title: MCF7/BUS, 10 micromolar genistein, 48 hours, biological replication 3

description: Gene expression data from MCF7 (BUS stock) exposed to 10 micromolar genistein for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 10 micromolar genistein. Total RNA was isolated 48 hours after E2 treatment.

tag: 10 micromolar genistein


title: MCF7/BUS, 10 nM para-nonylphenol, 48 hours, biological replication 2

status: Public on Jul 01 2006

type: RNA

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

country: USA

institute: MGH Cancer Center

description: Gene expression data from MCF7 (BUS stock) exposed to 10 nM para-nonylphenol for 48 hours.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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 150.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7/BUS cells, human breast adenocarcinoma cell line, estrogen receptor-positive

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: QIAGEN RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 10 nM para-nonylphenol. Total RNA was isolated 48 hours after E2 treatment.

tag: 10 nM para-nonylphenol


title: MCF7/BUS, 30 pM 17beta-estradiol, 48 hours, biological replication 1

description: Gene expression data from MCF7 (BUS stock) exposed to 30 pM 17beta-estradiolfor for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 30 pM 17beta-estradiol. Total RNA was isolated 48 hours after E2 treatment.

tag: 30 pM 17beta-estradiol


title: MCF7/BUS, 3 micromolar genistein, 48 hours, biological replication 1

description: Gene expression data from MCF7 (BUS stock) exposed to 3 micromolar genistein for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 3 micromolar genistein. Total RNA was isolated 48 hours after E2 treatment.

tag: 3 micromolar genistein


title: MCF7/BUS, 10 micromolar genistein, 48 hours, biological replication 2


title: MCF7/BUS, 1 micromolar daidzein, 48 hours, biological replication 1

description: Gene expression data from MCF7 (BUS stock) exposed to 1 micromolar daidzein for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 1 micromolar daidzein. Total RNA was isolated 48 hours after E2 treatment.

tag: 1 micromolar daidzein


title: MCF7/BUS, 3 micromolar genistein, 48 hours, biological replication 2


title: MCF7/BUS, 3 micromolar genistein, 48 hours, biological replication 3


title: MCF7/BUS, vehicle, 48 hours, biological replication 2

description: Gene expression data from MCF7 (BUS stock) exposed to 0.1% ethanol for 48 hours.

treatment_protocol: MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 0.1% ethanol. Total RNA was isolated 48 hours after E2 treatment.

tag: vehicle (0.1% ethanol)


title: MCF7/BUS, 10 micromolar genistein, 48 hours, biological replication 1


title: MCF7/BUS, 30 pM 17beta-estradiol, 48 hours, biological replication 2


title: MCF7/BUS, 30 pM 17beta-estradiol, 48 hours, biological replication 3


title: MCF7/BUS, vehicle, 48 hours, biological replication 1


title: MCF7/BUS, vehicle, 48 hours, biological replication 3

description: Gene expression data from MCF7 (BUS stock) exposed to 0.1% ethanol for for 48 hours.


title: Dkk-1_stg11.5_clutch4

status: Public on Jun 30 2006

city: Stanford

first: Andrew

middle: Lee

last: Hufton

state: CA

address: 300 Pasteur Dr., Alway Bldg, Rm M313

department: Genetics

institute: Stanford

hyb_protocol: Manufacturer's protocols (Affymetrix, Santa Clara, CA).

data_processing: RMA method, values in the GEO database have not been log transformed.

organism: Xenopus laevis

source_name: Ventral half of stg11.5 gastrula, injected with dkk-1

growth_protocol: Embryos were grown in 1/3 MR.

extract_protocol: RNA isolation described in Hufton et al. 2005,

treatment_protocol: Embryo was injected ventrally at the four-cell stage with dkk-1 plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 11.5 embryos were bisected and 10 ventral halves were saved for RNA isolation.

tag: Stage

tag: Clutch

tag: Tissue

value: Ventral half of gastrula embryo;

tag: Injection

value: dkk-1 and eGFP


title: Noggin+Dkk-1_stg11.5_clutch4

scan_protocol: Manufacturer's protocols (Affymetrix, Santa Clara, CA).

source_name: Ventral half of stg11.5 gastrula, injected with noggin and dkk-1

growth_protocol: Embryos were grown 1/3 MR.

treatment_protocol: Embryo was injected ventrally at the four-cell stage with noggin and dkk-1 plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 11.5 embryos were bisected and 10 ventral halves were saved for RNA isolation.

value: noggin, dkk-1, and eGFP


title: Dorsal_stg11.5_clutch4

description: The Ventral_stg11.5_clutch4 sample was derived from the same 10 eGFP injected embryos as this sample.

source_name: Dorsal half of stg11.5 gastrula

label_protocol: Manufacturer's protocols (Affymetrix, Santa Clara, CA).

treatment_protocol: Embryo was injected ventrally at the four-cell stage with eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 11.5 embryos were bisected and 10 dorsal halves were saved for RNA isolation.

value: Dorsal half of gastrula embryo;

value: eGFP


title: Noggin_stg11.5_clutch4

source_name: Ventral half of stg11.5 gastrula, injected with noggin

treatment_protocol: Embryo was injected ventrally at the four-cell stage with noggin plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 11.5 embryos were bisected and 10 ventral halves were saved for RNA isolation.

value: noggin and eGFP


title: Ventral_stg11.5_clutch4

description: The Dorsal_stg11.5_clutch4 sample was derived from the same 10 eGFP injected embryos as this sample.

source_name: Ventral half of stg11.5 gastrula

treatment_protocol: Embryo was injected ventrally at the four-cell stage with eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 11.5 embryos were bisected and 10 ventral halves were saved for RNA isolation.


title: Ventral_stg11.5_clutch3

description: The Dorsal_stg11.5_clutch3 sample was derived from the same 10 eGFP injected embryos as this sample.


title: Mets_NormalBone3

city: Toronto

first: Chung-Hae

last: Lee

state: ON

address: 9th Floor Rm. 717, 610 University Ave

department: Applied Molecular Oncology

country: Canada

institute: Ontario Cancer Institute, Princess Margaret Hospital

description:
hybridized biotin-labeled cDNA were detected with CPD-Star Chemiluminescent Detection Kit;
NOTE: this data is linked to supplementary excel file MetastasisPlatform_MetastaticGroup_atDiagnosis_atSurgery.xls

data_processing: the mean of signal intensities from empty spots (see platform description) were subtracted from the raw intensities after which normalization was performed with the mean signal intensity of ACTB

source_name: normal bone

tag: normal bone


title: Mets_Metast_Dx

source_name: tumor harvested at diagnosis from patient with metastasis at time of diagnosis

tag: Osteosarcoma harvested at time of diagnosis; patient was diagnosed with metastasis


title: Mets_Metast_SX

source_name: tumor harvested at surgery from patient with metastasis at time of diagnosis

tag: Osteosarcoma harvested at time of surgery; patient was diagnosed with metastasis


title: Dorsal_stg10_clutch2

description: The Ventral_stg10_clutch2 sample was derived from the same 10 eGFP injected embryos as this sample.

source_name: Dorsal half of stg10 gastrula

treatment_protocol: Embryo was injected ventrally at the four-cell stage with eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 10 embryos were bisected and 10 dorsal halves were saved for RNA isolation.


title: Dorsal_stg11.5_clutch3

description: The Ventral_stg11.5_clutch3 sample was derived from the same 10 eGFP injected embryos as this sample.


title: Testis from adult rat treated with 50 mg/kg b.w. Adjudin  8 h-2

status: Public on Jul 07 2006

city: New York

first: Weiliang

last: Xia

state: NY

address: 1230 York Avenue

institute: Population Council

description: normal adult rat testis

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

organism: Rattus norvegicus

source_name: Testis

label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 0.1 gram of frozen testis tissue extracted using Trizol (Invitrogen) and followed by RNeasy cleanup (Qiagen)

tag: Adult rats were treated with 50 mg/kg b.w. Adjudin [1-(2,4-dichlorobenzyl)-indazole-3-carbohydrazide] by gavage for 8 hour


title: Noggin_stg11.5_clutch3


title: Ventral_stg10_clutch2

description: The Dorsal_stg10_clutch2 sample was derived from the same 10 eGFP injected embryos as this sample.

source_name: Ventral half of stg10 gastrula

treatment_protocol: Embryo was injected ventrally at the four-cell stage with eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 10 embryos were bisected and 10 ventral halves were saved for RNA isolation.


title: Dkk-1_stg11.5_clutch3


title: Dorsal_stg10_clutch1

description: The Ventral_stg10_clutch1 sample was derived from the same 10 eGFP injected embryos as this sample.


title: Dkk-1_stg10_clutch2

source_name: Ventral half of stg10 gastrula, injected with dkk-1

treatment_protocol: Embryo was injected ventrally at the four-cell stage with dkk-1 plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 10 embryos were bisected and 10 ventral halves were saved for RNA isolation.


title: Noggin+Dkk-1_stg11.5_clutch3


title: Noggin+Dkk-1_stg10_clutch1

source_name: Ventral half of stg10 gastrula, injected with noggin and dkk-1

treatment_protocol: Embryo was injected ventrally at the four-cell stage with noggin and dkk-1 plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 10 embryos were bisected and 10 ventral halves were saved for RNA isolation.


title: A HID B_B017

city: Gainesville

first: Corinna

last: Burger

state: FL

address: 1600 SW Archer Red

institute: University of Florida

description:
A HID B_B017
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

source_name: CA1 hippocampus

label_protocol: two rounds of RNA  amplification were performed following the Affymetrix Small Sample Target Labeling version I protocol, which consists of two cycles of cDNA synthesis.  (The detailed protocol can be obtained at the Affymetrix website: http://www.affymetrix.com/index.affx).

growth_protocol: Fisher-344 male rats, 3 and 24 month old, were housed (2 per cage) in a 12:12 light-dark cycle with ad libitum access to food and water.  Behavioral testing occurred during the light phase of the cycle.

extract_protocol: Animals were sacrificed 24 hours after the last behavioral trial by decapitation, following a lethal dose of pentobarbital (100 mg/kg), and the brains were extracted from the skull and washed with ice-cold PBS.  The brains were sectioned into 1 mm slices and placed in RNAlater (Ambion).  The brain slices were stored at -20°C until ready for further dissection and RNA isolation.  The RNAlater gave the tissue a “fixed” consistency and allowed for clear visualization of the hippocampal cellular layers.  Three main anatomical areas of the hippocampus were dissected.  Using a 300 µm micro punch (Electron Microscopy Sciences), the main cell layer of the CA1 region from each animal was dissected out and placed in tubes containing 50 µl of RNAlater.  RNA was isolated using the Qiagen RNeasy protocol (Qiagen).  The tissue was homogenized in 400 µl of RLT buffer and 1% mercaptoethanol, and treated with 200 µg/ml proteinase K for 10 minutes at 55ºC.  After RNA isolation with the Qiagen RNeasy kit we assessed the quality of the RNA using an Agilent 2100 bioanalyzer using the RNA 6000 Nanochips assay kit (Agilent Technologies).  The RNA was stored at -80°C until further use.

treatment_protocol: animals were trained in the water maze. SIT = control rats stayed in cages, YOKE=swam with no platform, VIS= were trained with visible platform, HID= animals were trained in the hidden version of the paradigm

tag: A HID B_B017


title: Dkk-1_stg10_clutch1

value: Dkk-1 and eGFP


title: A HID B_B088

description:
A HID B_B088
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B088


title: A HID B_B021

description:
A HID B_B021
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B021


title: A SIT_B100

description:
A SIT_B100
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A SIT_B100


title: Noggin_stg10_clutch2

source_name: Ventral half of stg10 gastrula, injected with noggin

treatment_protocol: Embryo was injected ventrally at the four-cell stage with noggin plasmid and eGFP mRNA.  Embryos were sorted for proper ventral targeting at early stg. 10 by eGFP fluorescence.  At stg. 10 embryos were bisected and 10 ventral halves were saved for RNA isolation.

value: Noggin and eGFP


title: A HID B_B046

description:
A HID B_B046
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B046


title: Noggin_stg10_clutch1

source_name: Ventral half of stg10 gastrula, injected with Noggin


title: A HID B_B086

description:
A HID B_B086
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B086


title: A HID B_B013

description:
A HID B_B013
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B013


title: A HID B_B014

description:
A HID B_B014
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B014


title: Ventral_stg10_clutch1

description: The Dorsal_stg10_clutch1 sample was derived from the same 10 eGFP injected embryos as this sample.


title: A HID B_B012

description:
A HID B_B012
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B012


title: Noggin+Dkk-1_stg10_clutch2

tag: Stage


title: A HID B_B091

description:
A HID B_B091
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B091


title: A VIS _B097

description:
A VIS _B097
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B097


title: A HID B_B011

description:
A HID B_B011
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B011


title: Y SIT_B074

description:
Y SIT_B074
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y SIT_B074


title: Y SIT_B076

description:
Y SIT_B076
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y SIT_B076


title: A HID B_B009

description:
A HID B_B009
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B009


title: Y SIT_B070

description:
Y SIT_B070
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y SIT_B070


title: A HID B_B090

description:
A HID B_B090
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B090


title: A HID B_B043

description:
A HID B_B043
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B043


title: A YOKE_B063

description:
A YOKE_B063
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B063


title: A HID U_B042

description:
A HID U_B042
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B042


title: Y VIS _B030

description:
Y VIS _B030
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y VIS _B030


title: A HID B_B041

description:
A HID B_B041
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B041


title: A VIS _B033

description:
A VIS _B033
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B033


title: A SIT_B099

description:
A SIT_B099
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A SIT_B099


title: A SIT_B098

description:
A SIT_B098
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A SIT_B098


title: A HID U_B089

description:
A HID U_B089
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B089


title: A VIS _B068

description:
A VIS _B068
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B068


title: Y VIS _B065

description:
Y VIS _B065
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y VIS _B065


title: Y HID_B039

description:
Y HID_B039
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B039


title: Y YOKE_B058

description:
Y YOKE_B058
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B058


title: A YOKE_B062

description:
A YOKE_B062
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B062


title: A VIS _B069

description:
A VIS _B069
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B069


title: A HID U_B016

description:
A HID U_B016
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B016


title: A HID U_B020

description:
A HID U_B020
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B020


title: A HID I_B008

description:
A HID I_B008
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B008


title: A VIS _B096

description:
A VIS _B096
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B096


title: A HID I_B056

description:
A HID I_B056
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B056


title: A HID U_B054

description:
A HID U_B054
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B054


title: A YOKE_B095

description:
A YOKE_B095
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B095


title: Y YOKE_B059

description:
Y YOKE_B059
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B059


title: A YOKE_B093

description:
A YOKE_B093
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B093


title: A YOKE_B094

description:
A YOKE_B094
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B094


title: A HID B_B082

description:
A HID B_B082
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B082


title: A HID I_B087

description:
A HID I_B087
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B087


title: A VIS _B067

description:
A VIS _B067
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B067


title: A HID U_B084

description:
A HID U_B084
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B084


title: A HID I_B083

description:
A HID I_B083
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B083


title: A HID U_B045

description:
A HID U_B045
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B045


title: A HID I_B050

description:
A HID I_B050
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B050


title: A SIT_B035

description:
A SIT_B035
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A SIT_B035


title: Y HID_B037

description:
Y HID_B037
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B037


title: A HID I_B052

description:
A HID I_B052
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B052


title: A HID I_B051

description:
A HID I_B051
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B051


title: A HID B_B010

description:
A HID B_B010
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID B_B010


title: A SIT_B036

description:
A SIT_B036
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A SIT_B036


title: A HID I_B047

description:
A HID I_B047
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B047


title: A HID U_B081

description:
A HID U_B081
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B081


title: A HID U_B004

description:
A HID U_B004
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B004


title: A HID I_B048

description:
A HID I_B048
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B048


title: A HID U_B015

description:
A HID U_B015
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B015


title: A YOKE_B061

description:
A YOKE_B061
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B061


title: Y HID_B040

description:
Y HID_B040
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B040


title: A HID U_B007

description:
A HID U_B007
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B007


title: A VIS _B032

description:
A VIS _B032
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B032


title: A VIS _B031

description:
A VIS _B031
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A VIS _B031


title: A HID U_B049

description:
A HID U_B049
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B049


title: A YOKE_B025

description:
A YOKE_B025
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B025


title: Y VIS _B028

description:
Y VIS _B028
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y VIS _B028


title: Y VIS _B029

description:
Y VIS _B029
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y VIS _B029


title: Y YOKE_B060

description:
Y YOKE_B060
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B060


title: A YOKE_B027

description:
A YOKE_B027
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A YOKE_B027


title: Y HID_B038

description:
Y HID_B038
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B038


title: A HID U_B053

description:
A HID U_B053
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID U_B053


title: Y YOKE_B023

description:
Y YOKE_B023
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B023


title: A HID I_B044

description:
A HID I_B044
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: A HID I_B044


title: RPTEC control 220305

city: Munich

first: Andreas

last: Benesic

state: Bavaria

address: Marchioninistr. 15

department: Dept. of medicine 2

country: Germany

institute: University Hospital Grosshadern, Munich

description: Chronic renal damage is observed especially in children treated with the chemotherapeutic agent ifosfamide. Renal injury presents frequently as Fanconi´s syndrome with partial or complete loss of proximal tubule cell function. Since the ifosfamide metabolite chloroacetaldehyde is suspected to be the nephrotoxic agent, changes in signalling pathways after chloroacetaldehyde exposure in human RPTEC in primary cuilture were screened using cDNA Microarrays

hyb_protocol: according to user manual for Q-Series cDNA microarrays www.superarray.com

scan_protocol: After data acqusition on X-Ray Film using the CDP Star reagent, Films were scanned and TIF-Images analysed using spotfinder 3.1.0 (TIGR)

data_processing: Values were normalized for GAPDH

molecule: polyA RNA

source_name: human proximal tubule epithelial cells

label_protocol:
according to user manual for Q-Series cDNA microarrays, using the AMPO-Labelling Kit
www.superarray.com

growth_protocol: Cells were grown in DMEM/HAM F-12 medium supllemented with 0.5% fetal calf serum, supplemented with 1.1 g/l NaHCO3, 3.57 g/l, 4-(2-hydroxyethyl)-1-piperazineethanesulphonic acid (HEPES), 5 mg/l human apo-transferrin, 5 mg/l (bovine)insulin, 500 µg/l hydrocortisone, 10 µg/l mouse EGF, 5 µg/l Na-selenite, 0.5% fetal calf serum (Biochrom, Berlin, Germany), 6.5 µg/l thyroxin and 500 µg/l epinephrine under standard cell culture conditions (37 °C, 5% CO2)

extract_protocol:
Array Grade mRNA Extraction Kit available at www.superarray.com
procedures according to user manual

treatment_protocol: After 24 h serum starvation in DMEM/HAM F-12 medium without additives, cells were incubated for 24 h in presence an absence of 15 micromolar chloroacetaldehyde under standard cell culture conditions (37 °C, 5% CO2)

tag: human proximal tubule epithelial cells in primary culture


title: Y HID_B002

description:
Y HID_B002
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B002


title: Y YOKE_B024

description:
Y YOKE_B024
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B024


title: Y HID_B003

description:
Y HID_B003
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y HID_B003


title: Y YOKE_B022

description:
Y YOKE_B022
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

tag: Y YOKE_B022


title: CGH YJB9517 vs SC5314

type: genomic

city: Boston

first: Anna

last: Selmecki

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: CGH was performed as described previously (Selmecki et. al. Molecular Microbiology 55, 1553 (2005).  All test strains were compared to the reference control strain, SC5314.  Briefly, digested genomic DNA from the test strain and SC5314 were differentially labeled with Cy3-dUTP and Cy5-dUTP (Roche), respectively.  DNAs were mixed in a 1:1 ratio and co-hybridized to a whole genome C. albicans microarray printed in our lab.

data_processing: Fluorescense intensity ratios (mean log2 values) were obtained and analyzed using GenePixPro 5.1 and GeneTraffic 3.1.

molecule: genomic DNA

organism: Candida albicans

tag: Strain YJB9517

tag: Strain SC5314


title: 1-cell embryos polysomes  sample1

type: mixed

city: Philadelphia

first: Keith

middle: E

last: Latham

state: PA

address: 3307 N Broad St

department: The Fels Institute for Cancer Research and Molecular Biology

institute: Temple University School of Medicine

description: polysomal RNA from alpha-amanitin treated 1-cell embryos was subjected to 2 rounds of IVT amplification

data_processing: normalized to target average 150

molecule: other

organism: Mus musculus

source_name: 1-cell mouse embryo

tag: Polysomal mRNA isolated from 1-cell embryos of B6D2/F1xCF1 mice. 2 rounds of linear amplification.


title: CGH YJB9180 vs SC5314

tag: Strain YJB9180


title: MII oocyte polysomes  sample 4

description: polysomal RNA from metaphase II oocytes was subjected to 2 rounds of IVT amplification

source_name: Metaphase II mouse oocyte

tag: Polysomal mRNA isolated from metaphase II oocytes of CF1 female mice. 2 rounds of linear amplification.


title: 1-cell embryos polysomes  sample 3


title: CGH YJB8738 vs SC5314

tag: Strain YJB8738


title: MII oocytes polysomes  sample 3


title: 1-cell embryos polysomes  sample 2


title: CGH YJB8737 vs SC5314

tag: Strain YJB8737


title: CGH YJB8736 vs SC5314

tag: Strain YJB8736


title: 1-cell embryos polysomes  sample 4


title: MII oocyte polysomes  sample 2


title: CGH YJB9185 vs SC5314

tag: Strain YJB9185


title: CGH YJB8638 vs SC5314

tag: strain YJB8638

tag: strain SC5314


title: CGH YJB8640 vs SC5314

tag: Strain YJB8640


title: MII oocyte polysomes   sample 1

source_name: Metaphase II mouse oocytes


title: Female Ctrl1 labelled Cy3 vs Female Pheno1 labelled Cy5

status: Public on Jun 29 2006

city: Sophia-Antipolis

first: Gaelle

last: LE GOFF

address: 400 route des Chappes

country: France

institute: INRA

description: A cDNA microarray was constructed using expressed sequence tags (ESTs) of 1.8 kb average length and gene specific tags of 0.4 kb average length obtained by PCR amplification and plasmid cloning. This Drosophila toxicology microarray contained 319 genes that represent all cytochromes P450, glutathione S-transferases, esterases, other genes of interest including attacin or Ftz-F1 and several housekeeping genes as controls. Each insert was amplified by PCR with flanking universal primers, purified and then spotted using the ChipWriterPro Virtek (BioRad) spotter at three independent locations on Corning UltraGAPS slides (Corning).

hyb_protocol: Standard Operating Procedure Title: Hybridization pronto protocol Protocol from www.promega.com 1. Dry the appropriate amount of each dye-labeled cDNA using a speedvacuum concentrator, then dissolve the cDNA in the required volume of Pronto! Universal Hybridization Solution or in home made hybridization solution ( 1/3 ddH2O+ 2/3 DIGEasy). 2. Incubate the labeled cDNA solution at 95°C for 5 minutes, protecting samples from light. 3. Centrifuge the cDNA at 13,500g for two minutes to collect condensation. Do not place the solution on ice because this will cause precipitation of some of the components. 4. Place array in Corning® Hybridization Chamber (Cat.# 2551). Pipet the labeled cDNA gently up and down and then transfer onto the surface of the printed side of the slide. Carefully place the cover glass on the array. Avoid trapping air bubbles between the array and the cover glass. Small air bubbles that do form usually dissipate during hybridization. Assemble the chamber as described in its package insert.  5. Incubate the chamber-array assembly at 42°C for 14-20 hours using a water bath or a hybridization oven. Make sure you place the hybridization chamber horizontally . this can be checked with bubble in the middle of the stuff??

scan_protocol: Slides were scanned on a Genepix 4000b scanner and signal quantification was performed using the Genepix pro 4.1 software (Axon Instruments).

data_processing: Data files from Genepix were converted using Express Converter software and normalized in MIDAS (Microarray Data Analysis System), using two publicly available programs from TIGR. Three steps of normalization were performed in MIDAS, (a) a low intensity filter in which signal intensity < 1000 was removed; (b) a global lowess normalization was applied; (c) a flip dye consistency check, the Cy3 and Cy5 labels were swapped between controls versus treatments to account for potential differences in labelling efficiency. For statistical analysis, each array intensity was log-transformed, centred by their average value and reduced by their standard deviation. The resulting data for each gene were analyzed with a type III two-way (i.e., sex x treatment) analysis of variance (ANOVA) taking into account the presence of missing values. A gene was considered as differentially expressed if 50% or more of its variance was explained by the treatment effect with a corresponding P-value lower than 0.035. Data were removed when there was no consistency for a same gene represented on the array by PCR products of different size, as this may have reflected a different degree of specificity.

label: labelled with Cy3 dCTP from Amersham

organism: Drosophila melanogaster

source_name: Female untreated

label_protocol:
Standard Operating Procedure
Title: cDNA Labeling Protocol for Total RNA
Protocole from www.promega.com
1. For each Cy-dye labeling reaction, assemble the following reagents in a
microcentrifuge tube. Keep the reagents on ice, and mix the total RNA and
primers as follows:
Total RNA  10µg ( unless other specification)
Random Primers (3µg/µl) 	1µl
Oligo(dT) Primer (2µg/µl)	1µl
Nuclease-Free Water to a total volume of 20µl
2. Incubate RNA/primer solution at 70°C for 10 minutes ( use the PCR form the lab C314 with PRONTO program), click pause on the PCR machine, take the tubes and place them on ice.
3. While the RNA/primer solution is incubating at 70°C, prepare labeling mix
as follows. Perform Cy3 and Cy5 reactions in separate tubes.
Component				 Cy3 		Cy5
ChipShot Reverse Transcriptase
5X Reaction Buffer 			8µl 		8µl
MgCl2 (25mM)				4.8µl 		4.8µl
dNTP mix, Total RNA 			2µl 		3µl
Cy3 dCTP (1mM) 			1µl 		-
Cy5 dCTP (1mM)	 		-		1µl
ChipShot Reverse Transcriptase 	3.2µl		3.2µl
Nuclease-Free Water 			1µl 		-
final volume 				20µl 		20µl
4. Add the entire 20µl labeling mix to each tube of RNA/primer solution from step 3, vortex,
spin briefly and incubate at room temperature (22-25°C) for 10 minutes ( second step on the PRONTO program of the PCR machine from Lab C314) protected from light.
5. Incubate at 42°C for 2 hours protected from light ( step 3 from PRONTO program of the PCR machine from Lab C314).
6. Add 1.0µl RNase H and 0.35µl RNase Solution to each cDNA-synthesis reaction.
Mix gently and incubate at 37°C for 15 minutes ( step 4 from PRONTO program of the PCR machine from Lab C314).
Purifying Cy-Labeled cDNA

1. To 40µl of the synthesized, labeled cDNA, add the following components
in the order listed:
Binding Particles:		 18µl
Sodium Acetate, 3M (pH 5.2):       4µl
Binding Solution:		 310µl
2. Vortex gently for 5-10 seconds to mix.
3. Incubate at room temperature for 1 minute.
4. Repeat Steps 2 and 3.
5. Apply entire contents of tube (solution and Binding Particles) to a Spin-X column and cap the tube.
6. Spin at 10,000g for 1 minute.
7. Discard the column flowthrough.
8. Wash column with 500µl of 80% ethanol ( fresly prepared), mix 80%EtOH and binding particles by by up and down with the pipet, cap the tube, and centrifuge at 10,000g for 60 seconds.
9. Discard the column flowt hrough.
10. Repeat Step 8 and 9 twice for a total of 3 washes.
11. Centrifuge column at 10,000g for 1 minute to remove traces of ethanol.
12. Place column in a clean Collection Tube (provided).
13. To elute labeled cDNA, add 60µl of Elution Buffer , mix by up and down the EB with the particles and let the column stand at room temperature for 5 minutes. Centrifuge at 10,000 x gfor 1 minute, discard column. The eluted cDNA can be stored in a light-proof container at 4°C for several weeks.14. Quantitate absorbance at 260, 280, 320 550 and 650nm, and calculate frequency of
incorporation.
Frequency of incorporation (FOI) is defined as the number of Cy-labeled nucleotides incorporated per 1,000 nucleotides of cDNA. Best results are obtained with cDNAs having an FOI as recommended in Table 2. The FOI can be calculated as follows:
FOI = pmol of dye incorporated x 324.5 ng of cDNA
Amount of labeled cDNA (ng) = A260 x 37 x total volume (µl)
For Cy3: pmol of dye incorporated = [A550 x total volume (µl) ]/0.15
For Cy5: pmol of dye incorporated = [A650 x total volume (µl)]/0.25
Note: These equations were generated using the following constants: Average Molar Mass of
dNTP = 324.5; One A260 unit of single-stranded DNA = 37µg/ml; Extinction Coefficient of Cy3 =
150,000M-1cm-1 at 550nm; Extinction Coefficient of Cy5 = 250,000M-1cm-1 at 650nm.

growth_protocol: All fly stocks were maintained at 21°C on standard corn medium for a 12:12 h dark/light period. Oregon R flies were used as wild type strain.

extract_protocol:
Standard Operating Procedure
Title: RNA Isolation with TRIzol Reagent
Protocole from www.invitrogen.com
Material safety: When working with TRIzol Reagent use gloves and eye protection. Avoid contact with skin or clothing. Use in a chemical fume hood. Avoid breathing vapour.
1.	HOMOGENIZATION
Flies were crushed in liquid nitrogen with a mortar. The obtained powder was homogenized in 1 ml of TRIzol Reagent. The sample volume should not exceed 10% of the volume of TRIzol Reagent used for homogenization.
Following homogenization, remove insoluble material from the homogenate by centrifugation at 12,000 x g for 10 minutes at 2 to 8°C. The resulting pellet contains extracellular membranes, polysaccharides, and high molecular weight DNA, while the supernatant contains RNA. Transfer the cleared homogenate solution to a fresh tube.
2.	PHASE SEPARATION
Incubate the homogenized samples for 5 min at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 secondes and incubate them at 15 to 30°C for 2 to 3 min. Centrifuge the samples at no more than 12,000 x g for 15 min at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.
3.	RNA PRECIPITATION
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 min and centrifuge at no more than 12,000 x g for 10 min at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
4.	RNA WASH
Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 min at 2 to 8°C.
5.	REDISSOLVING THE RNA
At the end of the procedure, briefly dry the RNA pellet. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in RNA free water.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer  for 72 additional hours.

tag: Strain:Oregon R

tag: Gender

value: female

tag: Age

value: adult 6 days old

label: labelled with Cy5 dCTP from Amersham

source_name: Female treated with phenobarbital


title: CGH YJB9311 vs SC5314

tag: Strain YJB9311


title: Male Ctrl1 labelled Cy3 vs Male Atz1 labelled Cy5

hyb_protocol: Standard Operating Procedure Title: Hybridization pronto protocol Protocol from www.promega.com 1. Dry the appropriate amount of each dye-labeled cDNA using a speedvacuum concentrator, then dissolve the cDNA in the required volume of Pronto! Universal Hybridization Solution or in home made hybridization solution ( 1/3 ddH2O+ 2/3 DIGEasy). 2. Incubate the labeled cDNA solution at 95ï¿½C for 5 minutes, protecting samples from light. 3. Centrifuge the cDNA at 13,500g for two minutes to collect condensation. Do not place the solution on ice because this will cause precipitation of some of the components. 4. Place array in Corning Hybridization Chamber (Cat.# 2551). Pipet the labeled cDNA gently up and down and then transfer onto the surface of the printed side of the slide. Carefully place the cover glass on the array. Avoid trapping air bubbles between the array and the cover glass. Small air bubbles that do form usually dissipate during hybridization. Assemble the chamber as described in its package insert.  5. Incubate the chamber-array assembly at 42ï¿½C for 14-20 hours using a water bath or a hybridization oven. Make sure you place the hybridization chamber horizontally . this can be checked with bubble in the middle of the stuff??

source_name: Male untreated

label_protocol:
Standard Operating Procedure
Title: cDNA Labeling Protocol for Total RNA
Protocole from www.promega.com
1. For each Cy-dye labeling reaction, assemble the following reagents in a
microcentrifuge tube. Keep the reagents on ice, and mix the total RNA and
primers as follows:
Total RNA  10ï¿½g ( unless other specification)
Random Primers (3ï¿½g/ï¿½l) 	1ï¿½l
Oligo(dT) Primer (2ï¿½g/ï¿½l)	1ï¿½l
Nuclease-Free Water to a total volume of 20ï¿½l
2. Incubate RNA/primer solution at 70ï¿½C for 10 minutes ( use the PCR form the lab C314 with PRONTO program), click pause on the PCR machine, take the tubes and place them on ice.
3. While the RNA/primer solution is incubating at 70ï¿½C, prepare labeling mix
as follows. Perform Cy3 and Cy5 reactions in separate tubes.
Component				 Cy3 		Cy5
ChipShot Reverse Transcriptase
5X Reaction Buffer 			8ï¿½l 		8ï¿½l
MgCl2 (25mM)				4.8ï¿½l 		4.8ï¿½l
dNTP mix, Total RNA 			2ï¿½l 		3ï¿½l
Cy3 dCTP (1mM) 			1ï¿½l 		-
Cy5 dCTP (1mM)	 		-		1ï¿½l
ChipShot Reverse Transcriptase 	3.2ï¿½l		3.2ï¿½l
Nuclease-Free Water 			1ï¿½l 		-
final volume 				20ï¿½l 		20ï¿½l
4. Add the entire 20ï¿½l labeling mix to each tube of RNA/primer solution from step 3, vortex,
spin briefly and incubate at room temperature (22-25ï¿½C) for 10 minutes ( second step on the PRONTO program of the PCR machine from Lab C314) protected from light.
5. Incubate at 42ï¿½C for 2 hours protected from light ( step 3 from PRONTO program of the PCR machine from Lab C314).
6. Add 1.0ï¿½l RNase H and 0.35ï¿½l RNase Solution to each cDNA-synthesis reaction.
Mix gently and incubate at 37ï¿½C for 15 minutes ( step 4 from PRONTO program of the PCR machine from Lab C314).
Purifying Cy-Labeled cDNA

1. To 40ï¿½l of the synthesized, labeled cDNA, add the following components
in the order listed:
Binding Particles:		 18ï¿½l
Sodium Acetate, 3M (pH 5.2):       4ï¿½l
Binding Solution:		 310ï¿½l
2. Vortex gently for 5-10 seconds to mix.
3. Incubate at room temperature for 1 minute.
4. Repeat Steps 2 and 3.
5. Apply entire contents of tube (solution and Binding Particles) to a Spin-X column and cap the tube.
6. Spin at 10,000g for 1 minute.
7. Discard the column flowthrough.
8. Wash column with 500ï¿½l of 80% ethanol ( fresly prepared), mix 80%EtOH and binding particles by by up and down with the pipet, cap the tube, and centrifuge at 10,000g for 60 seconds.
9. Discard the column flowt hrough.
10. Repeat Step 8 and 9 twice for a total of 3 washes.
11. Centrifuge column at 10,000g for 1 minute to remove traces of ethanol.
12. Place column in a clean Collection Tube (provided).
13. To elute labeled cDNA, add 60ï¿½l of Elution Buffer , mix by up and down the EB with the particles and let the column stand at room temperature for 5 minutes. Centrifuge at 10,000 x gfor 1 minute, discard column. The eluted cDNA can be stored in a light-proof container at 4ï¿½C for several weeks.14. Quantitate absorbance at 260, 280, 320 550 and 650nm, and calculate frequency of
incorporation.
Frequency of incorporation (FOI) is defined as the number of Cy-labeled nucleotides incorporated per 1,000 nucleotides of cDNA. Best results are obtained with cDNAs having an FOI as recommended in Table 2. The FOI can be calculated as follows:
FOI = pmol of dye incorporated x 324.5 ng of cDNA
Amount of labeled cDNA (ng) = A260 x 37 x total volume (ï¿½l)
For Cy3: pmol of dye incorporated = [A550 x total volume (ï¿½l) ]/0.15
For Cy5: pmol of dye incorporated = [A650 x total volume (ï¿½l)]/0.25
Note: These equations were generated using the following constants: Average Molar Mass of
dNTP = 324.5; One A260 unit of single-stranded DNA = 37ï¿½g/ml; Extinction Coefficient of Cy3 =
150,000M-1cm-1 at 550nm; Extinction Coefficient of Cy5 = 250,000M-1cm-1 at 650nm.

growth_protocol: All fly stocks were maintained at 21ï¿½C on standard corn medium for a 12:12 h dark/light period. Oregon R flies were used as wild type strain.

extract_protocol:
Standard Operating Procedure
Title: RNA Isolation with TRIzol Reagent
Protocole from www.invitrogen.com
Material safety: When working with TRIzol Reagent use gloves and eye protection. Avoid contact with skin or clothing. Use in a chemical fume hood. Avoid breathing vapour.
1.	HOMOGENIZATION
Flies were crushed in liquid nitrogen with a mortar. The obtained powder was homogenized in 1 ml of TRIzol Reagent. The sample volume should not exceed 10% of the volume of TRIzol Reagent used for homogenization.
Following homogenization, remove insoluble material from the homogenate by centrifugation at 12,000 x g for 10 minutes at 2 to 8ï¿½C. The resulting pellet contains extracellular membranes, polysaccharides, and high molecular weight DNA, while the supernatant contains RNA. Transfer the cleared homogenate solution to a fresh tube.
2.	PHASE SEPARATION
Incubate the homogenized samples for 5 min at 15 to 30ï¿½C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 secondes and incubate them at 15 to 30ï¿½C for 2 to 3 min. Centrifuge the samples at no more than 12,000 x g for 15 min at 2 to 8ï¿½C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.
3.	RNA PRECIPITATION
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol reagent used for the initial homogenization. Incubate samples at 15 to 30ï¿½C for 10 min and centrifuge at no more than 12,000 x g for 10 min at 2 to 8ï¿½C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
4.	RNA WASH
Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 min at 2 to 8ï¿½C.
5.	REDISSOLVING THE RNA
At the end of the procedure, briefly dry the RNA pellet. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in RNA free water.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer    for 72 additional hours.

value: male

source_name: Male treated with atrazine

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer   at 5mM for atrazine for 72 additional hours.


title: Male Atz2 labelled Cy3 vs Male Ctrl2 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer     at 5mM for atrazine for 72 additional hours.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer     for 72 additional hours.


title: Male Atz3 labelled Cy3 vs Male Ctrl3 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer      at 5mM for atrazine for 72 additional hours.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer      for 72 additional hours.


title: Male Atz1 labelled Cy3 vs Male Ctrl1 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer    at 5mM for atrazine for 72 additional hours.


title: Female Ctrl3 labelled Cy3 vs Female Atz3 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer   for 72 additional hours.

source_name: Female treated atrazine

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer  at 5mM for atrazine for 72 additional hours.


title: CGH YJB8735 vs SC5314

tag: Strain YJB8735


title: Male Ctrl3 labelled Cy3 vs Male Atz3 labelled Cy5


title: Male Ctrl2 labelled Cy3 vs Male Atz2 labelled Cy5


title: Female Atz3 labelled Cy3 vs Female Ctrl3 labelled Cy5

source_name: Female treated with atrazine


title: Female Atz1 labelled Cy3 vs Female Ctrl1 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer at 5mM for atrazine for 72 additional hours.


title: Male Pheno3 labelled Cy3 vs Male Ctrl3 labelled Cy5

source_name: Male treated with phenobarbital

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer    at 10mM for phenobarbital for 72 additional hours.


title: Female Ctrl2 labelled Cy3 vs Female Atz2 labelled Cy5


title: Female Ctrl1 labelled Cy3 vs Female Atz1 labelled Cy5


title: Male Ctrl3 labelled Cy3 vs Male Pheno3 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer at 10mM for phenobarbital for 72 additional hours.


title: Female Atz2 labelled Cy3 vs Female Ctrl2 labelled Cy5


title: Male Ctrl2 labelled Cy3 vs Male Pheno2 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer at 10mM for phenobarbital  for 72 additional hours.


title: Male Pheno2 labelled Cy3 vs Male Ctrl2 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer for 72 additional hours.


title: Male Pheno1 labelled Cy3 vs Male Ctrl1 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer   at 10mM for phenobarbital for 72 additional hours.


title: Female Pheno2 labelled Cy3 vs Female Ctrl2 labelled Cy5

source_name: Female treated phenobarbital

growth_protocol: All fly stocks were maintained at 21Â°C on standard corn medium for a 12:12 h dark/light period. Oregon R flies were used as wild type strain.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer  at 10 mM for phenobarbital for 72 additional hours.

source_name: female untreated


title: Female Ctrl3 labelled Cy3 vs Female Pheno3 labelles Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing no inducer  for 72 additional hours.

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer  at 10mM for phenobarbital for 72 additional hours.


title: Female Pheno1 labelled Cy3 vs Female Ctrl1 labelled Cy5

treatment_protocol: Emerging flies were separated by sex and maintained on standard diet for 72h before induction. The flies were then placed on medium containing the inducer at 10 mM for phenobarbital for 72 additional hours.


title: Female Ctrl2 labelled Cy3 vs Female pheno2 labelled Cy5

hyb_protocol: Standard Operating Procedure Title: Hybridization pronto protocol Protocol from www.promega.com 1. Dry the appropriate amount of each dye-labeled cDNA using a speedvacuum concentrator, then dissolve the cDNA in the required volume of Pronto! Universal Hybridization Solution or in home made hybridization solution ( 1/3 ddH2O+ 2/3 DIGEasy). 2. Incubate the labeled cDNA solution at 95Â°C for 5 minutes, protecting samples from light. 3. Centrifuge the cDNA at 13,500g for two minutes to collect condensation. Do not place the solution on ice because this will cause precipitation of some of the components. 4. Place array in Corning Hybridization Chamber (Cat.# 2551). Pipet the labeled cDNA gently up and down and then transfer onto the surface of the printed side of the slide. Carefully place the cover glass on the array. Avoid trapping air bubbles between the array and the cover glass. Small air bubbles that do form usually dissipate during hybridization. Assemble the chamber as described in its package insert.  5. Incubate the chamber-array assembly at 42Â°C for 14-20 hours using a water bath or a hybridization oven. Make sure you place the hybridization chamber horizontally . this can be checked with bubble in the middle of the stuff??

label_protocol:
Standard Operating Procedure
Title: cDNA Labeling Protocol for Total RNA
Protocole from www.promega.com
1. For each Cy-dye labeling reaction, assemble the following reagents in a
microcentrifuge tube. Keep the reagents on ice, and mix the total RNA and
primers as follows:
Total RNA  10Âµg ( unless other specification)
Random Primers (3Âµg/Âµl) 	1Âµl
Oligo(dT) Primer (2Âµg/Âµl)	1Âµl
Nuclease-Free Water to a total volume of 20Âµl
2. Incubate RNA/primer solution at 70Â°C for 10 minutes ( use the PCR form the lab C314 with PRONTO program), click pause on the PCR machine, take the tubes and place them on ice.
3. While the RNA/primer solution is incubating at 70Â°C, prepare labeling mix
as follows. Perform Cy3 and Cy5 reactions in separate tubes.
Component				 Cy3 		Cy5
ChipShot Reverse Transcriptase
5X Reaction Buffer 			8Âµl 		8Âµl
MgCl2 (25mM)				4.8Âµl 		4.8Âµl
dNTP mix, Total RNA 			2Âµl 		3Âµl
Cy3 dCTP (1mM) 			1Âµl 		-
Cy5 dCTP (1mM)	 		-		1Âµl
ChipShot Reverse Transcriptase 	3.2Âµl		3.2Âµl
Nuclease-Free Water 			1Âµl 		-
final volume 				20Âµl 		20Âµl
4. Add the entire 20Âµl labeling mix to each tube of RNA/primer solution from step 3, vortex,
spin briefly and incubate at room temperature (22-25Â°C) for 10 minutes ( second step on the PRONTO program of the PCR machine from Lab C314) protected from light.
5. Incubate at 42Â°C for 2 hours protected from light ( step 3 from PRONTO program of the PCR machine from Lab C314).
6. Add 1.0Âµl RNase H and 0.35Âµl RNase Solution to each cDNA-synthesis reaction.
Mix gently and incubate at 37Â°C for 15 minutes ( step 4 from PRONTO program of the PCR machine from Lab C314).
Purifying Cy-Labeled cDNA

1. To 40Âµl of the synthesized, labeled cDNA, add the following components
in the order listed:
Binding Particles:		 18Âµl
Sodium Acetate, 3M (pH 5.2):       4Âµl
Binding Solution:		 310Âµl
2. Vortex gently for 5-10 seconds to mix.
3. Incubate at room temperature for 1 minute.
4. Repeat Steps 2 and 3.
5. Apply entire contents of tube (solution and Binding Particles) to a Spin-X column and cap the tube.
6. Spin at 10,000g for 1 minute.
7. Discard the column flowthrough.
8. Wash column with 500Âµl of 80% ethanol ( fresly prepared), mix 80%EtOH and binding particles by by up and down with the pipet, cap the tube, and centrifuge at 10,000g for 60 seconds.
9. Discard the column flowt hrough.
10. Repeat Step 8 and 9 twice for a total of 3 washes.
11. Centrifuge column at 10,000g for 1 minute to remove traces of ethanol.
12. Place column in a clean Collection Tube (provided).
13. To elute labeled cDNA, add 60Âµl of Elution Buffer , mix by up and down the EB with the particles and let the column stand at room temperature for 5 minutes. Centrifuge at 10,000 x gfor 1 minute, discard column. The eluted cDNA can be stored in a light-proof container at 4Â°C for several weeks.14. Quantitate absorbance at 260, 280, 320 550 and 650nm, and calculate frequency of
incorporation.
Frequency of incorporation (FOI) is defined as the number of Cy-labeled nucleotides incorporated per 1,000 nucleotides of cDNA. Best results are obtained with cDNAs having an FOI as recommended in Table 2. The FOI can be calculated as follows:
FOI = pmol of dye incorporated x 324.5 ng of cDNA
Amount of labeled cDNA (ng) = A260 x 37 x total volume (Âµl)
For Cy3: pmol of dye incorporated = [A550 x total volume (Âµl) ]/0.15
For Cy5: pmol of dye incorporated = [A650 x total volume (Âµl)]/0.25
Note: These equations were generated using the following constants: Average Molar Mass of
dNTP = 324.5; One A260 unit of single-stranded DNA = 37Âµg/ml; Extinction Coefficient of Cy3 =
150,000M-1cm-1 at 550nm; Extinction Coefficient of Cy5 = 250,000M-1cm-1 at 650nm.

extract_protocol:
Standard Operating Procedure
Title: RNA Isolation with TRIzol Reagent
Protocole from www.invitrogen.com
Material safety: When working with TRIzol Reagent use gloves and eye protection. Avoid contact with skin or clothing. Use in a chemical fume hood. Avoid breathing vapour.
1.	HOMOGENIZATION
Flies were crushed in liquid nitrogen with a mortar. The obtained powder was homogenized in 1 ml of TRIzol Reagent. The sample volume should not exceed 10% of the volume of TRIzol Reagent used for homogenization.
Following homogenization, remove insoluble material from the homogenate by centrifugation at 12,000 x g for 10 minutes at 2 to 8Â°C. The resulting pellet contains extracellular membranes, polysaccharides, and high molecular weight DNA, while the supernatant contains RNA. Transfer the cleared homogenate solution to a fresh tube.
2.	PHASE SEPARATION
Incubate the homogenized samples for 5 min at 15 to 30Â°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 secondes and incubate them at 15 to 30Â°C for 2 to 3 min. Centrifuge the samples at no more than 12,000 x g for 15 min at 2 to 8Â°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.
3.	RNA PRECIPITATION
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol reagent used for the initial homogenization. Incubate samples at 15 to 30Â°C for 10 min and centrifuge at no more than 12,000 x g for 10 min at 2 to 8Â°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
4.	RNA WASH
Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 min at 2 to 8Â°C.
5.	REDISSOLVING THE RNA
At the end of the procedure, briefly dry the RNA pellet. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in RNA free water.

extract_protocol:
Standard Operating Procedure
Title: RNA Isolation with TRIzol Reagent
Protocole from www.invitrogen.com
Material safety: When working with TRIzol Reagent use gloves and eye protection. Avoid contact with skin or clothing. Use in a chemical fume hood. Avoid breathing vapour.
1.	HOMOGENIZATION
Flies were crushed in liquid nitrogen with a mortar. The obtained powder was homogenized in 1 ml of TRIzol Reagent. The sample volume should not exceed 10% of the volume of TRIzol Reagent used for homogenization.
Following homogenization, remove insoluble material from the homogenate by centrifugation at 12,000 x g for 10 minutes at 2 to 8Ã¯Â°C. The resulting pellet contains extracellular membranes, polysaccharides, and high molecular weight DNA, while the supernatant contains RNA. Transfer the cleared homogenate solution to a fresh tube.
2.	PHASE SEPARATION
Incubate the homogenized samples for 5 min at 15 to 30Â°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 secondes and incubate them at 15 to 30Â°C for 2 to 3 min. Centrifuge the samples at no more than 12,000 x g for 15 min at 2 to 8Â°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.
3.	RNA PRECIPITATION
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol reagent used for the initial homogenization. Incubate samples at 15 to 30Â°C for 10 min and centrifuge at no more than 12,000 x g for 10 min at 2 to 8Â°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
4.	RNA WASH
Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 min at 2 to 8Â°C.
5.	REDISSOLVING THE RNA
At the end of the procedure, briefly dry the RNA pellet. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in RNA free water.


title: Delta4 ligand treatment for 6 hours APZ032

city: Villejuif

first: Cyril

last: Catelain

address: 39, rue Camille Desmoulins

institute: INSERM

description: aRNA sample from HSC was labeled in Cy3 and hybridized against aRNA sample from Lin- cells labeled in Cy5.

data_processing: lowess normalization using BioConductor with method printTipLowess and span 0.4

source_name: HSC-Lin-

tag: Organism Part:Bone marrow

tag: Lin- fresh cells were sorted by FACS and used as a commun reference for all experiments

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium without Delta4 ligand during 6 hours.


title: Delta4 ligand treatment for 6 hours APZ031


title: Delta4 ligand treatment for 6 hours APZ030

description: aRNA sample from HSC was labeled in Cy5 and hybridized against aRNA sample from Lin- cells labeled in Cy3.

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium with Delta4 ligand during 6 hours.


title: Delta4 ligand treatment for 6 hours APZ029


title: Delta4 ligand treatment for 6 hours APZ027


title: Delta4 ligand treatment for 6 hours APZ022

tag: Lin- Sca+ c-kit+ fresh cells were cultured in specific growth medium without Delta4 ligand during 6 hours.


title: Delta4 ligand treatment for 6 hours APZ024


title: Delta4 ligand treatment for 6 hours APZ026


title: Delta4 ligand treatment for 6 hours APZ028


title: Delta4 ligand treatment for 6 hours apz021


title: Delta4 ligand treatment for 6 hours APZ025


title: Delta4 ligand treatment for 6 hours APZ023


title: Untreated APZ015

source_name: HSC-LSK

tag: Hematopoietic stem cells (Lin-Sca+c-Kit+) were enriched by FACS from 30 mice.


title: Delta4 ligand treatment for 6 hours APZ019


title: Delta4 ligand treatment for 12 hours APZ013

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium with Delta4 ligand during 12 hours.


title: Delta4 ligand treatment for 12 hours APZ012


title: Delta4 ligand treatment for 12 hours APZ009


title: Untreated APZ016


title: Delta4 ligand treatment for 12 hours APZ014


title: Untreated APZ017


title: Delta4 ligand treatment for 6 hours APZ020


title: Delta4 ligand treatment for 12 hours APZ011


title: Delta4 ligand treatment for 12 hours APZ010

tag: Lin- fresh cells were sorted by FACS and used as a commun reference for all experiment


title: Male Ctrl1 labelled Cy3 vs Male Pheno1 labelled Cy5


title: Delta4 ligand treatment for 24 hours ARA004

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium without Delta4 ligand during 24 hours.


title: Delta4 ligand treatment for 24 hours ARA007


title: Delta4 ligand treatment for 24 hours ARA006


title: Untreated APZ018


title: Delta4 ligand treatment for 24 hours ARA005


title: Delta4 ligand treatment for 6 hours ARA002


title: Delta4 ligand treatment for 6 hours ARA003


title: Delta4 ligand treatment for 24 hours APV030

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium with Delta4 ligand during 24 hours.


title: Delta4 ligand treatment for 24 hours APV028


title: Delta4 ligand treatment for 24 hours APV027


title: Delta4 ligand treatment for 12 hours APV032


title: Delta4 ligand treatment for 12 hours APV031


title: Delta4 ligand treatment for 12 hours APV025

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium without Delta4 ligand during 12 hours.


title: Delta4 ligand treatment for 24 hours APV029


title: Female Pheno3 labelled Cy3 vs Female Ctrl3 labelled Cy5


title: Delta4 ligand treatment for 12 hours APV020


title: Delta4 ligand treatment for 12 hours APV023


title: Delta4 ligand treatment for 12 hours APV024


title: Delta4 ligand treatment for 12 hours APV022


title: Delta4 ligand treatment for 12 hours APV026


title: Delta4 ligand treatment for 12 hours APV021


title: Delta4 ligand treatment for 12 hours APV019


title: Delta4 ligand treatment for 24 hours APV018


title: Delta4 ligand treatment for 24 hours APV009


title: Delta4 ligand treatment for 24 hours APV017


title: Delta4 ligand treatment for 24 hours APV008


title: Marmoset SNc 2 h after MPTP

city: Kagoshima

first: Shin-ichi

last: Iwata

state: Kagoshima

address: Sakuragaoka 8-35-1

department: Pharmacology

country: Japan

institute: Kagoshima University

description: Total RNA was amplified using 2 rounds of in vitro transcription using the RiboAmp HS RNA Amplification Kit (Arcturus).

hyb_protocol: Hybridizations were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA were used.

scan_protocol: Agilent G2565BA Microarray Scanner System. Data were analyzed using the Agilent Feature Extraction Software version 7.1.

data_processing: A rank consistency filter and LOWESS were used for dye normalization.

organism: Callithrix jacchus

source_name: substantia nigra pars compacta, vehicle control

label_protocol: The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: Total RNA was extracted by the PicoPure RNA Isolation Kit and eluted in approximately 10 ul buffer as per the manufacturer's protocol.

treatment_protocol: vehicle administraion iv

value: male, Age:3 years, Tissue:substantia nigra pars compacta

source_name: substantia nigra pars compacta, 2 h after MPTP

treatment_protocol: 2 h after MPTP (2.5 mg/kg) iv


title: Delta4 ligand treatment for 24 hours APV011


title: Marmoset SNc 1 day after MPTP

source_name: substantia nigra pars compacta, 1 day after MPTP

treatment_protocol: 1 day after MPTP (2.5 mg/kg) iv


title: Decidual CD56+CD3-CD16- (Replicate B)

status: Public on Jun 28 2006

city: Jerusalem

first: Ofer

last: Mandelboim

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University of Jerusalem

description: Microarray analysis was performed on highly purified CD56brightCD16- decidual NK (dNK) cells pooled from 23 health elective 1st trimester elective terminations (6-10 weeks). Subsequently, each purified subset from all donors was pooled and used to obtain a total RNA extract. We confirmed that the cRNA samples were fragmented to uniform size by using Agilent Bioanalyzer before continuing with sample labeling and hybridization procedures.  The labeled cRNA samples were hybridized in duplicate to enhance the significance of the hybridization intensities and to eliminate random noise especially from probe sets at the borderline of expression. The aim of experiment to uncover genes expressed in this NK subset.

data_processing: Hybridization Intensity value after substracting average non-specific background value

source_name: Microarray analysis was performed on highly purified human CD56brightCD16- decidual NK (dNK) cells pooled from 23 health elective 1st trimester elective terminations


title: Delta4 ligand treatment for 24 hours APV010


title: Marmoset SNc 6 h after MPTP

source_name: substantia nigra pars compacta, 6 h after MPTP

treatment_protocol: 6 h after MPTP (2.5 mg/kg) iv