Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths.

Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths.

We current our work on {hardware} accelerated genomics pipelines, utilizing both FPGAs or GPUs to speed up execution of BWA-MEM, a widely-used algorithm for genomic brief learn mapping. The mapping stage can take as much as 40% of total processing time for genomics pipelines.

Our implementation offloads the Seed Extension perform, one of many predominant BWA-MEM computational features, onto an accelerator. Sequencers usually output reads with a size of 150 base pairs. Nonetheless, learn size is predicted to extend within the close to future. Right here, we examine the affect of learn size on BWA-MEM efficiency utilizing information units with learn size as much as 400 base pairs, and introduce strategies to ameliorate the affect of longer learn size.

For the industry-standard 150 base pair learn size, our implementation achieves an as much as two-fold improve in total application-level efficiency for techniques with at most twenty-two logical CPU cores. Longer learn size requires commensurately larger information buildings, which instantly impacts accelerator effectivity.

The 2-fold efficiency improve is sustained for learn size of at most 250 base pairs. To enhance efficiency, we carry out a classification of the inefficiency of the underlying systolic array structure. By eliminating idle areas as a lot as potential, effectivity is improved by as much as +95%. Furthermore, adaptive load balancing intelligently distributes work between host and accelerator to make sure use of an accelerator all the time leads to efficiency enchancment, which in GPU-constrained situations supplies as much as +45% extra efficiency.

Analysis of variant calling instruments for big plant genome re-sequencing

Background: Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a extensively used technique for creating genetic markers for a number of functions together with marker-assisted breeding, inhabitants range research for eco-geographical adaption, genotyping crop germplasm collections, and others. Precisely detecting SNPs from massive polyploid crop genomes reminiscent of wheat is essential and difficult.

A number of variant calling strategies have been beforehand developed however they present a low concordance between their variant calls. A gold customary of variant units generated from one human particular person pattern was established for variant calling device evaluations, nonetheless hitherto no gold customary of crop variant set is obtainable for wheat use.

Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths.

The intent of this examine was to judge seven SNP variant calling instruments (FreeBayes, GATK, Platypus, Samtools/mpileup, SNVer, VarScan, VarDict) with the 2 hottest mapping instruments (BWA-mem and Bowtie2) on wheat entire exome seize (WEC) re-sequencing information from allohexaploid wheat.

Outcomes: We discovered the BWA-mem mapping device had each a better mapping fee and a better accuracy fee than Bowtie2. With the identical mapping high quality (MQ) cutoff, BWA-mem detected extra variant bases in mapping reads than Bowtie2.

The reads preprocessed with high quality trimming or duplicate elimination didn’t considerably have an effect on the ultimate mapping efficiency when it comes to mapped reads. Primarily based on the concordance and receiver working attribute (ROC), the Samtools/mpileup variant calling device with BWA-mem mapping of uncooked sequence reads outperformed different checks adopted by FreeBayes and GATK when it comes to specificity and sensitivity. VarDict and VarScan had been the poorest performing variant calling instruments with the wheat WEC sequence information.

Conclusion: The BWA-mem and Samtools/mpileup pipeline, without having to preprocess the uncooked learn information earlier than mapping onto the reference genome, was ascertained the optimum for SNP calling for the advanced wheat genome re-sequencing. These outcomes additionally present helpful tips for dependable variant identification from deep sequencing of different massive polyploid crop genomes.

Sooner single-end alignment technology using multi-thread for BWA.

Because of next-generation sequencing (NGS) expertise, genome sequencing is ready to course of far more information at low price. In NGS information evaluation, the mapping of sequences right into a reference genome takes the most important period of time to course of.

Though the Burrows-Wheeler Aligner (BWA) device is among the most generally used open-source software program instruments to align learn sequences, it’s nonetheless restricted in that it doesn’t absolutely assist multi-thread mechanisms through the alignment steps. On this paper, we suggest a BWA-MT device, developed from BWA however supporting multi-thread computation, designed to totally make the most of the underlying multi-core structure of computing assets.

Through the use of multi-thread computation, BWA-MT can considerably shorten the time wanted to generate an alignment for single-end learn sequences. In the meantime, it generates an equivalent Sequence Alignment Map (SAM) outcome file as BWA. To judge BWA-MT, we use an analysis system geared up with twelve cores and 32 GB reminiscence.

As a workload, we used the hg19 human genome reference sequence and varied numbers of learn sequences from 1M to 40M. In our analysis, BWA-MT shows as much as 3.7 occasions quicker efficiency and generates an equivalent SAM outcome file to BWA.

Normal Goat Serum Sterile Filt

GWB-837593 500 ml Ask for price

Normal Horse Serum

88-NE21 100 ml Ask for price
  • Supplied as Serum, pH 7.5.
Description: Control Normal Horse Serum

Normal Horse Serum

88R-1020 10 ml
EUR 166
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Horse Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Horse Serum

MBS686282-10mL 10mL
EUR 210

Normal Horse Serum

MBS686282-2mL 2mL
EUR 135

Normal Horse Serum

MBS686282-5x10mL 5x10mL
EUR 805

Normal Horse Serum

MBS837801-10mL 10mL
EUR 325

Normal Horse Serum

MBS837801-5x10mL 5x10mL
EUR 1315

Horse normal serum (2 ml)

AS10-1561 2 ml
EUR 139

Horse normal serum (10 ml)

AS10-1562 10 ml
EUR 193

Serum - Normal - 0.2 Micron Filtered; Normal Serum

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Normal Sheep Serum Sterile Fil

GWB-EAD38B 100 ml Ask for price

Normal Rat Serum Filtered

GWB-CC0A9E 10 ml Ask for price

Normal Human Serum (filtered)

90-1013 100 ml Ask for price
  • Sterile filtered liquid serum.
Description: Human Serum Off The Clot from Normal Donors

Normal Mouse Serum Filtered

GWB-E7645B 10 ml Ask for price

Normal Mouse Serum, Filtered

MBS318415-10mL 10mL
EUR 320

Normal Mouse Serum, Filtered

MBS318415-5x10mL 5x10mL
EUR 1185

Normal Donkey Serum filtered

88R-D1052 100 ml
EUR 179
  • Supplied as a liquid, no preservatives.
Description: Control Normal Donkey Serum filtered

OOMA00002-10ML - Normal Mouse Serum, Filtered

OOMA00002-10ML 10ML
EUR 199
  • Normal Mouse Serum, Filtered

Horse Serum, US Orgin, Sterile Filtered, 0.2um Filtered

H0600-050 500ml
EUR 92

Normal Pig Serum

88-NP 500 ml
EUR 197
  • Supplied as sterile neat serum, no preservatives added, pH 6.8-8.2
Description: Normal Pig Serum collected from pigs in the USA

Normal Rat Serum

88-NR51 50 ml
EUR 330
  • Liquid Serum, sterile filtered through 0.2 um filter.
Description: Normal Rat Serum

Normal Rat Serum

88R-1010 5 ml
EUR 165
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 5.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove a
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Description: Normal Rat Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Pig Serum

88R-1023 2 ml
EUR 154
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 2.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove a
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Description: Normal Pig (Swine) Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Cat Serum

88R-1026 10 ml
EUR 235
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Cat Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Dog Serum

88R-1028 10 ml
EUR 234
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Dog Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Pig Serum

88R-P004 1 liter
EUR 724
  • Supplied as a liquid, no preservatives.
Description: Control Normal Pig Serum

Normal Rat Serum

BMS0100-10mL 10 mL
EUR 89
Description: High quality Normal rat serum processed from non-immunized normal adult rats is used as a blocking agent or as a negative control for immunoassays.

Normal Rat Serum

BMS0100-10mL10 10 mL×10
EUR 529
Description: High quality Normal rat serum processed from non-immunized normal adult rats is used as a blocking agent or as a negative control for immunoassays.

Normal Rat Serum

NRS 1 ml/vial
EUR 64

Normal Rat Serum

BMS0100-each each Ask for price

Serum, Rat, Normal

MBS638838-2mL 2mL
EUR 340

Serum, Rat, Normal

MBS638838-5x2mL 5x2mL
EUR 1390

Normal Rat Serum

MBS686270-2mL 2mL
EUR 150

Normal Rat Serum

MBS686270-5x2mL 5x2mL
EUR 535

Normal Rat Serum

MBS686316-5mL 5mL
EUR 175

Normal Rat Serum

MBS686316-5x5mL 5x5mL
EUR 630

Normal Cat Serum

MBS837783-10mL 10mL
EUR 455

Normal Cat Serum

MBS837783-5x10mL 5x10mL
EUR 1890

Normal Dog Serum

MBS837784-10mL 10mL
EUR 400

Normal Dog Serum

MBS837784-5x10mL 5x10mL
EUR 1655

Normal Pig Serum

MBS837793-2mL 2mL
EUR 270

Normal Pig Serum

MBS837793-5x2mL 5x2mL
EUR 1070

Normal Pig Serum

MBS837809-500mL 500mL
EUR 440

Normal Pig Serum

MBS837809-5x500mL 5x500mL
EUR 1760

Normal Rat Serum

MBS837812-5mL 5mL
EUR 280

Normal Rat Serum

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EUR 1115

Normal Rat Serum

MBS539311-50mL 50mL
EUR 730

Normal Rat Serum

MBS539311-5x50mL 5x50mL
EUR 3055

Normal Pig Serum

MBS539324-1L 1L
EUR 1540

Normal Pig Serum

MBS539324-5x1L 5x1L
EUR 6755

Normal Rat Serum

MBS9718945-10mL 10mL
EUR 135

Normal Rat Serum

MBS9718945-10x10mL 10x10mL
EUR 395

Normal Goat Serum

9067 50 ml
EUR 44
Description: Normal Goat Serum

Normal Goat Serum

88-B9999G000-S0 10 ml
EUR 95
  • Supplied delipidated, defibrinated and 0.2µm filtered, in 0.2M Tris, 0.5M NaCl , pH 7.7 with 0.09% NaN3
Description: Control Normal Goat serum

Normal Goat Serum

88-NG22 500 ml Ask for price
  • Supplied as Serum, pH 7.5.
Description: Control Normal Goat Serum

Normal Goat Serum

88-NG22S 500 ml
EUR 226
  • Supplied as Serum, pH 7.5.
Description: Control Normal Goat Serum

Normal Goat Serum

88R-1006 10 ml
EUR 166
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Goat Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Goat Serum

88R-NG001 50 ml Ask for price
  • Supplied as Serum, pH 7.5.
Description: Normal Goat Serum for use as a control or blocking reagent

Normal Goat Serum

BMS0050-10mL 10 mL
EUR 39
Description: High quality Normal goat serum processed from non-immunized normal adult goats is used as a blocking agent or as a negative control for immunoassays.

Normal Goat Serum

BMS0050-10mL10 10 mL×10
EUR 89
Description: High quality Normal goat serum processed from non-immunized normal adult goats is used as a blocking agent or as a negative control for immunoassays.

Normal Goat Serum

BMS0050-each each Ask for price

Serum, Goat, Normal

MBS638846-100mL 100mL
EUR 340

Serum, Goat, Normal

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EUR 1700

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EUR 510

Serum, Goat, Normal

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EUR 320

Serum, Goat, Normal

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EUR 2145

Normal Goat Serum

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Normal Goat Serum

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EUR 515

Normal Goat Serum

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Normal Goat Serum

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EUR 805

Normal Goat Serum

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Normal Goat Serum

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EUR 450

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Normal Goat Serum

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EUR 200

Normal Goat Serum

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Normal Goat Serum

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EUR 325

Normal Goat Serum

MBS837804-5x10mL 5x10mL
EUR 1315

Normal Goat Serum

MBS837811-500mL 500mL
EUR 405

Normal Goat Serum

MBS837811-5x500mL 5x500mL
EUR 1600

Normal Goat Serum

MBS9718941-10mL 10mL
EUR 100

Normal Goat Serum

MBS9718941-10x10mL 10x10mL
EUR 135

Normal Human Serum

90R-1002 10 ml
EUR 237
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove any precipitates.
Description: Normal Human Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Mouse Serum

88-NM35 50 ml
EUR 459
  • Liquid Serum, sterile filtered through 0.2 um filter.
Description: Normal Mouse Serum

Normal Sheep Serum

88-NS55 100 ml
EUR 287
  • Liquid Serum, sterile filtered through 0.2 um filter.
Description: Normal Sheep Serum

Normal Mouse Serum

88R-1002 5 ml
EUR 118
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 5.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove a
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Description: Normal Mouse Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Sheep Serum

88R-1008 10 ml
EUR 166
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Sheep Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Sheep Serum

88R-S002 100 ml
EUR 126
  • Supplied as a liquid, no preservatives.
Description: Control Normal Sheep Serum

Normal Mouse Serum

BMS0070-10mL 10 mL
EUR 89
Description: High quality Normal mouse serum processed from non-immunized normal adult mouses is used as a blocking agent or as a negative control for immunoassays.

Normal Mouse Serum

BMS0070-10mL10 10 mL×10
EUR 529
Description: High quality Normal mouse serum processed from non-immunized normal adult mouses is used as a blocking agent or as a negative control for immunoassays.

Normal Human Serum

NHS 1 ml/vial
EUR 50

Normal Mouse Serum

NMS 1 ml/vial
EUR 91

Normal Mouse Serum

BMS0070-each each Ask for price

Serum, Human, Normal

MBS638787-2mL 2mL
EUR 410

Serum, Human, Normal

MBS638787-5x2mL 5x2mL
EUR 1700

Serum, Mouse, Normal

MBS638791-2mL 2mL
EUR 340

Serum, Mouse, Normal

MBS638791-5mL 5mL
EUR 475

Serum, Mouse, Normal

MBS638791-5x5mL 5x5mL
EUR 1990

Serum, Mouse, Normal

MBS638800-05mL 0.5mL
EUR 465

Serum, Mouse, Normal

MBS638800-5x05mL 5x0.5mL
EUR 1950

Serum, Mouse, Normal

MBS638811-5mL 5mL
EUR 505

Serum, Mouse, Normal

MBS638811-5x5mL 5x5mL
EUR 2125

Serum, Sheep, Normal

MBS638820-1mL 1mL
EUR 380

Serum, Sheep, Normal

MBS638820-5x1mL 5x1mL
EUR 1560

Serum, Sheep, Normal

MBS638867-10mL 10mL
EUR 510

Serum, Sheep, Normal

MBS638867-2mL 2mL
EUR 320

Serum, Sheep, Normal

MBS638867-5x10mL 5x10mL
EUR 2145

Serum, Swine, Normal

MBS638868-1mL 1mL
EUR 380

Serum, Swine, Normal

MBS638868-5x1mL 5x1mL
EUR 1560

Normal Human Serum

MBS686120-2mL 2mL
EUR 150

Normal Human Serum

MBS686120-5x2mL 5x2mL
EUR 515

Normal Sheep Serum

MBS686140-2mL 2mL
EUR 135

Normal Sheep Serum

MBS686140-5x2mL 5x2mL
EUR 450

Normal Mouse Serum

MBS686158-5mL 5mL
EUR 180

Normal Mouse Serum

MBS686158-5x5mL 5x5mL
EUR 655

Normal Llama Serum

MBS686183-2mL 2mL
EUR 145

Normal Llama Serum

MBS686183-5x2mL 5x2mL
EUR 510

Normal Llama Serum

MBS686191-10mL 10mL
EUR 240

Normal Llama Serum

MBS686191-5x10mL 5x10mL
EUR 925

Normal Sheep Serum

MBS686202-10mL 10mL
EUR 210

Normal Sheep Serum

MBS686202-5x10mL 5x10mL
EUR 805

Normal Mouse Serum

MBS686304-2mL 2mL
EUR 150

Normal Mouse Serum

MBS686304-5x2mL 5x2mL
EUR 535

Normal Human Serum

MBS686347-10mL 10mL
EUR 195

Normal Human Serum

MBS686347-5x10mL 5x10mL
EUR 735

Normal Sheep Serum

MBS837800-10mL 10mL
EUR 325

Normal Sheep Serum

MBS837800-5x10mL 5x10mL
EUR 1315

Normal Mouse Serum

MBS837810-5mL 5mL
EUR 300

Normal Mouse Serum

MBS837810-5x5mL 5x5mL
EUR 1210

Normal Sheep Serum

MBS539321-100mL 100mL
EUR 565

Normal Sheep Serum

MBS539321-5x100mL 5x100mL
EUR 2315

Normal Mouse Serum

MBS539323-50mL 50mL
EUR 710

Normal Mouse Serum

MBS539323-5x50mL 5x50mL
EUR 2975

Normal Sheep Serum

MBS539327-100mL 100mL
EUR 290

Normal Sheep Serum

MBS539327-5x100mL 5x100mL
EUR 1160

Normal Mouse Serum

MBS9718943-10mL 10mL
EUR 135

Normal Mouse Serum

MBS9718943-10x10mL 10x10mL
EUR 395

Normal Bovine Serum

abx098263-100ml 100 ml
EUR 309.6
  • Shipped within 5-10 working days.

Normal Canine Serum

88-NC25 100 ml
EUR 493
  • Liquid Serum, sterile filtered through 0.2 um filter.
Description: Normal Canine Serum

Normal Rabbit Serum

88-NR50 100 ml
EUR 300
  • Liquid Serum, sterile filtered through 0.2 um filter.
Description: Normal Rabbit Serum

Normal Rabbit Serum

88R-1004 10 ml
EUR 188
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
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Description: Normal Rabbit Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Donkey Serum

88R-1022 10 ml
EUR 166
  • Lyophilized powder containing 10 mM Sodium Phosphate and 0.15 M Sodium Chloride. Protease/IgG free, pH 7.2 Rehydrate with 10.0 ml of deionized water. Swirl gentle and let stand for up to 2 hours at 18-25 °C. Centrifuge reconstituted serum to remove
  • Show more
Description: Normal Donkey Serum which has been lipid extracted and dialyzed against 10 mM Sodium Phosphate, 0.15 M Sodium Chloride, pH 7.2

Normal Bovine Serum

88R-B001 100 ml
EUR 490
  • Supplied as a liquid, no preservatives.
Description: Control Normal Bovine Serum

Normal Donkey Serum

88R-D001 100 ml
EUR 138
  • Supplied as a liquid, no preservatives.
Description: Control Normal Donkey Serum

Normal Donkey Serum

88R-D003 10 ml
EUR 125
  • Lyophilized from 0.01M Na3PO4, 0.25 M NaCl, pH 7.6, with 0.05% NaN3. Reconstitute with 10.0 ml of distilled Water.
Description: Control Normal Donkey Serum

Normal Rabbit Serum

89R-RM001 20 mg
EUR 470.4
Description: Normal Rabbit Serum (Mouse cell adsorbed)

Normal Rabbit Serum

89R-RM002 5 ml
EUR 289.2
Description: Normal Rabbit Serum (Mouse cell adsorbed)

Normal Rabbit Serum

89R-RR001 20 mg
EUR 418.8
Description: Normal Rabbit Serum (Rat cell adsorbed)

Normal Rabbit Serum

89R-RR002 5 ml
EUR 289.2
Description: Normal Rabbit Serum (Rat cell adsorbed)

Normal Donkey Serum

BMS0140-10mL 10 mL
EUR 39
Description: High quality Normal donkey serum processed from non-immunized normal adult donkeys is used as a blocking agent or as a negative control for immunoassays.

Normal Donkey Serum

BMS0140-10mL10 10 mL×10
EUR 89
Description: High quality Normal donkey serum processed from non-immunized normal adult donkeys is used as a blocking agent or as a negative control for immunoassays.

Normal Rabbit Serum

NRS-500 500 tests
EUR 34.56

Though the elevated velocity may be depending on computing assets, we verify that BWA-MT is extremely environment friendly and efficient.

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