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Sample GSM846065 Query DataSets for GSM846065
Status Public on Jan 04, 2012
Title Tet1-KD ES cells siRNA #1 96hr, rep1
Sample type RNA
 
Source name E14Tg2a Embryonic Stem Cells
Organism Mus musculus
Characteristics cell line: E14Tg2a
transfection: Tet1 siRNA #1
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 (http://www.bioconductor.org). 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
E-mail(s) jothi@mail.nih.gov
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
ID_REF
VALUE RMA Normalized signal value (log base 2)

Data table
ID_REF VALUE
100009600_at 6.483038489
100012_at 3.200728963
100017_at 7.29091907
100019_at 10.2504901
100034251_at 5.240308359
100036521_at 5.858603479
100037258_at 7.695201752
100037278_at 7.242974805
100038570_at 7.193618521
100038635_at 3.916036819
100038680_at 4.009746733
100038887_at 13.7487962
100038959_at 6.876585487
100039026_at 8.087521818
100039027_at 3.72836783
100039094_at 5.005635912
100039235_at 5.887565182
100039282_at 3.038631361
100039284_at 6.336415267
100039307_at 6.004715489

Total number of rows: 16556

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM846065_Tet1_siRNA1_96h_Rep_1.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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