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Chromium chip a

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The Chromium Chip A is a microfluidic device designed for use with the Chromium Controller instrument from 10x Genomics. The chip provides the necessary compartments and channels for encapsulating individual cells or nuclei into gel beads, which is a key step in the Chromium workflow for single-cell analysis.

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Lab products found in correlation

Countess 2 automated cell counter, by Thermo Fisher Scientific (3 mentions) Chromium single cell 5 reagent kit, by 10x Genomics (3 mentions) Novaseq 6000, by Illumina (1 mentions) Novaseq 6000, by Agilent Technologies (1 mentions) Nextseq 500 550 high output kit v2, by Illumina (1 mentions) Novaseq 6000 sp reagent kit, by Illumina (1 mentions) Bioanalyzer high sensitivity dna kit, by Agilent Technologies (1 mentions) Novaseq 6000 sequencing system, by Illumina (1 mentions)

Spelling variants of this product

Chromium Single Cell A Chip Kit (36 citations) Chromium Single Cell A Chip (16 citations) Chromium chip (15 citations)

5 protocols using chromium chip a

1

Single-cell RNA-seq of Activated T Cells

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Sorted T cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 2,700–11,000 cells proceeded using the Chromium Single Cell 5′ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 13–14 cycles and 11–50ng of the material was used to prepare sequencing libraries with 14–16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 or NextSeq 500 in a PE26/92, PE28/91 or PE100 run using the NovaSeq 6000 SP, S1, or S2 Reagent Kit (100, 200, or 500 cycles) or TG NextSeq 500/550 High Output Kit v2.5 (150 cycles) (Illumina). An average of 179 million reads was generated per sample.
Pai J.A., Hellmann M.D., Sauter J.L., Mattar M., Rizvi H., Woo H.J., Shah N., Nguyen E.M., Uddin F.Z., Quintanal-Villalonga A., Chan J.M., Manoj P., Allaj V., Baine M.K., Bhanot U.K., Jain M., Linkov I., Meng F., Brown D., Chaft J.E., Plodkowski A.J., Gigoux M., Won H.H., Sen T., Wells D.K., Donoghue M.T., de Stanchina E., Wolchok J.D., Loomis B., Merghoub T., Rudin C.M., Chow A, & Satpathy A.T. (2023). Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. Cancer cell, 41(4), 776-790.e7.
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2

Single-Cell RNA Sequencing Sample Preparation

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Cells were resuspended in 50 μl, counted, and loaded on Chromium Chip A (10x Genomics, 5′v3) for cell encapsulation. Complementary DNA libraries were prepared per the manufacturer’s recommendation. After quality checks with Bioanalyzer (Agilent, 2100), the libraries were pooled and sequenced with NovaSeq 6000.
Guo S.A., Bowyer G.S., Ferdinand J.R., Maes M., Tuong Z.K., Gillman E., Liao M., Lindeboom R.G., Yoshida M., Worlock K., Gopee H., Stephenson E., Gao C.A., Lyons P.A., Smith K.G., Haniffa M., Meyer K.B., Nikolić M.Z., Zhang Z., Wunderink R.G., Misharin A.V., Dougan G., Navapurkar V., Teichmann S.A., Conway Morris A, & Clatworthy M.R. (2022). Obesity Is Associated with Attenuated Tissue Immunity in COVID-19. American Journal of Respiratory and Critical Care Medicine, 207(5), 566-576.
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3

Single-cell RNA Sequencing Workflow

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Sorted cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 10,000 cells proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 16 cycles and 21.5-50ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NextSeq 500 in a 26bp/91bp paired end run using the NextSeq 500/550 High Output Kit v2.5 (150 cycles, Illumina). An average of 256 million paired reads was generated per sample.
Chow A., Schad S., Green M.D., Hellmann M.D., Allaj V., Ceglia N., Zago G., Shah N.S., Sharma S.K., Mattar M., Chan J., Rizvi H., Zhong H., Liu C., Bykov Y., Zamarin D., Shi H., Budhu S., Wohlhieter C., Uddin F., Gupta A., Khodos I., Waninger J.J., Qin A., Markowitz G.J., Mittal V., Balachandran V., Durham J.N., Le D.T., Zou W., Shah S.P., McPherson A., Panageas K., Lewis J.S., Perry J.S., de Stanchina E., Sen T., Poirier J.T., Wolchok J.D., Rudin C.M, & Merghoub T. (2021). Tim-4+ Cavity-Resident Macrophages Impair Anti-Tumor CD8+ T cell Immunity. Cancer cell, 39(7), 973-988.e9.
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4

CITE-seq of Cryopreserved Melanoma Samples

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Cryopreserved melanoma patient samples were individually hash-tagged and labeled with the TotalSeq-C human universal cocktail to enable protein detection of genes by cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Sorted T cells were stained with Trypan blue, and Countess II Automated Cell Counter (Thermo Fisher Scientific) was used to assess both cell number and viability. Following QC, the single-cell suspension was loaded onto Chromium Chip A (10X Genomics; PN 230027), and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 5,800–7,000 cells with 57% viability proceeded using the Chromium Single Cell 5′ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 50 ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a 28 bp/91 bp paired end run using the NovaSeq 6000 SP Reagent Kit (100 cycles; Illumina). An average of 273 million paired reads was generated per sample.
Schad S.E., Chow A., Mangarin L., Pan H., Zhang J., Ceglia N., Caushi J.X., Malandro N., Zappasodi R., Gigoux M., Hirschhorn D., Budhu S., Amisaki M., Arniella M., Redmond D., Chaft J., Forde P.M., Gainor J.F., Hellmann M.D., Balachandran V., Shah S., Smith K.N., Pardoll D., Elemento O., Wolchok J.D, & Merghoub T. (2022). Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. The Journal of Experimental Medicine, 219(6), e20212169.
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5

Single Cell RNA-Seq Library Prep Protocol

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17,000 cells per sample were loaded onto a Chromium Chip A (10x Genomics cat. 120236). Single cell gene expression was obtained using the Chromium Single Cell 3’ or 5′ Library & Gel Bead Kit (cat. 120237 or 1000006). Library preparations were performed according to manufacturer’s instructions. Following quality control with a Bioanalyzer High Sensitivity DNA Kit (Agilent), pooled libraries were sequenced on a (Illumina NovaSeq 6000 Sequencing System, RRID:SCR_016387) with 150 bp paired-end reads, and 8 bp for index 1.
Penter L., Gohil S.H., Lareau C., Ludwig L.S., Parry E.M., Huang T., Li S., Zhang W., Livitz D., Leshchiner I., Parida L., Getz G., Rassenti L.Z., Kipps T.J., Brown J.R., Davids M.S., Neuberg D.S., Livak K.J., Sankaran V.G, & Wu C.J. (2021). Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history. Cancer discovery, 11(12), 3048-3063.
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