Genomics platform

Manufactured by 10x Genomics

Sourced in United States

The 10x Genomics platform is a laboratory instrument designed for high-throughput genomic analysis. It utilizes microfluidic technology to encapsulate individual cells or nuclei in gel beads, enabling the parallel processing and analysis of thousands of samples simultaneously. The core function of the 10x Genomics platform is to facilitate the isolation, barcoding, and sequencing of genetic material from a large number of samples, allowing for comprehensive genomic profiling and insights.

Automatically generated - may contain errors

Lab products found in correlation

Novaseq 6000, by Illumina (5 mentions) Genomics chromium controller, by 10x Genomics (2 mentions) Cell ranger 3, by 10x Genomics (2 mentions) Polybrene, by Merck Group (1 mentions) Visium spatial platform, by 10x Genomics (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) S3e cell sorter, by Bio-Rad (1 mentions) Anti cd45 fitc, by BioLegend (1 mentions) Liberase, by Roche (1 mentions) Novaseq 6000 sp platform, by Illumina (1 mentions) Chromium single cell 5 library gel bead kit v2, by 10x Genomics (1 mentions) Novaseq 6000 sequencer, by Illumina (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Chromium single cell 3 reagent kit v3, by 10x Genomics (1 mentions) Nextseq, by Illumina (1 mentions) Cell ranger software, by 10x Genomics (1 mentions) Novaseq 6000 system, by Illumina (1 mentions) Single cell 3 library kit v3, by 10x Genomics (1 mentions) Cell ranger pipeline, by 10x Genomics (1 mentions) Gentlemacs dissociator, by Miltenyi Biotec (1 mentions)

Spelling variants of this product

10X Genomics Chromium platform (26 citations) 10x Genomics Visium platform (2 citations)

30 protocols using genomics platform

Single-cell RNA-seq of HIV-infected MDMs

Check if the same lab product or an alternative is used in the 5 most similar protocols

MDMs (2 × 10⁶) were spinoculated with A‐MLV‐pseudotyped DHIV3‐mCherry (MOI of 2) in the presence of 10 μg/mL polybrene (Millipore) for 2 h at room temperature. MDMs were washed 4–5 times with PBS to remove unbound virus and cultured in growth medium for 7 days. At day 7 postinfection, MDMS were gently detached from plates and resuspended at 1000 cells/μl in PBS with 0.4% BSA. scRNAseq was performed on the 10× Genomics platform using the 5′ Gene Expression reagent kit according to the manufacturer's instructions. Gene expression libraries were sequenced on the NovaSeq 6000 Illumina platform to obtain 150‐bp paired‐end reads at a depth of 200 million total read pairs. The raw gene sequencing data were processed using the 10x Genomics Cell Ranger software (v3.1.0) and analyzed using Loupe Browser 5.0 (10× Genomics). Data were further analyzed using databases available through Interferome.org with the following settings: IFN type: I, II, and III; subtype: all; treatment concentration: any; treatment time: any; in vivo/in vitro: all; species: human; system: hematopoietic/immune; organ: all; cell: all; cell lines: all; sample types: any.

Dickey L.L., Martins L.J., Planelles V, & Hanley T.M. (2022). HIV‐1‐induced type I IFNs promote viral latency in macrophages. Journal of Leukocyte Biology, 112(5), 1343-1356.

+ Open protocol

+ Expand

Multimodal Profiling of Colorectal Cancer

Check if the same lab product or an alternative is used in the 5 most similar protocols

Paired tumours and adjacent normal tissues from six MCA patients were fresh‐processed for scRNA‐seq. In practice, fresh normal mucosa and MCA tissue were washed with ice‐cold PBS and minced into small pieces. Then, the normal and tumour tissue pieces were digested with collagenase VIII at 0.38 mg/mL and DNase I at 0.1 mg/mL in 30% FBS for 1.0 h at 37°C. After digestion, tissue pieces were washed with PBS and processed according to the sample preparation instructions of the 10× Genomics platform. Moreover, one MCA tumour tissue sample and it's corresponding normal sample were fresh‐processed for spatial transcriptomics. The fresh tissue was first embedded through optical coherence tomography (OCT). Then, the tissue was cut into 10 μm sections in a cryostat and prepared based on the instructions of the Visium Spatial platform of 10x Genomics. In addition, twelve samples from six MCA patients were processed for multiplexed immunofluorescence. Three tissue microarray blocks that consisted of tumour and adjacent non‐tumour tissues from ninety MCA patients were analyzed by immunohistochemistry.

Zhou H., Shen Y., Zheng G., Zhang B., Wang A., Zhang J., Hu H., Lin J., Liu S., Luan X, & Zhang W. (2024). Integrating single‐cell and spatial analysis reveals MUC1‐mediated cellular crosstalk in mucinous colorectal adenocarcinoma. Clinical and Translational Medicine, 14(5), e1701.

+ Open protocol

+ Expand

Single-cell profiling of early-stage LUAD

Check if the same lab product or an alternative is used in the 5 most similar protocols

Five patients undergoing surgical resection for primary early-stage LUAD (I-IIIA) were carefully selected for the derivation of two to three uninvolved normal lung samples for single-cell analysis (n = 19 samples, Table S1). Samples were obtained from banked or residual specimens from patients evaluated at the University of Texas MD Anderson Cancer Center. Following tissue digestion and red blood cell removal, cells were sorted (by fluorescent-activated cell sorting) into viable singlets and, in samples from Patients 2 to 5, into separate viable epithelial (EPCAM+) and nonepithelial (EPCAM−) fractions. Single-cell gene expression libraries were generated from 35 sorted fractions using the 10× Genomics platform (Pleasanton, CA, USA) and sequenced on the Illumina NovaSeq 6000 platform (San Diego, CA, USA; Online Data Supplement).

Han G., Sinjab A., Hara K., Treekitkarnmongkol W., Brennan P., Chang K., Bogatenkova E., Sanchez-Espiridion B., Behrens C., Solis L.M., Gao B., Girard L., Zhang J., Sepesi B., Cascone T., Byers L.A., Gibbons D.L., Chen J., Moghaddam S.J., Ostrin E.J., Scheet P., Fujimoto J., Shay J., Heymach J.V., Minna J.D., Dubinett S., Wistuba I.I., Stevenson C.S., Spira A.E., Wang L, & Kadara H. (2021). Single-Cell Expression Landscape of SARS-CoV-2 Receptor ACE2 and Host Proteases in Normal and Malignant Lung Tissues from Pulmonary Adenocarcinoma Patients. Cancers, 13(6), 1250.

+ Open protocol

+ Expand

Single-cell RNA-seq of mouse epididymal immune cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

scRNA-seq was performed using a 10 × Genomics™ platform (10x Genomics, Pleasanton, California, USA) according to the manufacturer’s protocol (www.10xgenomics.com). Briefly, each batch of 10,000 single cells of epididymal IS pooled from four young and four old mice was loaded on a microfluidic chip to form the gel bead-in-emulsions reaction system. Constructed libraries were sequenced on an Illumina NovaSeq 6000 sequencing platform (Illumina Inc., San Diego, CA, USA) with a paired-end 150 bp read length.

Zhuang J., Li X., Yao J., Sun X., Liu J., Nie H., Hu Y., Tu X., Liu H., Qin W, & Xie Y. (2023). Single-cell RNA sequencing reveals the local cell landscape in mouse epididymal initial segment during aging. Immunity & Ageing : I & A, 20, 21.

+ Open protocol

+ Expand

Kidney Single-Cell Isolation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

The whole kidneys were minced and digested in 2 mL of Liberase (Roche) in RPMI-1640 medium at 37°C for 20 minutes. The resulting single-cell suspensions were filtered sequentially through 70 μm and 40 μm meshes before being incubated with FITC anti-CD45 (103108, BioLegend); cell viability was determined by exclusion of 7-aminoactinomycin (7-AAD, 00-6993-50, Thermo Fisher Scientific). These mixtures of living cells (CD45⁺/all cells = 1:4) sorted using the S3e Cell Sorter (Bio-Rad) were loaded onto a microfluidic chip by Berry Genomics, and a cDNA library was generated using the 10× Genomics platform (10× Genomics).

Wang W., Ren X., Chen X., Hong Q, & Cai G. (2024). Integrin β1–rich extracellular vesicles of kidney recruit Fn1+ macrophages to aggravate ischemia-reperfusion–induced inflammation. JCI Insight, 9(2), e169885.

+ Open protocol

+ Expand

Single-Cell RNA-Seq Analysis of Periodontitis

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

scRNA-seq was performed in a subset of the gingival tissue samples harvested. Specifically, periodontitis-affected and healthy gingival samples (one each) from three periodontitis patients were sequenced using a 10× Genomics platform (10× Genomics, San Francisco, CA, USA) as described.^{13 (link)} In addition, the gene raw counts and normalized gene expression matrix for previously reported single-cell analysis of periodontitis-affected and healthy gingival samples from two periodontitis patients and two periodontally healthy subjects, respectively, were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/).^{14 (link)}

Agrafioti P., Morin-Baxter J., Tanagala K.K., Dubey S., Sims P., Lalla E, & Momen-Heravi F. (2022). Decoding the role of macrophages in periodontitis and type 2 diabetes using single-cell RNA-sequencing. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 36(2), e22136.

+ Open protocol

+ Expand

Single-cell RNA-seq of Skin and Blood Immune Cells

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Single leucocyte suspensions were prepared from skin via enzymatic digestion and from whole blood using a Ficoll-Paque gradient, as previously described in detail.^{18 (link)} For sc-RNA-seq using the 10X Genomics platform (10X Genomics, Pleasanton, CA, USA), CD45⁺ live cells were sorted into phosphate-buffered saline (PBS)/10% fetal calf serum for library preparation with the Chromium™ Single Cell 5′ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s instructions. Briefly, sorted cells were partitioned into single-cell GEMs (Gel beads in EMulsion droplets) for cDNA synthesis and subsequently amplified and prepared for sequencing. The samples were sequenced at the Biomedical Sequencing Facility on the Illumina NovaSeq 6000 SP platform (Illumina, San Diego, CA, USA) in the 50-bp paired-end configuration. Raw sequencing data were processed as described below.

Strobl J., Gail L.M., Krecu L., Madad S., Kleissl L., Unterluggauer L., Redl A., Brazdilova K., Saluzzo S., Wohlfarth P., Knaus H.A., Mitterbauer M., Rabitsch W., Haniffa M, & Stary G. (2023). Diverse macrophage populations contribute to distinct manifestations of human cutaneous graft-versus-host disease. The British Journal of Dermatology, 190(3), 402-414.

+ Open protocol

+ Expand

Single-cell RNA-seq with 10x Genomics

Check if the same lab product or an alternative is used in the 5 most similar protocols

Single-cell gene expression profiling was performed using the 10x Genomics platform according to the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA). FACS sorted cells were captured in droplets that were emulsified with gel beads containing barcoded primers (https://www.nature.com/articles/ncomms14049). Single-cell expression libraries were prepared using the 10x genomics Chromium single-cell 3′ library and gel bead kit v3 reagents (10x Genomics, PN-1000075). Briefly, suspension containing 4,000–10,000 single cells were loaded into the 10x single-cell A chip and processed in the 10x Chromium controller. After reverse transcription, cDNAs were amplified by 12–14 PCR cycles. An aliquot of 10 ul cDNA product was then used for library construction, which included 14 cycles of sample index PCR to barcode samples. The quality of the cDNA library was checked by the Bioanalyzer (Agilent). KAPA qPCR was performed to measure the library quantities. A pool of all quantity-balanced libraries was then sequenced on the NovaSeq 6000 sequencer (Illumina) at an average sequencing depth of 45,889 reads/cell (post normalization). The single-cell RNA-sequencing steps were performed by the Genomics Resources Core Facility at Weill Cornell Medicine, New York.

Zhan L., Fan L., Kodama L., Sohn P.D., Wong M.Y., Mousa G.A., Zhou Y., Li Y, & Gan L. (2020). A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brain. eLife, 9, e51796.

+ Open protocol

+ Expand

Single-cell transcriptome profiling via 10x Genomics

Check if the same lab product or an alternative is used in the 5 most similar protocols

After droplet-based single-cell capture via the 10x Genomics platform, single-cell gene expression libraries were generated using the Chromium single cell 3′ reagent kit v3 (10x Genomics). To assess library quality, traces were analyzed traces using the LapChip GC Touch HT. Sequencing was performed on an Illumina NovaSeq 6000 at a target depth of 100,000 reads per cell with paired-end 75 bp reads. All steps for library preparation and sequencing were performed by the GRC at UMSOM IGS.

Rose K.P., Manilla G., Milon B., Zalzman O., Song Y., Coate T.M, & Hertzano R. (2023). Spatially distinct otic mesenchyme cells show molecular and functional heterogeneity patterns before hearing onset. iScience, 26(10), 107769.

+ Open protocol

+ Expand

Single-cell transcriptomics of human colon and tumor

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Paired human colon and tumour biopsies were obtained and made into single-cell suspensions. Cells were encapsulated into droplets and libraries prepared using the 10x Genomics platform, and libraries were sequenced on an Illumina NextSeq. BCL files were demultiplexed, aligned to mouse mm10 genome, filtered and unique molecular identifier-counted using CellRanger software (10x Genomics). Then downstream analysis was performed with Seurat v.3. Data were filtered to remove cells with high mitochondrial reads (>15%), low gene detection (<200) and high gene detection (>5,000). Normalization was performed with SCTransform and integrated. Subsequently, cells were clustered using Louvain clustering (0.5 resolution), and UMAP was used for visualization (assay, ‘SCT’; dims, 1:30). After normalization and clustering, we used adaptively thresholded low rank approximation^{36 (link)} to impute the RNA count matrix and fill in technical dropouts. Cells were then partitioned into epithelial, stromal and immune compartments based on expression of previously described marker genes in human colon single-cell RNA-seq data. The epithelial population for analysis of HOPX expression was positively selected for epithelial markers and negatively selected for markers of other populations. Cycling epithelial cells were identified by cell cycle scoring with canonical markers^{37 (link)–40 (link)}.

Dmitrieva-Posocco O., Wong A.C., Lundgren P., Golos A.M., Descamps H.C., Dohnalová L., Cramer Z., Tian Y., Yueh B., Eskiocak O., Egervari G., Lan Y., Liu J., Fan J., Kim J., Madhu B., Schneider K.M., Khoziainova S., Andreeva N., Wang Q., Li N., Furth E.E., Bailis W., Kelsen J.R., Hamilton K.E., Kaestner K.H., Berger S.L., Epstein J.A., Jain R., Li M., Beyaz S., Lengner C.J., Katona B.W., Grivennikov S.I., Thaiss C.A, & Levy M. (2022). β-Hydroxybutyrate suppresses colorectal cancer. Nature, 605(7908), 160-165.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!