Cecal mRNA was isolated using the miRNeasy mini kit (Qiagen Inc.). Libraries were created using the TrueSeq RNA Sample Preparation V2 Kit (Illumina, Inc.) and RNA-sequencing analysis was conducted in the University of Nebraska Medical Center Sequencing Core using the NextSeq 500 sequencer platform and a 150-bp single-end protocol (18 (link)). Sequencing data were analyzed as previously described (18 (link)). EBseq was used to identify transcripts that were differentially expressed in Mdr1a−/− ERS and ERD mice (33 (link)). Gene expression is presented in units of normalized expected counts, which indicates reads per kilobase of transcript per million mapped reads of an mRNA. Data were deposited in the BioProject database under accession ID PRJNA516639.
Trueseq rna sample preparation kit v2
Manufactured by Illumina
Sourced in United States
The TruSeq RNA Sample Preparation Kit v2 is a laboratory equipment product designed for RNA sample preparation. It provides a comprehensive solution for generating high-quality libraries from total RNA for downstream applications, such as next-generation sequencing.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2000, by Illumina (6 mentions)
2100 bioanalyzer, by Agilent Technologies (5 mentions)
Hiseq 2500, by Illumina (4 mentions)
Rnaeasy mini kit, by Qiagen (3 mentions)
Genome analyzer iix, by Illumina (2 mentions)
Library quantitative pcr qpcr quantification guide, by Illumina (2 mentions)
Rna mini kit, by Qiagen (2 mentions)
Agilent bioanalyzer, by Agilent Technologies (2 mentions)
Hiseq 4000, by Illumina (2 mentions)
Agilent 2100 bioanalyzer instrument, by Agilent Technologies (2 mentions)
Nanodrop 1000 spectrometer, by Thermo Fisher Scientific (2 mentions)
Rneasy micro kit, by Qiagen (2 mentions)
Nextseq 500 sequencer platform, by Illumina (1 mentions)
Mirneasy mini kit, by Qiagen (1 mentions)
Rnaqueous micro kit, by Thermo Fisher Scientific (1 mentions)
Lysis buffer, by Thermo Fisher Scientific (1 mentions)
Nextseq 500, by Illumina (1 mentions)
Tissueruptor, by Qiagen (1 mentions)
Rotor gene q, by Qiagen (1 mentions)
Kapa sybr fast qpcr master mix universal, by Roche (1 mentions)
17 protocols using trueseq rna sample preparation kit v2
1
Cecal mRNA Isolation and RNA-seq Analysis in Mdr1a Mice
2
Placodes RNA-seq Library Preparation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
About 100 placodes were collected from each stage for RNAseq library preparation. Immediately after dissection, tissues were lysed in lysis buffer (Ambion) and RNA was isolated using the RNAqueous-Micro Kit (Ambion). Libraries were prepared with TrueSeq RNA Sample Preparation V2 kit (Illumina) and sequenced with Illumina HiSeq 2000 (Illumina) to 1×50 cycles or HiSeq 2500 to 2×100 cycles.
3
Transcriptional Impact of BMP2 and E2 on Developing Ovaries
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To determine the effect of BMP2 and E2 on transcriptome of developing ovaries before the appearance of morphologically distinct PF, E16 ovaries were exposed to either vehicle, recombinant BMP2 (50 ng/μl), or E2 (3.67 nM) in vitro for 24 h. There were three replicates from different animals for each group. Total RNA was isolated using a Qiagen microkit and the quality of RNA was checked by a RNanalyzer (UNMC DNA Core). The RNA samples with RIN value >9 were used for making sequencing libraries with Illumina True-Seq RNA Sample Preparation V2 kit (UNMC DNA Core Facility). Libraries were sequenced using Illumina NextSeq500, yielding 75-bp single end reads in the UNMC DNA Core facility.
Reads were trimmed as necessary by Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by alignment using Tophat2 [36] . The aligned reads were counted by HTseqCount [37] and differential expression analysis was done by DESeq2 [38] using recommended parameters. The gene ontology (GO) pathway enrichment analysis was performed by ClusterProfiler [39] and Gene Set Enrichment Analysis (GSEA; 4.1.0) [40] . Subsetting and other data wrangling was performed in "R" (3.6.2) and with dplyr (0.8.3), data plots were made by using ggplot2 (3.2.1), ggpubr (0.2.4) and enhancedVolcano (1.4.0).
Reads were trimmed as necessary by Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by alignment using Tophat2 [36] . The aligned reads were counted by HTseqCount [37] and differential expression analysis was done by DESeq2 [38] using recommended parameters. The gene ontology (GO) pathway enrichment analysis was performed by ClusterProfiler [39] and Gene Set Enrichment Analysis (GSEA; 4.1.0) [40] . Subsetting and other data wrangling was performed in "R" (3.6.2) and with dplyr (0.8.3), data plots were made by using ggplot2 (3.2.1), ggpubr (0.2.4) and enhancedVolcano (1.4.0).
4
RNA-seq Libraries Construction and Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The cDNA libraries for RNA sequencing were constructed in triplicate for each condition (cultured keratinocytes and T. rubrum conidia as control and co-culture). The libraries were constructed using the TrueSeq® RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to manufacturer’s instructions and the libraries were validated according to the Library quantitative PCR (qPCR) Quantification Guide (Illumina). A pool of 11 pM of each library was distributed on the flowcell lanes and cluster amplification was performed in a cBot (Illumina) according to the manufacturer’s instructions.
Single read and paired-end sequencing were performed in a Genome Analyzer IIx and Hiseq 2000 (Illumina), respectively, according to the manufacturer’s instructions. The RNA-seq data are deposited in the GEO (Gene Expression Omnibus) database [15 (link)] under the accession number GSE110073
Single read and paired-end sequencing were performed in a Genome Analyzer IIx and Hiseq 2000 (Illumina), respectively, according to the manufacturer’s instructions. The RNA-seq data are deposited in the GEO (Gene Expression Omnibus) database [15 (link)] under the accession number GSE110073
5
RNA-seq of MBOAT7 siRNA in MDMs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated from MDMs transfected with MBOAT7 siRNA or control with and without LPS using the RNA mini kit (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer. Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina). Briefly, mRNA was purified, fragmented, and used for first- and second-strand cDNA synthesis followed by adenylation of 3′-ends. Samples were ligated to unique adaptors and subjected to PCR amplification. Libraries were validated using the 2100 BioAnalyzer (Agilent), normalized and pooled for sequencing. RNA-seq libraries prepared from three biological replicates for each condition were sequenced on the Illumina HiSeq 2000 using barcoded multiplexing and a 100 bp read length. Five biological replicates were performed.
6
Extracting mRNA from Tissue Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To extract messenger RNA from tissue samples, we removed liver and feathers from the RNAlater buffer and homogenized either a ∼5-mm3 portion of liver or two feathers per sample, in a Qiagen TissueRuptor, and used a Qiagen RNAeasy minikit, following manufacturer's instructions. RNA quality was assessed with the Agilent 2100 Bioanalyzer Instrument (Model G2939A, Agilent Technologies RNA). Concentrations were measured with a Nanodrop 1000 spectrometer (Thermo Fisher Scientific). About 1 µg of total RNA per sample was used to construct RNA sequencing libraries using the TrueSeq RNA Sample Preparation Kit, v2 (Illumina Inc., San Diego, CA, USA). The resulting libraries were barcoded then sequenced on Illumina Hiseq 2500 and HiSeq 4000 systems. The sequencing protocol was set to high output mode with paired-end 50- or 75-bp reads, with an output of 60–100 million reads per sample.
7
Library Preparation and Quantification
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Fourteen NGS libraries were prepared following the protocol of the TrueSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA). Libraries were qualified using the Bioanalyzer 2100 and DNA 1000 Kit (Agilent Technologies, Santa Clara, USA), according to the manufacturers’ instructions. In all libraries, the final product was an anticipated band at approximately 270 bp. The total concentration of the libraries was measured using the fluorometer Qubit and Qubit dsDNA BR Assay Kit (Life Technologies—Thermo Fisher Scientific), according to the manufacturers’ instructions. Libraries were additionally quantified with qPCR according to the Illumina recommended protocol, using Rotor-Gene Q (Qiagen) and KAPA SYBR FAST qPCR Master Mix Universal (Kapa Biosystems, Wilmington, MA, USA).
8
Transcriptome Profiling of Xpo4 and TGF-β1
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated from the JS1 cell line transfected with Xpo4 (NM_020506) Mouse Myc DDK-tagged ORF Clone (Origene CAT#: MR220257) or empty vector treated with or without TGF-β1 (5.0 ng/ml) using the RNA mini kit (Qiagen). RNA purity and integrity were confirmed using an Agilent Bioanalyzer. Sequencing libraries were prepared from 100–500 ng of total RNA using the TrueSeq RNA sample preparation kit v2 (Illumina). Briefly, mRNA was purified, fragmented, and used for first- and second-strand cDNA synthesis followed by adenylation of 3′ _ends. Samples were ligated to unique adaptors and subjected to PCR amplification. Libraries were then validated using the 2100 BioAnalyzer (Agilent), normalized and pooled for sequencing. RNA-seq libraries prepared from three biological replicates for each condition were sequenced on the Illumina HiSeq 2000 using barcoded multiplexing and a 100-bp read length.
9
RNA-seq analysis of primary iMB tumors
10
Gene Expression Analysis of iPSC-Derived Monocytes
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene expression analysis of FACS-sorted, CD14+ iPSC-derived monocytes (16–19 weeks of differentiation) was performed as published previously [33 (link)]. In brief, cells were lyzed in RLT buffer containing 1% β-mercaptoethanol and RNA was isolated in replicates of four, using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Preparation of the mRNA sequencing library was conducted using the TrueSeq RNA Sample Preparation Kit v2 (RS-122-2002, Illumina Inc, San Diego, USA) and sequencing was performed using the TruSeq SBS Kit HS e v3 (FC-401-3002, Illumina Inc.) on an Illumina HiSeq2000 instrument. The criteria used to identify genes which were expressed in iPSC-derived monocytes were mean reads per kilo base per million (RPKM) > 5.
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!