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Pooled Libraries文库质粒试剂盒Barcoding cDNA CRISPR Screening shRNA-BioVector

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Pooled Libraries文库质粒试剂盒Barcoding cDNA CRISPR Screening shRNA


In addition to the 80,000 plasmids in BioVector's repository, depositors have shared a variety of pooled libraries. To help you find what you're looking for, we've gathered our pooled plasmid libraries on one page. We hope you find it helpful! You can jump to the various types of libraries within the repository by using the top nav bar.</br>A pooled library is a set of plasmids all built with the same backbone and only differing in a small region. Pooled libraries are normally supplied as a single tube with all the plasmids in the library mixed together. The number of unique plasmids in a pooled library can range from a few hundred to millions. There are several different types of pooled libraries, including cDNA, shRNA, barcoding, phage display, and gRNA libraries.</br>Read our Pooled Library Guide for more information about:</br>Library amplification

Types of pooled library screens

Next-generation sequencing (NGS)</br>See our Pooled Library Amplification Protocol for BioVector's generalized library amplification protocol.</br>

Barcoding Libraries

Barcoded libraries contain very large numbers of unique barcodes used to mark individual cells. These barcodes will then be inherited by any daughter cells, making barcoded libraries ideal for lineage tracing. These libraries are also commonly used to monitor the dynamics of heterogeneous tumors.</br>Library ID Lentiviral Generation PI Description

LARRY Barcode Library Version 1 140024 3rd Camargo Lentiviral barcoding library for reconstructing transcriptional trajectories in differentiating cell populations.

CellTag Barcode Library 115643

115644

115645 3rd Morris Lentiviral barcoding libraries used to combinatorially index cells for single-cell analysis of clonal dynamics.

ClonTracer Library 67267 (2.5µg)</br>69830 (7.5µg) 3rd Stegmeier Lentiviral library used to conduct positive selection screens for cancer cells resistant to a given treatment.  This blog post about the ClonTracer Library describes how the library was used to identify pools cells that were resistant pre-treatment.

Perturb-seq Guide Barcodes (GBC) Library 85968 3rd Weissman Barcode library for cloning gRNA sublibraries for single cell CRISPR analysis.

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cDNA Libraries

cDNA libraries are created from an organism’s actively transcribed mRNA, as opposed to genomic libraries, which are created from genomic DNA. Since cDNA libraries lack introns and other nontranscribed sequences, they are smaller and easier to use than genomic libraries, but they don’t contain as much regulatory information. To make a cDNA library, cDNA is synthesized, then ligated to adapters, and cloned into a given vector.</br>Library ID Species PI Description

Monosiga cDNA Library 25864 Monosiga brevicollis Carroll and King Bacterial expression cDNA library created from the choanoflagellate Monosiga brevicollis.

Proterospongia cDNA library 25716 Proterospongia King Bacterial expression cDNA library created from Proterospongia, also referred to as Salpingoeca.

S. rosetta Col- cDNA amplified library 62843 Salpingoeca rosetta King Created from the choanoflagellate Salpingoeca rosetta. Col+ refers to DNA isolated from bacteria cultured with the colony-inducing bacteria Algoriphagus machipongonensis.

S. rosetta Col+ cDNA amplified library 62844 Salpingoeca rosetta King Created from the choanoflagellate Salpingoeca rosetta. The Col- library was created from S. rosetta cultured without bacteria.

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CRISPR Libraries

Like shRNA libraries, CRISPR knockout libraries are used for loss-of-function screens. Multiple gRNAs are present for each gene targeted by the library. In contrast to shRNA, the effects of CRISPR knockout are not easily reversible, as the targeted gene sequence is mutated by CRISPR. Current research suggests that CRISPR screens may have fewer off-target effects than shRNA screens. Variants of CRISPR knockout screens include CRISPR activation (CRISPRa) and inhibition (CRISPRi) screens. These screens use catalytically dead dCas9 to inhibit or activate given genes without direct genomic modification. As in shRNA screens, the effects are reversible.</br>When choosing your library, please be aware that some of the library vectors contain Cas9 (1 plasmid system), while others require co-infection with Cas9-expressing virus or use in cells expressing Cas9 (2 plasmid system).</br>Knockout

CRISPR knockout libraries are designed to create insertions or deletions in targeted genes across the genome, rendering them nonfunctional. Libraries are designed to target throughout the genome unless specified. To limit false positives or false negatives, each library contain multiple gRNAs for each gene targeted by the library. Each library also contains non-targeting control gRNAs.</br>Library ID Species Lentiviral Generation PI Genes Targeted gRNAs per gene Total gRNAs

Bassik Human CRISPR Knockout Library</br>Description  101926 — 101934 Human 3rd Bassik Varies (∼20,500 in total) ∼10 Varies

Bassik Mouse CRISPR Knockout Library</br>Description  1000000121 — 1000000130 Mouse 3rd Bassik Varies (∼23,000 in total) ∼10 Varies

Human Epigenetic Knockout Library</br>Description  162256 Human 3rd Birsoy 2,508 8 20,051

Mouse CRISPR Metabolic Gene Knockout Library</br>Description  160129 Mouse 3rd Birsoy 2,865 8 22,909

Bradley Human CRISPR Poison Exon Knockout Library</br>Description  138084 Human 3rd Bradley 963 exons targeted ~9 pairs/exon 9,508

Mouse Tumor Suppressor Gene CRISPR Knockout Library</br>Description  113584 EFS backbone

113585 TBG backbone Mouse N/A Chen 56 ∼4 286

Mouse Metastasis CRISPR-Cpf1(Cas12a) Double Knockout Library</br>Description  123361 Mouse 3rd Chen 26 4 11,934 arrays

Brie mouse genome-wide library</br>Description  73632 (1 plasmid)

73633 (2 plasmid) Mouse 3rd Doench and Root 19,674 4 78,637

Brie mouse kinome library</br>Description  75317 (1 plasmid)

75316 (2 plasmid) Mouse 3rd Doench and Root 713 4 2,852

Brunello human genome-wide library</br>Description  73179 (1 plasmid)

73178 (2 plasmid) Human 3rd Doench and Root 19,114 4 76,441

Brunello human kinome library</br>Description  75314 (Guides 1-4); 75315 (Guides 5-8)

(1 plasmid)</br>75312 (Guides 1-4); 75313 (Guides 5-8)

(2 plasmid)</br>1000000083

Guides 1-4 & 5-8

(1 plasmid)</br>1000000082

Guides 1-4 & 5-8

(2 plasmid) Human 3rd Doench and Root 763 4 3,052

Gattinara human genome-wide library</br>Description  136986 Human 3rd Doench 19,993 2 40,964

Gouda mouse genome-wide library</br>Description  136987 Mouse 3rd Doench 21,601 2 44,155

Mini-human AsCpf1-based Human Genome-wide Knockout Library</br>Description  130630 Human 3rd Draetta 16,977 3-4 17,032 arrays

Human Interferon-Stimulated Gene CRISPR Knockout Library</br>Description  125753 Human 3rd Emerman

OhAinle 1,902 8 15,416

Lin Human miRNA CRISPR Knockout Library</br>Description  112200 Human 3rd Lin 1,594 ∼5 8,382

Oxford Drosophila genome-wide library</br>Description  64750 D. melanogaster N/A J. Liu 13,501 3 40,279

Human CRISPR knockout library</br>Description  1000000132 Human 3rd X.S. Liu 18,436 10 185,634

CHyMErA Knockout Libraries</br>Description  155199

155200 Human 3rd Moffat

Blencowe 6,333

2,157 variable 92,746

91,948

Mouse Toronto KnockOut (mTKO) CRISPR Library</br>Description  159392

159393 Mouse 3rd Moffat 19,463 ~5 94,528

Mouse Validation (mVAL) CRISPR Library</br>Description  159391 Mouse 3rd Moffat 182 4 1,656

Toronto KnockOut (TKO) genome-wide library - Version 1</br>Description  1000000069 Human 3rd Moffat 17,661 12 176,500

Toronto KnockOut (TKO) genome-wide library - Version 3</br>Description  90294 (1 plasmid)

125517 (2 plasmid) Human 3rd Moffat 18,053 4 70,948

Human GlycoGene CRISPR Library</br>Description  140961 Human 3rd Neelamegham 347 10 3,637

Toxoplasma genome-wide library</br>Description  80636 T. gondii N/A Lourido 8,158 10 80,158

Human Genome-Wide Reduced Double-gRNA Library</br>Description  137999 Human 3rd Parts 19,657 3 59,576

Drosophila Cell CRISPR Knockout Libraries</br>Description  134582

134583

134584 D. melanogaster 3rd Perrimon 955

2979

9954 8

6

6 7,956

17,827

59,406

Mouse Cardiac Transcriptional Regulators CRISPR Knockout Library</br>Description  138015 Mouse N/A Pu 2,444 6 14,671

Activity-optimized human genome-wide library</br>Description  1000000100 Human 3rd Sabatini and Lander 18,663 10 187,535

Activity-optimized human genome-wide library</br>Discontinued - see #1000000100 for an improved version</br>1000000067 Human 3rd Sabatini and Lander 18,166 5 178,896

Human CRISPR Metabolic Gene Knockout Library</br>110066 Human 3rd Sabatini 2,981 ∼10 30,290

Two plasmid activity-optimized human genome-wide library</br>Description  1000000095 Human 3rd Sabatini and Lander 18,543 10 187,536

Two plasmid activity-optimized mouse genome-wide library</br>Description  1000000096 Mouse 3rd Sabatini and Lander 18,986 10 188,509

Focused Ras Synthetic Lethal Human CRISPR Knockout Library</br>Description  92352 Human 3rd Sabatini and Lander 132 50 6,661

Enriched human sub-pooled libraries</br>Description  51043 — 51048 Human 3rd Sabatini and Lander Varies 10 Varies

Human SLC Knockout Library</br>Description  132552 Human 3rd Superti-Furga 390 6-7 2,609

Mouse SLC Knockout Library</br>Description  141436 Mouse 3rd Superti-Furga 378 6-7 2,384

Retroviral Mouse Genome-wide CRISPR Knockout Library</br>Description  104861 Mouse N/A Teichmann 18,424 5 90,230

Human Kinase Domain-Focused CRISPR Knockout Library</br>Description  117725 Human 3rd Vakoc 482 ∼6 3,051

Human DNA Binding Domain-Focused CRISPR Knockout Library</br>Description  123334 Human 3rd Vakoc 1,427 ∼6 8,658

Human paired-guide RNA (pgRNA) Library for long non-coding RNAs (lncRNAs)</br>Description  89640 Human 3rd Wei 671 lncRNAs Varies 12,472 pairs

Human lncRNA Splicing-targeting CRISPR Library</br>Description  119977 Human 3rd Wei 10,996 lncRNAs Varies 126,773

Human Whole Genome sgRNA iBAR Library</br>Description  140633 Human 3rd Wei 19,210 3 58,630

Human genome-wide library v1</br>Description  69763 Human 3rd Wu 20,121 4 77,406

Mouse CRISPR/Cas9-assisted Removal of Mitochondrial DNA (CARM) Library</br>Description  82480 Mouse N/A Xie gRNAs target every ∼40bp over mitochondrial genome N/A 395

RNA-Binding Protein Pooled CRISPR Knockout Library</br>Description  141438 Human 3rd Yeo 1,078 10 12,472

Human improved genome-wide library v1</br>Description  67989 Human 3rd Yusa 18,010 5 90,709

Mouse genome-wide library</br>Discontinued 50947 Mouse 3rd Yusa 19,150 5 87,897

Mouse improved genome-wide library v2</br>Description  67988 Mouse 3rd Yusa 18,424 5 90,230

Cas13a/C2c2 Protospacer flanking site (PFS) Library</br>Description  79153 Bacterial N/A Zhang 4,096 Protospacer flanking sites N/A N/A

Human GeCKO v2 genome-wide library</br>Description  1000000048 (1 plasmid)

1000000049 (2 plasmid) Human 3rd Zhang 19,052 6 123,411

Mouse GeCKO v2 genome-wide library</br>Description  1000000052 (1 plasmid)

1000000053 (2 plasmid) Mouse 3rd Zhang 20,661 6 130,209

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Activation

CRISPR activation libraries use gRNAs to guide dCas9 bound to a transcriptional activator to target genes and thereby activate their expression. You can learn more CRISPR-based gene regulation on our CRISPR guide page.</br>Library ID Species Lentiviral Generation PI Genes targeted gRNAs per gene Total gRNAs</br></br>An Introduction to Pooled Libraries

Pooled libraries represent a powerful tool for forward genetic screening, or identifying previously unknown genes that contribute to a phenotype. At their simplest level, pooled libraries are single preparations of many different plasmids. Plasmids within a given library have the same backbone, but they express or target different genes. Some libraries cover the majority of the genome, while others are restricted to certain gene sets. In cDNA libraries, each plasmid contains a unique cDNA. In shRNA or gRNA libraries, each plasmid contains a unique gene targeting sequence, but there are multiple sequences targeting each gene in the overall library. Barcoding libraries contain plasmids with unique, semi-random sequences that can be used for applications like lineage tracing or parsing the effects of expressing multiple genes at once. A well-designed screen can help you begin to understand what genes are important to a certain phenotype, and allow you to design additional hypothesis-directed experiments.</br>As you might have guessed from their name, pooled libraries are supplied as a mixed population of plasmids in a single tube. Pooled libraries can be small, if they are designed to cover only a subset of genes, or very large (e.g. the Toronto KnockOut (TKO) library from the Moffat lab has over 175,000 different gRNA-containing plasmids).</br>Amplifying and Using the Library

Once you receive your library from BioVector, check the library information to see if it should be amplified before you conduct your screen. If you need to amplify the library, please refer to the depositor’s protocol for the best results.</br>For some libraries, plasmid DNA can be delivered directly to the cells of interest. With others, notably pooled lentiviral plasmid libraries, the plasmids must first be used to make virus. This pooled virus is subsequently used to deliver the plasmids to the cells of interest. In either case, next-generation sequencing of the maxiprep DNA is recommended to verify that the library is complete - an incomplete library may lead to false positives or false negatives in later experiments, and can also negatively affect data reproducibility.</br>Overview of pooled libraries

Types of Pooled Library Screens

In pooled library screens, cells are infected at a very low multiplicity of infection (MOI) to increase the odds that an infected cell receives only one plasmid. To make sure that every plasmid is adequately represented in the population, you’ll need to infect many more cells than the number of plasmids present in the library - for example, the Moffat lab uses 200x the number of cells as plasmids in the TKO library. Using large numbers of cells minimizes the effects of random chance that could lead to false positive or negative results - for a given plasmid, think of each cell carrying it as being a biological replicate for that plasmid.</br>Library screens can be divided into two types: positive screens and negative screens. Both types of screen employ a selection method relevant to the phenotype being studied. Examples of published selection mechanisms for lentiviral CRISPR libraries include: resistance to the  anti-cancer drug vemurafenib, resistance to  Clostridium septicum alpha-toxin, and resistance to to the  nucleotide analog 6-thioguanine. Next-generation sequencing is the only way to accurately evaluate which library components are influenced by selection, so it’s essential that you have access to this technology if you’re planning to conduct a pooled library screen.</br>positive and negative screening workflow

The figure above is an outline of how a gRNA library is used. Below are the general steps to take in the screening process.</br>Amplify the library (electroporation and maxiprep).

If delivering as virus, make virus; this creates a pooled lentiviral CRISPR library.

Apply pooled library to cells.

DIVERGE: Positive and negative screens</br>POSITIVE screen:</br>Apply library

Apply selection

Most cells die or do not pass selection (in the case of a reporter)

Sort “winning” cells

Sequence those cells that pass (“win”)

Get a list of genes involved in the selection

NEGATIVE screen:</br>Apply library

Perform Next Generation Sequencing (NGS) on a control sample (no selection)

In parallel, apply library

Apply selection; most cells will survive

Perform NGS on the surviving cells

Compare NGS results between experimental and control cells

Generate a list of gRNAs that disappear with addition of the selection mechanism

Positive Screen

In a positive screen, the goal is to identify those cells that survive post-selection. The selective pressure must be strong enough that most of the cells die, removing their plasmids from the population, and only a small fraction survive. After the surviving cells are collected, their plasmids are PCR-amplified and sequenced using NGS to identify their cDNA or target gene. Positive selection screens are generally very robust, and tens of thousands of genes that were initially present may be narrowed down to a few hundred or fewer ‘winners’.</br>Negative Screen

Negative screens are a little trickier than positive screens. In a negative screen, the goal is to identify those cells that do not survive the selection mechanism. You’ll infect two sets of cells and subject one set to selection while the other serves as a non-selected control. These two populations are then sequenced using NGS to determine which plasmids have been depleted by selection. In a CRISPR screen, negative screens are often used to identify genes that are essential for growth/survival under certain conditions.</br>Next-Generation Sequencing

Next-generation sequencing allows for parallel sequencing of millions of DNA fragments simultaneously in a single reaction. As discussed above, access to this technology is crucial for conducting pooled library screens. BioVector does not offer next-generation sequencing services. For an NGS company near you, please consult these links:</br> NGS Company Resources

AllSeq

Science Exchange

Scientist (formally Assay Depot)

Resources

Find additional resources on our website:</br>Read our CRISPR guide for more information on genome-wide screening with CRISPR/Cas9.

Browse our Viral Vector resources.

Check out our blog posts featuring some of our most popular libraries!

Genome-wide Screening Using CRISPR/Cas9

Lentiviral CRISPR Libraries Enable Genome-Scale, Knockout Screening

Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

New Tool for Lineage Tracing: The ClonTracer Library  

Calabrese p65-HSF human activation library</br>Description  92379 (Set A); 92379-LV (Lentiviral Prep)</br>92380 (Set B); 92380-LV (Lentiviral Prep)</br>1000000111

Set A & Set B Human 3rd Doench and Root 18,885 (Set A), 18,843 (Set B) 3-6 56,762 (Set A), 56,476 (Set B)

Caprano p65-HSF mouse activation library</br>Description  92383 (Set A)</br>92384 (Set B)</br>1000000113

Set A & Set B Mouse 3rd Doench and Root 22,774 (Set A), 22,658 (Set B) 3-6 67,187 (Set A), 66,889 (Set B)

Mouse Transcription Factor Activation Library</br>Description  122131 Mouse 3rd Qi 2,428 ∼20 51,762

Human SLC Activation Library</br>Description  132561 Human 3rd Superti-Furga 388 6-7 3,342

CRISPRa-v2 human genome-wide library</br>Description  83978

1000000091 Human 3rd Weissman 18,915 10 104,540

209,080

Subpooled CRISPRa-v2 human libraries</br>Description  83980 — 83986 Human 3rd Weissman Varies 5 Varies

CRISPRa-v2 mouse genome-wide library</br>Description  83996

1000000093 Mouse 3rd Weissman 19,939 10 107,105

214,210

Subpooled CRISPRa-v2 mouse libraries</br>Description  83998 — 84004 Mouse 3rd Weissman Varies 5 Varies

CRISPRa genome-wide library

Discontinued</br>60956 Human 3rd Weissman 15,977 10 198,810

Human Membrane Protein Activation Library</br>Description  113345 Human 3rd Wright 6,213 7-14 58,570

Human SAM genome-wide library (2-plasmid system)</br>Description  1000000078 Human 3rd Zhang 23,430 3 70,290

Human SAM genome-wide library (3-plasmid system)</br>Description  1000000057 (Zeocin)

1000000074 (Puromycin) Human 3rd Zhang 23,430 3 70,290

Human SAM lncRNA activation library (3-plasmid system)</br>Description  1000000106 (Zeocin) Human 3rd Zhang 10,504 10 96,458

Mouse SAM genome-wide library (3-plasmid system)</br>Description  1000000075 (Puromycin) Mouse 3rd Zhang 23,439 3 69,716

Repression

CRISPR repression libraries use gRNAs to guide dCas9 bound to a transcriptional repressor to target genes, block transcription initiation, and thereby repress, or knockdown, their expression. You can learn more CRISPR-based gene regulation on our CRISPR guide page.</br>Library ID Species Lentiviral Generation PI Genes Targeted gRNAs per gene Total gRNAs

Bikard E. coli Genome-wide Inhibition Library v1</br>Description  115927 E. coli N/A Bikard ∼4,500 ∼19 92,919

Bikard Lab EcoWG1: E. Coli Genome-wide Inhibition Library v2</br>Description  131625 E. coli N/A Bikard 4,444 ∼5 21,417

Dolcetto human inhibition library</br>Description  92385 (Set A)</br>92386 (Set B)</br>1000000114

Set A & Set B Human 3rd Doench and Root 18,901 (Set A), 18,899 (Set B) 3-6 57,050 (Set A), 57,011 (Set B)

Dolomiti mouse inhibition library</br>Description  104090 (Set A)</br>104091 (Set B)</br>1000000131

Set A & Set B Mouse 3rd Doench and Root 22,311 (Set A), 22,247 (Set B) 3-6 67,366 (Set A), 67,194 (Set B)

CRiNCL - Human CRISPRi Non-coding Libraries</br>Description  86538 — 86550 Human 3rd Weissman Varies 10 Varies

CRISPRi-v2 human genome-wide library</br>Description  83969

1000000090 Human 3rd Weissman 18,905 5

10 104,535

209,070

Subpooled CRISPRi-v2 human libraries</br>Description  83971 — 83977 Human 3rd Weissman Varies 5 Varies

CRISPRi-v2 mouse genome-wide library</br>Description  83987

1000000092 Mouse 3rd Weissman 20,003 5

10 107,415

214,830

Human CRISPRi Titration Libraries</br>Description  136478

136479 Human 3rd Weissman ~2,500 23-24

1-9 119,510

25,518

Subpooled CRISPRi-v2 mouse libraries</br>Description  83989 — 83995 Mouse 3rd Weissman Varies 5 Varies

CRISPRi genome-wide library

Discontinued</br>62217 Human 3rd Weissman 15,977 10 206,421

Chong Zhang E. coli Genome-wide Inhibition Library</br>Description  113134 — 113138

113146, 113147 E. coli N/A Chong Zhang Varies ∼15 Varies

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Screening Libraries

Screening libraries (non-CRISPR) can be used for different types of high-throughput experiments, including assay of protein-protein interactions or the effects of mutagenesis of a single gene. For example, phage display is a type of screening library that is used for finding binding partners for targets of interest. It relies on fusions of gene fragments and a bacteriophage coat protein.</br>Library ID Species Vector backbone PI Description

SPECS Library 127842 Synthetic Lentiviral Lu Library for high-throughput screening for identification of synthetic promoters with enhanced cell-state specificity.

TP53 Mutagenesis Library 113569 Human Lentiviral Hahn and Root Designed for the characterization of all possible p53 mutations

Synuclein VHH Immune Library 1000000071 Camelid Phagemid Messer and MJFF Created for research in Parkinson's Disease; For target validation and drug design

shRNA Libraries

shRNA libraries permit reversible loss-of-function screening to elucidate which genes are involved in a phenotype. Each library contains multiple shRNA sequences for each target gene; a true positive hit (a particular target gene) in an shRNA screen should show consistent results from the multiple shRNAs that target it. shRNA libraries may also be barcoded to allow for easy identification of the shRNA a given cell carries.</br>DECIPHER libraries are lentiviral barcoded shRNA libraries designed for RNAi screening. It’s important to note that these libraries are not genome-wide; instead, each library is enriched for a smaller set of biologically relevant genes. The DECIPHER barcoding system makes it easy to determine which shRNAs have been enriched or depleted in a cell population; each plasmid carries a unique 18 bp barcode that can be easily identified using next-generation sequencing.</br>As of October 2016, the DECIPHER libraries have been discontinued.</br>Library ID Species Lentiviral Generation PI Targets Total shRNAs

Decipher Mod 2: Disease Targets Discontinued</br>28286 Human 3rd Chenchik and Frango 5,412 27,500

Decipher Mod 3: Cell Surface, etc. Discontinued</br>29589 Human 3rd Chenchik 4,922 27,500

Decipher Mod 1: Pathway Targets Discontinued</br>28287 Mouse 3rd Chenchik and Frango 4,625 27,500

Decipher Mod 2: Disease Targets Discontinued</br>28288 Mouse 3rd Chenchik and Frango 4,520 27,500<br/></br>Supplier来源:BioVector NTCC Inc.<br/>TEL电话:+86-010-53513060<br/>Website网址: http://www.biovector.net


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