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Series GSE21554 Query DataSets for GSE21554
Status Public on Aug 30, 2012
Title An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Main Study)
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Expression profiling by array
Methylation profiling by array
Summary Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design For aCGH, 21 cases were done under accession number GSE35425.
21 fresh frozen splenic samples from patients with SMZL were hybridized against a reference control of pooled PBMC genomic DNA from 10 normal subjects. High-resolution oligonucleotide analysis of copy number variations in splenic marginal zone lymphoma (SMZL) in regions of recurrent alteration. Regions included on the array: 7q (2k resolution) and regions of interest on chromosomes 3q, 6q and 9q at 12k resolution.

For gene expression microarrays, 24 cases were done under accession number GSE35426.
A total of 48 cases of SMZL (including 15 with 7q deletion) were analysed using the Affymetrix HG-U133 Plus 2.0 platform (Affymetrix, Santa Clara, California, USA). Arrays were performed according to the manufacturer’s instructions. Briefly, RNA was extracted from snap frozen tissues with >70% tumour cells using the RNEasy extraction kit (Qiagen) and subjected to DNAse treatment (Turbo DNAse kit, Ambion). RNA integrity was assessed using an Agilent 2100 Bioanalyzer. cDNA synthesis was carried out with 2ug RNA using the GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix), followed by in vitro transcription with biotin-labelled nucleotides using GeneChip® IVT Labeling Kit. Biotinylated cRNA was purified and hybridized to the Affymetrix HG-U133 Plus 2.0 chips in a GeneChip® Hybridisation Oven 640 at 45oC for 14 hours. The arrays were then washed and stained using the Fluidics station 450 system (Affymetrix). The arrays were scanned using the Affymetrix GeneArray® Scanner 3000. Hybridisation and labelling controls were included according to the manufacturer’s instructions, and quality control analysis of microarrays was performed to published standards.

For methylation arrays, 24 cases were done under accession number GSE35424.
Epigenetic methylation analysis was performed using the Infinium Human Methylation 27 array (Illumina, San Diego, California, USA). The array contained 27,568 CpG islands within the proximal promoter regions of transcription start sites of 14,475 RefSeq genes, including 12,883 well annotated genes (NCBI CCDS database: Build 36). The methylation array was carried out in 12 SMZL (6 cases with 7q deletion), 6 follicular lymphomas (FL) and 6 mantle cell lymphomas (MCL) as per the manufacturer’s instructions. Briefly, 2μg genomic DNA extracted from frozen tissues with >70% tumour cells was bisulphite modified using the EZ DNA Methylation Kit (Zymo Research Corporation). Bisulphite modified DNA was then amplified using the MSM master mix (Illumina) and incubated at 37oC for 22 hours. Amplified DNA was then fragmented and hybridised to BeadChips in an Illumina Hybridisation Oven at 48oC for 18 hours. Following hybridisation, single base extension of hybridised DNA using hapten labelled bases was performed. Staining was then developed using immunochemical stains catalysed by the haptens, and the arrays washed. The chips were scanned using the BeadArray™ Reader (Illumina) and the BeadScan™ software (Illumina) using the Infinium Methylation Scan setting. The scanned data was then analysed in GenomeStudio™ (Illumina) using the Methylation analysis module.

**Samples from Series GSE35278 and GSE35348 was also used in this study:

GSE35278: Oligo aCGH on 35 SMZL cases were carried out by the Mayo clinic group using the Agilent Oligo aCGH 244A platform (6.4Kb resolution)

GSE35348: Gene expression profiling was carried out by the Mayo clinic group on 24 SMZL cases using the Affymetrix HG-U133 plus2 gene expression microarrays
 
Contributor(s) Watkins AJ, Hamoudi RA, Zeng N, Yan Q, Huang Y, Liu H, Zhang J, Braggio E, Fonseca R, de Leval L, Isaacson PG, Wotherspoon A, McPhail ED, Dogan A, Du MQ
Citation(s) 23028731
Submission date Apr 27, 2010
Last update date Mar 25, 2019
Contact name Alan J Watkins
E-mail(s) a.j.watkins@doctors.org.uk
Organization name University of Cambridge
Street address Addenbrooke's Hospital
City Cambridge
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platforms (3)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
GPL10383 Agilent MQD Lab Human 60K probes v1.0 - custom oligo array of 2Kb resolutoin covering 7q region
Samples (69)
GSM540686 Custom_Oligo_2Kb_aCGH_SMZL1
GSM540687 Custom_Oligo_2Kb_aCGH_SMZL2
GSM540688 Custom_Oligo_2Kb_aCGH_SMZL3
This SuperSeries is composed of the following SubSeries:
GSE35424 An integrated genomic and expression analysis of 7q deletion in SMZL (Illumina Infinium Human Methylation 27 array)
GSE35425 An integrated genomic and expression analysis of 7q deletion in SMZL (Oligo aCGH)
GSE35426 An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Affymetrix HG-U133plus2 gene expression microarray)
Relations
BioProject PRJNA126223

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21554_RAW.tar 242.9 Mb (http)(custom) TAR (of CEL, TXT)

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