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Chromium single cell 3 chip

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The Chromium Single Cell 3' Chip is a microfluidic device designed for the high-throughput analysis of single cells. It enables the isolation, barcoding, and library preparation of individual cells for subsequent sequencing.

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Lab products found in correlation

Chromium single cell 3 library gel bead kit v2, by 10x Genomics (3 mentions) Papain dissociation system kit, by Worthington (2 mentions) Bovine serum albumin (bsa), by Merck Group (2 mentions) Nextseq 500, by Illumina (2 mentions) Novaseq 6000, by Illumina (2 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Quantstudio 12k flex, by Agilent Technologies (1 mentions) Bioanalyzer high sensitivity dna kit, by Agilent Technologies (1 mentions) Luna fl dual fluorescence cell counter, by Logos Biosystems (1 mentions) Hiseq 4000, by Illumina (1 mentions) Chromium single cell 3 library gel bead kit v3, by 10x Genomics (1 mentions) 3 cellplex kit set a, by 10x Genomics (1 mentions)

Spelling variants of this product

Chromium chip (15 citations) Single Cell 3′ Chip (12 citations) Chromium Single Cell 3’ microfluidic chips (3 citations)

6 protocols using chromium single cell 3 chip

1

Single-nucleus RNA-seq of mouse brain

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RNA-seq of single nuclei was performed in two independent batches (batch 1, n = 1 NestinCre/+Il12rb2fl/fl and n = 1 Il12rb2fl/fl; batch 2, n = 3 NestinCre/+Il12rb2fl/fl and n = 3 Il12rb2fl/fl). Immediately after extraction, 17,500 sorted nuclei per sample were loaded onto a Chromium Single Cell 3′ Chip (10x Genomics) and processed for the single-nucleus cDNA library preparation (Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 protocol). Around 50,000 reads per nucleus were sequenced using the Illumina NovaSeq 6000 no. 1 platform according to the manufacturer’s instructions without modifications (R1 = 28, i7 = 10, i5 = 10, R2 = 90). Preparation of cDNA libraries and sequencing were performed at the Functional Genomics Center Zurich. Cell Ranger software (v6.0.2) was implemented for library demultiplexing, barcode processing, fastq file generation, gene alignment to the mouse genome (GENCODE reference build GRCm39) and UMI counts. We implemented the include-introns option for counting intronic reads, as the snRNA-seq assay captures unspliced pre-mRNA as well as mature mRNA. For each sample, a Cell Ranger report was obtained with all the available information regarding sequencing and mapping parameters. All samples were merged into a matrix using Cell Ranger (cellranger --aggr function).
Andreadou M., Ingelfinger F., De Feo D., Cramer T.L., Tuzlak S., Friebel E., Schreiner B., Eede P., Schneeberger S., Geesdorf M., Ridder F., Welsh C.A., Power L., Kirschenbaum D., Tyagarajan S.K., Greter M., Heppner F.L., Mundt S, & Becher B. (2023). IL-12 sensing in neurons induces neuroprotective CNS tissue adaptation and attenuates neuroinflammation in mice. Nature Neuroscience, 26(10), 1701-1712.
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2

Single-cell RNA-seq of brain organoids

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Individual brain organoids were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington Biochemical). A detailed description of the dissociation protocol is available at Protocol Exchange33 . Dissociated cells were resuspended in ice-cold PBS containing 0.04% BSA (Sigma) at a concentration of 1000 cells/μL, and approximately 17,400 cells per channel (to give estimated recovery of 10,000 cells per channel) were loaded onto a Chromium™ Single Cell 3’ Chip (10x Genomics, PN-120236) and processed through the Chromium Controller to generate single-cell GEMs (Gel Beads in Emulsion). Single-cell RNA-Seq libraries were prepared with the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics, PN-120237). Libraries from different samples were pooled based on molar concentrations and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read 1, 57 bases for read 2 and 8 bases for Index 1. After the first round of sequencing, libraries were re-pooled based on the actual number of cells in each and re-sequenced to give equal number of reads per cell in each sample and to reach a sequencing saturation of at least 50% (in most cases >70%).
Velasco S., Kedaigle A.J., Simmons S.K., Nash A., Rocha M., Quadrato G., Paulsen B., Nguyen L., Adiconis X., Regev A., Levin J.Z, & Arlotta P. (2019). Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature, 570(7762), 523-527.
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3

Single-Cell RNA Sequencing of Cells

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The cell concentrations were adjusted to 550 cells/μl and
approximately 10,000 cells per channel (to give estimated recovery of
5,000–8,000 cells per channel) were loaded onto a Chromium Single
Cell 3′ Chip (10x Genomics, PN-2000168) and processed through the
Chromium controller to generate single-cell gel beads in emulsion (GEMs).
scRNAseq libraries were prepared with the Chromium Single Cell 3′
Library & Gel Bead Kit v.2 (10x Genomics, PN-1000075). Each sample was
ligated and barcoded prior to performing library QC. The Agilent Bioanalyzer
and QuantStudio 12K Flex were used to assess the library quality prior to
sequencing. Libraries from different samples were pooled based on molar
concentrations and sequenced on a NovaSeq 6000 instrument (Illumina) with
151 bases for read 1, 151 bases for read 2 and 8 bases for index 1. After
the first round of sequencing, libraries were re-pooled on the basis of the
actual number of cells in each and re-sequenced to give an equal number of
reads per cell in each sample and to reach a sequencing saturation of at
least 50%.
Neely M.D., Xie S., Prince L.M., Kim H., Tukker A.M., Aschner M., Thimmapuram J, & Bowman A.B. (2021). Single cell RNA sequencing detects persistent cell type- and methylmercury exposure paradigm-specific effects in a human cortical neurodevelopmental model. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 154, 112288.
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4

Single-Cell RNA-Seq of Cell Viability

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Viability was confirmed to be >90% in all samples using acridine orange/propidium iodide dye with LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems, L20001). Single-cell suspensions were loaded on a Chromium Single Cell 3′ Chip (10X Genomics), and were run in the Chromium Controller to generate single-cell gel bead-in-emulsions using the 10x genomics 3′ Chromium v2.0 platform as per the manufacturer’s instructions. Single-cell RNA-seq libraries were prepared according to the manufacturer’s protocol, and the library quality was confirmed with a Bioanalyzer High-Sensitivity DNA Kit (Agilent, 5067-4627) and a Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851). Samples were pooled up to four, and sequenced on an Illumina HiSeq 4000 according to the standard 10X Genomics protocol.
Hong S.P., Chan T.E., Lombardo Y., Corleone G., Rotmensz N., Bravaccini S., Rocca A., Pruneri G., McEwen K.R., Coombes R.C., Barozzi I, & Magnani L. (2019). Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. Nature Communications, 10, 3840.
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5

Single-cell RNA-seq of brain organoids

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Individual brain organoids were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington Biochemical). A detailed description of the dissociation protocol is available at Protocol Exchange33 . Dissociated cells were resuspended in ice-cold PBS containing 0.04% BSA (Sigma) at a concentration of 1000 cells/μL, and approximately 17,400 cells per channel (to give estimated recovery of 10,000 cells per channel) were loaded onto a Chromium™ Single Cell 3’ Chip (10x Genomics, PN-120236) and processed through the Chromium Controller to generate single-cell GEMs (Gel Beads in Emulsion). Single-cell RNA-Seq libraries were prepared with the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics, PN-120237). Libraries from different samples were pooled based on molar concentrations and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read 1, 57 bases for read 2 and 8 bases for Index 1. After the first round of sequencing, libraries were re-pooled based on the actual number of cells in each and re-sequenced to give equal number of reads per cell in each sample and to reach a sequencing saturation of at least 50% (in most cases >70%).
Velasco S., Kedaigle A.J., Simmons S.K., Nash A., Rocha M., Quadrato G., Paulsen B., Nguyen L., Adiconis X., Regev A., Levin J.Z, & Arlotta P. (2019). Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature, 570(7762), 523-527.
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6

Single-Cell RNA Sequencing of Dissociated DFOs

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Individual DFOs were dissociated following a published protocol [38 (link)] with minor modifications. After dead cell removal (Miltenyi, Cat. no. 130-090-101), cells were subjected to multiplexing using 3′ CellPlex Kit Set A (10x Genomics, Cat. no. PN-1000261) following the manufacturer’s instructions. Equal proportions were loaded onto a Chromium Single Cell 3′ Chip (10x Genomics, Cat. no. PN-120236) and processed through the Chromium controller to generate single-cell gel beads in emulsion. scRNAseq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.3 (10x Genomics, Cat. no. PN-1000121). Libraries from different samples were pooled and sequenced on a NovaSeq6000 instrument (Illumina).
Sarieva K., Kagermeier T., Khakipoor S., Atay E., Yentür Z., Becker K, & Mayer S. (2023). Human brain organoid model of maternal immune activation identifies radial glia cells as selectively vulnerable. Molecular Psychiatry.
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