|
| Status |
Public on Apr 30, 2012 |
| Title |
NA12878 |
| Sample type |
RNA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: lymphoblastoid cell line
parent/child: HapMap CEU_children
coriell sample: NA12878
|
| Biomaterial provider |
Coriell sample NA12878
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12878
|
| Growth protocol |
RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
1.5 ug of total RNA from each sample was used in cDNA synthesis and IVT reaction using the Amino Allyl MessageAmpTMII aRNA Amplification kit (Ambion, Austin, TX 78744-1832, cat. no.1753). Single stranded aRNA labeled with Cy5 was generated using the Cy5 Mono-Reactive dye pack (Amersham. PA25001)
|
| |
|
| Hybridization protocol |
Ten micrograms of Cy5- labeled aRNA was fragmented (Ambion cat# 8740) and hybridized 16 hrs to Phalanx HOA arrays according to manufacturer’s instructions
|
| Scan protocol |
Arrays were scanned using Agilent DNA Microarray Scanner G2565B (Agilent Technologies, Inc. CA, USA) at settings of 60 PMT (for Cy5) and of 10 micron, and the resulting images were quantified using the software ProbeArrayer (an in-house tool developed by ITRI)
|
| Description |
no additional information
|
| Data processing |
log2 transformed intensities were normalized across technical replicates for each individual using a ComBat (Johnson et al. 2007) normalization. The normalized replicate values were merged by median as one chip per sample, and then sample-based chips were normalized by median across individuals (n=60 for parent or n=30 for children).
|
| |
|
| Submission date |
Apr 30, 2009 |
| Last update date |
Apr 30, 2012 |
| Contact name |
Li-Lan Li |
| E-mail(s) |
lilanli@itri.org.tw
|
| Organization name |
Industrial Technology Research Institute
|
| Street address |
195,Sec. 4, Chung Hsing Rd. Chutung
|
| City |
Hsinchu |
| ZIP/Postal code |
310 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6254 |
| Series (1) |
| GSE15905 |
A new genome wide expression array and its application to eQTL mapping, synergy to other platforms |
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