Bioscope 1

Manufactured by Thermo Fisher Scientific

The Bioscope 1.3.1 is a laboratory instrument designed for microscopic imaging and analysis. It features a high-resolution camera and advanced optics for capturing detailed images of biological samples.

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Lab products found in correlation

Solid total rna seq kit, by Thermo Fisher Scientific (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions)

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Bioscope (13 citations) BioScope software v.1.3 (2 citations)

2 protocols using bioscope 1

RNA-Seq Library Preparation and Sequencing

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mRNA-Seq library samples were prepared using a SOLiD Total RNA-Seq kit (Life Technologies). The amount of starting RNA material for RNA fragmentation was 500 ng. RNA samples were fragmented with RNase III, hybridized, and ligated to SOLiD adapters and ligation enzymes. cDNA was synthesized using ArrayScript Reverse Transcriptase and size-selected by separation on a TBE-urea gel. After amplification of cDNA, the yield and size distribution of the amplified cDNA were assessed using the Bioanalyzer. cDNA libraries were sequenced on SOLiD 3 plus (Life Technologies) with 50-bp single-end reads for whole-transcriptome sequencing (SRA accession number: SRX370383). Sequenced reads were uniquely aligned to the UCSC reference human genome (build hg19) using the whole-transcriptome mapping module in Bioscope 1.3.1 from Life Technologies, with default settings. BAM files were converted into BED files using BamTools.

Kim W.K., Kim D., Cui J., Jang H.H., Kim K.S., Lee H.J., Kim S.U, & Ahn S.M. (2014). Secretome Analysis of Human Oligodendrocytes Derived from Neural Stem Cells. PLoS ONE, 9(1), e84292.

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Whole Transcriptome Analysis by RNA-Seq

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Next-generation RNA deep sequencing for whole transcriptome analysis was performed according to the standard procedure instructed by Applied Biosystems. All RNA sequencing data were deposited to the Gene Expression Omnibus (GEO) data repository with accession number GSE109427. Briefly, total RNA was extracted from AsPC-1 cells as indicated. All RNA samples that passed quality tests with RIN-values greater than 8, as measured by Agilent Technologies Bioanalyzer, were subjected to RNA deep sequencing. SOLiD fragment colorspace transcriptome reads (50 nt) were mapped to the human genome (hg19) and assigned to ensemble transcripts using Bioscope 1.3.1 (Life Technologies). Unsupervised clustering was performed on the top 5,000 most variedly expressed genes (as determined by median absolute deviation) using Cluster and TreeView software (http://rana.lbl.gov/EisenSoftware.htm). Genes with significant change in expression after EGF/ANG treatment were identified by using R package limma with a cutoff p value of 0.05 and threshold fold change of 1.5. GSEA analysis was performed by using default conditions on AsPC-1 treated by EGF/ANG for 1 and 5 hr vs. AsPC-1 treated for 0 and 24 hr.

Wang Y.N., Lee H.H., Chou C.K., Yang W.H., Wei Y., Chen C.T., Yao J., Hsu J.L., Zhu C., Ying H., Ye Y., Wang W.J., Lim S.O., Xia W., Ko H.W., Liu X., Liu C.G., Wu X., Wang H., Li D., Prakash L.R., Katz M.H., Kang Y., Kim M., Fleming J.B., Fogelman D., Javle M., Maitra A, & Hung M.C. (2018). Angiogenin/ribonuclease 5 is an EGFR ligand and a serum biomarker for erlotinib sensitivity in pancreatic cancer. Cancer cell, 33(4), 752-769.e8.

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