|
| Status |
Public on Dec 31, 2014 |
| Title |
GM12878 cells gDNA Nsp array |
| Sample type |
genomic |
| |
|
| Source name |
GM12878 cells gDNA Nsp array
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
sample type: genomic DNA
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Treatment protocol |
Cells were grown to ~80% confluency and colleced after changing the media at -8hrs.
|
| Growth protocol |
Cells were grown in RPMI medium 1640 supplemented with 2mM L-glutamine and 15% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN Blood and Cell Culture Midi kit isolated
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard SNP array protocol
|
| |
|
| Hybridization protocol |
Affymetrix hybridization oven at 49C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450
|
| Scan protocol |
Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.
|
| Description |
QIAGEN Blood and Cell Culture Midi kit isolated
|
| Data processing |
Analyzing 250K Nsp and 250K Sty chip CEL files by Affymetrix Genotyping Console v4.1, we obtained the probe level intensity data for all match and mismatch probes. We applied quantile normalization to probe level ratios a=PMA/MMA and b=PMB/MMB. Then for each probeset or SNP, we computed the allelic intensities A=max(mean(log2(a)), 0) for allele A and B=max(mean(log2(b)), 0) for allele B based on the normalized ratios a and b. Finally, we obtained the total intensity A+B for each SNP on the 250K Nsp chips and the 250K Sty chips. The intensity data from two kind of chips were combined into one file.
The AplusB8GMs3types.ns.txt matrix file contains the total intensity data. It has 25 columns and 500568 rows. The Affymetrix SNP ids are in the first column. The rest columns contain 3 assays for each of the 8 CEPH samples.
|
| |
|
| Submission date |
Jan 13, 2012 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Howard Yang |
| E-mail(s) |
yanghow@mail.nih.gov
|
| Phone |
2402765257
|
| Organization name |
NCI
|
| Street address |
9609 Medical Center Dr.
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE35099 |
Allele specific RNA polymerase occupancy and gene expression analysis for 8 CEPH lymphoblastoid cell lines. |
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