For the RNA seq experiment, HAE were infected with MeV-GFP at an MOI of 1 for 4 h at 37 °C 5% CO2. Total RNA was extracted from infected HAE cultures at 0, 12, 24, 48, 72, and 120 hpi using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. RNA samples were treated with RQ1 RNAse-Free DNAse for 10–15 min at 37°C to remove genomic DNA contamination. The concentration and purity of the RNA were detected using a Nanodrop 2000 (Thermo Fisher Scientific, USA) and integrity was assessed via RNA integrity number (RIN) generated by capillary electrophoresis. Samples with RNA quantification ≥500 ng and an RIN ≥8 were used to generate Illumina-sequencing libraries. The cDNA libraries were prepared using the TruSeq RNA sample Prep (Illumina, San Diego, CA, USA) according to manufacturer’s instructions and submitted to Iowa Institute of Human Genetics Genomics Division at University of Iowa for sequencing. Adapter sequences and low-quality reads were discarded from the data set. Remaining reads were aligned to the human genome and normalized using RPKM method.
Truseq rna sample prep
Manufactured by Illumina
Sourced in United States
The TruSeq RNA Sample Prep is a lab equipment product manufactured by Illumina. It is designed for RNA sample preparation, a critical step in the process of generating data for RNA sequencing. The core function of this product is to prepare RNA samples for subsequent analysis, including library preparation and sequencing.
Automatically generated - may contain errors
Lab products found in correlation
Agilent model 2100 bioanalyzer, by Agilent Technologies (4 mentions)
Hiseq 2500, by Illumina (3 mentions)
Mirvanatm mirna isolation kit, by Thermo Fisher Scientific (2 mentions)
Bioanalyzer, by Thermo Fisher Scientific (2 mentions)
Truseq sbs kit v3, by Illumina (2 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Mirvana mirna isolation kit, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (1 mentions)
Nanodrop 8000 spectrophotometer, by Thermo Fisher Scientific (1 mentions)
Novaseq 6000 system, by Illumina (1 mentions)
Bioanalyzer 2100 system, by Agilent Technologies (1 mentions)
Genechip mouse gene 1.0 st array, by Thermo Fisher Scientific (1 mentions)
High pure rna isolation kit, by Roche (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Truseq rna library protocol, by Illumina (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Miseq instrument, by Illumina (1 mentions)
Olb v1, by Illumina (1 mentions)
Hiseq paired end read cluster generation kit, by Illumina (1 mentions)
Hiseq 2000, by Illumina (1 mentions)
18 protocols using truseq rna sample prep
1
RNA-seq Analysis of MeV-GFP Infection in HAE
2
Transcriptome Analysis of Bacterial Strains
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Transcriptome sequencing was performed at DNALINK, Inc. The purity and concentration of the RNA samples were measured with a NanoDrop™ 8,000 spectrophotometer (Thermo Fisher Scientific, Seoul, South Korea). Total RNA integrity was evaluated as an RNA Integrity Number (RIN) using a Bioanalyzer 2,100 system (Agilent, United States), and high quality RNA samples (RIN > 7) were used for the analysis. RNA samples were subjected to ribosomal RNA depletion using the Ribo-Zero Plus rRNA Depletion Kit for bacteria (Illumina), followed by cDNA library construction using TruSeq® RNA Sample Prep (Illumina) according to the manufacturer’s protocols. The resulting library was sequenced using a NovaSeq 6,000 System (Illumina). Raw reads were assembled and aligned with the reference AWRP genome using TopHat2 v2.0.13 with default parameters (Kim et al., 2013 (link)). Cufflinks v2.2.0 (Trapnell et al., 2010 (link)) was run with default parameters to calculate the fragments per kilobase of transcript per million (FPKM) values using the read data which were obtained with biological duplicate samples, and to identify differentially expressed genes (DEGs) between 46 T-a and AWRP for each phase. A differentially expressed gene was defined by the criteria of |log2(folds)| > 1 and false discovery rate (FDR) < 0.001.
3
Transcriptome Analysis of Mouse Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using a High Pure RNA Isolation Kit (Roche Applied Science); 5 µg of total RNA was utilized for RNA amplification and synthesis of double-stranded cDNAs according to the TruSeq RNA Sample Prep guidelines (Illumina, San Diego, CA). The paired-end reads of each sample were aligned to the mouse genome (mm10) using Subread25 (link), and transcript abundance was shown by the count data by using HTSeq26 (link). Expression data were adjusted by a total of 10 million counts. Gene chip analysis of MHCF1 cells, MHCF5 cells, and mouse liver was performed using a GeneChip Mouse Gene 1.0 ST Array (Affymetrix) as described previously27 (link). Functional ontology enrichment analysis was conducted to compare the BioCarta Pathway process distribution of the differentially expressed genes13 (link). LS/KS permutation tests were performed for pathway comparison (P < 0.05) (BRB-ArrayTools; https://brb.nci.nih.gov/BRB-ArrayTools ).
4
RNA-seq of porcine fetal lungs
5
RNA-Seq Protocol for Porcine Transcriptome
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The RNA-Seq samples were prepared following the manufacturer’s recommendation using the TruSeq RNA Sample Prep (Illumina, Hayward, CA, USA). Samples were sequenced on the Iseq platform, dividing the 60 samples across 7 lanes (i.e. 4 lanes with 9 samples and 3 lanes with 8 samples). Prior to alignment, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate < 0.5). After trimming, sequence reads shorter than 30 nucleotides were discarded. Remaining reads were aligned to the pig reference genome sequence assembly34 (link) (Sscrofa10.2) using the CLC Genomics Server program (Qiagen, Valencia, CA, USA). The total number of uniquely mapped reads per sample was 22,260,237 and on average across samples, 17,683,594 were mapped.
6
RNA-Seq Analysis of Primary Airway Cultures
7
RNA-Seq analysis of human pancreatic cancer cell lines
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The human pancreatic cancer cell lines MIA PaCA-2, Pa02C, Pa14C and Pa16C were seeded at ~50% confluency. The next day the cells were treated with the vehicle control DMSO (≤0.01%), LY3009120 (RAFi, 0.3 μM), SCH772984 (ERKi, 0.04 μM) or the combination of the two inhibitors for 4 or 24 hr. The cells were washed twice with ice-cold PBS and before scrape removal in ice-cold PBS. The cells were collected by centrifugation at 326 x g (500 rpm) at 4°C for 10 min, and the cell pellets were flash frozen by liquid nitrogen. Whole transcriptome libraries were generated from total RNA (50 ng) of the human pancreatic cancer cell lines by using Illumina’s Truseq RNA Sample Prep to perform RNA sequencing. Oligo(dT) magnetic beads were used to select Poly(A) mRNA, and TruSeq PCR Master Mix and primer cocktail were used to enrich the libraries. The Agilent Bioanalyzer and Invitrogen Qubit were used to clean and quantify the amplified products. The Illumina HiSeq 2500 was used to sequence the clustered flowcell for paired 100-bp reads by using Illumina’s TruSeq SBS Kit V3. Lane level fastq files were appended together if they were sequenced across multiple lanes. These fastq files were then aligned with STAR 2.3.1 to GRCh37.62 using ensembl.74.genes.gtf as GTF files. Transcript abundances were quantified by HTSeq in total read counts per transcript.
8
Isolation and Sequencing of Total RNA from CFBE Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated from CFBE cells using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA). Total RNA was tested on an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA integrity number (RIN) greater than 8.0 were selected for further processing. Libraries were prepared using the TruSeq RNA Sample Prep (Illumina, San Diego, CA, USA) and submitted to the Iowa Institute of Human Genetics Genomics Division for deep sequencing. Data were processed using Kallisto and Sleuth.19 , 20
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
The RNA samples from each cultivar grown under the same conditions were pooled in equimolar concentrations and 16 pooled RNA samples from the four cultivars under N, Al-4, Al-12, and Al-24 conditions were used for cDNA library preparation with TruSeq RNA SamplePrep (Illumina, USA). The quality of 16 libraries thus obtained was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies). Eventually, the libraries were sequenced on HiSeq2500 (Illumina) platform.
10
Transcriptome Analysis of Tongue Squamous Cell Carcinoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Transcriptome libraries for sequencing were constructed according to the TruSeq RNA library protocol (Illumina) outlined in TruSeq RNA Sample Prep (Illumina) performed as described previously [14] and detailed in supplementary material and methods . Transcriptome data analysis was performed using previously published a protocol for transcriptome sequencing data analysis [19] . First, to identify the bona fide expressed transcripts, we filtered all the transcripts which were lowly expressed (≤0.1 log 10 (RSEM + 1)) for each sample; second, transcript expressed in 10% of samples was considered as a candidate expressed gene in tongue tumor tissue. A list of 16,525 transcripts identified to be expressed in TSCC tumors were used to filter mutation and DNA copy number changes in this study.
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!