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P- Examples: E-MEXP-31, cancer
GSE23153- bioassay_data_transformation ID_REF = <br>VALUE = RMA signal
1
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P- Collagen or fibrin gels containing aortic rings were washed in PBS,
GSE23153- specified_biomaterial_action n Feedback
transferred to buffer RLT from the Qiagen RNAEasy kit, and snap l Login
2 frozen in liquid nitrogen.

Four to six individual aortic ring cultures from each treatment groupd
Functional genomics data
P- were combined to generate a sample. All cultures were grown in
GSE23153- grow serum free EBM medium (Lonza). Samples were divided into
3 treatment groups receiving 10ng/ml recombinant Rat TNFa or left
BIOSTUDIES / ARRAYEXPRESS / E-GEOD-23153 untreated.

P- Date: 20 July 2011 ▪ Modified: 9 MarchFollowing

Release 2022 ▪ pulverization
Views: 9 under liquid nitrogen, extraction of total RNA
GSE23153- nucleic_acid_extraction was performed with a microRNA Easy kit from Qiagen according to
[Cite] {JSON} →PageTab↲ FTP Globus
Gene expression in TNF
4 the manufacturer's instructions.

Biotinylated cRNA was prepared according to standard Affymetrix

treated
P- rat aortic rings cultured in collagen
Whole Transcript or fibrin
Sense Labeling Protocol gels.
from 200 ng of total RNA.
GSE23153- labeling
Alfred 1 (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay User
5 Aplin , Giovanni Ligresti, Roberto Nicosia
Manual, P/N 701880 Rev. 5)

Following fragmentation, 10ug of cRNA Data

1 University of Washington files
was hybridized for 17 hr at 45
P-
Accession E-GEOD-23153 degrees C on Affymetrix Rat Gene 1.0 ST Arrays.
Show 5 GeneChips
entries were
GSE23153- hybridization
washed and stained in the Affymetrix Gene Chip Fluidics Station
Search:
6
Study type transcription profiling by array
450.) EFO

P-
Organism Rattus norvegicus Affymetrix Rat Gene 1.0 ST Arrays were scanned using the Affymetrix
GSE23153- image_aquisition Name
GeneChip® 3000 scanner.
Description
7 Angiogenesis in cultures of rat aorta begins with
neovessels sprouting from the aortic explant within the
Raw microarray datafirst three
were GSM570077_Fib_TNF_GL18.CEL
processed with Bioconductor
days of culture. We used microarrys to examine the effects of
(http://www.bioconductor.org/) Probes were normalized with the
TNF-alpha on gene expression in both fibrin Robust Multi-Array
and collagen normalization
gels procedureGSM570076_Fib_TNF_GL14.CEL
(Irizarry RA, Gautier L,
Cope L, eds. An r package for analyses of affymetrix oligonucleotide
during the first 48 hours or culture. Rat aortic rings were cultured
P- arrays. London: Springer; 2003. Parmigiani RIG, Garrett ES, Zeger S,
in either collagen or fibrin maticies. Half eds.
of the GSM570075_Fib_TNF_GL10.CEL
GSE23153- feature_extraction Thecultures
analysis offrom
gene each
expression data: Methods and software.)
matrix
8 group were treated with 10ng/mlFrom recombinant rat TNF-
the normalized data, genes with significant evidence for
alpha, and half were cookies,
left untreated. Thesedifferential
cultures expression
were of weretoidentified usingGSM570074_Fib_Control_GL17.C
used the Bioconductor limma
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personal data in order to function. By using the site you are GSM570073_Fib_Control_GL13.C
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