WO2024138680A1 - Protein expression analysis method and related device - Google Patents

Abstract

A protein expression analysis method and a related device, relating to the technical field of biology. The method comprises: acquiring sequencing data from a sequencing chip sequencing a biological sample, the sequencing data comprising a sequence value and the position of a protein corresponding to the sequence value; according to a single-stranded DNA dyeing image of the biological sample, determining sequencing data belonging to the interior of a cell; comparing the sequence value in the sequencing data of the interior of the cell with a sequence value of the protein in a preset protein library, and obtaining a comparison result; and if the comparison result shows that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, acquiring an analysis result of protein expression, the analysis result comprising the type of the matched protein and the position in the interior of the cell. In said method, protein expression conditions can be analyzed.

Description

A protein expression analysis method and related equipment Technical Field

The present application relates to the field of biotechnology, and in particular to a protein expression analysis method and related equipment.

Background technique

Protein is the material basis of life, an organic macromolecule, the basic organic matter that constitutes cells, and the main bearer of life activities. Generally, after RNA is translated into protein, protein directly reflects physiological functions.

Currently, the technology used for protein detection is immunohistochemistry (immunofluorescence) technology. However, the number of proteins that can be detected simultaneously by this technology is limited, only about 40.

Although the existing technology can realize the detection of proteins, there is still a lack of relevant analysis methods, and it is impossible to analyze the protein expression.

Summary of the invention

The present application provides a protein expression analysis method and related equipment, which can analyze protein expression.

In a first aspect, the present application provides a method for analyzing protein expression, the method comprising:

Acquire sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a location of a protein corresponding to the sequence value;

Determining sequencing data belonging to the interior of the cell according to the single-stranded DNA staining image of the biological sample;

Comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a preset protein library to obtain a comparison result;

If the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, then the analysis result of protein expression is obtained, and the analysis result includes the type of the matched protein and the location inside the cell.

Optionally, the analysis result further includes: the expression abundance corresponding to each protein; the method further includes:

Obtaining a unique molecular identifier of a protein inside the cell;

According to the unique molecular identifier of the protein inside the cell, the protein inside the cell is deduplicated to obtain the expression abundance corresponding to each protein inside the cell.

Optionally, comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a preset protein library to obtain a comparison result includes:

If the degree of match between the sequence value in the sequencing data inside the cell and the sequence value of the protein in the preset protein library is greater than a preset threshold, a comparison result is determined that the sequence value in the sequencing data inside the cell matches the sequence value of the protein in the preset protein library.

Optionally, the sequence value in the sequencing data includes a coupled initial base sequence and a marked base sequence, and the marked base sequence is used to determine the type of protein corresponding to the sequence value.

Optionally, the method further includes:

Generate a protein expression heat map according to the analysis results of the protein expression, wherein the protein expression heat map is used to describe the type, location and expression abundance of the protein inside the cell;

The protein expression heat map is displayed.

Optionally, the method further includes:

Generate a protein in situ expression report based on the analysis results;

A report on the in situ expression level of the protein is displayed.

In a second aspect, the present application provides a protein expression analysis device, the device comprising:

An acquisition module, used to acquire sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a location of a protein corresponding to the sequence value;

A determination module, used to determine the sequencing data belonging to the interior of the cell according to the single-stranded DNA staining image of the biological sample;

A comparison module, used to compare the sequence value in the sequencing data inside the cell with the sequence value of the protein in the preset protein library to obtain a comparison result;

The analysis module is used to obtain the analysis result of protein expression if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, and the analysis result includes the type of the matched protein and the location inside the cell. The expression abundance of each protein is determined by calculating the number of sequencing data of the protein.

Optionally, the analysis result also includes: the expression abundance corresponding to each protein; the acquisition module is also used to obtain the unique molecular identifier of the protein inside the cell; the analysis module is also used to deduplicate the protein inside the cell according to the unique molecular identifier of the protein inside the cell to obtain the expression abundance corresponding to each protein inside the cell.

Optionally, the comparison module is specifically used to determine a comparison result that the sequence value in the sequencing data inside the cell matches the sequence value of the protein in the preset protein library if the degree of match between the sequence value in the sequencing data inside the cell and the sequence value of the protein in the preset protein library is greater than a preset threshold.

Optionally, the sequence value in the sequencing data includes a coupled initial base sequence and a marked base sequence, and the marked base sequence is used to determine the type of protein corresponding to the sequence value.

Optionally, the device further includes a display module, and the analysis module is further used to generate a protein expression heat map according to the analysis results of the protein expression, wherein the protein expression heat map is used to describe the type, location and expression abundance of the protein inside the cell;

The display module is used to display the protein expression heat map.

Optionally, the analysis module is further used to generate a protein in situ expression level report based on the analysis results; the display module is further used to display the protein in situ expression level report.

In a third aspect, the present application provides a device, the device comprising: a processor and a memory;

One or more computer programs are stored in the memory, and the one or more computer programs include instructions; when the instructions are executed by the processor, the electronic device executes the method as described in any one of the first aspects.

In a fourth aspect, the present application provides a computer storage medium, which includes computer instructions. When the computer instructions are executed on an electronic device, the electronic device executes the method as described in any one of the first aspects.

In a fifth aspect, the present application provides a computer program product. When the computer program product runs on a computer, the computer executes the method as described in any one of the first aspects.

The technical solution of this application has the following beneficial effects:

The present application provides a protein expression analysis method and related equipment, the method comprising: obtaining sequencing data of a biological sample sequenced by a sequencing chip, the sequencing data comprising a sequence value and the position of the sequence value; determining the sequencing data belonging to the inside of the cell according to the single-stranded DNA staining image of the biological sample; comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a pre-set protein library to obtain a comparison result; if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, then obtaining the analysis result of protein expression, the analysis result comprising the type of matched protein and the position inside the cell. The method comprehensively analyzes the protein expression inside the cell by sequencing, staining, and comparison with the protein library, and can obtain the protein expression situation inside the cell, such as the type, position, and expression abundance of the protein inside the cell.

It should be understood that the description of technical features, technical solutions, beneficial effects or similar language in this application does not imply that all features and advantages can be realized in any single embodiment. On the contrary, it is understood that the description of features or beneficial effects means that specific technical features, technical solutions or beneficial effects are included in at least one embodiment. Therefore, the description of technical features, technical solutions or beneficial effects in this specification does not necessarily refer to the same embodiment. Furthermore, the technical features, technical solutions and beneficial effects described in the present embodiment can also be combined in any appropriate manner. Those skilled in the art will understand that the embodiment can be realized without one or more specific technical features, technical solutions or beneficial effects of a specific embodiment. In other embodiments, additional technical features and beneficial effects can also be identified in a specific embodiment that does not embody all embodiments.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG1 is a flow chart of a protein expression analysis method provided in an embodiment of the present application;

FIG2 is a schematic diagram of a single-stranded DNA staining image provided in an embodiment of the present application;

FIG3 is a schematic diagram of a binary image provided in an embodiment of the present application;

FIG4 is a schematic diagram of a protein expression heat map provided in an embodiment of the present application;

FIG5 is a schematic diagram of a spatiotemporal proteomics analysis method provided in an embodiment of the present application;

FIG6 is a basic statistical diagram of data provided in an embodiment of the present application;

FIG7 is a schematic diagram of a protein data capture situation provided in an embodiment of the present application;

FIG8 is a saturation statistical diagram provided in an embodiment of the present application;

FIG9 is a schematic diagram of the proportion of protein types provided in an embodiment of the present application;

FIG. 10 is a schematic diagram of a protein expression analysis device provided in an embodiment of the present application.

Detailed ways

The terms "first", "second", "third", etc. in the specification, claims and drawings of this application are used to distinguish different objects rather than to limit a specific order.

In the embodiments of the present application, words such as "exemplary" or "for example" are used to indicate examples, illustrations or descriptions. Any embodiment or design described as "exemplary" or "for example" in the embodiments of the present application should not be interpreted as being more preferred or more advantageous than other embodiments or designs. Specifically, the use of words such as "exemplary" or "for example" is intended to present related concepts in a specific way.

In order to make the description of the following embodiments clear and concise, a brief introduction to the related technology is first given:

Spatiotemporal omics technology, used in the study of life sciences, was once named the technology of the year. Based on this, more and more studies using spatiotemporal omics technology have been conducted, promoting research in the fields of species evolution, embryonic development, disease mechanisms, etc. RNA will be translated into protein, and protein is the direct embodiment of physiological function.

Currently, immunohistochemistry (immunofluorescence) technology can be used to detect proteins. However, immunohistochemistry can detect a limited number of proteins at the same time, the detection area is small, and the resolution is low. Although protein detection can be achieved, there is still a lack of relevant analysis methods, and it is impossible to analyze the expression of proteins.

In view of this, the present application provides a protein expression analysis method, which aims to obtain the types of proteins inside cells, the locations of proteins, and the expression abundance of proteins.

Specifically, the method can be performed by an analysis device, and the method includes: the analysis device obtains sequencing data of a biological sample sequenced by a sequencing chip, and the sequencing data includes a sequence value and the position of the sequence value; according to the single-stranded DNA staining image of the biological sample, the sequencing data belonging to the inside of the cell is determined; the sequence value in the sequencing data inside the cell is compared with the sequence value of the protein in the pre-set protein library to obtain a comparison result; if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, the analysis result of the protein expression is obtained, and the analysis result includes the type of the matched protein and the position inside the cell. The method comprehensively analyzes the protein expression inside the cell by sequencing, staining, and comparison with the protein library, and can obtain the protein expression inside the cell, such as the type, position, and expression abundance of the protein inside the cell.

In order to make the technical solution of the present application clearer and easier to understand, the technical solution of the present application is introduced below from the perspective of analyzing the equipment in conjunction with the accompanying drawings.

As shown in FIG. 1 , this figure is a flow chart of a protein expression analysis method provided in an embodiment of the present application, the method comprising:

S101. An analysis device obtains sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a location of a protein corresponding to the sequence value.

The sequencing chip can be a spatiotemporal sequencing chip (e.g., a BGI spatiotemporal sequencing chip), and the biological sample is sequenced based on the sequencing chip to obtain sequencing data. The sequencing data includes a sequence value and the location of the protein corresponding to the sequence value. In some examples, the location of the protein can be represented by coordinates, such as abscissa and ordinate. The sequence value can be a base sequence, such as "GCCGCCCCAG". An embodiment of the present application provides a sequencing data, as shown in Table 1.

Table 1:

Barcode x y GCCCCCCCGCACCCCGCCGGAGAAG 67615 33826 CCTCCCCCGCCGCCCCTCGCGAAAG 67615 33827 CCTTCCCCCGACCCCCTCACATCGG 67615 33829 CTGTCCGCTCCCCTCTCCTCGTTCA 67615 33831 … … …

Wherein, barcode represents the sequence value, x represents the horizontal coordinate of the corresponding sequence value, and y represents the vertical coordinate of the corresponding sequence value.

S102. The analysis device determines the sequencing data belonging to the interior of the cell based on the single-stranded DNA staining image of the biological sample.

In some examples, the tissue sections of the biological sample can be pre-stained with single-stranded DNA, and then the biological sample can be microphotographed to obtain a single-stranded DNA staining image. As shown in Figure 2, this figure is a schematic diagram of a single-stranded DNA staining image provided in an embodiment of the present application.

The analysis device can perform binarization processing on the single-stranded DNA staining image to obtain a binarized image. As shown in Figure 3, this figure is a schematic diagram of a binarized image provided in an embodiment of the present application. Among them, the white part in the binarized image represents the inside of the cell, and the black part represents the outside of the cell.

Next, the sequencing data that does not belong to the interior of the cell can be filtered out, thereby obtaining the sequencing data that belongs to the interior of the cell. In some examples, the area inside the cell can be determined by binarizing the image, and the sequencing data obtained in S101 includes the position, and then the position corresponding to the interior of the cell is filtered out from the sequencing data, thereby obtaining the remaining sequencing data that belongs to the interior of the cell.

S103, the analysis device compares the sequence value in the sequencing data inside the cell with the sequence value of the protein in the preset protein library to obtain a comparison result.

The pre-set protein library can be a library that can detect proteins based on the screening of spatiotemporal proteomics technology. In some embodiments, the sequence values in Table 1 above can be compared with the sequence values of proteins in the pre-set protein library to obtain a comparison result. The comparison result can include two situations: matching and mismatching. In the case of matching, the type of protein corresponding to the sequence value in the sequencing data can be determined based on the protein library. In the case of mismatching, the protein corresponding to the sequence value is characterized as not existing.

In some embodiments, the analysis device can match the sequence value in the sequencing data inside the cell with the sequence value of the protein in the pre-set protein library to obtain a matching degree. If the matching degree is greater than a preset threshold, the comparison result that the sequence value in the sequencing data inside the cell matches the sequence value of the protein in the pre-set protein library is determined. The matching degree can be characterized by a percentage or other means. The preset threshold can be an empirical value or a value determined based on an error range, for example, it can be 95%, 90%, etc.

In some embodiments, the sequence value in the sequencing data includes a coupled initial base sequence and a marker base sequence, and the marker base sequence is used to determine the type of protein corresponding to the sequence value.

The marker base sequence may be a 15 bp base sequence, as shown in Table 2 below.

Table 2:

Base sequence type CTCATTGTAACTCCT Human-CD3 GCGCAACTTGATGAT Human-CD8 CTGGGCAATTACTCG Human-CD19 ACAGCGCCGTATTTA Human-PD-1 GTTGTCCGACAATAC Human-PD-L1 TTGCTTATTTCCGCA Mouse-P2RY12 … …

Among them, Table 2 is an example of an ADT tag library provided in an embodiment of the present application.

Before performing the comparison, the analysis device can couple the above-mentioned marked base sequence on the basis of the initial base sequence, so as to facilitate the comparison and subsequent processing.

S104. If the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, the analysis device obtains the analysis result of the protein expression, and the analysis result includes the type of the matched protein and the location inside the cell.

In some embodiments, the analysis results may also include the expression abundance corresponding to each protein. Based on this, the analysis device may also obtain the unique molecular identifier of the protein inside the cell, and then deduplicate the protein inside the cell based on the unique molecular identifier of the protein inside the cell to obtain the expression abundance corresponding to each protein inside the cell.

A unique molecular identifier is an identifier used to mark a protein. If a protein is obtained by replication, the same unique molecular identifier will exist. If two proteins are the same but not obtained by replication, the unique molecular identifiers of the two proteins are different. Therefore, based on the unique molecular identifier, the duplicate proteins generated by the PCR process can be removed to obtain the true number of proteins inside the cell. Based on the true number of proteins, the expression abundance of the protein can be obtained. Based on the above process, the analysis equipment can obtain a statistical table of protein expression, as shown in Table 3 below.

table 3:

x y ADT tag number UMI (Unique Molecular Identifier) Reads 6045 18653 17 253298 3 20103 16220 twenty two 686750 3 7052 17017 26 386504 3 12546 18367 31 699050 3 19839 15003 17 931045 3 9840 13305 17 643739 3 … … … … …

Among them, x represents the horizontal axis, y represents the vertical axis, the ADT tag number is used to represent different protein types, and is encoded with numbers. The UMI sequence, that is, the unique molecular identifier, is the number of reads. Each row can be interpreted as the number of reads of a certain protein value under the corresponding UMI sequence at the position corresponding to the x-coordinate and the y-coordinate.

After the analysis device completes the above deduplication processing, accurate analysis results can be obtained, wherein the analysis results are shown in Table 4 below.

Table 4:

GeneID x y MIDCount Mouse-CD8a 13607 14272 1 Mouse-CD4 12516 7941 1 Mouse-IgD 15646 10044 1 Mouse-CD19 12711 6853 1 Mouse-IgG2a 16100 12754 2 … … … …

Among them, GeneID represents the type of protein, x represents the horizontal coordinate of the protein, y represents the vertical coordinate of the protein, and MIDCount represents the expression abundance of the protein.

In some embodiments, the analysis device may generate a protein in situ expression report based on the above analysis results, and then display the above protein in situ expression report through a display device for user reference.

In some embodiments, the analysis device can also generate a protein expression heat map based on the analysis results of protein expression, which is used to describe the type, position and expression abundance of proteins inside the cell. In some examples, the analysis device can deliver the task of generating a protein expression heat map through a web page, and then obtain a protein expression heat map. Then, through a display device, the protein expression heat map is displayed for user reference. As shown in Figure 4, the figure is a schematic diagram of a protein expression heat map provided in an embodiment of the present application.

For ease of understanding, the spatiotemporal proteomic analysis method provided in an embodiment of the present application is introduced below, as shown in FIG5 , which is a schematic diagram of a spatiotemporal proteomic analysis method provided in an embodiment of the present application.

Among them, "1" means that based on the sequencing chip, the spatiotemporal sequencing chip sequence and position coordinate file are obtained. The sequencing chip can be a 1cm*1cm chip. The sequencing chip can include many points, each store corresponds to a probe, the sequence of the probe is random, and the probe at each position will correspond to a sequence.

"2" indicates an image obtained after microscopic photography after cell nucleus staining. The tissue section may be a section of a biological sample, which is stained with single-stranded DNA and then photographed under a microscope.

"3" indicates the antibody-coupled sequence sequencing data file. The protein and mRNA correspond to a .fastq file respectively, and the probe can capture the sequences of mRNA and protein at the same time.

“4” indicates an antibody library coupled with a 15 bp base sequence, which is used for comparison and determination of the types of proteins and mRNAs.

“5” indicates the statistical file of protein expression, see Table 3 above.

“6” indicates the microscopic photograph after registration with the expression matrix.

"7" indicates a binary image generated by tissue segmentation based on the ssDNA map. The inside of the cell is white, and the outside of the cell is black.

“8” indicates the expression level file after cell segmentation.

"9" means cell segmentation based on the registered microscopic photographs, with the value inside the cell being 1 and the value outside the cell being 0. Image file filled with 0 and 1.

“10” indicates the expression level file within the tissue, see Table 4 above.

It should be noted that spatiotemporal proteomics technology is mainly divided into three parts. First, based on the spatiotemporal sequencing chip, the spatiotemporal sequencing chip is sequenced for the first time to obtain the chip coordinate mask file (as shown in Table 1 above), in which the first column is the 25bp barcode sequence, the second column is the sequencing chip x coordinate, and the third column is the sequencing chip y coordinate; second, imaging microscopy photography. The tissue sections are stained with ssDNA and then photographed microscopically. The analysis equipment can obtain the nucleus imaging of cells on the tissue, also known as the ssDNA map (as shown in Figure 2), and then the cells are segmented according to the position of the nucleus shown on the ssDNA map. Third, the mRNA and ADT tag captured by the spatiotemporal sequencing chip are sequenced, where the ADT tag is a sequence used to mark the protein, that is, a 15bp base sequence. Each protein is coupled with a 15bp base sequence, and the spatiotemporal proteomics technology screens a library of some detectable proteins. The corresponding protein and the coupled 15bp base sequence are recorded (as shown in Table 2). ADT tag sequencing data fastq file Read1 35bp, where 1-25 are chip barcode sequences. 26-35 are UMI sequences. Read2 15bp, which is the ADT tag sequence.

Based on the above three parts, we can get the chip coordinate mask file, single-stranded DNA map and ADT tag fastq file. Then, the protein expression is analyzed based on the above chip coordinate mask file, single-stranded DNA map and ADT tag fastq file.

S201: The analysis device compares the Read1 1-25bp base sequence of the ADT tag fastq file with the first column of the chip barcode sequence of the chip coordinate mask file, and then obtains the in situ coordinates of the ADT tag sequence on the chip, wherein the comparison process allows a 1bp mismatch.

S202: The analysis device compares the Read2 15bp base sequence of the ADT tag fastq file with the screened library of detectable proteins to obtain the type of protein. The location of a certain protein on the chip can then be obtained by combining it with the chip coordinate mask file.

S203: Analyze the device to remove duplicates/ADT counts and calculate the in situ expression abundance of the protein. That is, for the detected ADT tag molecules, remove the duplications caused by PCR (which can be removed by UMI) to obtain the expression abundance of the protein at a specific location.

The embodiment of the present application provides an experimental example, which is introduced below.

The biological sample is a mouse thymus sample. Through the steps in the above embodiment, the fastq file read1 of the ADT tag and the chip mask file are obtained, and then compared to obtain Total Reads (the total number of original sequencing reads) and Valid CID Reads (the 1-25bp barcode sequence of Read1 is called CID. The number of valid CID Reads is the number of reads whose barcode of the read in Total Reads can match the barcode of the chip. That is: the number of reads that can find the corresponding position on the chip).

Compare the ADT tag fastq file read2 with the ADT tag database. Get the Valid PID Reads (the 1-15bp sequence of Read2 is the PID sequence. The number of valid PID reads, the reads at the corresponding position found on the chip, and the reads compared with the antibody library coupled with 15bp nucleic acid) and the basic quality of the data. In this example, 72.15% of the protein data was used for subsequent qualitative and quantitative analysis after quality control.

As shown in Figure 6, this figure is a basic statistical diagram of data provided by the embodiment of the present application. The English explanation in the figure can be found in Table 5 below.

table 5:

Then, tissue segmentation and cell segmentation are performed according to the single-stranded DNA image taken by the microscope, where the single-stranded DNA image can be seen in Figure 2 or Figure 3. Next, the capture of protein data is statistically analyzed based on the binsize of the spatiotemporal chip and the level of the cell after cell segmentation, as shown in Figure 7, which is a schematic diagram of a protein data capture provided in an embodiment of the present application. The English explanation can be seen in Table 6 below.

Table 6:

Based on the UMI, the captured reads are deduplicated, the types of UMI are calculated to obtain the expression of the protein, and the saturation is counted. As shown in Figure 8, this figure is a saturation statistical graph provided in an embodiment of the present application. Among them, the horizontal axis of Figure 8 (a) represents the amount of sequencing data, and the vertical axis represents the saturation; the horizontal axis of Figure 8 (b) represents the amount of sequencing data, and the vertical axis represents the number of unique reads under each bin.

The proportion of protein types and overall UMIs is statistically analyzed, as shown in FIG9 , which is a schematic diagram of the proportion of protein types provided in an embodiment of the present application.

Based on the above description, the embodiment of the present application provides a protein expression analysis method, which includes: obtaining sequencing data of sequencing a biological sample by a sequencing chip, the sequencing data including a sequence value and the position of the sequence value; determining the sequencing data belonging to the inside of the cell according to the single-stranded DNA staining image of the biological sample; comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a pre-set protein library to obtain a comparison result; if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, then obtaining the analysis result of protein expression, the analysis result including the type of matched protein and the position inside the cell. The method comprehensively analyzes the protein expression inside the cell by sequencing, staining, and comparison with the protein library, and can obtain the protein expression inside the cell, such as the type, position, and expression abundance of the protein inside the cell.

The present application also provides a protein expression analysis device, as shown in FIG10 , which is a schematic diagram of a protein expression analysis device provided in the present application, the device comprising:

An acquisition module 1001 is used to acquire sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a position of the sequence value;

A determination module 1002 is used to determine the sequencing data belonging to the interior of the cell according to the single-stranded DNA staining image of the biological sample;

A comparison module 1003 is used to compare the sequence value in the sequencing data inside the cell with the sequence value of the protein in the preset protein library to obtain a comparison result;

The analysis module 1004 is used to obtain the analysis result of protein expression if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, and the analysis result includes the type of the matched protein and the location inside the cell.

Optionally, the analysis result also includes: the expression abundance corresponding to each protein; the acquisition module 1001 is also used to obtain the unique molecular identifier of the protein inside the cell; the analysis module is also used to deduplicate the protein inside the cell according to the unique molecular identifier of the protein inside the cell to obtain the expression abundance corresponding to each protein inside the cell.

Optionally, the comparison module 1003 is specifically used to determine a comparison result that the sequence value in the sequencing data inside the cell matches the sequence value of the protein in the preset protein library if the degree of matching between the sequence value in the sequencing data inside the cell and the sequence value of the protein in the preset protein library is greater than a preset threshold.

Optionally, the sequence value in the sequencing data includes a coupled initial base sequence and a marked base sequence, and the marked base sequence is used to determine the type of protein corresponding to the sequence value.

Optionally, the device further includes a display module, and the analysis module 1004 is further used to generate a protein expression heat map according to the analysis results of the protein expression, wherein the protein expression heat map is used to describe the type, location and expression abundance of the protein inside the cell;

The display module is used to display the protein expression heat map.

Optionally, the analysis module 1004 is further used to generate a protein in situ expression level report according to the analysis results; the display module is further used to display the protein in situ expression level report.

The embodiment of the present application also provides a device, which includes: a processor and a memory;

One or more computer programs are stored in the memory, and the one or more computer programs include instructions; when the instructions are executed by the processor, the electronic device executes a method as described in any one of the method embodiments.

An embodiment of the present application further provides a computer storage medium, which includes computer instructions. When the computer instructions are executed on an electronic device, the electronic device executes a method as described in any one of the method embodiments.

An embodiment of the present application further provides a computer program product. When the computer program product is run on a computer, the computer executes a method as described in any one of the method embodiments.

It should also be noted that the device embodiments described above are merely schematic, wherein the units described as separate components may or may not be physically separated, and the components displayed as units may or may not be physical units, that is, they may be located in one place, or they may be distributed over multiple network units. Some or all of the modules may be selected according to actual needs to achieve the purpose of the scheme of this embodiment. In addition, in the drawings of the device embodiments provided by the present application, the connection relationship between the modules indicates that there is a communication connection between them, which may be specifically implemented as one or more communication buses or signal lines.

Through the description of the above implementation mode, the technicians in the field can clearly understand that the present application can be implemented by means of software plus necessary general hardware, and of course, it can also be implemented by special hardware including special integrated circuits, special CPUs, special memories, special components, etc. In general, all functions completed by computer programs can be easily implemented by corresponding hardware, and the specific hardware structure used to implement the same function can also be various, such as analog circuits, digital circuits or special circuits. However, for the present application, software program implementation is a better implementation mode in more cases. Based on such an understanding, the technical solution of the present application is essentially or the part that contributes to the prior art can be embodied in the form of a software product, which is stored in a readable storage medium, such as a computer floppy disk, a U disk, a mobile hard disk, a ROM, a RAM, a disk or an optical disk, etc., including a number of instructions to enable a computer device (which can be a personal computer, a training device, or a network device, etc.) to execute the methods described in each embodiment of the present application.

In the above embodiments, all or part of the embodiments may be implemented by software, hardware, firmware or any combination thereof. When implemented by software, all or part of the embodiments may be implemented in the form of a computer program product.

The computer program product includes one or more computer instructions. When the computer program instructions are loaded and executed on a computer, the process or function described in the embodiment of the present application is generated in whole or in part. The computer may be a general-purpose computer, a special-purpose computer, a computer network, or other programmable device. The computer instructions may be stored in a computer-readable storage medium, or transmitted from one computer-readable storage medium to another computer-readable storage medium. For example, the computer instructions may be transmitted from one website, computer, training equipment, or data center to another website, computer, training equipment, or data center by wired (e.g., coaxial cable, optical fiber, digital subscriber line (DSL)) or wireless (e.g., infrared, wireless, microwave, etc.) means. The computer-readable storage medium may be any available medium that a computer can store or a data storage device such as a training device, data center, etc. that includes one or more available media integrated. The available medium may be a magnetic medium (e.g., a floppy disk, a hard disk, a tape), an optical medium (e.g., a DVD), or a semiconductor medium (e.g., a solid-state drive (SSD)).

Claims (10)

A protein expression analysis method, characterized by comprising: Acquire sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a location of a protein corresponding to the sequence value; Determining sequencing data belonging to the interior of the cell according to the single-stranded DNA staining image of the biological sample; Comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a preset protein library to obtain a comparison result; If the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, then the analysis result of protein expression is obtained, and the analysis result includes the type of the matched protein and the location inside the cell. The method according to claim 1, characterized in that the analysis result further includes: the expression abundance corresponding to each protein; the method further includes: Obtaining a unique molecular identifier of a protein inside the cell; According to the unique molecular identifier of the protein inside the cell, the protein inside the cell is deduplicated to obtain the expression abundance corresponding to each protein inside the cell. The method according to claim 1 or 2, characterized in that the comparing the sequence value in the sequencing data inside the cell with the sequence value of the protein in a preset protein library to obtain the comparison result comprises: If the degree of match between the sequence value in the sequencing data inside the cell and the sequence value of the protein in the preset protein library is greater than a preset threshold, a comparison result is determined that the sequence value in the sequencing data inside the cell matches the sequence value of the protein in the preset protein library. The method according to claim 1 is characterized in that the sequence value in the sequencing data includes a coupled initial base sequence and a marked base sequence, and the marked base sequence is used to determine the type of protein corresponding to the sequence value. The method according to claim 2, characterized in that the method further comprises: Generate a protein expression heat map according to the analysis results of the protein expression, wherein the protein expression heat map is used to describe the type, location and expression abundance of the protein inside the cell; The protein expression heat map is displayed. The method according to any one of claims 1 to 5, characterized in that the method further comprises: Generate a protein in situ expression report based on the analysis results; A report on the in situ expression level of the protein is displayed. A protein expression analysis device, comprising: An acquisition module, used to acquire sequencing data of a biological sample sequenced by a sequencing chip, wherein the sequencing data includes a sequence value and a location of a protein corresponding to the sequence value; A determination module, used to determine the sequencing data belonging to the interior of the cell according to the single-stranded DNA staining image of the biological sample; A comparison module, used to compare the sequence value in the sequencing data inside the cell with the sequence value of the protein in the preset protein library to obtain a comparison result; The analysis module is used to obtain the analysis result of protein expression if the comparison result indicates that the sequence value in the sequencing data matches the sequence value of the protein in the protein library, wherein the analysis result includes the type of the matched protein and the position inside the cell. A device, comprising: a processor and a memory; One or more computer programs are stored in the memory, and the one or more computer programs include instructions; when the instructions are executed by the processor, the electronic device executes the method as described in any one of claims 1 to 6. A computer storage medium, characterized in that it includes computer instructions, and when the computer instructions are executed on an electronic device, the electronic device executes the method as described in any one of claims 1-6. A computer program product, characterized in that when the computer program product is run on a computer, the computer executes the method according to any one of claims 1 to 6.

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