Chromium system

Manufactured by 10x Genomics

Sourced in United States

The Chromium system is a lab equipment product offered by 10x Genomics. It is designed to enable high-throughput, single-cell analysis. The system utilizes microfluidic technology to encapsulate individual cells or nuclei in nanoliter-scale gel beads, facilitating the isolation and processing of genetic material from large numbers of individual cells simultaneously.

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Lab products found in correlation

Nextseq 500, by Illumina (7 mentions) Novaseq 6000, by Illumina (6 mentions) Hiseq 4000, by Illumina (5 mentions) Hiseq 2500, by Illumina (4 mentions) Single cell 3 reagent kit v2, by 10x Genomics (3 mentions) Nuclei ez lysis buffer, by Merck Group (3 mentions) Nextseq 500 machine, by Illumina (3 mentions) Nextseq 550, by Illumina (3 mentions) Hiseq 2500 platform, by Illumina (3 mentions) Chromium controller, by 10x Genomics (3 mentions) Novaseq 6000 platform, by Illumina (3 mentions) Tc20 automated cell counter, by Bio-Rad (2 mentions) 40 μm strainer, by Thermo Fisher Scientific (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Bioanalyzer, by Agilent Technologies (2 mentions) Single cell 3 reagent kit v3, by 10x Genomics (2 mentions) Gel bead kit v3, by 10x Genomics (2 mentions) Chromium single cell 3 library, by 10x Genomics (2 mentions) Novaseq, by Illumina (2 mentions) Chromium single cell platform, by 10x Genomics (2 mentions)

Spelling variants of this product

10x Genomics Chromium System (15 citations) Chromium Single Cell system (13 citations) 10x Genomics Chromium Single Cell System (8 citations) Chromium single cell sorting system (6 citations) Chromium Controller system (6 citations) Chromium Single Cell 3′ system (4 citations) Chromium microfluidic system (3 citations) Chromium Single-Cell 3′ Gene Expression system (2 citations) Chromium Single Cell 3′RNA-sequencing system (2 citations) 10X Genomics Chromium™ Controller Single Cell Sequencing System (2 citations)

72 protocols using chromium system

Single-Cell Immune Profiling of SARS-CoV-2 Infection

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VDJ, 5′, and probe feature libraries were prepared using the 10X Chromium System (10X Genomics). The Chromium Single Cell 5′ Library and Gel Bead v2 Kit, Human B Cell V(D)J Enrichment Kit, and Feature Barcode Library Kit were used. All steps were followed as listed in the manufacturer’s instructions. Specifically, user guide CG000186 Rev D was used. Severe acute infected samples were pooled post-sort and hashtagged (Biolegend), and run as a single sample, to account for low cell numbers. Final libraries were pooled and sequenced using the NextSeq550 (Illumina) with 26 cycles apportioned for read 1, 8 cycles for the i7 index, and 134 cycles for read 2.

Dugan H.L., Stamper C.T., Li L., Changrob S., Asby N.W., Halfmann P.J., Zheng N.Y., Huang M., Shaw D.G., Cobb M.S., Erickson S.A., Guthmiller J.J., Stovicek O., Wang J., Winkler E.S., Madariaga M.L., Shanmugarajah K., Jansen M.O., Amanat F., Stewart I., Utset H.A., Huang J., Nelson C.A., Dai Y.N., Hall P.D., Jedrzejczak R.P., Joachimiak A., Krammer F., Diamond M.S., Fremont D.H., Kawaoka Y, & Wilson P.C. (2021). Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets. Immunity, 54(6), 1290-1303.e7.

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Transcriptome Profiling of Zebrafish Telencephalon

Cited 3 times

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The telencephalon was dissected using ice-cold PBS, and cell dissociation was performed using the Neural Tissue Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) following the manufacturer’s instructions and as described previously [30 (link)]. Deep sequencing for whole transcriptome was performed as described [20 (link),30 (link)]. For single-cell sequencing, isolated cells were passed through a 40-μm cell strainer. Viability indicator (propidium iodide, Merck, Darmstadt, Germany) and GFP were used to sort live cells. Cell suspension was loaded into the 10X Chromium system (10X Genomics, Pleasanton, CA) [97 (link)]. The 10X libraries were prepared as per the manufacturer’s instructions. The raw sequencing data were processed by the cell ranger software provided by the 10X genomics with the default options. The reads were aligned to zebrafish reference transcriptome (ENSEMBL Zv10, release 91). Analyses matrices were used as input for downstream data analysis by Seurat (https://satijalab.org/seurat/) [98 (link)]. Analyses were performed as described [34 (link),99 (link)].

Bhattarai P., Cosacak M.I., Mashkaryan V., Demir S., Popova S.D., Govindarajan N., Brandt K., Zhang Y., Chang W., Ampatzis K, & Kizil C. (2020). Neuron-glia interaction through Serotonin-BDNF-NGFR axis enables regenerative neurogenesis in Alzheimer’s model of adult zebrafish brain. PLoS Biology, 18(1), e3000585.

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Single-Cell Transcriptomics of Wnt1 Tumor Models

Cited 2 times

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Whole Wnt1 (tamoxifen injected, Cre negative), DN-Wnt1, and K8iKOR-Wnt1 tumors were dissociated as described above and tumor cells were filtered with a 70 μm filter directly after dissociation to collect single cells from the entire tumor. Cells were captured using the 10X Chromium system (10X Genomics) and sequenced with the NextSeq 500 (Illumina). Raw reads were barcode deconvoluted and aligned to the reference genome (mm10) via cellranger (v3.1.0). All subsequent processing was performed using the Seurat package within R (v3.1.5). Low quality cells (cells with percentage of reads of mitochondrial origin >10%, with percentage of reads of ribosomal origin >45%, with <1000 feature counts, with >6000 feature counts) were filtered from the dataset, and read counts were normalized using the scTransform method (28 (link)). Samples were integrated with the Seurat integrate function (29 (link)) and clustered via UMAP according to nearest neighbors. Re-clustering was performed as above on subset clusters based on common annotation types.

Obr A.E., Bulatowicz J.J., Chang Y.J., Ciliento V., Lemenze A., Maingrette K., Shang Q., Gallagher E.J., LeRoith D, & Wood T.L. (2022). Breast tumor IGF1R regulates cell adhesion and metastasis: alignment of mouse single cell and human breast cancer transcriptomics. Frontiers in Oncology, 12, 990398.

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Single-cell RNA-seq protocol for transcription factor screens

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For screens conducted in mTeSR cells were harvested 5 days after transduction while for alternate media, EGM or ML, cells were harvested 6 days after transduction with the TF library. Cells were dissociated to single cell suspensions using Accutase (Innovative Cell Technologies). For samples sorted with magnetically assisted cell sorting (MACS), cells were labelled with anti-TRA-1–60 antibodies or with dead cell removal microbeads and sorted as per manufacturer’s instructions (Miltenyi Biotec). Samples were then resuspended in 1XPBS with 0.04% BSA at a concentration between 600–2000 per μl. Samples were loaded on the 10X Chromium system and processed as per manufacturer’s instructions (10X Genomics). Unused cells were centrifuged at 300 ref for 5 minutes and stored as pellets at −80 °C until extraction of genomic DNA.
Single cell libraries were prepared as per the manufacturer’s instructions using the Single Cell 3’ Reagent Kit v2 (10X Genomics). Prior to fragmentation, a fraction of the sample post-cDNA amplification was used to amplify the transcripts containing both the TF barcode and cell barcode. Single cell RNA-seq libraries and barcode amplicons were sequenced on an Illumina HiSeq platform.

Parekh U., Wu Y., Zhao D., Worlikar A., Shah N., Zhang K, & Mali P. (2018). Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single Cell RNA-Sequencing Readout. Cell systems, 7(5), 548-555.e8.

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Single-cell multiome analysis using 10X Chromium

Cited 1 time

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Single-cell multiome analysis was conducted using a 10X Chromium system (10X Genomics, Inc). Cryopreserved cells were thawed and washed as previously described.^{18 (link)} The cell suspensions were processed into RNA and ATAC libraries using the manufacturers standard protocol (Supplementary Materials). The resulting ATAC and cDNA libraries were sequenced separately, cDNA library for 28 bp and 91 bp paired-end and ATAC library for 50 bp paired-end sequencing on a NovaSeq 6000 (Illumina).

Johnson T.S., Sudha P., Liu E., Blaney P., Morgan G., Chopra V.S., Santos C.D., Nixon M., Huang K., Suvannasankha A., Zaid M.A., Abonour R, & Walker B.A. (2023). Identifying 1q amplification and PHF19 expressing high-risk cells associated with relapsed/refractory multiple myeloma. Research Square.

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Performing Single-Cell RNA-Seq Analysis

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After FACS, total cell concentration and viability were ascertained using a TC20 Automated Cell Counter (Bio-Rad). Samples were resuspended in 1XPBS with 10% bovine serum albumin (BSA) at a concentration between 8E²-3E³ cells per ml. Samples were loaded on the 10 X Chromium system and processed as per manufacturer’s instructions (10 X Genomics). Single-cell libraries were prepared per the manufacturer’s instructions using the Single Cell 3’ Reagent Kit v2 (10 X Genomics). Single-cell RNA-seq libraries and barcode amplicons were sequenced on an Illumina HiSeq2500 platform.

Sahai-Hernandez P., Pouget C., Eyal S., Svoboda O., Chacon J., Grimm L., Gjøen T, & Traver D. (2023). Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence. eLife, 12, e58300.

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Single-cell RNA-seq of Rat Cell Nuclei

Cited 1 time

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RIN14B cells were put on ice, washed with chilled PBS, and then lysed with chilled Nuclei EZ lysis buffer (Sigma-Aldrich, NUC-101). Single cells were isolated with a 40 µm filter and pelleted in a centrifuge for 8 min, 800 rcf, 4°C. The nuclei were resuspended using PBS with 1% BSA and counted using a hemocytometer with trypan blue viability dye. The nuclei were centrifuged and resuspended at an appropriate volume for the 10X Chromium system (10X Genomics). The nuclei were counted once more to check the number and quality before proceeding with 10X Chromium processing and library construction as per the manufacturer’s instructions. Next Gen sequencing with a Chromium V2 chemistry was carried out on an Illumina NextSeq 500. Illumina NextSeq 500 pre-mRNA sequencing data were aligned to the Rattus norvegicus genome using CellRanger. The data were then analyzed with Seurat V3.0 as described previously (Butler et al., 2018 (link)).

Nickolls A.R., O'Brien G.S., Shnayder S., Zhang Y., Nagel M., Patapoutian A, & Chesler A.T. (2022). Reevaluation of Piezo1 as a gut RNA sensor. eLife, 11, e83346.

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Comprehensive Single-Cell B Cell Profiling

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VDJ, 5’, and probe feature libraries were prepared using the 10X Chromium System (10X Genomics, Pleasanton, CA). The Chromium Single Cell 5’ Library and Gel Bead v2 Kit, Human B Cell V(D)J Enrichment Kit, and Feature Barcode Library Kit were used. All steps were followed as listed in the manufacturer’s instructions. Specifically, user guide CG000186 Rev D was used. Final libraries were pooled and sequenced using the NextSeq550 (Illumina, San Diego, CA) with 26 cycles apportioned for read 1, 8 cycles for the i7 index, and 134 cycles for read 2.

Stamper C.T., Dugan H.L., Li L., Asby N.W., Halfmann P.J., Guthmiller J.J., Zheng N.Y., Huang M., Stovicek O., Wang J., Madariaga M.L., Shanmugarajah K., Jansen M.O., Amanat F., Stewart I., Changrob S., Utset H.A., Huang J., Nelson C.A., Dai Y.N., Hall P.D., Jedrzejczak R.P., Joachimiak A., Krammer F., Fremont D.H., Kawaoka Y, & Wilson P.C. (2020). Distinct B cell subsets give rise to antigen-specific antibody responses against SARS-CoV-2. Research Square.

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Single-cell RNA-seq library preparation

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After sorting, cells were washed once with ice-cold PBS containing 10% FBS post-sorting and counted using hemocytometer. After that, the cells were loaded to 10X Chromium system (10X Genomics, San Francisco, CA) and run through the library preparation following guidance from the Chromium Single Cell 3’ Reagent Kits v2. The libraries were quantified using NEBNext Library Quant Kit (NEW ENGLAND Biolabs, Ipswich, MA) and sequenced via Illumina NextSeq 550 (Illumina, San Diego, CA).

Yang C., Siebert J.R., Burns R., Zheng Y., Mei A., Bonacci B., Wang D., Urrutia R.A., Riese M.J., Rao S., Carlson K.S., Thakar M.S, & Malarkannan S. (2020). Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature. eLife, 9, e51339.

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Single-cell dissociation of brain organoids

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Single cell dissociation was performed by pooling two organoids for each condition: 55-day H9 telencephalic organoids, 27-day H1 ChP, 46-day H1 ChP, and 53-day H1 ChP. Dissociated cells were resuspended in 0.04% BSA in PBS to load 16,000 cells on the 10X Chromium system (10X Genomics). Detailed methods for single cell RNA sequencing, bioinformatic analysis and comparison with in vivo datasets are included in the supplementary material.

Pellegrini L., Bonfio C., Chadwick J., Begum F., Skehel M, & Lancaster M.A. (2020). Human CNS barrier-forming organoids with cerebrospinal fluid production. Science (New York, N.Y.), 369(6500), eaaz5626.

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