Comment[ArrayExpressAccession]	E-GEOD-15808
Investigation Title	Transcription profiling of mouse lymphoid neoplasia shows changes in processing of 3 prime-UTR characterize clinically distinct tumor types
Comment[Submitted Name]	Global changes in processing of 3'-UTR characterize clinically distinct tumor types
Publication Title
Publication Author List
Publication DOI
PubMed ID
Experimental Design	unknown_experiment_design_type	transcription profiling by array
Experimental Design Term Source REF		EFO
Person Last Name	singh
Person First Name	priyam
Person Email	priyam.singh@jax.org
Person Address	Dr. Joel Graber, The Jackson Laboratory, 600 Main St, Bar Harbor, 04609, USA
Person Affiliation	The Jackson Laboratory
Person Roles	submitter
Public Release Date	2009-10-16
Comment[ArrayExpressSubmissionDate]	2009-04-24
Comment[GEOReleaseDate]	2009-10-08
Comment[SecondaryAccession]	GSE15808
Experiment Description	We used a novel probe-level microarray analysis, revealing connections between mRNA processing and lymphoid neoplasia, in a mouse leukemia model. Characteristic differences in mRNA processing, primarily in the 3’-untranslated region, distinguished histologically similar tumor subtypes with different survival characteristics. Gene sets with specific processing in each tumor subtype defined signatures useful for tumor subclassification, as demonstrated by internal cross-validation with up to 80% discrimination accuracy. A combination of mRNA expression and sequence analysis suggested that differences in isoform abundance likely arose from both alternative polyadenylation and differential degradation. Experiment Overall Design: 5 types of samples were analyzed with multiple biological replicates. Progenitor B-cells, mature B-cells were the control. LPC, APC, APN were the tumor cells. LPC (Lig4/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APC (Artemis/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APN (Artemis/P53 deficient cells developed pro-B lymphoma with N-myc amplification)
Protocol Name	P-G15808-3	P-G15808-1	P-G15808-2	P-G15808-4
Protocol Type	bioassay_data_transformation	specified_biomaterial_action	labeling	nucleic_acid_extraction
Protocol Description	MAS5 normalization	Single-cell suspensions for flow cytometric analysis of pro-B-cells, B-cells, and tumor samples were prepared by dispersion of bone marrow, spleen, or lymph nodes (respectively) using fine, sterile mesh.  Cell suspensions were prepared in RPMI 1640 medium containing with 10%fetal calf serum. Cell preparations were then stained with an antibody cocktail specific for B-lymphocytes, containing antibodies directed against the pan-B cell maker B220, and the developmental stage markers CD19, CD43, and IgM.  Flow cytometry was carried out using a Becton Dickinson FACSCalibur cytometer with CellQuest Pro acquisition software, and analyzed using FlowJo 2.0 software. Cell sorting to obtain purified populations of progenitor or mature B cells was carried out on a FACSvantage SE/DiVa cell sorter after staining of whole bone marrow or splenocyte preparations (respectively) with the same B-cell cocktail used for flow cytometry.  For histopathology, lymph node-derived tumor samples were treated with Bouin’s fixative and embedded in paraffin.  After sectioning, slides were stained with hematoxylin & eosin (H&E) prior to imaging.  At necropsy, lymphoma tissue samples were obtained from cervical lymphnode or thymus lymphoma foci, submerged in RNALater, and stored until processing for total RNA recovery. Normal pro-B-cells were sorted by fluorescence activated cell sorting (FACS) to obtain B220+ CD43+ IgM- cells from bone marrow of normal C57BL/6J mice and B-cells were the B220+ fraction from spleen of normal C57BL/6J mice, sorted by FACS.	Standard Affymetrix one-cycle labelling protocol	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Protocol Parameters				
Protocol Software				
SDRF File	E-GEOD-15808.sdrf.txt
Term Source Name	EFO
Term Source File	http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl