Tapestation d1000

Manufactured by Agilent Technologies

Sourced in United States

The TapeStation D1000 is a lab equipment product from Agilent Technologies. It is designed to provide automated sample analysis for DNA and RNA samples. The core function of the TapeStation D1000 is to assess the size and concentration of nucleic acid samples.

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Lab products found in correlation

Novaseq 6000, by Illumina (4 mentions) Hiseq 2000, by Illumina (4 mentions) Minielute pcr purification kit, by Qiagen (4 mentions) Nextera dna preparation kit, by Illumina (4 mentions) Miseq platform, by Illumina (4 mentions) Next gem chip g, by 10x Genomics (3 mentions) Liberase tl, by Roche (2 mentions) Dnase 1, by Roche (2 mentions) Chromium controller instrument, by 10x Genomics (2 mentions) Sp 100 cycles reagent kit, by Illumina (2 mentions) Ampure xp bead, by Beckman Coulter (2 mentions) Sequencing primer, by Illumina (2 mentions) Hiseq 4000, by Illumina (2 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Lipofectamine 2000, by Thermo Fisher Scientific (2 mentions) D5000 screentape, by Agilent Technologies (2 mentions) 2 step cells to ct, by Thermo Fisher Scientific (2 mentions) Q5 hot start high fidelity dna polymerase, by New England Biolabs (2 mentions) 96 well culture plates, by Avantor (2 mentions) Truseq stranded mrna sample preparation kit, by Illumina (2 mentions)

Spelling variants of this product

TapeStation (986 citations) TapeStation DNA screentape D1000 (22 citations) TapeStation D1000 Assay (13 citations) TapeStation High Sensitivity D1000 ScreenTape (13 citations) Agilent TapeStation D1000 DNA assay (3 citations) 4200 TapeStation High Sensitivity D1000 ScreenTape (3 citations) Agilent TapeStation High Sensitivity D1000 Assay (2 citations) Agilent 2200 TapeStation (HS D1000 ScreenTape, (2 citations) TapeStation High Sensitivity D1000 kit (2 citations) TapeStation D1000 screening tapes (2 citations)

36 protocols using tapestation d1000

Next-Gen Sequencing of Amplicon Libraries

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Massive parallel sequencing of the pooled amplicons was carried out on an Illumina NextSeq 500 analyser. Library preparation was performed at Genotypic Technology’s Genomics facility following Nextera XT DNA Library Preparation protocol (Cat #FC-131-1024). 1 ng of Qubit-quantified genomic DNA was tagmented (fragmented and tagged) using Amplicon Tagment Mix provided in the Nextera XT Kit. The adapter tagged DNA was subjected to 12 cycles of indexing-PCR [72°C for 3 min followed by denaturation at 95°C for 30 sec, cycling (95°C for 10 sec, 55°C for 30 sec, 72°C for 30 sec) and 72°C for 5 min] to enrich the adapter-tagged fragments. The PCR product was purified using HighPrep beads (Magbio Genomics, #AC-60050). Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Alampalli S.V., Thomson M.M., Sampathkumar R., Sivaraman K., U. K. J. A.J., Dhar C., D. Souza G., Berry N, & Vyakarnam A. (2017). Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India. PLoS ONE, 12(12), e0188603.

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Single-Cell RNA-seq of Auricular Lymph Nodes

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To prepare single cell suspensions for scRNA-seq using 10x Genomics system, auricular LNs were digested in IMDM containing 100 μg/mL Liberase TL and 100 μg/mL DNase I (both from Roche, Germany) for 20 minutes at 37°C. Last 5 minutes of incubation, EDTA was added at a final concentration of 10 mM. Cells were collected, filtered through a 70 μm cell strainer, washed with PBS + 0.04% BSA for a final concentration of 1000 cells/μL.
Cellular suspension was immediately loaded onto Next GEM Chip G targeting ~5000 cells and then ran on a Chromium controller instrument (10x Genomics) to generate GEM emulsion. Single cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol using the v3.1 Next GEM dual index workflow. Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Libraries were pooled and sequenced on an SP 100 cycles reagent kit on a NovaSeq6000 instrument (Illumina), aiming for ~ 50,000 reads per cell. Reads from raw FASTQ files were processed with Cell Ranger 4.0 and mapped to the mouse mm10–2020 reference (10x Genomics). No read depth normalization was applied when aggregating datasets.

Lopez R., Li B., Keren-Shaul H., Boyeau P., Kedmi M., Pilzer D., Jelinski A., David E., Wagner A., Addadi Y., Elhanani O., Fatelevich M., Yankielowicz-Keren L., Golani O., Ronchese F., Jordan M.I., Amit I, & Yosef N. (2022). DestVI identifies continuums of cell types in spatial transcriptomics data. Nature biotechnology, 40(9), 1360-1369.

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ATAC-seq Analysis of Stem Cells

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ATAC-seq libraries were made from freshly FACS-sorted SCs. Library preparation and analyses were performed as described (Buenrostro et al., 2013 (link)). Briefly, FACS-sorted cells were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were immediately subjected to a transposition reaction at 37°C for 30 min with 10 μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10–15 cycles. Library concentration and quality was assayed by D1000 Tape Station (Agilent) prior to sequencing. The samples were sequenced on Illumina HiSeq 2000 using a 50bp paired-end-reads setting. Extensive data analyses will be published elsewhere (Y Ge and E Fuchs). For the purposes of the current study, ATAC data were only used to substantiate the transcriptome differences that were found in 6 key regulatory genes (Figure 6F).

Yang H., Adam R.C., Ge Y., Hua Z.L, & Fuchs E. (2017). Epithelial-Mesenchymal Micro-Niches Govern Stem Cell Lineage Choices. Cell, 169(3), 483-496.e13.

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Single-cell RNA-seq library preparation

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Cells were counted and diluted to a final concentration in PBS supplemented with 0.04% BSA. Cellular suspension was loaded onto Next GEM Chip G and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3/v3.1 Chemistry). Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~50,000 reads per cell. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina).

Cohen K., Mouhadeb O., Shlomo S.B., Langer M., Neumann A., Erez N., Moshkovits I., Pelet R., Kedar D.J., Brazowski E., Guilliams M., Goodridge H.S., Gluck N, & Varol C. (2021). COMMD10 is critical for Kupffer cell survival and controls Ly6Chi monocyte differentiation and inflammation in the injured liver. Cell reports, 37(7), 110026.

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ATAC-seq Profiling of Stem Cells

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ATAC-seq libraries were made from freshly FACS-sorted stem cells, with two biologically independent replicates for cell population. Library preparations and analyses were performed as described (Buenrostro et al., 2013 (link)). Briefly, Freshly FACS-sorted cells (20K–200K) were subjected to tagmentation reactions with 2–10μl TnD transposase (Illumina), cleaned up with QIAquick PCR Purification Kit (Qiagen) and PCR-amplified with 10–15 cycles. Library concentrations and quality were confirmed with D1000 Tape Station (Agilent) prior to sequencing.

Ge Y., Gomez N.C., Adam R.C., Nikolova M., Yang H., Verma A., Lu C.P., Polak L., Yuan S., Elemento O, & Fuchs E. (2017). Stem Cell Lineage Infidelity Drives Wound-Repair and Cancer. Cell, 169(4), 636-650.e14.

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ATAC-seq Library Preparation Protocol

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ATAC-seq libraries were made from freshly FACS-sorted cells. Library preparation and analyses were performed as described (Buenrostro et al., 2013 (link)) with minor modifications. Briefly, FACS-sorted cells were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were immediately subjected to a transposition reaction at 37°C for 30 min with 10 μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10–15 cycles. Library concentration and quality was assayed by D1000 Tape Station (Agilent) prior to sequencing. The samples were sequenced on an Illumina HiSeq 2000 instrument using a 50bp paired-end-reads setting.

Adam R.C., Yang H., Ge Y., Lien W.H., Wang P., Zhao Y., Polak L., Levorse J., Baksh S.C., Zheng D, & Fuchs E. (2018). Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression. Cell stem cell, 22(3), 398-413.e7.

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Amplicon library preparation and sequencing

Cited 2 times

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Amplicon libraries were generated as described previously^{29 (link),45 (link),46 (link)}. The variable 4 (V4) region of the 16S rRNA gene was amplified in duplicate with the following PCR reaction components: 1× 5Prime Hotstart mastermix, 1× Evagreen, 500 nM forward primer, and 500 nM reverse primer. Amplification was monitored in a CFX96 RT–PCR machine (Bio-Rad) and samples were removed once fluorescence measurements reached ~10,000 RFU (late exponential phase). Cycling conditions were as follows: 94 °C for 3 min, up to 45 cycles of 94 °C for 45 s, 54 °C for 60 s, and 72 °C for 90 s. Duplicate reactions that amplified were pooled together and quantified with Kapa library quantification kit (Kapa Biosystems, KK4824) before equimolar sample mixing. Libraries were concentrated and cleaned using AMPureXP beads (Beckman Coulter). The final library was quantified using a High Sensitivity D1000 Tapestation (Agilent) chip. Sequencing was performed by Fulgent Genetics using the Illumina MiSeq platform and 2 × 300-bp reagent kit for paired-end sequencing.

Wu W.L., Adame M.D., Liou C.W., Barlow J.T., Lai T.T., Sharon G., Schretter C.E., Needham B.D., Wang M.I., Tang W., Ousey J., Lin Y.Y., Yao T.H., Abdel-Haq R., Beadle K., Gradinaru V., Ismagilov R.F, & Mazmanian S.K. (2021). Microbiota regulate social behaviour via stress response neurons in the brain. Nature, 595(7867), 409-414.

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ATAC-seq Library Preparation Protocol

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ATAC-seq libraries were made from freshly FACS-sorted cells. Library preparation and analyses were performed as described^{38 (link)} with minor modifications. Briefly, FACS-sorted cells were pelleted and incubated with cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were immediately subjected to a transposition reaction at 37°C for 30min with 10μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10–15 cycles. Library concentration and quality was assayed by D1000 Tape Station (Agilent) prior to sequencing. Samples were sequenced on an Illumina HiSeq 2000 instrument using a 50bp paired-end-reads setting.

Adam R.C., Yang H., Ge Y., Infarinato N.R., Gur-Cohen S., Miao Y., Wang P., Zhao Y., Lu C.P., Kim J.E., Ko J.Y., Paik S.S., Gronostajski R.M., Kim J., Krueger J.G., Zheng D, & Fuchs E. (2020). NFI Transcription Factors Provide Chromatin Access to Maintain Stem Cell Identity While Preventing Unintended Lineage Fate Choices. Nature cell biology, 22(6), 640-650.

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Optimized Illumina Library Preparation from 3C Samples

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3C samples and controls were quantified using Qubit (Invitrogen), run on a 1% agarose gel and tested by qPCR with KAPA SYBR Fast (Sigma) to determine library quality. qPCR primers are in Supplementary Data 1. Only libraries with a digestion efficiency >70% were used for Capture-C. Libraries were either indexed with NEBNext DNA Library Prep Master Mix for Illumina (New England Biolabs) using 6 µg input 3C DNA as previously described following manusfacture’s instructions or using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). When using the Ultra II kit 3 µg 3C material was sonicated to 200 bp using a Covaris S220 Focused Ultrasonicator, and purified using Ampure XP SPRI beads (Beckman Coulter). DNA was eluted into 53 µL with 1 µL used for D1000 TapeStation analysis (Agilent) and 2 µL used for Qubit quantification (Invitrogen). Fifty microliters of DNA ( ≤2 µg) was then indexed with the following modifications; for the End Prep reaction, the 20 °C incubation was lengthened to 45 min, 5 µL of NEBNext Adaptor was added and incubated for 30 min at 20 °C, the USER Enzyme incubation was extended to 30 min (37 °C), and indexing was performed in two reactions with Herculase II Fusion Polymerase (Agilent) using six cycles of amplification.

Downes D.J., Beagrie R.A., Gosden M.E., Telenius J., Carpenter S.J., Nussbaum L., De Ornellas S., Sergeant M., Eijsbouts C.Q., Schwessinger R., Kerry J., Roberts N., Shivalingam A., El-Sagheer A., Oudelaar A.M., Brown T., Buckle V.J., Davies J.O, & Hughes J.R. (2021). High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature Communications, 12, 531.

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Single-Cell RNA-Seq Library Preparation

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16 k cells were counted using a hemocytometer and loaded onto a 10× Genomics Chromium chip per manufacturer’s recommendations. Reverse transcription and library preparation was performed using the Chromium Next GEM Single-Cell 3ʹ Reagent Kits v3.1 (10× Gemomis, CG000204) according to manufacturer’s protocols. After a cleanup with SPRIselect Reagent Kit (C10640; Beckman), final libraries were quantified using a Qubit 1X dsDNA HS Assay Kit (Q33231; Invitrogen) and fragment size distribution was verified using a High Sensitivity D1000 Tapestation (5067-5582; Agilent).

Okafor A.E., Lin X., Situ C., Wei X., Xiang Y., Wei X., Wu Z, & Diao Y. (2023). Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state. The Journal of Cell Biology, 222(8), e202211073.

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