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Series GSE8293 Query DataSets for GSE8293
Status Public on Jun 14, 2008
Title Transcriptomic Analysis of the Effects of Cyclopamine Exposure on Xenopus Limb Development
Organism Xenopus laevis
Experiment type Expression profiling by array
Summary Study of the tetrapod limb has contributed a great deal to our understanding of developmental pathways and how changes to these pathways affect morphology. Most data on tetrapod limb development is known from amniotes, with far less known about genetic mechanisms of limb development in amphibians. To better understand the mechanisms of limb development in anuran amphibians, we use cyclopamine to inhibit Hedgehog signaling at various stages of limb development in Xenopus. We use transcriptomic analysis following cyclopamine exposure to understand the downstream effects of Hedgehog inhibition on gene expression. We find many aspects of Hedgehog function appear to be conserved with respect to amniotes, including the responses of ptc genes, gremlin, bmp2, and the autoregulatory property of shh. We show that, as was proposed based on experiments in chick, Sonic hedgehog plays two distinct roles in limb development – specification of digit number and specification of digit identity. In contrast to these points of conservation, we find that Hedgehog signaling is required for the maintenance of early limb bud outgrowth in Xenopus, a requirement not known for any other tetrapod.
Keywords: pharmacological signal inhibition response
 
Overall design Eight microarray experiments were performed using RNA extracted from batches of hindlimbs dissected from Xenopus laevis tadpoles. Four of these were experimental groups exposed to cyclopamine at 1 µg/ml for 24 hours before animal fixation, and four were experimental groups exposed to the ethanol, the cyclopamine vehicle, at the same concentration used for cyclopamine vehicle for 24 hours. Each pool of RNA consisted of material from 18-22 hindlimb buds. Two experimental groups and two control groups were from one clutch of tadpoles, and the other four pools were from another clutch. Both samples within each of four paired groups (experimental vs. control) were exposed and processed simultaneously.
 
Contributor(s) Stopper GF, Richards-Hrdlicka K, Wagner GP
Citation(s) 19393085
Submission date Jun 26, 2007
Last update date Mar 17, 2012
Contact name Geffrey Foresman Stopper
Organization name Yale University
Department Department of Ecology & Evolutionary Biology
Street address 165 Prospect St.
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platforms (1)
GPL1318 [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array
Samples (8)
GSM205790 Ethanol Control 1 (Clutch A, Group 1, N1)
GSM205791 Ethanol Control 2 (Clutch A, Group 2, N6)
GSM205792 Ethanol Control 3 (Clutch B, Group 1, P2)
Relations
BioProject PRJNA101257

Processed data matrix header descriptions
GeneChip Probe Set ID
Ethanol Control Mean Expression Value
Cyclopamine Experimental Mean Expression Value
Fold Change (Experimental/Control)
Paired t-test p-value
SAM q-value
Cyber-T Bayes p-value
Gene Title
Gene Symbol
Target Description
GO Terms

Data table
GeneChip Probe Set ID Ethanol Control Mean Expression Value Cyclopamine Experimental Mean Expression Value Fold Change (Experimental/Control) Paired t-test p-value SAM q-value Cyber-T Bayes p-value Gene Title Gene Symbol Target Description GO Terms
AFFX-BioB-3_at 257.4 249.95 0.971056721 0.690150229 87.49453611 0.8319433 --- --- E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2755-3052 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioB-5_at 292.75 357.375 1.220751494 0.198289253 73.7988289 0.1812656 --- --- E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2032-2305 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioB-M_at 353.85 375.45 1.061042815 0.625608162 84.98679812 0.6876334 --- --- E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2482-2739 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioC-3_at 945.65 935.875 0.989663195 0.745751804 87.49453611 0.9318484 --- --- E. coli /GEN=bioC /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4626-4878 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioC-5_at 843.475 840.175 0.996087614 0.957934706 83.76804834 0.9749382 --- --- E. coli /GEN=bioC /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4218-4566 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioDn-3_at 3001.625 2979.1 0.992495731 0.90456247 82.82396994 0.9426597 --- --- E. coli /GEN=bioD /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 5286-5570 of gb:J04423.1, not 100% identical /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-BioDn-5_at 2039.55 2012.1 0.986541149 0.772466244 87.49453611 0.9011158 --- --- E. coli /GEN=bioD /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4980-5256 of gb:J04423.1, not 100% identical /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. GO:0009102|GO:0008152|GO:0009058|GO:0009236|GO:0004015|GO:0008483|GO:0016740|GO:0030170|GO:0003824|GO:0004076|GO:0005506|GO:0046872|GO:0051536|GO:0051537|GO:0051539|GO:0008710|GO:0016769|GO:0008168|GO:0008757|GO:0000166|GO:0000287|GO:0004141|GO:0005524|GO:0016874|GO:0042242
AFFX-CreX-3_at 16150.475 13990.75 0.866274831 0.196640064 28.94853758 0.07857751 --- --- Bacteriophage P1 /GEN=cre /DB_XREF=gb:X03453.1 /NOTE=SIF corresponding to nucleotides 1089-1495 of gb:X03453.1 /DEF=Bacteriophage P1 cre gene for recombinase protein. GO:0006310|GO:0006313|GO:0015074|GO:0003677
AFFX-CreX-5_at 11764.55 11122.225 0.945401652 0.404498489 51.36686887 0.5214957 --- --- Bacteriophage P1 /GEN=cre /DB_XREF=gb:X03453.1 /NOTE=SIF corresponding to nucleotides 513-1047 of gb:X03453.1 /DEF=Bacteriophage P1 cre gene for recombinase protein. GO:0006310|GO:0006313|GO:0015074|GO:0003677
AFFX-DapX-3_at 18.775 11.325 0.603195739 0.564545743 87.49453611 0.3875494 --- --- B. subtilis /GEN=jojG /DB_XREF=gb:L38424.1 /NOTE=SIF corresponding to nucleotides 2684-3130 of gb:L38424.1 /DEF=Bacillus subtilis dihydropicolinate reductase (jojE) gene, complete cds; poly(A) polymerase (jojI) gene, complete cds; biotin acetyl-CoA-carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes, complete cds's. GO:0006350|GO:0006355|GO:0006464|GO:0008652|GO:0009085|GO:0009089|GO:0019877|GO:0001680|GO:0006396|GO:0008033|GO:0042245|GO:0019242|GO:0009058|GO:0005737|GO:0016020|GO:0016021|GO:0003677|GO:0003824|GO:0004077|GO:0016564|GO:0016874|GO:0008839|GO:0016491|GO:0000049|GO:0000166|GO:0000287|GO:0003723|GO:0004810|GO:0005524|GO:0016437|GO:0016740|GO:0016779|GO:0046872|GO:0008929|GO:0016829|GO:0016757
AFFX-DapX-5_at 10.8 12.8 1.185185185 0.693108042 84.98679812 0.759745 --- --- B. subtilis /GEN=dapB /DB_XREF=gb:L38424.1 /NOTE=SIF corresponding to nucleotides 1428-1926 of gb:L38424.1 /DEF=Bacillus subtilis dihydropicolinate reductase (jojE) gene, complete cds; poly(A) polymerase (jojI) gene, complete cds; biotin acetyl-CoA-carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes, complete cds's. GO:0006350|GO:0006355|GO:0006464|GO:0008652|GO:0009085|GO:0009089|GO:0019877|GO:0001680|GO:0006396|GO:0008033|GO:0042245|GO:0019242|GO:0009058|GO:0005737|GO:0016020|GO:0016021|GO:0003677|GO:0003824|GO:0004077|GO:0016564|GO:0016874|GO:0008839|GO:0016491|GO:0000049|GO:0000166|GO:0000287|GO:0003723|GO:0004810|GO:0005524|GO:0016437|GO:0016740|GO:0016779|GO:0046872|GO:0008929|GO:0016829|GO:0016757
AFFX-DapX-M_at 41.225 25.05 0.607640995 0.091783481 59.07429921 0.1432825 --- --- B. subtilis /GEN=dapB, jojF /DB_XREF=gb:L38424.1 /NOTE=SIF corresponding to nucleotides 2020-2580 of gb:L38424.1, not 100% identical /DEF=Bacillus subtilis dihydropicolinate reductase (jojE) gene, complete cds; poly(A) polymerase (jojI) gene, complete cds; biotin acetyl-CoA-carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes, complete cds's. GO:0006350|GO:0006355|GO:0006464|GO:0008652|GO:0009085|GO:0009089|GO:0019877|GO:0001680|GO:0006396|GO:0008033|GO:0042245|GO:0019242|GO:0009058|GO:0005737|GO:0016020|GO:0016021|GO:0003677|GO:0003824|GO:0004077|GO:0016564|GO:0016874|GO:0008839|GO:0016491|GO:0000049|GO:0000166|GO:0000287|GO:0003723|GO:0004810|GO:0005524|GO:0016437|GO:0016740|GO:0016779|GO:0046872|GO:0008929|GO:0016829|GO:0016757
AFFX-LysX-3_at 23.025 27.25 1.1834962 0.43051274 83.76804834 0.7015261 --- --- B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 1061-1343 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20). GO:0008652|GO:0009085|GO:0009089|GO:0003824|GO:0008836|GO:0016829|GO:0016831
AFFX-LysX-5_at 3.225 8.125 2.519379845 0.23640849 82.82396994 0.09721877 --- --- B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 387-658 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20). GO:0008652|GO:0009085|GO:0009089|GO:0003824|GO:0008836|GO:0016829|GO:0016831
AFFX-LysX-M_at 18.575 21.375 1.150740242 0.73074192 84.98679812 0.7840818 --- --- B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 720-990 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20). GO:0008652|GO:0009085|GO:0009089|GO:0003824|GO:0008836|GO:0016829|GO:0016831
AFFX-PheX-3_at 10.225 20.275 1.982885086 0.065778543 78.82515531 0.1916951 --- --- B. subtilis /GEN=pheB /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2885-3326 of gb:M24537.1, not 100% identical /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds. GO:0030435|GO:0050896|GO:0008152|GO:0008652|GO:0009073|GO:0009094|GO:0005622|GO:0016301|GO:0016740|GO:0000166|GO:0005525|GO:0004664|GO:0016597|GO:0016829
AFFX-PheX-5_at 6.025 4.3 0.713692946 0.489539262 87.49453611 0.4562762 --- --- B. subtilis /GEN=pheA /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2028-2375 of gb:M24537.1, not 100% identical /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds. GO:0030435|GO:0050896|GO:0008152|GO:0008652|GO:0009073|GO:0009094|GO:0005622|GO:0016301|GO:0016740|GO:0000166|GO:0005525|GO:0004664|GO:0016597|GO:0016829
AFFX-PheX-M_at 3.95 9.675 2.449367089 0.210867233 82.82396994 0.1646832 --- --- B. subtilis /GEN=pheA /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2437-2828 of gb:M24537.1 /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds. GO:0030435|GO:0050896|GO:0008152|GO:0008652|GO:0009073|GO:0009094|GO:0005622|GO:0016301|GO:0016740|GO:0000166|GO:0005525|GO:0004664|GO:0016597|GO:0016829
AFFX-r2-Bs-dap-3_at 1.925 10.5 5.454545455 0.429790487 82.82396994 0.1563597 --- --- B. subtilis /GEN=jojG /DB_XREF=gb:L38424.1 /NOTE=SIF corresponding to nucleotides 2634-3089 of gb:L38424.1 /DEF=Bacillus subtilis dihydropicolinate reductase (jojE) gene, complete cds; poly(A) polymerase (jojI) gene, complete cds; biotin acetyl-CoA-carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes, complete cds's. GO:0006350|GO:0006355|GO:0006464|GO:0008652|GO:0009085|GO:0009089|GO:0019877|GO:0001680|GO:0006396|GO:0008033|GO:0042245|GO:0019242|GO:0009058|GO:0005737|GO:0016020|GO:0016021|GO:0003677|GO:0003824|GO:0004077|GO:0016564|GO:0016874|GO:0008839|GO:0016491|GO:0000049|GO:0000166|GO:0000287|GO:0003723|GO:0004810|GO:0005524|GO:0016437|GO:0016740|GO:0016779|GO:0046872|GO:0008929|GO:0016829|GO:0016757
AFFX-r2-Bs-dap-5_at 10.475 5.25 0.501193317 0.183702267 86.59224873 0.2472724 --- --- B. subtilis /GEN=dapB /DB_XREF=gb:L38424.1 /NOTE=SIF corresponding to nucleotides 1439-1846 of gb:L38424.1 /DEF=Bacillus subtilis dihydropicolinate reductase (jojE) gene, complete cds; poly(A) polymerase (jojI) gene, complete cds; biotin acetyl-CoA-carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes, complete cds's. GO:0006350|GO:0006355|GO:0006464|GO:0008652|GO:0009085|GO:0009089|GO:0019877|GO:0001680|GO:0006396|GO:0008033|GO:0042245|GO:0019242|GO:0009058|GO:0005737|GO:0016020|GO:0016021|GO:0003677|GO:0003824|GO:0004077|GO:0016564|GO:0016874|GO:0008839|GO:0016491|GO:0000049|GO:0000166|GO:0000287|GO:0003723|GO:0004810|GO:0005524|GO:0016437|GO:0016740|GO:0016779|GO:0046872|GO:0008929|GO:0016829|GO:0016757

Total number of rows: 15611

Table truncated, full table size 5598 Kbytes.




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Supplementary file Size Download File type/resource
GSE8293_RAW.tar 17.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record
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