|
| Status |
Public on Feb 09, 2021 |
| Title |
Cord Blood_TD101 [methylation] |
| Sample type |
genomic |
| |
|
| Source name |
CBMC
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
batch: PL4
estimated bcell: 0.0756452925759608
estimated cd4t: 0.0621193837760734
estimated cd8t: 0.0287838203511467
estimated gran: 0.757480245158921
estimated mono: 0.0664013530433965
estimated nk: 0.0275850759093339
estimated nrbc: 0.046837674466466
have valid rna expression data?: Yes
gestational age: 23
birthweight sdscore: -1.27760215
parity: parous
delivery: Cesarean
maternal age: 38
maternal bmi: 23.63403301
paternal age: 41
paternal bmi: 26.81221871
assisted reproductive technology: No
smoking before pregnancy: No
smoking before pregnancy: No
gestational diabetes mellitus: No
chorioamnionitis: Yes
idiopathic prom without inflammation: No
preeclampsia: No
placenta previa: No
|
| Treatment protocol |
Mononuclear cells were separated by gradient centrifugation using Ficoll-Hypaque from cord blood and postnatal peripheral blood samples within 24 h of the sample collection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted by Qiagen AllPrep kit.
|
| Label |
Cy3, Cy5
|
| Label protocol |
Standard Illumina labelling 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 High Scan SQ using standard recommended Illumina scanner setting
|
| Description |
TD101C
|
| Data processing |
background correction and dye-bias equalization (Noob) was performed using minfi package (v. 1.20.2), and furthermore, beta-mixture quantile normalization (BMIQ) was performed using ChAMP package(v. 2.6.0).
|
| |
|
| Submission date |
Feb 20, 2018 |
| Last update date |
Feb 09, 2021 |
| Contact name |
Kohei Kashima |
| E-mail(s) |
KASHIMAK-PED@h.u-tokyo.ac.jp
|
| Phone |
+81-3-5800-8659
|
| Organization name |
The University of Tokyo Hospital
|
| Department |
Pediatrics
|
| Street address |
7-3-1 Hongo Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1138655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE110828 |
Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation] |
| GSE110829 |
Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period |
|
