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Sample GSM846064 Query DataSets for GSM846064
Status Public on Jan 04, 2012
Title Control ES cells 96hr, rep2
Sample type RNA
Source name E14Tg2a Embryonic Stem Cells
Organism Mus musculus
Characteristics cell line: E14Tg2a
transfection: control siRNA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNAeasy kit (Qiagen)
Label biotin
Label protocol Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.
Hybridization protocol One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
Scan protocol Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).
Data processing Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor ( Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 13 (Dai et al. (2005); Nucl Acids Res 33: e175). Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.
Submission date Dec 08, 2011
Last update date Jan 04, 2012
Contact name Raja Jothi
Organization name National Institutes of Health
Department National Institute of Environmental Health Sciences
Lab Systems Biology
Street address 111 TW Alexander Drive; A314
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL14661
Series (2)
GSE34267 Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
GSE34886 Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling]

Data table header descriptions
VALUE RMA Normalized signal value (log base 2)

Data table
100009600_at 6.905496008
100012_at 3.237949698
100017_at 7.020315006
100019_at 9.785624535
100034251_at 5.090985598
100036521_at 6.03252712
100037258_at 7.594728762
100037278_at 7.048437716
100038570_at 8.390628147
100038635_at 3.883415714
100038680_at 3.977125627
100038887_at 13.76324773
100038959_at 6.958876183
100039026_at 7.967168936
100039027_at 4.110669697
100039094_at 5.35044499
100039235_at 6.324061477
100039282_at 3.072405308
100039284_at 6.225762659
100039307_at 6.127068672

Total number of rows: 16556

Table truncated, full table size 343 Kbytes.

Supplementary file Size Download File type/resource
GSM846064_Control_siRNA_96h_Rep_2.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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