Chromium next gem single cell 5 library gel bead kit v1

Manufactured by 10x Genomics

The Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 is a laboratory equipment product designed for single-cell RNA sequencing. The kit enables the preparation of libraries for sequencing of the 5' end of transcripts from individual cells.

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Lab products found in correlation

Novaseq 6000 platform, by Illumina (2 mentions) Chromium controller, by 10x Genomics (2 mentions) Chromium microfluidic chips, by 10x Genomics (2 mentions) Nextseq 500, by Illumina (2 mentions) Cell strainer cap, by Corning (2 mentions) Tryple express, by Thermo Fisher Scientific (2 mentions) Novaseq s4, by Illumina (2 mentions) Nextseq 550, by Illumina (1 mentions) Tapestation 4200, by Agilent Technologies (1 mentions) Chromium controller instrument, by 10x Genomics (1 mentions)

Spelling variants of this product

Chromium Single Cell 5′ Library & Gel Bead Kit (29 citations) Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1 (5 citations) Chromium Single Cell 5′ Library & Gel Bead Kit v1 (4 citations) Single Cell 5′ Library & Gel Bead Kit (3 citations) Chromium Next GEM Single Cell 5′ beads (2 citations) 5’ v1 Gem beads (2 citations) Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 or v2 (2 citations)

5 protocols using chromium next gem single cell 5 library gel bead kit v1

Single-Cell Profiling of Tumor-Infiltrating CD8+ T Cells

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Tomato⁺ and tomato⁻ spleen and tumor CD8⁺ T cells were isolated from (CD137^−/− tomato⁺) and (CD137^+/+tomato⁻) mixed BM chimera bearing B16K1 for 19 days using FACSaria^™ Fusion.
Single-cell libraries (5′ gene expression) were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 according to the manufacturer’s protocol (10X Genomics). Additional Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell were used to generate TCR Libraries. Single-cell library size and quality were confirmed on the Tapestation 4200 (Agilent) and pooled to reach at least 20,000 read pairs for 5’ Gene Expression Library; 10,000 read pairs of Protein Library and 5,000 read pairs of V(D)J Library. Libraries were sequenced twice on a NextSeq 550 (Illumina) in pair-end sequencing 26 bp (read1) × 91 bp (read2) and a single index 8 bp in length. A similar workflow was performed on spleen memory CD8⁺ T cells (CD44^hi/PD1⁻), precursor exhausted T cells (CD44^hi/PD1⁺/Slamf6⁺/Tim3⁻), and exhausted T cells (CD44^hi/PD1⁺/Slamf6⁻/Tim3⁺) sorted using FACSaria^™ Fusion from C57BL/6 mice treated with anti-CD137 (10 μg, 3H3, BioXcell, twice a week, 5 mice) or with control IgG (100 μg, HRPN, BioXcell, twice a week, 10 mice) for 14 days.

Uchida S., Kwon H.M., Yamauchi A., Preston A.S., Marumo F, & Handler J.S. (1992). Molecular cloning of the cDNA for an MDCK cell Na(+)- and Cl(-)-dependent taurine transporter that is regulated by hypertonicity.. Proceedings of the National Academy of Sciences of the United States of America, 89(17), 8230-8234.

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Single-Cell Transcriptome and TCR Profiling from Frozen Mononuclear Cells

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Mononuclear cells were isolated from whole blood and bone marrow by centrifugation and resuspended with freezing medium. The cells were then frozen in a freezing container in a − 80 °C freezer. On the date of experiment, the cells were thawed using a water bath at 37 °C and loaded into Chromium microfluidic chips and barcoded within a 10X Chromium Controller (10X Genomics, US). For transcriptome, procedures were performed with reagents: Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 (10X Genomics, Cat. No. 1000165). TCR enrichment was carried out using the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10X Genomics, Cat. No. 1000005) for αβ transcripts, or customer primers for γδ TCR transcripts [9 (link)]^. All the libraries were sequenced in a PE150 mode (Pair-End for 150 bp read) on the NovaSeq 6000 platform (Illumina, US).

Song W., Zhang H., Yang F., Nakahira K., Wang C., Shi K, & Zhang R. (2022). Single cell profiling of γδ hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression. Cellular Oncology (Dordrecht), 46(1), 211-226.

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Single-Cell RNA-seq of Developing Heart

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Samples for single cell RNA sequencing were collected from three independent litters at E13.5. The heart was microdissected to obtain the interventricular septum (IVS), left ventricular (LV) and right ventricular (RV) regions. Each microdissected tissue was singularized with TrypLE Express (Life Technologies, Cat# 12604-013) at 37C and quenched with 1% FBS in PBS. The single cell suspension was then filtered through a cell strainer cap (Corning, Cat# 352235) and centrifuged at 300g for 5 minutes. The pellet was resuspended in 1% FBS in PBS and counted using an automated cell counter. A 30μL aliquot of the cell suspension was used to generate single cell droplet libraries with the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, according to manufacturer’s instructions (10X Genomics). After KAPA qPCR quantification, a shallow sequencing run was performed on a NextSeq 500 (Illumina) prior to deep sequencing on a NovaSeq S4 (Illumina).

Kathiriya I.S., Dominguez M.H., Rao K.S., Muncie-Vasic J.M., Devine W.P., Hu K.M., Hota S.K., Garay B.I., Quintero D., Goyal P., Matthews M.N., Thomas R., Sukonnik T., Miguel-Perez D., Winchester S., Brower E.F., Forjaz A., Wu P.H., Wirtz D., Kiemen A.L, & Bruneau B.G. (2024). A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects. bioRxiv.

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Single-cell Transcriptomics of Cardiac Ventricles

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Samples for single cell RNA sequencing were collected from three independent litters at E13.5. The heart was microdissected to obtain the interventricular septum (IVS), left ventricular (LV) and right ventricular (RV) regions. Control samples were Tbx5^CreERT2/+;Mef2cAHF-DreERT2;ROSA26^Ai66/Ai6 (n=3) and Tbx5^CreERT2/+;Mef2cAHF-DreERT2;ROSA26^Ai66/+ (n=1) for LV, RV and IVS each. Tbx5 mutant samples were Tbx5^CreERT2/flox;Mef2cAHF-DreERT2;ROSA26^Ai66/Ai6 for RV and LV (n=3 each) and IVS (n=2).
Each microdissected tissue was singularized with TrypLE Express (Life Technologies, Cat# 12604–013) at 37C and quenched with 1% FBS in PBS. The single cell suspension was then filtered through a cell strainer cap (Corning, Cat# 352235) and centrifuged at 300g for 5 minutes. The pellet was resuspended in 1% FBS in PBS and counted using an automated cell counter. A 30μL aliquot of the cell suspension was used to generate single cell droplet libraries with the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, according to manufacturer’s instructions (10X Genomics). After KAPA qPCR quantification, a shallow sequencing run was performed on a NextSeq 500 (Illumina) prior to deep sequencing on a NovaSeq S4 (Illumina). For control IVS+AVC, at E13.5, 3 samples were Tbx5^CreERT2/+;Mef2cAHF-DreERT2;ROSA26^Ai66/Ai6

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Single-cell RNA-seq and TCR profiling

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Mononuclear cells were isolated from whole blood and bone marrow by centrifugation and resuspended with freezing medium. The cells were then frozen in a freezing container in a -80°C freezer. On the date of experiment, the cells were thawed using a water bath at 37°C and loaded into Chromium microfluidic chips and barcoded within a 10X Chromium Controller (10X Genomics, US). For transcriptome, procedures were performed with reagents: Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 (10X Genomics, Cat. No. 1000165). TCR enrichment was carried out using the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10X Genomics, Cat. No. 1000005) for αβ transcripts, or customer primers for γδ TCR transcripts9. All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) on the NovaSeq 6000 platform (Illumina, US).

Song W., Zhang H., Yang F., Nakahira K., Wang C., Shi K., & Zhang R. (2022). Single cell profiling of γδ hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression.

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