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Sample GSM609800 Query DataSets for GSM609800
Status Public on Jan 21, 2011
Title CD8+ Effector Memory RA, sample 3
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics cell type: CD8+ Effector Memory RA
batch: HTA1
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 6.2196
1053_at 5.7852
117_at 5.7483
121_at 6.0495
1255_g_at 5.5506
1294_at 8.8798
1316_at 5.3412
1320_at 5.4784
1405_i_at 11.3695
1431_at 5.6649
1438_at 5.2106
1487_at 7.6174
1494_f_at 5.1863
1598_g_at 5.5351
160020_at 5.812
1729_at 7.8803
1773_at 5.1967
177_at 5.2498
179_at 5.4838
1861_at 5.3522

Total number of rows: 22944

Table truncated, full table size 408 Kbytes.




Supplementary file Size Download File type/resource
GSM609800_5202764006152214120704.F11.CEL.gz 2.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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