Comment[ArrayExpressAccession] E-GEOD-49253 MAGE-TAB Version 1.1 Public Release Date 2014-04-01 Investigation Title SUDHL-4 cells: suspension vs. co-cultured with HK cells Comment[Submitted Name] SUDHL-4 cells: suspension vs. co-cultured with HK cells Experiment Description We first performed miRNA analysis on SU-4 cells in suspension, and after 24 and 48 h of HK co-culture. To ensure that no HK cell contamination occurred, SU-4 cells in suspension and after co-culture were purified by CD19-positive magnetic selection, followed by total RNA isolation. Two-condition experiment, S4 vs. S4+HK cells. Biological replicates: 2 suspension controls, 2 co-cultured with HK cells, independently grown and harvested. One replicate per array. 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 tao Lin Lwin Tao Person First Name jianguo Jianhong Tint Jianguo Person Email jianguo.tao@moffitt.org Person Affiliation H Lee Moffitt Cancer Center Person Phone 813-745-3885 Person Address H Lee Moffitt Cancer Center, 12902 Magnolia Dr, Tampa, FL, USA Person Roles submitter Protocol Name P-GSE49253-1 P-GSE49253-4 P-GSE49253-5 P-GSE49253-2 P-GSE49253-3 P-GSE49253-6 Protocol Description Data were processed by subtracting background and normalizing the signals using a LOWESS filter (locally weighted regression) method to remove system-related variations.A detectable transcript was defined by fulfilling the following criteria: 1) signal intensity >3× background standard deviation; 2) spot CV (standard deviation/signal intensity) <0.5; and 3) signals from at least 50% of the repeating probes above detection level. ID_REF = VALUE = Normalized log2 ratio (Cy5/Cy3) RNA samples for comparison were labeled with tag-specific dendrimer Cy3 and Cy5 fluorescent dyes. The melting temperature of detection probes was balanced by incorporating varying numbers of modified nucleotides with increased binding affinities. For quality control, we hybridized a group of control oligos to evaluate array quality and mixed a fixed amount of 20-mer RNA oligos to samples as external controls. SU-4 cells in suspension and after 24 and 48 h of co-culture with HK cells were sorted out by CD19 magnet beads, and isolated total RNA was then applied for miRNA array assay. RNA samples for miRNA microarray or miRNA quantification, total RNA enriched with small RNAs was isolated by using mirVana miRNA isolation kit (Ambion) according to the manufacturer's protocol. Axon GenePix 4000B Microarray Scanner. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name TIME CELL TYPE GROWTH TYPE Experimental Factor Type time cell type growth type Publication Title A microenvironment-mediated c-Myc/miR-548m/HDAC6 amplification loop in non-Hodgkin B cell lymphomas. Publication Author List Lwin T, Zhao X, Cheng F, Zhang X, Huang A, Shah B, Zhang Y, Moscinski LC, Choi YS, Kozikowski AP, Bradner JE, Dalton WS, Sotomayor E, Tao J PubMed ID 24216476 Publication DOI 10.1172/JCI64210 Comment[SecondaryAccession] GSE49253 Comment[GEOReleaseDate] 2014-04-01 Comment[ArrayExpressSubmissionDate] 2013-07-26 Comment[GEOLastUpdateDate] 2014-04-01 Comment[AEExperimentType] transcription profiling by array Comment[AdditionalFile:Data1] GSE49253_readme.txt SDRF File E-GEOD-49253.sdrf.txt