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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PCDH20 Gene

protein-coding   GIFtS: 47
GCID: GC13M061983

protocadherin 20

 Explore 3 diseases affiliated with
PCDH20 via our new
 Human Malady Compendium 
Biological research products
for PCDH20
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Protocadherin 201 2     Protocadherin-133
PCDH131 2 3     Protocadherin-201
FLJ222181     Protocadherin-133
Protocadherin 132     

External Ids:    HGNC: 142571   Entrez Gene: 648812   Ensembl: ENSG000001979917   OMIM: 6144495   UniProtKB: Q8N6Y13   

Export aliases for PCDH20 gene to outside databases

Previous GC identifers: GC13M059951 GC13M055978 GC13M060920 GC13M059781 GC13M060881 GC13M042676


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PCDH20:
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a
protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from
those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal
receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain.
(provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
Function: Potential calcium-dependent cell-adhesion protein

Gene Wiki entry for PCDH20


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDH20 gene promoter:
         AML1a   GATA-3   CUTL1   GATA-2   GATA-1   MEF-2A   FOXO4   HSF2   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDH20 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDH20

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDH20


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q21   Ensembl cytogenetic band:  13q21.2   HGNC cytogenetic band: 13q21

PCDH20 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDH20 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M061983:  view genomic region     (about GC identifiers)

Start:
61,983,818 bp from pter      End:
62,002,220 bp from pter
Size:
18,403 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1 (See protein sequence)
Recommended Name: Protocadherin-20 precursor  
Size: 924 amino acids; 101927 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Sequence caution: Sequence=AAF89690.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=CAD38690.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAH73802.3;
Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B1AQU2 Q8NDN4 Q9NRT9

Explore the universe of human proteins at neXtProt for PCDH20: NX_Q8N6Y1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8N6Y1

  • PCDH20 Protein expression data from MOPED and PaxDb:    About this image 
    PCDH20 Protein Expression
    REFSEQ proteins: NP_073754.2  
    ENSEMBL proteins: 
     ENSP00000387250   ENSP00000386653  

    Human Recombinant Protein Products for PCDH20: 
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    Uscn Proteins for PCDH20

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--

    PCDH20 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for PCDH20


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    PCDH20 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR015919 Cadherin-like
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q8N6Y1

    ProtoNet protein and cluster: Q8N6Y1

    1 Blocks protein family: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
    Similarity: Contains 6 cadherin domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCD20_HUMAN, Q8N6Y1
    Function: Potential calcium-dependent cell-adhesion protein

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDH20 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for PCDH20 

    miRNA
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    hsa-miR-30c hsa-miR-3607-3p hsa-miR-30d hsa-miR-340 hsa-miR-4267 hsa-miR-649 hsa-miR-30a hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidPCDH20 3' UTR sequence
    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDH20


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDH20

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for PCDH20 (Q8N6Y13 ENSP000003866534) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RYKP349253, ENSP000002960844I2D: score=1 STRING: ENSP00000296084
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    PCDH20 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PCDH20

    1 HMDB Compound for PCDH20    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about PCDH20 / PCD20 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PCDH20 gene: 
    NM_022843.3  

    Unigene Cluster for PCDH20:

    Protocadherin 20
    Hs.391781  [show with all ESTs]
    Unigene Representative Sequence: AL833830
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409204(uc001vid.4) ENST00000409186(uc010thj.2) ENST00000472649


    miRNA
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    hsa-miR-30c hsa-miR-3607-3p hsa-miR-30d hsa-miR-340 hsa-miR-4267 hsa-miR-649 hsa-miR-30a hsa-miR-4325
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    Inhib. RNA
    Products:
         
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    OriGene siRNA: PCDH20
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDH20
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    Additional cDNA sequence: 

    AF169693.1 AK025871.1 AK094680.1 AK289924.1 AK314607.1 AL833830.1 BC027907.1 

    3 DOTS entries:

    DT.97768248  DT.99933397  DT.120763635 

    24/36 AceView cDNA sequences (see all 36):

    C16499 BU070294 T04933 AK094680 N34280 CK902366 BU608937 AA040057 
    AK025871 AI375140 BC038756 AI039143 AA040043 AA625076 BI766301 BC027907 
    AF169693 AL833830 Z43057 BX106673 BQ439228 AA453141 NM_022843 BP379279 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PCDH20 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    PCDH20 Expression
    About this image

    PCDH20 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneZeugopod Epiphyseal EndBone
    Head MesenchymeFrontonasal ProcessHead Mesenchyme
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    HyStem+BMP4-induced MEL2 cells (HyStem+BMP4 inductio...)Bone

    See PCDH20 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDH20

    SOURCE GeneReport for Unigene cluster: Hs.391781
        SABiosciences Custom PCR Arrays for PCDH20
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDH20

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for PCDH20 gene from 4/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PCDH201 protocadherin 20 75.13(n)
    80.89(a)
      428063  XM_425621.3  XP_425621.2 
    lizard
    (Anolis carolinensis)
    Reptilia PCDH206
    --
    77(a)
    1 ↔ 1
    3(76243203-76249608)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh201 protocadherin 20 60.51(n)
    59.23(a)
      100007362  XM_001345807.2  XP_001345843.2 
    worm
    (Caenorhabditis elegans)
    Secernentea cdh-16
    CaDHerin family member (cdh-1)
    7(a)
    1 → many
    III(2910962-2935598)


    ENSEMBL Gene Tree for PCDH20 (if available)
    TreeFam Gene Tree for PCDH20 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDH20 gene
    PCDH172  PCDH72  PCDH11X2  PCDH12  PCDH102  PCDH11Y2  PCDH122  PCDH182  
    PCDH92  PCDH192  PCDH82  
    5 SIMAP similar genes for PCDH20 using alignment to 2 protein entries:     PCD20_HUMAN (see all proteins):
    PCDH9    PCDH11X    PCDH11Y    PCDH1    PCDH7

    PCDH20 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/164 NCBI SNPs in PCDH20 are shown (see all 164    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1831546401,2
    --61983477(+) CATTGC/TTGCCT 1 -- int10--------
    rs79905361,2
    C,F,A,H--61983572(+) CTTGGT/CTGTTT 1 -- int18Minor allele frequency- C:0.35NA WA EA 504
    rs1878038161,2
    --61983649(+) TAACAA/GAGGAT 1 -- int10--------
    rs1388719131,2
    --61984000(+) GAAAAC/TATATA 1 -- ut310--------
    rs1179045451,2
    C,F--61984060(+) ATGCCA/GAAAAG 1 -- ut311Minor allele frequency- G:0.02NA 120
    rs1924268091,2
    --61984098(+) TTCCTG/TGTTTA 1 -- ut310--------
    rs1427384431,2
    --61984130(+) TCTCAC/TATAAA 1 -- ut310--------
    rs412934381,2
    C,F--61984275(+) NNNNAT/CCCAAA 1 -- ut311Minor allele frequency- C:0.02NA 120
    rs1849555901,2
    --61984320(+) AACCTA/GAACAA 1 -- ut310--------
    rs1473869411,2
    --61984365(+) AAAAGA/GCCCAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for PCDH20 (61983818 - 62002220 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for PCDH20: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDH20
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    PCDH20 for disorders           About GeneDecksing

    OMIM gene information: 614449    OMIM disorders: --

    3 diseases for PCDH20:    About MalaCards
    lung cancer    neuronitis    asthma


    Export disorders for PCDH20 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PCDH20 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with PCDH20)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Genome-wide association study identifies novel loci as sociated with circulating phospho- and sphingolipid concentrations. (PubMed id 22359512)1 Demirkan A....Schmitz G. (2012)
    3. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. (PubMed id 21907864)1 Ferreira M.A....Thompson P.J. (2011)
    4. Mindbomb 1, an E3 ubiquitin ligase, forms a complex w ith RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)1 Berndt J.D....Moon R.T. (2011)
    5. Joint influence of small-effect genetic variants on h uman longevity. (PubMed id 20834067)1 Yashin A.I....Ukraintseva S.V. (2010)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    7. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    8. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)2 Dunham A.... Ross M.T. (2004)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 64881 HGNC: 14257 AceView: PCDH20 Ensembl:ENSG00000197991 euGenes: HUgn64881
    ECgene: PCDH20 H-InvDB: PCDH20

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PCDH20 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDH20 gene:
    Search GeneIP for patents involving PCDH20

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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