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Tapestation high sensitivity dna tapes

Manufactured by Agilent Technologies
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The Tapestation high sensitivity DNA tapes are designed for the analysis of DNA samples. They provide a reliable and efficient way to assess the quality and quantity of DNA samples. The tapes are compatible with the Tapestation system and are used for the electrophoretic separation and detection of DNA fragments.

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Lab products found in correlation

Qubit high sensitivity dna kit, by Thermo Fisher Scientific (5 mentions) Dynabeads myone silane, by Thermo Fisher Scientific (5 mentions) Nextseq sequencer, by Illumina (5 mentions) Clc genomics workbench version 8.0.1 rna seq analysis software package, by Qiagen (4 mentions) Hiseq 2000, by Illumina (1 mentions) Rlt buffer, by Qiagen (1 mentions) Agencourt ampure xp bead clean up, by Beckman Coulter (1 mentions)

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TapeStation (986 citations)

5 protocols using tapestation high sensitivity dna tapes

1

RNA-seq Library Preparation and Analysis

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Samples were sorted as described above and each replicate indicates a biological replicate that was prepared using different sets of mice on different experimental days. RNA-seq library preparations were performed (Chevrier, N. manuscript in preparation). Briefly, RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented, and barcoded using 8bp barcodes in conjunction with standard Illumina adaptors. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was confirmed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA Sequencing reactions were sequenced on an Illumina HiSeq 2000 or Illumina NextSeq sequencer (Illumina) according to manufacturer’s instructions, sequencing 50bp reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff=5.0). Results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heatmaps.
Sage P.T., Ron-Harel N., Juneja V.R., Sen D.R., Maleri S., Sungnak W., Kuchroo V.K., Haining W.N., Chevrier N., Haigis M, & Sharpe A.H. (2016). Suppression by TFR cells leads to durable and selective inhibition of B cell effector functions. Nature immunology, 17(12), 1436-1446.
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2

RNA-seq Library Preparation and Analysis

Cited 1 time
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RNA-seq was performed as described previously15 (link). Briefly, RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented, and barcoded using 8bp barcodes in conjunction with standard Illumina adaptors. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was confirmed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA Sequencing reactions were sequenced on an Illumina NextSeq sequencer (Illumina) according to the manufacturer’s instructions, sequencing 50bp reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff=5.0). Results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heatmaps. The datasets generated during the current study are available on Gene Expression Omnibus (GEO) (Accession number GSE134153) and are available from the corresponding author on reasonable request.
Clement R.L., Daccache J., Mohammed M.T., Diallo A., Blazar B.R., Kuchroo V.K., Lovitch S.B., Sharpe A.H, & Sage P.T. (2019). Follicular regulatory T cells control humoral and allergic immunity by restraining early B cell responses. Nature immunology, 20(10), 1360-1371.
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3

RNA-seq library preparation and analysis

Cited 1 time
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RNAseq library preparations were performed as previously described75 (link). Briefly, samples were lysed with RLT Buffer (Qiagen) and RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented and barcoded with 8 bp barcodes. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt). Samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was assessed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA was sequenced on an Illumina NextSeq sequencer (Illumina) according to manufacturer’s instructions, sequencing 50 bp single end reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNAseq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff = 5.0). Results were normalized to reads per million.
Cai S., Choi J.Y., Borges T.J., Zhang H., Miao J., Ichimura T., Li X., Xu S., Chu P., Eskandari S.K., Allos H., Alhaddad J.B., Muhsin S.A., Yatim K., Riella L.V., Sage P.T., Chandraker A.K, & Azzi J.R. (2020). Donor myeloid derived suppressor cells (MDSCs) prolong allogeneic cardiac graft survival through programming of recipient myeloid cells in vivo. Scientific Reports, 10, 14249.
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4

RNA-seq Library Preparation and Analysis

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA-seq was performed as described previously15 (link). Briefly, RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific). RNA was fragmented, and barcoded using 8bp barcodes in conjunction with standard Illumina adaptors. Primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high sensitivity DNA kit (Invitrogen) and library quality was confirmed using Tapestation high sensitivity DNA tapes (Agilent Technologies). RNA Sequencing reactions were sequenced on an Illumina NextSeq sequencer (Illumina) according to the manufacturer’s instructions, sequencing 50bp reads. Analysis was performed using the CLC Genomics Workbench version 8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8) to the mouse genome and differential expression analysis was performed (total count filter cutoff=5.0). Results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heatmaps. The datasets generated during the current study are available on Gene Expression Omnibus (GEO) (Accession number GSE134153) and are available from the corresponding author on reasonable request.
Clement R.L., Daccache J., Mohammed M.T., Diallo A., Blazar B.R., Kuchroo V.K., Lovitch S.B., Sharpe A.H, & Sage P.T. (2019). Follicular regulatory T cells control humoral and allergic immunity by restraining early B cell responses. Nature immunology, 20(10), 1360-1371.
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5

RNA-seq workflow for mouse transcriptome

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RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher Scientific) and then fragmented and barcoded using eight-base pair barcodes together with standard Illumina adaptors. The primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and the samples were amplified with 14 PCR cycles. Libraries were gel purified and quantified using a Qubit high-sensitivity DNA kit (Invitrogen), and library quality was assessed using TapeStation high-sensitivity DNA tapes (Agilent Technologies). RNA-seq reactions were sequenced on an Illumina NextSeq sequencer (Illumina) according to the manufacturer’s instructions, sequencing 50-base pair reads. Analysis was performed using the CLC Genomics Workbench v.8.0.1 RNA-seq analysis software package (Qiagen). Briefly, reads were aligned (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8) to the mouse genome, and differential expression analysis was performed (total count filter cutoff = 5.0). The results were normalized to reads per million. Gene-e (Broad Institute) was used to generate heat maps. Datasets generated during the current study are available on the Gene Expression Omnibus (GSE134153) and are also available from the corresponding author upon reasonable request.
Geng J., Chen R., Yang F.F., Lin P., Zhu Y.M., Fu X., Wang K., Feng Z., Wu J., Zhang H., Li Q.J., Chen Z.N, & Zhu P. (2021). CD98-induced CD147 signaling stabilizes the Foxp3 protein to maintain tissue homeostasis. Cellular and Molecular Immunology, 18(12), 2618-2631.
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