I. gene lists to compare the microarray expression data with prior studies of gene expression. I. A. genes that are upregulated upon deflagellation in Chlamydomonas the first 22 genes are taken from various previously published studies of regeneration using Northern blots. The rest are taken from Li and Dutcher's comparative genomics paper in which they used RT-PCR to analyze a set of candidate genes. 164620 alpha-1 tubulin (probably the most strongly induced known gene) 170055 beta-2 tubulin 167398 outer dynein arm light chain DLC5 14,000kDa patel-king et al 1996 162279 Rsp3 156948 IFT57 154393 IFT52 166736 IC140 (IDA7) 164100 IC70 (a.k.a. ODA6) 157967 RSP4 157968 RSP6 153708 LF4 157052 MBO2 166131 PF20 171096 PF16 168923 PF6 158194 Fla10 157798 ODA3 165162 ODA5 160952 DC3 (outer arm docking complex subunit DC3) 159662 FA1 169516 (a.k.a. DHC2 dynein heavy chain) 156513 KPL2 induced during mammalian trachael ciliogenesis 158615 165004 165115 163193 164561 169293 153658 163664 164149 162703 159749 158670 168339 158863 164264 156043 153422 171602 159155 160297 171911 169882 153853 168565 156513 153053 171102 163277 165606 165905 158033 163484 159247 157793 159590 157246 161253 167776 171797 154949 160023 152526 157642 159573 161738 165091 164660 137687 166686 169489 162929 168165 156365 158752 165537 165684 I. B. genes that are known NOT to be upregulated after deflagellation the first four are taken from published studies of gene expression during regeneration using Northern blots. The rest are from the systematic RT-PCR analysis of Li and Dutcher. 168391 RBCS2 (should be an abundant transcript in all samples) 165904 CRY1 S14 ribosomal protein (RPS14) [the most commonly used ctrl] 165072 aldolase (note I corrected the ID from the first list) 165247 Cblp (chlamydomonas beta subunit-like polypeptide 158239 156671 165102 166667 153859 162058 157943 156530 164333 156598 155925 161779 171684 167053 171166 164526 155451 158560 171242 155468 168286 158402 159111 154789 155817 165569 168283 162907 157385 169453 156229 164197 170673 155464 164774 166044 162018 159566 164610 163738 165846 164517 167803 154013 162224 168715 171299 164928 161792 168343 169942 162000 166414 166774 160951 I. C. gene that should not be expressed AT ALL in this strain 156490 FUS1 (mating type + specific gene, samples are from mt- lack FUS1) II. Genes for which the localization of the gene product is known with respect to flagella in Chlamydomonas. Once the lists in section I are analyzed to show that the microarray method can mostly reproduce known expression patterns (i.e. a control for the technical methodology), an analysis of these lists will confirm our overall strategy of using gene expression as a way to identify likely flagellar components. II. A. gene products known to localize to flagella in Chlamydomonas 157469 ODA2 outer arm dynein heavy chain gamma 168602 DLC1 outer dynein arm light chain 1 156307 D1bLIC cytoplasmic dynein 1b light intermed chain (retro IFT) 169516 DHC1b cytoplasmic dynein 1b heavy chain (retro IFT) 160952 ODA15 outer arm docking complex subunit 3 ODA-DC3 155586 PF2 dynein regulatory complex component. trypanin related 165162 ODA5 associated with flagellar adenylated kinase 171763 ODA1 outer arm docking complex subunit 2 ODA-DC2 170981 FAP2 Tctex2-related light chain 157798 ODA3 outer arm docking complex subunit 1 ODA-DC1 168520 ODA11 outer dynein arm heavy chain alpha 164100 ODA6 outer dynein arm intermediate chain 2 (IC70) 158273 DLC4 outer dynein arm light chain 4 (18 kDa light chain) 164307 DLC3 outer dynein arm light chain 3 (16 kDa light chain) 169191 DHC9 inner arm dynein heavy chain 9 158922 IDA2 inner arm dynein 1 heavy chain beta (DHC1-beta) 169971 DLC7b dynein light chain related to Roadblock 161325 DHC7 inner arm heavy chain 7 C-terminus 161326 DHC7 inner arm dynein heavy chain, N-terminus (split gene model) 162594 DHC4 inner arm dynein heavy chain 4 164722 ODA13 outer dynein arm light chain 6 (11 kDa light chain) 171127 DHC2 inner arm dynein heavy chain 2 162407 DHC5 inner arm dynein heavy chain 5 159281 FLA14 outer dynein arm light chain 8 (LC8) [why is it fla?] 164295 ODA12 outer dynein arm light chain 2 (DLC2 or Tctex2) 167398 DLC5 outer dynein arm light chain 5 (14 kDa dynein light chain) 161759 DHC3 dynein heavy chain 3 (inner arm?) C-terminus 160289 ODA4 outer dynein arm heavy chain beta 153556 DHC1 inner arm dynein 1 heavy chain alpha (DHC1-alpha, PF9) 169795 DLC7a outer arm dynein light chain 7 (Roadblock-like outer arm) 163907 DHC6 inner arm dynein heavy chain 6 171599 DHC11 inner arm dynein heavy chain 11 176100 DHC8 inner arm dynein heavy chain 8 169383 IDA4 inner arm dynein light chain p28 171226 Tctex1 inner arm dynein light chain Tctex1 166736 IDA7 inner dynein arm I1 intermediate chain IC140 171680 ODA9 outer dynein arm intermediate chain 1 (IC78) 161758 DHC3 inner arm dynein heavy chain 3 192006 RSP1 radial spoke 1 (spoke head) 155416 RSP2 radial spoke 2 (spoke stalk, PF24) 156655 RSP2 radial spoke 2 (annotaed by lefebvre) which is right? 162279 RSP3 radial spoke 3 (spoke stalk, PF14, AKAP) 157967 RSP4 radial spoke 4 (spoke head, PF1) 157968 RSP6 radial spoke 6 (spoke head, PF26. dimer with pf4) 156214 IFT20 154393 IFT52 BLD1, Osm-6 156948 IFT57 homology with Hippi (huntingtin interacting protein 1) 164979 IFT74/72 159022 IFT81 169254 IFT88 homolog of Tg737 168243 IFT140 157911 IFT172 168012 KAP non-motor subunit of kinesin-II for IFT 157405 FLA8 kinesin-II subunit for IFT 158194 FLA10 kinesin-II subunit for IFT 170694 RIB43a pf ribbon protein with coiled-coil 168675 RIB72 pf ribbon protein 168923 PF6 central pair microtubule protein 171096 PF16 central pair microtubule protein (homolog to Spag6) 167565 KLP1 kinesin associated with the central pair 154251 MST1 mastigoneme protein 1 169341 FMG1A flagellar membrane glycoprotein 1A 169338 FMG1b flagellar membrane glycoprotein 1b 166131 PF20 central pair microtubule protein 159662 FA1 flagellar autotomy protein 171231 LF3 reported to downregulate during regen 160144 PP1a axonemal protein serine/threonine phosphatase 1a 153086 FA2 Nek kinase 152507 EB1 MT +end tracking protein (Pedersen et al) 167981 KAT2 katanin p60 subunit 157052 MBO2 mobe2 coiled-coil protein 168881 Tektin Chlamydomonas tektin annotated by Lefebvre II. B. control genes whose products localize to chloroplast 192023 RPS9 Chloroplast 30S ribosomal protein 154594 MINE2 MinE chloroplast division protein 192005 SBP sedoheptulose-bisphosphatase 169972 PETM cytochrome b6f subunit 165812 PETC cytochrome b6f Rieske Iron-sulfur protein 160286 THYL thylakoid lumenal 17.4 kDa protein 154244 PETN cytochrome b6f subunit 159627 CemA chloroplast integral membrane heme-binding protein 158611 PSBW photosystem II reaction center W protein 156157 PGK chloroplast phosphoglycerate kinase 169504 MET1 chloroplast resident DNA methyltransferase 165989 RbcS2 Rubisco small subunit II. C. control genes whose products localize to nucleus 170696 TOP1 topoisomerase I 169614 TOP2 topoisomerase II 162123 POLA2 DNA polymerase alpha subunit B 152784 HON1 histone H1 157840 HFO1 histone H4 153542 RPB1 RNA pol II large subunit 164104 RPB119aa RNA pol II 14.5 kD subunit 162121 TAF7 TF IID subunit TAF7 161483 TFIIAg TFIIA gamma subunit 164461 NUP98 nucleoporin nup98 163504 NUP155 nucleoporin nup155 157278 PCN1 PCNA homolog III. Genes corresponding to potential ciliary diseases 157469 ODA2 human DNAH5 (PCD, situs inversus) 169197 DIP13 deflag-inducible protein. Sjogren's syndrome NA 170819 SSD3 Niemann-pick related protein in arabidopsis 165845 PKHD1-3 fibrocystin (PKD & hepatic disease) 156686 PKHD1-2 fibrocystin 165102 PKHD1-1 fibrocystin 171797 BBS8 Bardet-Biedl TRP protein 8 158679 ARLB2 possible zebrafish Scorpion homolog (PKD, no cilia) 158670 TSLRP zebrafish Seahorse (PKD) testis specific LRR protein 158863 FAP22 zebrafish QiLin homolog (PKD) 165004 Hydin hydrocephalus inducing protein 154949 BBS7 152526 BBS1 159573 BBS2 161738 BBS5 137687 BBS4 164333 NPHP4 nephronophthisis (nephroretinin) 154789 RP2 retinitis pigmentosa 2 158816 NPHP3(?) possible nephrocystin 3 157801 OFD1 possible OFD1 (oro-facial_digital syndrome) 153344 CFTR atp binding cassette of cftr 157341 TBY1 Tubby like protein 1 163973 INVSb inversin isoform b 168613 PTCH patched homolog, Niemann-Pick 164661 insulin receptor 168988 NPHP3 nephrocystin 3 according to Pazour annotation 152452 RPGR retinitis pigmentosa GTPase regulator 168865 HIPI1 huntingtin interacting protein 1 156598 polycystin 1 precursor 159460 G-protein linked with obesity