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Sample GSM1718773 Query DataSets for GSM1718773
Status Public on Jul 01, 2015
Title HG01938 Replicate 1
Sample type genomic
 
Channel 1
Source name HG01938
Organism Homo sapiens
Characteristics coriell cell line: HG01938
Biomaterial provider Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=HG01938
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

Supplementary file Size Download File type/resource
GSM1718773_HG01938.txt.gz 102.4 Mb (ftp)(http) TXT
Processed data are available on Series record

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