Table 1.
Summary of WISH results. Clone_ID indicates cDNA clones that were used for cRNA probe preparation. U_ID is the identification of U cluster, which represents individual genes in the NIA Mouse Gene Index (Sharov et al., Genome Res., in press; http://lgsun.grc.nia.nih.gov/geneindex4). Log intensity is the mean value of signal intensities at log-scale measured in triplicate, which represents the expression of level of genes in mouse blastocyst (from the data in ref. (Hamatani et al., 2004)). Fold (ES/TS) indicates the ratio of signal intensities for each gene between ES cell and TS cell, averaged among biological replicates. The intensity of staining in ICM and TE in WISH are shown arbitrarily in 5 grades (−, +/−, +, ++ and +++, with “−“ as no staining and “+++” as the highest intensity for the amount of probe, either 1 or 5 μl). Non specific staining is shown as NS.
| Clone_ID | U_ID | Gene Symbol | Annotation | Transcription factor? | Log Intensity (Blastocyst) | Fold (ES/TS) | Oligo ID | ICM (1 ul) | TE (1 ul) | ICM (5 ul) | TE (5 ul) | ICM predominant? |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| H3028H01 | U017906 | Pou5f1 | POU domain, class 5, transcription factor 1 | Yes | 3.28 | 11.08 | Z04894 | ++ | − | ++ | +/− | Yes |
| H3123G03 | U042665 | 2310012P17Rik | RIKEN cDNA 2310012P17 gene | No | 3.13 | 2.40 | Z18099 | − | − | ++ | +/− | Yes |
| L0924F06 | U015681 | 4930548G07Rik | RIKEN cDNA 4930548G07 gene | Yes | 4.03 | 1.35 | Z12748 | ++ | − | ++ | + | Yes |
| H3101B05 | U036004 | 9930116P15Rik | Mus musculus ES cells cDNA, RIKEN full-length enriched library, clone:C330022M23 | No | 3.13 | 1.94 | Z10610 | − | − | ++ | +/− | Yes |
| H3030A05 | U037662 | Akap8 | A kinase (PRKA) anchor protein 8 | No | 2.95 | 1.58 | Z04916 | ++ | +/− | NS | NS | Yes |
| K0400H03 | U018590 | Ankhd1 | A062A08 GGTC Gene Trap Library GV03C04 Mus musculus cDNA clone A062A08 | Yes | 3.14 | 1.22 | Z15071 | +/− | − | ++ | +/− | Yes |
| H3123C11 | U030590 | Ankrd25 | ankyrin repeat domain 25 | Yes | 3.05 | 1.39 | Z11802 | + | − | ++ | +/− | Yes |
| C0866H11 | U038601 | BC024969 | MGC cDNA | Yes | 3.59 | 1.18 | Z04004 | − | − | ++ | +/− | Yes |
| C0202E10 | U089485,U013686,U119478 | BM199915 | Genbank number for EST | Yes | 3.98 | 1.21 | Z20771 | +/− | − | ++ | +/− | Yes |
| C0815H11 | U208874 | Cbfa2t2h (intron) | core-binding factor, runt domain, alpha subunit 2, translocated to, 2 homolog (human) | Yes | 2.91 | 1.46 | Z03694 | ++ | + | ++ | +/− | Yes |
| C0202D02 | U027935 | Csda | cold shock domain protein A | Yes | 3.72 | 1.26 | Z01041 | + | − | ++ | +/− | Yes |
| H3072H12 | U003038 | E2f5 | E2F transcription factor 5 | Yes | 3.12 | 1.74 | Z08851 | +/− | − | +++ | + | Yes |
| C0282F03 | U055077,U036911 | Etv5 | ets variant gene 5 | Yes | 3.60 | 2.93 | Z02758 | − | − | ++ | +/− | Yes |
| C0260F10 | U043544 | Gabpa | GA repeat binding protein, alpha | Yes | 3.34 | 1.70 | Z20218 | N/A | N/A | + | − | Yes |
| K0502H03 | U025592 | Gmeb1 | glucocorticoid modulatory element binding protein 1 | Yes | 3.74 | 1.17 | Z15720 | + | − | ++ | + | Yes |
| H3119G08 | U010777 | Gsta4 | glutathione S-transferase, alpha 4 | No | 3.69 | 21.43 | Z11620 | + | − | ++ | + | Yes |
| H3144B01 | U009246 | Gtf2e2 | general transcription factor II E, polypeptide 2 (beta subunit) | Yes | 3.27 | 1.46 | Z19185 | + | − | ++ | + | Yes |
| H8201G03 | U006190 | Gtf2h3 | general transcription factor IIH, polypeptide 3, 34kDa | Yes | 3.05 | 1.45 | Z19769 | + | − | + | +/− | Yes |
| H3140H12 | U026798 | Gtf2i | general transcription factor II I | Yes | 3.77 | 2.91 | Z19056 | ++ | − | +++ | + | Yes |
| K0406D08 | U030135 | Gtl3 | gene trap locus 3 | No | 3.64 | 1.47 | Z09177 | + | − | + | +/− | Yes |
| C0892A09 | U031153 | Ibtk | inhibitor of Bruton agammaglobulinemia tyrosine kinase | No | 3.85 | 1.49 | Z17931 | ++ | − | +/− | +/− | Yes |
| H3041C04 | U000832 | Jarid1b | jumonji, AT rich interactive domain 1B (Rbp2 like) | Yes | 3.27 | 2.22 | Z07056 | +/− | − | ++ | +/− | Yes |
| H3132F09 | U029275 | Kif22 | kinesin family member 22 | No | 2.67 | 1.75 | Z18589 | − | − | ++ | − | Yes |
| H3134C01 | U013196 | Mbtd1 | mbt domain containing 1 | No | 3.09 | 1.62 | Z18681 | − | − | ++ | +/− | Yes |
| H3057C11 | U026010 | Mll3 | myeloid/lymphoid or mixed-lineage leukemia 3 | Yes | 3.12 | 1.48 | Z07970 | − | − | ++ | +/− | Yes |
| H3144E01 | U002779,U095436,U165175 | Mybl2 | myeloblastosis oncogene-like 2 | Yes | 3.89 | 1.38 | Z19198 | ++ | − | +++ | + | Yes |
| H3050A07 | U007377,U125018 | Nanog | Nanog homeobox | Yes | 3.55 | 4.64 | Z07563 | ++ | − | ++ | − | Yes |
| H3146B03 | U032063 | Nfyb | nuclear transcription factor-Y beta | Yes | 3.40 | 1.41 | Z12544 | − | − | + | − | Yes |
| H4041A05 | U033813 | Nmyc1 | neuroblastoma myc-related oncogene 1 | Yes | 3.09 | 2.73 | Z21669 | + | − | NS | NS | Yes |
| H4028C12 | U037659 | Notch3 | Notch gene homolog 3 (Drosophila) | Yes | 4.00 | 1.22 | Z20375 | + | − | + | − | Yes |
| H3030H12 | U035481 | Otx2 | orthodenticle homolog 2 (Drosophila) | Yes | 3.25 | 4.59 | Z04978 | − | − | ++ | +/− | Yes |
| H3089E01 | U007921 | Polr2i | Mus musculus cDNA clone MGC:73656 IMAGE:3466417, complete cds. | Yes | 3.39 | 1.88 | Z10011 | − | − | ++ | +/− | Yes |
| K0417A05 | U036007 | Rai14 | retinoic acid induced 14 | Yes | 3.58 | 1.69 | Z19497 | − | − | ++ | +/− | Yes |
| H4070H09 | U018467 | Rnf138 | ring finger protein 138 | No | 3.43 | 1.32 | Z16641 | − | − | + | − | Yes |
| H4016B02 | U023697 | Sall4 | sal-like 4 (Drosophila) | No | 3.86 | 3.04 | Z13538 | +++ | + | +++ | + | Yes |
| C0341A10 | U008471 | Skd3 | suppressor of K+ transport defect 3 | Yes | 3.72 | 1.28 | Z02265 | +/− | − | + | − | Yes |
| C0402B01 | U010150 | Smarca4 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 | Yes | 3.55 | 1.67 | Z06449 | ++ | +/− | ++ | +/− | Yes |
| L0928B04 | U021771 | Sox13 | SRY-box containing gene 13 | Yes | 3.48 | 2.66 | Z05552 | ++ | +/− | +++ | ++ | Yes |
| H3081C12 | U012826 | Sox15 | SRY-box containing gene 15 | Yes | 3.49 | 2.27 | Z09444 | ++ | + | +++ | + | Yes |
| H3029B05 | U017472 | T | brachyury | Yes | 3.93 | 1.48 | Z06600 | ++ | +/− | ++ | + | Yes |
| H3071E08 | U038350 | Taf7 | TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor | Yes | 3.47 | 2.56 | Z14353 | +/− | − | ++ | +/− | Yes |
| K0240H01 | U017529 | Tbp | TATA box binding protein | Yes | 3.20 | 1.21 | Z09055 | + | − | +/− | − | Yes |
| H4005B08 | U004965 | Tcea3 | transcription elongation factor A (SII), 3 | Yes | 3.08 | 6.22 | Z14874 | + | − | ++ | +/− | Yes |
| H4061E07 | U043020 | Tfdp2 | transcription factor Dp 2 | Yes | 2.58 | 1.66 | Z03781 | − | − | + | − | Yes |
| L0949H07 | U008625 | Zfp143 | zinc finger protein 143 | Yes | 3.09 | 1.29 | Z09829 | + | − | +/− | − | Yes |
| H4040D10 | U043572 | Zfp206 | zinc finger protein 206 | Yes | 4.41 | 1.21 | Z02924 | − | − | + | − | Yes |
| H8176A06 | U072774 | Zfp322a | zinc finger protein 322a | No | 3.52 | 1.73 | Z04195 | N/A | N/A | + | − | Yes |
| H3058F11 | U018598 | Zmat2 | zinc finger, matrin type 2 | No | 3.13 | 1.47 | Z14005 | − | − | + | − | Yes |
| H3010D02 | U026912 | Actb | actin, beta, cytoplasmic | No | +++ | ++ | N/A | N/A | No | |||
| C0608A05 | U036682 | Krt2-8 | cytokeratin endo A | No | 4.92 | 0.09 | Z06684 | No | ||||
| H3093C04 | U025552 | 2410081M15Rik | RIKEN cDNA 2410081M15 gene | No | 3.06 | 3.82 | Z10249 | NS | NS | NS | NS | No |
| H3159D08 | U028390 | 2610014H22Rik | Mus musculus cDNA clone IMAGE:5704432, partial cds. | Yes | 3.30 | 1.19 | Z19782 | − | − | +/− | − | No |
| K0914F08 | U023323 | 2810405K07Rik | RIKEN cDNA 2810405K07 gene | Yes | 3.32 | 1.56 | Z15697 | − | − | +/− | − | No |
| K0122H01 | U029585 | Ankrd10 | ankyrin repeat domain 10 | Yes | 3.50 | 1.91 | Z01774 | − | − | − | − | No |
| C0326H11 | U108385 | Arid3b | AT rich interactive domain 3B (Bright like) | No | 3.60 | 1.50 | Z02467 | − | − | +/− | − | No |
| H3147F02 | U029672 | Ash2l | ash2 (absent, small, or homeotic)-like (Drosophila) | Yes | 3.83 | 1.46 | Z02226 | − | − | +/− | − | No |
| H3059D08 | U065275,U017890 | Bat4 | Mus musculus adult male epididymis cDNA, RIKEN full-length enriched library, clone:9230110P17 | Yes | 3.56 | 1.16 | Z08070 | − | − | + | +/− | No |
| H3056E10 | U025224 | Bnc2 | basonuclin 2 | No | 3.14 | 1.31 | Z13933 | N/A | N/A | − | − | No |
| H3125F02 | U215470,U183035 | Cbfa2t1h (3′-ext) | CBFA2T1 identified gene homolog | Yes | 3.51 | 1.29 | Z18223 | − | − | +/− | +/− | No |
| H3138A12 | U034741,U134034 | Dek | DEK oncogene (DNA binding) | Yes | 3.65 | 1.90 | Z12228 | − | − | + | + | No |
| H3015C12 | U021793 | Elf3 | E74-like factor 3 | Yes | 3.55 | 1.37 | Z06047 | − | − | + | +/− | No |
| C0407G11 | U018129,U012414 | Fem1a | feminization 1 homolog a (C. elegans) | Yes | 3.70 | 1.23 | Z01940 | − | − | + | +/− | No |
| H3038A09 | U039236 | Gata1 | GATA binding protein 1 | Yes | 4.48 | 1.29 | Z13445 | − | − | N/A | N/A | No |
| K0300F12 | U039463 | Hcfc1 | host cell factor C1 | No | 3.69 | 1.33 | Z00572 | − | − | NS | NS | No |
| H3029E05 | U003494 | Ilf2 | interleukin enhancer binding factor 2 | No | 3.71 | 1.60 | Z06628 | − | − | ++ | + | No |
| H3024A03 | U035555 | Jub | ajuba | No | 3.19 | 2.43 | Z06379 | NS | NS | NS | NS | No |
| H3024G07 | U042574 | Lmyc1 | lung carcinoma myc related oncogene 1 | Yes | 3.41 | 1.25 | Z06413 | − | − | − | − | No |
| K0110B04 | U002325 | Mga | MAX gene associated | Yes | 3.85 | 1.77 | Z19295 | − | − | +/− | − | No |
| K0232F02 | U018914 | Miz1 | Mus musculus Msx-interacting-zinc finger (Miz1), mRNA | Yes | 2.66 | 1.92 | Z06850 | +/− | +/− | +/− | +/− | No |
| H3039A04 | U019023 | Mrpl49 | mitochondrial ribosomal protein L49 | No | 3.15 | 1.50 | Z06929 | − | − | +/− | − | No |
| H3048E07 | U005938 | Mtf2 | metal response element binding transcription factor 2 | Yes | 4.03 | 4.22 | Z07461 | − | − | − | − | No |
| H3107B07 | U033300 | Myst2 | MYST histone acetyltransferase 2 | Yes | 3.45 | 1.23 | Z11023 | − | − | ++ | + | No |
| H3087G01 | U021824 | Nr5a2 | nuclear receptor subfamily 5, group A, member 2 | Yes | 2.94 | 3.28 | Z09889 | − | − | + | +/− | No |
| H3026F12 | U022570 | Nr6a1 | nuclear receptor subfamily 6, group A, member 1 | Yes | 3.50 | 2.49 | Z06529 | + | +/− | +++ | ++ | No |
| H3009B11 | U015867 | Nufip1 | nuclear fragile X mental retardation protein interacting protein | No | 3.29 | 1.58 | Z05791 | − | − | + | +/− | No |
| H3157C01 | U038334 | Pfdn1 | prefoldin 1 | Yes | 3.67 | 1.33 | Z13037 | − | − | − | − | No |
| H3153C03 | U042648 | Rest | RE1-silencing transcription factor | Yes | 3.05 | 2.21 | Z19589 | − | − | − | − | No |
| H8188D01 | U037958 | Rfx2 | regulatory factor X, 2 (influences HLA class II expression) | Yes | 3.77 | 1.60 | Z14719 | − | − | +/− | − | No |
| H4035E11 | U001816,U067822 | Slc4a10 | solute carrier family 4, sodium bicarbonate cotransporter-like, member 10 | Yes | 3.30 | 1.31 | Z21184 | − | − | − | − | No |
| C0234F10 | U043484 | Sp1 | trans-acting transcription factor 1 | Yes | 3.49 | 1.87 | Z01040 | − | − | ++ | + | No |
| H3128B05 | U043672 | Tcerg1 | transcription elongation regulator 1 (CA150) | Yes | 4.04 | 1.37 | Z18367 | − | − | − | − | No |
| H8244A10 | U031911 | Tfam | transcription factor A, mitochondrial | Yes | 2.66 | 1.22 | Z02399 | − | − | +/− | − | No |
| H3082D12 | U003889 | Ube2d3 | UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) | No | 2.28 | 1.39 | Z09504 | − | − | + | +/− | No |
| H3005G05 | U027470 | Usp39 | ubiquitin specific protease 39 | No | 3.20 | 1.33 | Z05697 | − | − | +/− | − | No |
| H3154D12 | U089830,U011188 | Zfp105 | zinc finger protein 105 | Yes | 3.40 | 2.58 | Z19647 | +/− | − | ++ | + | No |
| H3014D06 | U035530 | Zfp219 | zinc finger protein 219 | Yes | 3.58 | 1.77 | Z05989 | − | − | +++ | ++ | No |
| H4060F01 | U043940 | Zfp239 | zinc finger protein 239 | Yes | 3.02 | 2.90 | Z03653 | − | − | + | +/− | No |
| K0852A06 | U012241 | Zfp278 | zinc finger protein 278 | Yes | 3.45 | 2.02 | Z04975 | +/− | − | ++ | + | No |
| H3086D06 | U007769 | Zfp296 | zinc finger protein 296 | No | 3.82 | 3.71 | Z09785 | +/− | − | ++ | + | No |
| K0508E08 | U031463 | Zfp445 | zinc finger protein 445 | Yes | 3.27 | 1.71 | Z21112 | +/− | − | +/− | +/− | No |
| C0405D09 | U008795 | Zfp553 | zinc finger protein 553 | No | 3.18 | 1.56 | Z02818 | NS | NS | NS | NS | No |