A single cell/nuclei suspension containing 10,000 cells/nuclei was loaded on a Chromium Single Cell B Chip (10x Genomics, catalog no. 1000154) as follows: 75 μL of master mix + nuclei suspension was loaded into the row labeled 1, 40 μL of Chromium Single Cell 3 Gel Beads (10x Genomics, catalog no. PN-1000093) into the row labeled 2 and 280 μL of Partitioning Oil (10x Genomics, catalog no. 2000190) into the row labeled 3. This was followed by GEM generation and barcoding, post GEM-RT cleanup and cDNA amplification. Then 100 ng purified cDNA derived from 12 cycles of cDNA amplification was used for 3 Gene Expression Library Construction by using Chromium Single Cell 3 GEM, Library & Gel Bead Kit v3 (10x Genomics, catalog no. 1000092) according to the manufacturer’s manual (10x Genomics, catalog no. CG000183 Rev C). The barcoded short-read libraries were measured using a Qubit 2.0 with a Qubit dsDNA HS assay kit (Invitrogen, catalog no. Q32854) and the quality of the libraries was assessed on a Fragment analyzer (Agilent) using a high-sensitivity NGS Fragment Kit (1–6000bp) (Agilent, catalog no. DNF-474-0500). Sequencing libraries were loaded on an Illumina NovaSeq6000 with PE 2 × 50 paired-end kits by using the following read length: 28 cycles Read1, 8 cycles i7 index and 91 cycles Read2.
Chromium single cell 3 gel beads
Manufactured by 10x Genomics
The Chromium Single Cell 3 Gel Beads are a critical component of the Chromium Single Cell 3' Solution, which is used for single-cell RNA sequencing. These gel beads contain unique molecular identifiers (UMIs) and cell-specific barcodes that are used to label and identify individual cells and their transcripts during the sequencing process.
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Lab products found in correlation
2 protocols using chromium single cell 3 gel beads
1
Single-Cell RNA-Seq Library Preparation
2
Single-cell RNA-seq library preparation
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A single-cell/single-nucleus suspension containing 10,000 cells/10,000 nuclei was loaded on a Chromium Single Cell B Chip (10x Genomics, 1000154). Specifically, 75 µl of master mix + nuclei suspension was loaded into the row labeled 1, 40 µl of Chromium Single Cell 3′ Gel Beads (10x Genomics, PN-1000093) was loaded into the row labeled 2, and 280 µl of partitioning oil (10x Genomics, 2000190) was loaded into the row labeled 3. This was followed by GEM generation and barcoding after GEM-RT cleanup and cDNA amplification. Then, 100 ng of purified cDNA derived from 12 cycles of cDNA amplification was used for 3′ Gene Expression Library Construction by using Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3 (10x Genomics, 1000092) according to the manufacturer's manual (10x Genomics, CG000183 Rev C). The barcoded short-read libraries were measured using a Qubit 2.0 with a Qubit dsDNA HS assay kit (Invitrogen, Q32854), and library quality was assessed on a Fragment analyzer (Agilent) using a high-sensitivity NGS Fragment kit (1-6,000 base pairs (bp); Agilent, DNF-474-0500). Sequencing libraries were loaded on an Illumina NovaSeq6000 with PE 2 × 50 paired-end kits by using the following read lengths: 28 cycles read 1, 8 cycles i7 index and 91 cycles read 2.
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