Comment[ArrayExpressAccession]	E-GEOD-44048							
MAGE-TAB Version	1.1							
Public Release Date	2013-07-24							
Investigation Title	Human glioma cell line T98G: BAP-PCBP2 RIP vs. BAP-GFP RIP (Control)							
Comment[Submitted Name]	Human glioma cell line T98G: BAP-PCBP2 RIP vs. BAP-GFP RIP (Control)							
Experiment Description	RIP-Chip analysis of PCBP2 and identification of preferentially associated mRNAs. T98G cells were transfected transiently with BAP-tagged constructs. BAP-tagged proteins were biotinylated in vivo by the co-transfected hBirA enzyme. RNPs were recovered via precipitation with Steptavidin-sepharose beads. Finally, RNAs were purified and analyzed on microarrays. BAP-GFP as control was used in three independent sets of experiments. Two-condition experiment, BAP-PCBP2 vs. BAP-GFP cells. Biological replicates: 3 BAP-PCBP2 replicates, 3 BAP-GFP (Control) replicates							
Term Source Name	ArrayExpress	EFO						
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	peng	Han						
Person First Name	zhong	Wei						
Person Mid Initials	xiao							
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences							
Person Address	Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, China							
Person Roles	submitter							
Protocol Name	P-GSE44048-2	P-GSE44048-1	P-GSE44048-3	P-GSE44048-6	P-GSE44048-7	P-GSE44048-4	P-GSE44048-5	P-GSE44048-8
Protocol Description	Agilent Feature Extraction Software (v 7.0) was used for background subtraction and LOWESS normalization. ID_REF =  VALUE = normalized log2 ratio (Cy3/Cy5) representing test/reference B_G_7_13_1_NormSignal =  B_P_7_13_2_NormSignal =  flags = 	Agilent Feature Extraction Software (v 7.0) was used for background subtraction and LOWESS normalization. ID_REF =  VALUE = normalized log2 ratio (Cy3/Cy5) representing test/reference T-B+G-1_NormSignal =  T-B+P_NormSignal =  flags = 	Agilent Feature Extraction Software (v 7.0) was used for background subtraction and LOWESS normalization. ID_REF =  VALUE = normalized log2 ratio (Cy3/Cy5) representing test/reference B_G_7_17_1_NormSignal =  B_P_7_17_2_NormSignal =  flags = 	Add 2 μg of total RNA to a 1.5-mL microcentrifuge tube. Add 5 μL of T7 Primer into the tube that contain each tube now contains a total volume of 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Add 60 μL of Transcription Mix and incubate samples in a circulating water bath at 40°C for 2 hours. Add 10 μL DMSO to 4 μg above purified cRNA (6.6 μL), and add 3.4 μL 0.3M sodium bicarbonate (PH 9.0). Add the the 20 μL cRNA mixture to a fluorescent dye (Cy3 or Cy5), 25°C for 1 hours. Add 9 μL 4M Hydroxylamine, incubate for 15min at 25°C.	Mix 55 μL 2x GE Hybridization Buffer HI-RPM to 55 μL cRNA from Fragmentation Mix. Take the chip with 100 μL of the sample, 10rpm rolling hybridization for 17 hours at 65°C. Remove the chip to lotion 1, washing for 1 minutes. And take the chip into the lotion 2, washing for 1 minutes (37°C).	T98G cells were cultured in minimum essential medium and Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum, respectively. All cells were maintained at 37°C with 5% CO2.	Total RNA extracted using Trizol following manufacturer's instructions	Scanned on an Agilent G2565BA scanner.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Publication Title	RNA-binding protein PCBP2 modulates glioma growth by regulating FHL3.							
Publication Author List	Han W, Xin Z, Zhao Z, Bao W, Lin X, Yin B, Zhao J, Yuan J, Qiang B, Peng X							
PubMed ID	23585479							
Publication DOI	10.1172/JCI61820							
Comment[SecondaryAccession]	GSE44048							
Comment[GEOReleaseDate]	2013-07-24							
Comment[ArrayExpressSubmissionDate]	2013-02-04							
Comment[GEOLastUpdateDate]	2013-07-24							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-44048.sdrf.txt							
Experimental Factor Name	phenotype							
Experimental Factor Type	phenotype