|
| Status |
Public on Aug 17, 2015 |
| Title |
Preterm 3 (PT3) |
| Sample type |
genomic |
| |
|
| Source name |
preterm_umbilical cord blood DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
gestational_age (days): 193
oxytocin: Yes
initiation of labor: Spontaneous contractions
tissue: Umbilical cord blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from Umbilical Cord Blood was isolated by Gentra Autopure LS98TM system (Gentra Systems)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol
|
| Scan protocol |
standard Illumina Protocol
|
| Description |
Preterm sample
SAMPLE 3
|
| Data processing |
The quality control was performed using the array quality metrics and ChAMP R packages. 2 samples were excluded due to failed quality control. BMIQ normalization was performed on 22 samples and differential methylated values were calculated on M values (limma package). The non_normalized.txt contains unmethylated and methylated signal intensities (for all 24 samples).
|
| |
|
| Submission date |
Mar 03, 2015 |
| Last update date |
Aug 17, 2015 |
| Contact name |
Febilla Fernando |
| E-mail(s) |
j.f.fernando@amc.nl
|
| Phone |
+31205661882
|
| Organization name |
Academic Medical Center
|
| Department |
Reproductive Biology Laboratory
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE66459 |
The idiopathic preterm delivery methylation profile in umbilical cord blood |
|
