|
| Status |
Public on Jun 22, 2020 |
| Title |
Cord blood Nr_346 |
| Sample type |
RNA |
| |
|
| Source name |
cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
birthweight: 3700
hybridization date: 2016-07-14
|
| Extracted molecule |
total RNA |
| Extraction protocol |
not provided
|
| Label |
Cy3
|
| Label protocol |
0.2 μg total RNA was used to synthesize fluorescent cyanine-3-labeled cRNA following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies)
|
| |
|
| Hybridization protocol |
Cyanine-3 labelled cRNA was hybridized onto Agilent Whole Human Genome 8 × 60 K microarrays
|
| Scan protocol |
Microarray signals were detected using the Agilent DNA G2505C Microarray Scanner (Agilent Technologies).Scan images were converted into TXT files using the Agilent Feature Extraction Software (Version 10.7.3.1, Agilent Technologies, Amstelveen, Netherlands).
|
| Description |
excluded: missing covariates
|
| Data processing |
An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, flagging of bad spots and spots with too low intensity, log2 transformation and quantile normalization using arrayQC. More information about the flagging and the R-scripts of the pipeline are available at https://github.com/BiGCAT-UM/arrayQC_Module. Further preprocessing included removal of probes showing > 30% flagged data, merging of replicate probes based on the median, and imputation of missing values by means of K-nearest neighbor imputation (K = 15) resulting in 29,164 transcripts available for further analysis. Of the 200 samples, RNA extraction was not possible for 6 samples. After exclusion of samples failing preprocessing and missing covariates for denoising gene expression levels of 165 samples were left in our analyses.
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Michelle Plusquin |
| E-mail(s) |
michelle.plusquin@uhasselt.be
|
| Organization name |
Hasselt University
|
| Street address |
Campus Diepenbeek Agoralaan Gebouw D
|
| City |
Diepenbeek |
| ZIP/Postal code |
3590 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE151373 |
A cord blood multi-omic analysis of birthweight reveals new underlying mechanisms related to cholesterol metabolism [gene expression] |
|
