imported>BArsh |
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| = QPCR Data Relevant to Endomesoderm Network =
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| == Perturbation Ct:[Ub-C]-[Ub-Exp] ==
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| == May 18, 2010 ==
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| Ub, ubiquitin mRNA control used for internal standardization; C<sub>T</sub>, cycle no. at threshold; C, control embryo sample; Exp, sample from perturbed embryos. The quantity of transcript at any point in the reaction is I(1.94<sup>C<sub>T</sub></sup>), where I is the initial amount in the reaction mixture. A positive number means the number of transcripts is increased by the perturbation; a negative number means the number of transcripts is decreased. Data are listed that are considered significant where significant means more than three-fold increase or decrease from control transcript levels (normalized C<sub>T</sub> difference from control is <-1.6 or >+1.6). Smaller effects are shown as "NS", except where individual NS data are included together with other significant measurements to display scatter or inconsistencies amongst different batches of cDNA. Commas separate replicate measurements in the same cDNA batch; slashes indicate different batches of cDNA from independent experiments.
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| '''Note:''' Smaller effects are shown as "NS", except where individual NS data are included together with other significant measurements to display scatter or inconsistencies amongst different batches of cDNA. Commas separate replicate measurements in the same cDNA batch; slashes indicate different batches of cDNA from independent experiments, dashes indicate a missing data point
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| ===Perturbations===
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| {|
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| |width="50%"| '''Perturbation:'''
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| |width="50%"| '''Genes not affected or shown to be affected only indirectly (0 to 24h, unless otherwise noted)'''
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| |-
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| | '''Alx1 MASO'''
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| | ''L1 (18, 24, 30 h), cyclophillin, delta, endo16, ets1, eve, gatac, gcm, pmar1, sm/pm27, snail, tbr, [erg, foxA, foxN2/3, foxO, hex, hnf6, jun, not, pks, soxC, tel, z48 (18-24 h)]''
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| |-
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| | '''Blimp1b MASO'''
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| | ''bra, hox11/13b, lim1, [dac, delta, hesC, msx, notch (18-27 h)]''
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| |-
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| | '''Blimp1b-En'''
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| | ''dec, dpt, endo16, foxa, gatae, gcm, not, nrl, otx a, pks, pmar1, soxb1, tbr''
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| |-
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| | '''Bra MASO'''
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| | ''capk, dec, delta, dpt, ephx, ficolin, msp130-like, nrl, pks, sm50, tbr, [blimp1b, dac, eve, foxN2/3, gcm, hesC, myc, notch, soxB1, soxC, z188 (18-27 h)]''
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| |-
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| | '''Brn1/2/4 MASO'''
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| | ''[Brn1/2/4, otxb1/2 (18, 30, 45 h)], [gatae, hox11/13b (45 h)]''
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| |-
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| | '''Cad MOE'''
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| | ''dec, elk, endo16, foxc, hnf6, nrl, soxb1, tbr, z12-1''
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| |-
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| | '''Dac MASO'''
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| | ''[blimp1b, bra, delta, eve, foxN2/3, gataC, gcm, hesC, myc, notch, soxB1, soxC, wnt8, z188 (18-27 h)]''
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| |-
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| | '''DnN MOE'''
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| | ''blimp1, bra, capk, dec, delta, e(spl)-1, elk, endo16, eve, foxa, foxb, gatac, hmx, hox11/13b, not, notch, nrl, otx b1/2, su(h), tbr, wnt8''
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| |-
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| | '''Dri MASO'''
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| | ''N, bra, delta, dri (in pmc's), e(s), ets1, eve, foxa, gatae, gcm, hnf6, hox11/13b, lim1, pmar1, tbr, wnt8, z12-1, [elk, otx a, su(h) (16-20 h)], [alx1, erg, foxN2/3, msp130L, pks, soxC, tel, z48 (18-24 h)], [not, nrl (16-24 h)]''
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| |-
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| | '''Dri-En'''
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| | ''delta, dri (in pmc's), ets1, hnf6, pmar1, tbr, z12-1 (16-20 h)''
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| |-
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| | '''Elk-En'''
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| | ''delta, elk, hnf6''
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| |-
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| | '''Erg MASO'''
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| | ''[foxN2/3, gcm, pmar1, soxC, tbr, z48 (18-24 h)]''
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| |-
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| | '''Ets1 MASO'''
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| | ''delta, endo16, eve, foxb, gcm, pmar1, sm30, tbr, [jun, krl, pks, z48 (18-24 h)]''
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| |-
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| | '''Eve MASO'''
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| | ''alx1, cyclophilin, dri, ets1, foxc, gatac, gatac, gsc, hmx, msp130, not, otx a, otx b1/2, otx b3, pmar1, sm30, soxb1, tbr, [foxG, msx, myc, notch, soxC (15-27 h)]''
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| |-
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| | '''FoxA MASO'''
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| | ''b1/2otx, hmx, not (0-48 h), nrl, otx a, pks, tbr, [brn1/2/4, delta, eve, hox11/13b, wnt8 (18-27, 32, 48 h)], [blimp1, foxc (18, 24, 32, 48 h)], [alx1, blimp1b, dac, elk, foxN2/3, foxP, hesC, hnf1, msx, myc, notch, otxb1/2, soxB1, soxC, tgif, unc4.1, z188 (18-27 h)]''
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| |-
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| | '''FoxB MASO'''
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| | ''cyclophillin, endo16, ets1, ficolin, foxa, gatae, hox11/13b, sm27, sm50, tbr, wnt8''
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| |-
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| | '''FoxN2/3 MASO'''
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| | ''[cyclophillin, dri, foxA, foxN2/3, foxb, gatac, gcm, hex, hnf6, jun, krl, msp130, msp130L, not, pm27, pmar1, sm50, snail, soxC, tbr, tgif, z48 (18-24 h)]''
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| |-
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| | '''GataC MASO'''
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| | ''bra, capk, delta, dpt, elk, eve, gatae, gcm, not, pks''
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| |-
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| | '''GataE MASO'''
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| | ''??????, blimp1, capk, dec, dri, elk, ets1, eve, ferritin, gatae, gcm, hmx, nk1, otx a, [alx1, dac, delta, foxN2/3, hesC, soxB1, soxC (18-27 h)]''
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| |-
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| | '''Gcm MASO'''
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| | ''capk, dec, delta, elk, gatac, gatae, hmx, not, nrl''
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| |-
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| | '''Gsc MASO'''
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| | ''alx1, blimp1, bra, decorin, delta (in pmc's), dri, ets1, eve, foxb, fvmo, gatac, gcm, gsc, hmx, hnf6, krl, pks, pmar1, tbr, wnt8, z12-1 (17, 23 h)''
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| |-
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| | '''Hex MASO'''
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| | ''[dri, foxA, gcm, gsc, jun, krl, pmar1, tbr, z48 (18-24 h)]''
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| |-
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| | '''Hnf1 MASO'''
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| | ''[Brn1/2/4, alx1, blimp1b, bra, dac, delta, elk, endo16, eve, foxG, foxN2/3, foxP, foxa, foxb, gatac, gatae, gcm, hh, hox11/13b, krl, msx, myc, notch, otxb1/2, soxC, soxb1, tgif, unc4.1, wnt8, z188 (24-27 h)]''
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| |-
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| | '''Hnf6 MASO'''
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| | ''alx1, blimp1, bra, cyclophillin, delta, dri (in pmc's), elk, ets1, eve, foxa, gatae, gcm, hnf6 (in pmc's), otx a, pmar1, tbr, wnt8, [foxb, krl, z12-1 (19-20 h)]''
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| |-
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| | '''Hox11/13b MASO'''
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| | ''blimp1, otx a, otx b, soxb1, wnt8, [Brn1/2/4, alx1, dac, delta, elk, hnf6, otxb1/2, soxC, z188 (18-27 h)]''
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| |-
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| | '''Krl MASO'''
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| | ''alx1, blimp1, bra, dec, delta (12, 18-27 h), dri, ets1, eve, eve, gatae, gcm, gsc, hmx, krl, lim1, nrl, otx b1/2, pm27, pmar1, sm50, tbr, wnt8, z12-1, [dac, foxN2/3, foxP, gataC, hesC, msx, myc, notch, soxC, z188 (18-27 h)]''
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| |-
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| | '''MutantSu(H) MOE'''
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| | ''[endo16, sm50 (18, 24, 30 h)]''
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| |-
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| | '''Myc MASO'''
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| | ''[blimp1b, bra, dac, delta, endo16, eve, foxG, foxN2/3, foxP, gataC, gataE, gcm, hesC, hnf6, notch, soxB1, soxC, wnt8, z188 (18-27 h)]''
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| |-
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| | '''N MASO'''
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| | ''[foxa, foxb (18-27, 29, 41 h)], [bra, eve (21, 24-27, 29, 41 h)], [espl1, gatae, hmx, nrl, su (21, 29, 41 h)], [brn1/2/4, dac, foxN2/3, foxP, hesC, hh, myc, soxB1, soxC, wnt8 (18-27 h)]''
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| |-
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| | '''Otx-En'''
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| | ''dec, delta, elk, eve, gcm, otx a, pks, tbr''
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| |-
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| | '''OtxHD MASO'''
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| | ''[alx1, blimp1b, bra, dac, delta, elk, eve, foxN2/3, foxP, gatae, gcm, hnf6, hox11/13b, krl, myc, notch, otxb1/2, soxC, soxb1, unc4.1, wnt8, z188 (18-27 h)]''
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| |-
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| | '''Otxa MASO'''
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| | ''[alx1, blimp1b, bra, endo16, eve, foxG, foxP, foxa, foxb, gatac, gatae, gcm, hox11/13b, myc, soxC, soxb1, tgif, unc4.1, z188 (18-27 h)]''
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| |-
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| | '''Pmar1 MOE'''
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| | ''blimp1, elk, foxa, hnf6, krl, sm30, wnt8''
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| |-
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| | '''Pmar1-En'''
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| | ''blimp1, elk, foxa, hnf6, sm30, wnt8''
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| |-
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| | '''SoxC MASO'''
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| | ''[cyclophillin, dri, erg, ets1, foxO, hex, jun, msp130L, not, nrl, pm27, pmar1, sm50, snail, tbr, tel, vegfrII, z48 (18-24 h)], [alx1, blimp1b, bra, dac, delta, elk, endo16, eve, foxA, foxG, foxN2/3, foxP, foxb, gataC, gatae, gcm, hh, hnf1, hnf6, hox11/13b, krl, msx, myc, notch, otxb1/2, soxb1, unc4.1, wnt8, z188 (18-27 h)]''
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| |-
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| | '''Soxb1 MASO'''
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| | ''blimp1, bra, dec, dpt, dri, elk, endo16, foxa, foxb, foxc, gatac, krl, nrl, pmar1, wnt8, z12-1, [delta, gatae, gcm, hox11/13b, tbr (0-16 h)]''
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| |-
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| | '''Soxb1 MOE'''
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| | ''blimp1, dri, endo16, hnf6, tbr''
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| |-
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| | '''Soxb1-En'''
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| | ''alx1 (12 h), [bra, delta, endo16, ets-1, eve, foxa, foxb, gatac, gcm, hox11/13b, krl, msp130, pm27, sm50, wnt8 (18, 24 h)]''
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| | '''Tbr MASO'''
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| | ''alx1, cyclophilin, delta, endo16, ets1, ets1, eve, ficolin, gatae, gcm, msp130, msp130L, pm27, [cyclophillin, foxA, foxN2/3, foxO, gatac, hex, jun, not, pks, pmar1, soxC, tel, vegfrII, z48 (18-24 h)]''
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| | '''Tel MASO'''
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| | ''[cyclophillin, dri, erg, ets1, ficolin, foxA, foxB, foxN2/3, foxO, gcm, hex, hnf6, jun, krl, msp130, msp130L, not, pks, pmar1, pmar1, soxC, tbr, vegfrII, z48 (18-24 h)]''
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| | '''Tgif MASO'''
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| | ''[cyclophillin, ets1, jun, pmar1, tbr, tel (18-24 h)], [dac, delta, elk, endo16, eve, gatac, hesC, hox11/13b, msx, myc, notch, soxC, wnt8, z188 (18-27 h)]''
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| |}
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| === Footnotes ===
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| <sup>1</sup>Must be affected indirectly via intercellular signaling because Bra is not present in cells where these genes are active.
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| <sup>2</sup>At 30 h affected indirectly via cell signaling, since at 30 h Dri and Gsc are expressed only in OE.
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| <sup>3</sup>Thought to be indirect input, via GataE.
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| <sup>4</sup>Probably via GataC.
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| <sup>5</sup>Probably via Bra.
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| <sup>6</sup>Probably in OE where both Elk and Lim1 are expressed then.
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| <sup>7</sup>Probably indirect via Gcm.
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| <sup>8</sup>Probably indirect via ''gcm''.
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| <sup>9</sup>The inputs inferred from effects on ''endo16''.
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| <sup>10</sup>Effect on ''endo16'' is via Ui since no necessary GataE site in ''endo16''.
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| <sup>11</sup>Probably via ''ets1''; based on ECRA.
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| <sup>12</sup>Indirect, because rescued by ''blimp1'' MOE.
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| <sup>14</sup>Probably indirect via ''elk''.
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| <sup>15</sup>Weak effect 18 h only, probably not significant, since ''wnt''8 expression is disappearing in gatae domain at 18 h. Effect seen is probably via Otx which represses ''wnt8'' in this period.
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| <sup>17</sup>Likely indirect via ''gatae.''
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| <sup>18</sup>Late Krl effects likely to be indirect results of effects of Krl loss on endomesoderm specification (Howard ''et al''., 2000).
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| <sup>19</sup>Obviously indirect via ''pmar1.''
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| <sup>20</sup>Only when ''dri'' is expressed in OE (>30 h).
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| <sup>21</sup>Possibly indirect via, because if there were an Otx site in ''gatac'' gene effect would have been seen earlier than 24 h.
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| <sup>22</sup>Must be indirect because direct ''sm50'' inputs are known.
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| <sup>23</sup>Normalized to different standards in same run, i.e., ubiquitin and 18S rRNA.
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| <sup>24</sup> ''alx1'' expressed specifically in pmc's; discovered by Ettensohn ''et al''.
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| <sup>26</sup>In collaboration with R. and L. Angerer who provided the samples measured.
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| <sup>27</sup>Likely an artifact of expressing Blimp1-En MOE pmc's, since ''foxb'' is expressed only in pmc's at this stage (i.e., there could be a later interaction of Blimp1 and Soxb in hindgut where they are both expressed after gastrulation).
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| <sup>28</sup>Weak effect likely indirect since ''gatac'' is expressed in smc's at 27 h and ''foxb'' in pmc's, later hindgut on oral side (plus oral ectoderm).
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| <sup>30</sup>Not indirect via GataE because N MASO does not affect ''gatac'' though dnN does.
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| <sup>31</sup>Indirect effects on ''gatac'' does not turn on until after Tcf input is faded out, but all other inputs depend on endomesoderm specification.
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| <sup>32</sup>Effect on initial phase of ''gatac'' expression, before it becomes exclusive with ''gcm'' (oral vs aboral and lateral).
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| <sup>33</sup>Could be indirect via Ets1 effect on ''tbr''; effect of Ets1 on ''foxb'' is stronger than ''tbr'' effect on ''foxb''.
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| <sup>34</sup>At least early (<24 h) effects on the three ''fvmo'' genes probably via ''gcm''.
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| <sup>35</sup>Via ''dri'' (see Amore ''et al''., 2002).
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| <sup>37</sup>Implies late blastula pmc domain to mesoderm indirect effect on oral side, where ''gatac'' is then expressed in mesoderm: not yet understood.
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| <sup>38</sup>Since Gsc is a repressor (Angerer ''et al''.) implies existence of mid-late blastula repressor of skeletogenic function controlled by ''gsc'': perhaps a timing device.
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| <sup>40</sup>Very possibly indirect via ''dri''.
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| <sup>41</sup>Unlikely a direct transcriptional effect, since ''eve'' expression is not affected by Soxb1-Eng MOE.
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| <sup>42</sup>Possibly indirect.
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| <sup>43</sup>Likely via ''dri.''
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| <sup>45</sup>Probably in OE because most ''gsc'' expression at 24 h is there.
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| <sup>47</sup>Double perturbation results show both inputs, Alx1 and Ets1, are required when indicated.
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| <sup>48</sup>Data for mesenchyme blastula stage of Lytechinus variegatus
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| <sup>49</sup>Probably Indirect
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| <sup>50</sup>Unc4.1 is expressed in the aboral veg1 ectoderm, starting at 24h; effect must be indirect
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