|
| Status |
Public on Jul 01, 2015 |
| Title |
NA12878 Replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
NA12878
|
| Organism |
Homo sapiens |
| Characteristics |
coriell cell line: NA12878
|
| Biomaterial provider |
Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA12878
|
| Treatment protocol |
We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.
|
| Growth protocol |
We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.
|
| Label |
CY-5
|
| Label protocol |
1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.
|
| |
|
| Channel 2 |
| Source name |
NA10851
|
| Organism |
Homo sapiens |
| Characteristics |
coriell cell line: NA10851
|
| Biomaterial provider |
Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA10851
|
| Treatment protocol |
We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.
|
| Growth protocol |
We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.
|
| Label |
CY-3
|
| Label protocol |
1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.
|
| Scan protocol |
Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).
|
| Data processing |
Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)
|
| |
|
| Submission date |
Jun 23, 2015 |
| Last update date |
Jul 22, 2015 |
| Contact name |
Charles Lee |
| Organization name |
Jackson Laboratory for Genomic Medicine
|
| Lab |
Lee Lab
|
| Street address |
10 Discovery Dr.
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL20608 |
| Series (1) |
| GSE70188 |
1000 Genomes Phase 3 aCGH samples |
|
