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Bioanalyzer 2100 rna pico chip

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The Bioanalyzer 2100 RNA pico chip is a lab equipment product from Agilent Technologies. It is designed to perform automated analysis of RNA samples. The chip allows for the separation, detection, and quantification of RNA molecules in a small sample volume.

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Lab products found in correlation

Rneasy plus micro kit, by Qiagen (4 mentions) Nanodrop 2000, by Thermo Fisher Scientific (4 mentions) Anti ha 11, by BioLegend (3 mentions) Rneasy micro kit, by Qiagen (2 mentions) Zymo direct zol rna isolation kit, by Zymo Research (1 mentions) Hiseq 2500, by Illumina (1 mentions) Hiseq 4000 system, by Illumina (1 mentions) Dynabeads protein g magnetic beads, by Thermo Fisher Scientific (1 mentions) Ovation rna seq system v2, by Tecan (1 mentions) Ultimate 3000, by Thermo Fisher Scientific (1 mentions) Nanodrop nd 1000 spectrophotometer, by Avantor (1 mentions) Concentrator 5301, by Eppendorf (1 mentions) Truseq stranded mrna ht kit, by Illumina (1 mentions) Qubit rna hs assay kit, by Thermo Fisher Scientific (1 mentions) Epmotion 5075 robot, by Eppendorf (1 mentions) Hiseq 4000, by Illumina (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Dnase, by Qiagen (1 mentions) Rlt plus buffer, by Qiagen (1 mentions) β mercaptoethanol, by Merck Group (1 mentions)

11 protocols using bioanalyzer 2100 rna pico chip

1

RNA Extraction and Illumina Sequencing of Plant Samples

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The total RNA was extracted from the RH and Root-RH samples using Zymo Direct-Zol RNA isolation kit (Zymo Research, Irvine, CA, United States) as per the prescribed protocol. The isolated RNA samples were then analyzed using NanoDrop for their quantity and quality checks. To assess their integrity, samples were run on 1%TBE gel, and the RNA integrity (RIN) value was estimated using Bioanalyzer 2100 RNA pico chip as per the manufacturer’s instructions (Agilent Technologies, Palo Alto, CA, United States). The intact RNA samples with a RIN value of more than 7.9 (range: 7.9–9.5) were proceeded with the Illumina sequencing protocol (Supplementary Figure 1D). The libraries were generated using TruSeq Stranded Total RNA Library Prep Plant kit with plant rRNA depletion (Illumina Inc., United States) according to the manufacturer’s protocol. The libraries were sequenced to generate 150 bp paired-end reads using Illumina Hiseq2500 according to the manufacturer’s instructions. The Illumina reads generated from all the samples were submitted to the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/sra; BioProject ID: PRJNA857918).
Kohli P.S., Pazhamala L.T., Mani B., Thakur J.K, & Giri J. (2022). Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum. Frontiers in Plant Science, 13, 983969.
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2

RNA Extraction and Library Preparation for Embryo Transcriptomics

Cited 2 times
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We performed RNA extraction in TRIzol as previously
44 (link). All RNA quality was confirmed using a BioAnalyzer 2100 RNA Pico chip (Agilent).
We generated libraries of the
zld- embryos using the TruSeq mRNA unstranded kit (Illumina). As described previously, we added in 70 ng of yeast total RNA as a carrier and performed reactions in half-sized volumes to improve concentration
44 (link).
We generated libraries from the RNAi and overexpression embryos using the SMARTseq2 protocol; we skipped the cell lysis steps because RNA had already been extracted
45 (link),
46 (link). As described previously, tagmentation steps were performed at 1/5th volume to reduce costs
46 (link).
Combs P.A, & Eisen M.B. (2017). Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster. F1000Research, 6, 41.
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3

Ribosome Immunoprecipitation from Mouse Liver

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Three 30-day old Gfi1Cre/+;RiboTagHA/HA mice were euthanized by CO2 asphyxiation followed by cervical dislocation. Livers were harvested and immediately frozen on dry ice. Equal amounts of liver were used for input RNA extractions (RNeasy Plus Micro kit, QIAGEN USA, Germantown, MD, USA) or futher processed for ribosome immunoprecipitation (5 μg of purified anti-HA.11, BioLegend, San Diego, CA, USA) followed by RNA extraction as previously decribed in Sanz et al., 2009 [16 (link)]. The RNeasy Plus Micro kit is optimized for the removal of genomic DNA through a combination of high salt buffer and the gDNA Eliminator spin column. Quality of the RNA was assessed on an Agilent Technologies Bioanalyzer 2100 RNA pico chip as per the manufacturer’s instructions (Agilent Technologies, Palo Alto, CA, USA). All samples had a RIN score of 10 and no evidence of DNA contamination in the form of a high molecular weight DNA band. All RNA was equally aliquoted to test for the performance of five commercial kits and seven protocols.
Song Y., Milon B., Ott S., Zhao X., Sadzewicz L., Shetty A., Boger E.T., Tallon L.J., Morell R.J., Mahurkar A, & Hertzano R. (2018). A comparative analysis of library prep approaches for sequencing low input translatome samples. BMC Genomics, 19, 696.
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4

RiboTag Immunoprecipitation for Cochlear RNA

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RiboTag immunoprecipitations were performed as described in Chessum et al., 2018 (link). Briefly, cochlear ducts from eight mice were homogenized and centrifuged at 9400 g for 10 minutes at 4°C to pellet cell debris. Fifty microlitre of supernatant was stored at −80°C until RNA isolation (input sample) while 5 μg of haemagglutinin (HA) antibody (BioLegend Cat# 901502, RRID: AB_2565007) was added to the remaining supernatant and incubated at 4°C for 4 hours. Then the equivalent of 300 μl of rinsed Dynabeads Protein G magnetic beads (Thermo Fisher Scientific Cat# 10004D) were added to the sample and incubated overnight at 4°C. Following three washes in high-salt buffer, 350 μl of Buffer RLT (supplemented with β-mercaptoethanol) from the RNeasy Plus Micro kit (Qiagen Cat# 74034) was added to the beads and the input sample. RNA was extracted according to the manufacturer’s instructions. RNA integrity was assessed on a Bioanalyzer 2100 RNA pico chip (Agilent Technologies). The RNA was processed for RNA-seq using the Ovation RNA-Seq System V2 (NuGEN Cat# 7102-A01) to make the libraries and sequenced on a HiSeq 4000 system (Illumina) using a 75 bp paired end read configuration. Libraries and sequencing were performed at the Genomics Resource Center from the Institute for Genome Sciences at the University of Maryland.
Hertzano R., Gwilliam K., Rose K., Milon B, & Matern M.S. (2020). Cell Type–Specific Expression Analysis of the Inner Ear: A Technical Report. The Laryngoscope, 131(Suppl 5), S1-S16.
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5

tRNA Purification by Size Exclusion Chromatography

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The separation of tRNA by size exclusion chromatography (SEC) was performed as described previously[51] with minor modifications. Briefly, total RNA was loaded on a Thermo Scientific UltiMate 3000 LC system equipped with a diode array detector set to 260 nm, an autosampler, a column thermostat (60 °C), and a fraction collector. A size exclusion column (Agilent Bio SEC‐3, 3 μm, 300 Å, 7.8×300 mm, Agilent, Waldbronn) allowed the collection of the RNA fractions after isocratic elution with 100 mM ammonium acetate at pH 7. The peaks representing the mRNA+rRNA fraction as well as the tRNA fraction were collected and concentrated in a vacuum concentrator (Eppendorf Concentrator 5301). 5 M NH4OAc was added to a final concentration of 0.5 M, and after addition of 2× Vol. ice‐cold ethanol (100 %), the RNA was precipitated at −20 °C overnight. After centrifugation at 12,000×g for 30 min at 4 °C, the RNA pellet was subjected to an additional ethanol (80 %, v/v) wash step to verify the complete removal of the ammonium acetate and was then resuspended in pure water. The quality of the isolated tRNA was verified with chip gel electrophoresis (BioAnalyzer 2100, RNA Pico chip, Agilent, Waldbronn), RT‐qPCR analysis, agarose gel electrophoresis, and usage of the ▵trmN deletion mutant. RNA concentration was determined by NanoDrop ND1000 spectrophotometer (peqlab, Germany).
Petrov D.P., Kaiser S., Kaiser S, & Jung K. (2022). Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli. Chembiochem, 23(18), e202200270.
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6

Single-Cell Ribosome Profiling of Noise-Exposed Cochlea

Cited 1 time
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Six hours or 24 hours post-noise exposure, PrestinCreERT2/+;Rpl22HA/+;CBA and Sox2CreERT2/+;Rpl22HA/+;CBA mice (9 to 11 week-old) were euthanized by CO2 asphyxiation followed by cervical dislocation. Temporal bones were harvested, and cochlear ducts removed and immediately frozen on dry ice. Of note, while recombination occurs in supporting cells and glial cells with the Sox2-CreERT2 model, our dissection approach excludes the modiolus and thereby enriches for epithelial cells compared with neuronal tissue (as shown by the divergence in DEGs in Figure S7). Tissue from 8 animals (4 males and 4 females) for each biological replicate of the prestin line and 4 animals (2 males and 2 females) for each biological replicate of the Sox2 line were processed for ribosome immunoprecipitation (5 μg of purified anti-HA.11, BioLegend) followed by RNA extraction using the RNeasy Plus Micro kit (QIAGEN) as previously described (Song et al., 2018 (link)). RNA quality was determined using an Agilent Technologies Bioanalyzer 2100 RNA pico chip as per the manufacturer’s instructions (Agilent Technologies). All samples had a RIN score above 8.
Milon B., Shulman E.D., So K.S., Cederroth C.R., Lipford E.L., Sperber M., Sellon J.B., Sarlus H., Pregernig G., Shuster B., Song Y., Mitra S., Orvis J., Margulies Z., Ogawa Y., Shults C., Depireux D.A., Palermo A.T., Canlon B., Burns J., Elkon R, & Hertzano R. (2021). A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. Cell reports, 36(13), 109758.
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7

Single-Cell Ribosome Profiling of Noise-Exposed Cochlea

Cited 1 time
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Six hours or 24 hours post-noise exposure, PrestinCreERT2/+;Rpl22HA/+;CBA and Sox2CreERT2/+;Rpl22HA/+;CBA mice (9 to 11 week-old) were euthanized by CO2 asphyxiation followed by cervical dislocation. Temporal bones were harvested, and cochlear ducts removed and immediately frozen on dry ice. Of note, while recombination occurs in supporting cells and glial cells with the Sox2-CreERT2 model, our dissection approach excludes the modiolus and thereby enriches for epithelial cells compared with neuronal tissue (as shown by the divergence in DEGs in Figure S7). Tissue from 8 animals (4 males and 4 females) for each biological replicate of the prestin line and 4 animals (2 males and 2 females) for each biological replicate of the Sox2 line were processed for ribosome immunoprecipitation (5 μg of purified anti-HA.11, BioLegend) followed by RNA extraction using the RNeasy Plus Micro kit (QIAGEN) as previously described (Song et al., 2018 (link)). RNA quality was determined using an Agilent Technologies Bioanalyzer 2100 RNA pico chip as per the manufacturer’s instructions (Agilent Technologies). All samples had a RIN score above 8.
Milon B., Shulman E.D., So K.S., Cederroth C.R., Lipford E.L., Sperber M., Sellon J.B., Sarlus H., Pregernig G., Shuster B., Song Y., Mitra S., Orvis J., Margulies Z., Ogawa Y., Shults C., Depireux D.A., Palermo A.T., Canlon B., Burns J., Elkon R, & Hertzano R. (2021). A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. Cell reports, 36(13), 109758.
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8

RNA Extraction from Flow-Sorted Cells

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RNA was isolated from flow-cytometry-sorted cell populations by using the RNeasy Micro Kit from QIAGEN (74004) according to the manufacturer’s instructions, which included a step involving incubation with DNase. For whole-brain RNA purification, we generated 1 brain/pool samples. Purified RNA was quantified using a NanoDrop 2000 (Thermo Scientific) and Agilent Technologies Bioanalyzer 2100 RNA Pico chips (5067-1513, Agilent Technologies) according to manufacturer instructions; the RNA integrity number (RIN) in all cases was >9.
Pan J., Ma N., Zhong J., Yu B., Wan J, & Zhang W. (2021). Age-associated changes in microglia and astrocytes ameliorate blood-brain barrier dysfunction. Molecular Therapy. Nucleic Acids, 26, 970-986.
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9

RNA Isolation from Flow-Sorted Cells

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RNA was isolated from flow-cytometry-sorted cell populations by using an RNeasy Micro Kit (74004, Qiagen) according to the manufacturer’s instructions, which included a step involving incubation with DNase. For whole-brain RNA purification, we generated 1 brain/pool samples. Purified RNA was quantified using a NanoDrop 2000 (Thermo Scientific) and Agilent Technologies Bioanalyzer 2100 RNA Pico chips (5067-1513, Agilent Technologies), according to manufacturer instructions; the RNA integrity number (RIN) in all cases was > 9.
Pan J., Ma N., Yu B., Zhang W, & Wan J. (2020). Transcriptomic profiling of microglia and astrocytes throughout aging. Journal of Neuroinflammation, 17, 97.
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10

Whole Brain Transcriptome Profiling

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Whole brain RNA was extracted from the 600 µL homogenate in RLT buffer after an additional 30 s homogenization following the Qiagen RNeasy Mini Kit protocol, including a DNase (Qiagen) treatment to remove genomic DNA. RNA quantities were determined for each sample using a Qubit RNA HS Assay Kit (Invitrogen, Carlsbad, CA). High RNA integrity for all samples was confirmed with Bioanalyzer 2100 RNA Pico chips (Agilent, Santa Clara, CA) prior to library preparation.
RNAseq libraries were constructed and sequenced by the W.M. Keck Center for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Center (University of Illinois at Urbana-Champaign). Libraries were constructed from 500 ng RNA per sample using the TruSeq Stranded mRNA HT kit (Illumina, San Diego, CA) on an ePMotion 5075 robot (Eppendorf, Hamburg, Germany). Libraries were uniquely barcoded, quantified, and pooled for sequencing across 6 lanes with 100 nt single-end sequencing on the Illumina HiSeq 4000.
Jones B.M., Rao V.D., Gernat T., Jagla T., Cash-Ahmed A.C., Rubin B.E., Comi T.J., Bhogale S., Husain S.S., Blatti C., Middendorf M., Sinha S., Chandrasekaran S, & Robinson G.E. (2020). Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks. eLife, 9, e62850.
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