title: TGCT cell line 2102Ep/clone 2A6, treated 3 days with retinoic acid, undifferentiated

description:
Testicular germ cell tumor (embryonal carcinoma) cell line 2102Ep (clone 2A6). Embryonal carcinoma cell lines are generally pluripotent and share features with embryonic stem cells. However, the 2102Ep cell line is relatively nullipotent. Time point 3 days of culturing with retinoic acid (still undifferentiated). Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.
Keywords = cell line
Keywords = differentiation
Keywords = embryonal carcinoma
Keywords = embryonic stem cell
Keywords = nullipotency
Keywords = nullipotent
Keywords = pluripotency
Keywords = pluripotent
Keywords = retinoic acid
Keywords = seminoma
Keywords = teratocarcinoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis
Keywords = totipotency
Keywords = undifferentiated


title: TGCT cell line 2102Ep/clone 2A6, treated 7 days with retinoic acid

status: Public on Jul 01 2005

type: RNA

city: Oslo

first: Rolf

middle: I

last: Skotheim

department: Department of Cancer Prevention

country: Norway

institute: Rikshospitalet-Radiumhospitalet Medical Center, Institute for Cancer Research

description:
paste from 3 days...
Keywords = paste from 3 days...

molecule: total RNA

organism: Homo sapiens

source_name: Universal Human Reference RNA (Stratagene)


title: cow 6934a11, liver, day 28 relative to parturition

status: Public on Aug 10 2005

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

country: USA

institute: University of Illinois

description:
The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Keywords = cow
Keywords = liver
Keywords = bovine
Keywords = lactation
Keywords = cDNA

organism: Bos taurus

source_name: liver, day 28, labelled with Cy3

source_name: reference standard RNA, labelled with Cy5


title: cow 7079a9, liver, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy3


title: cow 7079a10, liver, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy5

source_name: reference standard RNA, labelled with Cy3


title: Ramp 7, ambient

status: Public on May 25 2005

city: Fargo

first: Steve

last: Travers

state: ND

address: 218 Stevens Hall

department: Biological Sciences

institute: North Dakota State University

description: Leaf sample collected from ambient treatment plant

organism: Andropogon gerardi

source_name: Andropogon gerardii


title: Yolk sac tumor 0307

description:
Testicular germ cell tumor; histological subtype yolk sac tumor
Keywords = endodermal sinus tumor
Keywords = nonseminoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis
Keywords = yolk sac tumor

source_name: Yolk sac tumor


title: Teratoma 0691

description:
Testicular germ cell tumor; histological subtype teratoma
Keywords = nonseminoma
Keywords = teratoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis

source_name: Teratoma


title: Yolk sac tumor 2110


title: Ramp 7, altered

description: Leaf sample collected from altered treatment plant


title: Ramp 8, ambient


title: Ramp 8, altered


title: Embryonal carcinoma 1838

description:
Testicular germ cell tumor; histological subtype embryonal carcinoma
Keywords = embryonal carcinoma
Keywords = nonseminoma
Keywords = pluripotency
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis

source_name: Embryonal carcinoma


title: Ramp 9, altered


title: Embryonal carcinoma 1017


title: cow 6934a14, liver, day 49 relative to parturition

source_name: liver, day 49, labelled with Cy5


title: Ramp 9, ambient


title: Testicular seminoma 1748

description:
Testicular germ cell tumor; histological subtype seminoma
Keywords = seminoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis

source_name: Testicular seminoma


title: Ramp 10, ambient


title: Choriocarcinoma 0915

description:
Testicular germ cell tumor; histological subtype choriocarcinoma
Keywords = choriocarcinoma
Keywords = nonseminoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis

source_name: Choriocarcinoma


title: Testicular seminoma 1113


title: Ramp 11, ambient

description: Leaf material sampled from ambient treatment plant


title: Yolk sac tumor 0216


title: Ramp 10, altered


title: Ramp 11, altered

description: Leaf material sampled from altered treatment plant


title: Ramp 12, ambient


title: Embryonal carcinoma 0502


title: Ramp 12, altered


title: Testicular intratubular germ cell neoplasia 3879

description:
Testicular intratubular germ cell neoplasia (alias carcinoma in situ or intratubular malignant germ cells), adjacent to a germ cell tumor
Keywords = carcinoma in situ
Keywords = intratubular germ cell neoplasia
Keywords = intratubular malignant germ cells
Keywords = testicular neoplasm
Keywords = testis


title: Embryonal carcinoma 0564


title: Testicular intratubular germ cell neoplasia 1692


title: Testicular intratubular germ cell neoplasia 3493


title: Normal testis 9013

description:
Normal testicular parenchyma from a 22 years old organ donor with no known history of cancer
Keywords = testis
Keywords = normal
Keywords = testicular neoplasm
Keywords = human

source_name: Normal testis, donor with no known history of cancer


title: Ramp 13, ambient


title: Ramp 14, ambient


title: Testicular seminoma 0737


title: Ramp 14, altered


title: Ramp 15, ambient


title: Ramp 17, altered


title: Ramp 19, ambient


title: Ramp 15, altered


title: Ramp 18, ambient


title: Ramp 19, altered


title: Ramp 18, altered


title: Ramp 17, ambient


title: Normal testis 0140

description:
Morphologically normal testicular parenchyma from area adjacent to a testicular germ cell tumor
Keywords = testis
Keywords = normal
Keywords = testicular neoplasm
Keywords = human

source_name: Normal testis, adjacent to germ cell tumor


title: ramp 4, altered

description: Leaf sample from altered rainfall plot


title: ramp 6, ambient

description: Leaf sample from ambient rainfall plot


title: Normal testis 9014

description:
Normal testicular parenchyma from a 29 years old organ donor with no known history of cancer
Keywords = testis
Keywords = normal
Keywords = testicular neoplasm
Keywords = human


title: ramp 4, ambient

description: Leaf sample from ambient rainfall plot


title: ramp 3, ambient

description: Leaf sample from ambient rainfall plot


title: Ramp 2, ambient

description: Leaf sample from ambient rainfall plot


title: ramp 2, alter

description: Leaf sample from altered rainfall plot


title: ramp 3, altered

description: Leaf sample from altered rainfall plot


title: Ramp 13, altered


title: Yolk sac tumor 0738


title: ramp 6, altered

description: Leaf sample from altered rainfall plot


title: nTE216vsHUE_2

status: Public on Mar 31 2005

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description:
Expression profiles in normal umbilical vein endothelial cells before (HUE142-2) and after immortalization with hTERT transfection (nTE4-5).
Keywords = endothelial cell
Keywords = cellular immortalization
Keywords = hTERT

source_name: nTE4_5 PDL216


title: nTE216vsHUE_1


title: TF1_216vsMJ90_2

description:
Expression profiles in normal fibroblasts before (MJ90) and after immortalization with hTERT transfection (TF1).
Keywords = fibroblast
Keywords = cellular immortalization
Keywords = hTERT

source_name: TF1 PDL216


title: nTE145vsHUE_2

source_name: nTE4_5 PDL145


title: nTE145vsHUE_1


title: TF1_148vsMJ90_1

source_name: TF1 PDL148


title: nTE105vsHUE_1

source_name: nTE4_5 PDL105


title: TF1_216vsMJ90_1


title: DNC_DABF3_1

status: Public on Mar 02 2005

city: Yongin

first: Ju-Kon

last: Kim

state: Kyonggi-do

address: 38-2 Nam-dong

department: Division of Bioscience and Bioinformatics

country: South Korea

institute: Myongji University

description:
Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::ABF3 and nontransgenic plants under drought stress condision.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles) were treated  with drought (air-dry) at the greenhouse continuous light for 2 h.
Total RNA (100 ¥ìg) was prepared from leaf tissues and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/) implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, ABF3

organism: Oryza sativa

source_name: Drought-stress treated Ubi1::ABF3 transgenic rice leaves

source_name: Drought-stress treated Nontransgenic rice leaves


title: nTE105vsHUE_2


title: TF1_148vsMJ90_2


title: baseline control 08

status: Public on Dec 31 2004

city: Stony Brook

first: Ira

last: Rampil

state: NY

institute: University at Stony Brook

description: Fear conditioning in rats leads to long term memory (LTM) formation. A central substrate for this type of LTM is the basolateral amygdala. We sought the expression changes specific to LTM at 6h following pain (a component of conditioning), following anesthesia with isoflurane (a general anesthetic and an effective amnestic agent), and following conditioning during isoflurane. For this also see GSE1779.

data_processing: raw data from Affymetrix

label: fluorscent label via ENZO BioArray RNA Transcript Labeling Kit

organism: Rattus norvegicus

source_name: basolateral amygdala


title: baseline control 09

label: fluorescent label via ENZO BioArray RNA Transcript Labeling Kit


title: baseline control 07


title: Embryonal carcinoma 1740

source_name: Universal Human Reference RNA (Stratagene)


title: baseline control 06


title: NC_CBF3_3

description:
Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::CBF3 and nontransgenic plants.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds were germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles).
Total RNA (100 ¥ìg) was prepared from leaf tissues of 14-day-old transgenic and nontransgenic seedlings (5-10 plants each) and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/)implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, CBF3

source_name: Ubi1::CBF3 transgenic rice leaves

source_name: Nontransgenic rice leaves


title: TF1_104vsMJ90_2

source_name: TF1 PDL104


title: baseline control 05


title: DNC_DCBF3_2

description:
Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::CBF3 and nontransgenic plants under drought stress condision.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds were germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles). Transgenic and NC plants were treated for 2 h with drought (air-dry) at the greenhouse continuous light.
Total RNA (100 ¥ìg) was prepared from leaf tissues of 14-day-old transgenic and nontransgenic seedlings (5-10 plants each) and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/)implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, CBF3

source_name: Drought stress treated Ubi1::CBF3 transgenic rice leaves

source_name: Drought stress treated Nontransgenic rice leaves


title: baseline control 04


title: NC_ABF3_2

description:
Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::ABF3 and nontransgenic plants.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds were germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles).
Total RNA (100 ¥ìg) was prepared from leaf tissues of 14-day-old transgenic and nontransgenic seedlings (5-10 plants each) and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/)implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, ABF3

source_name: Ubi1::ABF3 transgenic rice leaves


title: TF1_104vsMJ90_1


title: baseline control 03


title: baseline control 02


title: DNC_DABF3_2


title: DNC_DABF3_3


title: DNC_DCBF3_3


title: NC_CBF3_2


title: NC_ABF3_3


title: NC_CBF3_1


title: NC_ABF3_1


title: Stratagene Universal Reference (2)

city: Amsterdam

first: Fred

last: van Ruissen

department: Department of Neurogenetics

country: Netherlands

institute: Academic Medical Center

description: Gene expression analysis of Stratagene Universal Reference RNA Cat# 740000-41

source_name: Stratagene Universal Reference RNA


title: Stratagene Universal reference (1)

source_name: Stratagene Universal reference RNA


title: DNC_DCBF3_1

description:
Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::CBF3 and nontransgenic plants under drought stress condision.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles) were treated  with drought (air-dry) at the greenhouse continuous light for 2 h.
Total RNA (100 ¥ìg) was prepared from leaf tissues and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/) implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, CBF3

source_name: Drought-stress treated Ubi1::CBF3 transgenic rice leaves


title: RENAL_SNC12C

status: Public on Nov 24 2004

city: Research Triangle Park

first: Jennifer

last: Fostel

state: NC

institute: NIEHS

description: see Nature Genetics, volume 24 no. 3 pp 227 - 244.

source_name: Cy3-pool of 12 lines


title: OVARIAN_OVCAR4


title: Wilms' tumor (WT03) duplicate sample

description: Gene expression analysis of Wilms' tumor tissue after pre-operative chemotherapy

source_name: Bulk Wilms' tumor


title: PROSTATE_DU145


title: RENAL_TK10


title: baseline control 01


title: OVARIAN_OVCAR8


title: RENAL_ACHN


title: OVARIAN_OVCAR5


title: RENAL_CAKI_1


title: PROSTATE_PC3


title: BREAST_MCF7A_REPRO


title: RENAL_UO31


title: UNKNOWN_ADR_RES


title: RENAL_786_0


title: RENAL_A498


title: RENAL_RXF_393


title: Wilms tumor (WT03)


title: OVARIAN_SKOV3


title: NSCLC_NCI_H522


title: OVARIAN_OVCAR3


title: NSCLC_NCI_H460


title: NSCLC_NCI_H226


title: NSCLC_HOP92


title: OVARIAN_IGROV1


title: BREAST_MCF7D_REPRO


title: NSCLC_NCI_H23


title: NSCLC_HOP62


title: MELANOMA_SK_MEL5


title: MELANOMA_UACC257


title: NSCLC_EKVX


title: NSCLC_NCI_H322


title: MELANOMA_M14


title: MELANOMA_MALME_3M


title: MELANOMA_SK_MEL2


title: MELANOMA_SK_MEL28


title: NSCLC_A549


title: LEUKEMIA_K562


title: MELANOMA_UACC62


title: COLON_HCC2998


title: LEUKEMIA_K562B_REPRO


title: LEUKEMIA_K562A_REPRO


title: COLON_SW620


title: LEUKEMIA_HL60


title: MELANOMA_LOXIMVI


title: COLON_HCT116


title: LEUKEMIA_SR


title: LEUKEMIA_CCRF_CEM


title: COLON_HT29


title: COLON_KM12


title: LEUKEMIA_MOLT4


title: CNS_U251


title: COLON_COLO205


title: COLON_HCT15


title: CNS_SF539


title: CNS_SNB75


title: CNS_SNB19


title: mRNA abundance (wt, M9) no. 3

status: Public on Sep 09 2004

city: Saint Paul

first: Kyeong Soo

last: Jeong

state: MN

institute: University of Minnesota

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (wild type in M9)

organism: Escherichia coli

source_name: Genomic DNA from dnaC(ts) mutant

source_name: mRNA abundance (wt, M9)


title: BREAST_T47


title: BREAST_MDA_MB435


title: BR_HS578T


title: CNS_SF268


title: CNS_SF295


title: BREAST_MCF7


title: BREAST_MDA_N


title: LEUKEMIA_RPMI_8226


title: Transcription profile of wild type and gyrA (D82G) mutant no.4

description: Raw data for comparison of the transcriptional activity between wild type and gyrA (D82G) mutant in E. coli MG1655

source_name: mRNA abundance (gyrA D82G, LB)

source_name: mRNA abundance (wt, LB)


title: Transcription profile of wild type and gyrA (D82G) mutant no.5


title: BR_BT549


title: Transcription profile of wild type and gyrA (D82G) mutant no.7

source_name: mRNA abundance (gyrA D82G mutant, LB)


title: Transcription profile of wild type and gyrA (D82G) mutant no.6


title: Transcription profile of wild type and gyrA (D82G) mutant no.2


title: Transcription profile of wild type and gyrA (D82G) mutant


title: Transcription profile of wild type and gyrA (D82G) mutant no.8


title: mRNA abundance (wt, M9) no. 1


title: Transcription profile of wild type and gyrA (D82G) mutant no.3


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 7

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (wild type in LB, norfloxacin treat for 30min)


title: mRNA abundance (wt, M9) no. 2

source_name: Reference Genomic DNA


title: BREAST_MDA_MB231


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 8


title: mRNA abundance (wt, M9) no. 4


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 5


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 4

source_name: mRNA from wild type grown in LB


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 6


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 3


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 2

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (norfloxacin treat for 30 min in LB)


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 3

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (norfloxacin treat for 10 min in LB)


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 5


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 2


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 4


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 6


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 8


title: mRNA abundance (wt in LB, norfloxacin for 10 min) no. 7


title: mRNA abundance (gyrA D82G mutant, LB) no. 4

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (gyrA D82G mutant in LB)

source_name: mRNA from gyrA D82G mutant grown in LB


title: mRNA abundance (gyrA D82G mutant, LB) no. 6


title: mRNA abundance (gyrA D82G mutant, LB) no. 5


title: mRNA abundance (gyrA D82G mutant, LB) no. 2


title: mRNA abundance (gyrA D82G mutant, LB) no. 7


title: mRNA abundance (wild type, LB) no. 7

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (wild type in LB)


title: mRNA abundance (wild type, LB, norfloxacin treat for 10 min) no. 1


title: mRNA abundance (gyrA D82G mutant, LB) no. 1


title: mRNA abundance (wild type, LB) no. 8


title: mRNA abundance (wt in LB, norfloxacin for 30 min) no. 1


title: mRNA abundance (wild type, LB) no. 5


title: mRNA abundance (wild type, LB) no. 6


title: mRNA abundance (gyrA D82G mutant, LB) no. 3


title: mRNA abundance (wild type, LB) no. 2


title: mRNA abundance (wild type, LB) no. 3


title: mRNA abundance (wild type, LB) no. 4


title: mRNA abundance (wild type, LB)


title: MC3T3 cells day 3 GP prep 2.

status: Public on Jun 01 2004

city: Basel

first: Natasa

last: Zamurovic

department: Bone metabolism

country: Switzerland

institute: Novartis Institutes for BioMedical Research

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta-glycerol phosphate (GP) for 3 day; prep 2.

organism: Mus musculus

source_name: mouse calvarial MC3T3 cell line


title: MC3T3 cells day 1 GP/AA/BMP-2 prep 2.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 1 day; prep 2.


title: MC3T3 cells day 3 GP/AA/BMP-2 prep 2.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 3 days; prep 2.


title: MC3T3 cells day 1 GP prep 2.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP) for 1 day; prep 2.


title: Y6

status: Public on Oct 29 2003

city: Valhalla

first: Anna

last: Csiszar

department: Physiology

institute: New York Medical College

description: Total RNA was isolated from the septal coronary arteries of 3 month old F344 rats.

source_name: rat coronary artery


title: Y5


title: Y7


title: Y4


title: A3

description: Total RNA was isolated from the septal coronary arteries of 26 month old F344 rats. Increased endothelial apoptosis in coronary arteries was verified by TUNEL assay and DNA fragmentation assay.


title: A6


title: A5


title: MC3T3 cells day 1 GP prep 1.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate for 1 day; prep 1.


title: Y2


title: MC3T3 cells day 0 medium prep 2.

description:
Osteoblast differentiation experiment
MC3T3 clone 1b cells control medium day 0; prep 2.


title: Y1


title: MC3T3 cells day 3 GP/AA/BMP-2 prep 1.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 3 days; prep 1.


title: MC3T3 cells day 1 GP prep 3.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate for 1 day; prep 3.


title: MC3T3 cells day 0 medium prep 1.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells control medium day 0; prep 1.


title: Y3

source_name: rat coronary arteries


title: MC3T3 cells day 3 GP prep 3.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP) for 3 days; prep 3.


title: A1


title: MC3T3 cells day 0 medium prep 3.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells control medium, day 0; prep 3.


title: A2


title: T cells-BDC2.5/NOD lymph node-rep2

status: Public on Apr 17 2004

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Antigen specific T cells isolated from the pancreatic lymph nodes of mice developping a benign insulitis (BDC2.5-NOD at 22 days of age)

source_name: pancreatic lymph nodes

extract_protocol: RNA isolated with Trizol reagent and amplified twice

treatment_protocol: No treatment

tag: Genetic Background

value: NOD.

tag: Transgene:BDC2.5 T cell receptor genes.

tag: Age:22 days

tag: Tissue

value: pancreatic lymph nodes

tag: Isolation

value: FACS on CD4+, BDC2.5 clonotype high, Hoechst- (viable) cells


title: MC3T3 cells day 1 GP/AA/BMP-2 prep 1.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 1 day; prep 1.


title: MC3T3 cells day 1 GP/AA/BMP-2 prep 3.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 1 day; prep 3.


title: MC3T3 cells day 3 GP/AA/BMP-2 prep 3.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP), ascorbic acid (AA) and bone morphogenic protein 2 (BMP-2) for 3 days; prep 3.


title: A4


title: MC3T3 cells day 3 GP prep 1.

description:
Osteoblast differentiation experiment:
MC3T3 clone 1b cells treated with beta- glycerol phosphate (GP) for 3 days; prep 1.


title: Dahl_kidney_4_U94A

status: Public on Sep 20 2003

city: Montreal

first: Alan

middle: Y

last: Deng

country: Canada

institute: Research Centre-CHUM

description: Kidneys of 5 week old Dahl salt sensitive rat.

source_name: kidney


title: Dahl_kidney_3_U94A


title: Dahl_kidney_5_U94C

description: Kidneys of 5 week old congenic strain of Chr.10 of Dahl salt sensitive rat.


title: Dahl_kidney_5_U94B

description: Kidneys of 5 week old congenic strain Chr.10. of Dahl salt sensitive rat.


title: Dahl_kidney_2_U94C


title: Dahl_kidney_2_U94B


title: m1-adenoma2

status: Public on Sep 12 2003

city: Notre Dame

first: Matthew

last: Feldman

state: IN

address: 251 Nieuwland Science Hall

department: Chemistry and Biochemistry

institute: University of Notre Dame

description: Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step.

source_name: Ileum epithelials cells


title: Dahl_kidney_4_U94C


title: m1-adenoma4


title: m1-WT4


title: m1-adenoma1


title: m1-WT5


title: m1-carcinoma1


title: TAC-S_2B

status: Public on Aug 22 2003

first: Maria

last: Mirotsou

institute: Brigham and Women's Hospital, Harvard Medical School

description: Heart intra-ventricular septum from mouse model of transverse aortic constriction (TAC) 1 week post operation

source_name: HEART  INTRA-VENTRICULAR SEPTUM


title: m1-adenoma5


title: m1-carcinoma3


title: m1-WT3


title: UV_fhCMV-H-3

status: Public on Sep 08 2003

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
Target Source: human foreskin fibroblasts exposed to UV-inactivated cytomegalovirus.
Clinical  isolate fhCMV-H of CMV, genotype gB3.

HFF were plated in T75 flasks at approximately 80% confluence. The next day
the supernatant was removed and replaced with the CMV viral inoculum (MOI of
3) in a total volume of 7 mls of RPMI supplemented with 5% FBS. Virus was UV-inactivated on ice in a UV Stratalinker 2400. To ensure that the virus was UV-inactivated, yet not heat inactivated, pilot studies were conducted in which samples of each virus strain were subjected to increasing amount of UV light. These test samples were incubated with HFF for 2 hours at 37ºC and either fixed with 50% acetone/50% methanol at 8 hours post-infection (hpi) and stained using antibodies to CMV IE1 and pp65 or allowed to replicate for 24 hr. If the inoculum failed to produce CPE, was not positive for IE1 staining, but was positive for pp65 staining, it was considered UV-inactivated.The virus was permitted to absorb for 2 hours at 37 C and 5% CO2. The supernatants were incubated at the same time as the infected cultures. The inoculum was removed, the cells were washed 2 times with Hank's buffer, and media was replaced.
Uninfected and infected fibroblasts were harvested at 24 hpi by brief trypsinization followed by pelleting of the cells.
All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with
Superscript II reverse transcriptase for 2h at 42 C in the presence of 0.5mM
dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP.
After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with
a Microcon-30 concentrator. The cDNA from uninfected and infected fibroblasts
was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix
4000A fluorescent scanner and image intensity data were extracted and
analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression values were mean centered and linear transformed to obtain the log and linear values given in the data table.
Keywords = cytomegalovirus, glycoprotein B

source_name: UV-CMV exposed human foreskin fibroblasts (HFF)

source_name: uninfected HFF


title: m1-carcinoma2


title: UV-fhCMV-T-4

description:
Target Source: human foreskin fibroblasts exposed to UV-inactivated cytomegalovirus.
Clinical  isolate fhCMV-T of CMV, genotype gB1.

HFF were plated in T75 flasks at approximately 80% confluence. The next day
the supernatant was removed and replaced with the CMV viral inoculum (MOI of
3) in a total volume of 7 mls of RPMI supplemented with 5% FBS. Virus was UV-inactivated on ice in a UV Stratalinker 2400. To ensure that the virus was UV-inactivated, yet not heat inactivated, pilot studies were conducted in which samples of each virus strain were subjected to increasing amount of UV light. These test samples were incubated with HFF for 2 hours at 37ºC and either fixed with 50% acetone/50% methanol at 8 hours post-infection (hpi) and stained using antibodies to CMV IE1 and pp65 or allowed to replicate for 24 hr. If the inoculum failed to produce CPE, was not positive for IE1 staining, but was positive for pp65 staining, it was considered UV-inactivated.The virus was permitted to absorb for 2 hours at 37 C and 5% CO2. The supernatants were incubated at the same time as the infected cultures. The inoculum was removed, the cells were washed 2 times with Hank's buffer, and media was replaced.
Uninfected and infected fibroblasts were harvested at 24 hpi by brief trypsinization followed by pelleting of the cells.
All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with
Superscript II reverse transcriptase for 2h at 42 C in the presence of 0.5mM
dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP.
After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with
a Microcon-30 concentrator. The cDNA from uninfected and infected fibroblasts
was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix
4000A fluorescent scanner and image intensity data were extracted and
analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression values were mean centered and linear transformed to obtain the log and linear values given in the data table.
Keywords = cytomegalovirus, glycoprotein B


title: TAC-LV_2B

description: Heart left ventricle free wall from mouse model of transverse aortic constriction (TAC) 1 week post operation

source_name: HEART LV FREE WALL


title: TAC-S_1B


title: mRNA abundance (gyrA D82G mutant, LB) no. 8

description: Raw data for spatial pattern analysis of transcriptional activity in E. coli MG1655 (gyrA D82G mutant in LB)

source_name: Genomic DNA from dnaC(ts) mutant


title: TAC-S_1A


title: UV-fhCMV-T-3

source_name: uninfected fibroblasts


title: SHAM-S_3B

description: Heart intra-ventricular septum from mouse model of Sham myocardial infarction 1 week post operation


title: TAC-LV_1A


title: TAC-S_2A


title: m1-WT6


title: m1-carcinoma4


title: SHAM-S_3A


title: TAC-LV_1B


title: UV_fhCMV-H-4


title: UV_fhCMV-H-2

source_name: CMV-exposed human foreskin fibroblasts (HFF)


title: m1-WT2


title: SHAM-S_2B

description: Heart intra-ventricular septum from mouse model of Sham transverse aortic constriction (TAC) 1 week post operation


title: SHAM-S_1B


title: SHAM-S_1A


title: SHAM-S_4B


title: SHAM-LV_1B

description: Heart left ventricle free wall from mouse model of Sham myocardial infarction 1 week post operation


title: SHAM-S_4A


title: SHAM-LV_3B


title: SHAM-LV_2B

description: Heart left ventricle free wall from mouse model of Sham transverse aortic constriction (TAC) 1 week post operation


title: SHAM-LV_2A


title: MI-S_2B

description: Heart intra-ventricular septum from mouse model of myocardial infarction 1 week post operation


title: MI-S_2A


title: MI-S_1A


title: MI-LV_3B

description: Heart left ventricle free wall from mouse model of myocardial infarction 1 week post operation


title: 48h EC A

status: Public on Aug 18 2003

city: La Jolla

first: Richard

middle: Louis

last: Lieber

state: CA

address: 9500 Gilman Drive

department: Orthopaedics and Bioengineering

institute: University of California

description:
Mice were subjected to 50 eccentric contractions (EC) or 50 isometric contractions (IC) using a non-invasive model, and then sacrificed 48 hours later. RNA from the tibialis anterior of 4 animals were pooled and then split into two groups for hybridization onto two separate Affymetrix MGU74Av2 chips. Control samples were contralateral to the exercised legs, and were only subjected to enough contractions to measure isometric torque.
Keywords = mouse tibialis anterior muscle eccentric contraction

source_name: mouse skeletal muscle


title: 48h EC B


title: MI-LV_3A


title: MI-LV_2B


title: SHAM-LV_1A


title: SHAM-LV_3A


title: 48h IC A


title: 48h IC B


title: MI-S_1 B


title: MI-S_3A


title: 48h Control B


title: MI-LV_2A

description: Heart Left ventricle free wall from mouse model of myocardiac infarction 1 week post operation


title: E81a

status: Public on Jul 16 2003

city: Cambridge

first: Colin

last: Meiklejohn

address: 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Strains of Drosophila melanogaster were raised on standard medium at 25 C with no light/dark cycle.  Adult males were collected up to 24 hours after eclosing and separated from females where they were allowed to age an additional 3-4 days.  Total RNA was extracted by homogenizing 8-12 flies in TRIzol reagent (Invitrogen) followed by a chloroform extraction and isopropanol precipitation.  The resulting pellet was washed with 75% ethanol, air-dried, and resuspended in TE.  Individual extractions were pooled into one common RNA sample for each strain.  Poly-A RNA was purified from total RNA using the Oligotex Direct mRNA kit (Qiagen). mRNA samples were confirmed to be of high quality with a 2100 Bioanalyzer (Agilent).  The production of cDNA and hybridizations were done following a published protocol (Eisen and Brown, Methods in Enzymology 303:179-205).  2 µg of poly-A RNA was used as a template for SuperScript II reverse transcriptase (Invitrogen) in the presence of amino-allyl dUTP (Sigma) with random hexamer and oligo dT primers.  Reverse transcription was done at 42 C for 3 hours, followed by degradation of RNA by the addition of NaOH and EDTA and incubation at 65 C for 15 minutes.  The cDNA was concentrated and purified with Microcon-30 filters (Millipore).   Cyanine-3 or cyanine-5 fluorochromes (Amersham) were incorporated with the addition of 1 M NaHCO3 and a 75 minute incubation at room temperature with the cDNA probe.  The labeled probes were then purified using the QIAquick PCR Purification Kit (Qiagen), concentrated with Microcon-30 filters, and combined into one sample.  25 µL of probe was combined with 22 µg poly(A), 4.4 µL 20X SSC, 0.71 µL 1 M HEPES (pH 7.0), and 0.66 µL 10% SDS.  The probe was boiled at 100 C for 2 minutes and injected under a LifterSlip (Erie Scientific Company) placed over the array.  Slides were placed in a Telechem hybridization chamber with 3X SSC in the chamber wells to prevent drying, sealed, and placed in a 65 C water bath for 12 hours.  After hybridization, slides were washed with two wash solutions (0.6X SSC, 0.025% SDS [solution 1] and 0.05X SSC [solution 2]).  Slides were dried by centrifugation at 1000 rpm for 2 minutes and scanned within an hour of washing.  Fluorescence intensity was measured with Axon GenePix 4000A or 4000B scanners and the data was captured with GenePix 4.0 software. Following exclusion of suboptimal spots, intensity ratios were constructed by subtracting local background from foreground for each spot and normalizing one channel so that the mean foreground fluorescence of both channels across the slide was equal.

organism: Drosophila melanogaster

source_name: Zimbabwe2 adult males

source_name: Canton S adult males


title: E81b

source_name: St Louis adult males

source_name: Zimbabwe53 adult males


title: E87a

source_name: Zimbabwe30 adult males


title: E85a


title: E85b


title: Isoflurane single exposure 1 hr-1

status: Public on Jun 25 2003

city: Philadelphia

first: Roderic

last: Eckenhoff

state: PA

institute: University of Pennsylvania

description:
1 hr exposure to 2% isoflurane.  Rat was intubated.
Keywords = Eckenhoff, anesthetics

source_name: whole brain


title: Isoflurane single exposure 2 hr-2

description:
2 hr exposure to 2% isoflurane.  Rat was intubated.
Keywords = Eckenhoff, anesthetics

source_name: Whole brain


title: E70b

source_name: Oregon R adult males


title: E49b


title: jaw_1

status: Public on Jul 07 2003

city: Tuebingen

first: Javier

middle: Fernando

last: Palatnik

address: 37-39 Spemannstrasse

department: Molecular Biology

country: Germany

institute: Max Planck Institute

description:
Total RNA was extracted from the aerial parts of two weeks old jaw-d plants.
jaw-d is an activation tagged line.

organism: Arabidopsis thaliana

source_name: jaw-d


title: Isoflurane single exposure 1 hr-2


title: C121b


title: E114b

source_name: Zimbabwe29 adult males


title: C110b


title: jaw_2


title: E40b


title: Isoflurane single exposure 2 hr-1


title: Isoflurane single exposure control-2

description:
3 min exposure to isoflurane, immediate perfusion with ice cold saline.  Rat was intubated.
Keywords = Eckenhoff, anesthetics


title: Isoflurane single exposure 2 hr-3


title: C123b


title: C110a


title: C73a


title: E114a

source_name: Hikone R adult males


title: Isoflurane single exposure control-3


title: Control_2

description: Total RNA was extracted from the aerial parts of two weeks old plants.

source_name: Columbia


title: C58a


title: E103a


title: Isoflurane 5 exposures-3

description:
Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 2.5 days, for a total of 5 exposures
Keywords = Eckenhoff, anesthetics


title: C121a


title: Isoflurane 5 exposures-1

source_name: WHOLE BRAIN


title: Isoflurane single exposure control-1

description:
3 min exposure to isoflurane, immediate perfusion with ice cold saline.  Rat was intubated.
Keywords = Eckenhoff, anesthetic


title: Isoflurane 5 exposures-2


title: Isoflurane 10 exposures-3

description:
Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 5 days, for a total of 10 exposures
Keywords = Eckenhoff, anesthetics


title: Halothane 10 exposures-2

description:
Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 5 days, for a total of 10 exposures
Keywords = Eckenhoff, anesthetics


title: Halothane 10 exposure-1


title: Control 4

description:
3 min exposure to halothane, immediate perfusion with ice cold saline
Keywords = Eckenhoff, anesthetics


title: Control 7

description:
3 min exposure to halothane, immediate perfusion with ice cold saline
Keywords = Eckenhoff. anesthetics


title: Control 3


title: Halothane 10 exposures-3


title: Control 2


title: 408_1

status: Public on Apr 22 2003

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 408

source_name: Control


title: 307_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 307


title: 405_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 405


title: 290_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 290


title: Control 8


title: 290_2

description: Individual LCL vs Pooled Control LCLs


title: 407_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 407


title: 307_1

description: Individual LCL vs Pooled Control LCLs


title: Isoflurane 10 exposures-1


title: 440_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 440

source_name: control


title: 293_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 293


title: Control 9

source_name: whole brain


title: 293_2

description: Individual LCL vs Pooled Control LCLs


title: 287_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 287


title: 286_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 286


title: 407_2

description: Individual LCL vs Pooled Control LCLs


title: 287_2

description: Individual LCL vs Pooled Control LCLs


title: 408_2

description: Individual LCL vs Pooled Control LCLs


title: 436_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 436


title: 252_2

description: Individual LCL vs Pooled control LCLs

source_name: Individual 252


title: 286_1

description: Individual LCL vs Pooled Control LCLs


title: 435_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 435


title: 436_1

description: Individual LCL vs Pooled control LCLs


title: 440_1

description: Individual LCL vs Pooled Control LCLs


title: 432_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 432


title: 425_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 425


title: 434_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 434


title: 432_1

description: Individual LCL vs Pooled Control LCLs

source_name: Control


title: 434_2

description: Individual LCL vs Pooled Control LCLs


title: 435_1

description: Individual LCL vs Pooled Control LCLs


title: 412_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 412


title: 412_1

description: Individual LCL vs Pooled Control LCLs


title: 425_1

description: Individual LCL vs Pooled Control LCLs


title: 460_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 460


title: 411_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 411


title: 410_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 410


title: 411_2

description: Individual LCL vs Pooled Control LCLs


title: 430_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 430


title: 430_2

description: Individual LCL vs Pooled Control LCLs


title: 456_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 456

source_name: control


title: 460_1

description: Individual LCL vs Pooled Control LCLs


title: 410_1

description: Individual LCL vs Pooled Control LCLs


title: 456_1

description: Individual LCL vs Pooled Control LCLs


title: 443_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 443


title: 439_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 439


title: 443_1

description: Individual LCL vs Pooled Control LCLs


title: 438_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 438


title: 439_2

description: Individual LCL vs Pooled Control LCLs


title: 285_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 285


title: 285_2

description: Individual LCL vs Pooled Control LCLs


title: 437_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 437


title: 437_1

description: Individual LCL vs Pooled Control LCLs


title: E127a

source_name: Hikone R adult males

source_name: Canton S adult males


title: 284_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 284


title: Isoflurane 10 exposures-2

source_name: whole brain


title: 284_1

description: Individual LCL vs Pooled Control LCLs


title: 281_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 281


title: 277_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 277


title: 278_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 278


title: C123a

description: Strains of Drosophila melanogaster were raised on standard medium at 25 °C with no light/dark cycle.  Adult males were collected up to 24 hours after eclosing and separated from females where they were allowed to age an additional 3-4 days.  Total RNA was extracted by homogenizing 8-12 flies in TRIzol reagent (Invitrogen) followed by a chloroform extraction and isopropanol precipitation.  The resulting pellet was washed with 75% ethanol, air-dried, and resuspended in TE.  Individual extractions were pooled into one common RNA sample for each strain.  Poly-A RNA was purified from total RNA using the Oligotex Direct mRNA kit (Qiagen). mRNA samples were confirmed to be of high quality with a 2100 Bioanalyzer (Agilent).  The production of cDNA and hybridizations were done following a published protocol (Eisen and Brown, Methods in Enzymology 303:179-205).  2 µg of poly-A RNA was used as a template for SuperScript II reverse transcriptase (Invitrogen) in the presence of amino-allyl dUTP (Sigma) with random hexamer and oligo dT primers.  Reverse transcription was done at 42 °C for 3 hours, followed by degradation of RNA by the addition of NaOH and EDTA and incubation at 65 °C for 15 minutes.  The cDNA was concentrated and purified with Microcon-30 filters (Millipore).   Cyanine-3 or cyanine-5 fluorochromes (Amersham) were incorporated with the addition of 1 M NaHCO3 and a 75 minute incubation at room temperature with the cDNA probe.  The labeled probes were then purified using the QIAquick PCR Purification Kit (Qiagen), concentrated with Microcon-30 filters, and combined into one sample.  25 µL of probe was combined with 22 µg poly(A), 4.4 µL 20X SSC, 0.71 µL 1 M HEPES (pH 7.0), and 0.66 µL 10% SDS.  The probe was boiled at 100 °C for 2 minutes and injected under a LifterSlip (Erie Scientific Company) placed over the array.  Slides were placed in a Telechem hybridization chamber with 3X SSC in the chamber wells to prevent drying, sealed, and placed in a 65 °C water bath for 12 hours.  After hybridization, slides were washed with two wash solutions (0.6X SSC, 0.025% SDS [solution 1] and 0.05X SSC [solution 2]).  Slides were dried by centrifugation at 1000 rpm for 2 minutes and scanned within an hour of washing.  Fluorescence intensity was measured with Axon GenePix 4000A or 4000B scanners and the data was captured with GenePix 4.0 software. Following exclusion of suboptimal spots, intensity ratios were constructed by subtracting local background from foreground for each spot and normalizing one channel so that the mean foreground fluorescence of both channels across the slide was equal.


title: 277_1

description: Individual LCL vs Pooled Control LCLs


title: 438_1

description: Individual LCL vs Pooled Control LCLs


title: 278_2

description: Individual LCL vs Pooled Control LCLs


title: 280_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 280


title: 281_1

description: Individual LCL vs Pooled Control LCLs


title: 275_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 275


title: 259_1

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 259


title: 262_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 262


title: Control 5


title: 280_2

description: Individual LCL vs Pooled Control LCLs

source_name: control


title: 262_1

description: Individual LCL vs Pooled Control LCLs


title: 259_2

description: Individual LCL vs Pooled Control LCLs


title: 258_2

description: Individual LCL vs Pooled Control LCLs

source_name: Individual 258


title: delPPT1_hypo_osmotic_shock_15min

status: Public on Apr 15 2003

city: Stanford

first: Eran

last: Segal

address: Gates Building 1A

department: Computer Science

institute: Stanford University

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
delPPT1_hypo_osmotic_shock_15min

organism: Saccharomyces cerevisiae

source_name: reference


title: delUSV1_stationary_phase_5hours

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_5hours


title: delPPT1_hypo_osmotic_shock_0min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
delPPT1_hypo_osmotic_shock_0min


title: delPPT1_hypo_osmotic_shock_30min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
delPPT1_hypo_osmotic_shock_30min


title: 275_1

description: Individual LCL vs Pooled Control LCLs


title: DBY8778(wt)_stationary_phase_5hours

description:
Wild type and ypl230w mutant under stationary phase.
DBY8778(wt)_stationary_phase_5hours


title: delUSV1_stationary_phase_2hours

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_2hours


title: delKIN82_heat shock_0min_repeat

description:
Wild type and kin82 mutant under heat shock.
delKIN82_heat shock_0min_repeat

source_name: delKIN82_heat shock_0min_repeat


title: DBY8778(wt)_stationary_phase_7hours

description:
Wild type and ypl230w mutant under stationary phase.
DBY8778(wt)_stationary_phase_7hours


title: DBY8778(wt)_stationary_phase_1day

description:
Wild type and ypl230w mutant under stationary phase.
DBY8778(wt)_stationary_phase_1day


title: delPPT1_hypo_osmotic_shock_7min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
delPPT1_hypo_osmotic_shock_7min


title: delUSV1_stationary_phase_0hours

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_0hours


title: delUSV1_stationary_phase_1day

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_1day


title: delKIN82_heat shock_5min

description:
Wild type and kin82 mutant under heat shock.
delKIN82_heat shock_5min

source_name: delKIN82_heat shock_5min


title: delUSV1_stationary_phase_7hours

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_7hours


title: wt_hypo_osmotic_shock_60min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
wt_hypo_osmotic_shock_60min


title: wt_hypo_osmotic_shock_30min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
wt_hypo_osmotic_shock_30min


title: delKIN82_heat shock_15min

description:
Wild type and kin82 mutant under heat shock.
delKIN82_heat shock_15min

source_name: delKIN82_heat shock_15min


title: wt_hypo_osmotic_shock_7min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
wt_hypo_osmotic_shock_7min


title: wt_hypo_osmotic_shock_16min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
wt_hypo_osmotic_shock_16min


title: DBY8778_heat_shock2_60min

description:
Wild type and kin82 mutant under heat shock.
DBY8778_heat_shock2_60min


title: delKIN82_heat shock_60min_repeat

description:
Wild type and kin82 mutant under heat shock.
delKIN82_heat shock_60min_repeat

source_name: delKIN82_heat shock_60min_repeat


title: DBY8778_heat_shock2_15min

description:
Wild type and kin82 mutant under heat shock.
DBY8778_heat_shock2_15min


title: delUSV1_stationary_phase_9hours

description:
Wild type and ypl230w mutant under stationary phase.
delUSV1_stationary_phase_9hours


title: wt_hypo_osmotic_shock_0min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
wt_hypo_osmotic_shock_0min


title: leg muscle-adult Rat -L3

status: Public on Apr 02 2003

city: Cleveland

first: Sangeeta

last: Khanna

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

description:
Replicate 3 for control rat adult leg muscle;Gastroc/soleus were pooled for rna extraction; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray

source_name: Rat gastrocnemius/soleus


title: smooth muscle-adult Rat -S2

description:
Replicate 2 for control rat adult smooth muscle:source-stomach wall after removing the epithelium;raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray

source_name: Rat stomach wall


title: smooth muscle-adult Rat -S1

description:
Replicate 1 for control rat adult smooth muscle:source-stomach wall after removing the epithelium;raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: EOM-adult Rat -E2

description:
Replicate 2 for control rat adult extraocular muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray

source_name: Rat Extraocular Muscle


title: smooth muscle-adult Rat -S3

description:
Replicate 3 for control rat adult smooth muscle:source-stomach wall after removing the epithelium;raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: Cardiac muscle-adult Rat -H1

description:
Replicate 1 for control rat adult cardiac muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray

source_name: Rat Heart ventricle


title: leg muscle-adult Rat -L1

description:
Replicate 1 for control rat adult leg muscle;Gastroc/soleus were pooled for rna extraction; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: Cardiac muscle-adult Rat -H3

description:
Replicate 3 for control rat adult cardiac muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: leg muscle-adult Rat -L2

description:
Replicate 2 for control rat adult leg muscle;Gastroc/soleus were pooled for rna extraction; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: Cardiac muscle-adult Rat -H4

description:
Replicate 4 for control rat adult cardiac muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: EOM-adult Rat -E4

description:
Replicate 4 for control rat adult extraocular muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: EOM-adult Rat -E3

description:
Replicate 3 for control rat adult extraocular muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: Eye Discs iso4 lmC17

status: Public on Jan 21 2003

first: Lydia

last: Michaut

address: Klingelbergstrasse 70

department: Cell Biology

institute: Biozentrum

description: To analyze gene expression in Drosophila eye primordia (iso4 third instar wandering larvae), the eye part was separated from the antennal part of the eye-antennal disc. One hundred eye imaginal discs were dissected, immediately transferred into 800ul Trizol (GIBCO Life Technologies) and stored at –70°C. RNA extraction was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Two successive rounds of cDNA synthesis were applied to prepare 20ug of biotinylated target from one to two micrograms of total RNA (see Michaut et al., 2003).

source_name: Drosophila wandering larvae eye imaginal discs


title: Eye Discs iso4 lmC30


title: Leg Discs iso4 lmC50

description: To analyze gene expression in Drosophila control leg imaginal discs (iso4 third instar wandering larvae), one to two hundred leg imaginal discs were dissected and immediately transferred into 800ul Trizol (GIBCO Life Technologies). RNA extraction was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Biotinylated RNA targets were prepared from 15 to 20 ug total RNA (500-700 leg discs) according to the standard Affymetrix procedure (see Michaut et al., 2003).

source_name: Drosophila wandering larvae leg imaginal discs


title: Leg Discs iso4 lmC51


title: Leg Discs ectopic ey lmC52

description: To analyze gene expression in Drosophila leg discs where an eye field was ectopically induced  ([dppblink-GAL4, UAS-GAL4/UAS-ey] third instar wandering larvae), one to two hundred leg imaginal discs were dissected and immediately transferred into 800ul Trizol (GIBCO Life Technologies). RNA extraction, was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Biotinylated RNA targets were prepared from 15 to 20 ug total RNA (500-700 leg discs) according to the standard Affymetrix procedure (see Michaut et al., 2003).

source_name: [dppblink-GAL4, UAS-GAL4/UAS-ey] Drosophila wandering larvae leg imaginal discs


title: Leg Discs ectopic ey lmC53


title: Leg Discs iso4 lmC49


title: Leg Discs ectopic ey lmC54


title: Eye Discs iso4 lmC31


title: Eye Discs iso4 lmC45


title: Leg Discs ectopic ey lm54


title: Eye Discs iso4 lmC44


title: Leg Discs ectopic ey lm55


title: Eye Discs iso4 lm30

description: To analyze gene expression in Drosophila eye primordia (third instar wandering larvae), the eye part was separated from the antennal part of the eye-antennal disc. One hundred eye imaginal discs were dissected, immediately transferred into 800ul Trizol (GIBCO Life Technologies) and stored at –70°C. RNA extraction was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Two successive rounds of cDNA synthesis were applied to prepare 20ug of biotinylated target from one to two micrograms of total RNA (see Michaut et al., 2003).


title: wing/hinge 1

status: Public on Jan 11 2003

city: Columbus

first: Amanda

last: Simcox

address: 484 W 12th Ave

department: Molecular Genetics

institute: Ohio State University

description:
Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 1.
Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts

source_name: wing imaginal disc


title: body wall 3

description:
Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as NOTUM 3.
Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts

source_name: imaginal wing disc


title: Leg Discs iso4 lm51

description: To analyze gene expression in control leg imaginal discs (iso4 third instar wandering larvae), one to two hundred leg imaginal discs were dissected and immediately transferred into 800ul Trizol (GIBCO Life Technologies)  and stored at –70°C until RNA extraction, which was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Biotinylated RNA targets were prepared from 15 to 20 ug total RNA (500-700 leg discs) according to the standard Affymetrix procedure (see Michaut et al., 2003).


title: Leg Discs ectopic ey lm52

description: To analyze gene expression in Drosophila leg discs where an eye field was ectopically induced  ([dppblink-GAL4, UAS-GAL4/UAS-ey] third instar wandering larvae), one to two hundred leg imaginal discs were dissected and immediately transferred into 800ul Trizol (GIBCO Life Technologies)  and stored at –70°C until RNA extraction, which was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Biotinylated RNA targets were prepared from 15 to 20 ug total RNA (500-700 leg discs) according to the standard Affymetrix procedure (see Michaut et al., 2003).


title: Bladder sample 1238-1

status: Public on Dec 08 2002

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: T1 gr3 tumour

source_name: tumour


title: Bladder sample 1083-2

description: T1 gr3 tumour


title: wing/hinge 3

description:
Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 3.
Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts


title: body wall 2

description: Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as NOTUM 2R.


title: Leg Discs ectopic ey lm53


title: Bladder sample 1269-1

description: T1 gr3 tumour


title: wing/hinge 2

description:
Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 2
Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts


title: Bladder sample 967-3

description: Ta gr3 tumour


title: delPPT1_hypo_osmotic_shock_60min

description:
Wild type and ppt1 mutant under hypo-osmotic shock.
delPPT1_hypo_osmotic_shock_60min


title: Bladder sample 1134-1

description: T1 gr3 tumour


title: Bladder sample 956-2

description: Ta gr3 tumour


title: Bladder sample 934-1

description: Ta gr2 tumour


title: Bladder sample 1068-1

description: T2+ gr3 tumour


title: Bladder sample 968_1

description: Ta gr2 tumour


title: Bladder sample 930_1

description: Ta gr2 tumour


title: Bladder sample 880-1

description: T1 gr 3 tumour


title: Bladder sample 937-1

description: Ta gr2 tumour


title: Bladder sample 989-1

description: Ta gr3 tumour


title: Bladder sample 919-1

description: T1 gr3 tumour


title: Bladder sample 928_1

description: Ta gr2 tumour


title: Bladder sample 1166-1

description: Ta gr3 tumour


title: Bladder sample 847-1

description: T1 gr3 tumour


title: Bladder sample 812-1

description: T1 gr3 tumour


title: Bladder sample 716-2

description: Ta gr3 tumour


title: Bladder sample 875-1

description: T2+ gr3 tumour


title: Bladder sample 747-7

description: Ta gr3 tumour


title: Bladder sample 112-10

description: Ta gr3 tumour


title: Bladder sample 370-1

description: Ta gr2 tumour


title: Bladder sample 533-1

description: Ta gr2 tumour


title: Bladder sample 1070-1

description: Ta gr3 tumour


title: Bladder sample 1164-1

description: T2+ gr4 tumour


title: Bladder sample 524-1

description: Ta gr2 tumour


title: Bladder sample 1044-1

description: T2+ gr3 tumour


title: Bladder sample 1264-1

description: Ta gr3 tumour


title: Bladder sample 1117-1

description: T2+ gr 3 tumour


title: Bladder sample 1330-1

description: Ta gr3 tumour


title: Bladder sample 928-1

description: Ta gr2 tumour


title: Bladder sample 876-5

description: Ta gr3 tumour


title: Bladder sample 669-7

description: Ta gr3 tumour


title: H9SGK99091503

status: Public on Dec 06 2002

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
Large-scale analysis of the human transcriptome.
Leukemia lymphoblastic MOLT-4
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 116.74  Stdv: 4.66  Min: 108.45  Max: 126.14

source_name: Lymphoblastic molt-4


title: Cardiac muscle-adult Rat -H2

description:
Replicate 2 for control rat adult cardiac muscle; raw data from RGU34A array using antibody scan.
Keywords = skeletal muscle, extraocular muscle, microarray


title: Bladder sample 1060-1

description: Ta gr2 tumour


title: H9SGK99092001

description:
Large-scale analysis of the human transcriptome.
Umbilical vein endothelial cells
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 116.40  Stdv: 4.29  Min: 107.11  Max: 124.51

source_name: HUVEC


title: 258_1

description: Individual LCL vs Pooled control LCLs

source_name: Individual 258

source_name: control


title: Bladder sample 1078-1

description: T2+ gr3 tumour


title: H9SGK99091502

description:
Large-scale analysis of the human transcriptome.
Umbilical vein endothelial cells
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 131.19  Stdv: 4.79  Min: 121.06  Max: 139.47


title: Bladder sample 1062-2

description: Ta gr3 tumour


title: H9RGV00111005

description:
Large-scale analysis of the human transcriptome.
Promyelocytic leukemia
Source: ATCC
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 182.44  Stdv: 8.00  Min: 165.67  Max: 192.85


title: H9RGV00111404

description:
Large-scale analysis of the human transcriptome.
Brain, corpus callosum
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 184.68  Stdv: 10.68  Min: 161.62  Max: 197.95

source_name: corpus callosum


title: H9RGV00111502

description:
Large-scale analysis of the human transcriptome.
Brain, thalamus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 174.00  Stdv: 11.70  Min: 141.09  Max: 191.39

source_name: thalamus


title: H9RGV00111008

description:
Large-scale analysis of the human transcriptome.
Lymphoma Burkitt's Raji
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 124.96  Stdv: 7.76  Min: 113.67  Max: 138.77

source_name: Burkitt's Raji


title: H9RGV00110705

description:
Large-scale analysis of the human transcriptome.
Brain, corpus callosum
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 217.04  Stdv: 11.39  Min: 194.61  Max: 236.17


title: H9SGK99091504

description:
Large-scale analysis of the human transcriptome.
Promyelocytic leukemia
Source: ATCC
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 125.16  Stdv: 6.21  Min: 111.43  Max: 135.41


title: H9RGV00111001

description:
Large-scale analysis of the human transcriptome.
Dorsal root ganglia
Source: Analytical Biological Services; http://www.absbioreagents.com
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 155.22  Stdv: 8.99  Min: 133.06  Max: 168.20

source_name: DRG


title: H9RGV00111002

description:
Large-scale analysis of the human transcriptome.
Dorsal root ganglia
Source: Analytical Biological Services; http://www.absbioreagents.com
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 158.42  Stdv: 4.91  Min: 148.08  Max: 169.81


title: H9RGV00110702

description:
Large-scale analysis of the human transcriptome.
Brain, caudate nucleus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 233.03  Stdv: 9.77  Min: 206.76  Max: 246.58

source_name: caudate nucleus


title: H9RGV00111004

description:
Large-scale analysis of the human transcriptome.
Leukemia chronic myelogenous K-562
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 251.24  Stdv: 10.75  Min: 231.55  Max: 265.19

source_name: Myelogenous k562


title: H9RGV00102609

description:
Large-scale analysis of the human transcriptome.
Lymphoma Burkitt's Raji
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 265.32  Stdv: 7.55  Min: 249.92  Max: 277.42


title: H9RGV00111403

description:
Large-scale analysis of the human transcriptome.
Fetal brain
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 130.69  Stdv: 5.98  Min: 119.54  Max: 139.58

source_name: fetal brain


title: H9RGV00111402

description:
Large-scale analysis of the human transcriptome.
Fetal liver
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 152.40  Stdv: 6.72  Min: 140.82  Max: 163.89

source_name: fetal liver


title: H9RGV00110701

description:
Large-scale analysis of the human transcriptome.
Brain, amygdala
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 395.90  Stdv: 15.76  Min: 369.58  Max: 425.26

source_name: amygdala


title: H9RGV00110703

description:
Large-scale analysis of the human transcriptome.
Brain, caudate nucleus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 242.86  Stdv: 10.54  Min: 225.27  Max: 258.48


title: H9RGV00102608

description:
Large-scale analysis of the human transcriptome.
Pituitary gland
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 272.53  Stdv: 10.98  Min: 247.79  Max: 291.42

source_name: pituitary gland


title: H9RGV00102604

description:
Large-scale analysis of the human transcriptome.
Lymphoma Burkitt's, Daudi
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 259.98  Stdv: 8.04  Min: 246.43  Max: 276.51

source_name: Burkitt's Daudi


title: H9RGV00111003

description:
Large-scale analysis of the human transcriptome.
Lymphoma Burkitt's Daudi
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 344.37  Stdv: 16.95  Min: 316.61  Max: 376.49


title: H9RGV00102607

description:
Large-scale analysis of the human transcriptome.
Leukemia lymphoblastic, MOLT-4
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 359.81  Stdv: 15.09  Min: 334.81  Max: 383.57

source_name: lymphoblastic molt4


title: H9RGV00061306

description:
Large-scale analysis of the human transcriptome.
Pancreas
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 193.42  Stdv: 7.54  Min: 178.05  Max: 208.95

source_name: pancreas


title: H9LMS99102621

description:
Large-scale analysis of the human transcriptome.
Ovary, stroma-enriched
Source: CHTN, see PMID 11158614
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 133.93  Stdv: 5.74  Min: 122.53  Max: 142.72


title: H9RGV00102610

description:
Large-scale analysis of the human transcriptome.
Brain, thalamus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 114.50  Stdv: 4.21  Min: 105.65  Max: 118.77


title: H9LMS99090506

description:
Large-scale analysis of the human transcriptome.
Prostate
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 143.82  Stdv: 6.74  Min: 127.68  Max: 154.07

source_name: prostate


title: H9LMS99081101

description:
Large-scale analysis of the human transcriptome.
Prostate cancer
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 133.07  Stdv: 5.06  Min: 123.99  Max: 141.08

source_name: prostate cancer


title: H9LMS99090504

description:
Large-scale analysis of the human transcriptome.
Prostate
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 135.45  Stdv: 6.23  Min: 120.79  Max: 144.47


title: H9LMS99090508

description:
Large-scale analysis of the human transcriptome.
Prostate
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 139.08  Stdv: 10.57  Min: 122.14  Max: 169.09


title: H9LMS99080701

description:
Large-scale analysis of the human transcriptome.
Prostate cancer
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 114.93  Stdv: 3.44  Min: 109.69  Max: 119.51


title: H9LMS99102618

description:
Large-scale analysis of the human transcriptome.
Ovary pool
Source: CHTN, see PMID 11158614
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 121.54  Stdv: 5.29  Min: 111.41  Max: 130.65

source_name: ovary pool


title: H9LMS00121513

description:
Large-scale analysis of the human transcriptome.
CD34+Thy+ hematopoetic stem cells, GCSF-treated patients
Source: Internal GNF, mail mcooke@gnf.org
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 94.48  Stdv: 3.30  Min: 88.09  Max: 100.63

source_name: THY+


title: H9RGV00102601

description:
Large-scale analysis of the human transcriptome.
Trachea
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 105.12  Stdv: 3.59  Min: 98.45  Max: 110.41

source_name: trachea


title: H9RGV00061304

description:
Large-scale analysis of the human transcriptome.
Kidney
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 139.26  Stdv: 7.45  Min: 125.56  Max: 152.39

source_name: kidney


title: H9LMS99072808

description:
Large-scale analysis of the human transcriptome.
Prostate cancer
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 102.35  Stdv: 4.32  Min: 93.64  Max: 109.50


title: H9LMS00111701

description:
Large-scale analysis of the human transcriptome.
Spinal cord
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 188.45  Stdv: 7.54  Min: 172.74  Max: 197.83

source_name: spinal cord


title: H9LMS00111505

description:
Large-scale analysis of the human transcriptome.
Spinal cord
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 180.89  Stdv: 10.26  Min: 160.74  Max: 200.46


title: H9LMS00112901

description:
Large-scale analysis of the human transcriptome.
Heart
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 122.92  Stdv: 8.84  Min: 102.48  Max: 137.29

source_name: heart


title: H9LMS99081103

description:
Large-scale analysis of the human transcriptome.
Prostate cancer
Source: University of Virginia, see PMID 11507037
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 127.77  Stdv: 5.58  Min: 115.47  Max: 135.25


title: H9LMS00111506

description:
Large-scale analysis of the human transcriptome.
Uterus
Source: Research Genetics, http://www.resgen.com/products/DLmRNA.php3
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 223.30  Stdv: 9.40  Min: 195.15  Max: 234.28

source_name: uterus


title: H9LMS00111503

description:
Large-scale analysis of the human transcriptome.
Ovary, pooled
Source: CHTN, see PMID 11158614
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 281.10  Stdv: 26.00  Min: 240.25  Max: 341.39

source_name: ovary-pool


title: H9LMS00111006

description:
Large-scale analysis of the human transcriptome.
Salivary gland
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 146.86  Stdv: 8.51  Min: 131.54  Max: 162.87

source_name: salivary gland


title: Eye Discs iso4 lm31

description: To analyze gene expression in Drosophila eye primordia (third instar wandering larvae), the eye part was separated from the antennal part of the eye-antennal disc. One hundred eye imaginal discs were dissected, immediately transferred into 800ul Trizol (GIBCO Life Technologies) and stored at –70°C. RNA extraction was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Two successive rounds of cDNA synthesis were applied to prepare 20ug of biotinylated target from one to two micrograms of total RNA (see Michaut et al., 2003).

source_name: Drosophila wandering larvae eye imaginal discs


title: H9LMS00111001

description:
Large-scale analysis of the human transcriptome.
Adrenal gland
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 180.17  Stdv: 7.64  Min: 168.72  Max: 192.99

source_name: adrenal gland


title: H9LMS00110802

description:
Large-scale analysis of the human transcriptome.
CD34+Thy- progenitor cells, GCSF-treated patients
Source: Internal GNF, mail mcooke@gnf.org
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 247.69  Stdv: 13.39  Min: 213.38  Max: 265.42

source_name: THY-


title: H9LMS00110803

description:
Large-scale analysis of the human transcriptome.
CD34+THY+ hematopoietic stem cells, GCSF-treated patients
Source: Internal GNF, mail mcooke@gnf.org
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 134.39  Stdv: 6.08  Min: 119.69  Max: 144.12


title: H9LMS00111005

description:
Large-scale analysis of the human transcriptome.
Placenta
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 112.58  Stdv: 5.92  Min: 101.51  Max: 123.76

source_name: placenta


title: H9LMS00102617

description:
Large-scale analysis of the human transcriptome.
Uterus
Source: Research Genetics, http://www.resgen.com/products/DLmRNA.php3
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 117.02  Stdv: 3.93  Min: 108.08  Max: 124.24


title: H9LMS00111007

description:
Large-scale analysis of the human transcriptome.
Thyroid
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 123.40  Stdv: 4.93  Min: 115.06  Max: 130.09

source_name: thyroid


title: H9LMS00111002

description:
Large-scale analysis of the human transcriptome.
Kidney
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 148.60  Stdv: 7.22  Min: 138.96  Max: 166.76


title: Leg Discs ectopic ey lmC55

description: To analyze gene expression in Drosophila leg discs where an eye field was ectopically induced  ([dppblink-GAL4, UAS-GAL4/UAS-ey] third instar wandering larvae), one to two hundred leg imaginal discs were dissected and immediately transferred into 800ul Trizol (GIBCO Life Technologies). RNA extraction, was performed according to the manufacturer’s instructions. Quantity and quality of total RNA were determined by capillary electrophoresis on a RNA6000 bioanalyzer (Agilent Technologies). Biotinylated RNA targets were prepared from 15 to 20 ug total RNA (500-700 leg discs) according to the standard Affymetrix procedure (see Michaut et al., 2003).

source_name: [dppblink-GAL4, UAS-GAL4/UAS-ey] Drosophila wandering larvae leg imaginal discs


title: H9LMS00111501

description:
Large-scale analysis of the human transcriptome.
Brain, cerebellum
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 184.69  Stdv: 14.25  Min: 162.22  Max: 220.89

source_name: cerebellum


title: H9LMS00111004

description:
Large-scale analysis of the human transcriptome.
Pancreas
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 131.11  Stdv: 5.76  Min: 119.16  Max: 141.62

source_name: pancreas


title: H9LMS00111502

description:
Large-scale analysis of the human transcriptome.
Brain, cerebellum
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 178.26  Stdv: 9.71  Min: 157.32  Max: 190.35


title: H9LMS00102614

description:
Large-scale analysis of the human transcriptome.
Thyroid
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 172.35  Stdv: 5.64  Min: 160.35  Max: 181.49


title: H9LMS00102611

description:
Large-scale analysis of the human transcriptome.
Salivary gland
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 98.28  Stdv: 4.13  Min: 90.98  Max: 105.48


title: H9LMS00102608

description:
Large-scale analysis of the human transcriptome.
Liver
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 110.85  Stdv: 6.04  Min: 98.68  Max: 121.23

source_name: liver


title: H9LMS00102615

description:
Large-scale analysis of the human transcriptome.
Whole brain
Source: Research Genetics, http://www.resgen.com/products/DLmRNA.php3
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 116.33  Stdv: 5.23  Min: 102.93  Max: 122.67

source_name: whole brain


title: H9LMS00102612

description:
Large-scale analysis of the human transcriptome.
Spleen
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 85.69  Stdv: 4.11  Min: 77.77  Max: 93.67

source_name: spleen


title: H9LMS00102607

description:
Large-scale analysis of the human transcriptome.
Kidney
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 173.70  Stdv: 9.65  Min: 148.80  Max: 185.59

source_name: kidney


title: H9LMS00092712

description:
Large-scale analysis of the human transcriptome.
Thymus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 118.10  Stdv: 5.33  Min: 107.65  Max: 126.07

source_name: thymus


title: H9LMS00102606

description:
Large-scale analysis of the human transcriptome.
Heart
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 116.54  Stdv: 14.73  Min: 96.85  Max: 162.24

source_name: heart


title: H9LMS00092709

description:
Large-scale analysis of the human transcriptome.
Testis
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 215.15  Stdv: 8.48  Min: 197.86  Max: 228.62

source_name: testis


title: H9LMS00092711

description:
Large-scale analysis of the human transcriptome.
Thymus
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 371.69  Stdv: 69.90  Min: 296.08  Max: 566.98


title: H9LMS00061303

description:
Large-scale analysis of the human transcriptome.
Umbilical vein endothelial cells
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 115.75  Stdv: 4.68  Min: 105.64  Max: 124.99

source_name: HUVEC


title: H9LMS00061601

description:
Large-scale analysis of the human transcriptome.
Lung
Source: Contech
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 133.75  Stdv: 7.22  Min: 122.85  Max: 148.29

source_name: lung


title: H9LMS00092710

description:
Large-scale analysis of the human transcriptome.
Testis
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 205.42  Stdv: 7.66  Min: 192.17  Max: 217.78


title: H9LMS00102605

description:
Large-scale analysis of the human transcriptome.
Whole brain
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 163.68  Stdv: 7.52  Min: 148.81  Max: 175.06


title: H9DKG00061403

description:
Large-scale analysis of the human transcriptome.
Brain, cerebral cortex
Source: Mt. Sinai, see PMID 11296301
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 120.68  Stdv: 4.84  Min: 111.91  Max: 129.14

source_name: cortex


title: 22-oct-2002-BrainFsubB-ab150

status: Public on Nov 11 2002

city: Lausanne

first: David

last: Vilanova

institute: Nestle Research Center

description:
Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression, Lipids in Health and Disease 2002.
Diet contained 90% fat-free AIN93G rodent diet in powder form (Lot 9350-5, Dyets, Inc., Bethlehem, PA), 0.4% milk fat, 1.2% palm olein, 1.9% Trisun sunflower oil, 1.5% soybean oil and 2.1-5.1% medium chain triacylglycerol oil (all of the above ingredients except the AIN93G were from Nestlé affiliated companies). Part of the medium chain triacylglycerol oil in control diet was replaced with: 1.1% fungal oil and 1.9% fish oil. Food was maintained at -80°C in daily aliquots under liquid N2, thawed each afternoon before administration to mice, and uneaten food was discarded daily.
Prior to actual experimentation, test dissections were made on identical mice to perfect the dissection techniques at Porsolt & Partners Pharmacology (Paris, France).
Male Rj:NMRI mice from Elevage Janvier, Le Genest-Saint-Isle France, weighing 10-11 g at delivery and 33-51 grams on experimental d 42, were housed 10 per cage in wire cages with bedding and normal light cycle. Mice received ad libitum quantities of distilled water and purified powdered diets (7.5 g/mouse) in ceramic cups (10/group) from d 1-57 or 58, and were thereafter sacrificed in the morning by cervical dislocation over these last 2 experimental days. Food was not removed the night before, and since nocturnal mice are known to eat during the normal period dark cycle employed, the mice could have been fasted 0-6 h at sacrifice. Mice were thus not completely fasted at sacrifice, a complete fast being 12-16 h.  After feeding diets to 10 mice per group, 5 mice were randomly selected for inclusion in hippocampal gene expression analysis. From these same 5 mice, the hippocampus was dissected from the mice according to standard protocols (Porsolt & Partners Pharmacology, Boulogne-Billancourt, France), rinsed as described for livers, cut into 17-50 mg subsections, and frozen as described for livers.  Hippocampal lipid analysis was performed according to standard methods at Lipomics, Inc. (U.S.A) on individual mice (n=5).
Hippocampal tissue was extracted from 5 individual mice per group and extracted separately using Qiagen RNeasy mini-kits (Basel, Switzerland) according to manufacturer instructions, except that RNeasy columns were impregnated with DNase I (Roche, Basel, Switzerland) to remove any genomic DNA contamination. A pool of 10 mg total hippocampal RNA was created from the 5 individual extractions prior to GeneChip analysis. All RNA samples (individual and pooled) were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then analyzed via agarose gel electrophoresis for intact 18S and 28S rRNA. All study samples were judged to contain sufficient amounts of high-quality RNA for hybridization to GeneChips. As another quality control measure, prior to hybridization with Affymetrix GeneChips (Affymetrix, Inc., Santa Clara, CA), we confirmed that pooled samples gave strong signals using Affymetrix test chips.

source_name: brain/hippocampus


title: NIEHS_Rat_Tox_2w_Clofibrate-49-138

status: Public on Nov 20 2002

city: Thousand Oaks

first: Hisham

middle: K

last: Hamadeh

address: One Amgen Center Drive, Mailstop 5-1-A

department: Toxicology

institute: Currently at: Amgen Inc.

description:
Male Sprague-Dawley VAF+ albino rats (CRL:CD(SD) BR; Charles River, Kingston, NY) approximately 57 weeks old were maintained on certified rodent chow (PMI Feeds, Inc., Brentwood, MO) ad libitum in individual stainless steel wire bottom cages suspended on racks. The animals were kept under controlled lighting (12-h light-dark cycle), temperature (720 1 50F), and humidity (50 1 20%) and were acclimated to this environment for 47 days prior to the start of the study. Healthy rats were randomly assigned to dose groups (3 rats/group) by a computerized method. For the 2-week studies, a 1-week pretest involved dosing of all animals via oral gavage with 10 ml/kg vehicle. The 24-h studies did not have any pretest period. Clofibrate (CAS # 637070), gemfibrozil (CAS # 25812300), and phenobarbital (CAS # 57307) were obtained from Sigma (St. Louis, MO); Wyeth 14,643 (CAS # 50892234) was obtained from ChemSyn Laboratories (Lenexa, KS). Dosing suspensions of all compounds were prepared using a high speed homogenizer, and all dose suspensions were continuously stirred until completion of dosing. The peroxisome proliferators (clofibrate, gemfibrozil, and Wyeth 14,643) were prepared using 1% carboxymethylcellulose/0.2% Tween 80 as vehicle and phenobarbital was prepared using water as vehicle. Drug concentration and identity were verified via HPLC, as per United States Pharmacopeia (USP) methods for clofibrate, gemfibrozil, and phenobarbital. For Wyeth 14,643, a Waters 600E HPLC was equipped with a variable wavelength detector set at 235 nm, and a Symmetry Cs 4.6 x 250 mm column. Equal portions (approximately 10 ml) of standard and test solutions were injected separately into the column. Parameters of the run were as follows: mobile phase, 0.0738 M sodium acetate:acetonitrile (55:45 v/v); flow rate, 1 ml/min; column temperature, ambient; and run time, 6 min. The HPLC retention time of Wyeth 14,643 under these parameters was 3.4 1 0.1 min. Body weights and food consumption were measured weekly. Based on the most recently recorded body weights, the volume of drug administered was adjusted. Animals were observed 23 times daily for signs of overt toxicity. Experiments were performed according to the guidelines established in the NIH Guide for the Care and Use of Laboratory Animals. At the end of the drug phase of the study, each animal was fasted overnight before necropsy. Animals were taken to a deep plain of anesthesia with CO2, sacrificed by axillary vessel incision; exsanguination and necropsy immediately followed. A cross section of the left lateral lobe of the liver was collected in 10% neutral buffered formalin for histopathology. The remaining portions of liver were collected in RNase-free tubes and snap frozen in liquid nitrogen. Frozen tissues were stored at 700C until processed for RNA extraction. A control sample was generated by pooling livers of 9 vehicle-treated rats.
The liver tissues collected in formalin at necropsy were processed, embedded in paraffin, sectioned at 5 microns, and stained with hematoxylin and eosin (H&E). Histopathologic examinations of the liver sections were conducted by a pathologist and peer-reviewed.
Total RNA was isolated using QIAGEN (Qiagen, Valencia, CA) RNeasy kits. Liver sections of 130250 mg were used for midipreps and liver sections of approximately 800 mg were used for maxipreps. Homogenization buffer was added to frozen liver sections, and the tissue was immediately homogenized on ice (tissue did not thaw prior to homogenization) using a Cyclone homogenizer equipped with a rotor/stator shaft (VirTis Company, Gardiner, NY). Homogenates were processed as per the standard QIAGEN 3/99 protocol. Final product yielded 260 nm/280 nm ratios of 1.62.0, purity was confirmed via gels, and concentration was determined based on 260 nm absorbances.
For microarray hybridizations, each total RNA sample (3575 5g) was labeled with Cyanine 3 (Cy3)-or Cyanine 5 (Cy5)-conjugated dUTP (Amersham, Piscataway, NJ) by a reverse transcription reaction using reverse transcriptase, SuperScript (Invitrogen, Carlsbad, California), and the primer, Oligo dT (Amersham, Piscataway, NJ). Control samples were labeled with Cy3 while samples derived from chemically exposed animals were labeled with Cy5. The fluorescently labeled cDNAs were mixed and hybridized simultaneously to the cDNA microarray chip. Each RNA pair was labeled and hybridized independently in triplicate to a total of 3 arrays. The cDNA chips were scanned with an Axon Scanner (Axon Instruments, Foster City CA) using independent laser excitation of the 2 fluors at 532 and 635 nm wavelengths for the Cy3 and Cy5 labels, respectively.
The raw pixel intensity images were analyzed using the ArraySuite v1.3 extensions of the IPLab image processing software package (Scanalytics, Fairfax, VA). This program uses methods that were developed and previously described by Chen et al. (1997) to locate targets on the array, measure local background for each target, and subtract it from the target intensity value, and to identify differentially expressed genes using a probability-based method. After pixel intensity determination and background subtraction, the ratio of the intensity of the treated cells to the intensity of the control was calculated. We have previously determined that significant autofluorescence of the gene features on the array, attributed to spotting solution, occurs at high scanning power (Tucker et al., unpublished). We measured the pixel intensity level of "blank" spots comprised of spotting solution. The data was then filtered to provide a cut off at the intensity level just above the blank measurement values in order to remove from further analyses those genes having one or more intensity values in the background range.
--  taken largely verbatim from Hamadeh et al., Toxicological Sciences 67, 219-231 (2002)

source_name: reference

source_name: Liver 2w_Clofibrate-49-138


title: H9LMS00102609

description:
Large-scale analysis of the human transcriptome.
Lung
Source: Clontech, http://www.clontech.com/archive/OCT01UPD/pdf/PremiumRNA.pdf
Analyzed using the Affymetrix MAS4 algorithm.
Background: Avg: 127.25  Stdv: 5.50  Min: 113.26  Max: 137.25