|
| Status |
Public on Aug 05, 2015 |
| Title |
IPSC predisposition +JAK2V617F 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 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 |
|
