Epgfp and Endomes QPCR: Difference between pages

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= QPCR Data Relevant to Endomesoderm Network =


== EPGFP2 ==
== Perturbation Ct:[Ub-C]-[Ub-Exp] ==


[[image:Small_map.jpg||left|700x700px|EpGFPII plasmid vector]]
== May 18, 2010 ==


The plasmid vector used as a vehicle to test the cis-regulatory function of randomly cloned genomic DNA fragments was modified from a previous construct, EpGFP (Arnone et al., 1997; Arnone et al., 1998). The grand-parent of this plasmid was pCMV (Clontech); it has ampicillin resistance. EpGFP contains the region around the start of transcription of the endo16 gene (from -117 to +20).The activity of this element has been described in detail elsewhere (Yuh and Davidson, 1996; Yuh et al., 1996,1998, 2001). In addition to a TATA-containing basal promoter, it contains auxiliary sites for a ubiquitous sea urchin transcription factor which promotes DNA looping and has weak transcriptional enhancement activity(GCF1; Zeller et al., 1995). The vector also includes a sea urchin ribosome binding site from the cyIIa gene (Arnone et al., 1998), positioned at the start of the coding sequence of the GFP reporter. The original EpGFP construct was further modified by the addition of a double-stranded oligonucleotide polylinker inserted between the MluI and XmaI sites in the Multiple Cloning Site (MCS), so that the MCS contains the following restriction enzyme sites: 5'-KpnI-SacI-MluI-EcoRI-SpeI-BglII-SmaI/XmaI-3', situated just upstream of the endo16 basal promoter.
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.


<div class="toccolours mw-collapsible mw-collapsed" style="clear:both">
EpGFPII FASTA Sequence
<div class="mw-collapsible-content">>epgfpii
<pre>
1          11        21        31        41        51        61        71        81        90       
  |          |          |          |          |          |          |          |          |        |
  GGTACCGAGC TCTTACGCGT GAATTCACTA GTAGATCTCC CGGGTTAAAC TGTTTGAGTT TCGTCTCCTG ATTGTGCTAT CAAAGACAAA    90 epgfpii
  GGGGTGTAAC TTTACCCCCC TCATCAAGAG CGGAGGGTTA AATAGAGAAA GACTGGTCGA GGACAGGTCA TAATATTGCT AATTTTTAAG  180 epgfpii
  CTTATCATCA TGTGTGACGA CGACGTCGCC GCTCTTGTCG TCGACAACGG ATCTGCGGCC GCCGCCACCA TGAGCAAGGG CGAGGAACTG  270 epgfpii
  TTCACTGGCG TGGTCCCAAT TCTCGTGGAA CTGGATGGCG ATGTGAATGG GCACAAATTT TCTGTCAGCG GAGAGGGTGA AGGTGATGCC  360 epgfpii
  ACATACGGAA AGCTCACCCT GAAATTCATC TGCACCACTG GAAAGCTCCC TGTGCCATGG CCAACACTGG TCACTACCTT CACCTATGGC  450 epgfpii
  GTGCAGTGCT TTTCCAGATA CCCAGACCAT ATGAAGCAGC ATGACTTTTT CAAGAGCGCC ATGCCCGAGG GCTATGTGCA GGAGAGAACC  540 epgfpii
  ATCTTTTTCA AAGATGACGG GAACTACAAG ACCCGCGCTG AAGTCAAGTT CGAAGGTGAC ACCCTGGTGA ATAGAATCGA GCTGAAGGGC  630 epgfpii
  ATTGACTTTA AGGAGGATGG AAACATTCTC GGCCACAAGC TGGAATACAA CTATAACTCC CACAATGTGT ACATCATGGC CGACAAGCAA  720 epgfpii
  AAGAATGGCA TCAAGGTCAA CTTCAAGATC AGACACAACA TTGAGGATGG ATCCGTGCAG CTGGCCGACC ATTATCAACA GAACACTCCA  810 epgfpii
  ATCGGCGACG GCCCTGTGCT CCTCCCAGAC AACCATTACC TGTCCACCCA GTCTGCCCTG TCTAAAGATC CCAACGAAAA GAGAGACCAC  900 epgfpii
  ATGGTCCTGC TGGAGTTTGT GACCGCTGCT GGGATCACAC ATGGCATGGA CGAGCTGTAC AAGTGAGCGG CCGCGGCTCG AGGCTCTAGA  990 epgfpii
  GTCGGGGCGG CCGGCCGCTT CGAGCAGACA TGATAAGATA CATTGATGAG TTTGGACAAA CCACAACTAG AATGCAGTGA AAAAAATGCT  1080 epgfpii
  TTATTTGTGA AATTTGTGAT GCTATTGCTT TATTTGTAAC CATTATAAGC TGCAATAAAC AAGTTAACAA CAACAATTGC ATTCATTTTA  1170 epgfpii
  TGTTTCAGGT TCAGGGGGAG GTGTGGGAGG TTTTTTAAAG CAAGTAAAAC CTCTACAAAT GTGGTAAAAT CGATAAGGAT CCGTCGACCG  1260 epgfpii
  ATGCCCTTGA GAGCCTTCAA CCCAGTCAGC TCCTTCCGGT GGGCGCGGGG CATGACTATC GTCGCCGCAC TTATGACTGT CTTCTTTATC  1350 epgfpii
  ATGCAACTCG TAGGACAGGT GCCGGCAGCG CTCTTCCGCT TCCTCGCTCA CTGACTCGCT GCGCTCGGTC GTTCGGCTGC GGCGAGCGGT  1440 epgfpii
  ATCAGCTCAC TCAAAGGCGG TAATACGGTT ATCCACAGAA TCAGGGGATA ACGCAGGAAA GAACATGTGA GCAAAAGGCC AGCAAAAGGC  1530 epgfpii
  CAGGAACCGT AAAAAGGCCG CGTTGCTGGC GTTTTTCCAT AGGCTCCGCC CCCCTGACGA GCATCACAAA AATCGACGCT CAAGTCAGAG  1620 epgfpii
  GTGGCGAAAC CCGACAGGAC TATAAAGATA CCAGGCGTTT CCCCCTGGAA GCTCCCTCGT GCGCTCTCCT GTTCCGACCC TGCCGCTTAC  1710 epgfpii
  CGGATACCTG TCCGCCTTTC TCCCTTCGGG AAGCGTGGCG CTTTCTCAAT GCTCACGCTG TAGGTATCTC AGTTCGGTGT AGGTCGTTCG  1800 epgfpii
  CTCCAAGCTG GGCTGTGTGC ACGAACCCCC CGTTCAGCCC GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGTAAG  1890 epgfpii
  ACACGACTTA TCGCCACTGG CAGCAGCCAC TGGTAACAGG ATTAGCAGAG CGAGGTATGT AGGCGGTGCT ACAGAGTTCT TGAAGTGGTG  1980 epgfpii
  GCCTAACTAC GGCTACACTA GAAGGACAGT ATTTGGTATC TGCGCTCTGC TGAAGCCAGT TACCTTCGGA AAAAGAGTTG GTAGCTCTTG  2070 epgfpii
  ATCCGGCAAA CAAACCACCG CTGGTAGCGG TGGTTTTTTT GTTTGCAAGC AGCAGATTAC GCGCAGAAAA AAAGGATCTC AAGAAGATCC  2160 epgfpii
  TTTGATCTTT TCTACGGGGT CTGACGCTCA GTGGAACGAA AACTCACGTT AAGGGATTTT GGTCATGAGA TTATCAAAAA GGATCTTCAC  2250 epgfpii
  CTAGATCCTT TTAAATTAAA AATGAAGTTT TAAATCAATC TAAAGTATAT ATGAGTAAAC TTGGTCTGAC AGTTACCAAT GCTTAATCAG  2340 epgfpii
  TGAGGCACCT ATCTCAGCGA TCTGTCTATT TCGTTCATCC ATAGTTGCCT GACTCCCCGT CGTGTAGATA ACTACGATAC GGGAGGGCTT  2430 epgfpii
  ACCATCTGGC CCCAGTGCTG CAATGATACC GCGAGACCCA CGCTCACCGG CTCCAGATTT ATCAGCAATA AACCAGCCAG CCGGAAGGGC  2520 epgfpii
  CGAGCGCAGA AGTGGTCCTG CAACTTTATC CGCCTCCATC CAGTCTATTA ATTGTTGCCG GGAAGCTAGA GTAAGTAGTT CGCCAGTTAA  2610 epgfpii
  TAGTTTGCGC AACGTTGTTG CCATTGCTAC AGGCATCGTG GTGTCACGCT CGTCGTTTGG TATGGCTTCA TTCAGCTCCG GTTCCCAACG  2700 epgfpii
  ATCAAGGCGA GTTACATGAT CCCCCATGTT GTGCAAAAAA GCGGTTAGCT CCTTCGGTCC TCCGATCGTT GTCAGAAGTA AGTTGGCCGC  2790 epgfpii
  AGTGTTATCA CTCATGGTTA TGGCAGCACT GCATAATTCT CTTACTGTCA TGCCATCCGT AAGATGCTTT TCTGTGACTG GTGAGTACTC  2880 epgfpii
  AACCAAGTCA TTCTGAGAAT AGTGTATGCG GCGACCGAGT TGCTCTTGCC CGGCGTCAAT ACGGGATAAT ACCGCGCCAC ATAGCAGAAC  2970 epgfpii
  TTTAAAAGTG CTCATCATTG GAAAACGTTC TTCGGGGCGA AAACTCTCAA GGATCTTACC GCTGTTGAGA TCCAGTTCGA TGTAACCCAC  3060 epgfpii
  TCGTGCACCC AACTGATCTT CAGCATCTTT TACTTTCACC AGCGTTTCTG GGTGAGCAAA AACAGGAAGG CAAAATGCCG CAAAAAAGGG  3150 epgfpii
  AATAAGGGCG ACACGGAAAT GTTGAATACT CATACTCTTC CTTTTTCAAT ATTATTGAAG CATTTATCAG GGTTATTGTC TCATGAGCGG  3240 epgfpii
  ATACATATTT GAATGTATTT AGAAAAATAA ACAAATAGGG GTTCCGCGCA CATTTCCCCG AAAAGTGCCA CCTGACGCGC CCTGTAGCGG  3330 epgfpii
  CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG CTTTCTTCCC  3420 epgfpii
  TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGTGCTT TACGGCACCT  3510 epgfpii
  CGACCCCAAA AAACTTGATT AGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC  3600 epgfpii
  GTTCTTTAAT AGTGGACTCT TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT  3690 epgfpii
  TTCGGCCTAT TGGTTAAAAA ATGAGCTGAT TTAACAAAAA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CCCATTCGCC  3780 epgfpii
  ATTCAGGCTG CGCAACTGTT GGGAAGGGCG ATCGGTGCGG GCCTCTTCGC TATTACGCCA GCCCAAGCTA CCATGATAAG TAAGTAATAT  3870 epgfpii
  TAAGGTACGG GAGGTACTTG GAGCGGCCGC AATAAAATAT CTTTATTTTC ATTACATCTG TGTGTTGGTT TTTTGTGTGA ATCGATAGTA  3960 epgfpii
  CTAACATACG CTCTCCATCA AAACAAAACG AAACAAAACA AACTAGCAAA ATAGGCTGTC CCCAGTGCAA GTGCAGGTGC CAGAACATTT  4050 epgfpii
  CTCTATCGAT A                                                                                        4061 epgfpii
</pre></div>
</div>
[http://ftp.echinobase.org/pub/WikiDownloads/epgfpii.fasta Download FASTA file for EpGFPII]


=== REFERENCES ===


Yuh, C. H., Moore, J. G. and Davidson, E. H. Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene. Development 122, 4045-4056, 1996.<span class="newwin">[https://new.echinobase.org/literature/article.do?method=display&articleId=36543  [open<nowiki>]</nowiki>]</span>
'''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


Yuh, C.-H. and Davidson, E. H. Modular cis-regulatory organization of Endo16, a gut-specific gene of the sea urchin embryo. Development 122, 1069-1082, 1996.<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=36421  [open<nowiki>]</nowiki>]</span>
===Perturbations===


Yuh, C.-H., Bolouri, H. and Davidson, E. H. Genomic cis-regulatory logic: Functional analysis and computational model of a sea urchin gene control system. Science 279, 1896-1902, 1998.
{|
<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=36860  [open<nowiki>]</nowiki>]</span>
|width="50%"| '''Perturbation:'''
|width="50%"| '''Genes not affected or shown to be affected only indirectly (0 to 24h, unless otherwise noted)'''
|-
| '''Alx1 MASO'''
| ''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)]''
|-
| '''Blimp1b MASO'''
| ''bra, hox11/13b, lim1, [dac, delta, hesC, msx, notch (18-27 h)]''
|-
| '''Blimp1b-En'''
| ''dec, dpt, endo16, foxa, gatae, gcm, not, nrl, otx a, pks, pmar1, soxb1, tbr''
|-
| '''Bra MASO'''
| ''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)]''
|-
| '''Brn1/2/4 MASO'''
| ''[Brn1/2/4, otxb1/2 (18, 30, 45 h)], [gatae, hox11/13b (45 h)]''
|-
| '''Cad MOE'''
| ''dec, elk, endo16, foxc, hnf6, nrl, soxb1, tbr, z12-1''
|-
| '''Dac MASO'''
| ''[blimp1b, bra, delta, eve, foxN2/3, gataC, gcm, hesC, myc, notch, soxB1, soxC, wnt8, z188 (18-27 h)]''
|-
| '''DnN MOE'''
| ''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''
|-
| '''Dri MASO'''
| ''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)]''
|-
| '''Dri-En'''
| ''delta, dri (in pmc's), ets1, hnf6, pmar1, tbr, z12-1 (16-20 h)''
|-
| '''Elk-En'''
| ''delta, elk, hnf6''
|-
| '''Erg MASO'''
| ''[foxN2/3, gcm, pmar1, soxC, tbr, z48 (18-24 h)]''
|-
| '''Ets1 MASO'''
| ''delta, endo16, eve, foxb, gcm, pmar1, sm30, tbr, [jun, krl, pks, z48 (18-24 h)]''
|-
| '''Eve MASO'''
| ''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)]''
|-
| '''FoxA MASO'''
| ''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)]''
|-
| '''FoxB MASO'''
| ''cyclophillin, endo16, ets1, ficolin, foxa, gatae, hox11/13b, sm27, sm50, tbr, wnt8''
|-
| '''FoxN2/3 MASO'''
| ''[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)]''
|-
| '''GataC MASO'''
| ''bra, capk, delta, dpt, elk, eve, gatae, gcm, not, pks''
|-
| '''GataE MASO'''
| ''??????, 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)]''
|-
| '''Gcm MASO'''
| ''capk, dec, delta, elk, gatac, gatae, hmx, not, nrl''
|-
| '''Gsc MASO'''
| ''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)''
|-
| '''Hex MASO'''
| ''[dri, foxA, gcm, gsc, jun, krl, pmar1, tbr, z48 (18-24 h)]''
|-
| '''Hnf1 MASO'''
| ''[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)]''
|-
| '''Hnf6 MASO'''
| ''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)]''
|-
| '''Hox11/13b MASO'''
| ''blimp1, otx a, otx b, soxb1, wnt8, [Brn1/2/4, alx1, dac, delta, elk, hnf6, otxb1/2, soxC, z188 (18-27 h)]''
|-
| '''Krl MASO'''
| ''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)]''
|-
| '''MutantSu(H) MOE'''
| ''[endo16, sm50 (18, 24, 30 h)]''
|-
| '''Myc MASO'''
| ''[blimp1b, bra, dac, delta, endo16, eve, foxG, foxN2/3, foxP, gataC, gataE, gcm, hesC, hnf6, notch, soxB1, soxC, wnt8, z188 (18-27 h)]''
|-
| '''N MASO'''
| ''[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)]''
|-
| '''Otx-En'''
| ''dec, delta, elk, eve, gcm, otx a, pks, tbr''
|-
| '''OtxHD MASO'''
| ''[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)]''
|-
| '''Otxa MASO'''
| ''[alx1, blimp1b, bra, endo16, eve, foxG, foxP, foxa, foxb, gatac, gatae, gcm, hox11/13b, myc, soxC, soxb1, tgif, unc4.1, z188 (18-27 h)]''
|-
| '''Pmar1 MOE'''
| ''blimp1, elk, foxa, hnf6, krl, sm30, wnt8''
|-
| '''Pmar1-En'''
| ''blimp1, elk, foxa, hnf6, sm30, wnt8''
|-
| '''SoxC MASO'''
| ''[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)]''
|-
| '''Soxb1 MASO'''
| ''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)]''
|-
| '''Soxb1 MOE'''
| ''blimp1, dri, endo16, hnf6, tbr''
|-
| '''Soxb1-En'''
| ''alx1 (12 h), [bra, delta, endo16, ets-1, eve, foxa, foxb, gatac, gcm, hox11/13b, krl, msp130, pm27, sm50, wnt8 (18, 24 h)]''
|-
| '''Tbr MASO'''
| ''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)]''
|-
| '''Tel MASO'''
| ''[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)]''
|-
| '''Tgif MASO'''
| ''[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)]''
|}


Yuh, C.-H., Bolouri, H. and Davidson, E. H. cis-Regulatory logic in the endo16 gene: Switching from a specification to a differentiation mode of control. Development 128, 617-628, 2001.
=== Footnotes ===
<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=37679  [open<nowiki>]</nowiki>]</span>


Zeller, R. W., Coffman, J. A., Harrington, M. G., Britten, R. J. and Davidson, E. H. SpGCF1, a sea urchin embryo transcription factor, exists as five nested variants encoded by a single mRNA. Dev. Biol. 169, 713-727, 1995.
<sup>1</sup>Must be affected indirectly via intercellular signaling because Bra is not present in cells where these genes are active.
<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=35795  [open<nowiki>]</nowiki>]</span>


Arnone, M. and Davidson, E. H. The hardwiring of development: Organization and function of genomic regulatory systems. Development 124, 1851-1864, 1997.
<sup>2</sup>At 30 h affected indirectly via cell signaling, since at 30 h Dri and Gsc are expressed only in OE.


Arnone, M. I., Martin, E. L. and Davidson. E. H. Cis-regulation downstream of cell type specification: A single compact element controls the complex expression of the CyIIa gene in sea urchin embryos. Development 125, 1381-1395, 1998.
<sup>3</sup>Thought to be indirect input, via GataE.
<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=36858  [open<nowiki>]</nowiki>]</span>
 
<sup>4</sup>Probably via GataC.
 
<sup>5</sup>Probably via Bra.
 
<sup>6</sup>Probably in OE where both Elk and Lim1 are expressed then.
 
<sup>7</sup>Probably indirect via Gcm.
 
<sup>8</sup>Probably indirect via ''gcm''.
 
<sup>9</sup>The inputs inferred from effects on ''endo16''.
 
<sup>10</sup>Effect on ''endo16'' is via Ui since no necessary GataE site in ''endo16''.
 
<sup>11</sup>Probably via ''ets1''; based on ECRA.
 
<sup>12</sup>Indirect, because rescued by ''blimp1'' MOE.
 
<sup>14</sup>Probably indirect via ''elk''.
 
<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.
 
<sup>17</sup>Likely indirect via ''gatae.''
 
<sup>18</sup>Late Krl effects likely to be indirect results of effects of Krl loss on endomesoderm specification (Howard ''et al''., 2000).
 
<sup>19</sup>Obviously indirect via ''pmar1.''
 
<sup>20</sup>Only when ''dri'' is expressed in OE (>30 h).
 
<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.
 
<sup>22</sup>Must be indirect because direct ''sm50'' inputs are known.
 
<sup>23</sup>Normalized to different standards in same run, i.e., ubiquitin and 18S rRNA.
 
<sup>24</sup> ''alx1'' expressed specifically in pmc's; discovered by Ettensohn ''et al''.
 
<sup>26</sup>In collaboration with R. and L. Angerer who provided the samples measured.
 
<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).
 
<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).
 
<sup>30</sup>Not indirect via GataE because N MASO does not affect ''gatac'' though dnN does.
 
<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.
 
<sup>32</sup>Effect on initial phase of ''gatac'' expression, before it becomes exclusive with ''gcm'' (oral vs aboral and lateral).
 
<sup>33</sup>Could be indirect via Ets1 effect on ''tbr''; effect of Ets1 on ''foxb'' is stronger than ''tbr'' effect on ''foxb''.
 
<sup>34</sup>At least early (<24 h) effects on the three ''fvmo'' genes probably via ''gcm''.
 
<sup>35</sup>Via ''dri'' (see Amore ''et al''., 2002).
 
<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.
 
<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.
 
<sup>40</sup>Very possibly indirect via ''dri''.
 
<sup>41</sup>Unlikely a direct transcriptional effect, since ''eve'' expression is not affected by Soxb1-Eng MOE.
 
<sup>42</sup>Possibly indirect.
 
<sup>43</sup>Likely via ''dri.''
 
<sup>45</sup>Probably in OE because most ''gsc'' expression at 24 h is there.
 
<sup>47</sup>Double perturbation results show both inputs, Alx1 and Ets1, are required when indicated.
 
<sup>48</sup>Data for mesenchyme blastula stage of Lytechinus variegatus
 
<sup>49</sup>Probably Indirect
 
<sup>50</sup>Unc4.1 is expressed in the aboral veg1 ectoderm, starting at 24h; effect must be indirect

Revision as of 18:36, 26 March 2020

QPCR Data Relevant to Endomesoderm Network

Perturbation Ct:[Ub-C]-[Ub-Exp]

May 18, 2010

Ub, ubiquitin mRNA control used for internal standardization; CT, 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(1.94CT), 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 CT 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.


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

Perturbations

Perturbation: Genes not affected or shown to be affected only indirectly (0 to 24h, unless otherwise noted)
Alx1 MASO 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)]
Blimp1b MASO bra, hox11/13b, lim1, [dac, delta, hesC, msx, notch (18-27 h)]
Blimp1b-En dec, dpt, endo16, foxa, gatae, gcm, not, nrl, otx a, pks, pmar1, soxb1, tbr
Bra MASO 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)]
Brn1/2/4 MASO [Brn1/2/4, otxb1/2 (18, 30, 45 h)], [gatae, hox11/13b (45 h)]
Cad MOE dec, elk, endo16, foxc, hnf6, nrl, soxb1, tbr, z12-1
Dac MASO [blimp1b, bra, delta, eve, foxN2/3, gataC, gcm, hesC, myc, notch, soxB1, soxC, wnt8, z188 (18-27 h)]
DnN MOE 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
Dri MASO 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)]
Dri-En delta, dri (in pmc's), ets1, hnf6, pmar1, tbr, z12-1 (16-20 h)
Elk-En delta, elk, hnf6
Erg MASO [foxN2/3, gcm, pmar1, soxC, tbr, z48 (18-24 h)]
Ets1 MASO delta, endo16, eve, foxb, gcm, pmar1, sm30, tbr, [jun, krl, pks, z48 (18-24 h)]
Eve MASO 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)]
FoxA MASO 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)]
FoxB MASO cyclophillin, endo16, ets1, ficolin, foxa, gatae, hox11/13b, sm27, sm50, tbr, wnt8
FoxN2/3 MASO [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)]
GataC MASO bra, capk, delta, dpt, elk, eve, gatae, gcm, not, pks
GataE MASO ??????, 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)]
Gcm MASO capk, dec, delta, elk, gatac, gatae, hmx, not, nrl
Gsc MASO 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)
Hex MASO [dri, foxA, gcm, gsc, jun, krl, pmar1, tbr, z48 (18-24 h)]
Hnf1 MASO [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)]
Hnf6 MASO 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)]
Hox11/13b MASO blimp1, otx a, otx b, soxb1, wnt8, [Brn1/2/4, alx1, dac, delta, elk, hnf6, otxb1/2, soxC, z188 (18-27 h)]
Krl MASO 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)]
MutantSu(H) MOE [endo16, sm50 (18, 24, 30 h)]
Myc MASO [blimp1b, bra, dac, delta, endo16, eve, foxG, foxN2/3, foxP, gataC, gataE, gcm, hesC, hnf6, notch, soxB1, soxC, wnt8, z188 (18-27 h)]
N MASO [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)]
Otx-En dec, delta, elk, eve, gcm, otx a, pks, tbr
OtxHD MASO [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)]
Otxa MASO [alx1, blimp1b, bra, endo16, eve, foxG, foxP, foxa, foxb, gatac, gatae, gcm, hox11/13b, myc, soxC, soxb1, tgif, unc4.1, z188 (18-27 h)]
Pmar1 MOE blimp1, elk, foxa, hnf6, krl, sm30, wnt8
Pmar1-En blimp1, elk, foxa, hnf6, sm30, wnt8
SoxC MASO [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)]
Soxb1 MASO 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)]
Soxb1 MOE blimp1, dri, endo16, hnf6, tbr
Soxb1-En alx1 (12 h), [bra, delta, endo16, ets-1, eve, foxa, foxb, gatac, gcm, hox11/13b, krl, msp130, pm27, sm50, wnt8 (18, 24 h)]
Tbr MASO 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)]
Tel MASO [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)]
Tgif MASO [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)]

Footnotes

1Must be affected indirectly via intercellular signaling because Bra is not present in cells where these genes are active.

2At 30 h affected indirectly via cell signaling, since at 30 h Dri and Gsc are expressed only in OE.

3Thought to be indirect input, via GataE.

4Probably via GataC.

5Probably via Bra.

6Probably in OE where both Elk and Lim1 are expressed then.

7Probably indirect via Gcm.

8Probably indirect via gcm.

9The inputs inferred from effects on endo16.

10Effect on endo16 is via Ui since no necessary GataE site in endo16.

11Probably via ets1; based on ECRA.

12Indirect, because rescued by blimp1 MOE.

14Probably indirect via elk.

15Weak effect 18 h only, probably not significant, since wnt8 expression is disappearing in gatae domain at 18 h. Effect seen is probably via Otx which represses wnt8 in this period.

17Likely indirect via gatae.

18Late Krl effects likely to be indirect results of effects of Krl loss on endomesoderm specification (Howard et al., 2000).

19Obviously indirect via pmar1.

20Only when dri is expressed in OE (>30 h).

21Possibly indirect via, because if there were an Otx site in gatac gene effect would have been seen earlier than 24 h.

22Must be indirect because direct sm50 inputs are known.

23Normalized to different standards in same run, i.e., ubiquitin and 18S rRNA.

24 alx1 expressed specifically in pmc's; discovered by Ettensohn et al.

26In collaboration with R. and L. Angerer who provided the samples measured.

27Likely 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).

28Weak 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).

30Not indirect via GataE because N MASO does not affect gatac though dnN does.

31Indirect effects on gatac does not turn on until after Tcf input is faded out, but all other inputs depend on endomesoderm specification.

32Effect on initial phase of gatac expression, before it becomes exclusive with gcm (oral vs aboral and lateral).

33Could be indirect via Ets1 effect on tbr; effect of Ets1 on foxb is stronger than tbr effect on foxb.

34At least early (<24 h) effects on the three fvmo genes probably via gcm.

35Via dri (see Amore et al., 2002).

37Implies late blastula pmc domain to mesoderm indirect effect on oral side, where gatac is then expressed in mesoderm: not yet understood.

38Since Gsc is a repressor (Angerer et al.) implies existence of mid-late blastula repressor of skeletogenic function controlled by gsc: perhaps a timing device.

40Very possibly indirect via dri.

41Unlikely a direct transcriptional effect, since eve expression is not affected by Soxb1-Eng MOE.

42Possibly indirect.

43Likely via dri.

45Probably in OE because most gsc expression at 24 h is there.

47Double perturbation results show both inputs, Alx1 and Ets1, are required when indicated.

48Data for mesenchyme blastula stage of Lytechinus variegatus

49Probably Indirect

50Unc4.1 is expressed in the aboral veg1 ectoderm, starting at 24h; effect must be indirect