|
| Status |
Public on Jun 09, 2014 |
| Title |
Placenta_3.1_DG_M120_1 |
| Sample type |
genomic |
| |
|
| Source name |
Placenta_3.1_DG_M120
|
| Organism |
Homo sapiens |
| Characteristics |
tissue_id: Placenta_3.1
pregnancy stage: Third trimester
tissue collection method: DNAgard
time after removal from the uterus: 120 minutes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were lysed in ATL Buffer (DNeasy Blood and Tissue DNA Isolation kit, Qiagen), using a Mini-Beadbeater-16 (Biospec), with agitation for one minute in the presence of 1 mm zirconia beads. Samples were then centrifuged at maximum speed for one minute and the lysed solution was transferred to a new tube. The remainder of the extraction was followed per the DNeasy handbook using the animal tissue (spin column) protocol, without the optional RNase treatment. DNA was quantified using the Quant- iT kit (Life Technologies).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting
|
| Description |
SAMPLE 22
|
| Data processing |
We performed preprocessing and normalization utilizing the statistical programming language R (http://www.r-project.org/) (version 3.0.1) and the R package minfi (v.1.6.0). Briefly, IDATs files were control normalized and probes with detection p-values > 0.01 in at least one sample were discarded. The samples were then normalized using the SWAN normalization option in the minfi package and M-values were exported.
The non_normalized.txt contains Signal A, Signal B, Signal Intensity, and Detection P-value.
|
| |
|
| Submission date |
Feb 27, 2014 |
| Last update date |
Jun 09, 2014 |
| Contact name |
Rathi D Thiagarajan |
| E-mail(s) |
rthiagarajan@ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Reproductive Medicine
|
| Lab |
Louise Laurent
|
| Street address |
2880 Torrey Pines Scenic Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE55438 |
Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids [methylation] |
| GSE55440 |
Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids |
|
