NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM609768 Query DataSets for GSM609768
Status Public on Jan 21, 2011
Title Monocyte, sample 3
Sample type RNA
 
Source name umbilical cord blood
Organism Homo sapiens
Characteristics cell type: Monocyte
batch: HTA4
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from TriZol. The concentration of RNA was quantified using the RiboGreenĀ© RNA Quantitation Kit (Invitrogen, San Diego, CA)
Label biotin
Label protocol Ten nanograms of total RNA were amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA).
 
Hybridization protocol The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)
Scan protocol standard Affymetrix protocol
Data processing Transcript levels were processed from data image files using RMA method, implemented by Bioconductor R package. To reduce batch effects, transcript levels were further corrected with the ComBat method (Johnson, 2007), which applies empirical Bayes framework for adjusting data for batch effects. Final dataset which was used in the paper and contains 8968 genes is included in the supplementary file GSE24759_data.sort.txt.
 
Submission date Oct 18, 2010
Last update date Mar 22, 2017
Contact name Noa Novershtern
E-mail(s) noa.novershtern@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Molecular Genetics
Street address Weizmann Institute
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL4685
Series (1)
GSE24759 Densely interconnected transcriptional circuits control cell states in human hematopoiesis

Data table header descriptions
ID_REF
VALUE log2-transformed RMA data and normalized such that the mean of each gene is zero

Data table
ID_REF VALUE
1007_s_at 5.7028
1053_at 6.3859
117_at 7.9466
121_at 5.958
1255_g_at 5.0835
1294_at 6.7636
1316_at 5.6981
1320_at 5.5127
1405_i_at 7.1089
1431_at 5.4755
1438_at 5.4009
1487_at 7.7366
1494_f_at 5.1725
1598_g_at 5.7865
160020_at 5.9374
1729_at 6.1345
1773_at 5.5389
177_at 5.835
179_at 5.3373
1861_at 5.5388

Total number of rows: 22944

Table truncated, full table size 408 Kbytes.




Supplementary file Size Download File type/resource
GSM609768_5202764005790179113004.F07.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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