NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4576573 Query DataSets for GSM4576573
Status Public on Jun 22, 2020
Title Cord blood Nr_416
Sample type RNA
 
Source name cord blood
Organism Homo sapiens
Characteristics tissue: cord blood
birthweight: 4400
hybridization date: 2016-07-28
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]

Supplementary file Size Download File type/resource
GSM4576573_US10063773_253949447205_S01_GE1_107_Sep09_1_3.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data not provided for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap