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Truseq stranded total rna sample prep

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The TruSeq Stranded Total RNA Sample Prep is a laboratory equipment product designed for RNA sequencing. It prepares RNA samples for analysis by performing key steps such as RNA fragmentation, cDNA synthesis, and library preparation. The product enables the generation of stranded RNA-Seq libraries from total RNA samples.

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Lab products found in correlation

Hiseq 2500, by Illumina (2 mentions) Ribo zero rrna removal kit, by Illumina (1 mentions) Hiseq 2500 sequencing platform, by Illumina (1 mentions) Hiseq sr cluster kit v4 cbot, by Illumina (1 mentions) Hiseqv4, by Illumina (1 mentions) Hiseq sbs kit v4, by Illumina (1 mentions) Hiseq 3000, by Illumina (1 mentions) Hiseq 2000 sequencing, by Illumina (1 mentions)

6 protocols using truseq stranded total rna sample prep

1

Ribo-Zero RNA-seq of Gram-negative Bacteria

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Sequencing was completed at Brigham Young University (Provo, UT, United States). Briefly, ribosomal RNA was removed using the Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria. The resulting RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA Sample Prep and fragmented into 50-bp segments and reverse transcribed into cDNA. Sequence adapters used to initiate DNA polymerase binding were ligated to the cDNA, and the sequences were amplified with PCR. The cDNA library was sequenced in high output mode using Illumina sequencing technology (Illumina HiSeq 2500 sequencing platform), generating ∼12 million reads per sample. All sequence reads have been submitted to Genbank and can be found as BioSample accession: SAMN10686493, BioProject ID: PRJNA512538.
Rawle R., Saley T.C., Kang Y.S., Wang Q., Walk S., Bothner B, & McDermott T.R. (2021). Introducing the ArsR-Regulated Arsenic Stimulon. Frontiers in Microbiology, 12, 630562.
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2

Transcriptome Profiling with Illumina HiSeq

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Illumina TruSeq Stranded Total RNA Sample Prep with Ribo-Zero was used to prepare the library. Libraries were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot. After transfer of the flow cell to an Illumina HiSeq 2500, a 50-cycle single-read sequence run was performed (HiSeq SBS Kit v4). For data analysis, Rn5 Ensembl annotations (Build 75) were downloaded and converted to genePred format. Reads were aligned to the transcriptome reference index using NovoAlign (v2.08.01), allowing up to 50 alignments for each read. Read counts were generated using the USeq Defined Region Differential Seq application and used in DESeq2 to measure the differential expression between each condition, controlling for sample preparation batch. Data has been submitted to the GEO Database (Accession # GSE110804). For Ingenuity Pathway Analysis (IPA), differentially expressed gene lists were used as input to identify related pathways, diseases, and networks.
Pan H., Strickland A., Madhu V., Johnson Z.I., Chand S.N., Brody J.R., Fertala A., Zheng Z., Shapiro I.M, & Risbud M.V. (2018). RNA binding protein HuR regulates extracellular matrix gene expression and pH homeostasis independent of controlling HIF-1α signaling in nucleus pulposus cells. Matrix biology : journal of the International Society for Matrix Biology, 77, 23-40.
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3

Illumina TruSeq RNA Sequencing

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Sequencing libraries were constructed from RNA using Illumina TruSeq Stranded Total RNA Sample Prep and sequenced at the Clinical Microarray Core at UCLA by single-end sequencing on an Illumina HiSeq3000.
Balin S.J., Pellegrini M., Klechevsky E., Won S.T., Weiss D.I., Choi A.W., Hakimian J., Lu J., Ochoa M.T., Bloom B.R., Lanier L.L., Stenger S, & Modlin R.L. (2018). Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria. Science immunology, 3(26), eaat7668.
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4

RNA-Seq Protocol for Tumor Fusion Detection

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DNase-treated, ribo-depleted total tumor RNA was used as input for library construction using Illumina's TruSeq Stranded Total RNA Sample prep. RNA-seq data were processed using STAR-Fusion, and these data were used to detect putatively expressed gene fusions in the tumor (https://github.com/STAR-Fusion). We analyzed 125,302,701 RNA-seq reads.
Miller K.E., Kelly B., Fitch J., Ross N., Avenarius M.R., Varga E., Koboldt D.C., Boué D.R., Magrini V., Coven S.L., Finlay J.L., Cottrell C.E., White P., Gastier-Foster J.M., Wilson R.K., Leonard J, & Mardis E.R. (2018). Genome sequencing identifies somatic BRAF duplication c.1794_1796dupTAC;p.Thr599dup in pediatric patient with low-grade ganglioglioma. Cold Spring Harbor Molecular Case Studies, 4(2), a002618.
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5

RNA-seq Data Processing Pipeline

Cited 1 time
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Total RNA was sent to IntegraGen SA (Evry, France) for library construction with TruSeq Stranded Total RNA Sample Prep’ Illumina, and paired-end 2 × 75 nt sequencing was performed on HiSeq 2500 (Illumina). Reads were mapped with reference genome (GRCh38) using STAR mapper tool version 2.5.2a. To count reads that were aligned in each gene, the featureCounts tool (version 1.5.0) [37 (link)] were used with the GENCODE annotation (release 24, in GTF format) downloaded from gencodegens.org. Only read pairs that had both ends successfully aligned were considered. Chimeric reads as well as duplicated reads were not counted. All genes having 0 counts in all samples were filtered out before subsequent analysis. Raw counts were normalized using the size factor-based approach implemented in DESeq2 package (version 1.10.1) [38 (link)]. Normalized counts were then used to compute the enrichment ratio following the formula described above.
Meryet-Figuiere M., Vernon M., Andrianteranagna M., Lambert B., Brochen C., Issartel J.P., Guttin A., Gauduchon P., Brotin E., Dingli F., Loew D., Vigneron N., Wambecke A., Abeilard E., Barillot E., Poulain L., Martignetti L, & Denoyelle C. (2021). Network-Based Integration of Multi-Omics Data Identifies the Determinants of miR-491-5p Effects. Cancers, 13(16), 3970.
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6

Mouse RNA-seq Workflow with Illumina TruSeq

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Library preparation was performed using the Illumina TruSeq Stranded Total RNA Sample Prep and Ribo-Zero rRNA Removal Kit for mouse. Single-end 50-bp reads were generated on a Hiseq 2000 sequencing instrument at the University of Utah Microarray and Genomic Analysis Shared Resource using Illumina Version 4 flow cells. Reads were then aligned to the mouse reference genome (mm10) by Novoalign (http://www.novocraft.com). Quality of RNA sequencing was considered acceptable with an average of 22 million reads. After read alignment, DEGs were identified using the DRDS application (version 1.3.0) in the USeq software package (http://useq.sourceforge.net/).
Scoles D.R., Dansithong W., Pflieger L.T., Paul S., Gandelman M., Figueroa K.P., Rigo F., Bennett C.F, & Pulst S.M. (2020). ALS-associated genes in SCA2 mouse spinal cord transcriptomes. Human Molecular Genetics, 29(10), 1658-1672.
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