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Illumina Inc cdna library construction
Non-stranded versus stranded <t>RNA-seq</t> protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during <t>cDNA</t> synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries
Cdna Library Construction, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 981 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/cdna library construction/product/Illumina Inc
Average 95 stars, based on 981 article reviews
Price from $9.99 to $1999.99
cdna library construction - by Bioz Stars, 2020-07
95/100 stars

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1) Product Images from "Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap"

Article Title: Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

Journal: BMC Genomics

doi: 10.1186/s12864-015-1876-7

Non-stranded versus stranded RNA-seq protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during cDNA synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries
Figure Legend Snippet: Non-stranded versus stranded RNA-seq protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during cDNA synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries

Techniques Used: RNA Sequencing Assay, Polymerase Chain Reaction, Amplification

2) Product Images from "Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis"

Article Title: Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0158471

RT-PCR analysis of PKS gene expression in infected leaves and mycelial cultures. M . fijiensis isolate 10CR1-24 was used to infect banana tissue-culture plants, as well as to inoculate PDB medium. RT-PCR assays for each PKS or hybrid PKS-NRPS were performed on the resulting leaf lesions or mycelium from the PDB liquid culture. Where possible (for all genes except beta-tubulin and PKS10-1 ), primers were designed to span an intron, to distinguish cDNA from any gDNA contamination. Genomic DNA isolated from 10CR1-24 was used as a positive control, and reactions were also done with no added template, as a negative control. Each lane represents RNA isolated from individual infected leaves (left) or mycelium grown in flask culture (right).
Figure Legend Snippet: RT-PCR analysis of PKS gene expression in infected leaves and mycelial cultures. M . fijiensis isolate 10CR1-24 was used to infect banana tissue-culture plants, as well as to inoculate PDB medium. RT-PCR assays for each PKS or hybrid PKS-NRPS were performed on the resulting leaf lesions or mycelium from the PDB liquid culture. Where possible (for all genes except beta-tubulin and PKS10-1 ), primers were designed to span an intron, to distinguish cDNA from any gDNA contamination. Genomic DNA isolated from 10CR1-24 was used as a positive control, and reactions were also done with no added template, as a negative control. Each lane represents RNA isolated from individual infected leaves (left) or mycelium grown in flask culture (right).

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing, Infection, Isolation, Positive Control, Negative Control

3) Product Images from "sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide"

Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide

Journal: Scientific Reports

doi: 10.1038/s41598-017-04786-3

Antisense transcription detected on the opposite strand of some newly identified RNAs through MiSeq RNA sequencing. RT-PCR was performed on RNA extracted from cells collected at an OD 600nm of 6. Lanes 1 to 5 show IGR_1080208, IGR_1141547, IGR_1141775IGR, IGR_2019414 and 2019159, from left to right after cDNA synthesis (+) or after DNase treatment (−). The gel presented here was cropped for clarity purpose.
Figure Legend Snippet: Antisense transcription detected on the opposite strand of some newly identified RNAs through MiSeq RNA sequencing. RT-PCR was performed on RNA extracted from cells collected at an OD 600nm of 6. Lanes 1 to 5 show IGR_1080208, IGR_1141547, IGR_1141775IGR, IGR_2019414 and 2019159, from left to right after cDNA synthesis (+) or after DNase treatment (−). The gel presented here was cropped for clarity purpose.

Techniques Used: RNA Sequencing Assay, Reverse Transcription Polymerase Chain Reaction

Characterization of an sRNA transcription hotspot in Staphylococcus aureus Newman. ( A ) RNA mapping profile of IGR_11415444 visualized with Artemis. P1, P2, P3, as2, and as3 correspond to the position of probes and/or primers for northern blot and RT-qPCR experiments. ( B ) Identification of multiple transcripts expressed from the positive strand of the Newman genome. Total RNA were extracted from cells collected at an OD 600nm of 6 and tmRNA was used as an internal loading control. ( C ) Relative expression levels of the IGR_1141544 locus as a function of growth phase. The relative cDNA level was determined using HU as an internal control and OD 600nm of 0.5 as a calibrator. The data shown are the means of three independent experiments. A student t-test was performed to determine differences with condition at OD 600nm of 0.5 (* p
Figure Legend Snippet: Characterization of an sRNA transcription hotspot in Staphylococcus aureus Newman. ( A ) RNA mapping profile of IGR_11415444 visualized with Artemis. P1, P2, P3, as2, and as3 correspond to the position of probes and/or primers for northern blot and RT-qPCR experiments. ( B ) Identification of multiple transcripts expressed from the positive strand of the Newman genome. Total RNA were extracted from cells collected at an OD 600nm of 6 and tmRNA was used as an internal loading control. ( C ) Relative expression levels of the IGR_1141544 locus as a function of growth phase. The relative cDNA level was determined using HU as an internal control and OD 600nm of 0.5 as a calibrator. The data shown are the means of three independent experiments. A student t-test was performed to determine differences with condition at OD 600nm of 0.5 (* p

Techniques Used: Northern Blot, Quantitative RT-PCR, Expressing

4) Product Images from "Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection"

Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection

Journal: PLoS ONE

doi: 10.1371/journal.pone.0041645

Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.
Figure Legend Snippet: Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

Techniques Used: Sample Prep, cDNA Library Assay, Sequencing, Expressing

5) Product Images from "Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation"

Article Title: Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation

Journal: Molecular cell

doi: 10.1016/j.molcel.2018.06.001

Global profiling of tRNA m 7 G modifications by m 7 G MeRIP-Seq (A) Western blot of the control and Mettl1 KO samples with indicated antibodies. (B) Anti-m 7 G Northwestern blot of m 7 G modifications (Upper panel). RNA samples were separated on a TBE-urea gel, then transferred to nylon membrane for Western blotting using anti-m 7 G antibody. Northern blot of U6 snRNA was used a loading control (Lower panel). (C) Western blot of the METTL1 rescue samples with indicated antibodies. (D) Anti-m 7 G Northwestern blot of m 7 G modifications (Upper panel) and Northern blot of U6 snRNA (Lower panel). (E) Small RNA Northern blot of the anti-m 7 G IP products with indicated probes. (F) Schematic diagram of small RNA m 7 G MeRIP-seq to identify the m 7 G methylome. Small RNAs were isolated and treated with Alkb to remove modifications and then used for cDNA library construction. (G) Population of small RNA mapping in m 7 G MeRIP-Seq. Samples without Alkb treatment (Alkb-) were used as controls. n=2. (H) Scatter plot of tRNA relative enrichment of tRNA in m 7 G MeRIP-Seq. Relative enrichment was calculated by comparing the IP/Input ratio in the WT samples to the KO samples. (I) List of m 7 G modified tRNAs identified by m 7 G MeRIP-Seq. (J) Confirmation of m 7 G modified tRNAs by anti-m 7 G IP and Northern blot with indicated probes. No m 7 G modification was identified in GlnCTG, which was used as a control.
Figure Legend Snippet: Global profiling of tRNA m 7 G modifications by m 7 G MeRIP-Seq (A) Western blot of the control and Mettl1 KO samples with indicated antibodies. (B) Anti-m 7 G Northwestern blot of m 7 G modifications (Upper panel). RNA samples were separated on a TBE-urea gel, then transferred to nylon membrane for Western blotting using anti-m 7 G antibody. Northern blot of U6 snRNA was used a loading control (Lower panel). (C) Western blot of the METTL1 rescue samples with indicated antibodies. (D) Anti-m 7 G Northwestern blot of m 7 G modifications (Upper panel) and Northern blot of U6 snRNA (Lower panel). (E) Small RNA Northern blot of the anti-m 7 G IP products with indicated probes. (F) Schematic diagram of small RNA m 7 G MeRIP-seq to identify the m 7 G methylome. Small RNAs were isolated and treated with Alkb to remove modifications and then used for cDNA library construction. (G) Population of small RNA mapping in m 7 G MeRIP-Seq. Samples without Alkb treatment (Alkb-) were used as controls. n=2. (H) Scatter plot of tRNA relative enrichment of tRNA in m 7 G MeRIP-Seq. Relative enrichment was calculated by comparing the IP/Input ratio in the WT samples to the KO samples. (I) List of m 7 G modified tRNAs identified by m 7 G MeRIP-Seq. (J) Confirmation of m 7 G modified tRNAs by anti-m 7 G IP and Northern blot with indicated probes. No m 7 G modification was identified in GlnCTG, which was used as a control.

Techniques Used: Western Blot, Northern Blot, Isolation, cDNA Library Assay, Modification

6) Product Images from "Transcriptome Analysis of Portunus trituberculatus in Response to Salinity Stress Provides Insights into the Molecular Basis of Osmoregulation"

Article Title: Transcriptome Analysis of Portunus trituberculatus in Response to Salinity Stress Provides Insights into the Molecular Basis of Osmoregulation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0082155

Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.
Figure Legend Snippet: Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay, Expressing

7) Product Images from "De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock"

Article Title: De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-017-0828-7

Flowchart of the pipeline for the A. donax leaf transcriptome sequencing, de novo assembly, annotation, and analysis. The pipeline performs multiple operations from sampling and preparation to sequencing and de novo assembly to functional annotation and analysis. First, mRNA extraction from the first fully expanded leaf (5th from the top ) was carried out followed by cDNA preparation and library construction ( gray ). Sequencing was performed using an Illumina HiSeq platform. The sequenced reads were then subjected to quality control and filtering, and identical sequences were removed ( blue ). Next, de novo assemblies of transcripts were generated using a two-step approach: first, multi- k - mer (Trans-ABySS and rnaSPAdes) and single- k - mer (Trinity) methods were used to generate the pre-assemblies ( pink ); second, pre-assemblies were then concatenated and redundant transcripts were removed using CD-HIT and the EvidentialGene tr2aadcs pipeline ( purple ). The quality of the de novo assembled leaf transcriptome was then assessed ( green ). Finally, the non-redundant (NR) transcript dataset was functionally annotated by homology and gene ontology (GO), and metabolic pathways were analyzed ( mint blue ). Simple sequence repeats (SSRs) and polymorphic SSRs (PolySSRs) were also identified ( orange )
Figure Legend Snippet: Flowchart of the pipeline for the A. donax leaf transcriptome sequencing, de novo assembly, annotation, and analysis. The pipeline performs multiple operations from sampling and preparation to sequencing and de novo assembly to functional annotation and analysis. First, mRNA extraction from the first fully expanded leaf (5th from the top ) was carried out followed by cDNA preparation and library construction ( gray ). Sequencing was performed using an Illumina HiSeq platform. The sequenced reads were then subjected to quality control and filtering, and identical sequences were removed ( blue ). Next, de novo assemblies of transcripts were generated using a two-step approach: first, multi- k - mer (Trans-ABySS and rnaSPAdes) and single- k - mer (Trinity) methods were used to generate the pre-assemblies ( pink ); second, pre-assemblies were then concatenated and redundant transcripts were removed using CD-HIT and the EvidentialGene tr2aadcs pipeline ( purple ). The quality of the de novo assembled leaf transcriptome was then assessed ( green ). Finally, the non-redundant (NR) transcript dataset was functionally annotated by homology and gene ontology (GO), and metabolic pathways were analyzed ( mint blue ). Simple sequence repeats (SSRs) and polymorphic SSRs (PolySSRs) were also identified ( orange )

Techniques Used: Sequencing, Sampling, Functional Assay, Generated

8) Product Images from "Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery"

Article Title: Transcriptome Analysis of the Portunus trituberculatus: De Novo Assembly, Growth-Related Gene Identification and Marker Discovery

Journal: PLoS ONE

doi: 10.1371/journal.pone.0094055

Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, SSR and SNP analysis, etc.
Figure Legend Snippet: Schematic of Illumina deep sequencing and analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, SSR and SNP analysis, etc.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay

9) Product Images from "Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection"

Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection

Journal: PLoS ONE

doi: 10.1371/journal.pone.0041645

Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.
Figure Legend Snippet: Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

Techniques Used: Sample Prep, cDNA Library Assay, Sequencing, Expressing

10) Product Images from "Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge"

Article Title: Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge

Journal: PLoS ONE

doi: 10.1371/journal.pone.0038183

Combined taxonomic domain information of DNA and cDNA datasets. Total DNA sequences and cDNA sequences were assigned to Bacteria , Eukaryota , Archaea , viruses, and other sequences.
Figure Legend Snippet: Combined taxonomic domain information of DNA and cDNA datasets. Total DNA sequences and cDNA sequences were assigned to Bacteria , Eukaryota , Archaea , viruses, and other sequences.

Techniques Used:

11) Product Images from "Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to Changes in Water Salinity"

Article Title: Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to Changes in Water Salinity

Journal: Scientific Reports

doi: 10.1038/srep09836

Workflow of Illumina deep sequencing and bioinformatic analyses. It includes sample preparation, cDNA library construction, Illumina sequencing, and data analyses including transcriptome assembly, BLAST search, GO annotation, and gene expression analysis.
Figure Legend Snippet: Workflow of Illumina deep sequencing and bioinformatic analyses. It includes sample preparation, cDNA library construction, Illumina sequencing, and data analyses including transcriptome assembly, BLAST search, GO annotation, and gene expression analysis.

Techniques Used: Sequencing, Sample Prep, cDNA Library Assay, Expressing

Related Articles

RNA Sequencing Assay:

Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Article Snippet: .. cDNA library construction and Illumina RNA sequencing Overnight cultures of S. aureus were diluted in fresh BHI broth to an OD600nm of 0.1 then cultured at 160 rpm for 5 hr at 37 °C. .. Total RNA were extracted as described above and treated with Amplification Grade DNase I (Invitrogen) to remove genomic contaminations.

Article Title: Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Article Snippet: .. cDNA library construction and sequencing For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA , USA). .. For non-stranded RNA-seq, cDNA libraries were prepared with a TruSeq RNA sample preparation kit v2 (cat# RS-122-2001, Illumina).

Isolation:

Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Article Snippet: .. RNA Isolation, cDNA Library Construction and Illumina Deep Sequencing For each group, three spleens were randomly chosen and shipped on RNAlater (Applied Biosystems) to Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China), where total RNA was isolated from each spleen by trizol (Invitrogen, CA, USA). ..

Cell Culture:

Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Article Snippet: .. cDNA library construction and Illumina RNA sequencing Overnight cultures of S. aureus were diluted in fresh BHI broth to an OD600nm of 0.1 then cultured at 160 rpm for 5 hr at 37 °C. .. Total RNA were extracted as described above and treated with Amplification Grade DNase I (Invitrogen) to remove genomic contaminations.

Purification:

Article Title: Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation
Article Snippet: .. The RNA samples were purified by ethanol precipitation and used for cDNA library construction, followed by sequencing with Illumina Nextseq 500. .. Ribosome footprinting was performed using the TruSeq Ribo Profile kit from Illumina.

cDNA Library Assay:

Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Article Snippet: .. cDNA library construction and Illumina RNA sequencing Overnight cultures of S. aureus were diluted in fresh BHI broth to an OD600nm of 0.1 then cultured at 160 rpm for 5 hr at 37 °C. .. Total RNA were extracted as described above and treated with Amplification Grade DNase I (Invitrogen) to remove genomic contaminations.

Article Title: Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis
Article Snippet: .. cDNA Library Construction and Illumina HiSeq Sequencing Total RNA was submitted to the North Carolina State University Genomic Sciences Laboratory for sequencing. .. Quality of RNA was further confirmed using an Agilent Bioanalyzer, and then strand-specific libraries were created using the NEBNext Ultra Directional library prep kit (New England BioLabs).

Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Article Snippet: .. RNA Isolation, cDNA Library Construction and Illumina Deep Sequencing For each group, three spleens were randomly chosen and shipped on RNAlater (Applied Biosystems) to Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China), where total RNA was isolated from each spleen by trizol (Invitrogen, CA, USA). ..

Article Title: Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation
Article Snippet: .. The RNA samples were purified by ethanol precipitation and used for cDNA library construction, followed by sequencing with Illumina Nextseq 500. .. Ribosome footprinting was performed using the TruSeq Ribo Profile kit from Illumina.

Article Title: Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Article Snippet: .. cDNA library construction and sequencing For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA , USA). .. For non-stranded RNA-seq, cDNA libraries were prepared with a TruSeq RNA sample preparation kit v2 (cat# RS-122-2001, Illumina).

Formalin-fixed Paraffin-Embedded:

Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
Article Snippet: .. To further assess the utility of the immobilized enzymes method on more challenging samples, we have performed Illumina DNA library construction using human FFPE DNA with or without DNA repair as described previously . .. We used FFPE DNA samples as an example of challenging genomic DNA for which library preparation has been shown to be problematic and DNA has been shown to be extensively damaged, notably cytosine deamination .

DNA Sequencing:

Article Title: Absence of the KhpA and KhpB (JAG/EloR) RNA-Binding Proteins Suppresses the Requirement for PBP2b by Overproduction of FtsA in Streptococcus pneumoniae D39
Article Snippet: .. Genomic DNA preparation, DNA library construction, Illumina MiSeq or NextSeq DNA sequencing, and bioinformatics analyses were performed as described previously ( , ). ..

Ethanol Precipitation:

Article Title: Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation
Article Snippet: .. The RNA samples were purified by ethanol precipitation and used for cDNA library construction, followed by sequencing with Illumina Nextseq 500. .. Ribosome footprinting was performed using the TruSeq Ribo Profile kit from Illumina.

Sequencing:

Article Title: Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis
Article Snippet: .. cDNA Library Construction and Illumina HiSeq Sequencing Total RNA was submitted to the North Carolina State University Genomic Sciences Laboratory for sequencing. .. Quality of RNA was further confirmed using an Agilent Bioanalyzer, and then strand-specific libraries were created using the NEBNext Ultra Directional library prep kit (New England BioLabs).

Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Article Snippet: .. RNA Isolation, cDNA Library Construction and Illumina Deep Sequencing For each group, three spleens were randomly chosen and shipped on RNAlater (Applied Biosystems) to Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China), where total RNA was isolated from each spleen by trizol (Invitrogen, CA, USA). ..

Article Title: Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation
Article Snippet: .. The RNA samples were purified by ethanol precipitation and used for cDNA library construction, followed by sequencing with Illumina Nextseq 500. .. Ribosome footprinting was performed using the TruSeq Ribo Profile kit from Illumina.

Article Title: Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Article Snippet: .. cDNA library construction and sequencing For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA , USA). .. For non-stranded RNA-seq, cDNA libraries were prepared with a TruSeq RNA sample preparation kit v2 (cat# RS-122-2001, Illumina).

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    Illumina Inc cdna library construction
    Non-stranded versus stranded <t>RNA-seq</t> protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during <t>cDNA</t> synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries
    Cdna Library Construction, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 981 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cdna library construction/product/Illumina Inc
    Average 95 stars, based on 981 article reviews
    Price from $9.99 to $1999.99
    cdna library construction - by Bioz Stars, 2020-07
    95/100 stars
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    Non-stranded versus stranded RNA-seq protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during cDNA synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries

    Journal: BMC Genomics

    Article Title: Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

    doi: 10.1186/s12864-015-1876-7

    Figure Lengend Snippet: Non-stranded versus stranded RNA-seq protocol. The stranded protocol differs from the non-stranded protocol in two ways. First, during cDNA synthesis, the second-strand synthesis continues as normal except the nucleotide mix includes dUTPs instead of dTTPs. Second, after library preparation, a second-strand digestion step is added. This step ensures that only the first strand survives the subsequent PCR amplification step and hence the strand information of the libraries

    Article Snippet: cDNA library construction and sequencing For stranded RNA-seq, cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA , USA).

    Techniques: RNA Sequencing Assay, Polymerase Chain Reaction, Amplification

    RT-PCR analysis of PKS gene expression in infected leaves and mycelial cultures. M . fijiensis isolate 10CR1-24 was used to infect banana tissue-culture plants, as well as to inoculate PDB medium. RT-PCR assays for each PKS or hybrid PKS-NRPS were performed on the resulting leaf lesions or mycelium from the PDB liquid culture. Where possible (for all genes except beta-tubulin and PKS10-1 ), primers were designed to span an intron, to distinguish cDNA from any gDNA contamination. Genomic DNA isolated from 10CR1-24 was used as a positive control, and reactions were also done with no added template, as a negative control. Each lane represents RNA isolated from individual infected leaves (left) or mycelium grown in flask culture (right).

    Journal: PLoS ONE

    Article Title: Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis

    doi: 10.1371/journal.pone.0158471

    Figure Lengend Snippet: RT-PCR analysis of PKS gene expression in infected leaves and mycelial cultures. M . fijiensis isolate 10CR1-24 was used to infect banana tissue-culture plants, as well as to inoculate PDB medium. RT-PCR assays for each PKS or hybrid PKS-NRPS were performed on the resulting leaf lesions or mycelium from the PDB liquid culture. Where possible (for all genes except beta-tubulin and PKS10-1 ), primers were designed to span an intron, to distinguish cDNA from any gDNA contamination. Genomic DNA isolated from 10CR1-24 was used as a positive control, and reactions were also done with no added template, as a negative control. Each lane represents RNA isolated from individual infected leaves (left) or mycelium grown in flask culture (right).

    Article Snippet: cDNA Library Construction and Illumina HiSeq Sequencing Total RNA was submitted to the North Carolina State University Genomic Sciences Laboratory for sequencing.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Infection, Isolation, Positive Control, Negative Control

    Antisense transcription detected on the opposite strand of some newly identified RNAs through MiSeq RNA sequencing. RT-PCR was performed on RNA extracted from cells collected at an OD 600nm of 6. Lanes 1 to 5 show IGR_1080208, IGR_1141547, IGR_1141775IGR, IGR_2019414 and 2019159, from left to right after cDNA synthesis (+) or after DNase treatment (−). The gel presented here was cropped for clarity purpose.

    Journal: Scientific Reports

    Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide

    doi: 10.1038/s41598-017-04786-3

    Figure Lengend Snippet: Antisense transcription detected on the opposite strand of some newly identified RNAs through MiSeq RNA sequencing. RT-PCR was performed on RNA extracted from cells collected at an OD 600nm of 6. Lanes 1 to 5 show IGR_1080208, IGR_1141547, IGR_1141775IGR, IGR_2019414 and 2019159, from left to right after cDNA synthesis (+) or after DNase treatment (−). The gel presented here was cropped for clarity purpose.

    Article Snippet: cDNA library construction and Illumina RNA sequencing Overnight cultures of S. aureus were diluted in fresh BHI broth to an OD600nm of 0.1 then cultured at 160 rpm for 5 hr at 37 °C.

    Techniques: RNA Sequencing Assay, Reverse Transcription Polymerase Chain Reaction

    Characterization of an sRNA transcription hotspot in Staphylococcus aureus Newman. ( A ) RNA mapping profile of IGR_11415444 visualized with Artemis. P1, P2, P3, as2, and as3 correspond to the position of probes and/or primers for northern blot and RT-qPCR experiments. ( B ) Identification of multiple transcripts expressed from the positive strand of the Newman genome. Total RNA were extracted from cells collected at an OD 600nm of 6 and tmRNA was used as an internal loading control. ( C ) Relative expression levels of the IGR_1141544 locus as a function of growth phase. The relative cDNA level was determined using HU as an internal control and OD 600nm of 0.5 as a calibrator. The data shown are the means of three independent experiments. A student t-test was performed to determine differences with condition at OD 600nm of 0.5 (* p

    Journal: Scientific Reports

    Article Title: sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide

    doi: 10.1038/s41598-017-04786-3

    Figure Lengend Snippet: Characterization of an sRNA transcription hotspot in Staphylococcus aureus Newman. ( A ) RNA mapping profile of IGR_11415444 visualized with Artemis. P1, P2, P3, as2, and as3 correspond to the position of probes and/or primers for northern blot and RT-qPCR experiments. ( B ) Identification of multiple transcripts expressed from the positive strand of the Newman genome. Total RNA were extracted from cells collected at an OD 600nm of 6 and tmRNA was used as an internal loading control. ( C ) Relative expression levels of the IGR_1141544 locus as a function of growth phase. The relative cDNA level was determined using HU as an internal control and OD 600nm of 0.5 as a calibrator. The data shown are the means of three independent experiments. A student t-test was performed to determine differences with condition at OD 600nm of 0.5 (* p

    Article Snippet: cDNA library construction and Illumina RNA sequencing Overnight cultures of S. aureus were diluted in fresh BHI broth to an OD600nm of 0.1 then cultured at 160 rpm for 5 hr at 37 °C.

    Techniques: Northern Blot, Quantitative RT-PCR, Expressing

    Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

    Journal: PLoS ONE

    Article Title: Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection

    doi: 10.1371/journal.pone.0041645

    Figure Lengend Snippet: Schematic of Illumina EST analysis. It includes sample preparation, cDNA library construction and Illumina sequencing, data analysis including assemble, blast, GO annotation, gene expression analysis, etc.

    Article Snippet: RNA Isolation, cDNA Library Construction and Illumina Deep Sequencing For each group, three spleens were randomly chosen and shipped on RNAlater (Applied Biosystems) to Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China), where total RNA was isolated from each spleen by trizol (Invitrogen, CA, USA).

    Techniques: Sample Prep, cDNA Library Assay, Sequencing, Expressing