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Sample GSM712179 Query DataSets for GSM712179
Status Public on Jul 30, 2012
Title OZ
Sample type RNA
 
Source name DLBCL cell line
Organism Homo sapiens
Characteristics cell line: OZ
cell type: Diffuse Large B cell Lymphoma
genotype: TP53/BCL2/CMYC mutation
Treatment protocol All the cells were non-treated
Growth protocol All the cells were grown in supplemented media (RPMI or Iscove)
Extracted molecule total RNA
Extraction protocol RNA from cell lines was isolated using the RNeasy Plus MIni kit (QIAGEN). RNA integrity was determined using the RNA 6000 Nano LabChip Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies). Ten micrograms of total RNA was used to synthesize double-stranded cDNA using Superscript III (Invitrogen), but using a modified oligo-d(T) primer (Supplemental Table 2). The second strand was synthesized for 2 hours at 16°C in a reaction containing 30 μl of 5× second-strand buffer (Invitrogen), 90 μl of RNAse-free water, 3 μl dNTP (10 mM), 1 μl of BSA (1 μg/μl), 1 μl of E. coli DNA ligase (10 U/μl) (Invitrogen), 4 μl E. coli DNA polymerase I (10 U/μl) (Invitrogen), and 1 μl of RNAse H (2 U/μl) (Invitrogen). Finally, 2 μl of T4 DNA Polymerase (5 U/μl) (Invitrogen) was added and the reaction incubated at 16°C for another 10 minutes. Reactions were cleaned with QIAGEN’s QIAquick PCR Purification Kit
Label Cy3/Cy5
Label protocol Labeling was performed by NimbleGen Systems Inc., Reykjavik, Iceland, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Reykjavik,Iceland, following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description 2 biological replicates
Data processing The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and log2 transformation as implemented in the NimbleScan software package, version 2.3.16 (Roche NimbleGen, Inc.).
 
Submission date Apr 20, 2011
Last update date Jul 30, 2012
Contact name thomas clozel
E-mail(s) thc2014@med.cornell.edu
Phone 212-746-7622
Fax 212-746-8866
Organization name Weill Cornell Medical College
Department Hematology-Oncology
Lab Ari Melnick
Street address 1300 York Avenue
City New-York
State/province NY
ZIP/Postal code 10023
Country USA
 
Platform ID GPL6602
Series (2)
GSE28744 Chemosensitization of DLBCL cells in vitro and in vivo by demethylating nucleoside analogues [gene expression]
GSE31104 Chemosensitization of DLBCL cells in vitro and in vivo by demethylating nucleoside analogues

Data table header descriptions
ID_REF
VALUE RMA-normalized, log2 transformation, averaged between biological replicates gene-level signal intensity

Data table
ID_REF VALUE
HSAP0406S00000001 11.8814
HSAP0406S00000002 11.9775
HSAP0406S00000003 9.75465
HSAP0406S00000004 11.96105
HSAP0406S00000005 9.2604
HSAP0406S00000006 8.55915
HSAP0406S00000007 8.40545
HSAP0406S00000008 8.53185
HSAP0406S00000009 8.32585
HSAP0406S00000010 9.3373
HSAP0406S00000011 9.23755
HSAP0406S00000012 8.71665
HSAP0406S00000013 8.64215
HSAP0406S00000014 9.45
HSAP0406S00000015 8.74105
HSAP0406S00000016 9.0677
HSAP0406S00000017 8.5814
HSAP0406S00000018 8.92045
HSAP0406S00000019 8.77575
HSAP0406S00000020 8.29955

Total number of rows: 36846

Table truncated, full table size 931 Kbytes.




Supplementary file Size Download File type/resource
GSM712179_197769_532_OZ.pair.txt.gz 6.3 Mb (ftp)(http) TXT
GSM712179_197769_635_OZ.pair.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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