GEO DataSets

Analysis of breast tumor samples preserved using 2 different RNA stabilization methods (RNAlater or snap freezing) up to 3 hours post tumor excision. Results provide insight into the effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 11 individual, 35 other, 2 protocol, 6 time sets

Platform:

GPL96

Series:

GSE25011

86 Samples

Download data: CEL

(Submitter supplied) Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4088

Platform:

GPL96

86 Samples

Download data: CEL

(Submitter supplied) Previous studies have shown that ischemia alters gene expression in normal and malignant tissues. There are no studies that evaluated effects of ischemia in renal tumors. This study examines the impact of ischemia and tissue procurement conditions on RNA integrity and gene expression in renal cell carcinoma. We used microarray analysis to evaulate the effect of ischemia and tissue procurement conditions on the gene expression changes in renal cell carcinoma

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4547

Platform:

GPL570

140 Samples

Download data: CEL

Analysis of ten renal tumors that were resected then immediately frozen or stored at 4°C, 22°C, 37°C for up to 240 minutes. Results provide insight into the impact of tissue acquisition method on tumor gene expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 10 specimen, 4 temperature, 6 time sets

Platform:

GPL570

Series:

GSE41137

140 Samples

Download data: CEL

(Submitter supplied) A number of breast or colon specific genes predictive of the relapse status were used in comparing the outcome from matched fresh frozen and stored in RNAlater preservative. Keywords: disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

104 Samples

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(Submitter supplied) The aim of our study was to identify gene expression profiles of ductal and lobular carcinomas in relation to normal ductal and lobular cells. We examined ten mastectomy specimens from postmenopausal breast cancer patients. Ductal and lobular tumor and normal cells were microdissected from cryosections. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. GCOS pairwise comparison algorithm and rank products have identified multiple genes that are differentially expressed in comparisons between ductal and lobular tumor and normal cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2635

Platform:

GPL570

30 Samples

Download data: CEL, EXP

Analysis of invasive ductal carcinoma (IDC) cells, invasive lobular carcinoma (ILC) cells, and their normal counterparts. Cells obtained from postmenopausal breast cancer patients. Results provide insight into the molecular differences between IDC and ILC.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 disease state sets

Platform:

GPL570

Series:

GSE5764

30 Samples

Download data: CEL, EXP

(Submitter supplied) We created RNA with different degree of degradation and investigated if the RNA quality influenced gene expression We used oligo-cDNA-microarrays to compare gene expressions Keywords: RNA quality, breast cancer, gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5345

24 Samples

Download data: GPR

(Submitter supplied) Clones from the Research Genetics clone set (Research Genetics, Huntsville AL) were PCR amplified using universal primers, band size was verified, clones were precipitated, dissolved in 3 × SSC, and printed on poly-L-lysine (Sigma, St Louis, MO) coated slides. Microarrays consisted of 32 subarrays, each 18 rows by 18 columns, for a total of 10,368 spots.

Organism:

Homo sapiens

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

172 Samples

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(Submitter supplied) The study outcome was to evaluate the effect of the time on tumor samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

84 Samples

Download data: TXT

(Submitter supplied) The study outcome was to evaluate the effect of the time on normal colon mucosa samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

88 Samples

Download data: TXT

(Submitter supplied) Genome-wide gene expression changes were determined in histopathologically normal breast tissue in 33 women undergoing mastectomy for stage II and III primary invasive ductal carcinoma at serial distances in three dimensions from the tumor. Gene expression was determined by genome-wide mRNA analysis and subjected to metagene mRNA characterization

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

108 Samples

Download data: CEL

(Submitter supplied) We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage. By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1972

Platform:

GPL96

24 Samples

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Analysis of uterine myometrial tissue specimens stored in RNAlater preservative for 24 or 74 hours at room temperature. Results indicate RNALater did not contribute any systematic shift in quantitative RNA expression results relative to alternative tissue processing methods (fresh, snap-frozen).

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol, 3 time sets

Platform:

GPL96

Series:

GSE1296

24 Samples

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(Submitter supplied) Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

48 Samples

Download data: TXT

(Submitter supplied) This set of experiments includes 38 IDCs, 21 ILCs, 2 lymphnode metastases, and 3 normal breast samples. It is designed to compare gene expression profiles of IDCs and ILCs. Total RNAs from all samples were isolated using TRIzol, amplified using optimized T7 linear amplification protocol, and labeled with Cy5. Stratagen Universal Human Reference RNA was amplified the same way and labeled with Cy3. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

9 related Platforms

64 Samples

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(Submitter supplied) To obtain insight into the molecular basis of ductal carcinoma in situ (DCIS) and its progression by infiltrating surrounding tissue, we have performed cellular-based gene expression analysis of pure DCIS and DCIS with co-existing invasive ductal carcinoma (IDC) and compared the histological and molecular aspects between these morphologically identical lesions seeking to find key genes involved in DCIS progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1930

60 Samples

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(Submitter supplied) Analysis of 143 completely histologically-normal breast tissues resulted in the identification of a “malignancy risk” gene signature that may serve as a marker of subsequent risk of breast cancer development. Keywords: Tissue from breast cancer and adjacent regions

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

185 Samples

Download data: CEL

(Submitter supplied) we describe a mRNA profiling analysis of matched ductal carcinoma in situ and invasive duct carcinoma components of FFPE breast carcinomas with the purpose to identify potential prognostic markers

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8432

42 Samples

Download data: TXT