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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

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

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

Rat Brain Genomic DNA

RG-201 0.1mg
EUR 177

Rat Brain, whole Total RNA

RR-201 0.05mg
EUR 160

Rat-WS Brain, whole Total RNA

RR-201-WS 0.1mg
EUR 160

Total RNA - Rat Normal Tissue: Brain

R1434035-50 50 ug
EUR 156

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

Genomic DNA - Rat Normal Tissue: Brain

D1434035 100 ug
EUR 329

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

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

Human Brain Total RNA

HR-201 0.05mg
EUR 172

Dog Brain, Cerebellum RNA

DR-202 0.1mg
EUR 195

Total RNA - Rat Normal Tissue: Brain, cerebellum

R1434039-50 50 ug
EUR 156

Cat Brain Genomic DNA

FG-201 0.1mg
EUR 210

Dog Brain Genomic DNA

DG-201 0.1mg
EUR 210

Pig Brain Genomic DNA

PG-201 0.1mg
EUR 177

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

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

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

Dog Brain, Cerebral Cortex RNA

DR-210 0.1mg
EUR 195

Hamster Brain, Whole Total RNA

AR-201 0.1mg
EUR 160

Chicken Brain, Whole Total RNA

CR-201 0.1mg
EUR 160

Monkey Brain Total RNA, Rhesus

UR-201 0.1mg
EUR 195

Cat Brain, Cerebellum Total RNA

FR-202 0.1mg
EUR 195

Cat Brain, Hippocampus Total RNA*

FR-203 0.05mg
EUR 235

Bovine Brain, Striatum Total RNA*

BR-214 0.05mg
EUR 235

Cat Brain, Hypothalamus Total RNA*

FR-204 0.05mg
EUR 235

Sheep Brain, Cerebellum Total RNA

SR-202 0.1mg
EUR 160

Human Brain Cerebellum Total RNA

HR-202 0.05mg
EUR 172

MiniPig Brain, Striatum Total RNA

NR-214 0.05mg
EUR 319

Pig Brain, Hypothalamus Total RNA*

PR-204 0.05mg
EUR 235

Match cell/lid QS LP10mm 1.4ml - 1PR

CEL2120 1PR
EUR 386.29

Mini Pig Brain Genomic DNA

GN-201 0.1mg
EUR 210

Bovine Brain, Cerebellum Total RNA

BR-202 0.1mg
EUR 160

Total RNA - Alzheimer's Disease: Brain

R1236035Alz-50 50 ug
EUR 460

Monkey Brain Total RNA, Cynomolgus

KR-201 0.1mg
EUR 195

Mouse C57 Brain Genomic DNA

MG-201-C57 0.05mg
EUR 210

Bovine Brain, Hippocampus Total RNA*

BR-203 0.05mg
EUR 235

Sheep Brain, Hypothalamus Total RNA*

SR-204 0.05mg
EUR 160

MiniPig Brain, Cerebellum Total RNA

NR-202 0.1mg
EUR 231

Guinea Pig Brain Genomic DNA

GG-201 0.1mg
EUR 177

Match cell/stpr QS/GLP10mm 3.5ml - 1PR

CEL2052 1PR
EUR 511.14

Bovine Brain, Hypothalamus Total RNA*

BR-204 0.05mg
EUR 235

MiniPig Brain, Hypothalamus Total RNA

NR-204 0.05mg
EUR 319

RNase, RNA and DNA Remover

R504-01 250 ml
EUR 60

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

Monkey Rhesus Brain Genomic DNA

UG-201 0.1mg
EUR 210

Mouse CD1 Brain, whole Total RNA

MR-201 0.05mg
EUR 160

Guinea Pig Brain, Whole Total RNA

GR-201 0.1mg
EUR 160

Monkey Cynomolgus Brain Genomic DNA

KG-201 0.1mg
EUR 210

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

Cat Brain, Cerebral Cortex Total RNA

FR-210 0.1mg
EUR 195

Total RNA - Mouse Normal Tissue: Brain

R1334035-50 50 ug
EUR 156

Pig Brain, Cerebral Cortex Total RNA

PR-210 0.1mg
EUR 160

Pig Brain, Choroids Plexus Total RNA*

PR-243 0.05mg
EUR 235

Sheep Brain, Cerebral Cortex Total RNA

SR-210 0.1mg
EUR 160

Sheep Brain, Choroids Plexus Total RNA*

SR-243 0.05mg
EUR 160

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

Bovine Brain, Cerebral Cortex Total RNA

BR-210 0.1mg
EUR 160

Bovine Brain, Caudate Nucleus Total RNA*

BR-242 0.05mg
EUR 235

Bovine Brain, Choroids Plexus Total RNA*

BR-243 0.05mg
EUR 235

Rat Creatine kinase for muscle and brain (CKMB)

QY-E11888 96T
EUR 448.8

MiniPig Brain, Cerebral Cortex Total RNA

NR-210 0.1mg
EUR 231

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Lung

D8235152-PP-10 2x10 ug
EUR 478

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Colon

D8235090-PP-10 2x10 ug
EUR 478

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Liver

D8235149-PP-10 2x10 ug
EUR 478

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

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Breast

D8235086-PP-10 2x10 ug
EUR 478

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Kidney

D8235142-PP-10 2x10 ug
EUR 478

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Rectum

D8235206-PP-10 2x10 ug
EUR 478

Genomic DNA - Mouse Normal Tissue: Brain

D1334035 100 ug
EUR 329

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Lung

R8235152-PP-10 2x10 ug
EUR 500

Matched Pair - DNA - Human Primary Tumor and Normal Tissue: Stomach

D8235248-PP-10 2x10 ug
EUR 478

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

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Colon

R8235090-PP-10 2x10 ug
EUR 500

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Liver

R8235149-PP-10 2x10 ug
EUR 500

Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Lung

D8235152-PM-10 2x10 ug
EUR 794

Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Colon

D8235090-PM-10 2x10 ug
EUR 794

Matched Pair - DNA - Human Primary and Metastatic Tumor Tissue: Liver

D8235149-PM-10 2x10 ug
EUR 794

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Breast

R8235086-PP-10 2x10 ug
EUR 500

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Kidney

R8235142-PP-10 2x10 ug
EUR 500

Matched Pair - Total RNA - Human Primary Tumor and Normal Tissue: Rectum

R8235206-PP-10 2x10 ug
EUR 500

Brain Dissociation System 7 (Endothelial), Mouse and Rat

4-20227 ea Ask for price

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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