title: KO-Nrf2-Female-1

description:
Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease).

Keywords = Nrf2
Keywords = liver

source_name: Female Nrf2 Knock-out mice, liver sample


title: MF-16

status: Public on Dec 16 2003

type: RNA

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

description:
14 days age control
RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis.

molecule: total RNA

organism: Rattus norvegicus

source_name: soleus muscle, young female pathogen-free Wistar rats


title: WT-Nrf2-Female-2

city: Madison

first: Jiang

last: Li

state: WI

address: 777 Highland Ave.

department: School of Pharmacy

country: USA

institute: University of Wisconsin Madison

organism: Mus musculus

source_name: Female Nrf2 wild-type mice, liver sample


title: CL: Hela versus Brain - fetal [GenomeWideEVG_MRK2205]

status: Public on Dec 18 2003

city: Seattle

first: Stephen

middle: W

last: Edwards

state: WA

department: Research Genetics

institute: Rosetta Inpharmatics (Merck & Co.)

description:
Samples were purchased from Clontech as mRNA.
Hybridization material was generated through a random-priming amplification procedure (RP-AMP) using primers with a random sequence at the 3' end and a fixed motif at the 5' end.  shDNP256 (first strand synthesis): 5'- TAG ATG CTG TTG NNN NNN NNN -3'  shT7N9 (second strand synthesis): 5'- ACT ATA GGG AGA NNN NNN NNN -3'  1.5  g of mRNA was reverse-transcribed with Superscript II and the DP256 random primer for 20 minutes at 42 C (10 mM DTT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 5 U/ l Superscript II). The RNA was  degraded with the addition of 20 l volume of 0.5N sodium hydroxide and 0.25 M EDTA for 20 minutes at 65 C.  The single stranded cDNA was purified using a commercial kit (Qiagen Qiaquick).
The resulting product of single stranded cDNA was placed in its entirety in a second strand reaction. Second strand synthesis reactions utilized shT7N9 random primer and the Klenow fragment of DNA polymerase utilizing standard reaction conditions (37 C for 60 minutes, 0.2 mM DTT, 2.1 mM Tris-HCl pH 7.9, 2.1 mM MgCl2, 10.7 mM NaCl, 1.07 mM dNTPs, 0.1U/ l Klenow), followed by another Qiaquick purification.  Multiple polymerase chain reactions were run using 0.15  g of double stranded DNA and standard reaction conditions.  Amplification was achieved using 10 cycles of PCR with the DP256 and T7 primers (20 mM Tris-HCl pH 8.4, 50 mM KCl, 0.01 mM dNTPs, 1.5 mM MgCl2, 0.01 U/ l Taq Polymerase)  DP256: 5'- GTT CGA GAC CTC TAG ATG CTG TTG -3'  T7: 5'- AA TTA ATA CGA CTC ACT ATA GGG AGA -3'  followed by Qiaquick purification.
Further amplification was achieved using in vitro transcription reactions with X0.5  g dsDNA and T7 RNA Polymerase (7.5 mM DTT, 40 mM Tris-HCl pH 7.5, 14.25 mM MgCl2, 10 mM NaCl, 2 mM Spermidine, 125 U/ml RNAguard, 2.5 mM dNTPs, 15 U/ml IPPase, 25kU/ml T7 Polymerase) for 16 hours at 42 C. The cRNA was purified (RNeasy) and  reverse transcribed using Superscript and random 9-mers and amino-allyl dUTP (42 C for 20 minutes, 10 mM DTT, 50mM Tris-HCl pH 8.3, 75 mM KCl, 8 mM MgCl2, 0.5 mM dNTPs, 0.5 mM aa-dUTP, 5 U/ l Superscript II).
The cDNA for each channel was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 1M sodium bicarbonate, pH 9.0, followed by quenching with 4.0 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were purified with a QIAquick PCR purification kit and the percentage dye incorporation and total cDNA yield was determined spectrophotometrically. Cy5 and Cy3 labelled cDNAs were combined and added to 2 mls 30% formamide with Herring Sperm DNA for hybridization to the microarray.
Further details can be found in Castle et al., Genome Biol 2003;4(10):R66, http://genomebiology.com/2003/4/10/R66 , Roberts CJ et al., Science 2000, 287:873-880, and Schadt, Edwards, et al., unpublished.

organism: Homo sapiens

source_name: CL: Hela

source_name: Brain - fetal


title: Skeletal Muscle versus Adrenal gland [GenomeWideEVG_MRK2200]

source_name: Skeletal Muscle

source_name: Adrenal gland


title: M43

status: Public on Dec 12 2003

city: Daejon

first: Jin-Soo

last: Kim

country: South Korea

institute: ToolGen, Inc.

description: Lee, D-k et al. "Toward a functional annotation of the human genome using artificial transcription factors" Genome Res. In press.

source_name: Human 293 cell


title: M35


title: M37


title: M42


title: M39


title: M34


title: M36


title: M38


title: KO-Nrf2-Male-1

description:
Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease).
Keywords = Nrf2
Keywords = liver

source_name: Knock-out Nrf2 mice, liver sample


title: WT-Nrf2-Female-1

description:
Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2.  Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+).  Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle.  The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum.  All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease).
Keywords = Nrf2
Keywords = liver

source_name: wild-type Nrf2 mice, liver sample


title: M30


title: M31


title: M32


title: M18


title: M13


title: M33


title: M12


title: M14


title: F480_krab


title: M07


title: F475_vp16


title: F547_vp16


title: F505_p65


title: M06


title: F421_krab


title: F480_p65


title: F505_krab


title: M02


title: F561_p65


title: F324_p


title: F296_p65


title: F322_k


title: F320_p65


title: F301_p65


title: F293_p65


title: F320_krab


title: F324_k


title: F300_p65


title: F322_p


title: F291_p65


title: F290_p65


title: F295_p65


title: F294_krab


title: F295_krab


title: F285_krab


title: F285_p65


title: F278_p65


title: F253_krab


title: F291_krab


title: F290_krab


title: F231p_krab


title: F231_krab


title: F232_krab


title: F201_p65


title: F232_p65


title: F199_p65


title: F201_krab


title: F190_krab


title: F224_krab


title: F190_p65


title: F177_krab


title: F253_p65


title: F176_krab


title: F204_krab


title: F177_p65


title: F197_krab


title: F224_p65


title: F199_krab


title: F121_p65


title: F121m_p65


title: F121


title: F117_krab


title: F121_krab


title: F162_krab


title: F114_p65


title: F162_p65


title: F170_p65


title: F170_krab


title: F114_krab


title: F111_p65


title: F109_vp16


title: F104_p65


title: F105_krab


title: F109_krab


title: F108_krab


title: F105_p65


title: F109_p65


title: F103m11_krab


title: F102m01_p65


title: F108_p65


title: F063_krab


title: F101m03_krab


title: F081_p65


title: F101_krab


title: F102m15_p65


title: F036_p65


title: F026_p65


title: F103_krab


title: F103m04_p65


title: F036_krab


title: F032_p65


title: 11-B08_p65


title: F063_p65


title: 11-48-02


title: F062_p65


title: 10-H09_krab


title: 09-C10_p65


title: 08-E01_p65


title: 09-C10_krab


title: 08-A04_krab


title: 08-02


title: 05-E09_krab


title: 08-D05_krab


title: 05-G06_p65


title: 08-D05_p65


title: 05-E09_p65


title: 04-E03_p65


title: 08-A04_p65


title: 08-01


title: 05-G06_krab


title: 08-E01_krab


title: 07-G09_p65


title: 03-B04_p65


title: 05-H09_p65


title: 03-A10_p65


title: 07-G09_krab


title: 02-D01_p65


title: 02-H05_krab


title: 02-H05_p65


title: 02-E09_krab


title: 04-E03_krab


title: 03-G03_p65


title: 03-G03_krab


title: 01-A03_p65


title: 3d-2

status: Public on Dec 09 2003

city: Murray

first: William

middle: Clayton

last: Spencer

state: KY

address: P.O. Box 9

department: Department of Biological Sciences

institute: Murray State University

description:
Cultured on immobilized beta-amyloid peptide 25-35 fragment for 3 days.
Keywords = amyloid astrocytes rat

source_name: Cortical Type-I astrocytes


title: 1d-1

description:
Cultured on immobilized beta-amyloid peptide 25-35 fragment for 1 day.
Keywords = amyloid astrocytes rat


title: 1d-3


title: 5d-2

description:
Cultured on immobilized beta-amyloid peptide 25-35 fragment for 5 days.
Keywords = amyloid astrocytes rat


title: 5d-3


title: Control-6

description:
Cultured on laminin and nitrocellulose without exposure to beta-amyloid peptide 25-35 fragment
Keywords = amyloid astrocytes rat


title: 3d-1


title: Control-3

description:
Cultured on laminin and nitrocellulose without exposure to beta-amyloid peptide 25-35 fragment.
Keywords = amyloid astrocytes rat


title: Control-4


title: 1d-2


title: BALB2Cy5vsBL62Cy3

status: Public on Dec 10 2003

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Hybridization for gene expression variation between mouse inbred strains


title: 3d-3


title: Control-1 astrocytes

source_name: cerebral cortex


title: 12hr-1

description:
Cultured on immobilized beta-amyloid peptide 25-35 fragment for 12 hours.
Keywords = amyloid astrocytes rat


title: Control-5


title: 5d-1


title: BL61Cy5vsDBA2Cy3


title: 12hr-2


title: 12hr-3


title: BL102Cy5vsDBA1Cy3

description: hybridization for gene expression variation between mouse inbred strains


title: DBA1Cy5vsBL61Cy3


title: BALB1Cy5vsCBA2Cy3


title: Control-2 astrocytes


title: BL101Cy5vsBALB2Cy3


title: CBA2Cy5vsBL102Cy3


title: CBA1Cy5vsBL101Cy3


title: BL62Cy5vsCBA1Cy3

description: Variation in gene expression between mouse inbred strains


title: DBA2Cy5vsBALB1Cy3


title: Unirradiated HCT116-CloneK PartB R3

status: Public on Dec 08 2003

city: Ottawa

first: Felix

middle: M.

last: Mesak

state: ON

address: 503 Smyth Rd. 3rd Floor

department: Centre for Cancer Therapeutics

country: Canada

institute: Ottawa Regional Cancer Centre

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12192468_19k2iiB

source_name: Control HCT116-Clone10 cells (Cy3)

source_name: XR sensitive HCT116-CloneK cells (Cy5)


title: Unirradiated HCT116-CloneK PartA R3

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12191948_19k2iiA


title: Ileum 3B

status: Public on Dec 04 2003

city: Epalinges

first: Pascale

last: Anderle

institute: ISREC

description: 8 week-old male Hsd:ICR(CD-1) mice were fed ad libitum a standard chow (Harlan Teklad diet 2018S) and housed in groups of five. Animals were then divided into 3 pools (n=10) and sacrificed. The small intestine was extracted and divided into three sections, where the first 2-3 cm after the stomach comprised the duodenum, the middle third the jejunum, and the section before the ileo-ceco-colic junction comprised the ileum. Colon was not divided into proximal and distal sections and was treated as a single intestinal section.

source_name: Whole segment, ileum, pool of 10 mice


title: Ileum 2C


title: Colon 1C

source_name: Whole segment, colon, pool of 10 mice


title: Jejunum 1C

source_name: Whole segment, jejunum, pool of 10 mice


title: Duodenum 1C

source_name: Whole segment, duodenum, pool of 10 mice


title: Ileum 3C


title: Colon 2C


title: Duodenum 2B


title: Jejunum 2C


title: Jejunum 3B


title: Jejunum 3C


title: Duodenum 3C


title: Jejunum 2B


title: Duodenum 3B


title: Colon 3C


title: Ileum 1B


title: Unirradiated HCT116-CloneK PartB R1

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12167477_19k2iiB


title: Colon 3B


title: Duodenum 2C


title: Unirradiated HCT116-CloneK PartB R2

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12144939inv_19k2iiB

source_name: Control HCT116-Clone10 cells (Cy5)

source_name: XR sensitive HCT116-CloneK cells (Cy3)


title: Ileum 2B


title: Colon 1B


title: Ileum 1C


title: Jejunum 1B


title: Jejunum 3A


title: Duodenum 1B


title: Colon 2B


title: Unirradiated HCT116-CloneK PartA R2

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12167417inv_19k2iiA


title: Jejunum 2A


title: Duodenum 2A


title: 16 (Day 35)

status: Public on Dec 02 2003

city: Stanford

first: Peter

middle: N.

last: Kao

state: CA

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

institute: Stanford University Medical Center

description: Total rat lung

source_name: Total lung


title: 15 (Day 35)

description: Total rat lung


title: 19 (T)

description: Total rat lung


title: 18 (T)

description: Total rat lung


title: 20 (T)

description: Total rat lung


title: Duodenum 3A


title: 12 (Day 28)

description: Total rat lung


title: 14 (Day 28)

description: Total rat lung


title: 17 (Day 35)

description: Total rat lung


title: Ileum 1A


title: 13 (Day 28)

description: Total rat lung


title: 11 (Day 21)

description: Total rat lung


title: Jejunum 1A


title: Duodenum 1A


title: 10 (Day 21)

description: Total rat lung


title: Colon 2A


title: Colon 3A


title: Ileum 3A


title: Colon 1A


title: 07 (Day14)

description: Total rat lung


title: 05 (NL)

description: Total rat lung


title: Ileum 2A


title: 04 (NL)

description: Total rat lung


title: 02 (NL)

description: Total rat lung


title: 08 (Day14)

description: Total rat lung


title: 06 (NL)

description: Total rat lung


title: 09 (Day21)

description: Total rat lung


title: Normal (Day_0)

description: Total rat lung


title: 03 (NL)

description: Total rat lung


title: effect of age fat 2

status: Public on Dec 01 2003

city: Stockholm

first: Petra

middle: Elisabeth

last: Tollet-Egnell

address: CMM L8:01

department: Dept of Molecular Medicine

country: Sweden

institute: Karolinska Institute

description: effect of age in male rat adipose tissue

source_name: normal (2 months of age) male rat fat

source_name: old (18 months of age) male rat fat


title: effect of GH inj old liver 3

description: effect of hGH treatment (injections) in old (18 months of age) male rat livers

source_name: GH treated old (18 months of age) male rat liver

source_name: untreated old (18 months of age) male rat liver


title: effect of age fat 3

description: effect of aging in male rat adipose tissue


title: effect of age fat 1


title: effect of age skeletal muscle 2

description: effect of aging in male rat skeletal muscle

source_name: normal (2 months of age) male rat skeletal muscle

source_name: old (18 months of age) male rat skeletal muscle


title: effect of age skeletal muscle 3


title: effect of GH inj old liver 7

description: Effect of hGH treatment (injections) of old male rats in liver


title: effect of GH inj old skeletal muscle 2

description: effect of hGH treatment (injections) of old male rats in skeletal muscle

source_name: untreated old (18 months of age) male rat skeletal muscle

source_name: GH treated old (18 months of age) male rat skeletal muscle


title: effect of GH inj old skeletal muscle 1


title: EAE, 1,25(OH)2D2 treated #6

first: Karen

middle: Marie

last: Spach

address: 433 Babcock Drive

department: Nutritional Sciences / Biochemistry

institute: University of Wisconsin-Madison

description:
B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis.  Naive mice served as controls.
Keywords = Experimental autoimmune encephalomyelitis
Keywords = multiple sclerosis
Keywords = 1
Keywords = 25(OH)2D3

source_name: spinal cord


title: effect of age skeletal muscle 1

description: effect aging in male rat skeletal muscle


title: EAE, 1,25(OH)2D3-treated #8

source_name: mouse spinal cord


title: effect of GH inj old liver 2


title: effect of age liver 7

description: effect of aging in male rat liver

source_name: normal (2 months of age) male rat liver

source_name: old (18 months of age) male rat liver


title: effect of age liver 6

description: effect of aging in male rat liver


title: effect of GH inj old fat 2

description: effect of hGH treatment (injections) of old male rats in adipose tissue

source_name: untreated old (18 months of age) male rat fat

source_name: GH treated old (18 months of age) male rat fat


title: effect of GH inj old skeletal muscle 3


title: EAE, 1,25(OH)2D3-treated #7


title: effect of GH inj old liver 4

description: effect of hGH treatment (injections) of old male rats in liver


title: effect of GH inj old fat 3


title: Naive (control) #3


title: EAE, placebo-treated #10


title: effect of age liver 4

description: effect of aging in male rat liver


title: effect of GH inj old liver 5


title: Naive (control) #4


title: EAE, placebo treated #5


title: effect of GH inj old liver 1


title: effect of GH inj old fat 1


title: effect of age liver 5

description: effect of aging in male rat liver


title: effect of GH inj old liver 6

description: effect of hGH treatment (injections)of old male rats in liver


title: Naive (control) #2


title: effect of age liver 2

description: effect of aging in male rat liver


title: effect of age liver 3

description: effect of age in male rat liver


title: EAE, placebo-treated #1


title: Adn042

status: Public on Nov 30 2003

city: Paris

first: El Houdaigui

last: Fatiha

department: Immunology Department

country: France

institute: Institut Cochin

description: patient affected by rheumatoid arthritis

source_name: signal

source_name: control


title: Adn043

description: patient affected by osteoarthritis


title: Adn038

description: patient affected by osteoarthritis


title: Adn033


title: effect of age liver 1

description: the effect of aging in male rat liver


title: Experimental 5

city: New Orleans

first: Doan

last: Nguyen

state: LA

institute: LSU Eye Center/LSUHSC

description: Lacrimal Gland 7 days after greater superficial petrosal nerve sectioning.

source_name: Lacrimal Gland


title: Adn044


title: Experimental 4


title: Adn037

description: patient affected by osteoarthritis


title: Adn035

description: patient affected by osteoarthritis


title: Ack035


title: Ack037


title: Sham-operated

description: Sham, operated Lacrimal Gland -7 days after.


title: Ack032

description: patient affected by osteoarthritis


title: Ack038


title: Adn016

description: patient affected by osteoarthritis


title: Experimental 1


title: Adn039

description: patient affected by osteoarthritis


title: Experimental 3


title: Experimental 2


title: Adn031

description: patient affected by osteoarthritis


title: Normal Unoperated

description: Normal, unoperated Lacrimal Gland


title: Adn041

description: patient affected by osteoarthritis


title: Ack031

description: patient affected by osteoarthritis


title: Adn036

description: patient affected by osteoarthritis


title: Contralateral Control 3

description: Control Lacrimal Gland ipsilateral to the Experimental Side-7 days after greater superficial petrosal nerve sectioning.


title: Contralateral Control 2


title: Ack028

description: patient affected by osteoarthritis


title: Ack027

description: patient affected by osteoarthritis


title: Ack25

source_name: cy5 signal

source_name: cy3 control


title: Contralateral Control 1

source_name: Rat Lacrimal Gland


title: Ack026

description: patient affected by osteoarthritis


title: C4 Renal Clear Cell Carcinoma U133A

status: Public on Nov 25 2003

city: Boston

first: Marc

middle: E.

last: Lenburg

state: MA

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

description:
Age = 65; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Tumor Location: upper; Scaling Target = 500; Scaling Factor = 4.02; Raw Q = 4.35; Noise = 9.23; Background = 139.27.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638

source_name: Trizol isolation of total RNA from Renal Clear Cell Carcinoma tissue


title: N4 Renal Clear Cell Carcinoma U133A

description:
Age = 65; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: upper; Scaling Target = 500; Scaling Factor = 5.61; Raw Q = 2.68; Noise = 2.90; Background = 59.84.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076

source_name: Trizol isolation of total RNA from normal tissue adjacent to Renal Cell Carcinoma


title: C2 Renal Clear Cell Carcinoma U133A

description:
Age = 67; Gender = Male; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 2; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Tumor Location: lower; Scaling Target = 500; Scaling Factor = 6.80; Raw Q = 2.62; Noise = 2.73; Background = 59.31.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076


title: N2 Renal Clear Cell Carcinoma U133A

description:
Age = 67; Gender = Male; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 2; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: lower; Scaling Target = 500; Scaling Factor = 5.48; Raw Q = 3.09; Noise = 3.57; Background = 70.22.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076


title: N035 Normal Human Kidney U133A

description:
Age = 70; Gender = Female; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 3; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = true; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = true; Scaling Target = 500; Scaling Factor = 7.09; Raw Q = 2.39; Noise = 2.60; Background = 55.24.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: N3 Renal Clear Cell Carcinoma U133A

description:
Age = 50; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 2; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: mid; Scaling Target = 500; Scaling Factor = 4.76; Raw Q = 3.01; Noise = 3.72; Background = 72.11.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076


title: C011 Renal Clear Cell Carcinoma U133A

description:
Age = 55; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 7.02; Raw Q = 4.54; Noise = 11.06; Background = 142.4.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: N005 Normal Human Kidney U133A

description:
Age = 64; Gender = Male; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 7.48; Raw Q = 2.37; Noise = 2.54; Background = 56.14
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: C4 Renal Clear Cell Carcinoma U133B

description:
Age = 65; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Tumor Location: upper; Scaling Target = 500; Scaling Factor = 9.85; Raw Q = 3.7; Background = 122.40.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: N001 Normal Human Kidney U133A

description:
Age = 58; Gender = Male; Left Kidney; Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 9.94; Raw Q = 2.44; Noise = 2.47; Background = 55.43.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076


title: N4 Renal Clear Cell Carcinoma U133B

description:
Age = 65; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: upper; Scaling Target = 500; Scaling Factor = 22.68; Raw Q = 2.02; Noise = 1.71; Background = 43.92.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C035 Renal Clear Cell Carcinoma U133A

description:
Age = 70; Gender = Female; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = true; Scaling Target = 500; Scaling Factor = 4.44; Raw Q = 2.55; Noise = 3.07; Background = 60.24.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: N1 Normal Human Kidney U133A

description:
Age = 51; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 3; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = true; Adjacent Tumor Location: mid; Scaling Target = 500; Scaling Factor = 4.85; Raw Q = 3.04; Noise = 3.51; Background = 70.54.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004076


title: Unirradiated HCT116-CloneK PartA R1

status: Public on Nov 29 2003

description:
A cDNA microarray between unirradiated X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. Their total mRNA was collected from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12144787_19k2iiA

source_name: Control HCT116-Clone10 cells (Cy3)

source_name: XR sensitive HCT116-CloneK cells (Cy5)


title: C032 Renal Clear Cell Carcinoma U133A

description:
Age = 65; Gender = Female; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 4.18; Raw Q = 3.31; Noise = 4.66; Background = 88.8.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: C005 Renal Clear Cell Carcinoma U133A

description:
Age = 64; Gender = Male; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 11.09; Raw Q = 3.12; Noise = 4.65; Background = 76.41.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: N3 Renal Clear Cell Carcinoma U133B

description:
Age = 50; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 2; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: mid; Scaling Target = 500; Scaling Factor = 17.81; Raw Q = 2.19; Noise = 2.03; Background = 52.70.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1151

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

country: Australia

institute: SA Pathology

description:
HUVEC from 3 different umbilical cords were plated onto 100ul of bovine type I collagen in 96-well microtitre plates (15 wells/cord). At times 0, 0.5, 3, 6 and
24 hours after stimulation with PMA and RMAC11, total RNA was isolated using the TRIZOL procedure. Message Amp aRNA Kit was used to linearly amplify the mRNA approximately 400-fold. The aRNA was generated incorporating 5-(3-aminoallyl)-UTP
and subsequently coupled to Cy3 and Cy5 dyes.

The cDNAs used in this microarray were identified as part of collaborative project between the IMVS and Bionomics Limited. The project aims were to identify genes up-regulated during in vitro capillary tube formation as targets for angiogenesis-based therapeutics.

Any requests for further information regarding the data generated from this collaboration should be directed to Bionomics Limited (www.bionomics.com.au) at the
following address:

Bionomics Limited
31 Dalgleish Street
Thebarton, South Australia
Australia, 5031
Phone: 618 8354 6104
Fax: 618 8354 6199
Email: busdev@bionomics.com.au
Keywords = angiogenesis
Keywords = HUVEC
Keywords = in vitro
Keywords = capillary tube

source_name: time 0 hours

source_name: time 24 hours


title: C001 Renal Clear Cell Carcinoma U133A

description:
Age = 58; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Tumor Location: lower; Scaling Target = 500; Scaling Factor = 3.76; Raw Q = 4.10; Noise = 7.91; Background = 132.1.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: N023 Normal Human Kidney U133A

description:
Age = 72; Gender = Female; Right Kidney; Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 7.30; Raw Q = 2.49; Noise = 2.89; Background = 56.96.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: slide 1152


title: slide 1149

description:
HUVEC from 3 different umbilical cords were plated onto 100ul of bovine type I collagen in 96-well microtitre plates (15 wells/cord). At times 0, 0.5, 3, 6 and
24 hours after stimulation with PMA and RMAC11, total RNA was isolated using the TRIZOL procedure. Message Amp aRNA Kit was used to linearly amplify the mRNA approximately 400-fold. The aRNA was generated incorporating 5-(3-aminoallyl)-UTP
and subsequently coupled to Cy3 and Cy5 dyes.
Keywords = angiogenesis
Keywords = HUVEC
Keywords = in vitro
Keywords = capillary tube


title: C3 Renal Clear Cell Carcinoma U133B

description:
Age = 50; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 2; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 18.20; Raw Q = 2.03; Noise = 1.80; Background = 46.05.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: N2 Renal Clear Cell Carcinoma U133B

description:
Age = 67; Gender = Male; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 2; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = false; Adjacent Tumor Location: lower; Scaling Target = 500; Scaling Factor = 27.20; Raw Q = 1.85; Noise = 1.38; Background = 42.19.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1150


title: C023 Renal Clear Cell Carcinoma U133A

description:
Age = 72; Gender = Female; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 7.41; Raw Q = 3.76; Noise = 6.37; Background = 110.5.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: C2 Renal Clear Cell Carcinoma U133B

description:
Age = 67; Gender = Male; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 2; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Tumor Location: lower; Scaling Target = 500; Scaling Factor = 29.68; Raw Q = 1.83; Noise = 1.42; Background = 45.34.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: N1 Normal Human Kidney U133B

description:
Age = 51; Gender = Male; Left Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 3; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = true; Adjacent Tumor Renal Vein Invasion = true; Adjacent Tumor Location: mid; Scaling Target = 500; Scaling Factor = 22.09; Raw Q = 2.04; Noise = 1.74; Background = 46.76.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1154

description:
HUVEC from 3 different umbilical cords were plated onto 100ul of bovine type I collagen in 96-well microtitre plates (15 wells/cord). At times 0, 0.5, 3, 6 and
24 hours after stimulation with PMA and RMAC11, total RNA was isolated using the TRIZOL procedure. Message Amp aRNA Kit was used to linearly amplify the mRNA approximately 400-fold. The aRNA was generated incorporating 5-(3-aminoallyl)-UTP
and subsequently coupled to Cy3 and Cy5 dyes.

source_name: time 6 hours


title: N005 Normal Human Kidney U133B

description:
Age = 64; Gender = Male; Right Kidney; Adjacent Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = false; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 21.61; Raw Q = 2.11; Noise = 2.00; Background = 50.89.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C032 Renal Clear Cell Carcinoma U133B

description:
Age = 65; Gender = Female; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 10.31; Raw Q = 2.83; Noise = 3.35; Background = 69.63.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C011 Renal Clear Cell Carcinoma U133B

description:
Age = 55; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 19.66; Raw Q = 3.54; Noise = 6.02; Background = 110.7.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: N001 Normal Human Kidney U133B

description:
Age = 58; Gender = Male; Left Kidney; Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 22.09; Raw Q = 2.04; Noise = 1.74; Background = 46.76.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C001 Renal Clear Cell Carcinoma U133B

description:
Age = 58; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Tumor Location: lower; Scaling Target = 500; Scaling Factor = 11.56; Raw Q = 2.72; Noise = 3.47; Background = 68.43.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C035 Renal Clear Cell Carcinoma U133B

description:
Age = 70; Gender = Female; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 3; Tumor Capsule Penetration = true; Tumor Perinephric Fat Invasion = true; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = true; Scaling Target = 500; Scaling Factor = 14.77; Raw Q = 2.47; Noise = 2.53; Background = 57.93.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: C005 Renal Clear Cell Carcinoma U133B

description:
Age = 64; Gender = Male; Right Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 1; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = false; Tumor Renal Vein Invasion = false; Scaling Target = 500; Scaling Factor = 11.09; Raw Q = 3.12; Noise = 4.65; Background = 76.41
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1157

source_name: time 3 hours


title: #33 (isolate 36 rich media untreated)

status: Public on Nov 21 2003

city: Cambridge

first: Cristin

last: Print

country: United Kingdom

institute: Cambridge University

description: HUVEC isolate 36 rich media untreated

source_name: HUVEC


title: N035 Normal Human Kidney U133B

description:
N035 Normal Human Kidney U133B
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1161

source_name: time 0.5 hours


title: C3 Renal Clear Cell Carcinoma U133A

description:
Age = 50; Gender = Male; Left Kidney; Tumor Type = clear cell; Tumor Fuhrman Grade = 2; Tumor Capsule Penetration = false; Tumor Perinephric Fat Invasion = false; Tumor Renal Sinus Invasion = true; Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 4.77; Raw Q = 2.87; Noise = 3.57; Background = 70.69.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2004638


title: slide 1155


title: slide 1160


title: #26 (isolate Z low serum media PlGF 24hours)

description: HUVEC isolate Z low serum media PlGF 24hours cf. #25


title: slide 1163

source_name: time 0.5 hour


title: slide 1156


title: #32 (isolate 9 rich media untreated)

description: HUVEC isolate 9 rich media untreated


title: slide 1159


title: N023 Normal Human Kidney U133B

description:
Age = 72; Gender = Female; Right Kidney; Tumor Type = clear cell; Adjacent Tumor Fuhrman Grade = 1; Adjacent Tumor Capsule Penetration = true; Adjacent Tumor Perinephric Fat Invasion = false; Adjacent Tumor Renal Sinus Invasion = false; Adjacent Tumor Renal Vein Invasion = false; Tumor Location: mid; Scaling Target = 500; Scaling Factor = 7.30; Raw Q = 2.49; Noise = 2.89; Background = 56.96.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Lot batch = 2002912


title: slide 1158


title: slide 1167


title: slide 1164


title: #30 (isolate 8 low serum media PlGF 24hours)

description: HUVEC isolate 8 low serum media PlGF 24hours cf. #29


title: slide 1162


title: #29 (isolate 8 low serum media control)

description: HUVEC isolate 8 low serum media control for #30


title: slide 1153


title: #31 (isolate 22 rich media untreated)

description: HUVEC isolate 22 rich media untreated


title: #27 (isolate V low serum media control)

description: HUVEC isolate V low serum media control for #28


title: #24 (isolate H rich media PlGF 24hours)

description: HUVEC isolate H rich media PlGF 24hours cf. #23


title: slide 1166

description: HUVEC from 3 different umbilical cords were plated onto 100ul of bovine type I collagen in 96-well microtitre plates (15 wells/cord). At times 0, 0.5, 3, 6 and 24 hours after stimulation with PMA and RMAC11, total RNA was isolated using the TRIZOL procedure. Message Amp aRNA Kit was used to linearly amplify the mRNA approximately 400-fold. The aRNA was generated incorporating 5-(3-aminoallyl)-UTP and subsequently coupled to Cy3 and Cy5 dyes.

source_name: time 0 hour


title: #25 (isolate Z low serum media control)

description: HUVEC isolate Z low serum media control for #26


title: #16 (isolate 22 low serum media VEGF-A 24hours)

description: HUVEC isolate 22 low serum media VEGF-A 24hours cf. #15


title: #19 (isolate V rich media control)

description: HUVEC isolate V rich media control for #20


title: #12 (isolate 36 low serum media VEGF-A 4hours)

description: HUVEC isolate 36 low serum media VEGF-A 4hours cf. #11


title: #20 (isolate V rich media PlGF 24hours)

description: HUVEC isolate V rich media PlGF 24hours cf. #19


title: #18 (isolate 36 low serum media VEGF-A 42hours)

description: HUVEC isolate 36 low serum media VEGF-A 42hours cf. #17


title: #8 (isolate 9 low serum media VEGF-A 4hours)

description: HUVEC isolate 9 low serum media VEGF-A 4hours cf. #7


title: #13 (isolate 9 low serum media control)

description: HUVEC isolate 9 low serum media control for #14


title: #22 (isolate 8 rich media plGF 24hours)

description: HUVEC isolate 8 rich media plGF 24hours cf. #21


title: #10 (isolate 22 low serum media VEGF-A 4hours)

description: HUVEC isolate 22 low serum media VEGF-A 4hours cf. #9


title: #11 (isolate 36 low serum media control)

description: HUVEC isolate 36 low serum media control for #12


title: #3 (isolate 55 rich media control)

description: HUVEC isolate 55 rich media control for #4


title: #14 (isolate 9 low serum media VEGF-A 24hours)

description: HUVEC isolate 9 low serum media VEGF-A 24hours cf. #13


title: #15 (isolate 22 low serum media control)

description: HUVEC isolate 22 low serum media control for #16


title: #9 (isolate 22 low serum media control)

description: HUVEC isolate 22 low serum media control for #10


title: #23 (isolate H rich media control)

description: HUVEC isolate H rich media control for #24


title: #4 (isolate 55 rich media VEGF-A 24hours)

description: HUVEC isolate 55 rich media VEGF-A 24hours cf. #3


title: #17 (isolate 36 low serum media control)

description: HUVEC isolate 36 low serum media control for #18


title: #2 (isolate 52 rich media VEGF-A 24hours)

description: HUVEC isolate 52 rich media VEGF-A 24hours cf. #1


title: #7 (isolate 9 low serum media control)

description: HUVEC isolate 9 low serum media control for #8


title: #6 (isolate C rich media VEGF-A 24hours)

description: HUVEC isolate C rich media VEGF-A 24hours cf. #5


title: #1 (isolate 52 rich media control)

description: HUVEC isolate 52 rich media control for #2


title: #5 (isolate C rich media control)

description: HUVEC isolate C rich media control for #6


title: CA5_FA3_top

status: Public on Nov 15 2003

city: Urbana

first: Yewon

last: Cheon

state: IL

institute: University of Illinois at Urbana Champaign

organism: Sus scrofa

source_name: Porcine liver, 5 weeks, male, Yorkshire x Landrace, Clofibric Acid (0.5% w/w) treatment for 1 week

source_name: Porcine liver, 5 weeks, male, Yorkshire x Landrace, 24hr fasting


title: CA5_FE3_bot

source_name: Porcine liver, 5 weeks, male, Yorkshire x Landrace, fed


title: FA5_CA3_bot


title: FE5_FA3_top


title: FE5_CA3_top


title: 13_PAH

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description:
Pulmonary Arterial Hypertension PBMC sample
Sample_series_id: GSE703
Keywords = Pulmonary Arterial Hypertension
Keywords = PBMC

source_name: PBMC


title: 03_NOR


title: 01_NOR


title: FA5_FE3_bot


title: 12_PAH


title: 02_NOR


title: 06_NOR


title: 05_NOR


title: 05_PAH


title: 04_NOR


title: 10_PAH


title: 09_PAH


title: 06_PAH


title: 14_PAH


title: 11_PAH


title: 08_PAH


title: 04_PAH


title: 07_PAH


title: 03_PAH


title: 01_PAH


title: 02_PAH


title: IL4-treated primary aortic endothelial cells

status: Public on Nov 13 2003

city: Palo Alto

first: Terrill

middle: K.

last: McClanahan

address: 901 California Avenue

department: Experimental Pathology & Pharmacology

institute: DNAX Research Inc.

source_name: Control primary aortic endothelial cells


title: IL4-treated primary dermal endothelial cells

source_name: Control primary dermal endothelial cells


title: TNFa-treated primary colon endothelial cells

source_name: Control primary Colon endothelial cells

source_name: TNFa-treated primary Colon endothelial cells


title: TNFTG-3w-m-3

status: Public on Nov 09 2003

city: Philadelphia

first: Zhong

last: Tang

state: PA

address: 1025 Walnut Street

institute: Thomas Jefferson University

description: Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure.

source_name: heart


title: IL4-treated primary lung endothelial cells

source_name: Control primary lung endothelial cells

source_name: IL4-treated primary iliac endothelial cells


title: TNFTG-3w-m-2


title: TNFTG-3w-m-1


title: TNFTg-40w-f-3


title: TNFTG-3w-f-2


title: TNFTG-3w-f-3


title: TNF TG-13w-m-3


title: TNFTG-40w-f-2


title: TNFa-treated primary lung endothelial cells


title: TNF TG-13w-m-2


title: TNFTG-40w-f-1


title: IFNg-treated primary iliac endothelial cells

source_name: Control primary iliac endothelial cells


title: FVB-3wk-m-3

description: Cardiac-specific TNF-alpha transgenic mouse is an excellent model to study the pathologenesis of heart failure. Affytrix U74V2A was used to analyzed the gene expression profile of mice at the time point of compensated hypertrophy and dilated heart failure


title: TNF TG-13w-m-1


title: TNFa-treated primary iliac endothelial cells


title: TNFa-treated primary dermal endothelial cells


title: TNFa-treated primary aortic endothelial cells


title: IFNg-treated primary colon endothelial cells

source_name: Control primary colon endothelial cells


title: IFNg-treated primary lung endothelial cells


title: IFNg-treated primary aortic endothelial cells


title: TNFTG-3w-f-1


title: FVB-3wk-m-2


title: IL4-treated primary iliac endothelial cells


title: FVB-3w-f-2


title: ALS gray matter 2 Familial

status: Public on Nov 08 2003

first: Fernando

last: Dangond

institute: Brigham and Women's Hospital Laboratories

description: RNA isolated from post-mortem tissues

source_name: spinal cord


title: ALS gray matter 5 Sporadic

description: RNA isolated from post-mortem tissues


title: ALS gray matter 3 Sporadic

description: RNA isolated from post-mortem tissues


title: FVB-3wk-f-3


title: ALS gray matter 4 Sporadic

description: RNA isolated from post-mortem tissues


title: ALS gray matter 6 Sporadic

description: RNA isolated from post-mortem tissues


title: IFNg-treated primary dermal endothelial cells


title: FVB-3wk-m-1


title: ALS gray matter 1 Familial

description: RNA isolated from post-mortem tissues


title: Control gray matter 4

description: RNA isolated from post-mortem tissues


title: IL4-treated primary colon endothelial cells


title: Control gray matter 3

description: RNA isolated from post-mortem tissues


title: FVB-3w-f-1

description: Cardiac-specific TNF-alpha transgenic mice is an excellent model to study the pathologenesis of heart failure. Affymetrix U74V2A was used to analyzed the genes expression profile of mice at the time point of compensated hypertrophy and dilated heart failure.

source_name: mouse heart


title: Control gray matter 2

description: RNA isolated from post-mortem tissues


title: Normal Prostate Array B number N034

status: Public on Nov 07 2003

city: Rehovot

first: Orit

last: Shmueli

state: Israel

address: Rehovot

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: PolyA+ RNA samples from the twelve healthy human tissues were purchased from Clontech (Palo Alto, CA). Each RNA sample is typically composed of a pool of 10-25 individuals.

source_name: Normal Prostate


title: ALS gray matter 7 Sporadic

description: RNA isolated from post-mortem tissues


title: Normal Liver Array B number N020

source_name: Normal Liver


title: Normal Pancreas Array B number N037

source_name: Normal Pancreas


title: Normal Pancreas Array B number N035


title: Normal Kidney Array B number N026

source_name: Normal Kidney


title: Normal Bone marrow Array B number N021

source_name: Normal Bone marrow


title: Control gray matter 1

description: RNA isolated from post-mortem tissues


title: Normal Thymus Array B number N019

source_name: Normal Thymus


title: Normal Spinal cord Array B number N016

source_name: Normal Spinal cord


title: Normal Pancreas Array E number N037


title: Normal Brain Array B number N018

source_name: Normal Brain


title: Normal Prostate Array E number N036


title: Normal Spinal cord Array B number N010


title: Normal Brain Array B number N012


title: #28 (isolate V low serum media PlGF 24hours)

description: HUVEC isolate V low serum media PlGF 24hours cf. #27

source_name: HUVEC


title: Normal Prostate Array B number N036


title: Normal Kidney Array E number N026


title: Normal Thymus Array E number N019


title: Normal Prostate Array E number N034


title: Normal Skeletal muscle Array B number N009

source_name: Normal Skeletal muscle


title: Normal Spleen Array B number N008

source_name: Normal Spleen


title: Normal Bone marrow Array E number N021


title: Normal Lung Array E number N014

source_name: Normal Lung


title: Normal Pancreas Array E number N035


title: Normal Lung Array B number N014


title: Normal Thymus Array B number N011


title: Normal Skeletal muscle Array B number N013


title: Normal Heart Array B number N007

source_name: Normal Heart


title: Normal Liver Array E number N020


title: Normal Spinal cord Array E number N016


title: Normal Lung Array B number N005


title: Normal Brain Array E number N012


title: Normal Kidney Array B number N006


title: Normal Skeletal muscle Array E number N013


title: Normal Brain Array E number N018


title: #21 (isolate 8 rich media control)

description: HUVEC isolate 8 rich media control for #22


title: Normal Spinal cord Array E number N010


title: Normal Thymus Array E number N011


title: Normal Heart Array B number N003


title: Normal Liver Array B number N002


title: Normal Skeletal muscle Array E number N009


title: Normal Spleen Array E number N008


title: Normal Kidney Array E number N006


title: Normal Bone marrow Array D number N021


title: Normal Heart Array E number N007


title: Normal Prostate Array D number N034


title: Normal Prostate Array D number N036


title: Normal Bone marrow Array B number N001


title: Normal Pancreas Array D number N035


title: Normal Kidney Array D number N026


title: Normal Pancreas Array D number N037


title: Normal Liver Array D number N020


title: Normal Pancreas Array C number N035


title: Normal Brain Array D number N018


title: Normal Lung Array D number N014


title: Normal Thymus Array D number N019


title: Normal Lung Array E number N005


title: Normal Skeletal muscle Array D number N013


title: Normal Prostate Array C number N034


title: Normal Liver Array E number N002


title: Normal Pancreas Array C number N037


title: Normal Spleen Array E number N004


title: Normal Brain Array D number N012


title: Normal Heart Array E number N003


title: Normal Bone marrow Array E number N001


title: Normal Kidney Array C number N026


title: Normal Bone marrow Array C number N021


title: Normal Spinal cord Array D number N010


title: Normal Prostate Array C number N036


title: Normal Thymus Array D number N011


title: Normal Liver Array C number N020


title: Normal Spinal cord Array C number N016


title: Normal Thymus Array C number N019


title: Normal Skeletal muscle Array D number N009


title: Normal Skeletal muscle Array C number N013


title: Normal Spleen Array D number N008


title: Cry-deficient Circadian_Time_14

city: Tsukuba

first: Norio

last: Ishida

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description:
Cry deficient mice. male mice. 8- to 10-week-old.
Keywords = circatian rhythm

source_name: liver


title: Cry-deficient Circadian_Time_02

description:
Cry1 and Cry2 double knockout mice. male mice. 8- to 10-weeks-old.
Keywords = circatian rhythm


title: Normal Lung Array C number N014


title: Normal Brain Array C number N012


title: Normal Brain Array C number N018


title: Normal Spinal cord Array C number N010


title: Clock_mutant Circadian_Time_14

description:
Clock mutant mice. male mice. 8- to 10-week-old
Keywords = circatian rhythm


title: Normal Heart Array D number N007


title: Normal Spleen Array C number N008


title: Normal Thymus Array C number N011


title: Normal Kidney Array D number N006


title: Normal Heart Array C number N007


title: Normal Kidney Array C number N006


title: Normal Spleen Array D number N004


title: Normal Lung Array D number N005


title: Normal Skeletal muscle Array C number N009


title: Clock_mutant Circadian_Time_02

description:
Clock mutant mice. male mice. 8- to 10-week-old.
Keywords = circatian rhythm


title: Wild_Type Circadian_Time_14

description:
C57BL/6 background mice. male. 8- to 10-week-old.
Keywords = circatian rhythm


title: Normal Lung Array C number N005


title: Normal Heart Array D number N003


title: Normal Heart Array C number N003


title: Wild_Type Circadian_Time_02

description:
C57BL/6 background mice. male mice. 8- to 10-week-old.
Keywords = circatian rhythm


title: Normal Liver Array C number N002


title: Normal Bone marrow Array C number N001


title: Normal Spleen Array C number N004


title: Normal Liver Array D number N002


title: Normal Bone marrow Array D number N001


title: Normal Spinal cord Array D number N016


title: 3h HGF 3

status: Public on Nov 04 2003

first: David

last: Johnson

address: 415 Curie Blv

institute: University of Pennsylvania

description: MDCK epithelial cells were grown on Transwell filters for four days.  Cells were then treated with recombinant HGF for 3 hours. RNA was harvested and converted to cDNA and analyzed with the canine microarray described here.

organism: Canis lupus familiaris

source_name: MDCK cell line


title: 24h HGF 3

description: MDCK epithelial cells were grown on Transwell filters for four days.  Cells were then treated with recombinant HGF for 24 hours. RNA was harvested and converted to cDNA and analyzed with the canine microarray described here.

source_name: MDCK Cell Line


title: 24h HGF 2


title: 3h HGF 1


title: 3h HGF 2


title: Control 3

description: MDCK epithelial cells were grown on Transwell filters for four days. RNA was harvested and converted to cDNA and analyzed with the canine microarray described here.


title: Control 1


title: Early HF 4 (Mu11K-B)

status: Public on Nov 02 2003

city: Durham

first: Burns

last: Blaxall

state: NC

institute: Duke University Medical Center

description: The experiment was to test differential gene expression in early- and advanced-stage heart failure (HF), as well as in normal, HF, and transgenically "rescued" transgenic mice (please reference Blaxall, et al, Physiological Genomics 2003 for further information).  Each sample is from a single mouse left ventricle.  RNA was isolated using the guanidinium isothiocyanate method, and labeled and hybridized to Affymetrix Mu11K arrays as recommended by the manufacturer.

source_name: heart left ventricle


title: Advanced HF 5 (Mu11K-B)


title: Control 2


title: Early HF 5 (Mu11K-B)


title: Advanced HF 6 (Mu11K-B)


title: Early HF 3 (Mu11K-B)


title: Early HF 1 (Mu11K-B)


title: 24h HGF 1


title: Early HF 2 (Mu11K-B)


title: Transgenic 5 (Mu11K-B)


title: Advanced HF 4 (Mu11K-B)


title: Transgenic 6 (Mu11K-B)


title: Advanced HF 3 (Mu11K-B)


title: Transgenic 4 (Mu11K-B)


title: seedling leaf 8h UV-B-2

status: Public on Nov 03 2003

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Microarray hybridization was used to assess UV-B responses in directly exposed and shielded maize tissues. In this experiment, seedling leaves were tested for UV-B transcriptome changes after 8 h exposure

organism: Zea mays

source_name: control seedling leaves under no Uv-B

source_name: UV-B exposed seedling leaves


title: tassel 8 h UV-B-2

description: Microarray hybridization was used to assess UV-B responses in directly exposed and shielded maize tissues. In this experiment, emerging tassels were tested for UV-B transcriptome changes after 8 h exposure

source_name: no UV-B exposed tassels

source_name: UV-B exposed tassels


title: Transgenic 3 (Mu11K-B)


title: immature  ear-8h UV-B-2

description: Microarray hybridization was used to assess UV-B responses in directly exposed and shielded maize tissues. In this experiment, immature ears were tested for UV-B transcriptome changes after 8 h exposure

source_name: no UV-B treated ears

source_name: UV-B treated ears


title: Advanced HF 1 (Mu11K-B)


title: Transgenic 2 (Mu11K-B)


title: Advanced HF 2 (Mu11K-B)


title: Early HF 4 (Mu11K-A)


title: Rescue 10 (Mu11K-B)


title: Early HF 5 (Mu11K-A)


title: Rescue 11 (Mu11K-B)


title: Early HF 3 (Mu11K-A)


title: Rescue 9 (Mu11K-B)


title: Rescue 8 (Mu11K-B)


title: Rescue 7 (Mu11K-B)


title: Rescue 5 (Mu11K-B)


title: Heart Failure 12 (Mu11K-B)


title: Transgenic 1 (Mu11K-B)


title: Rescue 12 (Mu11K-B)


title: Rescue 2 (Mu11K-B)


title: Rescue 3 (Mu11K-B)


title: Rescue 6 (Mu11K-B)


title: Early HF 1 (Mu11K-A)


title: Early HF 2 (Mu11K-A)


title: Rescue 1 (Mu11K-B)


title: Heart Failure 11 (Mu11K-B)


title: Advanced HF 6 (Mu11K-A)


title: Heart Failure 10 (Mu11K-B)


title: Advanced HF 5 (Mu11K-A)


title: Advanced HF 4 (Mu11K-A)


title: Rescue 4 (Mu11K-B)


title: Advanced HF 2 (Mu11K-A)


title: Heart Failure 9 (Mu11K-B)


title: Advanced HF 3 (Mu11K-A)

description:
The experiment was to test differential gene expression in early- and advanced-stage heart failure (HF), as well as in normal, HF, and transgenically "rescued" transgenic mice (please reference Blaxall, et al, Physiological Genomics 2003 for further information).  Each sample is from a single mouse left ventricle.  RNA was isolated using the guanidinium isothiocyanate method, and labeled and hybridized to Affymetrix Mu11K arrays as recommended by the manufacturer.
Keywords = heart


title: Advanced HF 1 (Mu11K-A)


title: Heart Failure 8 (Mu11K-B)


title: Transgenic 5 (Mu11K-A)


title: Heart Failure 7 (Mu11K-B)


title: Transgenic 4 (Mu11K-A)


title: Normal Spleen Array B number N004

description: PolyA+ RNA samples from the twelve healthy human tissues were purchased from Clontech (Palo Alto, CA). Each RNA sample is typically composed of a pool of 10-25 individuals.


title: Transgenic 3 (Mu11K-A)


title: Heart Failure 5 (Mu11K-B)


title: Transgenic 2 (Mu11K-A)


title: Transgenic 6 (Mu11K-A)


title: Heart Failure 3 (Mu11K-B)


title: Heart Failure 4 (Mu11K-B)


title: Rescue 10 (Mu11K-A)


title: Heart Failure 2 (Mu11K-B)


title: Rescue 11 (Mu11K-A)


title: Rescue 8 (Mu11K-A)


title: Rescue 7 (Mu11K-A)


title: Transgenic 1 (Mu11K-A)


title: Rescue 12 (Mu11K-A)


title: Rescue 4 (Mu11K-A)


title: Rescue 3 (Mu11K-A)


title: Rescue 5 (Mu11K-A)


title: Rescue 9 (Mu11K-A)


title: Rescue 6 (Mu11K-A)


title: Rescue 2 (Mu11K-A)


title: Heart Failure 1 (Mu11K-B)


title: Heart Failure 6 (Mu11K-B)


title: Rescue 1 (Mu11K-A)


title: Normal 11 (Mu11K-B)


title: Heart Failure 10 (Mu11K-A)


title: Normal 12 (Mu11K-B)


title: Normal 10 (Mu11K-B)


title: Heart Failure 9 (Mu11K-A)


title: Heart Failure 12 (Mu11K-A)


title: Heart Failure 8 (Mu11K-A)


title: Normal 9 (Mu11K-B)


title: Normal 6 (Mu11K-B)


title: Normal 7 (Mu11K-B)


title: Heart Failure 11 (Mu11K-A)


title: Normal 8 (Mu11K-B)


title: Normal 12 (Mu11K-A)


title: Heart Failure 5 (Mu11K-A)


title: Normal 4 (Mu11K-B)


title: Heart Failure 1 (Mu11K-A)


title: Heart Failure 2 (Mu11K-A)


title: Normal 3 (Mu11K-B)


title: Normal 8 (Mu11K-A)


title: Normal 7 (Mu11K-A)


title: Normal 6 (Mu11K-A)


title: Normal 10 (Mu11K-A)


title: Normal 9 (Mu11K-A)


title: Heart Failure 4 (Mu11K-A)


title: Heart Failure 6 (Mu11K-A)


title: Normal 11 (Mu11K-A)


title: Normal 5 (Mu11K-B)


title: Heart Failure 3 (Mu11K-A)


title: Normal 4 (Mu11K-A)


title: Normal 1 (Mu11K-B)


title: Normal 2 (Mu11K-B)


title: Heart Failure 7 (Mu11K-A)


title: Normal 3 (Mu11K-A)


title: Normal 5 (Mu11K-A)


title: roots-8H UV-B-2

description: Microarray hybridization was used to assess UV-B responses in directly exposed and shielded maize tissues. In this experiment, roots were tested for UV-B transcriptome changes after 8 h exposure

source_name: roots from no UV-B treated plants

source_name: roots from UV-B exposed plants


title: Normal 2 (Mu11K-A)


title: Normal 1 (Mu11K-A)


title: RT 1-4

status: Public on Oct 30 2003

city: La Jolla

first: Jun

last: Lim

address: 10010 N. Torrey Pines Rd.

department: PBIO-E

institute: The Salk Institute for Biological Studies

description:
cRNA from Arabidopsis roots grown in Gamborg's liquid media
Keywords = Arabidopsis roots, tiling arrays

organism: Arabidopsis thaliana

source_name: Arabidopsis roots


title: FL 1-4

description:
cRNA from Arabidopsis flowers grown on soil
Keywords = Arabidopsis flowers, tiling arrays

source_name: Arabidopsis flowers


title: SC 1-4

description:
cRNA from Arabidopsis suspension cell culture
Keywords = Arabidopsis suspension cell culture, tiling arrays

source_name: Arabidopsis suspension cell culture


title: SC 1-6


title: SC 1-RC-6


title: SC 1-RC-1


title: RT 1-RC-1


title: RT 1-RC-6


title: SC 1-RC-5


title: FL 1-6


title: whole-genome 1-rc-1 L+

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

description: Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions.

source_name: Ecotype Columbia, Light grown 7-day old seedlings


title: whole-genome 1-rc-6 L+


title: FL 1-3


title: whole-genome 1-6 L+


title: RT 1-2


title: RT 1-3


title: RT 1-6


title: FL 1-RC-6


title: FL 1-RC-5


title: pilot 1C L-

source_name: Ecotype Columbia, Etiolated 7-day old seedlings


title: SC 1-3


title: RT 2C

description:
cRNA from Arabidopsis roots grown in Gamborg's liquid media
Keywords = Arabidopsis roots, pilot tiling arrays


title: SC 1-2


title: SC 1-5


title: RT 1-RC-4


title: FL 2C

description:
cRNA from Arabidopsis flowers grown on soil
Keywords = Arabidopsis flowers, pilot tiling arrays


title: pilot 1C L+


title: FL 1-RC-4


title: FL 1-2


title: RT 1-RC-5


title: whole-genome 1-4 L+


title: pilot 1C cold

source_name: Ecotype Columbia, Light grown 7-day old seedlings, treated at 4 degrees C for 24hrs


title: FL 1-1

description:
cRNA from Arabidopsis flowers
Keywords = Arabidopsis flowers


title: FL 1-5


title: SC 1-1


title: whole-genome 1-3 L+


title: SC 2C

description:
cRNA from Arabidopsis suspension cell culture
Keywords = Arabidopsis suspension cell culture, pilot tiling arrays


title: whole-genome 1-rc-5 L+


title: FL 1-RC-1


title: whole-genome 1-rc-4 L+


title: whole-genome 1-2 L+


title: SC 1-RC-3


title: pilot 1A L+


title: SC 1-RC-4


title: RT 1-1


title: RT 1-5


title: pilot 1B L+


title: pilot 1A L-


title: SC 1B


title: RT 1-RC-3


title: FL 1A


title: SC 2D


title: SC 1A


title: RT 1A


title: whole-genome 1-rc-3 L+


title: RT 1B


title: FL 1B


title: RT 2D


title: FL 1-RC-3


title: whole-genome 1-5 L+


title: 15208L

status: Public on Oct 29 2003

city: South San Francisco

first: Scott

middle: Curtis

last: Lohr

address: 290 Utah Ave.

department: Bioinformatics

institute: AGY Therapeutics Inc.

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 56
Sample_probe_id: 449

source_name: BV2, Abeta, 24h, control


title: 15208J

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 18
Sample_probe_id: 449


title: whole-genome 1-1 L+


title: 15208K

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 61
Sample_probe_id: 449


title: pilot 1D L-


title: FL 2D


title: pilot 1D L+


title: pilot 1D cold


title: pilot 1A cold


title: pilot 1B cold


title: 11552L

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 103
Sample_probe_id: 449


title: 11552K

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 184
Sample_probe_id: 449


title: pilot 1B L-


title: 11552W

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 62
Sample_probe_id: 467


title: 11552O

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 832
Sample_probe_id: 450

source_name: BV2, Abeta, 24h, stimulated


title: 15208O

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 22
Sample_probe_id: 450


title: 15208X

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 43
Sample_probe_id: 467


title: FL 1-RC-2


title: RT 1-RC-2

description:
cRNA from Arabidopsis roots grown in Gamborg's liquid media
Keywords = Arabidopsis roots, tiling arrays


title: 15208N

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 44
Sample_probe_id: 450


title: 15208V

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 58
Sample_probe_id: 467


title: 11552M

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 695
Sample_probe_id: 450


title: 11552N

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 651
Sample_probe_id: 450


title: 15208I

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 41
Sample_probe_id: 448


title: 11552V

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 74
Sample_probe_id: 467


title: 15208W

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 55
Sample_probe_id: 467


title: 15208H

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 27
Sample_probe_id: 448


title: 15208G

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 45
Sample_probe_id: 448


title: 11552I

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 59
Sample_probe_id: 448


title: 11552F

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 118
Sample_probe_id: 447


title: 15208E

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 70
Sample_probe_id: 447


title: 15208D

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 72
Sample_probe_id: 447


title: 11552G

description:
Probe Generation
Probes were generated from three independent BV2 cultures treated with freshly sonicated Abeta-42 peptide (California Peptide) along with controls. Briefly, mRNA was isolated from those cells as described previously.  Double-stranded cDNA (ds-cDNA) was generated by reverse transcription and second-strand synthesis, and digested with RsaI (New England Biolabs, Beverly, MA). Probes were generated through labeling with 33P-dCTP (Perkin Elmer Lifesciences, Boston, MA) using a Decamer labeling kit (Ambion, Austin, Texas).
Filter Hybridization
Hybridization of probes to filters was performed at 42.C for 24 hr in a hybridization solution containing 50% formamide.
Data Collection
A Cyclone phosphorimaging system (Packard Biosciences, Meriden, CT) and GenePix software analysis (GenePix Pro 3.0.6.24, Axon Instruments, Foster City, CA) were used to obtain densitometry of the 33P signal.
Sample_normalization_factor: 138
Sample_probe_id: 448