|
| Status |
Public on Apr 11, 2011 |
| Title |
Placenta IUGR Replicate 4 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Placenta Case
|
| Organism |
Homo sapiens |
| Characteristics |
sex: Male
gestational age: 37 wk
tissue: Placenta
birth weight percentile: 5
delivery: Vaginal delivery
pathology: Sm plac, Maternal Vascular Underperfusion
sample type: Methyl immunoprecipitated genomic DNA
antibody: anti-methylcytosine
antibody vendor: Eurogentec, San Diego, CA
antibody catalog #: BI-MECY-0100
|
| Growth protocol |
Samples were randomly collected from the villous portion of human placentae, washed with PBS and transferred and stored in RNAlater; later from each 3 mm fragment distal villi were macrodissected and stored at -80ºC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions; 10mg in a 100 ng/ml concentration was sonicated to sizes 200-1000 bp fragments; a 4mg fraction was immunoprecipitated (IP) using a Methylcytosine antiboidy, following a modified Weber et al., (2005) protocol. 21 ml of immunoprecipitated DNA and 250 ng of sonicated genomic DNA of corresponding sample was labeled using BioPrime® Array CGH Genomic Labeling (Cy3 and Cy5 respectively).
|
| |
|
| Channel 2 |
| Source name |
Placenta Case
|
| Organism |
Homo sapiens |
| Characteristics |
sex: Male
gestational age: 37 wk
tissue: Placenta
birth weight percentile: 5
delivery: Vaginal delivery
pathology: Sm plac, Maternal Vascular Underperfusion
sample type: total input genomic DNA
|
| Growth protocol |
Samples were randomly collected from the villous portion of human placentae, washed with PBS and transferred and stored in RNAlater; later from each 3 mm fragment distal villi were macrodissected and stored at -80ºC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions; 10mg in a 100 ng/ml concentration was sonicated to sizes 200-1000 bp fragments; a 4mg fraction was immunoprecipitated (IP) using a Methylcytosine antiboidy, following a modified Weber et al., (2005) protocol. 21 ml of immunoprecipitated DNA and 250 ng of sonicated genomic DNA of corresponding sample was labeled using BioPrime® Array CGH Genomic Labeling (Cy3 and Cy5 respectively).
|
| |
|
| |
| Hybridization protocol |
Purification of labelled products, array hybridization and scanning were performed at the Microarray facility, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada according to the Agilent Microarray Analysis of Methylated DNA Immunoprecipitation Manual (Version 1.0, May 2008)
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified by Agilent Feature Extraction software (v9.0) (Santa Clara, CA), using the Human Agilent CpG version 20070820 grid file and CGH V4-91 protocol
|
| Description |
n/a
|
| Data processing |
The background subtracted output raw data was imported to Partek® software, version 6.3 Copyright © 2008, Partek Inc., St. Louis, MO. The imported red and green signals raw data was normalized to baseline, by dividing the red signal (MeDIP fraction) by the green signal (total genomic DNA fraction), log2 transformed and quantile normalized between all the arrays.
|
| |
|
| Submission date |
Jun 14, 2010 |
| Last update date |
Apr 11, 2011 |
| Contact name |
Rosanna Weksberg |
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genome Biology
|
| Lab |
Weksberg Lab
|
| Street address |
555 University Ave.
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE22326 |
CpG Island methylation variation in placentae of Intra-Uterine Growth Restricted (IUGR) fetuses versus controls |
|
