Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., Hitchin, UK). mRNA was isolated using a Poly(A) RNA Selection Kit (LEXOGEN, Inc., Wien, Austria). The isolated mRNAs were used for cDNA synthesis and shearing following the manufacturer’s instructions. Indexing was performed using Illumina indexes 1–12. Enrichment was performed using PCR. Subsequently, libraries were examined using a TapeStation HS D1000 Screen Tape (Agilent Technologies, Amstelveen, The Netherlands) to evaluate the mean fragment size. Quantification was performed using a library quantification kit and StepOne Real-Time PCR System (Life Technologies, Inc., Carlsbad, CA, USA). High-throughput sequencing was performed via paired-end 100 sequencing using a NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA).
Tapestation hs d1000 screen tape
Manufactured by Agilent Technologies
Sourced in United States, Netherlands
The TapeStation HS D1000 Screen Tape is a lab equipment product from Agilent Technologies. It is designed to analyze the size and concentration of DNA samples. The product provides automated electrophoresis and data analysis for high-sensitivity DNA samples.
Automatically generated - may contain errors
Lab products found in correlation
Nebnext ultra 2 directional rna seq kit, by New England Biolabs (12 mentions)
Stepone real time pcr system, by Thermo Fisher Scientific (12 mentions)
Novaseq 6000, by Illumina (11 mentions)
Poly a rna selection kit, by Lexogen (9 mentions)
Indexes 1 12, by Illumina (5 mentions)
Trizol reagent, by Thermo Fisher Scientific (5 mentions)
8 nt dual indices, by Illumina (3 mentions)
Nd 2000 spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Qubit 2.0 dna hs assay, by Thermo Fisher Scientific (2 mentions)
Nextera xt library kit, by Illumina (2 mentions)
Kapa sybr fast qpcr with, by Thermo Fisher Scientific (2 mentions)
Quantstudio 5 system, by Thermo Fisher Scientific (2 mentions)
Novaseq platform, by Illumina (2 mentions)
Seqcap adapter kit, by Roche (2 mentions)
Tapestation genomic dna assay, by Agilent Technologies (1 mentions)
Novaseq, by Illumina (1 mentions)
Indices 1 12, by Illumina (1 mentions)
Trizol ls, by Thermo Fisher Scientific (1 mentions)
Novaseq 6000 sequencer, by Illumina (1 mentions)
19 protocols using tapestation hs d1000 screen tape
1
mRNA Isolation and RNA-Seq Library Prep
2
Directional RNA-Seq Library Preparation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK). The isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for the cDNA synthesis and shearing, following manufacture’s instruction. Indexing was performed using the Illumina indexes 1–12. The enrichment step was carried out using of PCR. Subsequently, libraries were checked using the TapeStation HS D1000 Screen Tape (Agilent Technologies, Amstelveen, The Netherlands) to evaluate the mean fragment size. Quantification was performed using the library quantification kit using a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 sequencing using NovaSeq 6000 (Illumina, Inc., USA).
A quality control of raw sequencing data was performed using FastQC [33 ]. Adapter and low quality reads (< Q20) were removed using FASTX_Trimmer and BBMap [34 , 35 ]. Then the trimmed reads were mapped to the reference genome using TopHat [36 (link)]. The RC (Read Count) data were processed based on FPKM + Geometric normalization method using EdgeR within R [37 ]. FPKM (Fragments Per kb per Million reads) values were estimated using Cufflinks [38 (link)].
A quality control of raw sequencing data was performed using FastQC [33 ]. Adapter and low quality reads (< Q20) were removed using FASTX_Trimmer and BBMap [34 , 35 ]. Then the trimmed reads were mapped to the reference genome using TopHat [36 (link)]. The RC (Read Count) data were processed based on FPKM + Geometric normalization method using EdgeR within R [37 ]. FPKM (Fragments Per kb per Million reads) values were estimated using Cufflinks [38 (link)].
3
Total RNA Library Construction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The NEB Next Ultra II Directional RNA-Seq Kit (New England BioLabs, Inc., Ipswich, MA, USA) was used to construct total RNA libraries. The mRNA was then isolated using a Poly (A) RNA Selection Kit (Lexogen Inc., Vienna, Austria). Complementary DNA (cDNA) was then synthesized from isolated mRNA and sheared according to the manufacture protocols. Indexing was performed by the Illumina indexes 1–12. PCR was used to enrich the samples. The libraries were then screened with a TapeStation HS D1000 Screen Tape (Agilent Technologies, Amstelveen, The Netherlands) to determine fragment size and quantified with a StepOne Real-Time PCR System (Life Technologies Inc., Carlsbad, CA, USA). Sequencing for high throughput was performed with NovaSeq 6000 (Illumina Inc., San Diego, CA, USA).
4
Illumina Library Preparation and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Isolated nucleic acid was quantified with Qubit 2.0 DNA HS Assay (Thermo Fisher) and the quality was assessed by Tapestation Genomic DNA Assay (Agilent Technologies, CA, USA). Library preparation was performed using the NexteraXT library kit (Illumina, CA, USA) according to the manufacturer’s recommendations. The final library quantity was measured by KAPA SYBR® FAST qPCR with QuantStudio® 5 System (Applied Biosystems, CA, USA), and library quality was evaluated by TapeStation HSD1000 ScreenTape (Agilent Technologies). Illumina® 8-nt dual indices were used. Equimolar pooling of libraries in the same run was performed based on QC values and sequenced on an Illumina® NovaSeq with a read length configuration of 150 paired-end.
5
RNA-seq Library Preparation and Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using TRIzol reagent (Invitrogen, 15596018), and RNA quality and quantification were performed using an Agilent 2100 bioanalyzer (Agilent Technologies) and an ND-2000 Spectrophotometer (Thermo). Library preparation was performed using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, E7760L). Using a Poly(A) RNA Selection Kit, mRNA was extracted (LEXOGEN, 157.96) and used according to the manufacturer’s instructions for cDNA synthesis and shearing. Indexing was performed using Illumina indices 1–12 and was enriched by PCR. The mean fragment sizes were evaluated, and libraries were checked using a TapeStation HS D1000 Screen Tape (Agilent Technologies). Quantification was performed using the StepOne Real-Time PCR System (Life Technologies), and high-throughput sequencing was performed using NovaSeq 6000 (Illumina). FastQC was used to control the quality of the raw sequencing data, and adapters and low-quality reads (
6
Ribosome-Profiling RNA-Seq Library Prep
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
10% of each lysate from the Ribo-seq sample was stored at −80°C with three volumes of TRIzol LS (Invitrogen). Purified RNA input sample was ribo-depleted using hybridizing rRNA complementary DNA oligo mix (final conc 16.5 μM) and thermostable RNaseH (10 U), as previously described.132 (link) Samples were purified with 2.2X RNA Clean XP beads (Beckman Coulter) and eluted with RNase-free water. Cleaned samples were DNase-treated with TuRBO DNase (Invitrogen), incubating at 37°C for 30 min. The samples were cleaned again using 2.2X RNA Clean XP beads and eluted in 22 μL 1x Elute Prime Fragment Buffer included in KAPA RNA Hyperprep library kit (Roche). Samples were fragmented by heating at 85°C for 6 min. RNA-seq libraries were generated per KAPA RNA Hyperprep library kit protocol, with Illumina compatible IDT-UBI adapters (KAPA Dual-Indexed Adapter Kit [Roche]) cDNA was amplified for ten cycles. PCR products were purified with 0.8X bead-based cleanup (KAPA Pure beads) and eluted in 10 mM Tris-HCl (pH 8.0–8.5). Samples were checked for quality control with Qubit dsDNA HS kit (Invitrogen) and Tapestation HS D1000 Screentape (Agilent). Libraries were sequenced on NovaSeq6000 Illumina sequencer at the Shared Genomics Core at the University of Colorado Anschutz.
7
Poly(A) mRNA Isolation and RNA-Seq Library Prep
8
Single-cell genome library preparation
9
RNA-seq Library Preparation and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands) and RNA quantification was performed using an ND-2000 Spectrophotometer (Thermo Inc., DE, USA). Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK). Isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for cDNA synthesis and shearing in accordance with the manufacturer’s instructions. Indexing was performed using the Illumina indexes 1–12. The enrichment step was carried out using PCR. Subsequently, libraries were checked using the TapeStation HS D1000 Screen Tape (Agilent Technologies, Amstelveen, The Netherlands) to evaluate the mean fragment size. Quantification was performed using the library quantification kit and a StepOne Real-Time PCR System (Life Technologies, Inc., Carlsbad, CA, USA). High-throughput sequencing was performed as paired-end 100 sequencing using NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA).
10
Amplicon-based Metagenomic Sequencing Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Library preparation and sequencing were performed by Admera Health (South Plainfield, NJ, USA). Isolated genomic DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Waltham, MA, USA) and DNA quality was evaluated by Genomic DNA ScreenTape analysis (Agilent Technologies, Santa Clara, CA, USA). Library preparation was performed using Nextera XT library kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations while barcoding was performed using Illumina 8-nt dual-indices. The final library was evaluated by Qubit 2.0 DNA HS Assay and the quality of the library generated was examined by TapeStation HSD1000 ScreenTape (Agilent Technologies). Final library quantity was measured by KAPA SYBR FAST qPCR with QuantStudio 5 System (Applied Biosystems, Waltham, MA, USA). Equimolar pooling of libraries was performed based on qPCR QC values before sequencing on an Illumina HiSeq with a read length configuration of 2 × 150 paired end reads, obtaining 1 M PE reads per sample.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!