Single index kit t set a

Manufactured by 10x Genomics

The Single Index Kit T Set A is a laboratory product from 10x Genomics designed for sample barcoding in genomic analyses. It provides a set of unique molecular identifiers (UMIs) and sample indices for labeling individual samples within a batch. The core function of this kit is to enable multiplexed sequencing and sample demultiplexing during data processing.

Automatically generated - may contain errors

Lab products found in correlation

10 protocols using single index kit t set a

Single-cell RNA-seq library preparation

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

Single-cell suspensions were adjusted to a final concentration of 50,000 cells in 50 μl and filtered using pluriStrainer mini (50 μm, pluoriSelect, Germany). Single cell reverse transcription and cDNA synthesis was performed using a Chromium platform (10x Genomics) and Chromium Single Cell 3′ library & Gel Bead kit v3 (10x Genomics, 1000075) following the manufacturer’s instructions. Samples were indexed using Single Index Kit T Set A (10x Genomics). An appropriate sequencing library size range and the cDNA concentration were determined using an Agilent 2100 Bioanalyzer. The libraries were sequenced at Novogene using Illumina HiSeq system, with 150 bp paired end read length at a 50,000 reads/cell sequencing depth.

Zhang L., Abedin M., Jo H.N., Levey J., Dinh Q.C., Chen Z., Angers S, & Junge H.J. (2023). A Frizzled4-LRP5 agonist promotes blood-retina barrier function by inducing a Norrin-like transcriptional response. iScience, 26(8), 107415.

+ Open protocol

+ Expand

Single-cell RNA-seq of SCI samples

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

Naive, Sham, and SCI1M samples were sequenced. Sample libraries were prepared by The University of Houston Sequencing and Editing Core (UH-SNEC) based on Chromium Single Cell 3′ Library and Gel Bead Kit instructions (v3-v3.1). All samples were indexed with Single Index Kit T Set A (10X Genomics; PN-1000213) or Chromium i7 Multiplex Kits (10X Genomics; PN-120262). Paired-end sequencing was performed using the NovaSeq6000 or NextSeq500 sequencing instrument at recommended settings (R1:28 cycles; i7 index: 8 cycles; i5 index: none; and R2: 91 cycles).

Wei H., Wu X., Withrow J., Duran R.C., Singh S., Chaboub L.S., Rakshit J., Mejia J., Rolfe A., Herrera J.J., Horner P.J, & Wu J.Q. (2023). Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury. Cell reports, 42(5), 112486.

+ Open protocol

+ Expand

Single-Cell Transcriptomics of Smarcb1 Mutant

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

Single-cell suspensions obtained from the supratentorial and infratentorial parts of two Smarcb1^{1148del/1148del} and two Smarcb1^+/+ P0 mice were stained with 7-Aminoactinomycin D (7-AAD) (eBioscience™, #00-6993-50). Non-viable, 7-AAD-positive cells were removed by fluorescence-activated cell sorting (BD FACS Aria II, BD FACS Diva Software), followed by manual counting with trypan blue staining (Sigma-Aldrich, #T8154). Approximately 25,000 single cells of each sample were processed for scRNA-seq using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, #1000121), the Chromium Next GEM Chip G (10X Genomics, #1000120) and the Single Index Kit T set A (10X Genomics, #1000213) according to the manufacturer’s instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library Construction. Quality, purity, size and concentrations of cDNA and libraries were measured by a tapestation 2200 (Agilent Technologies). All libraries were sequenced separately by the NextSeq 500 sequencing platform (v 2.5 chemistry, 75 cycle kit) at the Core Facility Genomics (Medical Faculty of the Westfälische Wilhelms-Universität Münster, Münster).

Brugmans A.K., Walter C., Moreno N., Göbel C., Holdhof D., de Faria F.W., Hotfilder M., Jeising D., Frühwald M.C., Skryabin B.V., Rozhdestvensky T.S., Wachsmuth L., Faber C., Dugas M., Varghese J., Schüller U., Albert T.K, & Kerl K. (2023). A Carboxy-terminal Smarcb1 Point Mutation Induces Hydrocephalus Formation and Affects AP-1 and Neuronal Signalling Pathways in Mice. Cellular and Molecular Neurobiology, 43(7), 3511-3526.

+ Open protocol

+ Expand

Single-Cell Transcriptome Profiling of Peritoneal Cells

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

Using a Chromium Next GEM Single Cell 3’ Kit v3.1, 4 rxns (1000269, 10X Genomics), Chromium Next GEM Single Cell 3ʹ Gel Bead Kit v3.1, 16 rxns (PN-1000122) and Chromium Next GEM Chip G Single Cell Kit (PN-1000120, 10X Genomics), the peritoneal cells suspensions in PBS, at 2000 cells per ul, were loaded onto a Chromium single cell controller (10X Genomics) to generate single-cell Gel beads-in-emulsion (GEMs) according to the manufacturer’s protocol. Briefly, approximately 10,000 cells per sample were added to a chip to create GEMs. Cells were lysed and the bead captured poly(A) RNA was barcoded during reverse transcription in Thermo Fisher Veriti 96-well thermal cycler at 53°C for 45 min, followed by 85°C for 5 min. cDNA was generated and amplified. Quality control and quantification of the cDNA was conducted using Agilent Genomic DNA ScreenTape Analysis kit (5067–5366 for Genomic DNA Reagents and 5067–5365 for Genomic DNA ScreenTape) in the TapeStation system. scRNA-seq libraries were constructed using a Chromium Next GEM Single Cell 3ʹ Library Kit v3.1 (PN-1000158, 10X Genomics) and Single Index Kit T Set A, 96 rxns (PN-1000213, 10X Genomics). 10x Genomics Single Cell Gene Expression libraries were sequenced on a NextSeq 2000 run. The sequencing run was setup as a 28 cycles + 90 cycles non-symmetric run. Demultiplexing was done allowing 1 mismatch in the barcodes.

Zhao M., Jankovic D., Hornick K.M., Link V.M., Souza C.O., Belkaid Y., Lack J, & Loke P. (2024). Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS. Research Square.

+ Open protocol

+ Expand

Single-Cell RNA-Seq Using 10x Genomics

Cited 2 times

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

The sorted IEL suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10,000 cells were loaded per channel. Single-cell RNA-Seq libraries were prepared using the following Single Cell 3’ Reagent Kits v3.1: Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, PN-1000121; Chromium Next GEM Chip G Single Cell Kit, PN-1000120 and Single Index Kit T Set A PN-1000213 (10x Genomics)^{54 (link)}, and following the Single Cell 3’ Reagent Kits v3.1 User Guide (Manual Part # CG000204 Rev D). Libraries were run on an Illumina NovaSeq 6000 paired-end reads, read1 is 28 cycles, i7 index is 8 cycles, and read2 is 91 cycles, one lane per sample). The Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting.
The data were analyzed as previously described^{55 (link)}. Briefly, the single cell count matrix was exported from 10x Genomics cell ranger version 3.0.0 output and subsequently analyzed in R version 3.4.1. Louvain clustering and differential expression analysis was performed with the standard functions from Seurat version 2.3.4.

Matsuzawa-Ishimoto Y., Yao X., Koide A., Ueberheide B.M., Axelrad J.E., Reis B.S., Parsa R., Neil J.A., Devlin J.C., Rudensky E., Dewan M.Z., Cammer M., Blumberg R.S., Ding Y., Ruggles K.V., Mucida D., Koide S, & Cadwell K. (2022). γδ IEL effector API5 masks genetic susceptibility to Paneth cell death. Nature, 610(7932), 547-554.

+ Open protocol

+ Expand

Single-cell RNA Sequencing Workflow

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

For each sample, the quantity and viability of the cells were evaluated. Absence of aggregated cells or cell debris was confirmed microscopically. Single cells were encapsulated into emulsion droplets using Chromium Connect (10x Genomics). scRNA-seq libraries were constructed using Chromium Next GEM Automated Single Cell 3′ Library and Gel Bead Kit v. 3.1 (10x Genomics), Chromium Next GEM Automated Chip G Single Cell Kit, and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s protocol. The libraries were sequenced using Illumina NextSeq 2000.

Hanai A., Kawabata A., Nakajima K., Masuda K., Urakawa I., Abe M., Yamazaki Y, & Fukumoto S. (2023). Single-cell RNA sequencing identifies Fgf23-expressing osteocytes in response to 1,25-dihydroxyvitamin D3 treatment. Frontiers in Physiology, 14, 1102751.

+ Open protocol

+ Expand

Single-Cell RNA-Seq Library Preparation

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

10,000 nuclei were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, PN-1000121). The cDNA and library were made using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262) according to the manufacturer’s protocol. Quality control for the libraries was performed using Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Libraries were sequenced on an Illumina Novaseq 6000 system with 2 × 150 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index and 91 bp Read2 for transcript.

Balzer M.S., Pavkovic M., Frederick J., Abedini A., Freyberger A., Vienenkötter J., Mathar I., Siudak K., Eitner F., Sandner P., Grundmann M, & Susztak K. (2023). Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution. Cell Reports Medicine, 4(4), 100992.

+ Open protocol

+ Expand

Single-cell RNA-seq of SCI samples

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

+ Open protocol

+ Expand

Single-Cell RNA-Seq of Immune Cells

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

Single-cell suspensions from sorted live CD45+ cells were loaded on a Chromium Controller (10x Genomics) to generate single-cell beads in emulsion, and scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1 Single Index Kit), Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Single Index Kit T Set A (10x Genomics) following the manufacturer’s protocol. Single-cell barcoded cDNA libraries were qualified and quantified using Agilent Bioanalyzer. cDNA libraries were sequenced on an Illumina NextSeq 500 (Illumina). Read lengths were 26 bp for read 1, 8 bp for i7 index, and 98 bp for read 2. Ten thousand cells from each sample were sequenced with greater than 50,000 reads per cell as recommended by the manufacturer.

Su C., Kent C.L., Pierpoint M., Floyd W., Luo L., Wiliams N.T., Ma Y., Peng B., Lazarides A.L., Subramanian A., Himes J.E., Perez V.M., Hernansaiz-Ballesteros R.D., Roche K.E., Modliszewski J.L., Selitsky S.R., Mari S.h.i.n.o.h.a.r.a., Wisdom A.J., Moding E.J., Mowery Y.M, & Kirsch D.G. (2024). Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma. bioRxiv.

+ Open protocol

+ Expand

Single Cell RNA-seq Library Generation

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

Following manufacturer’s protocol the Chromium Controller (10X Genomics, PN-120223) was used to load 30,000 cells into a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to generate single cell gel beads in the emulsion (10X Genomics, PN-1000121). The cDNA and library were created using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262), respectively⁵⁰.

Yan Y., Liu H., Abedini A., Sheng X., Palmer M., Li H, & Susztak K. (2024). Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. Nature Communications, 15, 873.

+ 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!