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

ODF1 Gene

protein-coding   GIFtS: 52
GCID: GC08P103633

outer dense fiber of sperm tails 1

(Previous name: outer dense fibre of sperm tails 1 )
 Explore 2 diseases affiliated with
ODF1 via our new
 Human Malady Compendium 
Biological research products
for ODF1
    

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

Aliases
Outer Dense Fiber Of Sperm Tails 11 2     ODF2
CT1331 2     ODF22
HSPB101 2     ODFPGA2
ODF271 2     ODFPGB2
ODFPG1 2     SODF2
RT71 2     Cancer/Testis Antigen 1332
ODFP2 3     Outer Dense Fiber Of Sperm Tails, 27-KD2
Outer Dense Fibre Of Sperm Tails 11     Outer Dense Fiber Protein 12

External Ids:    HGNC: 81131   Entrez Gene: 49562   Ensembl: ENSG000001550877   OMIM: 1828785   UniProtKB: Q149903   

Export aliases for ODF1 gene to outside databases

Previous GC identifers: GC08P102569 GC08P103632 GC08P103232 GC08P103520 GC08P098764


(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 ODF1:
The outer dense fibers are cytoskeletal structures that surround the axoneme in the middle piece and principal piece of
the sperm tail. The fibers function in maintaining the elastic structure and recoil of the sperm tail as well as in
protecting the tail from shear forces during epididymal transport and ejaculation. Defects in the outer dense fibers
lead to abnormal sperm morphology and infertility. The human outer dense fibers contains at least 10 major proteins
and this gene encodes the main protein. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990
Function: Component of the outer dense fibers (ODF) of spermatozoa. ODF are filamentous structures located on the
outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the
passive elastic structures and elastic recoil of the sperm tail

Gene Wiki entry for ODF1


(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_000008.10  NC_018919.1  NT_008046.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ODF1 gene promoter:
         c-Fos   RFX1   AP-1   Fra-1   FosB   MEF-2A   Nkx6-1   aMEF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidODF1 promoter sequence
   Search SABiosciences Chromatin IP Primers for ODF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ODF1


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

Entrez Gene cytogenetic band: 8q22.3   Ensembl cytogenetic band:  8q22.3   HGNC cytogenetic band: 8q22

ODF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ODF1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P103633:  view genomic region     (about GC identifiers)

Start:
103,563,800 bp from pter      End:
103,573,245 bp from pter
Size:
9,446 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: ODFP1_HUMAN, Q14990 (See protein sequence)
Recommended Name: Outer dense fiber protein 1  
Size: 250 amino acids; 28366 Da
Subunit: Interacts with SPAG4 and KLC3 (By similarity)
Secondary accessions: Q3SX72

Explore the universe of human proteins at neXtProt for ODF1: NX_Q14990

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q14990

  • ODF1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_077721.2  
    ENSEMBL proteins: 
     ENSP00000285402   ENSP00000430023  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for ODF1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001520outer dense fiber NAS--


    ODF1 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

    ODF1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR002068 a-crystallin/Hsp20_dom

    Graphical View of Domain Structure for InterPro Entry Q14990

    ProtoNet protein and cluster: Q14990

    1 Blocks protein family: IPB002068 Heat shock protein Hsp20

    UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990
    Domain: The C-terminal contains many C-X-P repeats


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990
    Function: Component of the outer dense fibers (ODF) of spermatozoa. ODF are filamentous structures located on the
    outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the
    passive elastic structures and elastic recoil of the sperm tail

         Genatlas biochemistry entry for ODF1:
    outer dense fiber protein 1,component of the filamentous structures of the sperm tail

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005198structural molecule activity NAS--
    GO:0019904protein domain specific binding IEA--


    ODF1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Odf1tm1Shf for ODF1
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Odf1):
     reproductive system 

    ODF1 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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Transcription_CREM signaling in testis
    Transcription_CREM signaling in testis1.00
    Transcription CREM signaling in testis0.96

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    1 EMD Millipore Pathway for ODF1
        Transcription CREM signaling in testis


    1 GeneGo (Thomson Reuters) Pathway for ODF1
        Transcription CREM signaling in testis



    ODF1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for ODF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for ODF1 (Q149903 ENSP000002854024) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KLC1Q078663, ENSP000004149824I2D: score=2 STRING: ENSP00000414982
    ODF2Q5BJF63, ENSP000003077814I2D: score=1 STRING: ENSP00000307781
    SPAG4Q9NPE63, ENSP000003633914I2D: score=2 STRING: ENSP00000363391
    SPAG5Q96R063, ENSP000003233004I2D: score=2 STRING: ENSP00000323300
    TRIP6Q156543, ENSP000002004574I2D: score=3 STRING: ENSP00000200457
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007283spermatogenesis NAS--
    GO:0030154cell differentiation IEA--


    ODF1 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

    ODF1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ODF1
    1 Novoseek chemical compound relationship for ODF1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    leucine 42.3 5 10373309 (2), 16211599 (1)

    Search CenterWatch for drugs/clinical trials and news about ODF1 / ODFP1 

    (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 ODF1 gene: 
    NM_024410.3  

    Unigene Cluster for ODF1:

    Outer dense fiber of sperm tails 1
    Hs.159274  [show with all ESTs]
    Unigene Representative Sequence: NM_024410
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000285402(uc003ykt.2) ENST00000518835

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    hsa-miR-3685 hsa-miR-22 hsa-miR-558 hsa-miR-3924 hsa-miR-3652
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    Inhib. RNA
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    OriGene siRNA: ODF1
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    Clone
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    Additional cDNA sequence: 

    AK315276.1 BC104456.1 BC104457.1 

    1 DOTS entry:

    DT.438515 

    14 AceView cDNA sequences:

    T29842 BX093384 NM_024410 BG214987 AW949852 AA383076 BU561235 AW951615 
    AW268564 AW665671 AW663738 AI285947 AA383166 BP369982 

    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

    ODF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCCCCTGTTG

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

    About this image
    See ODF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ODF1

    SOURCE GeneReport for Unigene cluster: Hs.159274

    UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990
    Tissue specificity: Testis

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF1

    (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 ODF1 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Odf11 , 5 outer dense fiber of sperm tails 11, 5 85.11(n)1
    95.74(a)1
      15 (15.14 cM)5
    182851  NM_008757.31  NP_032783.21 
     382192035 
    chicken
    (Gallus gallus)
    Aves E1BW80_CHICK6
    Uncharacterized protein
    41(a)
    1 ↔ 1
    2(134503622-134588515)
    lizard
    (Anolis carolinensis)
    Reptilia ODF16
    --
    44(a)
    1 ↔ 1
    4(13908825-13917823)


    ENSEMBL Gene Tree for ODF1 (if available)
    TreeFam Gene Tree for ODF1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/302 NCBI SNPs in ODF1 are shown (see all 302    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs121556441,2
    H,--98763077(+) agtggC/Taccaa 1 -- us2k15Minor allele frequency- T:0.00NS EA NA 540
    rs715188721,2
    C,F,--98763126(+) TCCTCC/GCTCAC 1 -- us2k13Minor allele frequency- G:0.05NA 124
    rs767135211,2
    F,--98763718(+) TTGAGG/AAATGA 1 -- us2k11Minor allele frequency- A:0.09WA 118
    rs756997761,2
    --98764097(+) TCATAC/TAAGGG 1 -- us2k10--------
    rs791822401,2
    --98764107(+) GAGACT/ACGAGA 1 -- us2k11Minor allele frequency- A:0.01WA 118
    rs1119194631,2
    --98764159(+) GCACCA/GAGAGC 1 -- us2k12Minor allele frequency- G:0.33CSA 3
    rs70182531,2
    C,H,--98764278(+) TGGCTA/GCAAGA 1 -- us2k14Minor allele frequency- G:0.00NS EA 414
    rs1139503541,2
    --98765507(+) CAATAG/ATTGAA 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs772300141,2
    F,--98765663(+) AGCAAG/AAATGC 1 -- int12Minor allele frequency- A:0.05WA NA 238
    rs562804391,2
    C,F,--98765687(+) AATGCG/AGCTTT 1 -- int11Minor allele frequency- A:0.10NA 120

    HapMap Linkage Disequilibrium report for ODF1 (103563800 - 103573245 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 5 variations for ODF1
         4 CNVs: 65215 7659 95610 82715
         1 Indel: 95611

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    ODF1 for disorders           About GeneDecksing

    OMIM gene information: 182878    OMIM disorders: --

    2 diseases for ODF1:    About MalaCards
    infertility    epididymitis

    1 Novoseek disease relationship for ODF1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    infertility male 51.4 1 9621304 (1)

    Human Genome Epidemiology (HuGE) Navigator: ODF1 (1 document)

    Export disorders for ODF1 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 ODF1 gene, integrated from 9 sources (see all 27):
    (articles sorted by number of sources associating them with ODF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sequence, expression, and chromosomal assignment of a human sperm outer dense fiber gene. (PubMed id 8305202)1, 2, 3, 9 Gastmann O....Hoyer-Fender S. (1993)
    2. 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)
    3. A homozygous deletion of 27 basepairs in the coding region of the human outer dense fiber protein gene does not result in a pathologic phenotype. (PubMed id 8111388)1, 2 Hofferbert S....Engel W. (1993)
    4. Spag4, a novel sperm protein, binds outer dense-fiber protein Odf1 and localizes to microtubules of manchette and axoneme. (PubMed id 10373309)1, 9 Shao X....van der Hoorn F.A. (1999)
    5. Outer dense fibre proteins from human sperm tail: molecular cloning and expression analyses of two cDNA transcripts encoding proteins of approximately 70 kDa. (PubMed id 10381817)1, 9 Petersen C.... Hoyer-Fender S. (1999)
    6. Isolation and partial characterization of the outer dense fiber proteins from human spermatozoa. (PubMed id 1418683)1, 9 Henkel R....Miska W. (1992)
    7. Keratins: unraveling the coordinated construction of scaffolds in spermatogenic cells. (PubMed id 11774369)1, 9 Kierszenbaum A.L. (2002)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    9. [Differential expression of ODF1 in human ejaculated spermatozoa and its clinical significance] (PubMed id 20112736)1 Chen J....Cai Z.M. (2009)
    10. ODF1 phosphorylation by Cdk5/p35 enhances ODF1-OIP1 interaction. (PubMed id 17762160)1 Rosales J.L....Lee K.Y. (2007)

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

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 4956 HGNC: 8113 AceView: ODF1 Ensembl:ENSG00000155087 euGenes: HUgn4956
    ECgene: ODF1 H-InvDB: ODF1

    (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 ODF1 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 ODF1 gene:
    Search GeneIP for patents involving ODF1

    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),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
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