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Related to cDNA library and ORF library construction - publications for Mammalian Gene Collection (MGC), ORFeome Collaboration (OC), Center for Cancer Systems Biology at Dana Farber Cancer Institute (CCSB), Broad Institute
A public genome-scale lentiviral expression library of human ORFs. Nat Methods. Jun 26;8(8):659-61. Yang, X. et al. (2011).
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234135/
Summary: Describes the production of a sequence-confirmed, clonal collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile Gateway vector system.
The international ORFeome Collaboration (OC)
Summary:
The international ORFeome Collaboration (OC) was founded to provide the research community with a comprehensive set of full-length, high quality human ORF clones.
Dana Farber Cancer Institute-Center for Cancer Systems Biology
Summary: Describes the undertaking of ORF verification and cloning projects for the entire genomes of multiple organisms. In the ORF-cloning pipeline
Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Molecular Cell. 20(6): 881–890. Ghigna, C. et al. (2005)
Additional Links:
https://www.ncbi.nlm.nih.gov/pubmed/16364913
Summary: Skipping of exon 11 that is controlled by a silencer and an enhancer of splicing located in the constitutive exon 12, show that abnormal accumulation of DeltaRon mRNA occurs in breast and colon tumors
Human ORFeome V8.1 Libraries
Relating to transOMIC cDNA/ORF clones used in research
PDZD7-MYO7A complex identified in enriched stereocilia membranes. Morgan, C. P., Krey, J. F., Grati, M., Zhao, B., Fallen, S., Kannan-Sundhari, A., … Barr-Gillespie, P. G. (2016).
eLife, 5, e18312.

Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005036/

Summary: MGC premier human MYO7A ORF and full-length cDNA clones purchased from transOMIC, tagged by the authors and transfected into COS7 cells. This was subsequently used to detect association with other proteins by immunoprecipitation.
Determination of the CD148-Interacting Region in Thrombospondin-1.Takahashi, K., Sumarriva, K., Kim, R., Jiang, R., Brantley-Sieders, D. M., Chen, J., Takahashi, T. (2016). PLoS ONE, 11(5), e0154916.
Summary: The pCMV-Myc-C expression plasmid for human CD36 was purchased from transOMIC technologies Inc. (Huntsville, AL).
Post-transcriptional m6A editing of HIV-1 mRNAs enhances viral gene expression. Kennedy, E. M., Bogerd, H. P., Kornepati, A. V. R., Kang, D., Ghoshal, D., Marshall, J. B., Cullen, B. R. (2016). Cell Host & Microbe, 19(5), 675–685. http://doi.org/10.1016/j.chom.2016.04.002
Summary: MGC cDNA clones purchased from transOMIC Technologies (Huntsville, AL) BC050284; BC002559; BC052970, were used to show their cis interaction in regulating viral replication.
Aldose Reductase acts as a Selective Derepressor of PPARγ and Retinoic Acid Receptor. Thiagarajan, D., Ananthakrishnan, R., Zhang, J., O’Shea, K. M., Quadri, N., Li, Q., … Ramasamy, R. (2016). Cell Reports15(1), 181–196.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826833/?report=classic

Summary: Transgenic expression of human cDNAS in mice. cDNA clones were purchased from transOMIC and subcloned by authors.
Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation. Heard, M. E., Besio, R., Weis, M., Rai, J., Hudson, D. M., Dimori, M., … Morello, R. (2016). PLoS Genetics12(4), e1006002.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847768/
Summary:
pCMV-SC65-DDK-C plasmid (murine, SC65-FLAG) was purchased from transOMIC. Author cloned full-length LH1 and CypB cDNAs into the pCMV-HA-C plasmid (transOMIC). Direct co-immunoprecipitation assays and western blotting was performed in vitro and anti-DDDK (cat# A190-102A, Bethyl Laboratories, Montgomery, TX, USA) and anti-HA (cat# sc-7392, Santa Cruz Biotechnologies) antibodies were used. Note: Suggestion of proven antibodies for detection of DDK (FLAG) and HA tags
DDB2 modulates TGF-β signal transduction in human ovarian cancer cells by downregulating NEDD4L. Zhao, R., Cui, T., Han, C., Zhang, X., He, J., Srivastava, A. K., Wang, Q.-E. (2015). Nucleic Acids Research43(16), 7838–7849.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652750/
Summary:
The human NEDD4L cDNA was subcloned into pTCP vector (transOMIC) to construct a pTCP-NEDD4L expression plasmid. This plasmid was transiently transfected into CP70-DDB2-3H cells to establish an overexpression cell line. Positional binding to the NEDD4L promoter by DDB2 was then studied.
Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Bochkov, Y. A., Watters, K., Ashraf, S., Griggs, T. F., Devries, M. K., Jackson, D. J., … Gern, J. E. (2015). Proceedings of the National Academy of Sciences of the United States of America, 112(17), 5485–5490.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418890/

Summary: Identification of the association of trans-membrane protein CDHR3 and a mutated form in rhinovirus infections and asthma. Both CDHR3 and its mutated version were obtained from transOMIC in pLX304 and used in transfection studies. The mutant construct was used to create a stable cell line; and was packaged with psPAX2 and pMD2.G.
MDA-9/Syntenin (SDCBP) modulates small GTPases RhoA and Cdc42 via transforming growth factor β1 to enhance epithelial-mesenchymal transition in breast cancer. Menezes, M. E., Shen, X.-N., Das, S. K., Emdad, L., Sarkar, D., & Fisher, P. B. (2016). Oncotarget, 7(49), 80175–80189.
Summary: FLAG-tagged full length and PDZ-1 deleted constructs were obtained from transOMIC (Huntsville, AL).
Related to cDNA/ORF clones used in protein/DNA association studies
PDZD7-MYO7A complex identified in enriched stereocilia membranes. Morgan, C. P., Krey, J. F., Grati, M., Zhao, B., Fallen, S., Kannan-Sundhari, A., … Barr-Gillespie, P. G. (2016).
eLife, 5, e18312.

Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005036/

Summary: MGC premier human MYO7A ORF and full-length cDNA clones purchased from transOMIC, tagged by the authors and transfected into COS7 cells. This was subsequently used to detect association with other proteins by immunoprecipitation.
Determination of the CD148-Interacting Region in Thrombospondin-1.Takahashi, K., Sumarriva, K., Kim, R., Jiang, R., Brantley-Sieders, D. M., Chen, J., Takahashi, T. (2016). PLoS ONE, 11(5), e0154916.
Summary: The pCMV-Myc-C expression plasmid for human CD36 was purchased from transOMIC technologies Inc. (Huntsville, AL).
Post-transcriptional m6A editing of HIV-1 mRNAs enhances viral gene expression. Kennedy, E. M., Bogerd, H. P., Kornepati, A. V. R., Kang, D., Ghoshal, D., Marshall, J. B., Cullen, B. R. (2016). Cell Host & Microbe, 19(5), 675–685. http://doi.org/10.1016/j.chom.2016.04.002
Summary: MGC cDNA clones purchased from transOMIC Technologies (Huntsville, AL) BC050284; BC002559; BC052970, were used to show their cis interaction in regulating viral replication.
Related to cDNA/ORF clones used in protein association studies
Aldose Reductase acts as a Selective Derepressor of PPARγ and Retinoic Acid Receptor. Thiagarajan, D., Ananthakrishnan, R., Zhang, J., O’Shea, K. M., Quadri, N., Li, Q., … Ramasamy, R. (2016). Cell Reports15(1), 181–196.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826833/?report=classic

Summary: Transgenic expression of human cDNAS in mice. cDNA clones were purchased from transOMIC and subcloned by authors.
Related to transOMIC cDNA/ORF tagged clones
Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation. Heard, M. E., Besio, R., Weis, M., Rai, J., Hudson, D. M., Dimori, M., … Morello, R. (2016). PLoS Genetics12(4), e1006002.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847768/
Summary:
pCMV-SC65-DDK-C plasmid (murine, SC65-FLAG) was purchased from transOMIC. Author cloned full-length LH1 and CypB cDNAs into the pCMV-HA-C plasmid (transOMIC). Direct co-immunoprecipitation assays and western blotting was performed in vitro and anti-DDDK (cat# A190-102A, Bethyl Laboratories, Montgomery, TX, USA) and anti-HA (cat# sc-7392, Santa Cruz Biotechnologies) antibodies were used. Note: Suggestion of proven antibodies for detection of DDK (FLAG) and HA tags
Related to cDNA clones in pTCP vector - view protein/DNA interactions
DDB2 modulates TGF-β signal transduction in human ovarian cancer cells by downregulating NEDD4L. Zhao, R., Cui, T., Han, C., Zhang, X., He, J., Srivastava, A. K., Wang, Q.-E. (2015). Nucleic Acids Research43(16), 7838–7849.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652750/
Summary:
The human NEDD4L cDNA was subcloned into pTCP vector (transOMIC) to construct a pTCP-NEDD4L expression plasmid. This plasmid was transiently transfected into CP70-DDB2-3H cells to establish an overexpression cell line. Positional binding to the NEDD4L promoter by DDB2 was then studied.
Related to ORF clones in pLX304 vector and mutated versions - view protein/DNA interactions
Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Bochkov, Y. A., Watters, K., Ashraf, S., Griggs, T. F., Devries, M. K., Jackson, D. J., … Gern, J. E. (2015). Proceedings of the National Academy of Sciences of the United States of America, 112(17), 5485–5490.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418890/

Summary: Identification of the association of trans-membrane protein CDHR3 and a mutated form in rhinovirus infections and asthma. Both CDHR3 and its mutated version were obtained from transOMIC in pLX304 and used in transfection studies. The mutant construct was used to create a stable cell line; and was packaged with psPAX2 and pMD2.G.
Related to transOMIC cDNA/ORF clones - tagged and/or mutated
MDA-9/Syntenin (SDCBP) modulates small GTPases RhoA and Cdc42 via transforming growth factor β1 to enhance epithelial-mesenchymal transition in breast cancer. Menezes, M. E., Shen, X.-N., Das, S. K., Emdad, L., Sarkar, D., & Fisher, P. B. (2016). Oncotarget, 7(49), 80175–80189.
Summary: FLAG-tagged full length and PDZ-1 deleted constructs were obtained from transOMIC (Huntsville, AL).