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Supplemental Table 1: Genes That Show Altered Expression in Hepg2 Cells in the Presence of Exogenously Added Let-7

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Supplemental Table 1: Genes that show altered expression in HepG2 cells in the presence of exogenously added let-7 Gene Title Gene Symbol RefSeq Transcriptp- IDvalue(TREAp-TMENTvalue(Let7bS) - negativLog2 Reatio control1) (Let7b - negativp-value(Let7be control1) - negativLog2 Reatio control2) (Let7b - negative control2) aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase) AKR1D1 NM_005989 3.28E-12 2.52E-12 -3.85007 3.59E-12 -3.73727 lin-28 homolog B (C. elegans) LIN28B NM_001004317 6.13E-15 8.29E-15 -3.29879 1.55E-15 -3.79656 high mobility group AT-hook 2 /// high mobility group AT-hook 2 HMGA2 NM_001015886 /// NM_0034833.74E-14 /// NM_0034844.29E-14 -3.06085 4.56E-14 -3.04538 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 HECW2 NM_020760 1.27E-13 6.65E-13 -2.94724 4.47E-12 -2.50907 cell division cycle 25A CDC25A NM_001789 /// NM_2015672.01E-11 7.32E-11 -2.88831 1.99E-11 -3.22735 hypothetical protein FLJ21986 FLJ21986 NM_024913 1.05E-09 5.19E-10 -2.80277 1.18E-09 -2.61084 solute carrier family 2 (facilitated glucose transporter), member 3 SLC2A3 NM_006931 1.59E-13 3.49E-13 -2.78111 1.84E-12 -2.41734 Transcribed locus --- --- 2.58E-13 1.08E-13 -2.59794 1.69E-13 -2.50248 Hypothetical protein LOC145786 LOC145786 --- 4.23E-12 1.07E-11 -2.58849 3.00E-12 -2.88135 Dicer1, Dcr-1 homolog (Drosophila) DICER1 NM_030621 /// NM_1774381.06E-08 4.37E-09 -2.5442 4.49E-09 -2.53796 mannose-binding lectin (protein C) 2, soluble (opsonic defect) MBL2 NM_000242 9.73E-10 1.48E-09 -2.53211 9.84E-10 -2.62363 cell division cycle 25A CDC25A NM_001789 /// NM_2015677.44E-14 8.65E-14 -2.49891 3.90E-14 -2.67164 hypothetical protein LOC145786 LOC145786 --- 9.68E-11 2.10E-10 -2.49462 6.21E-11 -2.7689 Dicer1, Dcr-1 homolog (Drosophila) DICER1 NM_030621 /// NM_1774382.79E-14 2.51E-14 -2.45436 3.21E-14 -2.40416 haloacid dehalogenase-like hydrolase domain containing 1A HDHD1A NM_012080 9.61E-15 1.00E-14 -2.44389 1.23E-14 -2.40192 Dicer1, Dcr-1 homolog (Drosophila) DICER1 NM_030621 /// NM_1774384.46E-08 2.78E-08 -2.43541 1.49E-08 -2.57479 dual specificity phosphatase 9 DUSP9 NM_001395 8.85E-13 7.63E-13 -2.42489 6.76E-13 -2.4497 solute carrier organic anion transporter family, member 4C1 SLCO4C1 NM_180991 4.23E-10 4.73E-10 -2.41257 9.91E-11 -2.75897 solute carrier family 2 (facilitated glucose transporter), member 3 SLC2A3 NM_006931 6.99E-14 2.93E-13 -2.37509 1.06E-12 -2.13093 hyaluronan-mediated motility receptor (RHAMM) HMMR NM_012484 /// NM_0124851.53E-11 1.48E-11 -2.35937 8.98E-12 -2.46154 Putative neuronal cell adhesion molecule PUNC NM_004884 1.13E-08 1.31E-08 -2.33991 2.42E-08 -2.21604 aurora kinase B AURKB NM_004217 1.04E-11 9.53E-12 -2.29164 8.71E-12 -2.30913 solute carrier family 2 (facilitated glucose transporter), member 3 /// solute c SLC2A3 /// SLC2A14NM_006931 /// NM_1534492.53E-11 1.17E-10 -2.28343 3.73E-10 -2.06781 pleiomorphic adenoma gene-like 2 PLAGL2 NM_002657 2.13E-12 1.62E-12 -2.25936 1.43E-12 -2.28277 cyclin A2 CCNA2 NM_001237 5.19E-13 4.88E-13 -2.24473 6.29E-13 -2.19724 ubiquitin-like, containing PHD and RING finger domains, 1 UHRF1 NM_013282 6.16E-14 1.70E-13 -2.22165 2.84E-13 -2.12743 tubulin tyrosine ligase-like family, member 4 TTLL4 NM_014640 1.97E-14 1.49E-14 -2.15645 7.76E-15 -2.27775 similar to RIKEN cDNA 1200014N16 gene MGC14289 NM_080660 3.62E-13 7.78E-13 -2.14115 6.29E-13 -2.17971 E2F transcription factor 5, p130-binding E2F5 NM_001951 1.92E-13 1.19E-13 -2.12946 5.24E-13 -1.8803 CDC6 cell division cycle 6 homolog (S. cerevisiae) CDC6 NM_001254 4.82E-13 8.52E-12 -2.12602 7.53E-12 -2.14828 deiodinase, iodothyronine, type I DIO1 NM_000792 /// NM_2135931.70E-09 3.42E-09 -2.123 1.02E-09 -2.35815 denticleless homolog (Drosophila) DTL NM_016448 4.35E-11 6.78E-10 -2.07975 9.03E-10 -2.02875 RAD18 homolog (S. cerevisiae) RAD18 NM_020165 6.73E-09 6.63E-09 -2.07149 5.77E-09 -2.09708 serine/threonine kinase 6 STK6 NM_003600 /// NM_1984332.06E-13 /// NM_1984344.75E-13 /// NM_198435 ///-2.06623 NM_198436 /// 6.77E-13NM_198437 -2.00555 S-phase kinase-associated protein 2 (p45) SKP2 NM_005983 /// NM_0326371.46E-11 3.79E-10 -2.0565 1.90E-10 -2.18265 dopa decarboxylase (aromatic L-amino acid decarboxylase) DDC NM_000790 6.92E-14 3.77E-14 -2.05118 4.33E-14 -2.02728 APin protein APIN NM_017855 7.25E-11 5.75E-11 -2.04877 3.38E-11 -2.14365 DNA replication complex GINS protein PSF2 Pfs2 NM_016095 7.74E-14 3.73E-13 -2.02611 8.01E-13 -1.89993 activator of S phase kinase ASK NM_006716 7.22E-12 4.16E-12 -2.02005 3.28E-12 -2.061 solute carrier family 2 (facilitated glucose transporter), member 3 /// solute c SLC2A3 /// SLC2A14NM_006931 /// NM_1534492.55E-13 3.64E-13 -2.01819 2.97E-12 -1.69067 solute carrier family 35, member F5 SLC35F5 NM_025181 9.35E-11 3.24E-11 -2.01487 6.50E-11 -1.89889 ribonucleotide reductase M2 polypeptide RRM2 NM_001034 2.28E-15 4.66E-15 -2.01117 2.93E-15 -2.09111 CDNA FLJ11381 fis, clone HEMBA1000501 --- --- 3.88E-09 3.07E-09 -2.01062 2.27E-09 -2.06382 hypermethylated in cancer 2 HIC2 NM_015094 1.37E-08 8.34E-09 -2.01005 4.96E-09 -2.1038 Galactosidase, beta 1 GLB1 NM_000404 1.29E-10 1.15E-10 -2.00307 3.31E-11 -2.22704 denticleless homolog (Drosophila) DTL NM_016448 6.33E-15 1.38E-13 -1.99945 9.77E-14 -2.05806 solute carrier family 2 (facilitated glucose transporter), member 3 SLC2A3 NM_006931 2.27E-12 2.57E-12 -1.99809 1.58E-11 -1.71314 GAJ protein GAJ NM_032117 5.28E-11 5.62E-11 -1.99004 3.34E-11 -2.0803 hypothetical protein LOC253842 LOC253842 --- 5.23E-10 6.50E-10 -1.98709 1.90E-10 -2.20856 putative small membrane protein NID67 NID67 NM_032947 1.09E-08 5.41E-09 -1.9577 5.69E-09 -1.9489 hyaluronan-mediated motility receptor (RHAMM) HMMR NM_012484 /// NM_0124857.93E-10 7.69E-10 -1.9564 3.72E-10 -2.08276 hypermethylated in cancer 2 HIC2 NM_015094 5.01E-11 6.78E-11 -1.95061 9.35E-11 -1.89784 Paternally expressed 3 PEG3 NM_006210 2.40E-09 2.51E-08 -1.94183 1.45E-07 -1.65871 polymerase (DNA directed), epsilon 2 (p59 subunit) POLE2 NM_002692 6.07E-14 8.40E-14 -1.93668 7.40E-14 -1.95732 proteasome (prosome, macropain) activator subunit 4 PSME4 NM_014614 9.93E-07 4.19E-05 -1.93116 2.76E-05 -2.01839 lysyl oxidase LOX NM_002317 8.52E-11 4.31E-08 -1.9294 6.44E-08 -1.8609 zinc finger, CSL-type containing 2 ZCSL2 NM_206831 8.86E-12 1.11E-11 -1.92796 4.35E-12 -2.08693 paternally expressed 3 PEG3 NM_006210 4.00E-09 1.69E-07 -1.92223 3.93E-07 -1.77804 phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria) /// p PIGA NM_002641 /// NM_0204721.47E-09 /// NM_0204736.90E-10 -1.91851 7.63E-10 -1.90193 Supplemental Table 1: Genes that show altered expression in HepG2 cells in the presence of exogenously added let-7 chromosome 14 open reading frame 46 C14orf46 NM_001024674 5.54E-11 2.76E-11 -1.91644 6.40E-11 -1.78396 chromosome 7 open reading frame 23 C7orf23 NM_024315 3.17E-13 1.22E-13 -1.916 3.48E-13 -1.75473 solute carrier family 39 (zinc transporter), member 14 SLC39A14 NM_015359 7.43E-06 0.000232616 -1.88947 0.000491779 -1.72679 family with sequence similarity 54, member A FAM54A NM_138419 2.76E-13 4.73E-13 -1.8867 5.36E-13 -1.86698 microtubule associated serine/threonine kinase-like MASTL NM_032844 6.54E-11 1.15E-10 -1.88332 5.66E-11 -2.00108 suppressor of variegation 3-9 homolog 2 (Drosophila) SUV39H2 NM_024670 3.71E-11 2.14E-11 -1.87873 1.38E-11 -1.95024 hypothetical protein MGC13204 MGC13204 NM_031465 1.93E-09 9.57E-10 -1.87292 9.86E-10 -1.8682 apolipoprotein B (including Ag(x) antigen) APOB NM_000384 5.43E-05 0.0286114 -1.86773 0.0284021 -1.87074 ribonucleotide reductase M2 polypeptide RRM2 NM_001034 1.98E-11 1.68E-10 -1.86737 2.02E-10 -1.83802 nucleoporin 98kDa NUP98 NM_005387 /// NM_0163202.33E-12 /// NM_1391312.98E-12 /// NM_139132 -1.86591 4.20E-12 -1.81269 solute carrier family 6 (amino acid transporter), member 14 SLC6A14 NM_007231 1.94E-11 3.56E-09 -1.86071 2.02E-07 -1.29761 MCM10 minichromosome maintenance deficient 10 (S. cerevisiae) MCM10 NM_018518 /// NM_1827511.82E-12 2.79E-11 -1.85807 2.49E-11 -1.87586 ring finger and WD repeat domain 3 RFWD3 NM_018124 2.04E-11 1.60E-11 -1.85037 1.26E-11 -1.8882 coproporphyrinogen oxidase CPOX NM_000097 4.48E-11 5.67E-11 -1.84531 5.30E-11 -1.85604 cell division cycle associated 7 /// cell division cycle associated 7 CDCA7 NM_031942 /// NM_1458101.16E-10 7.53E-11 -1.84512 2.41E-10 -1.67017 LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM6 NM_007080 1.18E-10 6.77E-11 -1.83721 6.61E-11 -1.84092 CDC6 cell division cycle 6 homolog (S.
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    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
  • Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

    Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

    RESEARCH ARTICLE Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data David L. A. Wood1*, Katia Nones1, Anita Steptoe1, Angelika Christ1, Ivon Harliwong1, Felicity Newell1, Timothy J. C. Bruxner1, David Miller1, Nicole Cloonan2, Sean M. Grimmond3,1 1 Queensland Centre for Medical Genomics, University of Queensland, Brisbane, Australia, 2 QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia, 3 Translational Research Centre, University of Glasgow, Glasgow, Scotland a11111 * [email protected] Abstract Genetic variation modulates gene expression transcriptionally or post-transcriptionally, and OPEN ACCESS can profoundly alter an individual’s phenotype. Measuring allelic differential expression at Citation: Wood DLA, Nones K, Steptoe A, Christ A, heterozygous loci within an individual, a phenomenon called allele-specific expression Harliwong I, Newell F, et al. (2015) (ASE), can assist in identifying such factors. Massively parallel DNA and RNA sequencing Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq and advances in bioinformatic methodologies provide an outstanding opportunity to mea- Data. PLoS ONE 10(5): e0126911. doi:10.1371/ sure ASE genome-wide. In this study, matched DNA and RNA sequencing, genotyping ar- journal.pone.0126911 rays and computationally phased haplotypes were integrated to comprehensively and Academic Editor: I. King Jordan, Georgia Institute of conservatively quantify ASE in a single human brain and liver tissue sample. We describe a Technology, UNITED STATES methodological evaluation and assessment of common bioinformatic steps for ASE quantifi- Received: February 3, 2014 cation, and recommend a robust approach to accurately measure SNP, gene and isoform Accepted: April 9, 2015 ASE through the use of personalized haplotype genome alignment, strict alignment quality control and intragenic SNP aggregation.
  • UNC93A (NM 018974) Human Tagged ORF Clone – RC217002L3

    UNC93A (NM 018974) Human Tagged ORF Clone – RC217002L3

    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC217002L3 UNC93A (NM_018974) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: UNC93A (NM_018974) Human Tagged ORF Clone Tag: Myc-DDK Symbol: UNC93A Synonyms: dJ366N23.1; dJ366N23.2; Unc-93A Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC217002). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_018974 ORF Size: 1371 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 UNC93A (NM_018974) Human Tagged ORF Clone – RC217002L3 OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_018974.2 RefSeq Size: 2011 bp RefSeq ORF: 1374 bp Locus ID: 54346 UniProt ID: Q86WB7 Protein Families: Transmembrane MW: 50.1 kDa This product is to be used for laboratory only.