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Products Content

 1. Home
 2. Applications
 3. InTraSeq™ Single Cell Analysis Overview


INTRASEQ™ SINGLE CELL ANALYSIS OVERVIEW

ANALYSIS OF ISOLATED CD4+ AND CD8+ CELLS USING INTRASEQ INTRACELLULAR AND
SIGNALING PATHWAY ANTIBODIES TO IDENTIFY CELLULAR STATES THAT WOULD BE DIFFICULT
TO STUDY USING RNA ALONE. THE INTRASEQ ASSAY OFFERS ADDITIONAL INSIGHTS INTO
CELLULAR SUBPOPULATIONS, BY MEASURING PTMS AND INTRACELLULAR PROTEIN LEVELS IN
SINGLE CELLS WHICH CAN ENABLE A DEEPER UNDERSTANDING OF DISEASE DEVELOPMENT
MECHANISMS.


SEQ WHAT YOU’VE BEEN MISSING

Intracellular protein and Transcriptomic Sequencing (InTraSeq) is a novel
technology developed by CST that identifies signaling pathways and reveals
molecular mechanisms in disease development in a single experiment. It enables
simultaneous detection of RNA as well as both intracellular and surface proteins
in thousands of cells, allowing researchers to investigate signaling pathways
with the transcriptome—all at a single-cell resolution.

InTraSeq facilitates deeper understanding of cell biology by:

 * Uncovering biological insights not revealed with traditional single-cell RNA
   sequencing (scRNA-seq) methods
 * Highlighting the dynamics between transcription and translation in
   single-cell datasets
 * Dissecting cell signaling mechanisms by quantifying post-translational
   modifications at the single-cell level

InTraSeq 3’ technology is developed and validated by CST, using the 10x Genomics
Chromium Single Cell 3' Reagent Kits with Feature Barcoding technology.


WHAT MAKES INTRASEQ UNIQUE?

A)MOST SINGLE-CELL ANALYSIS TECHNIQUES CURRENTLY AVAILABLE DETECT RNA AND USE
BARCODED ANTIBODIES TO MEASURE SURFACE PROTEINS FOR PHENOTYPING PURPOSES. B)
MANY HAVE TRIED DEVELOPING METHODS TO DETECT INTRACELLULAR PROTEINS, BUT THESE
METHODS TYPICALLY SUFFER FROM SIGNIFICANT RNA LOSS AND DEGRADATION. C) INTRASEQ™
SINGLE CELL ANALYSIS DETECTS RNA ALONGSIDE INTRACELLULAR AND SURFACE PROTEINS
WHILE PRESERVING RNA.

Most currently available single-cell analysis technologies are limited to
phenotyping a sample because they only identify RNA and, occasionally, surface
marker expression levels. Additionally, other technologies are not able to
determine and measure important signaling cascades activated during a disease
state or by pharmacologic perturbation. By combining transcriptomic, protein,
and post-translational modifications quantification into a single assay,
InTraSeq technology goes beyond phenotyping and dissects the cellular mechanisms
that distinguish cellular differences—all in one experiment. With InTraSeq
technology, scientists can readily explore multiple signaling pathways along
with genetic expression changes to efficiently identify key molecular mechanisms
underlying physiologic responses and discern downstream protein modifications.

SINGLE-CELL ANALYSIS (SCA) FOR INTRACELLULAR PROTEINS AND POST-TRANSLATIONAL
MODIFICATIONS

Single-cell RNA sequencing (scRNA-seq) is commonly utilized to determine
cellular responses to pharmacologic and environmental perturbations. However,
protein expression levels often do not directly correlate with RNA expression,
leaving a gap in the understanding of complex physiologic systems. Determining
how single-cell protein expression and post-translational modifications differ
from single-cell gene expression can offer functional insight into pathway
activation that cannot be obtained from scRNA-seq alone.

Post-translational modifications (PTMs) can alter protein activity, longevity,
and expression levels. Understanding the interplay between genetic expression
and protein activity is crucial to determine the underlying cellular
heterogeneity and functional state of complex biological systems. The InTraSeq
3' Conjugate Antibody Cocktail is formulated with 31 of our most popular
antibodies that bind to both human and mouse targets, including PTMs. Scientists
can quantify dozens of critical signaling proteins in a single assay with ease
and without bias.

CO-QUANTIFICATION OF SINGLE-CELL PTMS AND MRNA

Many cells can exhibit similar levels of RNA expression, but some may differ in
which proteins are ultimately expressed and subsequently modified to regulate
activity after pharmacologic or environmental perturbations. Co-quantification
of RNA, protein, and post-translational modifications facilitates a more
thorough understanding of complex physiologic interactions that RNA expression
alone cannot elucidate.

RNA DOES NOT NECESSARILY CORRELATE WITH PROTEIN LEVELS

CO-QUANTITATION OF MRNA AND CELLULAR PROTEINS WITH INTRASEQ REVEALS DIFFERENTIAL
EXPRESSION LEVELS OF MRNA AND PROTEIN WHERE THE TWO VALUES OFTEN DO NOT
CORRELATE.


INTRASEQ SINGLE CELL ANALYSIS ADVANTAGES

Reduced Hands-On Time with a Streamlined Workflow

A STRAIGHTFORWARD, FOUR-STEP PROTOCOL

THE INTRASEQ™ 3’ ASSAY KIT IS OPTIMIZED TO PROVIDE A ROBUST MRNA AND PROTEIN
SIGNAL IN A STRAIGHTFORWARD PROTOCOL THAT REQUIRES MINIMAL BENCH TIME. THE TWO
CONVENIENT STOPPING POINTS ALLOW FOR FLEXIBILITY AND SAMPLE STORAGE FOR UP TO
SEVEN DAYS, PROVIDING MAXIMUM WORKFLOW FLEXIBILITY.

The InTraSeq protocol requires approximately one hour of hands-on bench time and
includes multiple stopping points, providing maximum time flexibility when
performing single-cell experiments. Samples can be stored for up to seven days
after the fixation step without compromising RNA integrity. Unlike currently
available single-cell analysis protocols, the convenience offered by InTraSeq
eliminates the need to coordinate staff and equipment with long single-day
protocols. The ability to store samples for longer periods of time can also
facilitate high-throughput applications by allowing bulk sample and single-cell
processing protocols to be performed on sequential days without compromising
quality.

The straightforward immunostaining protocol includes the following steps:

Step 1: Fix the cells overnight.

 * ~5 min hands-on benchwork
 * Cells can be stored in the freezer for up to seven days.

Step 2: Incubate with scBlock.

 * ~10 min hands-on benchwork
 * This step is optimized to obtain high-quality single-cell readout of both RNA
   and proteins.

Step 3: Add CST® InTraSeq™ 3’ Conjugate Antibody Cocktail, and incubate
overnight.

 * ~5 min hands-on benchwork

Step 4: Wash the cells.

 * ~20 min hands-on benchwork
 * At this point the cells are ready for a single-cell 10x Genomics 3’
   experiment.

Investigate Intracellular Protein Signaling while Guaranteeing Robust RNA Signal

Preserving RNA integrity in single-cell multiomic experiments has been a
persistent and significant challenge. Many single-cell assays utilize harsh
chemicals to disrupt the membrane resulting in RNA degradation and loss.
InTraSeq reagents have been rigorously optimized to gently permeabilize the cell
and nuclear membranes. This allows the conjugated antibodies to enter the cell
and bind to their targets while maintaining RNA levels throughout the assay.
This enables accurate quantitation of both RNA and protein expression.

INTRASEQ PRESERVES THE TRANSCRIPT ABUNDANCE IN THE SAMPLE COMPARED TO LIVE CELL
CONTROL



  Live PBMCs InTraSeq™ PBMCs Relative Median Genes/Cell (matched reads/cell)
100% 86.2% Fraction Reads in Cells 94.9% 85% Antibody Reads in Cells N/A 60%
Reads Mapped Confidently to Genome 89.9% 85.5%

AVERAGE GENE EXPRESSION WAS QUANTIFIED IN LIVE AND INTRASEQ PREPARED SAMPLES OF
PMBCS. INTRASEQ REAGENTS PRESERVE THE GENETIC PROFILE OF LIVE CELLS IN DIFFICULT
SAMPLES SUCH AS PBMCS, WITH MINIMAL LOSS OF MRNA.

Identify Hard-To-Detect Cells with Unbiased Depth-of-Coverage

The power of InTraSeq single-cell analysis technology lies in the ability to
detect and quantify both intracellular and surface proteins in conjunction with
single-cell gene expression to differentiate heterogeneous cell populations. In
contrast to CITE-Seq, which only detects cell surface proteins, InTraSeq
provides scientists with tools to study complex intracellular signaling pathways
without bias.

INTRASEQ METHOD PRESERVES CELLULAR HETEROGENEITY

UMAP DISPLAYING CELL TYPES IN PBMCS FROM THE SAME DONOR BEFORE AND AFTER THE
INTRASEQ PROTOCOL. THE SPLIT UMAP SHOWS THAT THE PROPORTION OF EACH CELL TYPE
WAS SIMILAR AND NOT IMPACTED BY THE INTRASEQ PROTOCOL.

Explore Multiple Molecular Mechanisms In One Experiment

Combined with CST expertise in intracellular signaling and post-translational
modification antibodies, the InTraSeq technology enables researchers to study
and quantify intricate intracellular, nuclear, and surface protein interactions
together with gene expression. Simultaneously measuring transcriptomics changes
and protein expression, including post-translational modifications, generates
more comprehensive data sets, enriching the knowledge of complex signaling
systems in a way not possible with other assays and deepens our understanding of
disease mechanisms.

IDENTIFYING CELL STATES WITHIN CD4+ AND CD8+ CELLS USING SINGLE-CELL
INTRACELLULAR PROTEIN READOUT



ANALYSIS OF ISOLATED CD4+ AND CD8+ CELLS USING INTRASEQ INTRACELLULAR AND
SIGNALING PATHWAY ANTIBODIES TO IDENTIFY CELLULAR STATES THAT WOULD BE DIFFICULT
TO STUDY USING RNA ALONE. THE INTRASEQ ASSAY OFFERS ADDITIONAL INSIGHTS INTO
CELLULAR SUBPOPULATIONS, BY MEASURING PTMS AND INTRACELLULAR PROTEIN LEVELS IN
SINGLE CELLS WHICH CAN ENABLE A DEEPER UNDERSTANDING OF DISEASE DEVELOPMENT
MECHANISMS.

Of the 31 validated antibodies in InTraSeq 3' Conjugate Antibody Cocktail, 2
target surface proteins, and the other 29 target intracellular proteins,
including PTMs. The antibody cocktail is designed for unbiased quantitation of
proteins along signaling pathways commonly studied in immunology and cancer
research providing accurate and reliable data sets.



PBMCS WERE STIMULATED WITH LPS AND PROCESSED USING THE INTRASEQ™ ASSAY KIT, RNA,
TOTAL PROTEIN, AND PTMS WERE QUANTIFIED WITH SCRNA-SEQ AND THE INTRASEQ™ 3'
CONJUGATE ANTIBODY COCKTAIL. THE HEATMAPS DISPLAY THE PTM LEVELS OF STAT3 AND
MAPK BEFORE AND AFTER STIMULATION, AS WELL AS WHICH RNA AND PROTEINS CORRELATE
WITH THOSE SHIFTS IN PHOSPHORYLATION LEVELS.


HOW DOES INTRASEQ SUPPORT MY RESEARCH?

InTraSeq can be a unique and powerful screening tool when starting a project. It
enables researchers to understand a specific genetic phenotype by offering an
unbiased approach that determines which signaling pathway is perturbed and can
help determine where to focus.

InTraSeq can also measure acute cellular perturbations that occur within short
periods of time (< 20 minutes) since PTMs responses occur before mRNA. These
acute responses would otherwise not be observed in RNA alone in single cells and
outlines the importance and uniqueness of InTraSeq technology.

Trust Your Results with the CST-Validated InTraSeq™ 3' Conjugate Antibody
Cocktail

CST scientists rigorously validate and optimize all InTraSeq antibodies and
reagents to provide consistent, high-quality results. The InTraSeq™ 3' Conjugate
Antibody Cocktail is formulated such that all the included antibodies and
reagents are at optimal concentrations and ready to use in your experiments.
InTraSeq removes the guesswork and enables scientists to collect trustworthy
data without the need for time-consuming optimization experiments.


INTRASEQ SINGLE CELL ANALYSIS PRODUCT OFFERINGS

Find the right solution for your workflow below.

InTraSeq™ 3' Conjugate Antibody Cocktail

Contains 31 primary antibodies against popular signaling pathway proteins and
reacts with both human and mouse samples.

InTraSeq™ 3' Assay Kit

A buffer kit specially formulated for single-cell analysis.

InTraSeq™ 3' Conjugates

Besides the thirty-one 3' conjugated antibodies included in the InTraSeq 3'
Conjugate Antibody Cocktail 1 (human and mouse reactive), seven additional
InTraSeq 3' conjugates (human reactive) are also available individually.

Surface Targets Species Reactivity Included in Cocktail? CD3 (UCHT1) Mouse mAb
(InTraSeq™ 3' Conjugate 3028) H No CD4 (RPA-T4) Mouse mAb (InTraSeq™ 3'
Conjugate 3029) H No CD8α (SK1) Mouse mAb (InTraSeq™ 3' Conjugate 3030) H No
CD19 (Intracellular Domain) (D4V4B) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3010)
H, M Yes CD68 (D4B9C) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3012) H No NCAM1
(CD56) (E7X9M) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3025) H, M Yes T-bet/TBX21
(D6N8B) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3009) H No

Intracellular Targets (non-PTM) Species Reactivity Included in Cocktail? Aiolos
(D1C1E) Rabbit mAb #15103 (InTraSeq™ 3' Conjugate 3027) H, M Yes FoxO1 (C29H4)
Rabbit mAb (InTraSeq™ 3' Conjugate 3037) H, M Yes GAPDH (14C10) Rabbit mAb
(InTraSeq™ 3' Conjugate 3007) H, M Yes Iba1/AIF-1 (E4O4W) XP® Rabbit mAb
(InTraSeq™ 3' Conjugate 3003) H, M Yes Ikaros (D6N9Y) Rabbit mAb #14859
(InTraSeq™ 3' Conjugate 3026) H, M Yes NFAT1 (D43B1) XP® Rabbit mAb (InTraSeq™
3' Conjugate 3032) H, M Yes S100A9 (D5O6O) Rabbit mAb (InTraSeq™ 3' Conjugate
3004) H No TCF1/TCF7 (C63D9) Rabbit mAb (InTraSeq™ 3' Conjugate 3013) H, M Yes
Vimentin (D21H3) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3011) H, M Yes

PTM-related Targets Species Reactivity Included in Cocktail? Phospho-4E-BP1
(Thr37/46) (236B4) Rabbit mAb (InTraSeq™ 3' Conjugate 3021) H, M Yes Akt (pan)
(C67E7) Rabbit mAb (InTraSeq™ 3' Conjugate 3018) H, M Yes Phospho-Akt (Ser473)
(D9E) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3014) H, M Yes CREB (48H2) Rabbit
mAb (InTraSeq™ 3' Conjugate 3008) H, M Yes Phospho-CREB (Ser133) (87G3) Rabbit
mAb (InTraSeq™ 3' Conjugate 3006) H, M Yes Glucocorticoid Receptor (D6H2L) XP®
Rabbit mAb (InTraSeq™ 3' Conjugate 3035) H, M Yes Phospho-Glucocorticoid
Receptor (Ser226) (D9D3V) Rabbit mAb (InTraSeq™ 3' Conjugate 3036) H, M Yes
Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3020) H,
M Yes Phospho-Histone H3 (Ser10) (D2C8) XP® Rabbit mAb (InTraSeq™ 3' Conjugate
3024) H, M Yes Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (InTraSeq™ 3'
Conjugate 3017) H, M Yes NF-κB p65 (D14E12) XP® Rabbit mAb (InTraSeq™ 3'
Conjugate 3033) H, M Yes Phospho-NF-κB p65 (Ser536) (93H1) Rabbit mAb (InTraSeq™
3' Conjugate 3034) H, M Yes p44/42 MAPK (Erk1/2) (137F5) Rabbit mAb (InTraSeq™
3' Conjugate 3016) H, M Yes Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (197G2)
Rabbit mAb (InTraSeq™ 3' Conjugate 3023) H, M Yes S6 Ribosomal Protein (54D2)
Mouse mAb (InTraSeq™ 3' Conjugate 3005) H, M Yes Phospho-S6 Ribosomal Protein
(Ser235/236) (D57.2.2E) XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3019) H, M Yes
Stat1 (D1K9Y) Rabbit mAb (InTraSeq™ 3' Conjugate 3038) H, M Yes Phospho-Stat1
(Ser727) (D3B7) Rabbit mAb (InTraSeq™ 3' Conjugate 3039) H, M Yes Stat3 (124H6)
Mouse mAb (InTraSeq™ 3' Conjugate 3022) H, M Yes Phospho-Stat3 (Tyr705) (D3A7)
XP® Rabbit mAb (InTraSeq™ 3' Conjugate 3015) H, M Yes Phospho-Stat3 (Ser727)
(D4X3C) Rabbit mAb (InTraSeq™ 3' Conjugate 3031) H, M Yes

Isotype Control Species Reactivity Included in Cocktail? Mouse (G3A1) mAb IgG1
Isotype Control (InTraSeq™ 3' Conjugate 3001) H No

Controls Included In Assay Kit (not for individual sale) Species Reactivity
Included in Cocktail? Histone H3 (D1H2) XP® Rabbit mAb (InTraSeq™ 3' Conjugate
3002) H, M No Rabbit (DA1E) mAb IgG XP® Isotype Control (InTraSeq™ 3' Conjugate
3000) H, M No


TECHNICAL SUPPORT

Visit the Technical Support page to search InTraSeq Single Cell Analysis-related
troubleshooting information, answers to technical questions, and how to contact
us.

CELL SIGNALING TECHNOLOGY, CST, AND INTRASEQ ARE TRADEMARKS OF CELL SIGNALING
TECHNOLOGY, INC. ALL RIGHTS RESERVED. 10X GENOMICS, 10X, FEATURE BARCODE, AND
CHROMIUM ARE THE TRADEMARKS OR REGISTERED TRADEMARKS OF 10X GENOMICS, INC. ALL
OTHER TRADEMARKS ARE THE PROPERTY OF THEIR RESPECTIVE OWNERS. VISIT
CELLSIGNAL.COM/TRADEMARKS FOR MORE INFORMATION.

SUBJECT TO PATENTS LICENSED FROM 10X GENOMICS, INC., FOR USE WITH SINGLE-CELL
(I.E., CHROMIUM) 10X PRODUCTS.

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