|
Status |
Public on Feb 09, 2021 |
Title |
Cord Blood_TD045 [methylation] |
Sample type |
genomic |
|
|
Source name |
CBMC
|
Organism |
Homo sapiens |
Characteristics |
gender: female batch: PL1 estimated bcell: 0.16316127525185 estimated cd4t: 0.440337309198085 estimated cd8t: 0.277837630233229 estimated gran: 0 estimated mono: 0.142827168867263 estimated nk: 6.91778541329858e-18 estimated nrbc: 0.0483828772670804 have valid rna expression data?: No gestational age: 39.71428571 birthweight sdscore: -0.900220323 parity: parous delivery: Vaginal maternal age: 37 maternal bmi: 17.36044134 paternal age: 37 paternal bmi: 21.2244898 assisted reproductive technology: No smoking before pregnancy: No smoking before pregnancy: No gestational diabetes mellitus: No chorioamnionitis: No 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 |
TD045C
|
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 |
|