|
| Status |
Public on Feb 01, 2012 |
| Title |
12939.s1 |
| Sample type |
genomic |
| |
|
| Source name |
leukocyte
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: leukocyte
sample id: s1
gender: Male
sentrix id: 4953087006
sentrix position: E
experiment: 8
group: 2
family: 12939
distribution: 6
site: hv
cpea dx: 1-autism-sib
age at collection (months): 71
ethnicity: asian
|
| Treatment protocol |
Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR
|
| Label |
biotin nucleotide or dinitrophenyl labeled
|
| Label protocol |
A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications
|
| |
|
| Hybridization protocol |
Followed the manufacturer's (Illumina) specifications
|
| Scan protocol |
Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan
|
| Description |
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.
|
| Data processing |
Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).
|
| |
|
| Submission date |
Feb 03, 2011 |
| Last update date |
Feb 01, 2012 |
| Contact name |
Benjamin G Barwick |
| E-mail(s) |
benjamin.barwick@emory.edu
|
| Phone |
(404) 285-2964
|
| Organization name |
Emory University
|
| Department |
Hematology and Medical Oncology
|
| Lab |
Barwick Lab
|
| Street address |
1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE27044 |
Methylation Profiling of Blood DNA from Sibling Discordant for Autism |
| GSE27097 |
Pediatric age-associated DNA methylation |
|
