|
| Status |
Public on Jun 09, 2015 |
| Title |
genomic DNA from human cerebellum sample 14 |
| Sample type |
genomic |
| |
|
| Source name |
Cerebellum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cerebellum
age: 61
hivstatus: Positive
dnamage: 47.14772956
gender: female
ageaccelerationvscontrols: 1.954503521
ageaccelerationresidual: 0.511007399
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA Minikit from Qiagen
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
genomic DNA from human cerebellum sample 14
Fresh frozen human cerebellum
Sample14
|
| Data processing |
BeadStudio software v3.2. The unmethylated and methylated signal intensities can be found in the file datSignal_cerebellum.csv available on the series record. Data were processed as follows: Background corrected, average beta values (no special processing)
The data matrix with normalized beta values differs from the file with raw signal intensities with respect to 65 CpG probes that are labelled by Refseq ID such as rs10033147 rs1019916. Unfortunately, the raw signal intensities are not available for these 65 SNPs because our pre-processing pipeline automatically removes these probes. In contrast, we used GenomeStudio to generate the normalized beta values. Therefore, these data are complete.
|
| |
|
| Submission date |
Apr 10, 2015 |
| Last update date |
Jun 09, 2015 |
| Contact name |
Steve Horvath |
| E-mail(s) |
shorvath@altoslabs.com
|
| Organization name |
University of California, Los Angeles
|
| Department |
Human Genetics
|
| Lab |
Horvath
|
| Street address |
695 Charles E. Young Drive South, Box 708822
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7088 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE67748 |
Cerebellum Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects |
|
