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Trinean dropsense96 spectrophotometer

Manufactured by PerkinElmer
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The Trinean DropSense96 is a high-throughput spectrophotometer designed for the quantification of nucleic acids and proteins in microplates. It features a compact, integrated design and utilizes 96-well microplate technology to enable rapid and efficient sample analysis.

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Lab products found in correlation

Agilent 2200 tapestation, by Agilent Technologies (8 mentions) Humanht 12 expression beadchip, by Illumina (3 mentions) Iscan system, by Illumina (3 mentions) Agilent 4200 tapestation, by Agilent Technologies (3 mentions) Sciclone ngsx workstation, by PerkinElmer (2 mentions) Invitrogen qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Rneasy mini kit, by Qiagen (2 mentions) Hiseq 2500, by Illumina (2 mentions) Truseq rna sample prep kit v2, by Illumina (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Real time analysis v1, by Illumina (1 mentions) Bcl2fastq conversion software v1, by Illumina (1 mentions) Nextseq 2000, by Illumina (1 mentions) Truseq stranded mrna kit, by Illumina (1 mentions) Tissuelyser lt, by Qiagen (1 mentions) Quant it picogreen dsdna assay kit, by Thermo Fisher Scientific (1 mentions) Nd 1000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Allprep dna rna mini kit, by Qiagen (1 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions)

11 protocols using trinean dropsense96 spectrophotometer

1

RNA-seq Library Preparation and Sequencing

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RNA was extracted and purified from the Ptm lymphocytes using the RNeasy Mini kit (Qiagen) following manufacturer's protocol. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences). RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) and a Sciclone NGSx Workstation (PerkinElmer). Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies). Additional library QC, blending of pooled indexed libraries, and cluster optimization were performed using Life Technologies’ Invitrogen Qubit 2.0 Fluorometer (Life Technologies-Invitrogen). RNA-seq libraries were pooled (6-plex) onto a flow cell lane. Sequencing was performed using an Illumina HiSeq 2500 in rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy. Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4.
Sharma A., McLaughlin RN J.r., Basom R.S., Kikawa C., OhAinle M., Yount J.S., Emerman M, & Overbaugh J. (2019). Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner. PLoS Pathogens, 15(7), e1007925.
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2

RNA Integrity Assessment and Microarray Analysis

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RNA integrity was assessed using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and was quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). High quality RNA samples were converted to cDNA and biotin-labeled for microarray analysis using Ambion’s Illumina TotalPrep RNA Amplification Kit (Life Technologies, Grand Island, NY). Labeled cRNAs were processed on a Human HT-12 Expression BeadChip (Illumina, Inc., San Diego, CA) and imaged using an Illumina iScan system.
Burwick N., Zhang M.Y., de la Puente P., Azab A.K., Hyun T.S., Ruiz-Gutierrez M., Sanchez-Bonilla M., Nakamura T., Delrow J.J., MacKay V.L, & Shimamura A. (2017). The eIF2-alpha kinase HRI is a novel therapeutic target in multiple myeloma. Leukemia research, 55, 23-32.
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3

Liver Transcriptome Profiling in Nrf2 Mice

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Total RNA derived from the livers of wild-type, C151S, and Nrf2-knockout mice treated with vehicle (n = 5) and CDDO-Me (n = 5) in each genotype were used. RNA quality check, library construction, and sequencing were performed at the Fred Hutchinson Cancer Center Shared Resources Cores for Genomics and Bioinformatics. Total RNA integrity was affirmed and quantified using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA), respectively. RNA-seq libraries were prepared from total RNA (TruSeq Stranded mRNA kit, Illumina, Inc., San Diego, CA), and library size distribution was validated (Agilent 4200 TapeStation, Agilent Technologies, Santa Clara, CA). Additional quality control of the library, combining of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA). RNA-seq libraries were pooled (30-plex) and clustered onto a P3 flow cell. Samples were sequenced using an Illumina NextSEq 2000 using a paired-end, 50 base read-length strategy. Raw data have been deposited in Gene Expression Omnibus; the accession number is GSE222256.
Gatbonton-Schwager T., Yagishita Y., Joshi T., Wakabayashi N., Srinivasan H., Suzuki T., Yamamoto M, & Kensler T.W. (2023). A Point Mutation at C151 of Keap1 of Mice Abrogates NRF2 Signaling, Cytoprotection in Vitro, and Hepatoprotection in Vivo by Bardoxolone Methyl (CDDO-Me). Molecular Pharmacology, 104(2), 51-61.
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4

Microarray Analysis of Transcriptome

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Total RNA integrity was tested using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and was quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). High quality RNA samples were converted to cDNA and biotin-labeled for microarray analysis using Ambion’s Illumina To-talPrep RNA Amplification kit (Life Technologies, Grand Island, NY). Labeled cRNAs were processed on a HumanHT-12 Expression BeadChip (Illumina, Inc., San Diego, CA) and imaged using an Illumina iScan system. Microarray data was assessed for quality and quantile normalized using the Bioconductor package lumi Initial filtering included flagging probes that were below a signal “noise floor,” which was calculated as the 75th percentile of the negative control probe signals within each array. We subsequently filtered the dataset by employing a variance filter using the “shorth” function of the Biocon-ductor package genefilter. Differential gene expression was determined using the Bio-conductor package limma, and a false discovery rate (FDR) method was used to correct for multiple testing. Significant differential gene expression was defined as |log2 (ratio) ≥ 0.585 (± 1.5-fold) with the FDR set to 5%.
Kotini A.G., Chang C.J., Boussaad I., Delrow J.J., Dolezal E.K., Nagulapally A.B., Perna F., Fishbein G.A., Klimek V.M., Hawkins R.D., Huangfu D., Murry C.E., Graubert T., Nimer S.D, & Papapetrou E.P. (2015). Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells. Nature biotechnology, 33(6), 646-655.
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5

RNA Isolation and Sequencing of CD34+ Cells

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Isolation of total RNA from human and nonhuman primate bulk CD34+ cells and sort-purified HSC-enriched cell fractions was performed according to manufacturer instructions (>Supplemental Methods. Total RNA integrity was analyzed using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). RNA-Seq expression analysis was performed in Shared Recources at the Fred xgHutchinson Cancer Research Center. Detailed protocols for data analyses can be found in Suxgpplemental Methods. All custom R and Python codes are available on request. All other codes are publicly available and cited in the appropriate methods description (see Supplemental Methods).
Radtke S., Adair J.E., Giese M.A., Chan Y.Y., Norgaard Z.K., Enstrom M., Haworth K.G., Schefter L.E, & Kiem H.P. (2017). A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates. Science translational medicine, 9(414), eaan1145.
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6

Total RNA Extraction from Mouse Tumor

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Total RNA extraction from flash frozen mouse tumor tissue was done using the RNEasy Mini kit (Qiagen, Valencia, CA). The method involved using 5 mm stainless beads in conjunction with the TissueLyser LT (Qiagen, Valencia, CA) to achieve tissue lysis and homogenization. On-column DNase I digestion and RNA extraction was carried out following the manufacturer’s recommended protocol. Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).
Wagner M.J., Lyons Y.A., Siedel J.H., Dood R., Nagaraja A.S., Haemmerle M., Mangala L.S., Chanana P., Lazar A.J., Wang W.L., Ravi V., Holland E.C, & Sood A.K. (2021). Combined VEGFR and MAPK pathway inhibition in angiosarcoma. Scientific Reports, 11, 9362.
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7

Comprehensive Nucleic Acid Extraction

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DNA and RNA from the primary tumor and HNSCC cell lines were extracted using the AllPrep DNA/RNA Mini kit (QIAGEN, Valencia, CA). DNA was also extracted from the patient’s tumor-free salivary gland formalin-fixed block using QIAamp® DNA FFPE Tissue kit (QIAGEN). Extracted DNA and RNA were assessed with ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA). Quantity of double stranded DNA was determined by Quant-iT™ PicoGreen® dsDNA Assay Kit (Thermo Fisher Scientific). Quantity of RNA was also determined by Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA) before sequencing.
Xu C., Nikolova O., Basom R.S., Mitchell R.M., Shaw R., Moser R.D., Park H., Gurley K.E., Kao M.C., Green C.L., Schaub F.X., Diaz R.L., Swan H.A., Jang I.S., Guinney J., Gadi V.K., Margolin A.A., Grandori C., Kemp C.J, & Méndez E. (2018). Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 24(12), 2828-2843.
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8

RNA Isolation and Quality Assessment

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Total RNA was isolated by acid phenol method from 10 ml cultures of WT and pbs2Δ mutant grown in YEPD (5.5 hrs), YEP-GAL (5.5 hrs), YEPD+Tunicamycin (3 hrs) and YEPD+salt (10 min). Isolated RNA was purified over a RNAeasy column (Qiagen). RNA concentration was measured using the NanoDrop2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and purity was established by the A260/A280 ratio. RNA was detected by running samples on an 8M Urea 6%polyacylamide gel, stained by ethidium bromide. Three independent inductions were evaluated for RNA-seq analysis. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).
Adhikari H, & Cullen P.J. (2014). Metabolic Respiration Induces AMPK- and Ire1p-Dependent Activation of the p38-Type HOG MAPK Pathway. PLoS Genetics, 10(10), e1004734.
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9

Microarray Analysis of Transcriptome

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Total RNA integrity was tested using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and was quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). High quality RNA samples were converted to cDNA and biotin-labeled for microarray analysis using Ambion’s Illumina To-talPrep RNA Amplification kit (Life Technologies, Grand Island, NY). Labeled cRNAs were processed on a HumanHT-12 Expression BeadChip (Illumina, Inc., San Diego, CA) and imaged using an Illumina iScan system. Microarray data was assessed for quality and quantile normalized using the Bioconductor package lumi Initial filtering included flagging probes that were below a signal “noise floor,” which was calculated as the 75th percentile of the negative control probe signals within each array. We subsequently filtered the dataset by employing a variance filter using the “shorth” function of the Biocon-ductor package genefilter. Differential gene expression was determined using the Bio-conductor package limma, and a false discovery rate (FDR) method was used to correct for multiple testing. Significant differential gene expression was defined as |log2 (ratio) ≥ 0.585 (± 1.5-fold) with the FDR set to 5%.
Kotini A.G., Chang C.J., Boussaad I., Delrow J.J., Dolezal E.K., Nagulapally A.B., Perna F., Fishbein G.A., Klimek V.M., Hawkins R.D., Huangfu D., Murry C.E., Graubert T., Nimer S.D, & Papapetrou E.P. (2015). Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells. Nature biotechnology, 33(6), 646-655.
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10

RNA Integrity Analysis Protocol

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Total RNA integrity was analyzed using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA, USA).
Radtke S., Pande D., Cui M., Perez A.M., Chan Y.Y., Enstrom M., Schmuck S., Berger A., Eunson T., Adair J.E, & Kiem H.P. (2020). Purification of Human CD34+CD90+ HSCs Reduces Target Cell Population and Improves Lentiviral Transduction for Gene Therapy. Molecular Therapy. Methods & Clinical Development, 18, 679-691.
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