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Sample GSM1162221 Query DataSets for GSM1162221
Status Public on Dec 01, 2015
Title siFip1-2_121812
Sample type RNA
 
Source name mESCs_Fip1 depletion
Organism Mus musculus
Characteristics cell line: E14Tg2a.4
cell type: mouse embryonic stem cells (mESCs)
transfected with: Fip1L1 siRNA
Treatment protocol Lipofectamine 2000-mediated transfections were performed as previously described (PMID 22367759). Mock transfections were performed using lipofectamine but without siRNAs.
Growth protocol ESCs were cultured in gelatin-coated plates in M15 medium.
Extracted molecule total RNA
Extraction protocol Cells were harvested for RNA extraction on day 4, post-transfection. For quality assessment, extracts were checked using qRT-PCR for Fip1 expression as well as appropriate expression markers
Label biotin
Label protocol Affymetrix Whole Mouse Genome oligo arrays using the Affymetrix 1-color microarray-based gene expression analysis protocol.
 
Hybridization protocol standard Affymetrix protocol
Scan protocol standard Affymetrix protocol
Description Fip1L1_2_1; Fip1L1 siRNA2, replicate 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 Jun 13, 2013
Last update date Dec 01, 2015
Contact name Georgette Mona Charles
E-mail(s) georgette.charles@nih.gov
Phone 919-361-4741
Organization name National Institutes of Environmental Health Sciences
Department Laboratory of Molecular Carcinogenesis
Lab Stem Cell Biology
Street address 111 T.W. Alexander Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL14661
Series (1)
GSE47907 Fip1 regulates mRNA alternative polyadenylation to promote embryonic stem cell self-renewal and somatic cell reprogramming.

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

Data table
ID_REF VALUE
100009600_at 6.013437403
100012_at 3.28437402
100017_at 7.581154786
100019_at 8.96568491
100034251_at 4.764255939
100036521_at 4.753131145
100037258_at 7.109330252
100037278_at 6.200374981
100038570_at 6.940540464
100038635_at 4.039417084
100038680_at 3.474523339
100038887_at 13.1923381
100038959_at 6.709779684
100039026_at 8.164123547
100039027_at 3.375283214
100039094_at 4.65529775
100039235_at 5.125016085
100039282_at 3.216029738
100039284_at 5.226042839
100039307_at 5.154465137

Total number of rows: 16556

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM1162221_12143_fip_1218_2_Mouse430_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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