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No Probe Set Accession UNIGENE LocusLink Gene Name Symbol Description RefSeq Transcript ID FSK1 FSK2 CTRL1 CTRL2 FSK_mean CTRL_mean Fold Change T-test Note Link
1 1387760_a_at NM_02267148812 25231"one cut domain, family member 1" Onecut1 "gb:NM_022671.1 /DB_XREF=gi:12083604 /GEN=Hnf6 /FEA=FLmRNA /CNT=1 /TID=Rn.48812.1 /TIER=FL /STK=1 /UG=Rn.48812 /LL=25231 /DEF=Rattus norvegicus Hepatocyte nuclear factor 6 (Hnf6), mRNA. /PROD=hepatocyte nuclear factor 6 /FL=gb:NM_022671.1" NM_022671 72.8 69.7 59.9 58.7 71.2 59.3 1.2 0.048 "all, " Rat_CRE_Prediction PC12_Expression_B
2 1371034_at BF39618948812 25231"one cut domain, family member 1" Onecut1 gb:BF396189 /DB_XREF=gi:11381201 /DB_XREF=UI-R-BS2-bdv-g-06-0-UI.s1 /CLONE=UI-R-BS2-bdv-g-06-0-UI /FEA=mRNA /CNT=7 /TID=Rn.48812.2 /TIER=ConsEnd /STK=0 /UG=Rn.48812 /LL=25231 /UG_GENE=Hnf6 /UG_TITLE=Hepatocyte nuclear factor 6 NM_022671 62.3 60.5 52.7 55.2 61.4 54.0 1.1 0.178 "all, " Rat_CRE_Prediction PC12_Expression_B

The PC12 data is from the following source (GSE2071 at GEO)::
See reference: Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S,
Dunn JJ, Mandel G, Goodman RH.

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell. 2004 Dec 29;119(7):1041-54.

Sample Description:
A comparison of forskolin-induced mRNA vs. an inactive control in the rat PC12 cell pheochromocytoma cell line.
PC12 cells (passage 22) were cultured at 5% CO2 in a 37 C incubator. The growth medium was DMEM (high glucose, Invitrogen) supplemented with 25mM HEPES, 10% FCS, 5% FBS and 1x Pen/Strep (Invitrogen). 1x106 cells were starved overnight in DMEM+25 mM HEPES and treated with 10 uM 1,9 dideoxy forskolin or forskolin for 60 min. The final DMSO concentration was 0.05%. Total RNA was purified using Trizol (Invitrogen) according to the manufacturers protocol. An additional round of purification was conducted using Rneasy columns (Qiagen) according to the manufacturers protocol. cRNA was synthesized and labeled according to standard Affymetrix protocols. 2 biological replicates for the forskolin and 1,9 dideoxy forskolin conditions were run on Affymetrix RAE230 A and B chips for a total of 8 hybridizations.

Microarray Analysis:
Array data was analyzed using the RMA method. Expression values showing here are transformed back from log range.

Guidelines for Choosing cAMP Induced Genes in this Data Set:
Note the values are transformed back from log range (2^RMA_value) so it is easiler to read for human eyes.
The fold change of Forskolin treated sample over control is listed, as well as the p-value from T-test. User can choose an fold change cutoff (e.g. 1.5) together with p-value cutoff (e.g. 0.05) to pick cAMP induced genes.