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Sample GSM1354601 Query DataSets for GSM1354601
Status Public on Mar 24, 2015
Title genomic DNA from T-ALL sample 29
Sample type genomic
 
Source name clinical T-ALL sample
Organism Homo sapiens
Characteristics tissue/cell type: clinical T-cell acute lymphoblastic leukemia (T-ALL)
sample type: Tumor
cimp subgroup: CIMP+
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted according to standard protocols and DNA purity and concentration determined by spechtrophotometry.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.
Scan protocol Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting
Description 29
BM T-ALL sample
Data processing GenomeStudio software v2010.3 with the Methylation module. Intergenic CpG-sites, CpG-sites at chromosome X and Y, Detection P-value > 0.05 and nbeads<=3 were filtered (set to NA). Probe type normalization was performed using the BMIQ Method.
 
Submission date Mar 20, 2014
Last update date Mar 24, 2015
Contact name Sofie Degerman
E-mail(s) sofie.degerman@umu.se
Organization name Umeå University
Department Medical Biosciensces
Lab Pathology
Street address NUS, Blg 6M, 2nd floor
City Umeå
State/province Sweden
ZIP/Postal code 90185
Country Sweden
 
Platform ID GPL13534
Series (2)
GSE56068 Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias [methylation]
GSE56070 Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias

Data table header descriptions
ID_REF
VALUE Average Beta (processed)
29.Detection.Pval

Data table
ID_REF VALUE 29.Detection.Pval
cg00000029 0.71704548 0
cg00000108 0.988940605 0
cg00000109 0.923815439 0
cg00000165 0
cg00000236 0.915210843 0
cg00000289 0.585801152 0
cg00000292 0.96501392 0
cg00000321 0.628674294 0
cg00000363 0
cg00000622 0.01121717 0
cg00000658 0.908474336 0
cg00000714 0.14265088 0
cg00000721 0.985658877 0
cg00000734 0.041921004 0
cg00000769 0.02726444 0
cg00000807 0.888628571 0
cg00000884 0.953125303 0
cg00000905 0.048604242 0
cg00000924 0.716951385 0
cg00000948 0

Total number of rows: 485577

Table truncated, full table size 10019 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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