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Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Background: Much learning has emerged as a versatile approach for predicting complex biological phenomena. However, the utility of biological discoveries so far been limited, given that generic neural network in providing some insight into the biological mechanisms that underlie successful predictions.

Here we demonstrate in-depth study on the biological network, where each node has an equivalent molecules, such as proteins or genes, and each edge has a mechanistic interpretation, such as regulatory interactions along the signal path.


Results: With the knowledge-primed neural network (KPNNs), we exploit the ability of deep learning algorithm to assign significant weight in the multi-layered network, thus broadly applicable approach to learning in the interpretation. We present a method of learning that increases the interpretability of KPNNs trained by stabilizing the node weights in the presence of redundancy, improve the interpretability quantitative node weights, and control for connectivity are uneven in biological tissue. We validate KPNNs simulated data with known ground truth and show their practical use and utility in five applications with single-cell biology of RNA-seq data for cancer and immune cells.


Conclusions: We introduce KPNNs as a method that combines the predictive power of deep learning with biological tissue interpretability. While shown here at the single-cell sequencing data, this method is broadly relevant to other research fields in which domain knowledge before it can be represented as a network.


neuroendocrine neoplasms (NENs) is a clinical cancer incomplete diverse and characterized challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancer. More recently, morphology-based classification framework to evaluate NENs from different anatomical sites proposed by the experts, the need for enhanced integration of molecular data.

Here, we collected 378 miRNA expression profiling to examine the classification of Nen through a comprehensive miRNA profiling and data mining. The following data preprocessing, our final study cohort included 221 and 114 Nen-Nen non samples, representing 15 Nen type of pathological and 5 non-site-matched control group Nen.

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data

Use Whole Genome Sequencing data for First Silico Evaluation Test Specificity of RT-qPCR Used for SARS-CoV-2 Detection

Disease coronavirus Flow 2019 (COVID-19) pandemic started in December 2019. COVID 19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, a limited number of SARS-CoV-2 genome is available as RT-qPCR method was first developed in January 2020 to early in silico evaluation of specificity and to verify whether the target locus highly conserved.

Now that the genome data more completely available, we use the tools of bioinformatics filtered and total 4755 publicly available SARS-CoV-2 genome, download at two different time points to evaluate the specificity 12 tests RT-qPCR (comprised of a total of 30 primary and probe sets) used for SARS-CoV-2 detection and the impact of the genetic evolution of the virus’ on four of them.

Trypin for Mass & Sequencing
T9600-112 12x100ug
EUR 1988.4

Trypin for Mass & Sequencing
T9600-400 4x100ug
EUR 781.2

sequencing system 20x50 cm
ESEQ1200-SYS ea
EUR 1842

Sequencing Grade V8 Protease
RE014 50ug
EUR 209

TNM Sequencing Primers for SE
TMS002-C1-1rxn 1 rxn
EUR 115

TNM Sequencing Primers for PE
TMS002-C2-1rxn 1 rxn
EUR 143.88

Chymotrypsin for Sequencing grade
C4001-010 4x25ug
EUR 375.6

Chymotrypsin for Sequencing grade
C4001-100 100ug
EUR 343.2

Sequencing Grade Modified Trypsin
RE012 100ug
EUR 229

Oligo, Sequencing Primer, SK (17mer)
MBS634188-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SK (17mer)
MBS634188-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, KS (17mer)
MBS634192-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, KS (17mer)
MBS634192-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, SK (20mer)
MBS634219-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SK (20mer)
MBS634219-5x0033mg 5x0.033mg
EUR 1240

Oligo, Sequencing Primer, T3 (17mer)
MBS634243-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T3 (17mer)
MBS634243-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, T7 (17mer)
MBS634247-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T7 (17mer)
MBS634247-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, KS (19mer)
MBS634259-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, KS (19mer)
MBS634259-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, T3 (20mer)
MBS634261-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T3 (20mer)
MBS634261-5x0033mg 5x0.033mg
EUR 1240

Sequencing Grade Carboxypeptidase B
RE011 100ug
EUR 99

PCR Clean Up for DNA Sequencing
BT5100 100preps
EUR 114.82

PCR Clean Up for DNA Sequencing
BT5101 1000Preps, 1000prep
EUR 553.3

ACES Sequencing Buffer 10X, pH 7.7
21420000-1 1 L
EUR 138.62

ACES Sequencing Buffer 10X, pH 7.7
21420000-2 4 L
EUR 456.17

TBE-Buffer 5X for DNA Sequencing
40121072-1 100 mL
EUR 26.54

TBE-Buffer 5X for DNA Sequencing
40121072-2 500 mL
EUR 44.84

TBE-Buffer 5X for DNA Sequencing
40121072-3 1 L
EUR 72.29

TBE-Buffer 5X for DNA Sequencing
40121072-4 4 L
EUR 192.14

SequaGel Sequencing System 1L Kit - 1KIT
NAT1136 1KIT
EUR 187.65

SequaGel Sequencing System 2.2L Kit - EACH
NAT1138 EACH
EUR 318.6

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ100UG each
EUR 148
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ1MG each
EUR 765
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
IBOTRYSEQ400UG each
EUR 419
Description: Bovine Trypsin Purified Sequencing Grade

Bovine Trypsin Purified Sequencing Grade
MBS136298-01mg 0.1mg
EUR 255

Bovine Trypsin Purified Sequencing Grade
MBS136298-04mg 0.4mg
EUR 540

Bovine Trypsin Purified Sequencing Grade
MBS136298-1mg 1mg
EUR 935

Bovine Trypsin Purified Sequencing Grade
MBS136298-5x1mg 5x1mg
EUR 4010

HCV-N-G3/10 (residues 2-119)
PR-1140 100µg
EUR 300.7
Description: recombinant, E. coli

EpiNext Bisulfite Sequencing Kit (Illumina)
P-1056
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  • 24 Reactions
  • 12 Reactions
  • 24 Reactions

Oligo, Sequencing Primer, T7 Universal (20mer)
MBS634194-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, T7 Universal (20mer)
MBS634194-5x0033mg 5x0.033mg
EUR 1240

Oligo, Sequencing Primer, SP6 Promoter (19mer)
MBS634260-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, SP6 Promoter (19mer)
MBS634260-5x0033mg 5x0.033mg
EUR 1235

DNA Library Prep Kit for IIlumina Sequencing
K1475-12 12 Rxns
EUR 576

Trifluoroacetic Acid (TFA) for HPLC & Sequencing, 99.9%
23947 10 x1 ml
EUR 165.03
Description: Part A

Oligo, Sequencing Primer, Lambda gt11, Reverse (24mer)
MBS634120-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt11, Reverse (24mer)
MBS634120-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt10, Reverse (31mer)
MBS634167-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt10, Reverse (31mer)
MBS634167-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt11, Forward (24mer)
MBS634252-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt11, Forward (24mer)
MBS634252-5x0033mg 5x0.033mg
EUR 1245

Oligo, Sequencing Primer, Lambda gt10, Forward (27mer)
MBS634255-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, Lambda gt10, Forward (27mer)
MBS634255-5x0033mg 5x0.033mg
EUR 1240

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY100UG each
EUR 130
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY1MG each
EUR 640
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
IBOTRYSEQLY400UG each
EUR 344
Description: Bovine Trypsin Purified Sequencing Grade Lyophilized

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-01mg 0.1mg
EUR 235

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-04mg 0.4mg
EUR 465

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-1mg 1mg
EUR 795

Bovine Trypsin Purified Sequencing Grade Lyophilized
MBS136299-5x1mg 5x1mg
EUR 3400

Oligo, Sequencing Primer, pBR322 (EcoR I), Clockwise (16mer)
MBS634158-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (EcoR I), Clockwise (16mer)
MBS634158-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, pBR322 (BamH I), Clockwise (20mer)
MBS634234-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, pBR322 (BamH I), Clockwise (20mer)
MBS634234-5x0033mg 5x0.033mg
EUR 1240

HCV-N-G4 (residues 2-119)
PR-1137 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G5 (residues 2-119)
PR-1138 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G1a (residues 2-119)
PR-1130 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G1b (residues 2-119)
PR-1132 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G2b (residues 2-119)
PR-1134 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G3a (residues 2-119)
PR-1135 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G3b (residues 2-119)
PR-1136 100µg
EUR 300.7
Description: recombinant, E. coli

HCV-N-G6a (residues 2-119)
PR-1139 100µg
EUR 300.7
Description: recombinant, E. coli

Oligo, Sequencing Primer, pBR322 (Pst I), Counterclockwise (16mer)
MBS634143-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (Pst I), Counterclockwise (16mer)
MBS634143-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, pBR322 (BamH I), Counterclockwise (16mer)
MBS634262-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (BamH I), Counterclockwise (16mer)
MBS634262-5x0033mg 5x0.033mg
EUR 1230

Oligo, Sequencing Primer, pBR322 (Hind III), Counterclockwise (16mer)
MBS634154-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, pBR322 (Hind III), Counterclockwise (16mer)
MBS634154-5x0033mg 5x0.033mg
EUR 1230

Genorise® Customized PCR primers for cloning and sequencing
GR108023 2 nmol
EUR 65

HCV-N-G2a (residues 2-119)GST
PR-1133 100µg
EUR 300.7
Description: recombinant, E. coli

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
IBOCHYTLCKSG100UG each
EUR 297
Description: Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
MBS136223-01mg 0.1mg
EUR 400

Bovine Alpha Chymotrypsin 3X Crystallized TLCK Treated Sequencing Grade
MBS136223-5x01mg 5x0.1mg
EUR 1605

Oligo, Sequencing Primer, M13 Reverse (16mer) [5'-AAC AGC TAT GAC CAT G-3']
MBS634131-0033mg 0.033mg
EUR 305

Oligo, Sequencing Primer, M13 Reverse (16mer) [5'-AAC AGC TAT GAC CAT G-3']
MBS634131-5x0033mg 5x0.033mg
EUR 1230

Anti-TAF2(N-terminal-middle residues) Polyclonal Antibody
AB1J129 0.1mg
EUR 399

Oligo, Sequencing Primer, M13 (-20) Forward (17mer) [5'-GTA AAA CGA CGG CCA GT-3']
MBS634146-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, M13 (-20) Forward (17mer) [5'-GTA AAA CGA CGG CCA GT-3']
MBS634146-5x0033mg 5x0.033mg
EUR 1235

Oligo, Sequencing Primer, M13 Reverse (19mer) [5'-GGA AAC AGC TAT GAC CAT G-3']
MBS634148-0033mg 0.033mg
EUR 310

Oligo, Sequencing Primer, M13 Reverse (19mer) [5'-GGA AAC AGC TAT GAC CAT G-3']
MBS634148-5x0033mg 5x0.033mg
EUR 1235

RV gE2 (residues 31-105)
PR-1229 100µg
EUR 300.7
Description: recombinant, E. coli

RV-C (residues 1-123)
PR-1230 100µg
EUR 300.7
Description: recombinant, E. coli

TG MIC3 (residues 234-306)
PR-1243 100µg
EUR 300.7
Description: Toxoplasma gondii, recombinant, E. coli

EBV-EA (residues 306-390)
PR-1224 100µg
EUR 300.7
Description: recombinant, E. coli

CMV pp28 (residues 130-160)
PR-1248 100µg
EUR 300.7
Description: recombinant, E. coli

CMV pp65 (residues 297-510)
PR-1251 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-P2C (residues 1121-1234)
PR-1115 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-P3C (residues 1643-1743)
PR-1121 100µg
EUR 300.7
Description: recombinant, E. coli

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
IBCTCLOSGPF10UG each
EUR 165
Description: Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
MBS136171-01mg 0.1mg
EUR 270

Bacteria-Derived Clostripain (Endoproteinase-Arg-C) Sequencing Grade Purified
MBS136171-5x001mg 5x0.01mg
EUR 1035

SARS-ACM (residues 182-216)
PR-1101 100µg
EUR 300.7
Description: recombinant, E. coli

HEV-ORF3 (residues 92-123)
PR-1187 100µg
EUR 300.7
Description: recombinant, E. coli

Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized
IBCTV8SEQLY250UG each
EUR 784
Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized
IBCTV8SEQLY50UG each
EUR 304
Description: Bacteria-Derived V8 Protease (Endoprotease Glu-C) Sequencing Grade Lyophilized

AF6-RBDGST (residues 1-141)
PR-398 50µg
EUR 271.4
Description: human, recombinant, E. coli

SARS-ACE (residues 1-76)
PR-1100 100µg
EUR 300.7
Description: recombinant, E. coli

Clenbuterol Residues [BSA]
DAGA-004B 1mg
EUR 936

Clenbuterol Residues [HRP]
DAGA-004H 1mg
EUR 1404

Clenbuterol Residues [KLH]
DAGA-004K 1mg
EUR 1248

HIV-1 Nef (residues 3-190)
PR-1214 100µg
EUR 300.7
Description: recombinant, E. coli

TG GRA1/p24 (residues 57-149)
PR-1244 100µg
EUR 300.7
Description: Toxoplasma gondii, recombinant, E. coli

TG GRA7/p29 (residues 24-100)
PR-1245 100µg
EUR 300.7
Description: Toxoplasma gondii, recombinant, E. coli

SARS-ACN/1 (residues 340-390)
PR-1102 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-VP1-P2A (residues 722-830)
PR-1113 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-VP1-P2A (residues 669-782)
PR-1114 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-P2C-P3B (residues 1492-1606)
PR-1118 100µg
EUR 300.7
Description: recombinant, E. coli

HAV-VP4-VP2 (residues 55-164)
PR-1120 100µg
EUR 300.7
Description: recombinant, E. coli

SARS-ACN/2 (residues 1-49)
PR-1103 100µg
EUR 300.7
Description: recombinant, E. coli

VZV ORF9 (residues 6-28/76-100)
PR-1254 100µg
EUR 300.7
Description: recombinant, E. coli

Histone H3 Peptide (residues 15-39) 
R-1005
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  • 200 µl
  • 100 ul
  • 200 ul

VZV ORF26 (residues 9-33/184-208)
PR-1255 100µg
EUR 300.7
Description: recombinant, E. coli

HBV-Core 18 kDa (residues 1-183)
PR-1123 100µg
EUR 300.7
Description: recombinant, E. coli

Histone H3 Peptide (residues 1-21) 
R-1003
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  • 400 µl
  • 200 ul
  • 400 ul

Clenbuterol residues ELISA Kit
DEIANJ44 96T
EUR 1039.2
Description: This ELISA kit is used for quantitative determination of Clenbuterol residues.

SARS-ACN/3 (residues 1-49/192-220)
PR-1104 100µg
EUR 300.7
Description: recombinant, E. coli

SARS-ACSMS(M) (residues 408-470/540-573)
PR-1106 100µg
EUR 300.7
Description: recombinant, E. coli

HTLV-1 Mosaic (residues 374-400/190-207)
PR-1221 100µg
EUR 300.7
Description: recombinant, E. coli

HBV-Core delta 14 kDa (residues 1-144)
PR-1124 100µg
EUR 300.7
Description: recombinant, E. coli

EBV-EBNA1 Mosaic (residues 1-90/408-498)
PR-1223 100µg
EUR 300.7
Description: recombinant, E. coli

Histone H3 Peptide (residues 21-44), Biotinylated
R-1006
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  • 200 µl
  • 100 ul
  • 200 ul

Histone H3 Peptide (residues 69-89), Biotinylated
R-1057 200 µl
EUR 267.06

Sulfonamides residues (SAs) ELISA Kit
AE81013SF-48Tests 48 Tests
EUR 245
Description: Food Safety

Sulfonamides residues (SAs) ELISA Kit
AE81013SF-96Tests 96 Tests
EUR 450
Description: Food Safety

Sulfonamides residues (SAs) ELISA Kit
JOT-SAs-FS-48T 48T
EUR 390.4

Sulfonamides residues (SAs) ELISA Kit
JOT-SAs-FS-96T 96T
EUR 558.4

Sulfonamides residues (SAs) ELISA Kit
RDFS-SAs-48T 48T
EUR 488
Description: Animal tissue, aquatic tissue, honey, etc.

Sulfonamides residues (SAs) ELISA Kit
RDFS-SAs-96T 96T
EUR 698
Description: Animal tissue, aquatic tissue, honey, etc.

Sulfonamides residues (SAs) ELISA Kit
AE81013SF-48T 48T
EUR 265
Description: 0.5-40.5 ppb

Sulfonamides residues (SAs) ELISA Kit
AE81013SF-96T 96T
EUR 450
Description: 0.5-40.5 ppb

Sulfonamides residues (SAs) ELISA Kit
MBS282405-10x96StripWells 10x96-Strip-Wells
EUR 4880

Sulfonamides residues (SAs) ELISA Kit
MBS282405-48StripWells 48-Strip-Wells
EUR 360

Sulfonamides residues (SAs) ELISA Kit
MBS282405-5x96StripWells 5x96-Strip-Wells
EUR 2555

Sulfonamides residues (SAs) ELISA Kit
MBS282405-96StripWells 96-Strip-Wells
EUR 570

RV gE1 Mosaic (residues 157-176/374-390/213-239)
PR-1228 100µg
EUR 300.7
Description: recombinant, E. coli

SARS-ACSMS(C) (residues 1051-1076/1121-1154/1162-1190)
PR-1105 100µg
EUR 300.7
Description: recombinant, E. coli

Xylosyl residues (monoclonal, clone LM23)
AS22-4751 1 ml
EUR 246

Histone H3 Peptide (residues 1-21), Biotinylated
R-1004
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  • 200 µl
  • 100 ul
  • 200 ul

Histone H4 Peptide (residues 1-21), Biotinylated
R-1007
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  • Ask for price
  • 200 µl
  • 100 ul
  • 200 ul

Sulfonamides residues ELISA Kit (OKAO00112)
OKAO00112 96 Wells
EUR 669.6
Description: Description of target: The related sulfinamides (R(S=O)NHR) are amides of sulfinic acids (R(S=O)OH) (see sulfinyl). Chiral sulfinamides such as tert-butanesulfinamide, p-toluenesulfinamide and 2,4,6-trimethylbenzenesulfinamide are relevant to asymmetric synthesis.;Species reactivity: General;Application: ;Assay info: Assay Methodology: Competitive Inhibition ELISA;Sensitivity:
ComponentAmount
Tissue0.4 ppb
Honey, egg0.4 ppb
Serum, urine1.6 ppb
Milk8 ppb

SEPTA MAT, FOR 96 WELL PCR PLATES, SILICONE, GREY, NONSTERILE, FOR ABI MULTI-CAPILLARY SEQUENCING INSTRUMENTS, BULK
AM-96-SEPTA-3100 10/pk
EUR 639.6
Description: Sealing Products; Sealing mats - Axygen

Sulfonamides residues (SAs) ELISA Test Kit
LSY-10009 96 well/kit Ask for price

Anti- HBB(Middle residues) Polyclonal Antibody
AB5FOBP2 0.1mg
EUR 399

Anti- OGCP(Middle residues) Polyclonal Antibody
AB2E152 0.1mg
EUR 399

OKAO00112-96W - Sulfonamides residues ELISA Kit
OKAO00112-96W 96Wells
EUR 475

Exclusivity This method was also assessed using the human reference genome and the genomes of closely related 2624 other respiratory viruses. Specificity of this test is generally good and stable over time. The exception is the method was first developed by the Chinese Center for Disease Control and Prevention (CDC), which showed three primary discrepancy is present in 358 SARS-CoV-2 genome sequencing, especially in Europe from February 2020 onwards.

MarK

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