title: 3ARS02080774a_globus_pallidus


title: 3AMH02022205_Brain Amygdala

status: Public on Mar 19 2004

type: RNA

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

description: Brain Amygdala

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

scan_protocol: standard Affymetrix procedures

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 3AMH02022205_Brain Amygdala

label_protocol: Five micrograms of total RNA was used to synthesize cDNA that was then used as a template to generate biotinylated cRNA using Enzo kits.

extract_protocol: Human tissue samples were obtained from several sources: Clinomics Biosciences (Pittsfield, MA), Clontech, AllCells (Berkeley, CA), Clonetics/BioWhittaker (Walk-ersville, MD), AMS Biotechnology (Abingdon, Oxfordshire, U.K.), and the University of California at San Diego. When samples from four or more subjects were available, equal numbers of male and female subjects were used to make two independent pools; when fewer than four samples were available, RNA samples were pooled, and duplicate amplifications were performed for each pool (detailed annotation for human samples is on our web site, http:\\symatlas.gnf.org)  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).

tag: 3AMH02022205_Brain Amygdala


title: 3AJZ02022870_  brain, caudate nucleus

description: brain, caudate nucleus

source_name: 3AJZ02022870_  brain, caudate nucleus

tag: 3AJZ02022870_  brain, caudate nucleus


title: 3AMH02082802_BM_CD71EarlyErythroid

description: bone marrow-CD71EarlyErythroid


title: 3AJZ02022865_bone marrow

description: bone marrow

source_name: 3AJZ02022865_bone marrow

tag: 3AJZ02022865_bone marrow


title: 3ARS02080774b_globus_pallidus


title: 3AJZ02030474_bonemarrow

description: bonemarrow


title: 3AJZ02022750_fetal liver

description: fetal liver

source_name: 3AJZ02022750_fetal liver

tag: 3AJZ02022750_fetal liver


title: 3AJZ02022647_cerebellum

description: cerebellum


title: 3AJZ02051604_CerebellumPeduncles

description: CerebellumPeduncles


title: 3AJZ02081484a_TemporalLobe

description: TemporalLobe


title: 3AJZ02022633_fetal liver

description: fetal liver

source_name: 3AJZ02022633_fetal liver

tag: 3AJZ02022633_fetal liver


title: 3AJZ02051605_ParietalLobe

description: ParietalLobe


title: 3AJZ02081484b_TemporalLobe

description: TemporalLobe


title: 3AJZ02022115_  lymph node

description: lymph node

source_name: 3AJZ02022115_  lymph node

tag: 3AJZ02022115_  lymph node


title: 3AJZ02052116_Tonsil

description: Tonsil


title: 3AJZ02022232_  lymph node

description: lymph node

source_name: 3AJZ02022232_  lymph node

tag: 3AJZ02022232_  lymph node


title: 3AMH02082801_BM_CD71EarlyErythroid

description: bone marrow-CD71EarlyErythroid


title: 3AJZ02022758_thymus

description: thymus


title: 3AJZ02031411_thymus

description: thymus


title: 3AJZ02051715_Tonsil

description: Tonsil


title: 3AJZ02031099_ lymphomaburkittsDaudi

description: lymphomaburkittsDaudi

source_name: 3AJZ02031099_ lymphomaburkittsDaudi

tag: 3AJZ02031099_ lymphomaburkittsDaudi


title: 3AJZ02022222_  leukemia, chronic Myelogenous K-562

description: leukemia, chronic Myelogenous K-562


title: 3AJZ02031302_lymphomaburkittsDaudi

description: lymphomaburkittsDaudi


title: 3AMH02022603_LymphomaRaji

description: LymphomaRaji


title: 1BJZ02061909_pituitary

description: pituitary


title: 3AJZ02022220_leukemia, promyelocytic-HL-60

description: leukemia, promyelocytic-HL-60


title: 1BJZ02061809_pituitary

description: pituitary


title: 3AMH02030602_LymphomaRaji

description: LymphomaRaji


title: 1BJZ02083089b_Uterus_Corpus


title: 1BJZ02060414_OlfactoryBulb

description: OlfactoryBulb


title: 1BJZ02081478b_Superior_Cervical_Ganglion


title: 1BJZ02083089a_Uterus_Corpus


title: 3AMH02082102_BM_CD34

description: bone marrow-CD34


title: 1BJZ02060511_OlfactoryBulb

description: OlfactoryBulb


title: 3AMH02082810_721_BLymphoblasts


title: 1BJZ02083092b_Skeletal_Muscle_Psoas


title: 1BJZ02081478a_Superior_Cervical_Ganglion


title: 1BJZ022987A_TONGUE

description: TONGUE


title: 3AMH02082001_BM_CD34

description: bone marrow-CD34


title: 1BJZ02083092a_Skeletal_Muscle_Psoas


title: 1BRS02081536f_DRG

description: DRG


title: 3AJZ02022218_leukemia lymphoblastic (MOLT-4)

description: leukemia lymphoblastic (MOLT-4)


title: 3AJZ02022105_  leukemia, chronic Myelogenous K-562

description: leukemia, chronic Myelogenous K-562


title: 3AMH02082108_PB_CD19BCells

description: peripheral blood-CD19BCells


title: 1BJZ022987B_TONGUE

description: TONGUE


title: 3AMH02082103_BM_CD105Endothelial

description: bone marrow-CD105Endothelial


title: 3AJZ02022869_leukemia lymphoblastic (MOLT-4)

description: leukemia lymphoblastic (MOLT-4)


title: 1BRS02080872a_atrioventricular_node


title: 1BRS02081536e_DRG

description: DRG


title: 3AJZ02022103_leukemia, promyelocytic-HL-60

description: leukemia, promyelocytic-HL-60


title: 3AMH02082805_PB_CD8TCells

description: peripheral blood-CD8TCells


title: 1BRS02080872b_atrioventricular_node


title: 3AMH02082107_PB_CD19BCells

description: peripheral blood-CD19BCells


title: 1BJZ02081483b_Trigeminal_Ganglion


title: 3AMH02082809_721_BLymphoblasts


title: 3AMH02082806_PB_CD8TCells

description: peripheral blood-CD8TCells


title: 1BRS02080873a_ciliary_ganglion


title: 1BJZ02081483a_Trigeminal_Ganglion


title: 3AMH02082804_PB_CD4TCells

description: peripheral blood-CD4TCells


title: 3AMH02082803_PB_CD4TCells

description: peripheral blood-CD4TCells


title: 1BJZ02081482b_Appendix

description: Appendix


title: 1BRS02080876a_skin

description: skin


title: 1BRS02080876b_skin

description: skin


title: 3AMH02082316_PB_CD14Monocytes

description: peripheral blood-CD14Monocytes


title: 3AMH02082104_BM_CD105Endothelial

description: bone marrow-CD105Endothelial


title: 1BRS02080873b_ciliary_ganglion


title: 3AMH02082109_PB_CD56NKCells

description: peripheral blood-CD56NKCells


title: 1BJZ02052208_Ovary

description: Ovary


title: 3AMH02082111_PB_BDCA4DentriticCells

description: peripheral blood-BDCA4DentriticCells


title: 3AMH02082110_PB_CD56NKCells

description: peripheral blood-CD56NKCells


title: 3AMH02082315_PB_CD14Monocytes

description: peripheral blood-CD14Monocytes


title: 1BJZ02081482a_Appendix

description: Appendix


title: 3AMH02082012_PB_BDCA4DentriticCells

description: peripheral blood-BDCA4DentriticCells


title: 3AMH02082105_BM_CD33Myeloid

description: bone marrow-CD33Myeloid


title: 3AMH02082106_BM_CD33Myeloid

description: bone marrow-CD33Myeloid


title: 1BJZ02050813_Ovary

description: Ovary


title: 1BJZ02022640_trachea

description: trachea


title: 3AMH02022201_Colorectal Adenocarc

description: Colorectal Adenocarc

source_name: 3AMH02022201_Colorectal Adenocarc

tag: 3AMH02022201_Colorectal Adenocarc


title: 1BJZ02041227_salivarygland

description: salivarygland


title: 1BJZ02050809_AdrenalCortex

description: AdrenalCortex


title: 1BJZ02052201_AdrenalCortex

description: AdrenalCortex


title: 1BJZ02022755_trachea

description: trachea


title: 3AJZ02052320_WHOLEBLOOD(JJV)

description: WHOLEBLOOD


title: 1BJZ02052113_TestiSeminiferousTubule

description: TestiSeminiferousTubule


title: 3AJZ02052318_WHOLEBLOOD(JJV)

description: WHOLEBLOOD


title: 1BJZ02060515_IsletCell

description: IsletCell


title: 3AMH02030601_Colorectal Adenocarcinoma

description: Colorectal Adenocarcinoma

source_name: 3AMH02030601_Colorectal Adenocarcinoma

tag: 3AMH02030601_Colorectal Adenocarcinoma


title: 1BJZ02022636_testis

description: testis


title: 1BJZ02051712_Testi_LeydigCell


title: 1BJZ02051710_Testi_Intersitial


title: 1BJZ02051708_Testi_GermCell


title: 1BJZ02022751_testis

description: testis


title: 1BJZ02052107_TestiGermCell

description: TestiGermCell


title: 1BJZ02052111_TestiLeydigCell

description: TestiLeydigCell


title: 1BJZ02053102_HBEC

description: HBEC


title: 1BJZ02052109_TestiIntersitial

description: TestiIntersitial


title: 1BJZ02052311_HUMANCULTUREDADIPOCYTE

description: HUMANCULTUREDADIPOCYTE


title: 1BJZ02052308_Islet

description: Islet


title: 1BJZ02060602_CardiacMyocytes

description: CardiacMyocytes


title: 1BJZ02040822_salivarygland

description: salivarygland


title: 1BJZ02060601_SmoothMuscle

description: SmoothMuscle


title: 1BJZ02060501_Pancreas

description: Pancreas


title: 1BJZ02052313_HUMANCULTUREDADIPOCYTE

description: HUMANCULTUREDADIPOCYTE


title: 1BRS0207253IB_PLACENTA

description: PLACENTA


title: 1BRS0207253HB_PLACENTA

description: PLACENTA


title: 1BMH02022702_Pancreas

description: Pancreas


title: 1BJZ02053106_SmoothMuscle

description: SmoothMuscle


title: 1BJZ02031305_fetallung

description: fetallung


title: 1BJZ02053104_HBEC

description: HBEC


title: 1BJZ02061205_fetalThyroid

description: fetalThyroid


title: 1BJZ02052324_FETALTHYROID

description: FETALTHYROID


title: 1BJZ02053108_CardiacMyocytes

description: CardiacMyocytes


title: 1BMH02022803_Uterus

description: Uterus


title: 1BJZ02022114_fetallung

description: fetallung


title: 1BMH02022809_Uterus

description: Uterus


title: 1BMH02022104_thyroid

description: thyroid


title: 1BMH02030601_Prostate

description: Prostate


title: 1BMH02022804_Prostate

description: Prostate


title: 1BJZ02030684_KIDNEY

description: KIDNEY


title: 1BMH02022704_Thyroid

description: Thyroid


title: 1BMH02022808_Heart

description: Heart


title: 1BJZ02022644_kidney

description: kidney


title: 1BJZ02022223_spinalcord

description: spinalcord


title: 1BMH02022806_Liver

description: Liver


title: 1BJZ02022227_fetalbrain

description: fetalbrain


title: 1BMH02022812_Liver

description: Liver


title: 1BMH02022811_Lung

description: Lung


title: 1BJZ02022761_adrenalgland

description: adrenalgland


title: 1BJZ02040818_brainThalamus

description: brainThalamus


title: 1BJZ02021377_brainThalamus

description: brainThalamus


title: 1BMH02022802_Heart

description: Heart


title: 1BJZ02022108_spinalcord

description: spinalcord


title: 1BJZ02022646_adrenalgland

description: adrenalgland


title: 1BJZ02081480b_Pons

description: Pons


title: 1BJZ02060408_CingulateCortex

description: CingulateCortex


title: 1BJZ02072563_Hypothalamus

description: Hypothalamus


title: 1BJZ02081480a_Pons

description: Pons


title: 1BJZ02060505_CingulateCortex

description: CingulateCortex


title: 1BRS02080877b_subthalamic_nucleus


title: 1BMH02022805_Lung

description: Lung


title: 1BJZ02051609_OccipitalLobe

description: OccipitalLobe


title: 1BJZ02022112_fetalbrain

description: fetalbrain


title: 1BMH02022705_Brain Amygdala

description: Brain Amygdala

source_name: 1BMH02022705_Brain Amygdala

tag: 1BMH02022705_Brain Amygdala


title: 1BJZ02060406_Hypothalamus

description: Hypothalamus


title: 1BJZ02053110_PrefrontalCortex

description: PrefrontalCortex


title: 1BJZ02051610_OccipitalLobe

description: OccipitalLobe


title: 1BJZ02053112_PrefrontalCortex

description: PrefrontalCortex


title: 1BMH02022105_Brain Amygdala

description: Brain Amygdala

source_name: 1BMH02022105_Brain Amygdala

tag: 1BMH02022105_Brain Amygdala


title: 1BJZ02081479b_Medulla_Oblongata


title: 1BJZ02051614_ParietalLobe

description: ParietalLobe


title: 1BJZ02051613_ParietalLobe

description: ParietalLobe


title: 1BJZ02061808_caudatenucleus

description: caudatenucleus


title: 1BJZ02022648_cerebellum

description: cerebellum


title: 1BMH02022801_Whole Brain

description: Whole Brain

source_name: 1BMH02022801_Whole Brain

tag: 1BMH02022801_Whole Brain


title: 1BJZ02081484a_TemporalLobe

description: TemporalLobe


title: 1BJZ02022634_fetalliver

description: fetalliver


title: 1BJZ02022866_bonemarrow

description: bonemarrow


title: 1BMH02083002_BM_CD71EarlyErythroid

description: bone marrow-CD71EarlyErythroid


title: 1BJZ02081479a_Medulla_Oblongata


title: 1BRS02080877a_subthalamic_nucleus


title: 1BJZ02022763_cerebellum

description: cerebellum


title: 1BJZ02051612_CerebellumPeduncles

description: CerebellumPeduncles


title: 1BJZ02051611_CerebellumPeduncles

description: CerebellumPeduncles


title: 1BRS02080874a_globus_pallidus


title: 1BJZ02081484b_TemporalLobe

description: TemporalLobe


title: 1BMH02083001_BM_CD71EarlyErythroid

description: bone marrow-CD71EarlyErythroid


title: 1BRS02080874b_globus_pallidus


title: 1BJZ02022231_lymphnode

description: lymphnode


title: 1BJZ02030473_bonemarrow

description: bonemarrow


title: 1BMH02022807_Whole Brain

description: Whole Brain

source_name: 1BMH02022807_Whole Brain

tag: 1BMH02022807_Whole Brain


title: 1BJZ02022757_thymus

description: thymus


title: 1BJZ02051716_Tonsil

description: Tonsil


title: 1BJZ02022749_fetalliver

description: fetalliver


title: 1BJZ02022116_lymphnode

description: lymphnode


title: 1BJZ02061908_caudatenucleus

description: caudatenucleus


title: 1BJZ02022219_leukemiapromyelocytic(hl60)


title: 1BJZ02031303_lymphomaburkittsDaudi

description: lymphomaburkittsDaudi


title: 1BJZ02022642_thymus

description: thymus


title: 1BMH02083010_721_Blymphoblasts


title: 1BJZ02022221_leukemiachronicmyelogenous(k562)


title: 1BJZ02031098_lymphomaburkittsDaudi

description: lymphomaburkittsDaudi


title: 1BJZ02022102_leukemialymphoblastic(molt4)


title: 1BMH02083009_721_Blymphoblasts


title: 1BJZ02030679_LEUKEMIALYMPHOBLASTIC(MOLT4)


title: 1BMH02020805_LymphomaRaji

description: LymphomaRaji


title: 1BJZ02022106_leukemiachronicmyelogenous(k562)


title: 1BJZ02052115_Tonsil

description: Tonsil


title: 1BMH02022103_LymphomaRaji

description: LymphomaRaji


title: 1BMH02082903_BM_CD105endothelial

description: bone marrow-CD105endothelial


title: 1BJZ02022104_leukemiapromyelocytic(hl60)


title: 1BMH02082908_PB_CD19BCells

description: peripheral blood-CD19BCells


title: 1BMH02082907_PB_CD19BCells

description: peripheral blood-CD19BCells


title: 1BMH02083006_PB_CD8TCells

description: peripheral blood-CD8TCells


title: 1BMH02082902_BM_CD34

description: bone marrow-CD34


title: 1BMH02083007_PB_CD4TCells

description: peripheral blood-CD4TCells


title: 1BMH02082904_BM_CD105endothelia

description: bone marrow-CD105endothelia


title: 1BMH02082901_BM_CD34

description: bone marrow-CD34


title: 1BMH02082910_PB_CD56NKCells

description: peripheral blood-CD56NKCells


title: 1BMH02082909_PB_CD56NKCells

description: peripheral blood-CD56NKCells


title: 1BMH02082912_PB_BDCA4DendriticCells

description: peripheral blood-BDCA4DendriticCells


title: 1BMH02083005_PB_CD8TCells

description: peripheral blood-CD8TCells


title: 1BMH02082906_BM_CD33myeloid

description: bone marrow-CD33myeloid


title: 1BMH02083008_PB_CD4TCells

description: peripheral blood-CD4TCells


title: 1BMH02022101_Colorectal Adenocarc

description: Colorectal Adenocarc

source_name: 1BMH02022101_Colorectal Adenocarc

tag: 1BMH02022101_Colorectal Adenocarc


title: 1BMH02022701_Colorectal Adenocarc

description: Colorectal Adenocarc

source_name: 1BMH02022701_Colorectal Adenocarc

tag: 1BMH02022701_Colorectal Adenocarc


title: 1BMH02082911_PB_BDCA4DendriticCells

description: peripheral blood-BDCA4DendriticCells


title: 1BMH02083004_PB_CD14Monocytes

description: peripheral blood-CD14Monocytes


title: 1BMH02082905_BM_CD33myeloid

description: bone marrow-CD33myeloid


title: 1BMH02083003_PB_CD14Monocytes

description: peripheral blood-CD14Monocytes


title: 1BJZ02052319_WHOLEBLOOD(JJV)

description: WHOLEBLOOD(JJV)


title: 0hHypo_0hReox_4

status: Public on Feb 18 2004

city: San Antonio

first: Phillip

last: Bowman

state: TX

address: 3400 Rawley E. Chambers Ave

institute: Institute of Surgical Research

description: Human umbilical vein endothelial cells (HUVEC) were cultivated on 1%-gelatin-coated 75-cm2 culture flasks in Medium 200 supplemented with 2% fetal calf serum, penicillin (100 units/ml), streptomycin (100 units/ml) and Funizone (0.25 μg/ml) supplied by Cascade Biologics (Portland, OR).   Prior to an experiment, HUVECs were subcultivated with Trypsin/EDTA onto 1% gelatin coated glass 30-mm glass coverslips in 60 mm glass Petri dishes.

source_name: HUVEC control with no hypoxia and no reoxygenation

source_name: Human universal reference RNA (Stratagene, La Jolla, CA)


title: 1hHypo_24hReox_2

source_name: HUVEC with 1 hour hypoxia and 24 hours reoxygenation


title: rlm1 mutant 4 hours exposure to congo red 4

status: Public on Feb 16 2004

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: S. cerevisiae rlm1Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

organism: Saccharomyces cerevisiae

source_name: BY4741 -rlm1 Strain (4 hours Congo Red treatment)

source_name: BY4741 -rlm1 Strain (Control mRNA: no treatment)


title: 0hHypo_0hReox_2


title: 1hHypo_24hReox_3


title: 0hHypo_0hReox_3


title: 1hHypo_12hReox_4

source_name: HUVEC with 1 hour hypoxia and 12 hours reoxygenation


title: 1hHypo_12hReox_3


title: 1hHypo_12hReox_1


title: 1hHypo_12hReox_2


title: 0hHypo_0hReox_1


title: rlm1 mutant 4 hours exposure to congo red 3


title: slt2 mutant 4 hours exposure to congo red 4

description: S. cerevisiae slt2Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 -slt2 Strain (4 hours Congo Red treatment)

source_name: BY4741 -slt2 Strain (Control mRNA: no treatment)


title: 1hHypo_0hReox_1

description:
Human umbilical vein endothelial cells (HUVEC) were cultivated on 1%-gelatin-coated 75-cm2 culture flasks in Medium 200 supplemented with 2% fetal calf serum, penicillin (100 units/ml), streptomycin (100 units/ml) and Funizone (0.25 μg/ml) supplied by Cascade Biologics (Portland, OR).   Prior to an experiment, HUVECs were subcultivated with Trypsin/EDTA onto 1% gelatin coated glass 30-mm glass coverslips in 60 mm glass Petri dishes.
The hypoxic treatment was performed in airtight chambers from Mitsubishi Gas Chemical Co. Inc (Remel Scientific, Baton Rouge, LA) Preconditioning consisted of 1-hour hypoxia followed by various periods of reoxygenation (0, 3, 5, 12 and 24 hrs) for gene expression analysis.
Total RNA was extracted from cultured HUVECs with TRITM reagent according to the manufacture’s instructions (Molecular Research Center, Cincinnati, OH). Cy5 and Cy3 labeled cDNA probes were generated from total RNA by reverse transcription in the presence of aminoallyl-dUTP according to the method described by Xiang, et al,15.  Human universal reference RNA (Stratagene, La Jolla, CA) was Cy3-labeled and used as reference RNA and RNA isolated from HUVEC at 0, 3, 5, 12 and 24 hour following reoxygenation were Cy5-labeled. The high-resolution scans of hybridized microarrays were acquired with a GenePix scanner 4000B (Axon Instruments, Inc., Union City, CA) and tabulated with GenePix pro 5.1 software.

source_name: HUVEC with 1 hour hypoxia and no reoxygenation


title: 1BJZ02052321_WHOLEBLOOD(JJV)

description: WHOLEBLOOD(JJV)


title: 1hHypo_3hReox_3

source_name: HUVEC with 1 hour hypoxia and 3 hours reoxygenation


title: 1hHypo_0hReox_4


title: 1hHypo_5hReox_1

source_name: HUVEC with 1 hour hypoxia and 5 hours reoxygenation


title: 1hhypo_3hReox_1


title: 1hHypo_24hReox_1


title: 1hHypo_0hReox_3


title: 1hHypo_5hReox_4


title: slt2 mutant 4 hours exposure to congo red 3


title: 1hHypo_0hReox_2


title: slt2 mutant 4 hours exposure to congo red 2


title: 1hHypo_3hReox_2


title: 1hHypo_5hReox_3


title: 1hHypo_5hReox_2


title: wild type 4 hours exposure to congo red 4

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 Strain (Control mRNA: no treatment)

source_name: BY4741 Strain (4 hours Congo Red treatment)


title: 72-h-3

status: Public on Jan 27 2004

city: Ypsilanti

first: Stephen

middle: James

last: McGregor

state: MI

address: 318 Porter Bldg

department: HPERD

institute: Eastern Michigan University

description:
I.  Experimental Design:
a. Type of experiment:  Time course
b. Experimental factors:  3 month old mice subjected to lengthening contractions of the extensor digitorum longus muscle (EDL).  Samples of EDL collected at 6 and 72 h and compared to non-treated control.
c.  How many hybridizations in exp: 9
d.  Common reference used for all hyb: no
e.  Quality control steps:  All arrays used from same lot.  Triplicate hybridizations performed for each time point.

II. Samples used, extracts, preparation and labeling:
Animals.  Nine male C57BL/6 mice (3-4 mo of age, 27.8 ± 3.3 g body mass, Harlan Sprague-Dawley, Indianapolis, IN).
Muscle Injury.  The extensor digitorum longus (EDL) muscle of six mice were exposed to lengthening contractions.  Mice were anesthetized with 2% avertin (0.015 ml/kg) and supplemental doses were administered if the mouse responded to a toe pinch.  Animals were placed on a plexiglass platform that was maintained at 37°C.  The distal femur of the right hindlimb was fixed between screws and the foot was taped to the platform.  The distal tendons of the EDL were exposed by incision and tied to the lever arm of a servomotor (Aurora Scientific, Richmond Hill ON, Canada) with 4-0 silk suture.  Needle electrodes were placed adjacent to the peroneal nerve to stimulate dorsiflexor contraction (Grass Instruments, West Warwick, RI).  Maximal isometric force (Po) was determined by stimulating the dorsiflexors maximally at optimum length (Lo) for force development.
To induce muscle injury, 75 lengthening contractions were performed at 0.25 Hz for 5 min.  For each lengthening contraction, the muscle was stimulated at 150 Hz and stretched 100 ms after the initiation of stimulation.  Muscle stretch involved 20 % strain relative to Lo.  Force deficit was evaluated 10 min after the 75 contractions and then the incision was closed with 7-0 silk suture.  Animals were returned to their cage to recover until the time of sacrifice.  Prior to sacrifice by cervical dislocation, animals were anesthetized with avertin and the EDL muscles were excised and flash frozen in liquid nitrogen.  Muscles were stored in liquid nitrogen until RNA isolation.
RNA Isolation.  Total RNA was isolated from EDL muscles from control mice (n=3) and mice sacrificed at 6 h (n=3) and 72 h (n=3) after lengthening contractions according to the modified protocol of  Chomzynski et al..  Frozen muscles were added to preweighed tubes containing TriReagent (Sigma-Aldrich, St. Louis, MO).  Tissue was homogenized in TriReagent using a Tissue Tearor (Fischer, Pittsburgh, PA) at 30,000 rpm for 1 minute.  Homogenates were transferred to sterile, RNAase free microcentrifuge tubes and incubated for 10 min at room temperature.  Chloroform (0.2 ml; Sigma-Aldrich, St. Louis, MO) was added and after incubation, the samples were centrifuged for 15 min at 12,000 g and 4°C.  Total RNA was precipitated from the aqueous phase by the addition of isopropanol (Sigma-Aldrich), and pelleted by centrifugation.  Pellets were washed in ethanol (75 and 95 %) and air dried before resuspension in diethylpyrocarbonate (DEPC) treated water.  RNA concentration was determined by optical density at 260 nm.

III. Hybridization procedures and parameters:
Microarray Hybridization and Analysis.  To reduce measurement error, all membranes (Atlas mouse 1.2; Clontech, Palo Alto, CA) were prepared from the same lot.  Additionally, each membrane was hybridized only once to avoid errors associated with stripping and multiple hybridizations.  In order to minimize individual biological variability, total RNA was pooled from three animals for hybridization of arrays.  Three arrays were used for the pooled sample at each time point.  First strand cDNA probe generation from total RNA and microarray hybridization were performed according to manufacturer’s instructions (Atlas cDNA Expression Arrays User Manual, Clontech).  33P labeled cDNA was generated from sample RNA using [33P]-dATP (3000 Ci/mmol; ICN, Costa Mesa, CA) and Maloney murine leukemia virus (MMLV) reverse transcriptase (Clontech).  Labeled probes were purified using nucleospin columns (Clontech).
Array membranes were prehybridized in Express Hyb containing sheared Salmon testes DNA (Gibco BRL, Rockville, MD) for 30 min at 71°C in rotating hybridization tubes.  Radiolabeled probe (3 x 106 cpm) was incubated in denaturing solution (Clontech) for 20 min at 71°C, after which Cot1 DNA/neutralizing solution was added and incubation continued for 10 min.  The probe mixture was added to the hybridization tube and incubated with rotation overnight.
Following hybridization, membranes were washed four times for 30 min in 2X saturated sodium citrate (SSC) and 1 % sodium dodecyl sulphate (SDS) at 71°C, once for 30 min in 0.1X SSC and 0.5% SDS at 71°C, and once for 5 min in 2X SSC at room temperature.  Membranes were removed and immediately wrapped in plastic and exposed to a phosphor storage screen (Molecular Dynamics, Sunnyvale, CA) for four days.

IV. Measurement data and specifications:
Data Analysis.  The membrane image was acquired using a Storm phosporimager (Molecular Dynamics) and Image Quant software.  Array images were analyzed using Atlas Image 2.0 (Clontech) software to determine raw intensity levels of expression.  Raw intensity data was imported into GeneSpring (Silicon Genetics, Redwood City, CA) expression analysis software.  Intensity levels were normalized to the median expressed intensity on each of the arrays and averaged for the three arrays at each time point.  Normalized expression levels for control arrays were established as a value of 1 and data from 6 and 72 h were expressed as fold changes relative to control.
In order to simplify interpretation of the resulting dataset, a k-means cluster analysis was employed to group genes based on similarities in patterns of expression.
To reduce the likelihood of false positives, the data was filtered using a criterion 2 fold change in expression prior to clustering.  Miller et al. (61) have calculated that using an array of 10,000 features with a coefficient of variation (CV) of 20 percent, a 2 fold criterion for altered gene expression would result in zero false positives.  The mean and median CV (15.8 and 14.3%, respectively) for all arrays in the current study fell within these guidelines for the elimination of false positives.

organism: Mus musculus

source_name: Extensor digitorum longus muscle of C57B/6 mouse


title: 6-h-3


title: wild type 4 hours exposure to congo red 2


title: 72-h-2


title: rlm1 mutant 4 hours exposure to congo red 1


title: wild type 4 hours exposure to congo red 3


title: wild type 6 hours exposure to congo red 4

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 6 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 Strain (6 hours Congo Red treatment)


title: wild type 6 hours exposure to congo red 2


title: wild type 6 hours exposure to congo red 1

source_name: BY4741 Strain (2hours Congo Red treatment)


title: 72-h-1


title: 6-h-1

description:
II.  Experimental Design:
a. Type of experiment:  Time course
b. Experimental factors:  3 month old mice subjected to lengthening contractions of the extensor digitorum longus muscle (EDL).  Samples of EDL collected at 6 and 72 h and compared to non-treated control.
c.  How many hybridizations in exp: 9
d.  Common reference used for all hyb: no
e.  Quality control steps:  All arrays used from same lot.  Triplicate hybridizations performed for each time point.

II. Samples used, extracts, preparation and labeling:
Animals.  Nine male C57BL/6 mice (3-4 mo of age, 27.8 ± 3.3 g body mass, Harlan Sprague-Dawley, Indianapolis, IN).
Muscle Injury.  The extensor digitorum longus (EDL) muscle of six mice were exposed to lengthening contractions.  Mice were anesthetized with 2% avertin (0.015 ml/kg) and supplemental doses were administered if the mouse responded to a toe pinch.  Animals were placed on a plexiglass platform that was maintained at 37°C.  The distal femur of the right hindlimb was fixed between screws and the foot was taped to the platform.  The distal tendons of the EDL were exposed by incision and tied to the lever arm of a servomotor (Aurora Scientific, Richmond Hill ON, Canada) with 4-0 silk suture.  Needle electrodes were placed adjacent to the peroneal nerve to stimulate dorsiflexor contraction (Grass Instruments, West Warwick, RI).  Maximal isometric force (Po) was determined by stimulating the dorsiflexors maximally at optimum length (Lo) for force development.
To induce muscle injury, 75 lengthening contractions were performed at 0.25 Hz for 5 min.  For each lengthening contraction, the muscle was stimulated at 150 Hz and stretched 100 ms after the initiation of stimulation.  Muscle stretch involved 20 % strain relative to Lo.  Force deficit was evaluated 10 min after the 75 contractions and then the incision was closed with 7-0 silk suture.  Animals were returned to their cage to recover until the time of sacrifice.  Prior to sacrifice by cervical dislocation, animals were anesthetized with avertin and the EDL muscles were excised and flash frozen in liquid nitrogen.  Muscles were stored in liquid nitrogen until RNA isolation.
RNA Isolation.  Total RNA was isolated from EDL muscles from control mice (n=3) and mice sacrificed at 6 h (n=3) and 72 h (n=3) after lengthening contractions according to the modified protocol of  Chomzynski et al..  Frozen muscles were added to preweighed tubes containing TriReagent (Sigma-Aldrich, St. Louis, MO).  Tissue was homogenized in TriReagent using a Tissue Tearor (Fischer, Pittsburgh, PA) at 30,000 rpm for 1 minute.  Homogenates were transferred to sterile, RNAase free microcentrifuge tubes and incubated for 10 min at room temperature.  Chloroform (0.2 ml; Sigma-Aldrich, St. Louis, MO) was added and after incubation, the samples were centrifuged for 15 min at 12,000 g and 4°C.  Total RNA was precipitated from the aqueous phase by the addition of isopropanol (Sigma-Aldrich), and pelleted by centrifugation.  Pellets were washed in ethanol (75 and 95 %) and air dried before resuspension in diethylpyrocarbonate (DEPC) treated water.  RNA concentration was determined by optical density at 260 nm.

III. Hybridization procedures and parameters:
Microarray Hybridization and Analysis.  To reduce measurement error, all membranes (Atlas mouse 1.2; Clontech, Palo Alto, CA) were prepared from the same lot.  Additionally, each membrane was hybridized only once to avoid errors associated with stripping and multiple hybridizations.  In order to minimize individual biological variability, total RNA was pooled from three animals for hybridization of arrays.  Three arrays were used for the pooled sample at each time point.  First strand cDNA probe generation from total RNA and microarray hybridization were performed according to manufacturer’s instructions (Atlas cDNA Expression Arrays User Manual, Clontech).  33P labeled cDNA was generated from sample RNA using [33P]-dATP (3000 Ci/mmol; ICN, Costa Mesa, CA) and Maloney murine leukemia virus (MMLV) reverse transcriptase (Clontech).  Labeled probes were purified using nucleospin columns (Clontech).
Array membranes were prehybridized in Express Hyb containing sheared Salmon testes DNA (Gibco BRL, Rockville, MD) for 30 min at 71°C in rotating hybridization tubes.  Radiolabeled probe (3 x 106 cpm) was incubated in denaturing solution (Clontech) for 20 min at 71°C, after which Cot1 DNA/neutralizing solution was added and incubation continued for 10 min.  The probe mixture was added to the hybridization tube and incubated with rotation overnight.
Following hybridization, membranes were washed four times for 30 min in 2X saturated sodium citrate (SSC) and 1 % sodium dodecyl sulphate (SDS) at 71°C, once for 30 min in 0.1X SSC and 0.5% SDS at 71°C, and once for 5 min in 2X SSC at room temperature.  Membranes were removed and immediately wrapped in plastic and exposed to a phosphor storage screen (Molecular Dynamics, Sunnyvale, CA) for four days.

IV. Measurement data and specifications:
Data Analysis.  The membrane image was acquired using a Storm phosporimager (Molecular Dynamics) and Image Quant software.  Array images were analyzed using Atlas Image 2.0 (Clontech) software to determine raw intensity levels of expression.  Raw intensity data was imported into GeneSpring (Silicon Genetics, Redwood City, CA) expression analysis software.  Intensity levels were normalized to the median expressed intensity on each of the arrays and averaged for the three arrays at each time point.  Normalized expression levels for control arrays were established as a value of 1 and data from 6 and 72 h were expressed as fold changes relative to control.
In order to simplify interpretation of the resulting dataset, a k-means cluster analysis was employed to group genes based on similarities in patterns of expression.
To reduce the likelihood of false positives, the data was filtered using a criterion 2 fold change in expression prior to clustering.  Miller et al. (61) have calculated that using an array of 10,000 features with a coefficient of variation (CV) of 20 percent, a 2 fold criterion for altered gene expression would result in zero false positives.  The mean and median CV (15.8 and 14.3%, respectively) for all arrays in the current study fell within these guidelines for the elimination of false positives.


title: Control-3


title: 6-h-2

source_name: Extensor digitorum longus of C57B/6 mouse


title: wild type 0 hours exposure to congo red 2

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. At this time cells were collected t=0h.

source_name: BY4741 Strain (0 hours Congo Red treatment)


title: wild type 0 hours exposure to congo red 1


title: wild type 6 hours exposure to congo red 3


title: wild type 4 hours exposure to congo red 1


title: wild type 2 hours exposure to congo red 4

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 2hours of growth, frozen at -80 °C and processed for RNA extraction.


title: wild type 2 hours exposure to congo red 2


title: Control-2


title: 50uM ABA_23

status: Public on Feb 05 2004

city: Tsukuba

first: Junshi

last: Yazaki

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Absisic acid
Keywords = Dormancy
Lot batch = US22502511_16011538011023_S01_A01

organism: Oryza sativa

source_name: Non treated sample labeled by green (Cy3)

source_name: ABA treated sample labeled by red (Cy5)


title: wild type 2 hours exposure to congo red 3


title: wild type 2 hours exposure to congo red 1

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 2hours of growth, frozen at -80 °C and processed for RNA extraction.


title: 50uM ABA_24

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Absisic acid
Keywords = Dormancy
Lot batch = US22502511_16011538011024_S01_A01

source_name: ABA treated sample labeled by green (Cy3)

source_name: Non treated sample labeled by red (Cy5)


title: 50uM ABA_19

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Absisic acid
Keywords = Dormancy
Lot batch = US22502511_16011538011019_S01_A01


title: 50uM ABA_20

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Absisic acid
Keywords = Dormancy
Lot batch = US22502511_16011538011020_S01_A01


title: rlm1 mutant 4 hours exposure to congo red 2

source_name: BY4741 -rlm1 Strain (Control mRNA: no treatment)

source_name: BY4741 -rlm1 Strain (4 hours Congo Red treatment)


title: RT4 cells grown on plastic, Replicate 1

status: Public on Nov 02 2003

city: Oklahoma City

first: Robert

middle: Evan

last: Hurst

state: OK

address: 920 S. L. Young Blvd

department: Urology

institute: Oklahoma University Health Sciences Center

description:
RNA was isolated from the cells growing on plastic using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 31664.11 +/- 1770.29
Keywords = Bladder cancer

source_name: RT4 cells grown on plastic


title: J82 cells grown on Matrigel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array.  Mean background = 43154.91 +/- 3494.00
Keywords = Bladder cancer

source_name: J82 cells grown on Matrigel


title: JP 253 cells grown on SISgel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 27162.50 +/- 1422.43
Keywords = Bladder cancer

source_name: JP 253 cells grown on SISgel


title: JB-V cells grown on Matrigel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 48174.13 +/- 9833.44
Keywords = Bladder cancer

source_name: JB-V cells grown on Matrigel


title: J82 cells grown on SISgel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 43121.97 +/- 2348.13
Keywords = Bladder cancer

source_name: J82 cells grown on SISgel


title: J82 grown on Matrigel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 46196.63 +/- 4644.43
Keywords = Bladder cancer

source_name: J82 grown on Matrigel


title: slt2 mutant 4 hours exposure to congo red 1

description: S. cerevisiae slt2Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 -slt2 Strain (Control mRNA: no treatment)

source_name: BY4741 -slt2 Strain (4 hours Congo Red treatment)


title: J82 cells grown on SISgel, Replicate 2

description: RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 40879.38 +/- 4400.70


title: Control-1

description:
I.  Experimental Design:
a. Type of experiment:  Time course
b. Experimental factors:  3 month old mice subjected to lengthening contractions of the extensor digitorum longus muscle (EDL).  Samples of EDL collected at 6 and 72 h and compared to non-treated control.
c.  How many hybridizations in exp: 9
d.  Common reference used for all hyb: no
e.  Quality control steps:  All arrays used from same lot.  Triplicate hybridizations performed for each time point.

II. Samples used, extracts, preparation and labeling:
Animals.  Nine male C57BL/6 mice (3-4 mo of age, 27.8 ± 3.3 g body mass, Harlan Sprague-Dawley, Indianapolis, IN).
Muscle Injury.  The extensor digitorum longus (EDL) muscle of six mice were exposed to lengthening contractions.  Mice were anesthetized with 2% avertin (0.015 ml/kg) and supplemental doses were administered if the mouse responded to a toe pinch.  Animals were placed on a plexiglass platform that was maintained at 37°C.  The distal femur of the right hindlimb was fixed between screws and the foot was taped to the platform.  The distal tendons of the EDL were exposed by incision and tied to the lever arm of a servomotor (Aurora Scientific, Richmond Hill ON, Canada) with 4-0 silk suture.  Needle electrodes were placed adjacent to the peroneal nerve to stimulate dorsiflexor contraction (Grass Instruments, West Warwick, RI).  Maximal isometric force (Po) was determined by stimulating the dorsiflexors maximally at optimum length (Lo) for force development.
To induce muscle injury, 75 lengthening contractions were performed at 0.25 Hz for 5 min.  For each lengthening contraction, the muscle was stimulated at 150 Hz and stretched 100 ms after the initiation of stimulation.  Muscle stretch involved 20 % strain relative to Lo.  Force deficit was evaluated 10 min after the 75 contractions and then the incision was closed with 7-0 silk suture.  Animals were returned to their cage to recover until the time of sacrifice.  Prior to sacrifice by cervical dislocation, animals were anesthetized with avertin and the EDL muscles were excised and flash frozen in liquid nitrogen.  Muscles were stored in liquid nitrogen until RNA isolation.
RNA Isolation.  Total RNA was isolated from EDL muscles from control mice (n=3) and mice sacrificed at 6 h (n=3) and 72 h (n=3) after lengthening contractions according to the modified protocol of  Chomzynski et al..  Frozen muscles were added to preweighed tubes containing TriReagent (Sigma-Aldrich, St. Louis, MO).  Tissue was homogenized in TriReagent using a Tissue Tearor (Fischer, Pittsburgh, PA) at 30,000 rpm for 1 minute.  Homogenates were transferred to sterile, RNAase free microcentrifuge tubes and incubated for 10 min at room temperature.  Chloroform (0.2 ml; Sigma-Aldrich, St. Louis, MO) was added and after incubation, the samples were centrifuged for 15 min at 12,000 g and 4°C.  Total RNA was precipitated from the aqueous phase by the addition of isopropanol (Sigma-Aldrich), and pelleted by centrifugation.  Pellets were washed in ethanol (75 and 95 %) and air dried before resuspension in diethylpyrocarbonate (DEPC) treated water.  RNA concentration was determined by optical density at 260 nm.

III. Hybridization procedures and parameters:
Microarray Hybridization and Analysis.  To reduce measurement error, all membranes (Atlas mouse 1.2; Clontech, Palo Alto, CA) were prepared from the same lot.  Additionally, each membrane was hybridized only once to avoid errors associated with stripping and multiple hybridizations.  In order to minimize individual biological variability, total RNA was pooled from three animals for hybridization of arrays.  Three arrays were used for the pooled sample at each time point.  First strand cDNA probe generation from total RNA and microarray hybridization were performed according to manufacturer’s instructions (Atlas cDNA Expression Arrays User Manual, Clontech).  33P labeled cDNA was generated from sample RNA using [33P]-dATP (3000 Ci/mmol; ICN, Costa Mesa, CA) and Maloney murine leukemia virus (MMLV) reverse transcriptase (Clontech).  Labeled probes were purified using nucleospin columns (Clontech).
Array membranes were prehybridized in Express Hyb containing sheared Salmon testes DNA (Gibco BRL, Rockville, MD) for 30 min at 71°C in rotating hybridization tubes.  Radiolabeled probe (3 x 106 cpm) was incubated in denaturing solution (Clontech) for 20 min at 71°C, after which Cot1 DNA/neutralizing solution was added and incubation continued for 10 min.  The probe mixture was added to the hybridization tube and incubated with rotation overnight.
Following hybridization, membranes were washed four times for 30 min in 2X saturated sodium citrate (SSC) and 1 % sodium dodecyl sulphate (SDS) at 71°C, once for 30 min in 0.1X SSC and 0.5% SDS at 71°C, and once for 5 min in 2X SSC at room temperature.  Membranes were removed and immediately wrapped in plastic and exposed to a phosphor storage screen (Molecular Dynamics, Sunnyvale, CA) for four days.

IV. Measurement data and specifications:
Data Analysis.  The membrane image was acquired using a Storm phosporimager (Molecular Dynamics) and Image Quant software.  Array images were analyzed using Atlas Image 2.0 (Clontech) software to determine raw intensity levels of expression.  Raw intensity data was imported into GeneSpring (Silicon Genetics, Redwood City, CA) expression analysis software.  Intensity levels were normalized to the median expressed intensity on each of the arrays and averaged for the three arrays at each time point.  Normalized expression levels for control arrays were established as a value of 1 and data from 6 and 72 h were expressed as fold changes relative to control.
In order to simplify interpretation of the resulting dataset, a k-means cluster analysis was employed to group genes based on similarities in patterns of expression.
To reduce the likelihood of false positives, the data was filtered using a criterion 2 fold change in expression prior to clustering.  Miller et al. (61) have calculated that using an array of 10,000 features with a coefficient of variation (CV) of 20 percent, a 2 fold criterion for altered gene expression would result in zero false positives.  The mean and median CV (15.8 and 14.3%, respectively) for all arrays in the current study fell within these guidelines for the elimination of false positives.

source_name: Extensor digitorum longus muscle of C57B/6 mice


title: JP 253 cells grown on Matrigel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 26934.50 +/= 1522.78
Keywords = Bladder cancer

source_name: JP 253 cells grown on Matrigel


title: JP 253 cells grown on Matrigel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 25183.87 +/- 1221.67
Keywords = Bladder cancer


title: JP 253 cells grown on SISgel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 35678.56 +/- 1815.53
Keywords = Bladder cancer


title: RT4 cells grown on Matrigel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 24873.73 +/- 1657.26
Keywords = Bladder cancer

source_name: RT4 cells grown on Matrigel


title: RT4 cells grown on plastic, Replicate 2

description:
RNA was isolated from the cells growing on plastic using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array.  Mean background = 33022.53 +/- 3560.75
Keywords = Bladder cancer


title: JBV cells grown on SISgel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array.  Mean background = 75081.31 +/- 4347.75
Keywords = Bladder cancer

source_name: JBV cells grown on SISgel


title: JBV cells grown on Matrigel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array.
Keywords = Bladder cancer

source_name: JBV cells grown on Matrigel


title: 50uM GA_07

status: Public on Jan 08 2004

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA (Gibberellin) and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Gibberellin
Keywords = Germination
Lot batch = 16011538011007_S01_A01.xls

source_name: Non treated sample labeled by green (Cy3)

source_name: GA treated sample labeled by red (Cy5)


title: TCCSUP cells grown on SISgel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 36977.24 +/- 2156.99
Keywords = Bladder cancer

source_name: TCCSUP cells grown on SISgel


title: TCCSUP cells grown on Matrigel, Replicate 2

source_name: TCCSUP cells grown on Matrigel


title: RT4 cells grown on SISgel, replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 23206.86 +/- 998.45
Keywords = Bladder cancer

source_name: RT4 cells grown on SISgel


title: 50uM GA_08

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA (Gibberellin) and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Gibberellin
Keywords = Germination
Lot batch = 16011538011008_S02_A01


title: JBV cells grown on SISgel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 24777.53 +/- 1498.94
Keywords = Bladder cancer


title: 50uM GA_04

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA (Gibberellin) and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Gibberellin
Keywords = Germination
Lot batch = 16011538011004_S01_A01

source_name: GA treated sample labeled by green (Cy3)

source_name: Non treated sample labeled by red (Cy5)


title: 50uM GA_05

description:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA (Gibberellin) and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/).　We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Gibberellin
Keywords = Germination
Lot batch = 16011538011005_S01_A01


title: RT4 cells grown on SISgel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 22993.99 +/- 914.57
Keywords = Bladder cancer


title: HUC Cells on Matrigel, Replicate 2

description:
RNA was isolated from the cells growing on SISgel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 36610.58+/- 2218.36
Keywords = Bladder cancer

source_name: HUC Cells grown on Matrigel


title: RT4 cells grown on Matrigel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 25158.70 +/- 1801.94
Keywords = Bladder cancer


title: TCCSUP cells grown on Matrigel, Replicate 1

description:
RNA was isolated from the cells growing on SISgel or Matrigel using the QIAeasy kit (Qiagen) by adding 300 microliter lysis buffer and pipeting up and down to lyse the cells and dissolve the gel. The RNA was isolated from the lysate by use of a QIAshredder spin column to complete homogenization, proteinase K digestion, ethanol precipitation, an RNeasy mini spin column, DNase I digestion, and a final spin column. Yield of total RNA and the purity were assessed by spectrophotometry. The yield was approximately 2.4 - 6 microg RNA per culture in 30 microliter. First strand synthesis was carried out at 42 C for 1 h. with reagents supplied by Clontech as part of the SMART II kit except that Superscript II (Invitrogen) reverse transcriptase (a version of MMLV reverse transcriptase engineered for increased stability) was substituted for the one supplied. The SMART II oligonucleotide is included to capture full length cDNA at the 5’end and to permit amplification in the next step. A proportional amplification (2000 to 5000 fold) was then used to produce sufficient probe for analysis using the Clontech SMART (Switch Mechanism At the 5' end of Reverse Transcript) system. Labeled probe is produced from an aliquot of the amplified probe with Klenow fragment and 32P-labeled nucleotide. After probe purification, 15 × 10**6 cpm of probe is hybridized in duplicate to the Clontech Human Cancer 1.2 array on nylon following the protocol provided by the company. The results are visualized by exposing a phosphorimager screen approximately 16 hours overnight and then reading with the Packard Cyclone phosphoimager and Optiquant software. The background was subtracted from each of the densitometer counts by iteratively eliminating all points that are over 3 standard deviations above the mean of the 280 background measurements provided for each array. Mean background = 43154.91 +/- 3494.00
Keywords = Bladder cancer