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Sample GSM1659028 Query DataSets for GSM1659028
Status Public on Aug 05, 2015
Title IPSC predisposition +JAK2V617F+TET2 mutation clone a
Sample type genomic
 
Channel 1
Source name IPS
Organism Homo sapiens
Characteristics gender: F
pathology: Essential thrombocythemia
cell status: iPS
biosource: undifferentiated
Growth protocol IPSC (passage between P15 and P33) were cultured on MEF layers in the presence of FGF2
Extracted molecule genomic DNA
Extraction protocol DNA extraction was performed using the DNEasy Mini Kit (Qiagen). DNA was purified using the ChargeSwitch Forensic DNA Purification Kit (Invitrogen, Carlsberg, CA). Concentration and purity of DNA was determined using a Qubit dsDNA BR kit (Life Technologies).
Label Cy5
Label protocol DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP, whereas sex-matched normal reference DNA from Promega was labeled with Cy3-dUTP). Samples with unknown gender where hybridized with labeled male reference DNA.
 
Channel 2
Source name Commercial DNA (Promega)
Organism Homo sapiens
Characteristics gender: F
Growth protocol IPSC (passage between P15 and P33) were cultured on MEF layers in the presence of FGF2
Extracted molecule genomic DNA
Extraction protocol DNA extraction was performed using the DNEasy Mini Kit (Qiagen). DNA was purified using the ChargeSwitch Forensic DNA Purification Kit (Invitrogen, Carlsberg, CA). Concentration and purity of DNA was determined using a Qubit dsDNA BR kit (Life Technologies).
Label Cy3
Label protocol DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP, whereas sex-matched normal reference DNA from Promega was labeled with Cy3-dUTP). Samples with unknown gender where hybridized with labeled male reference DNA.
 
 
Hybridization protocol Pooled test and reference labeled DNA samples were hybridized for 40 hours at 65°C on Agilent 244K high density oligo microarrays (G4411B, AMADID 014693), and washed with Agilent Wash Buffers 1 & 2 and acetonitril.
Scan protocol Washed arrays were dried using a nitrogen pulse gun and scanned on an Agilent G2565CA scanner (Agilent, Palo Alto, CA) using a resolution of 3µm per pixel and 100% of the photomultiplicator for both signals.
Description Sample name in figure S3a : P3-CNV-VF-TET2 a
Data processing Intensity aquisition and data normalization and transformation were performed using Feature Extraction v10.7.3.1 (Agilent Sotware) using default protocol.
 
Submission date Apr 15, 2015
Last update date Aug 06, 2015
Contact name Bastien Job
E-mail(s) bastien.job@gustaveroussy.fr
Phone +330142114211
Organization name Institut Gustave Roussy
Lab Bioinformatics Core Facility
Street address 39 rue Camille Desmoulins
City VILLEJUIF
ZIP/Postal code 94800
Country France
 
Platform ID GPL9777
Series (1)
GSE67938 Germline duplication of ATG2B and GSKIP predisposes to familial essential thrombocythemia rapidly progressing to acute leukemia

Data table header descriptions
ID_REF
VALUE Values correspond to normalized log2(test/ref), where test and ref correspond to pathological samples and Promega commercial normal intensities, respectively.

Data table
ID_REF VALUE
4 0.495408334
5 0.457038099
6 -0.588272507
7 0.135632601
8 -0.139536792
9 -0.305846546
10 0.211986168
11 0.000403998
12 -0.830512973
13 0.061594425
14 0.259481656
15 0.172017862
16 -0.218188924
17 -0.541364822
18 -0.672212506
19 0.12158378
20 -0.546386291
21 0.778417338
22 -0.47203107
23 -0.429324014

Total number of rows: 415056

Table truncated, full table size 7746 Kbytes.




Supplementary file Size Download File type/resource
GSM1659028_US82900153_252185016643_S01_CGH_107_Sep09_1_2.txt.gz 43.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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