NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM846066 Query DataSets for GSM846066
Status Public on Jan 04, 2012
Title Tet1-KD ES cells siRNA #1 96hr, rep2
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 6.564098106
100012_at 3.267220796
100017_at 7.234723419
100019_at 10.48446801
100034251_at 5.024279262
100036521_at 5.482423764
100037258_at 7.619966146
100037278_at 7.292630662
100038570_at 6.94450146
100038635_at 3.706289961
100038680_at 3.899697946
100038887_at 13.73247248
100038959_at 6.779440422
100039026_at 8.172807442
100039027_at 3.795963293
100039094_at 5.090325539
100039235_at 6.081735521
100039282_at 3.21923704
100039284_at 6.180531728
100039307_at 5.965274802

Total number of rows: 16556

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM846066_Tet1_siRNA1_96h_Rep_2.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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