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10x Genomics - Crossref

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Last Updated: 10 June 2022

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10X Genomics Single-Nucleus Multiome (RNA + ATAC) Assay for Profiling Adult Human Tissues v2

RNA sequencing from single nuclei "10X Genomics Single Cell 3' RNA sequencing is a microdroplet-based process that allows for the efficient capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. The total RNA content in a nucleus is just 10% of that in a whole cell, but has been found to accurately reflect whole cell expression levels in adult human tissues [2,3], including the kidney [4]. The 10x Genomics Single Cell ATAC sequencing is a microdroplet-based procedure that allows for the rapid capture, sequencing, and profiling of accessible chromatin in single nuclei. Both RNA expression and epigenomic data from the same nuclei can be retrieved by the 10X Multiome ATAC + Gene Expression assay for a deeper analysis of cell type or state gene regulation. ".

Source link: https://doi.org/10.17504/protocols.io.5qpvoby69l4o/v2


Dissociation of neuronal culture to single cells for scRNA-seq (10x Genomics) v1

"This protocol outlines a procedure for dissociating a human pluripotent stem cell-derived neuronal culture from single cells for loading onto a Chromium 10x chip for single cell RNA-sequencing. " DNase Vial - PDS Kit Papain Vial Note: These include: iPS cells were cultured in our labs and were cultured under'mature' conditions from day 20 to day 11, and as "early neuronal progenitors" on day 11.

Source link: https://doi.org/10.17504/protocols.io.bh32j8qe


10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues v3

"10X Genomics Single Cell 3' RNA sequencing is a microdroplet-based method that allows the effective capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. RNA molecules are transcribed and processed within the nucleus before exporting to the United Kingdom for translation into proteins. As such, nuclear RNA is a blend of nascent transcripts, partially or entirely digested mRNA, and several non-coding RNA molecules. The kidney's total RNA content within the nucleus is about 10% of the RNA content in a whole cell, but it has been shown to accurately represent whole cell expression levels in adult human tissues [2,3] including the kidney [4]. Here we offer a modified version of the published 10X protocol [1] that we have modified for the processing of adult human kidney nuclei. [1].

Source link: https://doi.org/10.17504/protocols.io.86khzcw


10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues v2

"10X Genomic Single Cell 3' RNA sequencing is a microdroplet-based technology that allows for the safe capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. paraphrasedoutput:RNA molecules are transcribed and processed within the nucleus before exporting to ER for translation into proteins. Nuclear RNA is a blend of nascent transcripts, partially or fully processed mRNA, and several non-coding RNA molecules. As such, nuclear RNA is a blend of nascent transcripts, partially or fully processed mRNA, as well as other non-coding RNA molecules. The total RNA content within the nucleus is about 10% of the RNA content in a single cell, but it has been found to accurately depict whole cell expression values in adult human tissues [2,3], including the kidney [4]. Here we have a modified version of the widely circulated 10X protocol [1] that we have modified for the processing of adult human kidney nuclei.

Source link: https://doi.org/10.17504/protocols.io.8xthxnn


10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues v1

"10X Genoomics Single Cell 3' RNA sequencing is a microdroplet-based technology that enables the safe capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. Nuclear RNA is a blend of nascent transcripts, partially or completely processed mRNA, and a number of non-coding RNA molecules. The total RNA content within the nucleus is less than 10% of the RNA content in a whole cell, but it has been shown to accurately reflect whole cell expression values in adult human tissues [2,3], including the kidney [4]. Nuclei can be easily isolated from frozen tissue using a combination of chemical and physical methods that can effectively avoid solid tissue dissociation into single cells, as well as RNA breakdown or artefacts during dissociation. Here we present a modified version of the well-established 10X protocol [1] that we've modified for the processing of adult human kidney nuclei.

Source link: https://doi.org/10.17504/protocols.io.8v2hw8e


Protocol for nuclei isolation from fresh and frozen tissues using Salty-Ez10 or Salty-Ez50 buffer: compatible with snRNA-Seq and Multiome workflows from 10x Genomics v5

"I labelled DTT as optional in this version because after further testing I haven't noticed any difference with or without in the snRNA-Seq workflow. " Also, I recommend WRB1 for snRNA-Seq workflow only and WRB2 for both snRNA-Seq and Multiome workflows. Since WRB2 is 10x Genomics' recommendation for Multiome, I have used it for this workflow. During the cDNA amp, I include a discussion about cycling. This has been especially useful for samples where lysis in SaltyEz10 proved to be suboptimal," SaltyEz50's option was particularly useful.

Source link: https://doi.org/10.17504/protocols.io.bx64prgw


10X Genomics Single-Nucleus Assay of Transposase Accessible Chromatin-Sequencing for Epigenetic Profiling of Adult Human Tissues v1

"10x Genomics Single Cell ATAC sequencing is a microdroplet-based method that allows for the efficient capture, sequencing, and profiling of accessible chromatin in single nuclei. " Chromatin availability is a key determinant of gene regulation, determining the transcriptional regulatory networks that control cellular identity and function as well as other biological processes. Chromatin accessibility sequencing provides insight into the upstream regulatory landscape associated with open and accessible chromatin regions.

Source link: https://doi.org/10.17504/protocols.io.bvssn6ee


10X Genomics Single-Nucleus Multiome (RNA + ATAC) Assay for Profiling Adult Human Tissues v1

"10X Genomics Single Cell 3' RNA sequencing is a microdroplet-based method that enables the efficient capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. Nuclear RNA is a blend of nascent transcripts, partially or entirely processed mRNA, and a number of non-coding RNA molecules. The total RNA content within the nucleus accounts for approximately 10% of the total RNA content in a single cell, but it has been found to accurately represent whole cell expression values in adult human tissues [2,3], including the kidney [4]. Genomics Single Cell ATAC sequencing, a microdroplet-based procedure that permits the efficient capture, sequencing, and profiling of accessible chromatin in single nuclei. The 10X Multiome ATAC + Gene Expression assay captures both RNA expression and epigenomic data from the same nucleus for a deeper analysis of cell type or state gene regulation. ".

Source link: https://doi.org/10.17504/protocols.io.b4dqqs5w


Protocol for nuclei isolation from fresh and frozen tissues using Salty-Ez10 buffer: compatible with snRNA-Seq and Multiome workflows from 10x Genomics v4

"I labelled DTT as optional in this version because after further testing, I haven't noticed any difference with or without in the snRNA-Seq workflow, whether it be black or white. " For both snRNA-Seq and Multiome workflows, I recommend WRB1 for snRNA-Seq workflow and WRB2 for both snRNA-Seq and Multiome workflows. Since WRB2 is 10x Genomics' suggestion for Multiome, I have adopted this for this workflow. During the cDNA amp, I include a discussion about cycling. ".

Source link: https://doi.org/10.17504/protocols.io.bw6qphdw


PBMC 10X Genomics Single Cell CUT&Tag Protocol v1

"While the nuclei isolation protocol is designed to produce single nuclei solutions with low relative centrifugal force spins that will prevent nuclei clumping," the nuclei isolation protocol is expected to produce two million PBMC-isolated nuclei spins that will prevent nuclei clumping, but will not pellet all nuclei after multiple washes, the goal is to produce double the number of live PBMCs. ".

Source link: https://doi.org/10.17504/protocols.io.bwdhpa36

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions