A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs.
Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets.
Match cell/lid QS LP10mm 1.4ml |
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CEL2120 | Scientific Laboratory Supplies | 1PR | EUR 343.37 |
Match cell/stpr QS/GLP10mm 3.5ml |
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CEL2052 | Scientific Laboratory Supplies | 1PR | EUR 454.35 |
Total RNA - Mouse Normal Tissue: Brain |
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R1334035-50 | Biochain | 50 ug | EUR 130 |
Rat Creatine kinase for muscle and brain (CKMB) |
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QY-E11888 | Qayee Biotechnology | 96T | EUR 448.8 |
Genomic DNA - Mouse Normal Tissue: Brain |
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D1334035 | Biochain | 100 ug | EUR 286 |
Total RNA - Human Adult Normal Tissue: Brain |
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R1234035-50 | Biochain | 50 ug | EUR 170 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Lung |
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D8235152-PP-10 | Biochain | 2x10 ug | EUR 416 |
Total RNA - Monkey (Rhesus) Normal Tissue: Brain |
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R1534035-50 | Biochain | 50 ug | EUR 191 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Colon |
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D8235090-PP-10 | Biochain | 2x10 ug | EUR 416 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Liver |
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D8235149-PP-10 | Biochain | 2x10 ug | EUR 416 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Lung |
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R8235152-PP-10 | Biochain | 2x10 ug | EUR 463 |
Brain Dissociation System 7 (Endothelial), Mouse and Rat |
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4-20227 | CHI Scientific | ea | Ask for price |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Breast |
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D8235086-PP-10 | Biochain | 2x10 ug | EUR 416 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Kidney |
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D8235142-PP-10 | Biochain | 2x10 ug | EUR 416 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Rectum |
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D8235206-PP-10 | Biochain | 2x10 ug | EUR 416 |
Brain and Acute Leukemia, Cytoplamatic |
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PR27238 | Neuromics | 2 ug | EUR 229.2 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Colon |
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R8235090-PP-10 | Biochain | 2x10 ug | EUR 463 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Liver |
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R8235149-PP-10 | Biochain | 2x10 ug | EUR 463 |
Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Stomach |
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D8235248-PP-10 | Biochain | 2x10 ug | EUR 416 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Breast |
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R8235086-PP-10 | Biochain | 2x10 ug | EUR 463 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Kidney |
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R8235142-PP-10 | Biochain | 2x10 ug | EUR 463 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Rectum |
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R8235206-PP-10 | Biochain | 2x10 ug | EUR 463 |
Total RNA - Monkey (Cynomolgus) Normal Tissue: Brain |
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R1534035-Cy | Biochain | 50 ug | EUR 191 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Lung |
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D8235152-PM-10 | Biochain | 2x10 ug | EUR 690 |
Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Stomach |
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R8235248-PP-10 | Biochain | 2x10 ug | EUR 463 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Colon |
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D8235090-PM-10 | Biochain | 2x10 ug | EUR 690 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Liver |
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D8235149-PM-10 | Biochain | 2x10 ug | EUR 690 |
Brain tumor and brain tissue array(2016 WHO CNS tumor classification) |
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GL208a | TissueArray | each | EUR 546 |
Description: Brain tumor and brain tissue array(2016 WHO CNS tumor classification), including pathology grade, 69 cases/207 cores (cores size 1.0mm), replacing GL208 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Lung |
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R8235152-PM-10 | Biochain | 2x10 ug | EUR 716 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Breast |
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D8235086-PM-10 | Biochain | 2x10 ug | EUR 690 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Kidney |
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D8235142-PM-10 | Biochain | 2x10 ug | EUR 690 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Rectum |
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D8235206-PM-10 | Biochain | 2x10 ug | EUR 690 |
Brain tumor and normal tissue array |
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GL1002 | TissueArray | each | EUR 306 |
Description: Brain tumor and normal tissue array, 50 cases/100 cores |
Brain tumor and normal tissue array |
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GL1201 | TissueArray | each | EUR 330 |
Description: Brain tumor and normal tissue array, including Meningioma and Astrocytoma, Oligodendroglioma, Glioblastoma, Neurilemmoma, Medulloblastoma, Ependymoma, lymphoma, Choroids plexus papilloma, Pituitary adenoma, Germ cell tumours, Acoustic neuroma, craniopharyngioma, Haemangioblastoma, Primal neuroectodermal tumor, with pathology grade, 120 cases/120 cores (core size 1.5mm),replacing BC17013 |
Brain tumor and normal tissue array |
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GL721 | TissueArray | each | EUR 306 |
Description: Brain tumor and normal tissue array, including pathology grade, 24 cases/72 cores |
FFPE and Frozen Matched Pair Genomic DNA: Human Tumor Tissue: Lung |
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D8235152-FP | Biochain | 2 x 2 ug | EUR 2374 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Colon |
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R8235090-PM-10 | Biochain | 2x10 ug | EUR 716 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Liver |
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R8235149-PM-10 | Biochain | 2x10 ug | EUR 716 |
Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Stomach |
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D8235248-PM-10 | Biochain | 2x10 ug | EUR 690 |
Brain cancer and normal tissue array |
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GL1001a | TissueArray | each | EUR 306 |
Description: Brain cancer and normal tissue array, including pathology grade, 100 cases/100 cores, replacing GL1001 |
FFPE and Frozen Matched Pair Genomic DNA: Human Tumor Tissue: Colon |
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D8235090-FP | Biochain | 2 x 2 ug | EUR 2374 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Breast |
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R8235086-PM-10 | Biochain | 2x10 ug | EUR 716 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Kidney |
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R8235142-PM-10 | Biochain | 2x10 ug | EUR 716 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Rectum |
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R8235206-PM-10 | Biochain | 2x10 ug | EUR 716 |
Total RNA - Human Adult Normal Tissue: Brain: Pons |
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R1234071-10 | Biochain | 10 ug | EUR 183 |
FFPE and Frozen Matched Pair Total RNA: Human Adult Normal Tissue: Liver |
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R8234149-FP | Biochain | 2x1 ug | EUR 1664 |
Brain Dissociation System 2 (Glial, Schwann), Mouse and Rat |
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4-20222 | CHI Scientific | ea | Ask for price |
FFPE and Frozen Matched Pair Genomic DNA: Human Tumor Tissue: Breast |
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D8235086-FP | Biochain | 2 x 2 ug | EUR 2374 |
Matched Pair - Total RNA - Human Primary and Metastatic Tumor Tissue: Stomach |
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R8235248-PM-10 | Biochain | 2x10 ug | EUR 716 |
FFPE and Frozen Matched Pair Genomic DNA: Human Tumor Tissue: Stomach |
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D8235248-FP | Biochain | 2 x 2 ug | EUR 2520 |
Brain Dissociation System 5 (Cerebral cortex), Mouse and Rat |
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4-20225 | CHI Scientific | ea | Ask for price |
Kidney And Brain Protein (KIBRA) Antibody |
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20-abx177265 | Abbexa |
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Kidney And Brain Protein (KIBRA) Antibody |
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20-abx131689 | Abbexa |
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Total RNA - Human Adult Normal Tissue: Brain: Thalamus |
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R1234079-50 | Biochain | 50 ug | EUR 170 |
Recombinant Kidney And Brain Protein (KIBRA) |
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4-RPL824Mu01 | Cloud-Clone |
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Description: Recombinant Mouse Kidney And Brain Protein expressed in: E.coli |
Total RNA - Human Adult Normal Tissue: Brain: Cerebellum |
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R1234039-50 | Biochain | 50 ug | EUR 170 |
Rat Brain PrimaCell1: Normal Brain Fibroblasts |
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2-82511 | CHI Scientific | 1 Kit | Ask for price |
Brain Dissociation System 3 (Hippocampal neurons), Mouse and Rat |
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4-20223 | CHI Scientific | ea | Ask for price |
Baalc ELISA Kit| Rat Brain and acute leukemia cytoplasmic prote |
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EF018386 | Lifescience Market | 96 Tests | EUR 826.8 |
Total RNA - Human Adult Normal Tissue: Brain: Hippocampus |
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R1234052-10 | Biochain | 10 ug | EUR 643 |
Total RNA - Human Adult Normal Tissue: Brain: Diencephalon |
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R1234049-10 | Biochain | 10 ug | EUR 183 |
Brain astrocytoma and meningioma tissue array |
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BC17013 | TissueArray | each | EUR 306 |
Description: Brain astrocytoma and meningioma tissue array, 120 cases/120 cores |
Rat Brain And Acute Leukemia Cytoplasmic Protein (BAALC) ELISA Kit |
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abx391033-96tests | Abbexa | 96 tests | EUR 1093.2 |
Brain and Acute Leukemia, Cytoplasmatic Protein |
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20-abx262869 | Abbexa |
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Brain Dissociation System 4 (Endothelial, Microvessels), Mouse and Rat |
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4-20224 | CHI Scientific | ea | Ask for price |
FFPE and Frozen Matched Pair Genomic DNA: Human Adult Normal Tissue: Liver |
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D8234149-FP | Biochain | 2 x 2 ug | EUR 2099 |
Total RNA - Human Adult Normal Tissue: Brain: Frontal Lobe |
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R1234051-50 | Biochain | 50 ug | EUR 170 |
Mouse Kidney And Brain Protein (KIBRA) Protein |
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20-abx650801 | Abbexa |
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Total RNA - Human Adult Normal Tissue: Brain: Parietal Lobe |
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R1234066-50 | Biochain | 50 ug | EUR 170 |
Total RNA - Human Adult Normal Tissue: Brain: Temporal Lobe |
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R1234078-50 | Biochain | 50 ug | EUR 170 |
Brain Dissociation System 6 (Brain), Fetal Rat |
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4-20226 | CHI Scientific | ea | Ask for price |
Total RNA - Human Adult Normal Tissue: Brain: Occipital Lobe |
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R1234062-50 | Biochain | 50 ug | EUR 170 |
Total RNA - Human Adult Normal Tissue: Brain: Cerebellum (left) |
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R1234040-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Cerebral Cortex |
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R1234042-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Corpus Callosum |
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R1234045-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Cerebellum (right) |
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R1234041-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Olfactory (region) |
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R1234063-10 | Biochain | 10 ug | EUR 286 |
Total RNA - Human Adult Normal Tissue: Brain: Precentral Gyrus |
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R1234073-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Cerebral Meninges |
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R1234043-10 | Biochain | 10 ug | EUR 183 |
Total RNA - Human Adult Normal Tissue: Brain: Medulla oblongata |
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R1234057-50 | Biochain | 50 ug | EUR 170 |
Total RNA - Human Adult Normal Tissue: Brain: Postcentral Gyrus |
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R1234072-10 | Biochain | 10 ug | EUR 183 |
Pituitary And Brain Cadherin (PB Cadherin) Antibody |
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20-abx133389 | Abbexa |
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Total RNA - Human Adult Normal Tissue 5 Donor Pool: Brain |
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R1234035-P | Biochain | 50 ug | EUR 370 |
Mouse Kidney And Brain Protein (KIBRA) CLIA Kit |
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20-abx495976 | Abbexa |
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Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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20-abx154290 | Abbexa |
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Brain And Muscle ARNT-Like 1 (BMAL1) Antibody |
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abx148343-100ug | Abbexa | 100 ug | EUR 526.8 |
Brain And Muscle ARNT-Like 1 (BMAL1) Antibody |
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abx430327-200ul | Abbexa | 200 ul | EUR 460.8 |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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DLR-KIBRA-Mu-48T | DL Develop | 48T | EUR 679.2 |
Description: A sandwich quantitative ELISA assay kit for detection of Mouse Kidney And Brain Protein (KIBRA) in samples from tissue homogenates, cell lysates or other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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DLR-KIBRA-Mu-96T | DL Develop | 96T | EUR 889.2 |
Description: A sandwich quantitative ELISA assay kit for detection of Mouse Kidney And Brain Protein (KIBRA) in samples from tissue homogenates, cell lysates or other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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SEL824Mu-10x96wellstestplate | Cloud-Clone | 10x96-wells test plate | EUR 6400.37 |
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Kidney And Brain Protein (KIBRA) in Tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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SEL824Mu-1x48wellstestplate | Cloud-Clone | 1x48-wells test plate | EUR 632.27 |
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Kidney And Brain Protein (KIBRA) in Tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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SEL824Mu-1x96wellstestplate | Cloud-Clone | 1x96-wells test plate | EUR 851.81 |
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Kidney And Brain Protein (KIBRA) in Tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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SEL824Mu-5x96wellstestplate | Cloud-Clone | 5x96-wells test plate | EUR 3473.14 |
Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Mouse Kidney And Brain Protein (KIBRA) in Tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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4-SEL824Mu | Cloud-Clone |
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Description: Enzyme-linked immunosorbent assay based on the Double-antibody Sandwich method for detection of Mouse Kidney And Brain Protein (KIBRA) in samples from Tissue homogenates, cell lysates and other biological fluids. with no significant corss-reactivity with analogues from other species. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RDR-KIBRA-Mu-48Tests | Reddot Biotech | 48 Tests | EUR 723.6 |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RDR-KIBRA-Mu-96Tests | Reddot Biotech | 96 Tests | EUR 1008 |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RD-KIBRA-Mu-48Tests | Reddot Biotech | 48 Tests | EUR 692.4 |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RD-KIBRA-Mu-96Tests | Reddot Biotech | 96 Tests | EUR 962.4 |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RD-KIBRA-Mu-48T | Reddot Biotech | 48T | EUR 506.3 |
Description: tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RD-KIBRA-Mu-96T | Reddot Biotech | 96T | EUR 723.3 |
Description: tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RDR-KIBRA-Mu-48T | Reddot Biotech | 48T | EUR 531.62 |
Description: tissue homogenates, cell lysates and other biological fluids. |
Mouse Kidney And Brain Protein (KIBRA) ELISA Kit |
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RDR-KIBRA-Mu-96T | Reddot Biotech | 96T | EUR 759.47 |
Description: tissue homogenates, cell lysates and other biological fluids. |
Brain Dissociation System 8 (Capillary endothelium, Pericytes), Mouse and Rat |
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4-20228 | CHI Scientific | ea | Ask for price |
Genomic DNA - Dementia: Brain: Thalamus, from a single donor |
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D1236079Dem | Biochain | 50 ug | EUR 489 |
Genomic DNA - Alzheimer's Disease: Brain, from a single donor |
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D1236035Alz | Biochain | 50 ug | EUR 489 |
Genomic DNA - Parkinson's Disease: Brain, from a single donor |
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D1236035Par | Biochain | 50 ug | EUR 489 |
Rat Brain PrimaCell1: Normal Brain Fibroblasts Growth Medium |
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9-25011 | CHI Scientific | 5 x 100 ml | Ask for price |
Creatine Kinase, Muscle and Brain (CKM/CKB) Antibody |
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abx411275-01mg | Abbexa | 0.1 mg | EUR 526.8 |
Recombinant Human Brain and Acute Leukemia, Cytoplasmatic |
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7-04471 | CHI Scientific | 2µg | Ask for price |
Recombinant Human Brain and Acute Leukemia, Cytoplasmatic |
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7-04472 | CHI Scientific | 10µg | Ask for price |
Recombinant Human Brain and Acute Leukemia, Cytoplasmatic |
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7-04473 | CHI Scientific | 1mg | Ask for price |
Genomic DNA - Depression: Brain: Thalamus, from a single donor |
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D1236079Dep | Biochain | 50 ug | EUR 489 |
Kin17 DNA And RNA Binding Protein (KIN) Protein |
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20-abx260971 | Abbexa |
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Kin17 DNA And RNA Binding Protein (KIN) Antibody |
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abx234575-100ug | Abbexa | 100 ug | EUR 610.8 |
Kin17 DNA And RNA Binding Protein (KIN) Antibody |
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20-abx113374 | Abbexa |
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Rat Brain Tissue Lysate |
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LYSATE0002 | BosterBio | 200ug | EUR 180 |
Description: This cell lysate is prepared from Rat Brain Tissue using Boster's RIPA Lysis Buffer (AR0105) using a standard whole cell lysate protocol. The concentration was determined using the BCA assay process and then diluted using Dithiothreitol (DTT) and a reducing SDS sample loading buffer, heated for 5 minutes at 100˚C. |
Rat Brain Tissue Preparation Buffer 1: Normal Brain Fibroblasts |
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9-80218 | CHI Scientific | 1 x 100 ml | Ask for price |
ELISA kit for Mouse KIBRA (Kidney And Brain Protein) |
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ELK8022 | ELK Biotech | 1 plate of 96 wells | EUR 518.4 |
Description: A sandwich ELISA kit for detection of Kidney And Brain Protein from Mouse in samples from blood, serum, plasma, cell culture fluid and other biological fluids. |
Kidney And Brain Protein (KIBRA) Polyclonal Antibody (Mouse) |
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4-PAL824Mu01 | Cloud-Clone |
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Description: A Rabbit polyclonal antibody against Mouse Kidney And Brain Protein (KIBRA) |
Genomic DNA - Dementia: Brain: Frontal Lobe, from a single donor |
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D1236051Dem | Biochain | 50 ug | EUR 489 |
Total RNA - Human Adult Normal Tissue: Brain, Ambient temperature shipping |
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ATR1234035-50 | Biochain | 50 ug | EUR 185 |
Genomic DNA - Dementia: Brain: Parietal Lobe, from a single donor |
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D1236066Dem | Biochain | 50 ug | EUR 489 |
Genomic DNA - Alzheimer's Disease: Brain: Pons, from a single donor |
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D1236071Alz | Biochain | 50 ug | EUR 489 |
Genomic DNA - Parkinson's Disease: Brain: Pons, from a single donor |
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D1236071Par | Biochain | 50 ug | EUR 489 |
Genomic DNA - Dementia: Brain: Temporal Lobe, from a single donor |
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D1236078Dem | Biochain | 50 ug | EUR 489 |
The 1982 revised criteria for the classification of systemic lupus erythematosus
The 1971 preliminary criteria for the classification of systemic lupus erythematosus (SLE) were revised and updated to incorporate new immunologic knowledge and improve disease classification. The 1982 revised criteria include fluorescence antinuclear antibody and antibody to native DNA and Sm antigen. Some criteria involving the same organ systems were aggregated into single criteria.
Raynaud’s phenomenon and alopecia were not included in the 1982 revised criteria because of low sensitivity and specificity. The new criteria were 96% sensitive and 96% specific when tested with SLE and control patient data gathered from 18 participating clinics. When compared with the 1971 criteria, the 1982 revised criteria showed gains in sensitivity and specificity.