title: MammaryCarcinoma_PrepubertalIrradiationInduced_2

status: Public on Jan 19 2011

type: RNA

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression of carcinoma induced by irradiation at 3 weeks of age

hyb_protocol: Labeled RNA was hybridized to DNA microarrays (Whole Rat Genome Microarray Kit, Agilent) using the Gene Expression Hybridization Kit (Agilent) at 65°C for 17 h and washed with Gene Expression Wash Buffers 1 and 2 (Agilent).

scan_protocol: Microarrays were then scanned (DNA Microarray Scanner, Model G2565BA; Agilent) using one color scan setting for 4x44K array slides (scan area, 61x21.6 mm; scan resolution, 5 um; scanning mode, single pass; extended dynamic range, on; dye channel, Green; Green PMT for XDR-Hi, 100%; and Green PMT for XDR-Lo, 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and grid 014879_D_F_20100118) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as not positive and significant or not above background were excluded. The median normalized signal intensity from the three non-irradiated control signals were compared with each hybridized sample and log2 transformed.

organism: Rattus norvegicus

source_name: Mammary carcinoma, 3 weeks of age

label_protocol: Cyanine 3–labeled complementary RNA was generated from total RNA samples of tumors and normal mammary tissues from age-matched rats using the Low RNA Input Linear Amplification Kit Plus (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Total RNA was extracted from frozen carcinomas and from frozen normal mammary tissues of 7-week-old rats using the Maxwell 16 Total RNA Purification kit (Promega Co., Madison, WI).

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (2 Gy, 0.6 Gy/min) at 3 or 7 weeks of age. Rats were fed AIN-76A diet containing 23.5% corn oil  after 9 weeks of age. At 50 weeks of age, rats with palpable tumors were killed using ether anesthesia and tumors were collected.

value: mammary

tag: gender

value: female

tag: age at irradiation

value: 3 weeks

source_name: Normal mammary tissue, non-irradiated, mean value of 3 Samples

value: non-irradiated


title: MammaryCarcinoma_PostpubertalIrradiationInduced_6

description: Gene expression of carcinoma induced by irradiation at 7 weeks of age

molecule: total RNA

source_name: Mammary carcinoma, 7 weeks of age

tag: tissue

value: 7 weeks


title: NormalMammaryTissue_NonIrradiated_3

description: Gene expression of control normal tissue

source_name: Normal mammary tissue, non-irradiated


title: MammaryCarcinoma_PostpubertalIrradiationInduced_5


title: MammaryCarcinoma_PostpubertalIrradiationInduced_2


title: MammaryCarcinoma_PostpubertalIrradiationInduced_3


title: MammaryCarcinoma_PostpubertalIrradiationInduced_4


title: MammaryCarcinoma_PostpubertalIrradiationInduced_1


title: MammaryCarcinoma_PrepubertalIrradiationInduced_3


title: NormalMammaryTissue_NonIrradiated_1


title: MammaryCarcinoma_PrepubertalIrradiationInduced_1


title: MammaryCarcinoma_PrepubertalIrradiationInduced_4