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1 Table S5. Genes Upregulated in Lectin+, KRT5-Gfphi Bcs

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Rock et al., PNAS 2009 Table S5. Genes upregulated in lectin+, KRT5-GFPhi BCs versus non-BCs with p<0.001 and >21.5 fold change. Probe Symbol Name Fold 1435479_at --- --- 28.242 1436092_at --- Transcribed locus 13.519 1434848_at --- Transcribed locus 12.162 1438577_at --- Transcribed locus 8.387 1436651_at --- --- 6.605 1420194_at --- --- 4.812 1434209_at --- --- 3.904 1443669_at --- Transcribed locus 3.893 1439887_at --- 16 days embryo head cDNA, RIKEN full-length enriched library, clone:C130025B04 3.820 1441574_at --- Adult male diencephalon cDNA, RIKEN full-length enriched library, clone:9330190O21 3.767 1443529_at --- --- 3.683 1447314_at --- --- 3.680 1440485_at --- --- 3.596 1440371_at --- 2 days neonate sympathetic ganglion cDNA, RIKEN full-length enriched library, clone:7120457A19 3.595 1447988_at --- --- 3.554 1439990_at --- 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130065P14 3.544 1447204_at --- --- 3.539 1439769_at --- Transcribed locus 3.521 1439714_at --- --- 3.428 1458599_at --- --- 3.274 1445154_at --- --- 3.260 1445697_at --- Transcribed locus 3.253 1444425_at --- 0 day neonate kidney cDNA, RIKEN full-length enriched library, clone:D630017L16 3.233 1460556_at --- --- 3.163 1441341_at --- Transcribed locus 3.128 1446834_at --- Transcribed locus 3.113 1440592_at --- Transcribed locus 3.110 1456186_at --- --- 2.972 1447544_at --- Transcribed locus 2.862 1444479_at --- Transcribed locus 2.857 1436772_at --- Transcribed locus 2.851 1441368_at --- 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430084D06 2.841 1416805_at 1110032E23Rik RIKEN cDNA 1110032E23 gene 6.252 1429087_at 1110054O05Rik RIKEN cDNA 1110054O05 gene 2.861 1424318_at 1110067D22Rik RIKEN cDNA 1110067D22 gene 3.283 1438511_a_at 1190002H23Rik RIKEN cDNA 1190002H23 gene 8.796 1428922_at 1200009O22Rik RIKEN cDNA 1200009O22 gene 5.444 1429764_at 1500005K14Rik RIKEN cDNA 1500005K14 gene 6.663 1449074_at 1700019N12Rik RIKEN cDNA 1700019N12 gene 3.401 1436431_at 1700025G04Rik RIKEN cDNA 1700025G04 gene 48.804 1436677_at 1810032O08Rik RIKEN cDNA 1810032O08 gene 4.003 1454013_at 1810062O18Rik RIKEN cDNA 1810062O18 gene 3.666 1435089_at 2010111I01Rik RIKEN cDNA 2010111I01 gene 4.389 1456023_at 2210010B09Rik RIKEN cDNA 2210010B09 gene 3.011 1 Rock et al., PNAS 2009 1424968_at 2210023G05Rik RIKEN cDNA 2210023G05 gene 5.144 1429637_at 2210419I08Rik RIKEN cDNA 2210419I08 gene 5.629 1453008_at 2300002D11Rik RIKEN cDNA 2300002D11 gene 3.618 1452924_at 2310007D09Rik RIKEN cDNA 2310007D09 gene 2.915 1431299_a_at 2310014H01Rik RIKEN cDNA 2310014H01 gene 4.108 1429835_at 2310033E01Rik RIKEN cDNA 2310033E01 gene 13.737 1432976_at 2310038E17Rik RIKEN cDNA 2310038E17 gene 62.254 1432975_at 2310038E17Rik RIKEN cDNA 2310038E17 gene 12.437 1429844_at 2310043J07Rik RIKEN cDNA 2310043J07 gene 3.030 1429909_at 2600010E01Rik RIKEN cDNA 2600010E01 gene 16.946 1419032_at 2610018G03Rik RIKEN cDNA 2610018G03 gene 4.201 1419033_at 2610018G03Rik RIKEN cDNA 2610018G03 gene 3.720 1453261_at 2610035D17Rik RIKEN cDNA 2610035D17 gene 3.092 1436216_s_at 2610204M08Rik RIKEN cDNA 2610204M08 gene /// similar to INF2 15.338 1435639_at 2610528A11Rik RIKEN cDNA 2610528A11 gene 22.236 1453745_at 2700038G22Rik RIKEN cDNA 2700038G22 gene 3.165 1427141_at 2700099C18Rik RIKEN cDNA 2700099C18 gene 3.561 1417218_at 2810048G17Rik RIKEN cDNA 2810048G17 gene 5.771 1430655_at 4631405K08Rik RIKEN cDNA 4631405K08 gene 8.062 1422628_at 4632417K18Rik RIKEN cDNA 4632417K18 gene 6.160 1435261_at 4732416N19Rik RIKEN cDNA 4732416N19 gene 3.832 1437900_at 4930523C07Rik RIKEN cDNA 4930523C07 gene 3.509 1435773_at 4930547N16Rik RIKEN cDNA 4930547N16 gene 5.877 1453557_at 4930562F07Rik RIKEN cDNA 4930562F07 gene 3.282 1419745_at 4933428G20Rik RIKEN cDNA 4933428G20 gene 2.899 1439675_at 4933429D07Rik RIKEN cDNA 4933429D07 gene 3.714 1428694_at 5033413D16Rik RIKEN cDNA 5033413D16 gene 7.046 1435830_a_at 5430435G22Rik RIKEN cDNA 5430435G22 gene 16.506 1424987_at 5430435G22Rik RIKEN cDNA 5430435G22 gene 5.274 1439738_at 5630401D24Rik RIKEN cDNA 5630401D24 gene 3.641 1434797_at 6720469N11Rik RIKEN cDNA 6720469N11 gene 18.377 1418879_at 9030611O19Rik RIKEN cDNA 9030611O19 gene 4.668 1446088_at 9430081I23Rik RIKEN cDNA 9430081I23 gene 3.111 1438337_x_at 9930032O22Rik RIKEN cDNA 9930032O22 gene 17.713 1457319_at A130038J17Rik RIKEN cDNA A130038J17 gene 3.152 1439808_at A130090K04Rik RIKEN cDNA A130090K04 gene 3.856 1459145_at A930033H14Rik RIKEN cDNA A930033H14 gene 3.102 1421840_at Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 7.829 1418872_at Abcb1b ATP-binding cassette, sub-family B (MDR/TAP), member 1B 8.632 1423570_at Abcg1 ATP-binding cassette, sub-family G (WHITE), member 1 9.958 1427053_at Abi3bp ABI gene family, member 3 (NESH) binding protein 54.075 1427054_s_at Abi3bp ABI gene family, member 3 (NESH) binding protein 36.603 1434013_at Ablim3 actin binding LIM protein family, member 3 5.888 1424451_at Acaa1b acetyl-Coenzyme A acyltransferase 1B 4.077 1455328_at Accn2 amiloride-sensitive cation channel 2, neuronal 3.078 1416454_s_at Acta2 actin, alpha 2, smooth muscle, aorta 4.867 2 Rock et al., PNAS 2009 1438266_at Adamtsl5 ADAMTS-like 5 9.149 1423420_at Adrb1 adrenergic receptor, beta 1 4.159 1433939_at Aff3 /// LOC638024 AF4/FMR2 family, member 3 /// similar to AF4/FMR2 family member 3 3.957 1436520_at Ahnak2 AHNAK nucleoprotein 2 6.743 1436614_at AI843639 expressed sequence AI843639 3.661 1428785_at Amotl1 angiomotin-like 1 16.486 1422573_at Ampd3 AMP deaminase 3 4.575 1427044_a_at Amph amphiphysin 7.192 1433742_at Ankrd15 ankyrin repeat domain 15 5.026 1436294_at Ankrd29 ankyrin repeat domain 29 5.524 1433543_at Anln anillin, actin binding protein (scraps homolog, Drosophila) 5.015 1449070_x_at Apcdd1 adenomatosis polyposis coli down-regulated 1 3.736 1418382_at Apcdd1 adenomatosis polyposis coli down-regulated 1 3.520 1454822_x_at Apcdd1 adenomatosis polyposis coli down-regulated 1 2.848 1417889_at Apobec2 apolipoprotein B editing complex 2 4.838 1417561_at Apoc1 apolipoprotein C-I 6.625 1432466_a_at Apoe apolipoprotein E 25.858 1422007_at Aqp3 aquaporin 3 11.065 1422008_a_at Aqp3 aquaporin 3 8.365 1418687_at Arc activity regulated cytoskeletal-associated protein 3.052 1435108_at Arhgap22 Rho GTPase activating protein 22 6.384 1424842_a_at Arhgap24 Rho GTPase activating protein 24 3.627 1437072_at Arhgap25 Rho GTPase activating protein 25 5.064 1426454_at Arhgdib Rho, GDP dissociation inhibitor (GDI) beta 7.544 1427167_at Armcx4 armadillo repeat containing, X-linked 4 15.620 1434409_at Armcx6 armadillo repeat containing, X-linked 6 3.630 1429688_at Arntl2 aryl hydrocarbon receptor nuclear translocator-like 2 4.538 1432032_a_at Artn artemin 7.629 1432018_at Ascl2 achaete-scute complex homolog 2 (Drosophila) 22.433 1449475_at Atp12a ATPase, H+/K+ transporting, nongastric, alpha polypeptide 3.861 1420083_at AU016916 expressed sequence AU016916 3.802 1423586_at Axl AXL receptor tyrosine kinase 34.575 1438989_s_at B130021B11Rik RIKEN cDNA B130021B11 gene 8.481 1436515_at Bach2 BTB and CNC homology 2 2.948 1437667_a_at Bach2 BTB and CNC homology 2 2.831 1421761_a_at Barx2 BarH-like homeobox 2 5.390 1417688_at BC004044 cDNA sequence BC004044 3.474 1460713_at BC048355 cDNA sequence BC048355 2.882 1424791_a_at Bcam basal cell adhesion molecule 7.469 1457072_at Bcl11a /// Ppfia3 Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3 3.024 1435227_at Bcl11b B-cell leukemia/lymphoma 11B 19.855 1438784_at Bcl11b B-cell leukemia/lymphoma 11B 6.276 1428512_at Bhlhb9 basic helix-loop-helix domain containing, class B9 2.951 1424278_a_at Birc5 baculoviral IAP repeat-containing 5 3.044 1426238_at Bmp1 bone morphogenetic protein 1 6.425 1418910_at Bmp7 bone morphogenetic protein 7 20.989 3 Rock et al., PNAS 2009 1424890_at Bnc1 basonuclin 1 76.989 1422490_at Bnip2 BCL2/adenovirus E1B interacting protein 1, NIP2 3.796 1453993_a_at Bnip2 BCL2/adenovirus E1B interacting protein 1, NIP2 2.867 1428377_at Btbd11 BTB (POZ) domain containing 11 15.435 1447363_s_at Bub1b budding uninhibited by benzimidazoles 1 homolog, beta (S. cerevisiae) 3.638 1439422_a_at C1qdc2 C1q domain containing 2 3.647 1439104_at C230081A13Rik RIKEN cDNA C230081A13 gene 3.040 1433988_s_at C230098O21Rik RIKEN cDNA C230098O21 gene 6.673 1431497_at C330022C24Rik RIKEN cDNA C330022C24 gene 3.136 1417066_at Cabc1 chaperone, ABC1 activity of bc1 complex like (S. pombe) 5.593 1433643_at Cacna2d1 calcium channel, voltage-dependent, alpha2/delta subunit 1 27.283 1424768_at Cald1 caldesmon 1 4.581 1433971_at Camta1 calmodulin binding transcription activator 1 36.957 1433972_at Camta1 calmodulin binding transcription activator 1 13.811 1450355_a_at Capg capping protein (actin filament), gelsolin-like 2.961 1418981_at Casp12 /// LOC100044205 caspase 12 /// hypothetical protein LOC100044205 3.431 1449297_at Casp12 /// LOC100044205 caspase 12 /// hypothetical protein LOC100044205 3.021 1449145_a_at Cav1 caveolin, caveolae protein 1 3.866 1434116_at Cbx2 chromobox homolog 2 (Drosophila Pc class) 3.436 1424699_at Ccdc136 coiled-coil domain containing 136 3.037 1428549_at Ccdc3 coiled-coil domain containing 3 84.184 1439109_at Ccdc68 coiled-coil domain containing 68 3.203 1436025_at Ccdc88a coiled coil domain containing 88A 3.334 1422029_at Ccl20 chemokine (C-C motif) ligand 20 3.514 1450920_at Ccnb2 cyclin B2 3.371 1436789_at Ccnjl cyclin J-like 9.986 1436346_at Cd109 CD109 antigen 99.435 1425658_at Cd109 CD109
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    39th Meeting of the Polish Biochemical Society Gdañsk 16–20 September 2003 SESSION 6 Metabolism of purines and pyrimidines in health and disease Organized by A. C. Sk³adanowski, A. Guranowski 182 Session 6. Metabolism of purines and pyrimidines in health and disease 2003 323 Lecture The role of DNA methylation in cytotoxicity mechanism of adenosine analogues in treatment of leukemia Krystyna Fabianowska-Majewska Zak³ad Chemii Medycznej IFiB, Uniwersytet Medyczny, ul. Mazowiecka 6/8, 92 215 £ódŸ Changes in DNA methylation have been recognized tory effects of cladribine and fludarabine on DNA as one of the most common molecular alterations in hu- methylation, after 48 hr growth of K562 cells with the man neoplastic diseases and hypermethylation of drugs, are non-random and affect mainly CpG rich is- gene-promoter regions is one of the most frequent lands or CCGG sequences but do not affect sepa- mechanisms of the loss of gene functions. For this rea- rately-located CpG sequences. The analysis showed son, DNA methylation may be a tool for detection of that cladribine (0.1 mM) reduced the methylated early cell transformations as well as predisposition to cytosines in CpG islands and CCGG sequences to a sim- metastasis process. Moreover, DNA methylation seems ilar degree. The inhibition of cytosine methylation by to be a promissing target for new preventive and thera- fludarabine (3 mM) was observed mainly in CCGG se- peutic strategies. quences, sensitive to HpaII, but the decline in the meth- Our studies on DNA methylation and cytotoxicity ylated cytosine, located in CpG island was 2-fold lower mechanism of antileukemic drugs, cladribine and than that with cladribine.
  • 0.5) in Stat3∆/∆ Compared with Stat3flox/Flox

    0.5) in Stat3∆/∆ Compared with Stat3flox/Flox

    Supplemental Table 2 Genes down-regulated (<0.5) in Stat3∆/∆ compared with Stat3flox/flox Probe ID Gene Symbol Gene Description Entrez gene ID 1460599_at Ermp1 endoplasmic reticulum metallopeptidase 1 226090 1460463_at H60c histocompatibility 60c 670558 1460431_at Gcnt1 glucosaminyl (N-acetyl) transferase 1, core 2 14537 1459979_x_at Zfp68 zinc finger protein 68 24135 1459747_at --- --- --- 1459608_at --- --- --- 1459168_at --- --- --- 1458718_at --- --- --- 1458618_at --- --- --- 1458466_at Ctsa cathepsin A 19025 1458345_s_at Colec11 collectin sub-family member 11 71693 1458046_at --- --- --- 1457769_at H60a histocompatibility 60a 15101 1457680_a_at Tmem69 transmembrane protein 69 230657 1457644_s_at Cxcl1 chemokine (C-X-C motif) ligand 1 14825 1457639_at Atp6v1h ATPase, H+ transporting, lysosomal V1 subunit H 108664 1457260_at 5730409E04Rik RIKEN cDNA 5730409E04Rik gene 230757 1457070_at --- --- --- 1456893_at --- --- --- 1456823_at Gm70 predicted gene 70 210762 1456671_at Tbrg3 transforming growth factor beta regulated gene 3 21378 1456211_at Nlrp10 NLR family, pyrin domain containing 10 244202 1455881_at Ier5l immediate early response 5-like 72500 1455576_at Rinl Ras and Rab interactor-like 320435 1455304_at Unc13c unc-13 homolog C (C. elegans) 208898 1455241_at BC037703 cDNA sequence BC037703 242125 1454866_s_at Clic6 chloride intracellular channel 6 209195 1453906_at Med13l mediator complex subunit 13-like 76199 1453522_at 6530401N04Rik RIKEN cDNA 6530401N04 gene 328092 1453354_at Gm11602 predicted gene 11602 100380944 1453234_at
  • Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S

    Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S

    www.nature.com/scientificreports OPEN Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S. Adav 1, Roopa S. Subbaiaih2, Swat Kim Kerk 2, Amelia Yilin Lee 2,3, Hui Ying Lai3,4, Accepted: 12 January 2018 Kee Woei Ng3,4,7, Siu Kwan Sze 1 & Artur Schmidtchen2,5,6 Published: xx xx xxxx Human hair is laminar-fbrous tissue and an evolutionarily old keratinization product of follicle trichocytes. Studies on the hair proteome can give new insights into hair function and lead to the development of novel biomarkers for hair in health and disease. Human hair proteins were extracted by detergent and detergent-free techniques. We adopted a shotgun proteomics approach, which demonstrated a large extractability and variety of hair proteins after detergent extraction. We found an enrichment of keratin, keratin-associated proteins (KAPs), and intermediate flament proteins, which were part of protein networks associated with response to stress, innate immunity, epidermis development, and the hair cycle. Our analysis also revealed a signifcant deamidation of keratin type I and II, and KAPs. The hair shafts were found to contain several types of histones, which are well known to exert antimicrobial activity. Analysis of the hair proteome, particularly its composition, protein abundances, deamidated hair proteins, and modifcation sites, may ofer a novel approach to explore potential biomarkers of hair health quality, hair diseases, and aging. Hair is an important and evolutionarily conserved structure. It originates from hair follicles deep within the der- mis and is mainly composed of hair keratins and KAPs, which form a complex network that contributes to the rigidity and mechanical properties.
  • Determining HDAC8 Substrate Specificity by Noah Ariel Wolfson A

    Determining HDAC8 Substrate Specificity by Noah Ariel Wolfson A

    Determining HDAC8 substrate specificity by Noah Ariel Wolfson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2014 Doctoral Committee: Professor Carol A. Fierke, Chair Professor Robert S. Fuller Professor Anna K. Mapp Associate Professor Patrick J. O’Brien Associate Professor Raymond C. Trievel Dedication My thesis is dedicated to all my family, mentors, and friends who made getting to this point possible. ii Table of Contents Dedication ....................................................................................................................................... ii List of Figures .............................................................................................................................. viii List of Tables .................................................................................................................................. x List of Appendices ......................................................................................................................... xi Abstract ......................................................................................................................................... xii Chapter 1 HDAC8 substrates: Histones and beyond ...................................................................... 1 Overview ..................................................................................................................................... 1 HDAC introduction