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Sample GSM520724 Query DataSets for GSM520724
Status Public on Mar 12, 2010
Title fibroblasts_miRNA transfected_rep2
Sample type RNA
 
Source name AG01522 normal human fibroblasts, miRNA-transfected
Organism Homo sapiens
Characteristics cell type: cultured fibroblasts
cell line: AG01522
supplier: Coriell
passage: 20
transfection: miRNA
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG01522
Treatment protocol Typically, for a 60 mm plate, 500 µl of optiMEM (Invitrogen) was mixed with 2.5 µl of TransIT-siQUEST (Mirus) and incubated for 10 min. The small RNA fraction (800 ng in ~15 µl) was added to this mixture and incubated for 10 more min. This mixture was placed on the bottom of a 60 mm plate and immediately 500,000 cells in 3.5 ml of complete media were added followed by incubation of the cells for 38 h. The media was changed after 24 h. Control cells were mock-transfected using the same conditions without the addition of RNA.
Growth protocol Human fibroblasts (AG01522) were received as cell cultures from Coriell at passage (PDL) 16 and expanded until PDL 20 by culturing in EEMEM (Invitrogen) supplemented with 15% FBS (ATCC).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Ribopure kit (Applied Biosystems), following the manufacturer's instructions.
Label Cy3
Label protocol For array analysis, 0.3 µg RNA was used to produce Cyanine-3 (Cy3)-labeled cRNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).
 
Hybridization protocol Following the manufacturer’s recommendations, 1.5 µg labeled cRNA (>9 pmol Cy3 per µg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit.
Scan protocol Microarrays with labeled cRNA were scanned at 5 µm resolution with an Agilent DNA Microarray Scanner (G2505B).
Description Gene expression after transfection with endogenous small RNA fraction.
mir_3_14_1
Data processing Default parameters of Feature Extraction v. 10.5 software (Agilent) were used for image analysis, data extraction, background correction, and flagging of non-uniform features. Background-corrected intensities were log2-transformed and median-normalized using BRB-ArrayTools v. 3.8.0. Non-uniform outliers or features not significantly above background intensity in 25% or more of the hybridizations were removed, leaving a set of 5800 features that were used for subsequent analyses.
 
Submission date Mar 11, 2010
Last update date Mar 22, 2010
Contact name Thomas Templin
E-mail(s) tt2308@columbia.edu
Phone 212-305-5661
Fax 212-305-3229
URL http://www.crr-cu.org/templin.htm
Organization name Columbia University Medical Center
Street address 630 West 168th Street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL6480
Series (1)
GSE20755 Identification and analysis of miRNA target genes in a cell system

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P100056 6.255778313
A_23_P100127 7.524620056
A_23_P100141 7.445242882
A_23_P100189 5.21781826
A_23_P100220 7.036252975
A_23_P100408 6.918828487
A_23_P100522 13.44874954
A_23_P100660 14.04493523
A_23_P100754 9.796739578
A_23_P101054 12.2956543
A_23_P101084 5.709715843
A_23_P101237 11.83456802
A_23_P101297 9.702320099
A_23_P101303 10.06012154
A_23_P101407 9.225250244
A_23_P101671 8.905658722
A_23_P101761 14.0735817
A_23_P101783 6.146051884
A_23_P101972 5.888262272
A_23_P102071 12.36923218

Total number of rows: 5773

Table truncated, full table size 138 Kbytes.




Supplementary file Size Download File type/resource
GSM520724.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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