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Surecell scatac seq procedure

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The SureCell scATAC-seq procedure is a workflow designed for single-cell analysis of chromatin accessibility. It enables the identification and profiling of accessible chromatin regions within individual cells.

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Lab products found in correlation

Basespace, by Illumina (3 mentions)

3 protocols using surecell scatac seq procedure

1

Systematic Removal of ATAC-seq Biases

Cited 2 times
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Per-read bead barcodes were parsed and trimmed using UMI-tools v1.0.041 (link). Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to 1 mismatch per 6-mer or 7-mer (mean >99% parsing efficiency across experiments). Paired-end reads were aligned to hg19 using BWA v0.7.1742 (link) on the Illumina BaseSpace online application. Bead-based ATAC-seq processing (BAP)17 (link) was used to identify systematic biases (i.e., reads aligning to an inordinately large number of barcodes) and barcode-aware deduplicate reads, as well as perform merging of multiple bead barcode instances associated with the same cell. Barcode merging was necessary due to the nature of the BioRad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet. BAP was given an alignment (.bam) file for a given experiment with a bead barcode identifier indicated by a SAM tag as input. Aligned reads were combined using samtools merge (v1.9).
Lal A., Chiang Z.D., Yakovenko N., Duarte F.M., Israeli J, & Buenrostro J.D. (2021). Deep learning-based enhancement of epigenomics data with AtacWorks. Nature Communications, 12, 1507.
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2

Bead-based ATAC-seq data processing

Cited 1 time
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Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools),77 (link) and the remaining read fragments were aligned using BWA (https://github.com/lh3/bwa) on the Illumina BaseSpace online application. Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to one mismatch per 6-mer or 7-mer (mean > 99% parsing efficiency across experiments). All sequence libraries were aligned to the hg19 reference genome. We then used bead-based ATAC-seq data processing (BAP, v0.6.4) (https://github.com/caleblareau/bap)13 (link) to help identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplication of reads, and to perform merging of multiple bead barcode instances associated with the same cell (barcode merging is necessary due to the nature of the Bio-Rad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet). For a detailed description of the bead barcode merging strategy see.13 (link) We ran BAP using a single input alignment (.bam) file for a given experiment with a bead barcode identifier indicated by the SAM tag “DB”, and default parameters.
Kartha V.K., Duarte F.M., Hu Y., Ma S., Chew J.G., Lareau C.A., Earl A., Burkett Z.D., Kohlway A.S., Lebofsky R, & Buenrostro J.D. (2022). Functional inference of gene regulation using single-cell multi-omics. Cell Genomics, 2(9), 100166.
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3

Bead Barcode Processing and Deduplication for scATAC-seq

Cited 1 time
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Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools),77 (link) and the remaining read fragments were aligned using BWA (https://github.com/lh3/bwa) on the Illumina BaseSpace online application. Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to one mismatch per 6-mer or 7-mer (mean > 99% parsing efficiency across experiments). All sequence libraries were aligned to the hg19 reference genome. We then used bead-based ATAC-seq data processing (BAP, v0.6.4) (https://github.com/caleblareau/bap)13 (link) to help identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplication of reads, and to perform merging of multiple bead barcode instances associated with the same cell (barcode merging is necessary due to the nature of the Bio-Rad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet). For a detailed description of the bead barcode merging strategy see.13 (link) We ran BAP using a single input alignment (.bam) file for a given experiment with a bead barcode identifier indicated by the SAM tag “DB”, and default parameters.
Kartha V.K., Duarte F.M., Hu Y., Ma S., Chew J.G., Lareau C.A., Earl A., Burkett Z.D., Kohlway A.S., Lebofsky R, & Buenrostro J.D. (2022). Functional inference of gene regulation using single-cell multi-omics. Cell Genomics, 2(9), 100166.
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