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Supplementary Table 1A. Genes Significantly Altered in A4573 ESFT

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Supplementary Table 1A. Genes significantly altered in A4573 ESFT cells following BMI-1knockdown genesymbol genedescription siControl siBMI1 FC Direction P-value AASS aminoadipate-semialdehyde synthase | tetra-peptide repeat homeobox-like6.68 7.24 1.5 Up 0.007 ABCA2 ATP-binding cassette, sub-family A (ABC1), member 2 | neural5.44 proliferation,6.3 differentiation1.8 and Upcontrol, 1 0.006 ABHD4 abhydrolase domain containing 4 7.51 6.69 1.8 Down 0.002 ACACA acetyl-Coenzyme A carboxylase alpha | peroxiredoxin 5 | similar6.2 to High mobility7.26 group2.1 protein UpB1 (High mobility0.009 group protein 1) (HMG-1) (Amphoterin) (Heparin-binding protein p30) | Coenzyme A synthase ACAD9 acyl-Coenzyme A dehydrogenase family, member 9 9.25 8.59 1.6 Down 0.008 ACBD3 acyl-Coenzyme A binding domain containing 3 7.89 8.53 1.6 Up 0.008 ACCN2 amiloride-sensitive cation channel 2, neuronal 5.47 6.28 1.8 Up 0.005 ACIN1 apoptotic chromatin condensation inducer 1 7.15 7.79 1.6 Up 0.008 ACPL2 acid phosphatase-like 2 6.04 7.6 2.9 Up 0.000 ACSL4 acyl-CoA synthetase long-chain family member 4 6.72 5.8 1.9 Down 0.001 ACTA2 actin, alpha 2, smooth muscle, aorta 9.18 8.44 1.7 Down 0.003 ACYP1 acylphosphatase 1, erythrocyte (common) type 7.09 7.66 1.5 Up 0.009 ADA adenosine deaminase 6.34 7.1 1.7 Up 0.009 ADAL adenosine deaminase-like 7.88 6.89 2.0 Down 0.006 ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif, 1 6.57 7.65 2.1 Up 0.000 ADARB1 adenosine deaminase, RNA-specific, B1 (RED1 homolog rat) 6.49 7.13 1.6 Up 0.008 ADCY9 adenylate cyclase 9 6.5 7.18 1.6 Up 0.002 ADCYAP1R1 adenylate cyclase activating polypeptide 1 (pituitary) receptor 5.71type I 6.38 1.6 Up 0.002 ADI1 acireductone dioxygenase 1 6.65 7.35 1.6 Up 0.009 ADRBK1 adrenergic, beta, receptor kinase 1 | ankyrin repeat domain 136.95 family, member7.59 D 1.6 Up 0.002 AES amino-terminal enhancer of split 7.72 8.45 1.7 Up 0.005 AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 9.42 8.76 1.6 Down 0.003 AGPAT5 1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic7.16 acid acyltransferase,8.23 2.1 epsilon) Up 0.005 AKAP2 A kinase (PRKA) anchor protein 2 | paralemmin 2 | PALM2-AKAP26.55 protein7.14 1.5 Up 0.005 AKAP8 A kinase (PRKA) anchor protein 8 6.08 7.13 2.1 Up 0.001 AKT1S1 AKT1 substrate 1 (proline-rich) 6.56 7.37 1.8 Up 0.001 ALDH1A3 aldehyde dehydrogenase 1 family, member A3 5.95 6.55 1.5 Up 0.006 ALDH9A1 aldehyde dehydrogenase 9 family, member A1 8.55 9.96 2.7 Up 0.000 AMDHD2 amidohydrolase domain containing 2 | cementum protein 1 7.39 6.66 1.7 Down 0.003 ANAPC1 anaphase promoting complex subunit 1 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase7.61 6.95 1.6 Down 2 0.007 ANGPTL2 angiopoietin-like 2 5.95 6.67 1.6 Up 0.007 ANKDD1A ankyrin repeat and death domain containing 1A 5.33 5.97 1.6 Up 0.005 ANKH ankylosis, progressive homolog (mouse) | CHK1 checkpoint homolog6.1 (S. pombe)6.63 1.4 Up 0.006 ANKRD29 ankyrin repeat domain 29 6.05 6.78 1.7 Up 0.002 ANKS1A ankyrin repeat and sterile alpha motif domain containing 1A 6.65 5.85 1.7 Down 0.006 AOF2 amine oxidase (flavin containing) domain 2 | similar to TFIIH basal8.9 transcription9.84 factor 1.9complex Upp44 subunit (Basic0.000 transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) APAF1 apoptotic peptidase activating factor 1 8.76 6.92 3.6 Down 0.000 APBB3 amyloid beta (A4) precursor protein-binding, family B, member8.97 3 8.07 1.9 Down 0.002 APCDD1 adenomatosis polyposis coli down-regulated 1 9.22 9.87 1.6 Up 0.002 APEH N-acylaminoacyl-peptide hydrolase | macrophage stimulating, 6.77pseudogene7.46 9 1.6 Up 0.002 API5 apoptosis inhibitor 5 9.69 8.46 2.3 Down 0.000 APLP1 amyloid beta (A4) precursor-like protein 1 5.76 6.6 1.8 Up 0.010 APOBEC3D apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like7.17 3D (putative)6.64 1.4 Down 0.006 ARG2 arginase, type II | similar to High mobility group protein B1 (High5.9 mobility6.78 group protein1.8 1) (HMG-1)Up (Amphoterin)0.001 (Heparin-binding protein p30) | similar to protein kinase C, eta ARHGAP17 Rho GTPase activating protein 17 7.07 8.23 2.2 Up 0.003 ARHGAP19 Rho GTPase activating protein 19 8.94 7.94 2.0 Down 0.004 ARHGAP19 Rho GTPase activating protein 19 7.92 7.29 1.5 Down 0.003 ARID1B AT rich interactive domain 1B (SWI1-like) | similar to AT rich interactive5.67 domain6.22 1B (SWI1-like)1.5 Up isoform 1 0.008 ARL1 ADP-ribosylation factor-like 1 9.21 8.33 1.8 Down 0.008 ARL13B ADP-ribosylation factor-like 13B 7.36 8.3 1.9 Up 0.000 ARL5B ADP-ribosylation factor-like 5B | similar to Programmed cell death8.28 protein6.98 8, mitochondrial2.5 precursorDown (Apoptosis-inducing0.000 factor) ARL6IP1 ADP-ribosylation factor-like 6 interacting protein 1 11.42 10.76 1.6 Down 0.005 ARMCX1 armadillo repeat containing, X-linked 1 7.93 7.16 1.7 Down 0.007 ARNTL aryl hydrocarbon receptor nuclear translocator-like 6.15 5.56 1.5 Down 0.008 ASH1L ash1 (absent, small, or homeotic)-like (Drosophila) | KIAA17516.25 | TL132 pseudogene6.89 1.6 Up 0.005 ATE1 arginyltransferase 1 | KIAA1529 6.15 7.12 2.0 Up 0.001 ATF1 activating transcription factor 1 5.82 6.58 1.7 Up 0.001 ATF2 activating transcription factor 2 7.22 8.4 2.3 Up 0.001 ATG9A ATG9 autophagy related 9 homolog A (S. cerevisiae) | ATP-binding6.81 cassette,7.51 sub-family1.6 B (MDR/TAP),Up member0.004 6 ATP10D ATPase, Class V, type 10D 7.22 6.28 1.9 Down 0.006 ATP11C ATPase, Class VI, type 11C 7.34 8.9 2.9 Up 0.000 ATP13A3 ATPase type 13A3 7.94 8.75 1.8 Up 0.002 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide 6.06 6.68 1.5 Up 0.004 ATP6V0D1 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1 9.11 8.2 1.9 Down 0.008 ATP6V1A ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A 9.92 9.22 1.6 Down 0.005 AYTL2 acyltransferase like 2 7.18 8.07 1.9 Up 0.001 AZIN1 antizyme inhibitor 1 10.53 9.28 2.4 Down 0.000 B3GAT1 beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase P) 5.84 6.84 2.0 Up 0.000 B4GALNT3 beta-1,4-N-acetyl-galactosaminyl transferase 3 5.44 5.9 1.4 Up 0.008 B4GALT5 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide7.49 5 8.35 1.8 Up 0.009 B4GALT6 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide7.8 6 6.82 2.0 Down 0.002 BAALC brain and acute leukemia, cytoplasmic | hypothetical protein FLJ104895.89 7.07 2.3 Up 0.001 BAG4 BCL2-associated athanogene 4 8.15 9.01 1.8 Up 0.003 BAI2 brain-specific angiogenesis inhibitor 2 | collagen, type XVI, alpha5.79 1 6.45 1.6 Up 0.003 BARX1 BarH-like homeobox 1 6.4 7.07 1.6 Up 0.003 BASP1 brain abundant, membrane attached signal protein 1 | similar 8.26to Aurora kinase9.65 A-interacting2.6 proteinUp (AURKA-interacting0.000 protein) BCL2L13 BCL2-like 13 (apoptosis facilitator) | hypothetical protein ZD77D087.87 | CHK16.85 checkpoint 2.0homologDown (S. pombe) | 0.005ring finger protein 141 BCL9 B-cell CLL/lymphoma 9 7.05 7.64 1.5 Up 0.008 BCOR BCL6 co-repressor | hypothetical protein LOC730590 | hypothetical7.57 protein8.1 LOC7280681.4 Up 0.006 BET1 7.96 8.46 1.4 Up 0.010 BGN biglycan 6.6 7.66 2.1 Up 0.001 BHLHB5 basic helix-loop-helix domain containing, class B, 5 8.22 9.28 2.1 Up 0.001 BIRC2 baculoviral IAP repeat-containing 2 9.28 8.13 2.2 Down 0.010 BIRC3 baculoviral IAP repeat-containing 3 10.15 8.02 4.4 Down 0.000 BMI1 B lymphoma Mo-MLV insertion region (mouse) | COMM domain8.31 containing 36.2 4.3 Down 0.000 BMP7 bone morphogenetic protein 7 (osteogenic protein 1) 6.18 6.95 1.7 Up 0.001 BOC Boc homolog (mouse) 5.3 6.14 1.8 Up 0.002 BPGM 2,3-bisphosphoglycerate mutase 8.77 8.25 1.4 Down 0.008 BST2 bone marrow stromal cell antigen 2 7.14 6.2 1.9 Down 0.002 BTBD5 BTB (POZ) domain containing 5 8.26 6.76 2.8 Down 0.000 BTN3A1 butyrophilin, subfamily 3, member A1 8.28 7.18 2.1 Down 0.001 BVES blood vessel epicardial substance 6.92 6.14 1.7 Down 0.006 C10orf72 chromosome 10 open reading frame 72 5.82 6.55 1.7 Up 0.001 C11orf24 chromosome 11 open reading frame 24 6.99 7.86 1.8 Up 0.003 C11orf51 chromosome 11 open reading frame 51 7.49 8.3 1.8 Up 0.003 C11orf59 chromosome 11 open reading frame 59 7.46 8.44 2.0 Up 0.001 C11orf60 chromosome 11 open reading frame 60 8.57 7.8 1.7 Down 0.008 C12orf49 chromosome 12 open reading frame 49 6.61 7.39 1.7 Up 0.001 C14orf100 chromosome 14 open reading frame 100 9.32 7.89 2.7 Down 0.001 C14orf122 chromosome 14 open reading frame 122 7.06 8.22 2.2 Up 0.000 C14orf32 chromosome 14 open reading frame 32 9.12 9.7 1.5 Up 0.010 C15orf39 chromosome 15 open reading frame 39 | similar to COMM domain5.91 containing6.38 4 1.4 Up 0.010 C16orf58 chromosome 16 open reading frame 58 7.85 7.12 1.7 Down 0.004 C17orf68 chromosome 17 open reading frame 68 8.17 7.36 1.8 Down 0.002 C18orf25 chromosome 18 open reading frame 25 7.13 6.24 1.9 Down 0.001 C19orf24 chromosome 19 open reading frame 24 7.63 8.28 1.6 Up 0.008 C1orf124 chromosome 1 open reading frame 124 7.63 6.55 2.1 Down 0.003 C1orf128 chromosome 1 open reading frame 128 | SET domain containing7.51 5 | lysophospholipase8.4 1.9 II | lysophospholipaseUp 0.004 II pseudogene 1 | similar to Acyl-protein thioesterase 2 (Lysophospholipase II) (LPL-I) C1orf38 chromosome 1 open reading frame 38 5.26 5.84 1.5 Up 0.008 C1orf55 chromosome 1 open reading frame 55 8.76 8.01 1.7 Down 0.005 C1orf75 chromosome 1 open reading frame 75 6.93 7.6 1.6 Up 0.005 C1orf86 chromosome 1 open reading frame 86 6 6.67 1.6 Up 0.007 C1QL1 complement component 1, q subcomponent-like 1 6.26 7.17 1.9 Up 0.005 C20orf55 chromosome 20 open reading frame 55 6.69 7.31 1.5 Up 0.009 C20orf77 chromosome 20 open reading frame 77 7.54 6.99 1.5 Down 0.007 C21orf25
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  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Inborn Errors of Metabolism Test Requisition

    Inborn Errors of Metabolism Test Requisition

    LABORATORY OF GENETICS AND GENOMICS Mailing Address: For local courier service and/or inquiries, please contact 513-636-4474 • Fax: 513-636-4373 3333 Burnet Avenue, Room R1042 www.cincinnatichildrens.org/moleculargenetics • Email: [email protected] Cincinnati, OH 45229 INBORN ERRORS OF METABOLISM TEST REQUISITION All Information Must Be Completed Before Sample Can Be Processed PATIENT INFORMATION ETHNIC/RACIAL BACKGROUND (Choose All) Patient Name: ___________________ , ___________________ , ________ European American (White) African-American (Black) Last First MI Native American or Alaskan Asian-American Address: ____________________________________________________ Pacific Islander Ashkenazi Jewish ancestry ____________________________________________________ Latino-Hispanic _____________________________________________ Home Phone: ________________________________________________ (specify country/region of origin) MR# __________________ Date of Birth ________ / ________ / _______ Other ____________________________________________________ (specify country/region of origin) Gender: Male Female BILLING INFORMATION (Choose ONE method of payment) o REFERRING INSTITUTION o COMMERCIAL INSURANCE* Insurance can only be billed if requested at the time of service. Institution: ____________________________________________________ Policy Holder Name: _____________________________________________ Address: _____________________________________________________ Gender: ________________ Date of Birth ________ / ________ / _______
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).