold change values vs TaqMan qPCR measurements. The boxes are coloured by protocol: red for RNA Access, green for Ribo-Zero, and blue for TruSeq. Darker shades indicate boxes for samples to which a more severe degradation protocol was applied

    Article Snippet: Sequencing libraries Poly-A enriched strand-specific libraries were generated with the TruSeq mRNA V2 sample preparation kit (#RS-122-2001, Illumina), ribosomal RNA depleted strand-specific RNA libraries with the TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (#RS-122-2301and (#RS-122-2302, Illumina), and transcriptome capture based libraries with the TruSeq RNA Access Library Prep Kit (#RS-301-2001, Illumina).

    Techniques: RNA Sequencing Assay, Real-time Polymerase Chain Reaction

    Viremia measurement in experimentally ZIKV-infected Callithrix penicilata collected from day −1 until 19 dpi. One-step qRT-PCR was used to measure semi quantitatively the ZIKV RNA loads in the serum of four animals at indicated days p.i. and represented as viral RNA copies per mL of sample standard curve. The curve was obtained from a standard sample with known titer after serial dilutions (5 × 10 1 to 5 × 10 6 copies/mL) on the plasma of the non-infected marmosets.Values are expressed by RNA genome copies per mL for all the infected marmosets. Viremia was detected in the serum of marmosets 1, 3 and 4 on day 2 p.i. and in all infected marmosets on day 3 p.i. The figure shows that viremia increased on day 5 p.i. when compared to other evaluated days for all the infected marmosets. p.i.: post infection. NHP: non-human primates. Day −1: day before the infection.

    Journal: Scientific Reports

    Article Title: Evidence of natural Zika virus infection in neotropical non-human primates in Brazil

    doi: 10.1038/s41598-018-34423-6

    Figure Lengend Snippet: Viremia measurement in experimentally ZIKV-infected Callithrix penicilata collected from day −1 until 19 dpi. One-step qRT-PCR was used to measure semi quantitatively the ZIKV RNA loads in the serum of four animals at indicated days p.i. and represented as viral RNA copies per mL of sample standard curve. The curve was obtained from a standard sample with known titer after serial dilutions (5 × 10 1 to 5 × 10 6 copies/mL) on the plasma of the non-infected marmosets.Values are expressed by RNA genome copies per mL for all the infected marmosets. Viremia was detected in the serum of marmosets 1, 3 and 4 on day 2 p.i. and in all infected marmosets on day 3 p.i. The figure shows that viremia increased on day 5 p.i. when compared to other evaluated days for all the infected marmosets. p.i.: post infection. NHP: non-human primates. Day −1: day before the infection.

    Article Snippet: Then, libraries were prepared with the Illumina®TruSeq® RNA Access Library Prep kit (Illumina, San Diego, CA, USA), with ZIKV-specific probes, according to the manufacturer’s instructions, skipping the first step that cleaves the RNA molecules.

    Techniques: Infection, Quantitative RT-PCR

    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques: Expressing

    Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques:

    Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques: Generated

    Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques:

    Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques:

    Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques: Expressing

    Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) with 4 ng of RNA,NuGEN Ovation® RNA-Seq System V2 with 4 ng of RNA (NuGEN) with 4 ng of RNA, TaKaRa SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian with 4 ng of RNA (SMARTer), TaKaRa SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing with 4 ng and 0.25 ng of RNA (SMARTseq4 and SMARTseq0.25) and Illumina TruSeq RNA Library Prep Kit v2 with 4 ng and 70 ng of RNA (TruSeq4 and TruSeq70).

    Techniques: