Genomics chromium controller instrument

Manufactured by 10x Genomics

Sourced in United States

The 10X Genomics Chromium Controller Instrument is a laboratory device designed to automate the partitioning of single cells or nuclei into nanoliter-scale droplets. It is used to prepare samples for downstream genomic analysis by 10X Genomics' Chromium platforms.

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Lab products found in correlation

Bioanalyzer 2200, by Agilent Technologies (10 mentions) Qubit high sensitivity dna assay, by Thermo Fisher Scientific (9 mentions) Chromium single cell 3 v3.1 reagent kit, by 10x Genomics (7 mentions) Chromium single cell 3 reagent kit v3, by 10x Genomics (4 mentions) Hiseq x ten, by Illumina (3 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) D5000 dna screen tape analysis, by Agilent Technologies (2 mentions) Nextseq 500, by Illumina (1 mentions) High output v2 kit, by Illumina (1 mentions) Hiseq 4000, by Illumina (1 mentions) Novaseq, by Illumina (1 mentions) Fluorescence cell analyzer, by Countstar (1 mentions) Dsdna hs assay kit, by Agilent Technologies (1 mentions) Agilent 2100 bioanalyzer high sensitivity dna kit, by Agilent Technologies (1 mentions) Novaseq 6000, by Illumina (1 mentions) Novaseq 6000 sequencer, by Illumina (1 mentions) Chromium single cell 5 library gel bead kit, by 10x Genomics (1 mentions) Chromium single cell 5 v2 reagent kit, by 10x Genomics (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Chromium single cell 3 reagent kit v2, by 10x Genomics (1 mentions)

Close spelling variants of this product

Chromium Controller (506 citations) Chromium instrument (59 citations) Chromium Controller instrument (38 citations) 10x Genomics Chromium Controller (24 citations) 10x Genomics Chromium (12 citations) 10x Genomics Chromium instrument (8 citations) 10x Genomics Controller (2 citations) 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3′ V3 Reagent Kits (2 citations)

22 protocols using genomics chromium controller instrument

Single-cell RNA-seq Library Preparation

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The scRNA-seq libraries were generated using the 10× Genomics Chromium Controller Instrument and Chromium Single Cell 3′ V3 Reagent Kits (10× Genomics). Briefly, cells were concentrated to 1,000 cells/μL and approximately 8,000–10,000 cells were loaded into each channel to generate single-cell gel bead-in-emulsions (GEM), which resulted in the expected mRNA barcoding of 3,000–8,000 single cells for each sample. After the reverse transcription step, GEMs were broken and barcoded cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using a Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of these libraries was determined by a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were then sequenced by an Illumina sequencer (Illumina) on a 150 bp paired-end run.

Xu J., Fang Y., Chen K., Li S., Tang S., Ren Y., Cen Y., Fei W., Zhang B., Shen Y, & Lu W. (2022). Single-Cell RNA Sequencing Reveals the Tissue Architecture in Human High-Grade Serous Ovarian Cancer. Clinical Cancer Research, 28(16), 3590-3602.

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High-Molecular-Weight DNA Sequencing

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Visayan warty pig’s genomic DNA was size selected for fragments >40 kb on a BluePippin instrument (Sage Sciences, Beverly, MA, USA) and Illumina sequencing libraries were constructed using the 10× Genomics Chromium Controller instrument with the Genome Reagents Kit v2 chemistry (10× Genomics, Pleasanton, CA, USA) according to the manufacturer’s recommendations. The resulting Illumina library was sequenced on a NextSeq500 using a High Output Kit v2 for paired-end, 2 × 151 bp run (Illumina, San Diego, CA, USA).

Liu L., Megens H.J., Crooijmans R.P., Bosse M., Huang Q., van Sonsbeek L., Groenen M.A, & Madsen O. (2022). The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs. Molecular Biology and Evolution, 39(6), msac110.

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Single-Cell RNA Sequencing of Cells and Clusters

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Single cells or Clusters were captured using the 10× Genomics Chromium Controller Instrument (10× Genomics, Pleasanton, CA) and ChromiumTM Single Cell 30 Reagent Kits v1 or v2 according to manufacturer’s instructions. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified (14 PCR cycles) on the operative day. Subsequently, the cDNA was fragmented, A-tailed and ligated with adaptors. Finally, ten and 14 cycles of PCR amplification for the single cell and cluster derived libraries was performed to enable sample indexing. The libraries were sequenced on an Illumina HiSeq 4000 or NovaSeq instruments. Information on the number of single cells or Clusters captured, total cDNA yield as well as number of reads per cell or cluster can be found in Supplementary Fig. 1b.

Sanchez-Ferras O., Pacis A., Sotiropoulou M., Zhang Y., Wang Y.C., Bourgey M., Bourque G., Ragoussis J, & Bouchard M. (2021). A coordinated progression of progenitor cell states initiates urinary tract development. Nature Communications, 12, 2627.

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Single-cell 3' RNA-seq library prep

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The snRNA-seq libraries were built using the 10× Genomics Chromium Controller Instrument (PN-120223, 10×Genomics) and chromium single-cell 3′ V3.1 reagent kits (PN-1000121, 10× Genomics). Please refer to manufacturer's instructions.

Yang Q., Zhang L., Li M., Xu Y., Chen X., Yuan R., Ou X., He M., Liao M., Zhang L., Dai H., Lv M., Xie X., Liang W, & Chen X. (2023). Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury. Genome Research, 33(10), 1818-1832.

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Single-cell RNA-seq analysis of mouse liver

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As described previously, mouse livers were digested to obtain single-cell suspensions A [20 (link)]. Dissociated single cells were stained with AO/PI for viability assessment using a Countstar Fluorescence Cell Analyzer. The scRNA-seq libraries were generated using the 10× Genomics Chromium Controller Instrument and Chromium Single Cell 3’V3.1 Reagent Kits (10× Genomics, Pleasanton, CA, USA) according to the recommendations of the manufacturer. scRNA-seq data analysis, including cell communication analysis, quantitative set analysis of gene expression (QuSAGE) analysis, and pathway analysis were performed by NovelBio Bio-Pharm Technology Co., Ltd., using the NovelBrain Cloud Analysis Platform as previous procedures [29 (link)–32 (link)]. To characterize the relative activation of a given gene set, such as pathway activation, we performed QuSAGE analysis, in which gene sets, including ferroptosis, described previously, were added. Pathway analysis was used to identify the significant pathways of the marker genes and differentially expressed genes according to the kyoto encyclopedia of genes and genomes (KEGG) database. Fisher’s exact test was used to select significant pathways, and the threshold of significance was defined by the P-value and false discovery rate (FDR).

Jia K.W., Yao R.Q., Fan Y.W., Zhang D.J., Zhou Y., Wang M.J., Zhang L.Y., Dong Y., Li Z.X., Wang S.Y., Wang M., Li Y.H., Zhang L.X., Lei T., Gui L.C., Lu S., Yang Y.Y., Wang S.X., Yu Y.Z., Yao Y.M, & Hou J. (2024). Interferon-α stimulates DExH-box helicase 58 to prevent hepatocyte ferroptosis. Military Medical Research, 11, 22.

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Single-Cell RNA-Seq Library Preparation and Sequencing

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ScRNA-seq libraries were generated from each time point using the 10× Genomics Chromium Controller
Instrument (10× Genomics, Pleasanton, CA) and Chromium^™ Single Cell 3’ Reagent Kits v1
(65,781 cells experiment) and v2 (259,155 cells experiment) according to manufacturer’s instructions. Reverse
transcription and sample indexing were performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module.
Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel
Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified
barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable
sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher
Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent
2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing. All
samples were sequenced to an average depth of 87 million paired-end reads per sample (see Experimental Methods), with 98 bp on the first read and 10 bp on the second read. In the larger experiment, we
profiled 259,155 cells to an average depth of 46,523 reads per cell.

Schiebinger G., Shu J., Tabaka M., Cleary B., Subramanian V., Solomon A., Gould J., Liu S., Lin S., Berube P., Lee L., Chen J., Brumbaugh J., Rigollet P., Hochedlinger K., Jaenisch R., Regev A, & Lander E.S. (2019). Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming. Cell, 176(4), 928-943.e22.

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Single-cell RNA Sequencing Protocol

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The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3′ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA). Concentrated cells to ~1 000 cells/μL. Then loaded the cells into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). The RT step broke GEMs and the barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adapters and index PCR amplified. Quantified the final libraries by using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and determined the size distribution of the libraries by using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). Sequenced all libraries by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

Zhang X., Xiao Y., Hu B., Li Y., Zhang S., Tian J., Wang S., Tao Z., Zeng X., Liu N.N., Li B, & Liu S. (2024). Multi-omics analysis of human tendon adhesion reveals that ACKR1-regulated macrophage migration is involved in regeneration. Bone Research, 12, 27.

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scRNA-seq Library Generation with 10X Chromium

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The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3′ V3 Reagent Kits (10X Genomics, Pleasanton, CA).⁵⁸ (link) Briefly, the cell concentration was adjusted to 1000 cells/uL. Then, the single-cell Gel Bead-In-Emulsions (GEMs) were generated after loading more than 8,000 cells into each channel. Barcoded-cDNA was purified and amplified in the RT step after breaking the GEMs. The amplified barcoded cDNA was modified (Fragmentation, A-tailing, and linking with adaptors) and index PCR amplified. The final libraries were quantified and were analyzed the size distribution by the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). Subsequently, all libraries were sequenced using HiSeq Xten (Illumina, San Diego, CA).

Liao J., Wang J., Xu Y., Wu Y., Wang M., Zhao Q., Tan X., Meng Y., Wei L, & Huang A. (2023). LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma. iScience, 26(6), 106754.

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Single-cell RNA-sequencing Library Preparation

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The scRNA-Seq libraries were generated through the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA, USA). Briefly, cells were concentrated to 1000 cells/µL and approximately 8000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 6000 single cells for each sample. After the RT step, GEMs were broken and barcoded cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA), and the size distribution of the libraries was determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by Illumina sequencer (Illumina, San Diego, CA, USA) on a 150-bp paired-end run.

Shi J.W., Lai Z.Z., Yang H.L., Zhou W.J., Zhao X.Y., Xie F., Liu S.P., Chen W.D., Zhang T., Ye J.F., Zhou X.Y, & Li M.Q. (2022). An IGF1-expressing endometrial stromal cell population is associated with human decidualization. BMC Biology, 20, 276.

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High-throughput Single-cell RNA Sequencing

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The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA). Cells were concentrated to approximately 1000 cells/uL. Single-cell Gel Bead-In-Emulsions (GEMs) were generated by loading the cells into each channel. GEMs were subsequently ruptured by an RT step, followed by purification and amplification of the barcoded-cDNA. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries was determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). Lastly, all libraries were sequenced on an Illumina sequencer (Illumina, San Diego, CA) using a 150 bp paired-end run (Fig. S9).

Pang S., Wu R., Lv W., Zou J., Li Y., Li Y., Zhang P., Ma X., Wang Y, & Liu S. (2024). Use of a pH-responsive imatinib mesylate sustained-release hydrogel for the treatment of tendon adhesion by inhibiting PDGFRβ/CLDN1 pathway. Bioactive Materials, 38, 124-136.

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