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

CHODL Gene

protein-coding   GIFtS: 49
GCID: GC21P019166

chondrolectin

(Previous name: chromosome 21 open reading frame 68 )
(Previous symbol: C21orf68)
 Explore 2 diseases affiliated with
CHODL via our new
 Human Malady Compendium 
Biological research products
for CHODL
    

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

Aliases
Chondrolectin1     FLJ126271
C21orf681 2 3     PRED121
MT751 2     Chromosome 21 Open Reading Frame 681
Transmembrane Protein MT752 3     

External Ids:    HGNC: 178071   Entrez Gene: 1405782   Ensembl: ENSG000001546457   OMIM: 6072475   UniProtKB: Q9H9P23   

Export aliases for CHODL gene to outside databases

Previous GC identifers: GC21P016281 GC21P018538 GC21P018539 GC21P018195 GC21P005005


(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 CHODL:
This gene encodes a type I membrane protein with a carbohydrate recognition domain characteristic of C-type lectins in
its extracellular portion. In other proteins, this domain is involved in endocytosis of glycoproteins and exogenous
sugar-bearing pathogens. This protein localizes predominantly to the perinuclear region. Several transcript variants
encoding a few different isoforms have been found for this gene. (provided by RefSeq, Feb 2011)

Gene Wiki entry for CHODL


(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_000021.8  NC_018932.1  NT_011512.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CHODL gene promoter:
         LHX3b/Lhx3b   RP58   Pax-2   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   Pax-2a   Nkx2-5   E47   Sox9   LHX3a/Lhx3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCHODL promoter sequence
   Search SABiosciences Chromatin IP Primers for CHODL

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


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

Entrez Gene cytogenetic band: 21q11.2   Ensembl cytogenetic band:  21q21.1   HGNC cytogenetic band: 21q11.2

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

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P019166:  view genomic region     (about GC identifiers)

Start:
19,165,801 bp from pter      End:
19,639,690 bp from pter
Size:
473,890 bases      Orientation:
plus 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: CHODL_HUMAN, Q9H9P2 (See protein sequence)
Recommended Name: Chondrolectin precursor  
Size: 273 amino acids; 30431 Da
Subcellular location: Cytoplasm. Membrane; Single-pass type I membrane protein (Potential)
Miscellaneous: A protein of the expected size has been detected by antibody binding and Western blot in at least one of
the analyzed tissues or cells (PubMed:22042635)
Secondary accessions: B2R9C0 B4DJB8 Q7Z798 Q7Z799 Q7Z7A0 Q9HCY3
Alternative splicing: 4 isoforms:  Q9H9P2-1   Q9H9P2-2   Q9H9P2-3   Q9H9P2-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CHODL: NX_Q9H9P2

Post-translational modifications:

  • N-glycosylated1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H9P2

  • CHODL Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (6 alternative transcripts): 
    NP_001191103.1  NP_001191104.1  NP_001191105.1  NP_001191106.1  NP_001191107.1  NP_079220.2  

    ENSEMBL proteins: 
     ENSP00000415566   ENSP00000417423   ENSP00000390957   ENSP00000382993   ENSP00000382996  
     ENSP00000383001   ENSP00000382992   ENSP00000299295   ENSP00000443566   ENSP00000339975  

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    Uscn Proteins for CHODL

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--
    GO:0016021integral to membrane IEA--
    GO:0048471perinuclear region of cytoplasm IDA12079284


    CHODL for ontologies           About GeneDecksing



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

    CHODL for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR016187 C-type_lectin_fold
     IPR016186 C-type_lectin-like
     IPR001304 C-type_lectin

    Graphical View of Domain Structure for InterPro Entry Q9H9P2

    ProtoNet protein and cluster: Q9H9P2

    UniProtKB/Swiss-Prot: CHODL_HUMAN, Q9H9P2
    Similarity: Contains 1 C-type lectin domain


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

    miRNA
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    hsa-miR-3910 hsa-miR-323-3p hsa-miR-431 hsa-miR-507 hsa-miR-374a* hsa-miR-548m hsa-miR-124 hsa-miR-641
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005540NOT hyaluronic acid binding IDA12079284
    GO:0030246carbohydrate binding IEA--


    CHODL for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Chodltm1Lex for CHODL
         1 MGI phenotypic allele for Chodl (no phenotypes)

    CHODL for phenotypes           About GeneDecksing


    (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 CHODL

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

    1 Interacting protein for CHODL (ENSP000002992954) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SIRT5ENSP000003685524STRING: ENSP00000368552
    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:0007517muscle organ development NAS12079284


    CHODL 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 CHODL
    Search CenterWatch for drugs/clinical trials and news about CHODL 

    (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, 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 CHODL gene (6 alternative transcripts): 
    NM_001204174.1  NM_001204175.1  NM_001204176.1  NM_001204177.1  NM_001204178.1  NM_024944.2  

    Unigene Cluster for CHODL:

    Chondrolectin
    Hs.283725  [show with all ESTs]
    Unigene Representative Sequence: NM_024944
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000452759 ENST00000465099 ENST00000427223 ENST00000400128(uc002ykr.3 uc002yks.3 uc021whr.1 uc002ykt.3 uc002yku.3)
    ENST00000400131 ENST00000400135 ENST00000400127(uc021whs.1) ENST00000299295(uc002ykv.3)
    ENST00000543733 ENST00000338326

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    hsa-miR-3910 hsa-miR-323-3p hsa-miR-431 hsa-miR-507 hsa-miR-374a* hsa-miR-548m hsa-miR-124 hsa-miR-641
    SwitchGear 3'UTR luciferase reporter plasmidCHODL 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AF257472.1 AF523313.1 AF523314.1 AF523315.1 AK022689.1 AK296009.1 AK313725.1 AY358608.1 
    BC009418.1 

    4 DOTS entries:

    DT.91679032  DT.100748590  DT.100748591  DT.100694217 

    24/54 AceView cDNA sequences (see all 54):

    BC009418 AF257472 AI089920 AI332692 AK022689 AA235925 CA446379 AU125569 
    NM_024944 AW452240 AI378795 AA976845 AI093869 AY358608 W07506 BF979864 
    BE313146 AL700069 T84923 AI147017 AA405716 BI828968 AW449247 AF523315 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CHODL    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
    SP1:                                          
    SP2:                          -               


    ECgene alternative splicing isoforms for CHODL

    (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

    CHODL expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTTATTTTGC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CHODL expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeInner Nuclear LayernGnG Amacrine CellsAmacrine, Retina
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Cartilage-like cells (Differentiation of s...)Cartilage

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

    SOURCE GeneReport for Unigene cluster: Hs.283725

    UniProtKB/Swiss-Prot: CHODL_HUMAN, Q9H9P2
    Tissue specificity: Found in spleen, testis, prostate and fetal liver. Expression limited to vascular muscle of testis,
    smooth muscle of prostate stroma, heart muscle, skeletal muscle, crypts of small intestine, and red pulp of spleen

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    (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 chordates.

    Orthologs for CHODL gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Chodl1 , 5 chondrolectin1, 5 87.67(n)1
    92.67(a)1
      16 (45.39 cM)5
    2460481  NM_139134.31  NP_624360.21 
     789309485 
    chicken
    (Gallus gallus)
    Aves CHODL1 chondrolectin 76.24(n)
    76.49(a)
      418474  XM_001231434.2  XP_001231435.1 
    lizard
    (Anolis carolinensis)
    Reptilia CHODL6
    --
    76(a)
    1 ↔ 1
    3(153447448-153455794)
    zebrafish
    (Danio rerio)
    Actinopterygii chodl1 chondrolectin 64.83(n)
    66.93(a)
      550240  NM_001017578.1  NP_001017578.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CHODL gene
    LAYN2  
    1 SIMAP similar gene for CHODL using alignment to 1 protein entry:     CHODL_HUMAN:
    LAYN

    CHODL 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

    10/6986 NCBI SNPs in CHODL are shown (see all 6986    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs560794361,2
    C,--19287670(+) CTTATG/ATATTA 4 -- us2k12Minor allele frequency- A:0.09WA 120
    rs1487748861,2
    --19287673(+) ATGTAG/TTATTA 4 -- us2k10--------
    rs72804901,2
    C,F,A,H,--19287750(+) TTTACG/ATGGTA 4 -- us2k111Minor allele frequency- A:0.42NA WA CSA EA 374
    rs99842381,2
    C,F,A,H,--19287753(+) ACGTGG/ATAAAT 4 -- us2k19Minor allele frequency- A:0.38NA WA EA 370
    rs1130339381,2
    C,--19287762(+) ATATGG/CTACTT 4 -- us2k12Minor allele frequency- C:0.09WA 120
    rs1922932821,2
    --19287904(+) GAAAAC/TATATA 4 -- us2k10--------
    rs1420935971,2
    --19287907(+) AACATA/GTATGT 4 -- us2k10--------
    rs1463639561,2
    --19287976(+) GCCAGA/GGCTGA 4 -- us2k10--------
    rs1832555871,2
    --19288011(+) CCAGGA/CAGAGA 4 -- us2k10--------
    rs758043301,2
    --19288084(+) ATAACA/CCTGGA 4 -- us2k10--------

    HapMap Linkage Disequilibrium report for CHODL (19165801 - 19415801 bp, first 250kb of CHODL)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for CHODL
         2 CNVs: 59037 9325

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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

    CHODL for disorders           About GeneDecksing

    OMIM gene information: 607247    OMIM disorders: --

    2 diseases for CHODL:    About MalaCards
    prostatitis    neuronitis


    Export disorders for CHODL 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 CHODL gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with CHODL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of human chondrolectin, a novel type I transmembrane protein homologous to C-type lectins. (PubMed id 12079284)1, 2, 3 Weng L.... Merregaert J. (2002)
    2. A novel alternative spliced chondrolectin isoform lacking the transmembrane domain is expressed during T cell maturation. (PubMed id 12621022)1, 2, 9 Weng L.... Merregaert J. (2003)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    6. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PubMed id 11707072)1, 2 Reymond A....Antonarakis S.E. (2001)
    7. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M....Yaspo M.L. (2000)
    8. Expression and localization of CHODLDeltaE/CHODLfDeltaE, the soluble isoform of chondrolectin. (PubMed id 17606388)1, 9 Claessens A....Merregaert J. (2007)
    9. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
    10. Antibody-based protein profiling of the human chromosome 21. (PubMed id 22042635)2 Uhlen M....Sivertsson A. (2012)

    (in PubMed, OMIM, and 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: 140578 HGNC: 17807 AceView: CHODL Ensembl:ENSG00000154645 euGenes: HUgn140578
    ECgene: CHODL H-InvDB: CHODL

    (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 CHODL Pharmacogenomics, SNPs, Pathways
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_185

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

    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, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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