title: MDA-MB-453 (U133B)

status: Public on Mar 05 2007

city: Princeton

first: Fei

last: Huang

institute: Bristol-Myers Squibb Co

description: Gene expression data from cultured breast cancer cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained using the Affymetrix Fluidics Station 400 according to Affymetrix standard procedures

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: cultured human breast cancer cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA isolated from cell culture using RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

tag: Dasatinib resistant


title: ZR-75-1 (U133B)

type: RNA

state: NJ

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens


title: P3_AS_HeLaS3_RCyP+_C03_B1

status: Public on May 25 2007

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

state: CA

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: See publication for details

hyb_protocol: See publication for details

scan_protocol: See publication for details

data_processing: See publication for details

molecule: polyA RNA

source_name: Total Cytoplasmic RNA from HeLa cell line

label_protocol: See publication for details

extract_protocol: Long RNA protocol - see publication for details

tag: See publication for details


title: MDA-MB-436 (U133B)


title: P3_AS_HDF_RCyP+_C17_B1

description: See publication for details

source_name: Total RNA from HDF cell line


title: P3_AS_HDF_RCyP+_C80_B1

description: See publication for details


title: MCF7 (U133B)


title: MCF7/Her2 (U133B)


title: Pooled glp-1 C elegans embryos_bleach NaOH prep_rep1

status: Public on May 16 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: Data were processed using the Rosetta Resolver® system (version 5.1), as described in Weng (2004).  Weng, L. (2004). Data processing and analysis methods in the Rosetta Resolver system, Rosetta Biosoftware Technical Note, http://www.rosettabio.com/tech/default.htm

organism: Caenorhabditis elegans

source_name: Pooled glp-1 C elegans embryos obtained by bleach sodium hydroxide treatment.

growth_protocol: Obtained from adults raised at 15ºC, grown on K agar plates with OP50 bacteria.

extract_protocol: After bleach-NaOH treatment and washing, eggs were resuspended in ~500uL K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.

treatment_protocol: Normal culturing conditions.

tag: Pool of ~5000 eggs at various developmental stages, Strain

value: JK1107, Genotype:glp-1(q224) III


title: ZR-75-30 (U133B)


title: P3_AS_HDF_RCyP+_C10_B1

description: See publication for details


title: P3_AS_HeLaS3_RCyP+_C02_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C08_B1

description: See publication for details


title: H3396 (U133B)


title: BT-549 (U133B)


title: MDA-MB-453 (U133A)


title: MDA-MB-435S (U133B)


title: HCC1428 (U133B)


title: ZR-75-1 (U133A)


title: MDA-MB-468 (U133B)


title: MDA-MB-436 (U133A)


title: BT-474 (U133B)


title: P3_AS_HeLaS3_RCyP+_C89_B1

description: See publication for details


title: AU-565 (U133B)


title: SK-BR-3 (U133B)


title: MCF7 (U133A)


title: HCC38 (U133B)


title: H3396 (U133A)


title: HCC70 (U133B)

tag: Dasatinib sensitive


title: P3_AS_HeLaS3_RCyP+_C01_B1

description: See publication for details


title: P3_AS_HDF_RCyP+_C81_B1

description: See publication for details


title: HCC1419 (U133B)


title: MCF7/Her2 (U133A)


title: HCC1428 (U133A)


title: HCC1954 (U133B)


title: MDA-MB-468 (U133A)


title: HCC38 (U133A)


title: MDA-MB-435S (U133A)


title: BT-474 (U133A)


title: MDA-MB-231 (U133B)


title: HS578T (U133B)


title: P3_AS_HeLaS3_RNuP+_C01_B1

description: See publication for details

source_name: Total Nuclear RNA from HeLa cell line


title: P3_AS_HDF_RCyP+_C89_B1

description: See publication for details


title: ZR-75-30 (U133A)


title: AU-565 (U133A)


title: MDA-MB-157 (U133B)


title: BT-549 (U133A)


title: HS578T (U133A)


title: HCC1806 (U133A)


title: BT-20 (U133A)


title: HCC1419 (U133A)


title: MDA-MB-231 (U133A)


title: P3_AS_HDF_RCyP+_C01_B1

description: See publication for details


title: HCC1954 (U133A)


title: HCC70 (U133A)


title: P3_AS_HDF_RCyP+_C79_B1

description: See publication for details


title: hGRB con 2/23/05 vs. U-off con 2/10/05 (ExpID 2834)

status: Public on Mar 02 2007

description: Total RNA was extracted from U-OFF or U-2OSbeta cells treated with ethanol vehicle for 6 hours using the RNAqueous Total RNA Isolation Kit.  RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents prior to use with the microarray.

data_processing: Gene expression analysis was conducted using Agilent Human1Av2 arrays. Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

tag: hGRB con 2/23/05


title: U-off con 2/3/05 vs. hGRB con 2/7/05 (ExpID 2832)

tag: U-off con 2/3/05

source_name: hGRB con 2/7/05 (Cy5)

tag: hGRB con 2/7/05


title: MDA-MB-157 (U133A)


title: U-off RU 2/10/05 vs. U-off con 2/10/05 (ExpID 2799)

description: Total RNA was extracted from U-OFF cells treated with either ethanol vehicle or 1uM RU-486 for 6 hours using the RNAqueous Total RNA Isolation Kit.  RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents prior to use with the microarray.


title: hGRB con 2/16/05 vs. U-off con 2/8/05 (ExpID 2833)

tag: hGRB con 2/16/05

tag: U-off con 2/8/05


title: SK-BR-3 (U133A)


title: U-off RU 2/3/05 vs. U-off con 2/3/05 (ExpID 2795)


title: U-off RU 2/8/05 vs. U-off con 2/8/05 (ExpID 2797)


title: hGRB con 2/7/05 vs. U-off con 2/3/05 (ExpID 2832)

source_name: hGRB con 2/7/05 (Cy3)


title: U-off con 1/26/05 vs. hGRB con 1/27/05 (ExpID 2831)

tag: hGRB con 1/27/05


title: U-off con 2/3/05 vs. U-off RU 2/3/05 (ExpID 2795)


title: hGRB RU 2/23/05 vs. hGRB con 2/23/05 (ExpID 2803)

description: Total RNA was extracted from U-2OSbeta cells treated with either ethanol vehicle or 1uM RU-486 for 6 hours using the RNAqueous Total RNA Isolation Kit.  RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents prior to use with the microarray.


title: U-off con 2/10/05 vs. hGRB con 2/23/05 (ExpID 2834)


title: U-off con 1/26/05 vs. U-off RU 1/26/05 (ExpID 2793)


title: U-off RU 1/26/05 vs. U-off con 1/26/05 (ExpID 2793)


title: hGRB con 2/23/05 vs. hGRB RU 2/23/05 (ExpID 2803)


title: U-off con 2/8/05 vs. hGRB con 2/16/05 (ExpID 2833)


title: U-off con 2/10/05 vs. U-off RU 2/10/05 (ExpID 2799)


title: hGRB con 2/16/05 vs. hGRB RU 2/16/05 (ExpID 2802)


title: hGRB con 1/27/05 vs. U-off con 1/26/05 (ExpID 2831)


title: hGRB RU 2/7/05 vs. hGRB con 2/7/05 (ExpID 2801)

tag: hGRB RU 2/7/05


title: hGRB RU 2/16/05 vs. hGRB con 2/16/05 (ExpID 2802)


title: U-off con 2/8/05 vs. U-off RU 2/8/05 (ExpID 2797)


title: hGRB con 2/7/05 vs. hGRB RU 2/7/05 (ExpID 2801)


title: hGRB RU 1/27/05 vs. hGRB con 1/27/05 (ExpID 2800)


title: hGRB con 1/27/05 vs. hGRB RU 1/27/05 (ExpID 2800)

description: Total RNA was extracted from U-OFF or U-2OSbeta cells treated with either ethanol vehicle or 1uM RU-486 for 6 hours using the RNAqueous Total RNA Isolation Kit.  RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents prior to use with the microarray.


title: In vitro erythroid differentiation at day 9, biological replicate 3

status: Public on Nov 09 2006

city: Philadelphia

first: Sankar

last: Addya

state: PA

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

description: Gene expression data from human adult-derived peripheral blood CD34+ hematopoietic progenitor cells after in vitro erythroid differentiation for 11 days with samples at days 1, 3, 5, 7, 9 and 11

hyb_protocol: Fragmented and biotin-labeled 2.5 µg target in 200 µl hybridization cocktail was used for each Affymetrix U133 Plus 2.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix Gene-Array scanner 3000

data_processing: The data were analyzed with Gene Chip Operating Software (GCOS v3.0) using Affymetrix default analysis settings.

label: Biotin

source_name: Human adult-derived peripheral blood CD34+ hematopoietic progenitor cells

label_protocol: Biotinylated cDNA was prepared from 50 ng total RNA using Ovation biotin RNA amplification and labeling system.

growth_protocol: Cells cultured for 11 days with samples at days 1, 3, 5, 7, 9 and 11.

extract_protocol: RNA was extracted by Qiagen RNAeasy micro kit according to the manufacturer's instructions.

treatment_protocol: CD34+ cells were cultured in serum-free medium in the presence of  dexamethasone (1µM), holo transferrin (0.3 mg/ml), erythropoietin (4 unit/ml), stem cell factor (10 ng/ml) and interleukin 3 (10 ng/ml).

tag: Human adult


title: In vitro erythroid differentiation at day 9, biological replicate 2


title: In vitro erythroid differentiation at day 7, biological replicate 2


title: In vitro erythroid differentiation at day 9, biological replicate 1


title: In vitro erythroid differentiation at Culture 3, biological replicate 3


title: In vitro erythroid differentiation at day 7, biological replicate 3


title: In vitro erythroid differentiation at day 5, biological replicate 2


title: In vitro erythroid differentiation at day 11, biological replicate 1


title: In vitro erythroid differentiation at day 5, biological replicate 3


title: In vitro erythroid differentiation at day 1, biological replicate 2


title: In vitro erythroid differentiation at day 3, biological replicate 1


title: BT-20 (U133B)


title: In vitro erythroid differentiation at day 1, biological replicate 3


title: HCC1806 (U133B)


title: In vitro erythroid differentiation at day 11, biological replicate 2


title: SO2122 vs. Fred Pep8 peritoneal mesothial (ExpID 2560)

status: Public on Apr 20 2006

description: Following exposure to 2000 ppm of o-nitrotoluene (o-NT) for two years, total RNA from rat peritoneal mesotheliomas was compared to a non-transformed mesothelial cell line (Fred-PE). RNAs were isolated with the RNeasy kit according to the manufacturer's protocols.

data_processing: Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

organism: Rattus norvegicus

source_name: Fred Pep8 peritoneal mesothial (Cy5)

tag: Fred Pep8 peritoneal mesothial


title: In vitro erythroid differentiation at day 1, biological replicate 1


title: Fred Pep8 peritoneal mesothial vs. SO2122 (ExpID 2560)

source_name: Fred Pep8 peritoneal mesothial (Cy3)


title: Fred Pep8 peritoneal mesothial vs. SO2274 (ExpID 2561)


title: Fred Pep8 peritoneal mesothial vs. SO2213 (ExpID 2557)

description: Following exposure to 1250 ppm of o-nitrotoluene (o-NT) for two years, total RNA from rat peritoneal mesotheliomas was compared to a non-transformed mesothelial cell line (Fred-PE). RNAs were isolated with the RNeasy kit according to the manufacturer's protocols.


title: Fred Pep8 peritoneal mesothial vs. SO2038 (ExpID 2558)


title: so2038 vs. Fred Pep8 peritoneal mesothial (ExpID 2558)


title: SO2213 vs. Fred Pep8 peritoneal mesothial (ExpID 2557)


title: Protonemata_1

status: Public on Aug 15 2006

city: University Park

first: Michael

middle: J

last: Axtell

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: Construction of small RNA cDNA libraries derived from polyacrylamide gel electrophoresis (PAGE) fractionated total RNA, adapter ligation, reverse transcription, and pyrosequencing was performed as described by Axtell et al. (2006) Cell 127: 565-577

hyb_protocol: none - direct sequencing

scan_protocol: none - direct sequencing

data_processing: NONE .. VALUE reflects number of times the given small RNA was sequenced in this sample.

organism: Physcomitrium patens

source_name: 7 day protonemata

label_protocol: none - direct sequencing

growth_protocol: samples cultivated on minimal media agar  overlaid with cellophane discs under standard conditions (16hr day, 8 hr night).  P. patens minimal media agar was composed of 10mM MgSO4, 184mM KH2PO4, 0.45mM FeSO4, 100mM KNO3, 0.22μM CuSO4*5H2O, 10μM H3BO3, 0.23μM CoCl2*6H2O, 0.1μM Na2MoO4*2H2O, 0.19μM ZnSO4*7H2O, 2μM MnCl2*4H2O, 0.17μM KI , 1mM CaCl2, 10mM NH4-tartarate.

extract_protocol: Total RNA was extracted from P. patens by grinding specimens in 100mM Tris-HCl pH 9.0, 2% hexadecyltrimethylammonium bromide (CTAB), 0.5% SDS, 2% polyvinyl pyrrilidone 40 (PVP-40), 5mM EDTA, 10mM β-mercaptoethanol.  The resulting slurry was phenol-chloroform extracted, followed by addition of sodium acetate (pH 5.2) to 300mM, followed by ethanol precipitation.  The resulting pellet was resuspended in 250mM NaCl, and placed on ice for 20 minutes to precipitate carbohydrates.  After centrifugation, the supernatant was ethanol precipitated to recover total RNA.

tag: 7 day wild-type protonemata


title: SO2542 vs. Fred Pep8 peritoneal mesothial (ExpID 2562)

description: Following exposure to 500 mg/l of bromochloracetic acid (BCA) for two years, total RNA from rat peritoneal mesotheliomas was compared to a non-transformed mesothelial cell line (Fred-PE).  RNAs were isolated with the RNeasy kit according to the manufacturer's protocols.


title: In vitro erythroid differentiation at day 3, biological replicate 3


title: Fred Pep8 peritoneal mesothial vs. SO2732 (ExpID 2565)

description: Following exposure to 250 mg/l of bromochloracetic acid (BCA) for two years, total RNA from rat peritoneal mesotheliomas was compared to a non-transformed mesothelial cell line (Fred-PE).  RNAs were isolated with the RNeasy kit according to the manufacturer's protocols.


title: In vitro erythroid differentiation at day 7, biological replicate 1


title: SO2274 vs. Fred Pep8 peritoneal mesothial (ExpID 2561)


title: Fred Pep8 peritoneal mesothial vs. SO2726 (ExpID 2564)


title: In vitro erythroid differentiation at day 5, biological replicate 1


title: SO2545 vs. Fred Pep8 peritoneal mesothial (ExpID 2563)

description: Following exposure to 1000 mg/l of bromochloracetic acid (BCA) for two years, total RNA from rat peritoneal mesotheliomas was compared to a non-transformed mesothelial cell line (Fred-PE).  RNAs were isolated with the RNeasy kit according to the manufacturer's protocols.


title: SO2726 vs. Fred Pep8 peritoneal mesothial (ExpID 2564)


title: Fred Pep8 peritoneal mesothial vs. SO2545 (ExpID 2563)


title: GamteophoresSporophytes_1

description:
Construction of small RNA cDNA libraries derived from polyacrylamide gel electrophoresis (PAGE) fractionated total RNA, adapter ligation, reverse transcription, and pyrosequencing was performed as described by Axtell et al. (2006) Cell 127: 565-577
UPDATED JULY 9, 2007 TO INCLUDE SMALL RNAS THAT DO NOT HAVE EXACT MATCHES TO THE GENOME

source_name: ~60 day Gametophores and Sporophytes

growth_protocol: samples cultivated on minimal media agar overlaid with cellophane discs under standard conditions (16hr day, 8 hr night). P. patens minimal media agar was composed of 10mM MgSO4, 184mM KH2PO4, 0.45mM FeSO4, 100mM KNO3, 0.22μM CuSO4*5H2O, 10μM H3BO3, 0.23μM CoCl2*6H2O, 0.1μM Na2MoO4*2H2O, 0.19μM ZnSO4*7H2O, 2μM MnCl2*4H2O, 0.17μM KI , 1mM CaCl2, 10mM NH4-tartarate.

extract_protocol: Total RNA was extracted from P. patens by grinding specimens in 100mM Tris-HCl pH 9.0, 2% hexadecyltrimethylammonium bromide (CTAB), 0.5% SDS, 2% polyvinyl pyrrilidone 40 (PVP-40), 5mM EDTA, 10mM β-mercaptoethanol. The resulting slurry was phenol-chloroform extracted, followed by addition of sodium acetate (pH 5.2) to 300mM, followed by ethanol precipitation. The resulting pellet was resuspended in 250mM NaCl, and placed on ice for 20 minutes to precipitate carbohydrates. After centrifugation, the supernatant was ethanol precipitated to recover total RNA.

tag: ~60 day old wild-type mature gametophores and sporophytes


title: In vitro erythroid differentiation at day 11, biological replicate 3


title: SO2732 vs. Fred Pep8 peritoneal mesothial (ExpID 2565)


title: Fred Pep8 peritoneal mesothial vs. SO2542 (ExpID 2562)


title: time course control vs. E, 24 hr (ExpID 2706)

status: Public on Apr 14 2006

description: Mice were treated with sesame oil or E2 and uteri were collected 24 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

data_processing: Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using default for all parameters.

organism: Mus musculus

source_name: time course control (Cy3)

tag: time course control

tag: E, 24 hr


title: E, 12 hr vs. time course control (ExpID 2705)

description: Mice were treated with sesame oil or E2 and uteri were collected 12 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

tag: E, 12 hr

source_name: time course control (Cy5)


title: time course control vs. E, 2 hr (ExpID 2703)

description: Mice were treated with sesame oil or E2 and uteri were collected two hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: E, 2 hr (Cy5)

tag: E, 2 hr


title: time course control vs. E, 6 hr (ExpID 2704)

description: Mice were treated with sesame oil or E2 and uteri were collected six hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: E, 6 hr (Cy5)

tag: E, 6 hr


title: time course control vs. E, 12 hr (ExpID 2705)


title: E, 24 hr vs. time course control (ExpID 2706)


title: E, 6 hr vs. time course control (ExpID 2704)

source_name: E, 6 hr (Cy3)


title: time course control vs. E, 30 min (ExpID 2702)

description: Mice were treated with sesame oil or E2 and uteri were collected 30 minutes after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: E, 30 min (Cy5)

tag: E, 30 min


title: alpha ERKO 19NT 24h vs. alpha ERKO V

status: Public on Apr 07 2006

description: Mice were treated with sesame oil or 19NT and uteri were collected 24 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

data_processing: Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v8.1), using default for all parameters.

source_name: alpha ERKO 19NT 24h (Cy3)

tag: alpha ERKO 19NT 24h

source_name: alpha ERKO V (Cy5)

tag: alpha ERKO V


title: E, 2 hr vs. time course control (ExpID 2703)

source_name: E, 2 hr (Cy3)


title: E, 30 min vs. time course control (ExpID 2702)

source_name: E, 30 min (Cy3)


title: WT 19NT 24h vs. WT V

source_name: WT 19NT 24h (Cy3)

tag: WT 19NT 24h

source_name: WT V (Cy5)

tag: WT V


title: alphaERKO E2, 2h vs. alphaERKO Vehicle control

description: Mice were treated with sesame oil or E2 and uteri were collected 2 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: alphaERKO E2, 2h (Cy3)

tag: alphaERKO E2, 2h

source_name: alphaERKO Vehicle control (Cy5)

tag: alphaERKO Vehicle control


title: WT V vs. WT 19NT 24h

source_name: WT V (Cy3)

source_name: WT 19NT 24h (Cy5)


title: Protonemata-YoungGametophores_1

description:
Construction of small RNA cDNA libraries derived from polyacrylamide gel electrophoresis (PAGE) fractionated total RNA, adapter ligation, reverse transcription, and pyrosequencing was performed as described by Axtell et al. (2006) Cell 127: 565-577
UPDATED JULY 9, 2007 TO INCLUDE SEQUENCED SMALL RNAS THAT DO NOT HAVE EXACT MATCHES TO THE GENOME

source_name: 14 day old P. patens

tag: 14 day old wild-type P. patens -- Protonemata and young Gametophores


title: alpha ERKO V vs. alpha ERKO 19NT 24h

source_name: alpha ERKO V (Cy3)

source_name: alpha ERKO 19NT 24h (Cy5)


title: alphaERKO Estren, 2h vs. alphaERKO Vehicle control

description: Mice were treated with sesame oil or estren and uteri were collected 2 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: alphaERKO Estren, 2h (Cy3)

tag: alphaERKO Estren, 2h


title: alphaERKO E2, 24h vs. alphaERKO Vehicle control

source_name: alphaERKO E2, 24h (Cy3)

tag: alphaERKO E2, 24h


title: alphaERKO Vehicle control vs. alphaERKO Estren, 24h

description: Mice were treated with sesame oil or estren and uteri were collected 24 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: alphaERKO Vehicle control (Cy3)

source_name: alphaERKO Estren, 24h (Cy5)

tag: alphaERKO Estren, 24h


title: DHT 24 h vs. Vehicle

description: Mice were treated with sesame oil or DHT and uteri were collected 24 hours after treatment and snap frozen in liquid nitrogen.  Three or four uteri from each treatment group were pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: DHT 24 h (Cy3)

tag: DHT 24 h

source_name: Vehicle (Cy5)

tag: Vehicle


title: Vehicle vs. DHT 24 h

source_name: Vehicle (Cy3)

source_name: DHT 24 h (Cy5)


title: alphaERKO Estren, 24h vs. alphaERKO Vehicle control

source_name: alphaERKO Estren, 24h (Cy3)


title: alphaERKO Vehicle control vs. alphaERKO Estren, 2h

source_name: alphaERKO Estren, 2h (Cy5)


title: alphaERKO Vehicle control vs. alphaERKO E2, 24h

source_name: alphaERKO E2, 24h (Cy5)


title: alphaERKO Vehicle control vs. alphaERKO E2, 2h

source_name: alphaERKO E2, 2h (Cy5)


title: WT E2, 24h vs. WT Vehicle control

tag: WT E2, 24h

source_name: WT Vehicle control (Cy5)

tag: WT Vehicle control


title: WT E2, 2h vs. WT Vehicle control

source_name: WT E2, 2h (Cy3)

tag: WT E2, 2h"


title: WT Vehicle control vs. WT Estren, 2h

source_name: WT Vehicle control (Cy3)

source_name: WT Estren, 2h (Cy5)

tag: WT Estren, 2h


title: WT Vehicle control vs. WT E2, 2h

source_name: WT E2, 2h (Cy5)

tag: WT E2, 2h


title: WT Vehicle control vs. WT E2, 24h


title: hGRalpha-D3 vehicle vs. hGRalpha-D3 DEX, Array 2, Biorep 2

status: Public on Jun 20 2005

description:
This experiment was used to compare cytoplasmic RNA samples from a U-2 OS cell line stably expressing hGRalpha-D3 treated with 100 nM DEX or vehicle for 6 hours.
Keywords = Glucocorticoid Receptor Isoforms

molecule: cytoplasmic RNA

source_name: Cy3: hGRalpha-D3 DEX

source_name: Cy5: hGRalpha-D3 vehicle


title: hGRalpha-B vehicle vs. hGRalpha-B DEX, Array 1, Biorep 2

description:
This experiment was used to compare cytoplasmic RNA samples from a U-2 OS cell line stably expressing hGRalpha-B treated with 100 nM DEX or vehicle for 6 hours.
Keywords = Glucocorticoid Receptor Isoforms

source_name: Cy3: hGRalpha-B vehicle

source_name: Cy5: hGRalpha-B DEX


title: hGRalpha-C3 vehicle vs. hGRalpha-C3 DEX, Array 2, Biorep 2

description:
This experiment was used to compare cytoplasmic RNA samples from a U-2 OS cell line stably expressing hGRalpha-C3 treated with 100 nM DEX or vehicle for 6 hours.
Keywords = Glucocorticoid Receptor Isoforms

source_name: Cy3: hGRalpha-C3 DEX

source_name: Cy5: hGRalpha-C3 vehicle


title: hGRalpha-D3 vehicle vs. hGRalpha-D3 DEX, Array 1, Biorep 2

source_name: Cy3: hGRalpha-D3 vehicle

source_name: Cy5: hGRalpha-D3 DEX


title: hGRalpha-A vehicle vs. hGRalpha-A DEX, Array 2, Biorep 2

description:
This experiment was used to compare cytoplasmic RNA samples from a U-2 OS cell line stably expressing hGRalpha-A treated with 100 nM DEX or vehicle for 6 hours.
Keywords = Glucocorticoid Receptor Isoforms

source_name: Cy3: hGRalpha-A DEX

source_name: Cy5: hGRalpha-A vehicle


title: hGRalpha-A vehicle vs. hGRalpha-A DEX, Array 1, Biorep 2

source_name: Cy3: hGRalpha-A vehicle

source_name: Cy5: hGRalpha-A DEX


title: WT Estren, 24h vs. WT Vehicle control

source_name: WT Estren, 24h (Cy3)

tag: WT Estren, 24h

source_name: WT Vehicle control (Cy5)


title: hGRalpha vehicle vs. hGRalpha DEX, Array 2, Biorep 2

description:
This experiment was used to compare cytoplasmic RNA samples from a U-2 OS cell line stably expressing hGRalpha treated with 100 nM DEX or vehicle for 6 hours.
Keywords = Glucocorticoid Receptor Isoforms

source_name: Cy3: hGRalpha DEX

source_name: Cy5: hGRalpha vehicle


title: WT Estren, 2h vs. WT Vehicle control

source_name: WT Estren, 2h (Cy3)


title: hGRalpha-C3 vehicle vs. hGRalpha-C3 DEX, Array 2, Biorep 1


title: hGRalpha-C3 vehicle vs. hGRalpha-C3 DEX, Array 1, Biorep 1


title: hGRalpha-C3 vehicle vs. hGRalpha-C3 DEX, Array 1, Biorep 2

source_name: Cy3: hGRalpha-C3 vehicle

source_name: Cy5: hGRalpha-C3 DEX


title: WT Vehicle control vs. WT Estren, 24h

source_name: WT Vehicle control (Cy3)

source_name: WT Estren, 24h (Cy5)


title: hGRalpha-D3 vehicle vs. hGRalpha-D3 DEX, Array 2, Biorep 1

source_name: Cy3: hGRalpha-D3 DEX

source_name: Cy5: hGRalpha-D3 vehicle


title: hGRalpha-D3 vehicle vs. hGRalpha-D3 DEX, Array 1, Biorep 1

source_name: Cy3: hGRalpha-D3 vehicle


title: hGRalpha-B vehicle vs. hGRalpha-B DEX, Array 2, Biorep 2

source_name: Cy3: hGRalpha-B DEX

source_name: Cy5: hGRalpha-B vehicle


title: hGRalpha vehicle vs. hGRalpha DEX, Array 1, Biorep 1

source_name: Cy3: hGRalpha vehicle

source_name: Cy5: hGRalpha DEX


title: hGRalpha-A vehicle vs. hGRalpha-A DEX, Array 2, Biorep 1

source_name: Cy3: hGRalpha-A DEX

source_name: Cy5: hGRalpha-A vehicle


title: hGRalpha-B vehicle vs. hGRalpha-B DEX, Array 2, Biorep 1


title: hGRalpha vehicle vs. hGRalpha DEX, Array 1, Biorep 2


title: hGRalpha vehicle vs. hGRalpha DEX, Array 2, Biorep 1


title: hGRalpha-A vehicle vs. hGRalpha-A DEX, Array 1, Biorep 1

source_name: Cy3: hGRalpha-A vehicle

source_name: Cy5: hGRalpha-A DEX


title: hGRalpha-B vehicle vs. hGRalpha-B DEX, Array 1, Biorep 1

source_name: Cy3: hGRalpha-B vehicle

source_name: Cy5: hGRalpha-B DEX


title: SHR-3week vs. SHR-9week (Array 4)

status: Public on Dec 01 2004

description: Age-related gene expression profile of spontaneously-hypertensive rats (SHR) between a pre-hypertensive stage (3 weeks of age) and a hypertensive stage (9 weeks of age).

source_name: SR: SHR-9week (Cy5)

source_name: SG: SHR-3week (Cy3)


title: WKY-9week vs. SHR-9week (Array 4)

description: Renal gene expression profile between spontaneously-hypertensive rats (SHR) and Wistar-Kyoto (WKY) control rats at a hypertensive stage (9 weeks of age).

source_name: SR: SHR-9week (Cy3)

source_name: SG: WKY-9week (Cy5)


title: SHR-3week vs. SHR-9week (Array 1)

source_name: SG: SHR-3week (Cy5)


title: WKY-3week vs. WKY-9week (Array 4)

description: Age-related gene expression profile of Wistar-Kyoto (WKY) control rats between a pre-hypertensive stage (3 weeks of age) and a hypertensive stage (9 weeks of age).

source_name: SR: WKY-9week (Cy5)

source_name: SG: WKY-3week (Cy3)


title: WKY-3week vs. WKY-9week (Array 3)


title: SHR-3week vs. SHR-9week (Array 3)


title: WKY-9week vs. SHR-9week (Array 3)


title: WKY-3week vs. WKY-9week (Array 2)

source_name: SR: WKY-9week (Cy3)

source_name: SG: WKY-3week (Cy5)


title: SHR-3week vs. SHR-9week (Array 2)


title: WKY-3week vs. WKY-9week (Array 1)


title: WKY-3week vs. SHR-3week (Array 1)

description: Renal gene expression profile between spontaneously-hypertensive rats (SHR) and Wistar-Kyoto (WKY) control rats at a pre-hypertensive stage (3 weeks of age).

source_name: SR: SHR-3week (Cy5)


title: WKY-3week vs. SHR-3week (Array 4)

source_name: SR: SHR-3week (Cy3)


title: WKY-3week vs. SHR-3week (Array 3)


title: WKY-9week vs. SHR-9week (Array 2)

source_name: SG: WKY-9week (Cy3)


title: WKY-9week vs. SHR-9week (Array 1)


title: Parent vs. Rpn4-Null (Array#1)

status: Public on Nov 01 2004

description: Comparison of RNA from Rpn4-null S.cerevisiae (strain BY4741) cultures to RNA from S.cerevisiae (strain BY4741) parent cultures.

organism: Saccharomyces cerevisiae

source_name: Cy3: Parent

source_name: Cy5: Rpn4-Null


title: Arr1-Null vs. Parent (Array#2)

description: Comparison of RNA from Arr1-null S.cerevisiae (strain BY4741) cultures to RNA from S.cerevisiae (strain BY4741) parent cultures.

source_name: Cy3: Arr1-Null

source_name: Cy5: Parent


title: Cad1-Null vs. Parent (Array#2)

description: Comparison of RNA from Cad1-null S.cerevisiae (strain BY4741) cultures to RNA from S.cerevisiae (strain BY4741) parent cultures.

source_name: Cy3: Cad1-Null


title: Yap1-Null vs. Parent (Array#2)

description: Comparison of RNA from Yap1-null S.cerevisiae (strain BY4741) cultures to RNA from S.cerevisiae (strain BY4741) parent cultures.

source_name: Cy3: Yap1-Null


title: Parent AsIII vs. Parent Control (Array#4)

description: Comparison of RNA from S.cerevisiae (strain BY4741) cultures treated with 100uM NaAsO2 for 2hrs (AsIII) to untreated RNA from S.cerevisiae (strain BY4741) cultures.

source_name: Cy3: Parent AsIII

source_name: Cy5: Parent Control


title: Parent vs. Cad1-Null (Array#1)

source_name: Cy5: Cad1-Null


title: Parent AsIII vs. Parent Control (Array#2)


title: Parent vs. Yap1-null (Array#1)

source_name: Cy5: Yap1-Null


title: Rpn4-Null vs. Parent (Array#2)

source_name: Cy3: Rpn4-Null


title: 4hr Control vs. 4hr 100uM AsIII (Array 4)

description: A S.cerevisiae strain BY474 culture was treated with 100uM NaAsO2 (AsIII) for 4 hours and compared to the untreated control culture.

source_name: SR: 4hr 100uM AsIII (Cy5)

source_name: SG: 4hr Control (Cy3)


title: 4hr Control vs. 4hr 100uM AsIII (Array 3)


title: Rpn4-Null AsIII vs. Rpn4-Null Control (Array #2)

description: Comparison of RNA from Rpn4-null S.cerevisiae (strain BY4741) cultures treated with 100uM NaAsO2 for 2hrs (AsIII) to untreated RNA from Rpn4-null S.cerevisiae (strain BY4741) cultures.

source_name: Cy3: Rpn4-Null AsIII

source_name: Cy5: Rpn4-Null Control


title: Parent Control vs. Parent AsIII (Array#3)

source_name: Cy3: Parent Control

source_name: Cy5: Parent AsIII


title: Parent Control vs. Parent AsIII (Array#1)


title: Cad1-Null Control vs. Cad1-Null AsIII (Array#1)

description: Comparison of RNA from Cad1-null S.cerevisiae (strain BY4741) cultures treated with 100uM NaAsO2 for 2hrs (AsIII) to untreated RNA from Cad1-null S.cerevisiae (strain BY4741) cultures.

source_name: Cy3: Cad1-Null Control

source_name: Cy5: Cad1-Null AsIII


title: Arr1-Null Control vs. Arr1-Null AsIII (Array #1)

description: Comparison of RNA from Arr1-null S.cerevisiae (strain BY4741) cultures treated with 100uM NaAsO2 for 2hrs (AsIII) to untreated RNA from Arr1-null S.cerevisiae (strain BY4741) cultures.

source_name: Cy3: Arr1-Null Control

source_name: Cy5: Arr1-Null AsIII


title: Parent vs. Arr1-Null (Array#1)

source_name: Cy3: Parent

source_name: Cy5: Arr1-Null


title: Yap1-Null AsIII vs. Yap1-Null Control (Array#2)

description: Comparison of RNA from Yap1-null S.cerevisiae (strain BY4741) cultures treated with 100uM NaAsO2 for 2hrs (AsIII) to untreated RNA from Yap1-null S.cerevisiae (strain BY4741) cultures.

source_name: Cy3: Yap1-Null AsIII

source_name: Cy5: Yap1-Null Control


title: Rpn4-Null Control vs. Rpn4-Null AsIII (Array #1)

source_name: Cy3: Rpn4-Null Control

source_name: Cy5: Rpn4-Null AsIII


title: 4hr Control vs. 4hr 100uM AsIII (Array 1)

source_name: SR: 4hr 100uM AsIII (Cy3)

source_name: SG: 4hr Control (Cy5)


title: Cad1-Null AsIII vs. Cad1-Null Control (Array#2)

source_name: Cy3: Cad1-Null AsIII

source_name: Cy5: Cad1-Null Control


title: 2hr Control vs. 2hr 100uM AsIII (Array 4)

description: A S.cerevisiae strain BY474 culture was treated with 100uM NaAsO2 (AsIII) for 2 hours and compared to the untreated control culture.

source_name: SR: 2hr 100uM AsIII (Cy5)

source_name: SG: 2hr Control (Cy3)


title: Arr1-Null AsIII vs. Arr1-Null Control (Array#2)

source_name: Cy3: Arr1-Null AsIII

source_name: Cy5: Arr1-Null Control


title: 2hr Control vs. 2hr 100uM AsIII (Array 3)


title: 2hr Control vs. 2hr 100uM AsIII (Array 2)

source_name: SR: 2hr 100uM AsIII (Cy3)

source_name: SG: 2hr Control (Cy5)


title: Yap1-Null Control vs. Yap1-Null AsIII (Array#1)

source_name: Cy3: Yap1-Null Control

source_name: Cy5: Yap1-Null AsIII


title: 30min Control vs. 30min 1mM AsIII (Array 4, Biorep 2)

description: A S.cerevisiae strain BY474 culture was treated with 1mM NaAsO2 (AsIII) for 30 minutes and compared to the untreated control culture.

source_name: SR: 30min 1mM AsIII (Cy5)

source_name: SG: 30min Control (Cy3)


title: 4hr Control vs. 4hr 100uM AsIII (Array 2)


title: 30min Control vs. 30min 1mM AsIII (Array 3, Biorep 2)


title: 30min Control vs. 30min 1mM AsIII (Array 2, Biorep 2)

source_name: SR: 30min 1mM AsIII (Cy3)

source_name: SG: 30min Control (Cy5)


title: 30min Control vs. 30min 100uM AsIII (Array 4)

description: A S.cerevisiae strain BY474 culture was treated with 100uM NaAsO2 (AsIII) for 30 minutes and compared to the untreated control culture.

source_name: SR: 30min 100uM AsIII (Cy5)


title: 30min Control vs. 30min 1mM AsIII (Array 1, Biorep 2)


title: 30min Control vs. 30min 1mM AsIII (Array 4, Biorep 1)


title: 30min Control vs. 30min 100uM AsIII (Array 1)

source_name: SR: 30min 100uM AsIII (Cy3)


title: 30min Control vs. 30min 1mM AsIII (Array 2, Biorep 1)


title: 30min Control vs. 30min 1mM AsIII (Array 3, Biorep 1)


title: 30min Control vs. 30min 100uM AsIII (Array 3)


title: 30min Control vs. 30min 100uM AsIII (Array 2)


title: 30min Control vs. 30min 1mM AsIII (Array 1, Biorep 1)

description: A S.cerevisiae strain BY4741 culture was treated with 1mM NaAsO2 (AsIII) for 30 minutes and compared to the untreated control culture.


title: 2hr Control vs. 2hr 100uM AsIII (Array 1)


title: KT1027_AR3

status: Public on Jun 16 2003

city: Stanford

first: Xin

last: Chen

department: Biochemistry

institute: Stanford University

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17333.gif
Disease State: Acute rejection type III

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: CRG

label_protocol: not provided

extract_protocol: not provided

tag: CRG

source_name: SFK27-2W (AR)

tag: SFK27-2W (AR)


title: Hst5-Cy5 vs CAI4-Cy3

status: Public on Jul 18 2007

city: Buffalo

first: Wansheng

last: Li

state: NY

address: 3435 main st.

department: Oral Biology

institute: University at Buffalo

description: Candida albicans Hst5 treated wild-type strain compared to wild-type strain CAI4

hyb_protocol: The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before application to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and scanned.

scan_protocol: As described in the the manufacturer's instructions of GenePix 4200A scanner (Axon Instruments).

data_processing: Slides have been scanned by Axon scanner 4200A and image analysis analyzed by GenePix Version 6.0. Post analysis was performed using TIGR microarray software suite(http://www.tm4.org). ExprConverter v1.7 to transform GPR format to Mev file, Midias 2.19 to normalize the data, and Mev4.0 to do statistical analysis. The VALUE column is the log2 based expression level after background correction, total intensity normaliztion,Lowess normalization. if VALUE=null, then this spot was bad.

organism: Candida albicans

source_name: wild-type strain CAI4

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy3 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

extract_protocol: cDNA was synthesized from total RNA samples using Superscript II RT (Invitrogen) in reaction mixtures containing 0.5 mM deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates). After cDNA synthesis, RNA was hydrolyzed with 1 M NaOH and 0.5 M EDTA, followed by neutralization with 1 M HCl. The cDNA was purified using the Qiagen QIAquick PCR purification kit and dried by SpeedVac.

tag: Candida albicans wild-type strain CAI4

source_name: Hst5 treated wild-type strain

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy5 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

growth_protocol: Cells were grown overnight in 10 ml of YNB medium, 2% glucose with the addition of uridine when required. AFTER this, the cells were treated using Hst5.

treatment_protocol: wild-type CAI4 cells were harvested, washed twice with 10 mM NaPB, pH 7.4 and reconstituted in the same buffer. About 3x10^8 cells were incubated with 500uM Hst 5 (an LD40 dose) for 60 min.

tag: wild-type strain CAI4 treated 60min. with Hst5.


title: KT1023a_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17448.gif
Disease State: Chronic allograft nephropathy


title: KT1021b_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17330.gif
Disease State: Chronic allograft nephropathy


title: KT1007c_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17296.gif
Disease State: Chronic allograft nephropathy


title: KT126_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17444.gif
Disease State: Acute rejection type I


title: KT94_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16329.gif
Disease State: Acute rejection type I


title: KT95b_AR2/DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16330.gif
Disease State: Acute rejection type II/DT/Infection


title: KT116_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17329.gif
Disease State: Acute rejection type I


title: KT89_AR2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16327.gif
Disease State: Acute rejection type II


title: KT12b_AR2/DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16325.gif
Disease State: Acute rejection type II/DT/Infection


title: KT138_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17450.gif
Disease State: Acute rejection type I


title: KT1008c_DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17264.gif
Disease State: Nephrotoxic effects of drugs/Infection


title: KT99_CAN/AR3

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15986.gif
Disease State: Acute rejection type III/Chronic allograft nephropathy


title: KT65_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16249.gif
Disease State: Nephrotoxic effects of drugs

source_name: KT65 (DT/D)

tag: KT65 (DT/D)


title: KT100_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15988.gif
Disease State: Chronic allograft nephropathy


title: KT82_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16328.gif
Disease State: Nephrotoxic effects of drugs


title: KT96_AR2/DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17248.gif
Disease State: Acute rejection type II/DT/Infection


title: KT87_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15976.gif
Disease State: Acute rejection type I


title: KT84b_CAN/AR3

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17253.gif
Disease State: Acute rejection type III/Chronic allograft nephropathy

source_name: KT#84b (DT/CR)

tag: KT#84b (DT/CR)


title: KT138b_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17294.gif
Disease State: Acute rejection type I


title: KT95_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15982.gif
Disease State: Chronic allograft nephropathy


title: KT102_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17251.gif
Disease State: Nephrotoxic effects of drugs


title: KT86_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15420.gif
Disease State: Acute rejection type I


title: KT84_AR2/DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15307.gif
Disease State: Acute rejection type II/DT/Infection


title: KT34b_AR2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16326.gif
Disease State: Acute rejection type II


title: KT86b_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15979.gif
Disease State: Chronic allograft nephropathy


title: KT126b_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15304.gif
Disease State: Acute rejection type I


title: KT25b_AR2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15230.gif
Disease State: Acute rejection type II


title: KT28c_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15300.gif
Disease State: Chronic allograft nephropathy


title: KT38_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15226.gif
Disease State: Chronic allograft nephropathy


title: KT40_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15225.gif
Disease State: Chronic allograft nephropathy


title: KT10_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14924.gif
Disease State: Acute rejection type I


title: KT63_AR2

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15229.gif
Disease State: Acute rejection type II


title: KT15_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14929.gif
Disease State: Nephrotoxic effects of drugs


title: KT1009_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14824.gif
Disease State: Normal kidney


title: KT1009a_DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14725.gif
Disease State: Nephrotoxic effects of drugs/Infection


title: KT9_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14921.gif
Disease State: Chronic allograft nephropathy


title: KT1013_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14827.gif
Disease State: Normal kidney


title: KT14_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14926.gif
Disease State: Normal kidney


title: KT26b_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14919.gif
Disease State: Chronic allograft nephropathy


title: KT1006c_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14818.gif
Disease State: Nephrotoxic effects of drugs


title: KT78b_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14721.gif
Disease State: Nephrotoxic effects of drugs


title: KT1003d_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14819.gif
Disease State: Chronic allograft nephropathy


title: KT72_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14723.gif
Disease State: Nephrotoxic effects of drugs

source_name: KT72 (DT)

tag: KT72 (DT)


title: KT76_AR2/DT/IN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14726.gif
Disease State: Acute rejection type II/DT/Infection


title: KT80_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14727.gif
Disease State: Acute rejection type I

source_name: KT80 (AR Rx)

tag: KT80 (AR Rx)


title: KT38b_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14517.gif
Disease State: Normal kidney


title: KT18_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14537.gif
Disease State: Normal kidney


title: KT32_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14512.gif
Disease State: Normal kidney


title: KT36_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14515.gif
Disease State: Normal kidney


title: KT87b_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14514.gif
Disease State: Normal kidney


title: KT1001d_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14378.gif
Disease State: Chronic allograft nephropathy


title: KT28_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14438.gif
Disease State: Normal kidney


title: KT1001a(2)_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14373.gif
Disease State: Acute rejection type I


title: KT12_CAN/AR3

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14326.gif
Disease State: Acute rejection type III/Chronic allograft nephropathy


title: KT31_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14440.gif
Disease State: Normal kidney


title: KT3_AR3

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14324.gif
Disease State: Acute rejection type III


title: KT1001b_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14376.gif
Disease State: Normal kidney


title: KT1001a_AR1

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20900.gif
Disease State: Acute rejection type I

source_name: SFK1-1M (SAR)

tag: SFK1-1M (SAR)


title: KT30_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14439.gif
Disease State: Chronic allograft nephropathy


title: KT1002a_DT

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14313.gif
Disease State: Nephrotoxic effects of drugs


title: KT1007a_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14728.gif
Disease State: Normal kidney


title: KT1002b_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14321.gif
Disease State: Normal kidney


title: KT1001_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14375.gif
Disease State: Chronic allograft nephropathy


title: KT1002c_CAN

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14318.gif
Disease State: Chronic allograft nephropathy


title: KT1002_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14315.gif
Disease State: Normal kidney


title: KT1008a_N

description:
Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14730.gif
Disease State: Normal kidney


title: PPAR in Rat  Quad_d03_Bezafibrate_250.0mkd_#1259

status: Public on Jul 12 2007

city: Rahway

first: Olivia

last: Fong

department: Molecular Profiling

institute: Merck & Co.

description: Quad_d03_ vehicle control pool_000.0mkd_n=12 vs. Quad_d03_Bezafibrate_250.0mkd_#1259

hyb_protocol: All treated individual samples were hybridized against a pool of RNA from time-matched (concurrent) control animals (e.g., animals treated for 3 days were hybridized against a pool of animals dosed for 3 days with vehicle). The ratio of individual animal expression to control pool expression was used for all data analysis. All hybridizations (Hughes et al., 2001, PMID: 11283592) were performed in duplicate, with fluor reversal (Cy3 or Cy5) in the second hybridization.

scan_protocol: Arrays were scanned using a DNA microarray scanner (Model G2565AA; Agilent Technologies), and feature intensities (background subtracted) were determined using feature extraction software developed at Rosetta.

data_processing: Local background correction

source_name: Quad

label_protocol: Cy3- or Cy5-labeled cRNA was created from total RNA using reverse transcription followed by in vitro transcription and a two-step label incorporation method (Hughes et al., 2001, PMID: 11283592).

extract_protocol: tissues were collected for RNA extraction (snap frozen in liquid nitrogen). RNA was extracted from tissues using a combination of TRIzol RNA extraction (Invitrogen Life Technologies, Carlsbad, CA) with the RNeasy RNA extraction kit (Qiagen, Valencia, CA). Briefly, tissue was incubated in TRIzol reagent (1 ml/100 mg tissue) for 15 s at room temperature and homogenized with a Polytron homogenizer followed by an ~ 5-min room temperature incubation. After the addition of 100 µl chloroform, 500 µl of homogenate was mixed by shaking for 15 s, incubated at room temperature for 2–3 min, and centrifuged at 10,000 x g for 10 min at 2–8°C. The supernatant was used as the input material for the RNeasy RNA extraction kit and RNA isolated according to the manufacturer's protocol. Following isolation, RNA quantity, purity, and quality were determined using a SpectraMax Plus384 (Molecular Devices, Sunnyvale, CA) spectrophotometer and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, Quad

label_protocol: same as for channel_1

extract_protocol: same as for channel_1

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, Quad


title: PPAR in Rat  Soleus_d04_ vehicle control_000.0mkd_#1048

description: Soleus_d04_ vehicle control pool_000.0mkd_(n=14) vs. Soleus_d04_ vehicle control_000.0mkd_#1048

source_name: Soleus

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, Soleus

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, Soleus


title: WKY-3week vs. SHR-3week (Array 2)

description: Renal gene expression profile between spontaneously-hypertensive rats (SHR) and Wistar-Kyoto (WKY) control rats at a pre-hypertensive stage (3 weeks of age).

source_name: SR: SHR-3week (Cy5)

source_name: SG: WKY-3week (Cy3)