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Truseq cdna library construction

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The TruSeq cDNA library construction kit is a tool designed for the preparation of cDNA libraries from total RNA samples. The kit provides a streamlined workflow for the conversion of RNA to cDNA and the subsequent generation of a sequencing-ready library.

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Lab products found in correlation

Hiseq 2000 sequencer, by Illumina (2 mentions) Nextseq 500 550 high output kit v2, by Illumina (1 mentions)

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Illumina TruSeq library construction (22 citations)

3 protocols using truseq cdna library construction

1

Xenograft Transcriptome Analysis Pipeline

Cited 1 time
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RNA was extracted from white and thermogenic implants using the TRIzol method. Library preparation was performed using the TruSeq cDNA library construction (Illumina). Samples were processed on the Illumina HiSeq 550 sequencing system with the NextSeq 500/550 High Output kit v2.5 (Illumina, Cat. No. 20024906). The generated fastq files were loaded into the DolphinNext platform (https://dolphinnext.umassmed.edu/) and the Bulk RNA sequencing pipeline was used. The. fastq files were aligned to both the human (hg38) and the mouse (mm10) genome. The resulting alignments were processed using the R-package XenofilteR to classify reads as either of human or mouse origin. Reference (https://github.com/PeeperLab/XenofilteR; Netherlands Cancer Institute - Genomics Core Facilty, 2022 ; Kluin et al., 2018 (link)) for more details on XenofilteR source code. Once aligned, the files were run through RSEM for normalization. Differential expression analysis was performed using the DEBrowser platform (https://debrowser.umassmed.edu/). Gene ontology analysis was performed by combining results from TopFunn (https://toppgene.cchmc.org/).
Solivan-Rivera J., Yang Loureiro Z., DeSouza T., Desai A., Pallat S., Yang Q., Rojas-Rodriguez R., Ziegler R., Skritakis P., Joyce S., Zhong D., Nguyen T, & Corvera S. (2022). A neurogenic signature involving monoamine Oxidase-A controls human thermogenic adipose tissue development. eLife, 11, e78945.
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2

RNA-seq Analysis of Adipocyte Transcriptome

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RNA (1000 ng) was extracted from adipocytes using the Trizol method. RNA sequencing was performed by BGI (Hong Kong) using 1000 ng RNA for the TruSeq cDNA library construction (Illumina). 3Gb data was generated per sample on a HiSeq 2000 sequencer (Illumina). A 91-paired end sequencing strategy was used for the project. Overall read quality was assessed using FastQC http://www.bioinformatics.babraham.ac.uk and the following pre-processing steps where performed using the Fastx toolkit (http://hannonlab.cshl.edu) and PRINSEQ: 7 nt were clipped off from the 5’ end of every read 52 . The reads were then filtered to remove all N-reads. The 3´ ends were then trimmed and the reads filtered to minimum Q25 and 50 bp length. Reads were then mapped with tophat2 to the human genome GRCh38 Ensembl release 77 53 . Read counts were imported into R, and DESeq2 was used for identifying differential expression 54 , as implemented in DEBrowser55 . For the isoform analysis, fpkm values from cufflinks were used 56 ,57 .
Tran K.V., Brown E.L., DeSouza T., Jespersen N.Z., Nandrup-Bus C., Yang Q., Yang Z., Desai A., Min S.Y., Rojas-Rodriguez R., Lundh M., Feizi A., Willenbrock H., Larsen T.J., Severinsen M.C., Malka K., Mozzicato A.M., Deshmukh A.S., Emanuelli B., Pedersen B.K., Fitzgibbons T., Scheele C., Corvera S, & Nielsen S. (2020). Human thermogenic adipocyte regulation by the long noncoding RNA LINC00473. Nature metabolism, 2(5), 397-412.
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3

RNA-seq Analysis of Adipocyte Transcriptome

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RNA (1000 ng) was extracted from adipocytes using the Trizol method. RNA sequencing was performed by BGI (Hong Kong) using 1000 ng RNA for the TruSeq cDNA library construction (Illumina). 3Gb data was generated per sample on a HiSeq 2000 sequencer (Illumina). A 91-paired end sequencing strategy was used for the project. Overall read quality was assessed using FastQC http://www.bioinformatics.babraham.ac.uk and the following pre-processing steps where performed using the Fastx toolkit (http://hannonlab.cshl.edu) and PRINSEQ: 7 nt were clipped off from the 5’ end of every read 52 . The reads were then filtered to remove all N-reads. The 3´ ends were then trimmed and the reads filtered to minimum Q25 and 50 bp length. Reads were then mapped with tophat2 to the human genome GRCh38 Ensembl release 77 53 . Read counts were imported into R, and DESeq2 was used for identifying differential expression 54 , as implemented in DEBrowser55 . For the isoform analysis, fpkm values from cufflinks were used 56 ,57 .
Tran K.V., Brown E.L., DeSouza T., Jespersen N.Z., Nandrup-Bus C., Yang Q., Yang Z., Desai A., Min S.Y., Rojas-Rodriguez R., Lundh M., Feizi A., Willenbrock H., Larsen T.J., Severinsen M.C., Malka K., Mozzicato A.M., Deshmukh A.S., Emanuelli B., Pedersen B.K., Fitzgibbons T., Scheele C., Corvera S, & Nielsen S. (2020). Human thermogenic adipocyte regulation by the long noncoding RNA LINC00473. Nature metabolism, 2(5), 397-412.
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