Following granulocyte depletion, PBMCs were split into two fractions to generate single cell V(D)J T-cell and B-cell libraries or multiomic (GEX and ATAC) libraries. To capture T-cell and B-cell V(D)J repertoire, single cell gel beads-in-emulsion and libraries were performed according to...
Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). Next quenching reagent (Multiome 10x kit) was used to stop the reaction. After quenching, single-cell droplets were dissolved and ...
aggregates1.png" style="width: 276px; height:200px"/> Cell Ranger combines the aggregate barcodes identified from both aforementioned steps and removes them from the final feature-barcode matrix. The fraction of reads associated with these barcodes is reported as the "Antibody: Fraction ...
https://support10xgenomics.com/single-cell- multiome-atac-gex/datasets/100/pbmc_granulocyte_sorted_10k. 2020. LeCun Y, Misra I. Self-supervised learning: The dark matter of intelligence. Meta AI. 2021. p. Web blog post. 10X Genomics. Frozen human healthy brain tissue (3k), single cell ...
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4A). Signatures GEX-1 and GEX-4 were removed from further consideration, as they corresponded to either a generic immune cell activation module (GEX-1) or monocytic contamination (GEX-4). For the remaining six signatures, key marker genes included CXCR4; the tumor suppressor RASSF6; AHNAK, ...
A SPRI selection clean-up was done to separate the amplified cDNA molecules for 3’ Gene Expression (GEX) and the CMO-derived cDNA (CellPlex). 100 ng of mRNA-derived cDNA were used for GEX library construction while 5 μl of CMO-derived cDNA were used to amplify the corresponding Cell...
The cell-barcode RNA reads were processed with the standard CellRanger (version: 7.2.0) pipeline (14) using the hg38 reference genome (refdata-gex-GRCh38-2020-A). The resulting gene-barcode matrices served as input of Seurat (version: 5.0.1) (15) for cell filtration, data integration, ...
Cryosections were cut at 10 μm thickness and mounted onto the GEX arrays. Sections were then placed on a Thermocycler Adaptor with the active surface facing up, incubated for 1 min at 37°C, fixed for 30 min with methyl alcohol at -20°C, and stained with hematoxylin and eosin (H&E...
Gene Expression (GEX) libraries were indexed with 13 cycles of amplification using the Dual Index Plate TT Set A (10 × Genomics; PN-3000431). The size distribution and concentration of full-length GEX libraries were verified on an Agilent Bioanalyzer High Sensitivity chip. Finally, ...