Log In Sign up
The largest database of trusted experimental protocols

Chromium single cell sorting system

Manufactured by 10x Genomics
Visit Supplier

The Chromium single cell sorting system is a laboratory instrument designed for the high-throughput isolation and processing of individual cells. It facilitates the encapsulation of single cells into nanoliter-scale droplets, enabling the subsequent analysis of gene expression profiles and other cellular characteristics at the single-cell level.

Automatically generated - may contain errors

Lab products found in correlation

Anti mouse cd16 32 fc block, by BD (2 mentions) Totalseq c antibodies, by BioLegend (2 mentions) Lobind, by Eppendorf (1 mentions) Flow cell, by Illumina (1 mentions) Facsaria 3, by BD (1 mentions) Novaseq 6000, by Illumina (1 mentions)

Spelling variants of this product

Chromium system (72 citations)

6 protocols using chromium single cell sorting system

1

Single-Cell RNA-Seq of Activated T Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Activated (CD44+) T cells (TCRβ+) were FACS-sorted from the spleens of control or Trib1 cKO mice at day 15 post-clone 13 infection into 1.5ml Lo-Bind Eppendorf tubes containing complete RPMI (10% FBS). Two biological replicates were pooled for each genotype to create one sample per genotype. 750,000 cells per genotype were sorted, collected, washed twice with RPMI, diluted in RPMI to 1,000 cells/μl, and loaded onto the Chromium single cell sorting system (10x Genomics) with a standard loading targeting 5,000 cells for recovery. Library construction was performed using the Chromium Single Cell 5′ Library & Gel Bead Kit according to the manufacturer’s protocol. The final pooled library (containing control and Trib1 cKO samples) was sequenced on a NextSeq 550 using paired-end sequencing on one high output FlowCell (Illumina).
Rome K.S., Stein S.J., Kurachi M., Petrovic J., Schwartz G.W., Mack E.A., Uljon S., Wu W.W., DeHart A.G., McClory S.E., Xu L., Gimotty P.A., Blacklow S.C., Faryabi R.B., Wherry E.J., Jordan M.S, & Pear W.S. (2020). Trib1 regulates T cell differentiation during chronic infection by restraining the effector program. The Journal of Experimental Medicine, 217(5), e20190888.
+ Open protocol
+ Expand
2

Single-cell RNA sequencing of tumor and spleen

Check if the same lab product or an alternative is used in the 5 most similar protocols
Spleens and tumors from mice that had been boosted one day prior were collected and processed into single cell suspensions by mechanical dissociation. Samples were stained with LIVE/DEAD Fixable Blue Dead Cell Stain Kit for 10 min at room temperature. Then samples were washed with FACS buffer (2% FBS in PBS) and stained with Fc block (Anti-mouse CD16/32, BD Biosciences) prior to addition of a surface stain. The surface stain antibody master mix contained: CD3 BUV395, CD19 BUV395, CD45 BUV661, CD11c PE, and CD11b AF700. Each sample was also stained with a unique hashtag antibody. Samples were incubated in surface stain for 20 minutes at room temperature after which all surface stain antibodies were washed off. Samples were resuspended in FACS buffer and sorted by fluorescence activated cell sorting to isolate the live CD45+ CD11b+ CD11c+ cells. Sorted samples were pooled together by tissue prior to loading in duplicate into a Chromium single cell sorting system (10x Genomics). Expression and hashtag library construction was performed following the Chromium Single Cell VDJ Library protocol with a loading target of 1 × 104 per lane. At the conclusion, there were 4 expression and hash tag libraries from spleen samples and another 4 from tumor samples. The libraries were sequenced on a NovaSeq 6000 S2 chip.
van Dijk K, & Nelson E.B. (2000). Fatty Acid Competition as a Mechanism by Which Enterobacter cloacae Suppresses Pythium ultimum Sporangium Germination and Damping-Off. Applied and Environmental Microbiology, 66(12), 5340-5347.
+ Open protocol
+ Expand
3

Bulk and Single-Cell RNA Sequencing of T Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
For bulk RNA sequencing, sample cDNA libraries were prepared following poly-A selection to enrich for mRNA and then sequenced as 150 bp paired-end reads on a NovaSeq 6000 (Illumina). For scRNA-seq, tumors and spleens were processed into single cell suspension. Biological replicates (n=10) for each experimental condition were pooled together at the tissue processing stage. Around 5000 live CD3+CD8+P1A35-43- LPYLGWLVF+ cells from each condition were sorted by fluorescence activated cell sorting using a BD FACSAria III (BD Biosciences). Sorted cells from each experimental condition were loaded into a Chromium single-cell sorting system (10× Genomics). Single-cell RNA libraries were prepared using 10× Genomics Chromium platform and reagents according to the manufacturer’s instructions by the Oxford Genomics Centre, University of Oxford. Details of sequencing data analysis are described in the online supplemental materials.
McAuliffe J., Chan H.F., Noblecourt L., Ramirez-Valdez R.A., Pereira-Almeida V., Zhou Y., Pollock E., Cappuccini F., Redchenko I., Hill A.V., Leung C.S, & Van den Eynde B.J. (2021). Heterologous prime-boost vaccination targeting MAGE-type antigens promotes tumor T-cell infiltration and improves checkpoint blockade therapy. Journal for Immunotherapy of Cancer, 9(9), e003218.
+ Open protocol
+ Expand
4

Immune Cell Profiling of Mouse Spleen and Tumor

Check if the same lab product or an alternative is used in the 5 most similar protocols
Spleens and tumors from mice that had been boosted one day prior were collected and processed into single cell suspensions by mechanical dissociation. Samples were stained with LIVE/DEAD Fixable Blue Dead Cell Stain Kit for 10 min at room temperature. Then samples were washed with FACS buffer (2% FBS in PBS) and stained with Fc block (Anti-mouse CD16/32, BD Biosciences) prior to addition of a surface stain. The surface stain antibody master mix contained: CD3 BUV395, CD19 BUV395, CD45 BUV661, CD11c PE, and CD11b AF700. Each sample was also stained with a unique hashtag antibody. Samples were incubated in surface stain for 20 minutes at room temperature after which all surface stain antibodies were washed off. Samples were resuspended in FACS buffer and sorted by fluorescence activated cell sorting to isolate the live CD45+ CD11b+ CD11c+ cells. Sorted samples were pooled together by tissue prior to loading in duplicate into a Chromium single cell sorting system (10x Genomics). Expression and hashtag library construction was performed following the Chromium Single Cell VDJ Library protocol with a loading target of 1 × 104 per lane. At the conclusion, there were 4 expression and hash tag libraries from spleen samples and another 4 from tumor samples. The libraries were sequenced on a NovaSeq 6000 S2 chip.
Baharom F., Ramirez-Valdez R.A., Khalilnezhad A., Khalilnezhad S., Dillon M., Hermans D., Fussell S., Tobin K.K., Dutertre C.A., Lynn G.M., Müller S., Ginhoux F., Ishizuka A.S, & Seder R.A. (2022). Systemic vaccination induces CD8+ T cells and remodels the tumor microenvironment. Cell, 185(23), 4317-4332.e15.
+ Open protocol
+ Expand
5

Transcriptomic Analysis of Mouse Splenocytes

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Spleens from mice vaccinated with SNP via SC or IV injections were collected 2 weeks post boost and processed into a single cell suspension by mechanical dissociation. Splenocytes were stained with Reps1 tetramer and hashtag antibodies (Biolegend Total-Seq-C antibodies 1–5)52 (link). CD8+ T were isolated by fluorescence activated cell sorting (FACS) into 1.5 mL Eppendorf tubes containing staining buffer (2% FBS/PBS). Up to 4×104 cells were sorted per mouse. Cells from mice in both treatment groups with distinct hashtags were mixed to form two pools with an aim for equivalent numbers of cells from each mouse. Each pool of cells was loaded in duplicate in a Chromium single cell sorting system (10X Genomics). Expression and hashtag library construction was performed following Chromium Single Cell VDJ Library protocol with a loading target of 1 ×104 cells per lane. The resulting 4 libraries were pooled prior to sequencing on a Novaseq 6000 S1 chip.
Baharom F., Ramirez-Valdez R.A., Tobin K.K., Yamane H., Dutertre C.A., Khalilnezhad A., Reynoso G.V., Coble V.L., Lynn G.M., Mulè M.P., Martins A.J., Finnigan J.P., Zhang X.M., Hamerman J.A., Bhardwaj N., Tsang J.S., Hickman H.D., Ginhoux F., Ishizuka A.S, & Seder R.A. (2020). Intravenous Nanoparticle Vaccination Generates Stem-Like TCF1+ Neoantigen-Specific CD8+ T Cells. Nature immunology, 22(1), 41-52.
+ Open protocol
+ Expand
6

Transcriptomic Analysis of Mouse Splenocytes

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Spleens from mice vaccinated with SNP via SC or IV injections were collected 2 weeks post boost and processed into a single cell suspension by mechanical dissociation. Splenocytes were stained with Reps1 tetramer and hashtag antibodies (Biolegend Total-Seq-C antibodies 1–5)52 (link). CD8+ T were isolated by fluorescence activated cell sorting (FACS) into 1.5 mL Eppendorf tubes containing staining buffer (2% FBS/PBS). Up to 4×104 cells were sorted per mouse. Cells from mice in both treatment groups with distinct hashtags were mixed to form two pools with an aim for equivalent numbers of cells from each mouse. Each pool of cells was loaded in duplicate in a Chromium single cell sorting system (10X Genomics). Expression and hashtag library construction was performed following Chromium Single Cell VDJ Library protocol with a loading target of 1 ×104 cells per lane. The resulting 4 libraries were pooled prior to sequencing on a Novaseq 6000 S1 chip.
Baharom F., Ramirez-Valdez R.A., Tobin K.K., Yamane H., Dutertre C.A., Khalilnezhad A., Reynoso G.V., Coble V.L., Lynn G.M., Mulè M.P., Martins A.J., Finnigan J.P., Zhang X.M., Hamerman J.A., Bhardwaj N., Tsang J.S., Hickman H.D., Ginhoux F., Ishizuka A.S, & Seder R.A. (2020). Intravenous Nanoparticle Vaccination Generates Stem-Like TCF1+ Neoantigen-Specific CD8+ T Cells. Nature immunology, 22(1), 41-52.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!