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A framework for variation discovery and genotyping using next-generation DNA sequencing data.

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.

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Mouse Thymus, match set of RNA, DNA, Protein

MS-702-RDP 20µg/20µg/100µg
EUR 422

Mouse Kidney, match set of RNA, DNA, Protein

MS-901-RDP 20µg/20µg/100µg
EUR 422

Mouse Stomach, match set of RNA, DNA, Protein

MS-302-RDP 20µg/20µg/100µg
EUR 422

Mouse S. Muscles, match set of RNA, DNA, Protein

MS-102-RDP 20µg/20µg/100µg
EUR 422

Mouse S. Intestine, match set of RNA, DNA, Protein

MS-306-RDP 20µg/20µg/100µg
EUR 422

Tissue Set, BioAssay, DNA, RNA, Protein, Rat Adult Normal, Brain

MBS640997-1Set 1Set
EUR 650

Tissue Set, BioAssay, DNA, RNA, Protein, Rat Adult Normal, Brain

MBS640997-5x1Set 5x1Set
EUR 2970

Rat Brain Region Total RNA Panel, Set of any 5 Regions

RR-201-005 5X0.015mg
EUR 707

Rat Brain Region Total RNA Panel, Set of any 10 Regions

RR-201-010 10x0.015mg
EUR 984

Rat Brain Region Total RNA Panel, Set of any 15 Regions

RR-201-015 15X0.015mg
EUR 1275

Tissue Set, BioAssay, DNA, RNA, Protein, Human Adult Normal, Brain

MBS639448-1Kit 1Kit
EUR 730

Tissue Set, BioAssay, DNA, RNA, Protein, Human Adult Normal, Brain

MBS639448-5x1Kit 5x1Kit
EUR 3075

Tissue Set, BioAssay, DNA, RNA, Protein, Mouse Adult Normal, Brain

MBS640986-1Set 1Set
EUR 650

Tissue Set, BioAssay, DNA, RNA, Protein, Mouse Adult Normal, Brain

MBS640986-5x1Set 5x1Set
EUR 2970

Rat-WS Brain Region Total RNA Panel, Set of any 5 Regions

RR-201-005-WS 5X0.015mg
EUR 707

Rat-WS Brain Region Total RNA Panel, Set of any 10 Regions

RR-201-010-WS 10x0.015mg
EUR 984

Rat-WS Brain Region Total RNA Panel, Set of any 15 Regions

RR-201-015-WS 15X0.015mg
EUR 1275

Syringe Caps (Package of 100)

T311 each
EUR 32

Safe-Wrap® Blood Collection Tubes (Package of 100 Tubes)

CT220 each
EUR 191

Rat Brain Genomic DNA

RG-201 0.1mg
EUR 177

End Caps for use with Safe-Wrap® Blood Collection Tubes (Package of 200) Caps)

EC220 each
EUR 78

Safe-Wrap® Combo Blood Collection Tubes for i•-STAT® (Package of 50 Tubes) 95μL

CT095 each
EUR 85

Rat Brain, whole Total RNA

RR-201 0.05mg
EUR 160

Mouse CD1 Brain Region Total RNA Panel, Set of any 5 Regions

MR-201-005 5X0.010mg
EUR 707

Mouse C57 Brain Region Total RNA Panel, Set of any 5 Regions

MR-201-005-C57 5X0.010mg
EUR 875

Mouse CD1 Brain Region Total RNA Panel, Set of any 10 Regions

MR-201-010 10x0.010mg
EUR 852

Mouse C57 Brain Region Total RNA Panel, Set of any 10 Regions

MR-201-010-C57 10x0.010mg
EUR 1092

Mouse CD1 Brain Region Total RNA Panel, Set of any 15 Regions

MR-201-015 15X0.010mg
EUR 1142

Mouse C57 Brain Region Total RNA Panel, Set of any 15 Regions

MR-201-015-C57 15X0.010mg
EUR 1384

Mouse Balbc Brain Region Total RNA Panel, Set of any 5 Regions

MR-201-005-BLC 5X0.010mg
EUR 875

Mouse Balbc Brain Region Total RNA Panel, Set of any 10 Regions

MR-201-010-BLC 10x0.010mg
EUR 1092

Mouse Balbc Brain Region Total RNA Panel, Set of any 15 Regions

MR-201-015-BLC 15X0.010mg
EUR 1384

Rat-WS Brain, whole Total RNA

RR-201-WS 0.1mg
EUR 160

Rat Brain Region cDNA Panel, Set of any 5 Regions

RD-201-005 5X10 reactions
EUR 655

Rat Brain Region cDNA Panel, Set of any 10 Regions

RD-201-010 10X10 reactions
EUR 1091

Rat Brain Region cDNA Panel, Set of any 15 Regions

RD-201-015 15X10 reactions
EUR 1324

Genomic DNA - Rat Normal Tissue: Brain

D1434035 100 ug
EUR 241.5

ESA LEADCARE II ANALYZER KIT

706760 each Ask for price

ESA LEADCARE II TEST KIT

706762 each Ask for price

Calibration Verification Controls (BG, Electrolyte, Metabolite Analyzers)

CVC123 each
EUR 565

CO‐Oximeter Calibration Verification Controls

CVC223 each
EUR 396

Multi‐Level, 10 ampuls each level (Levels 1, 2, 3)

CC527 each
EUR 169

Level 1, 30 ampuls

CC527-1 each
EUR 169

Level 2, 30 ampuls

CC527-2 each
EUR 169

Level 3, 30 ampuls

CC527-3 each
EUR 169

Multi‐Level, 10 ampuls each level (Levels 1, 2, 3)

QC253 each
EUR 221

Level 1, 30 ampuls

QC253-1 each
EUR 221

Level 2, 30 ampuls

QC253-2 each
EUR 221

Level 3, 30 ampuls

QC253-3 each
EUR 221

Multi-Level, 10 ampuls each level (Levels 1, 2, 3)

QC623 each
EUR 150

Level 1, 30 ampuls

QC623-1 each
EUR 150

Level 2, 30 ampuls

QC623-2 each
EUR 150

Level 3, 30 ampuls

QC623-3 each
EUR 150

Multi-Level, 10 ampuls each level (Levels 1, 2, 3)

QC823 each
EUR 153

Level 1, 30 ampuls

QC823-1 each
EUR 153

Level 2, 30 ampuls

QC823-2 each
EUR 153

Level 3, 30 ampuls

QC823-3 each
EUR 153

Multi-Level, 2 bottles each level (Low, Normal, High)

QCHGB each
EUR 121

Low, 6 bottles

QCHGB-1 each
EUR 121

Normal, 6 bottles

QCHGB-2 each
EUR 121

High, 6 bottles

QCHGB-3 each
EUR 121

Pre-Treated Syringes (100 per Box)

T310 each
EUR 145

Rat WS Brain Region cDNA Panel, Set of any 5 Regions

RD-201-005-WS 5X10 reactions
EUR 655

Rat WS Brain Region cDNA Panel, Set of any 10 Regions

RD-201-010-WS 10X10 reactions
EUR 1091

Rat WS Brain Region cDNA Panel, Set of any 15 Regions

RD-201-015-WS 15X10 reactions
EUR 1324

Rat Brain Region Total Protein Panel, Set of any 5 regions

RT-201-005 5x0.1mg
EUR 567

Rat Brain Region Total Protein Panel, Set of any 10 Regions

RT-201-010 10x0.1mg
EUR 858

Rat Brain Region Total Protein Panel, Set of any 15 Regions

RT-201-015 15x0.1mg
EUR 1149

Brain tumor with matched adjacent normal tissue array

GL808 each
EUR 306
Description: Brain tumor with matched adjacent normal tissue array, including pathology grade, 80 cases/80 cores, replacing GL801

Rat Brain Frozen Coronal Sections Panel, Set of any 7 regions

RF-201-007 7x4 slides
EUR 720

Rat Brain Frozen Coronal Sections Panel, Set of any 14 regions

RF-201-014 14X4 slides
EUR 1158

Cross match determination (FCXM)

FCXM-100T 100 test
EUR 806.18

Cross match determination (FCXM)

FCXM-25T 25 test
EUR 412.04

Cross match determination (FCXM)

FCXMPU 0,5 mg
EUR 620.04

Rat WS Brain Region Total Protein Panel, Set of any 5 regions

RT-201-005-WS 5x0.1mg
EUR 567

Rat WS Brain Region Total Protein Panel, Set of any 10 Regions

RT-201-010-WS 10x0.1mg
EUR 858

Rat WS Brain Region Total Protein Panel, Set of any 15 Regions

RT-201-015-WS 15x0.1mg
EUR 1149

Rat Kidney and Brain Protein ELISA Kit

MBS048807-10x96StripWells 10x96-Strip-Wells
EUR 6725

Rat Kidney and Brain Protein ELISA Kit

MBS048807-48StripWells 48-Strip-Wells
EUR 550

Rat Kidney and Brain Protein ELISA Kit

MBS048807-5x96StripWells 5x96-Strip-Wells
EUR 3420

Rat Kidney and Brain Protein ELISA Kit

MBS048807-96StripWells 96-Strip-Wells
EUR 765

Rat WS Brain Frozen Coronal Sections Panel, Set of any 7 regions

RF-201-007-WS 7x4 slides
EUR 720

Rat WS Brain Frozen Coronal Sections Panel, Set of any 14 regions

RF-201-014-WS 14X4 slides
EUR 1158

Human Brain Total RNA

HR-201 0.05mg
EUR 172

Dog Brain, Cerebellum RNA

DR-202 0.1mg
EUR 195

Dog Brain Genomic DNA

DG-201 0.1mg
EUR 210

Cat Brain Genomic DNA

FG-201 0.1mg
EUR 210

Pig Brain Genomic DNA

PG-201 0.1mg
EUR 177

Tissue, Total RNA, Rat Adult Normal, Brain, BioGenomics

MBS638727-005mg 0.05mg
EUR 435

Tissue, Total RNA, Rat Adult Normal, Brain, BioGenomics

MBS638727-5x005mg 5x0.05mg
EUR 1735

Human Brain Genomic DNA

HG-201 0.05mg
EUR 210

Mouse Brain Genomic DNA

MG-201 0.1mg
EUR 177

Sheep Brain Genomic DNA

SG-201 0.1mg
EUR 177

Human Brain Genomic DNA  

X11001
  • Ask for price
  • Ask for price
  • 10 µg
  • 10 ul

Bovine Brain Genomic DNA

BG-201 0.1mg
EUR 177

Equine Brain Genomic DNA

GE-201 0.1mg
EUR 210

Rabbit Brain Genomic DNA

TG-201 0.1mg
EUR 177

Hamster Brain Genomic DNA

GA-201 0.1mg
EUR 177

Chicken Brain Genomic DNA

GC-201 0.1mg
EUR 177

Tissue, Genomic DNA, Rat Adult Normal, Brain, BioGenomics

MBS654502-01mg 0.1mg
EUR 575

Tissue, Genomic DNA, Rat Adult Normal, Brain, BioGenomics

MBS654502-5x01mg 5x0.1mg
EUR 2440

Rat Creatine kinase for muscle and brain -CKMB-

QY-E11888 96T
EUR 420

Tissue, Array, Human Tumor, Different Types of Tumor, Multi, tissue I (8), brain, control, kidney, control, liver, control, lung, control (matched with Total RNA Northern Blot) (Paraffin)

MBS639557-5Arrays 5Arrays
EUR 805

Tissue, Array, Human Tumor, Different Types of Tumor, Multi, tissue I (8), brain, control, kidney, control, liver, control, lung, control (matched with Total RNA Northern Blot) (Paraffin)

MBS639557-5x5Arrays 5x5Arrays
EUR 3465

Mouse C57 Brain Total RNA

MR-201-C57 0.05mg
EUR 180

Bovine Brain Stem Total RNA*

BR-215 0.05mg
EUR 235

Mouse Balbc Brain Total RNA

MR-201-BLC 0.1mg
EUR 180

Equine Brain, Whole Total RNA

ER-201 0.1mg
EUR 195

Pig Brain, Striatum Total RNA*

PR-214 0.05mg
EUR 160

Rabbit Brain, whole Total RNA

TR-201 0.1mg
EUR 160

Chicken Brain, Whole Total RNA

CR-201 0.1mg
EUR 160

Hamster Brain, Whole Total RNA

AR-201 0.1mg
EUR 160

Dog Brain, Cerebral Cortex RNA

DR-210 0.1mg
EUR 195

Monkey Brain Total RNA, Rhesus

UR-201 0.1mg
EUR 195

Mini Pig Brain Genomic DNA

GN-201 0.1mg
EUR 210

Brain Dissociation System 7 (Endothelial), Mouse and Rat

4-20227 ea
EUR 144.82

Cat Brain, Cerebellum Total RNA

FR-202 0.1mg
EUR 195

Mouse C57 Brain Genomic DNA

MG-201-C57 0.05mg
EUR 210

Bovine Brain, Striatum Total RNA*

BR-214 0.05mg
EUR 235

Cat Brain, Hippocampus Total RNA*

FR-203 0.05mg
EUR 235

Rat Brain and muscle ARNT like 1,BMAL1 ELISA KIT

E2919Ra-1096T 10*96T
EUR 4122

Rat Brain and muscle ARNT like 1,BMAL1 ELISA KIT

E2919Ra-48wells 48 wells
EUR 300

Rat Brain and muscle ARNT like 1,BMAL1 ELISA KIT

E2919Ra-596T 5*96T
EUR 2061

Rat Brain and muscle ARNT like 1,BMAL1 ELISA KIT

E2919Ra-96wells 96 wells
EUR 458

Rat Brain and muscle ARNT like 1,BMAL1 ELISA KIT

JOT-EK2919Ra 96 wells Ask for price
Description: Rat

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.
 

Translating the histone code

Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states.
 
The combinatorial nature of histone amino-terminal modifications thus reveals a “histone code” that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.

Genomic sequencing

Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a short 32P-labeled single-stranded probe produces the image of a DNA sequence “ladder” extending from the 3′ or 5′ end of one restriction site in the genome. Numerous different sequences can be obtained from a single membrane by reprobing.
 
Each band in these sequences represents 3 fg of DNA complementary to the probe. Sequence data from mouse immunoglobulin heavy chain genes from several cell types are presented. The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution.
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