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Sample GSM307182 Query DataSets for GSM307182
Status Public on Jul 29, 2008
Title pLXSN/HuR/3
Sample type RNA
 
Source name Breast epithelial cells MCF10A, RNA from IP reactions using an anti-HuR antibody and pLXSN empty vector transfected cells.
Organism Homo sapiens
Characteristics RNA from IP reactions using an anti-HuR antibody and pLXSN empty vector transfected cells. Biological repeat 3.
Treatment protocol pLXSN empty vector stable transfected cells
Extracted molecule total RNA
Extraction protocol After IP with HuR antibody, beads were incubated with 100 ul NT2 buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40) containing 20 U RNase-free DNase I for 5 min at 37°C, washed with NT2 buffer, and incubated in 100 ul NT2 buffer containing 0.1% SDS and 0.5 mg/ml proteinase K (15 min, 55°C). RNA was extracted using acid phenol-ChCl (Ambion) and precipitated in the presence of glycoblue.
Label biotin
Label protocol standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol standard Illumina protocol. In short, a total of 0.75 ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description Breast epithelial cells MCF10A
Data processing Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection score of 0.98 and below. The natural log of all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores included in the supplementary file..
 
Submission date Jul 23, 2008
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6102
Series (1)
GSE12215 Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.

Data table header descriptions
ID_REF
RAW_VALUE Raw Intensity value from the Beadstudio software
VALUE Z transformation of the natural log of the raw signal values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1804663 137.9 -0.3340321
ILMN_1840887
ILMN_1867201
ILMN_1900605
ILMN_1651799 1876.7 2.93786361
ILMN_1818166 121.5 -0.492711
ILMN_1782558
ILMN_1827636 157.4 -0.1682761
ILMN_1821792
ILMN_1833080
ILMN_1895660
ILMN_1850244
ILMN_1812262 242.5 0.37339015
ILMN_1712803 233.1 0.3238442
ILMN_1842171
ILMN_1873045 112.5 -0.5891619
ILMN_1774757 114.9 -0.5627072
ILMN_1905009
ILMN_1867479
ILMN_1875979

Total number of rows: 48688

Table truncated, full table size 1054 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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