title: Tubulogenesis at 4 hours (A)

status: Public on Apr 08 2006

city: Argonne

first: suneeta

last: mandava

state: IL

address: 9700 S Cass ave

department: Bio

institute: Argonne National Lab

description: HMVEC induced with matrigel

source_name: HMVEC

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 4 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.

tag: HMVECs induced with matrigel


title: FETAL_DAY21_21%_OXYGEN_sample1

status: Public on Apr 30 2006

type: RNA

city: Boston

first: Elizabeth

middle: D

last: George

state: MA

address: 715 Albany St

department: Bioinformatics

country: USA

institute: Boston University

description: whole fetal lung taken at day 21 of gestation.  RNA extracted for hybridization.

label: affy kit

molecule: total RNA

organism: Mus musculus

source_name: fetal mouse lung

tag: Strain

tag: Age

value: fetal day 21

tag: Tissue

value: Lung


title: NEWBORN2_21%_OXYGEN_sample2

description: whole lung taken from mouse 2 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 2 hours after birth

tag: strain

tag: age

value: 2 hours after birth

tag: tissue

value: whole lung


title: Proloferation at 0 hours (A)

description: HMVEC induced with VEGF

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Homo sapiens

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 0 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.

tag: HMVECs induced with VEGF


title: Tubulogenesis at 8 hours (B)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 8 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed b


title: Proloferation at 4 hours (A)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 4 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: Tubulogenesis at 2 hours (B)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 2 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed b


title: Proloferation at 0 hours (B)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 0 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:


title: Tubulogenesis at 8 hours (A)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 8 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: NEWBORN24_21%_OXYGEN_sample1

description: whole lung taken from mouse at 24 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 24 hours after birth

value: 24 hours after birth


title: Proloferation at 2 hours (A)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 2 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: FETAL_DAY21_21%_OXYGEN_sample2

source_name: mouse lung fetal day 21

value: Fetal day 21


title: Proloferation at 1 hour (B)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 1 hour.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1


title: Tubulogenesis at 4 hours (B)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 4 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed b


title: Proloferation at 4 hours (B)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 4 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:


title: Proloferation at 30 minutes (B)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 30 minutes.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by


title: NEWBORN6_21%_OXYGEN_sample2

description: whole lung taken from mouse 6 hours after birth.  RNA extracted for hybridization.

source_name: mouse lung 6 hours after birth

value: 6 hours after birth


title: Proloferation at 2 hours (B)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 2 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:


title: NEWBORN6_21%_OXYGEN_sample3


title: Tubulogenesis at 1 hour (A)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 1 hour.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: NEWBORN2_21%_OXYGEN_sample3


title: Proloferation at 30 minutes (A)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 30 minutes.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: Tubulogenesis at 1 hour (B)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 1 hour.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by


title: Proloferation at 1 hour (A)

description: HMVEC induced with VEGF

extract_protocol: 1.35E6 HMVEC cells were plated onto gelatin–coated plates and the cells were allowed to attach for 1 hour.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: NEWBORN24_21%_OXYGEN_sample3

description: whole lung taken from mouse 24 hours after birth.  RNA extracted for hybridization.


title: RY47

status: Public on Apr 07 2006

city: Tokyo

first: Tokuzo

last: Arao

address: Tsukiji 5-1-1, Chuo-ku

department: Shien lab

country: Japan

institute: National Cancer Center Hospital

data_processing: log 10 cy3/cy5

source_name: normal brain RNA, control

tag: normal brain RNA, control

source_name: tumor RNA

tag: tumor RNA


title: Tubulogenesis at 30 minutes (B)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 30 minutes.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followe


title: RY48


title: SJJNE056


title: RY305


title: RY130


title: RY340


title: RY125


title: RY24


title: RY129


title: RY348


title: RY133


title: RY137


title: RY54


title: RY63


title: RY139


title: RY122


title: Tubulogenesis at 2 hours (A)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 2 hours.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.


title: RY44


title: RY121


title: RY124


title: gHvxb455


title: RY311


title: RY138


title: LITgM533


title: RY123


title: LKMqK563


title: ajhfA459

status: Public on Apr 06 2006

tag: glioma


title: gdKJL617


title: cvWvz529


title: MMPvK094


title: Mock infected murine liver-MO30k-(6508)-6 hpi

status: Public on Apr 04 2006

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Sample is MyD88 Heterozygous murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.

hyb_protocol: Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

data_processing: VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.

source_name: Cy5 labeled Liver RNA

label_protocol: The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.

extract_protocol: RNA isolation was accomplished by homogenizing liver in liquid nitrogen, then extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was purified using an RNeasy Kit (Qiagen) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: MyD88 Heterozygous murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock)

source_name: Murine Reference RNA

label_protocol: The RNA was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.

tag: Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.


title: Ad infected murine liver-MO30k-(6415)-6 hpi

description: Sample is MyD88 Homozygous murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

tag: MyD88 Homozygous murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.


title: Ad infected murine liver-MO30k-(6515)-6 hpi

description: Sample is MyD88 Heterozygous murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

tag: MyD88 Heterozygous murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.


title: Mock infected murine liver-MO30k-(6412)-6 hpi

description: Sample is MyD88 Homozygous murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.

tag: MyD88 Homozygous murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock)


title: Ad infected murine liver-MO30k-(712)-6 hpi


title: Ad infected murine liver-MO30k-(679)-6 hpi

tag: MyD88 Heterozygote murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.


title: Mock infected murine liver-MO30k-(6413)-6 hpi


title: Ad infected murine liver-MO30k-(6449)-6 hpi

description: Sample is MyD88 Homozygous murine liver RNA extract after Ad infection with 1.5x10E11 particles of LacZ Ad at 6 hpi.

tag: MyD88 Homozygous murine Liver RNA- 6 hours post-injection after injection with 1.5x10E11 particles of LacZ 1st generation adenovirus


title: Ad infected murine liver-MO30k-(846)-6 hpi


title: Mock infected murine liver-MO30k-(6416)-6 hpi


title: Mock infected murine liver-MO30k-(6414)-6 hpi


title: Ad infected murine liver-MO30k-(6450)-6 hpi


title: Ad infected murine liver-MO30k-(848)-6 hpi


title: Ad infected murine liver-MO30k-(6417)-6 hpi


title: Ad infected murine liver-MO30k-(711)-6 hpi


title: Ad infected murine liver-MO30k-(710)-6 hpi


title: Ad infected murine liver-MO30k-(6411)-6 hpi


title: Ad infected murine liver-MO30k-(6451)-6 hpi


title: DCN_U7_A

city: Wako-shi

first: Jin-Sung

last: Park

state: Saitama

address: 2-1 Hirosawa

department: BSI

institute: RIKEN

description: Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles

data_processing: Affy version 1.3.25. with default parameters.

label: Biotin

source_name: anterior interpositus nucleus-centered deep cerebellar nuclei, trained with unpaired paradigm of delayed-type eyeblink conditioning for 7 days

label_protocol: 15ug Biotin-labeled cRNA was synthesized with BioArray HighYield RNA Transcript Labeling Kit (ENZO Diagnostics Inc., Farmingdale, NY) according to the manufacturer’s instructions

growth_protocol: Mice were individually housed in a ventilated plastic cage, which was placed in a temperature and humidity-controlled room with 12-h light/dark cycle (light on from 8:00 AM to 8:00 PM). All animals were fed laboratory chow and water ad libitum

extract_protocol: 10~15 anterior interpositus-centered deep cerebellar nuclei ipsilateral to the eye implanted with four wires were pooled. Total RNA was extracted using an RNeasy Mini Kit (QIAGEN, Hilden, Germany) and QIAshredder (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After 3days’ recovery, they were trained with unpaired paradigm of conditioned stimulus (CS) and unconditioned stimulus (US) for 7days: A 352-ms tone CS (1kHz, 83~85dB) and a 100ms periorbital shock US (100kHz square pluses) were delivered in an explicitly unpaired, pseudorandomized manner. After the last trial was given, anterior interpositus was immediately sampled in 10 to 30 min from the sacrifice.

tag: Strain

tag: Gender

value: Male


title: DCN_P3_A

source_name: anterior interpositus nucleus-centered deep cerebellar nuclei, trained with paired paradigm of delayed-type eyeblink conditioning for 3 days

label_protocol: 18ug Biotin-labeled cRNA was synthesized with BioArray HighYield RNA Transcript Labeling Kit (ENZO Diagnostics Inc., Farmingdale, NY) according to the manufacturer’s instructions

treatment_protocol: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After 3days’ recovery, they were trained with paired paradigm of conditioned stimulus (CS) and unconditioned stimulus (US) for 3days: A 352-ms tone CS (1kHz, 83~85dB) was delivered first and a 100ms periorbital shock US (100kHz square pluses) were delivered with 252ms after the onset of CS, and they co-terminated. After the last trial was given, anterior interpositus was immediately sampled in 10 to 30 min from the sacrifice.

tag: Age

tag: Tissue

value: Anterior interpositus nucleus-centered deep cerebellar nuclei


title: DCN_U7_C


title: DCN_P7_A

source_name: anterior interpositus nucleus-centered deep cerebellar nuclei, trained with paired paradigm of delayed-type eyeblink conditioning for 7 days

treatment_protocol: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After 3days’ recovery, they were trained with paired paradigm of conditioned stimulus (CS) and unconditioned stimulus (US) for 7days: A 352-ms tone CS (1kHz, 83~85dB) was delivered first and a 100ms periorbital shock US (100kHz square pluses) were delivered with 252ms after the onset of CS, and they co-terminated. After the last trial was given, anterior interpositus was immediately sampled in 10 to 30 min from the sacrifice.


title: DCN_P7_C


title: DCN_SHAM_A

description: Anterior interpositus nucleus-centered deep cerebellar nuclei were sampled using syringe needles.

data_processing: Affy version 1.3.25 with default parameters.

source_name: anterior interpositus nucleus-centered deep cerebellar nuclei, sham negative control

growth_protocol: Mice were individually in a ventilated plastic cage, which was placed in a temperature and humidity-controlled room with 12-h light/dark cycle (light on from 8:00 AM to 8:00 PM). All animals were fed laboratory chow and water ad libitum

extract_protocol: 10~15 anterior interpositus nucleus-centered deep cerebellar nuclei ipsilateral to the eye implanted with four wires were pooled. Total RNA was extracted using an RNeasy Mini Kit (QIAGEN, Hilden, Germany) and QIAshredder (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After recovery, anterior interpositus nculeus-centered deep cerebellar nuclei were immediately sampled in 10 to 30 min from the sacrifice.


title: DCN_SHAM_C

treatment_protocol: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After recovery, anterior interpositus nucleus-centered deep cerebellar nuclei were immediately sampled in 10 to 30 min from the sacrifice.


title: DCN_P3_C


title: DCN_U7_B


title: DCN_P7_B


title: Mock infected murine liver-MO30k-(6507)-6 hpi


title: DCN_SHAM_B


title: DCN_P3_B


title: PND28 Rat Testis_Rat230-2_6hr MEHP_Animal#31_04005

status: Public on Apr 01 2006

city: Research Triangle Park

first: Kamin

last: Johnson

address: 6 Davis Drive

department: Biological Sciences

institute: CIIT Centers for Health Research

description: KJ_1_6_31_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

data_processing: Affymetrix GCOS 1.0

organism: Rattus norvegicus

source_name: Sample Type: tissue, Tissue: testis

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen RNeasy Maxi Kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:00, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.28, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: ug

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: excellent

tag: Strain or Line

value: Fischer

tag: Individual

tag: Sacrifice Method

tag: Units of Age

value: PND


title: PND28 Rat Testis_Rat230-2_3hr MEHP_Animal#51_04005

description: KJ_1_3_51_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:16, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.225, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_2hr MEHP_Animal#45_04005

description: KJ_1_2_45_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:14, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.225, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

value: good


title: PND28 Rat Testis_Rat230-2_1hr MEHP_Animal#39_04005

description: KJ_1_1_39_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:12, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_6hr MEHP_Animal#33_04005

description: KJ_1_6_33_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:10, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.29, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg body weight


title: PND28 Rat Testis_Rat230-2_2hr Corn Oil_Animal#7_04005

description: KJ_1_2_ 7_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:00, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.235, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: Rat vestibular ganglia_calretinin_negative_rep2

city: Milwaukee

first: Ashley

last: Wackym

state: WI

address: 9200 W. Wisconsin Ave

department: Otolaryngology

institute: Medical College of Wisconsin

description: Rat vestibular ganglia stained with calretinin.  Tissue is LCM captured, calretinin positive cells

data_processing: Raw values represent the final number of the spot after the background is subtracted out.  Normalized values represent median global normalization method, i.e. raw intensity/median intensity of all spots on the array

source_name: Rat vestibular ganglia

tag: Brown norwary rats, 6-8 weeks old, vestibular ganglia


title: PND28 Rat Testis_Rat230-2_2hr MEHP_Animal#44_04005

description: KJ_1_2_44_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:08, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: Rat vestibular ganglia_calretinin_positive_rep1.


title: PND28 Rat Testis_Rat230-2_2hr MEHP_Animal#43_04005

description: KJ_1_2_43_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:02, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_1hr MEHP_Animal#37_04005

description: KJ_1_1_37_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:00, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg oodyweight


title: Rat vestibular ganglia_calretinin_negative_rep1


title: Rat vestibular ganglia_calretinin_positive_rep2


title: PND28 Rat Testis_Rat230-2_12hr MEHP_Animal#57_04005

description: KJ_1_12_57_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:10, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_6hr Corn Oil_Animal#36_04005

description: KJ_0_6_36_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:25, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.305, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_2hr Corn Oil_Animal#48_04005

description: KJ_0_2_48_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:32, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.178, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_12hr MEHP_Animal#58_04005

description: KJ_1_12_58_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:15, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.265, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_6hr Corn Oil_Animal#35_04005

description: KJ_0_6_35_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:20, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.285, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_1hr MEHP_Animal#38_04005

description: KJ_1_1_38_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:06, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_3hr Corn Oil_Animal#53_04005

description: KJ_0_3_53_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:28, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_3hr Corn Oil_Animal#52_04005

description: KJ_0_3_52_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:22, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_12hr MEHP_Animal#59_04005

description: KJ_1_12_59_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:20, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_6hr Corn Oil_Animal#34_04005

description: KJ_0_6_34_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:15, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.28, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_2hr Corn Oil_Animal#47_04005

description: KJ_0_2_47_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:26, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_3hr Corn Oil_Animal#54_04005

description: KJ_0_3_54_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration:  hour, Treatment Time: 1:34, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.22, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: Tubulogenesis at 30 minutes (A)

description: HMVEC induced with matrigel

extract_protocol: 1.35E6 HMVEC cells were plated onto Matrigel™ – coated plates and the cells were allowed to attach for 30 minutes.  Cells were collected by scraping, washed with PBS, and RNA prepared using Trizol (Invitrogen) extraction followed by 1:1 phenol/chloroform and ethanol precipitation.  RNA integrity was monitored using an Agilent 2100 Bioanalyzer.

tag: HMVECs induced with matrigel


title: PND28 Rat Testis_Rat230-2_1hr Corn Oil_Animal#42_04005

description: KJ_0_1_42_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:30, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_1hr Corn Oil_Animal#40_04005

description: KJ_0_1_40_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:18, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: SR786

status: Public on Mar 31 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Analysis of differential gene expression in human non-Hodgkin`s lymphoma cell lines and a primary leukaemic tumor sample of large cell anaplastic type in comparison with Hodgkin`s lymphoma cell lines and other non-Hodgkin`s lymphoma samples and non-neoplastic lymphocytes

data_processing: MAS5.0, scaled to a target value of 1000

source_name: SR786 cell line

treatment_protocol: no treatment

tag: cell line established from malignant lymphoma cells of a patient diagnosed with large cell anaplastic non-Hodgkin`s lymphoma, carrying the t2;5 translocation


title: 13218881_mak_MAUI Hyb_083105

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

hyb_protocol: 10 micrograms, NSH ester Cy3 (Ambion), Chemical conjugation"

data_processing: Ch1 Intensities read directly from the Microarray scanner.

organism: Tursiops truncatus

tag: peripheral blood lymphocytes, male, captive, adult"


title: PND28 Rat Testis_Rat230-2_1hr Corn Oil_Animal#41_04005

description: KJ_0_1_41_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:24, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: PND28 Rat Testis_Rat230-2_12hr Corn Oil_Animal#60_04005

description: KJ_0_12_60_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:25, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.235, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: 13218984_952post_10C_110105

hyb_protocol: 10 micrograms, NSH ester Cy3 (Ambion), Chemical conjugation

tag: peripheral blood lymphocytes, male, 18 years old, wild, adult


title: SuDHL1

source_name: SuDHL1 cell line


title: LeukALCL

source_name: Leukaemic ALCL (primary tumor cells from peripheral blood)

tag: Lymphoma cells from peripheral blood of a 30 year old female patient diagnosed with large cell anaplastic non-Hodgkin`s lymphoma carrying the t2;5 translocation, suffering a leukaemic course


title: 13222791_control oven_090705

tag: peripheral blood lymphocytes, male, 16 years old, skin, adult, 37C, 5%CO2, 1/1 micture RPMI 1640 and cheratinocyte free medium


title: Karpas299

source_name: Karpas299 cell line


title: PND28 Rat Testis_Rat230-2_3hr MEHP_Animal#49_04005

description: KJ_1_3_49_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:04, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.188, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

tag: Array Type

tag: Age


title: 13218856_mak_MAUI Hyb_083105

tag: peripheral blood lymphocytes, male, captive, adult


title: PND28 Rat Testis_Rat230-2_6hr MEHP_Animal#32_04005

description: KJ_1_6_32_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:05, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.265, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

tag: Amount to Core

tag: Units of Amount

tag: Ratio


title: PND28 Rat Testis_Rat230-2_12hr Corn Oil_Animal#61_04005

description: KJ_0_12_61_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:30, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.245, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

tag: RNA Integrity Number

tag: Bioanalyzer Results

tag: Strain or Line


title: YUMAC_1

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: This is a comparison of YUMAC melanoma cells versus melanocytes

data_processing: VALUE data calculated using Excel

molecule: polyA RNA

source_name: metastatic melanoma culture

tag: Gender

value: male

tag: Source tissue

value: recurrent metastasis at the site of excision.

source_name: normal melanocyte culture

value: foreskin


title: 13218857_mak_MAUI Hyb_083105


title: 13218986_952post_10B_110105


title: PND28 Rat Testis_Rat230-2_12hr Corn Oil_Animal#62_04005

description: KJ_0_12_62_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:35, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.245, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

tag: Individual

tag: Sacrifice Method

tag: Units of Age


title: YUSIT1_1

description: This is a comparison of YUSIT1 melanoma cells versus melanocytes

value: unknown


title: YUHEIK_1

description: This is a comparison of YUHEIK melanoma cells versus melanocytes

value: female

value: metastatic melanoma, from maxillary gingiva lymph node.


title: PND28 Rat Testis_Rat230-2_3hr MEHP_Animal#50_04005

description: KJ_1_3_50_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

treatment_protocol: in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:10, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight


title: WW165_2

description: This is a comparison of WW165 melanoma cells versus melanocytes

source_name: primary melanoma culture

value: primary melanoma, 2.25mm lesion removed from the back.


title: YUSIT1_2


title: 13218987_952post_10A_110105

tag: peripheral blood lymphocytes, male, 18 years old, wild, adult


title: 13222786_control oven_090705


title: YUCAL_1

description: This is a comparison of YUCAL melanoma cells versus melanocytes

value: soft tissue metastasis of melanoma.


title: LS-126

status: Public on Mar 30 2006

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

institute: Veridex, LLC

description: lung squamous carcinoma

source_name: lung

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

extract_protocol: Total RNA was isolated from lung squamous cell carcinoma samples according to Standard Trizol protocol.

tag: Cancer


title: LS-138

description: lung squamous carcinoma


title: LS-140

description: lung squamous carcinoma


title: LS-122

description: lung squamous carcinoma


title: LS-118

description: lung squamous carcinoma


title: LY3 CARD11 shRNA Day5 - mAdbID:72244

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 72244

hyb_protocol: protocol_name: NCI cDNA Microarray Hybridization other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual": http://nciarray.nci.nih.gov/reference/nciarrayspacket01-04A.pdf)

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Dox treated - 120 hours (day 5)

label_protocol: protocol_name: Cy5 Sample Labeling Protocol - generic

extract_protocol: protocol_name: Sample Extraction Protocol

treatment_protocol:
treatment_type: compound
compound: Doxycycline
treatment_dose: 20 ng/ml
treatment_time: 120 hours
in_vitro_treatments: Doxycycline treated every 48 hours - sample taken at 120 hours

value: B-cell

value: Lymphoma

source_name: Untreated-120 hours (day 5)

label_protocol: protocol_name: Cy3 Sample Labeling Protocol - generic


title: LS-116

description: lung squamous carcinoma


title: LY3 CARD11 shRNA Day3 - mAdbID:72281

description: mAdb experiment ID: 72281

source_name: Dox treated - 72 hours (day 3)

treatment_protocol:
treatment_type: compound
compound: Doxycycline
treatment_dose: 20 ng/ml
treatment_time: 72 hours
in_vitro_treatments: Doxycycline treated every 48 hours - sample taken at 72 hours

source_name: Untreated-72 hours (day 3)


title: LS-124

description: lung squamous carcinoma


title: LS-132

description: lung squamous carcinoma


title: LY3 CARD11 shRNA Day4 - mAdbID:72242

description: mAdb experiment ID: 72242

source_name: Dox treated - 96 hours (day 4)

treatment_protocol:
treatment_type: compound
compound: Doxycycline
treatment_dose: 20 ng/ml
treatment_time: 96 hours
in_vitro_treatments: resupplemented doxycycline every 48 hours

source_name: Untreated-96 hours (day 4)


title: LS-128

description: lung squamous carcinoma


title: LS-120

description: lung squamous carcinoma


title: WW165_1


title: LS-130

description: lung squamous carcinoma


title: LS-136

description: lung squamous carcinoma


title: LS-100

description: lung squamous carcinoma


title: MNT1_2

description: This is a comparison of MNT1 melanoma cells versus melanocytes

value: lymph node


title: LS-102

description: lung squamous carcinoma


title: LS-114

description: lung squamous carcinoma


title: LY3 CARD11 shRNA Day2 - replicate - mAdbID:71519

description: mAdb experiment ID: 71519

source_name: Untreated-48 hours (day 2)

source_name: Dox treated - 48 hours (day 2)

treatment_protocol:
treatment_type: compound
compound: Doxycycline
treatment_dose: 20 ng/ml
treatment_time: 48 hours
in_vitro_treatments: resupplemented with Doxycycline every 48 hours


title: LY3 CARD11 shRNA Day2 - mAdbID:72279

description: mAdb experiment ID: 72279


title: LS-106

description: lung squamous carcinoma


title: LS-108

description: lung squamous carcinoma


title: LS-104

description: lung squamous carcinoma


title: LS-98

description: lung squamous carcinoma


title: LS-72

description: lung squamous carcinoma


title: LS-94

description: lung squamous carcinoma


title: LY3 CARD11 shRNA Day4 - replicate - mAdbID:71523

description: mAdb experiment ID: 71523


title: LS-62

description: lung squamous carcinoma


title: LS-86

description: lung squamous carcinoma


title: LS-70

description: lung squamous carcinoma


title: LS-68

description: lung squamous carcinoma


title: LS-82

description: lung squamous carcinoma


title: MNT1_3


title: LS-96

description: lung squamous carcinoma


title: LS-64

description: lung squamous carcinoma


title: LS-80

description: lung squamous carcinoma


title: LS-54

description: lung squamous carcinoma


title: LS-56

description: lung squamous carcinoma


title: LS-88

description: lung squamous carcinoma


title: LS-60

description: lung squamous carcinoma


title: MNT1_1


title: LS-66

description: lung squamous carcinoma


title: LS-58

description: lung squamous carcinoma


title: LS-48

description: lung squamous carcinoma


title: LS-74

description: lung squamous carcinoma


title: LS-92

description: lung squamous carcinoma


title: LS-78

description: lung squamous carcinoma


title: LS-90

description: lung squamous carcinoma


title: LS-46

description: lung squamous carcinoma


title: LS-134

description: lung squamous carcinoma


title: LS-50

description: lung squamous carcinoma


title: LS-40

description: lung squamous carcinoma


title: LS-34

description: lung squamous carcinoma


title: LS-38

description: lung squamous carcinoma


title: LS-42

description: lung squamous carcinoma


title: LS-32

description: lung squamous carcinoma


title: LS-44

description: lung squamous carcinoma


title: LS-16

description: lung squamous carcinoma


title: LS-22

description: lung squamous carcinoma


title: LS-28

description: lung squamous carcinoma


title: LS-20

description: lung squamous carcinoma


title: LS-6

description: lung squamous carcinoma


title: LS-18

description: lung squamous carcinoma


title: LS-8

description: lung squamous carcinoma


title: LS-24

description: lung squamous carcinoma


title: LS-10

description: lung squamous carcinoma


title: LS-2

description: lung squamous carcinoma


title: LS-135

description: lung squamous carcinoma


title: LS-12

description: lung squamous carcinoma


title: LS-36

description: lung squamous carcinoma


title: LS-14

description: lung squamous carcinoma


title: LS-26

description: lung squamous carcinoma


title: LS-129

description: lung squamous carcinoma


title: LS-131

description: lung squamous carcinoma


title: LS-125

description: lung squamous carcinoma


title: LS-123

description: lung squamous carcinoma


title: LS-127

description: lung squamous carcinoma


title: LS-139

description: lung squamous carcinoma


title: LS-121

description: lung squamous carcinoma


title: LS-115

description: lung squamous carcinoma


title: LS-117

description: lung squamous carcinoma


title: LS-113

description: lung squamous carcinoma


title: LS-105

description: lung squamous carcinoma


title: LS-111

description: lung squamous carcinoma


title: LS-133

description: lung squamous carcinoma


title: LS-109

description: lung squamous carcinoma


title: LS-30

description: lung squamous carcinoma


title: LS-101

description: lung squamous carcinoma


title: LS-87

description: lung squamous carcinoma


title: LS-91

description: lung squamous carcinoma


title: LS-79

description: lung squamous carcinoma


title: LS-103

description: lung squamous carcinoma


title: LS-89

description: lung squamous carcinoma


title: LS-97

description: lung squamous carcinoma


title: LS-95

description: lung squamous carcinoma


title: LS-107

description: lung squamous carcinoma


title: LS-81

description: lung squamous carcinoma


title: LS-85

description: lung squamous carcinoma


title: LS-99

description: lung squamous carcinoma


title: LS-75

description: lung squamous carcinoma


title: LS-73

description: lung squamous carcinoma


title: LS-77

description: lung squamous carcinoma


title: LS-69

description: lung squamous carcinoma


title: LS-67

description: lung squamous carcinoma


title: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 3

city: Rockville

first: Francoise

last: Thibaud-Nissen

address: 9712 Medical Center Dr

institute: The Institute for Genomic Research

description: salicylic-treated plants, replicate 3 of 3

data_processing: RMA, quantile normalization, median polish summary of probes

organism: Arabidopsis thaliana

source_name: leaf tissue of 3- to 4-week old plants, sprayed with 1 mM SA and 0.01% Silwet 2 hours before harvest

extract_protocol: Phenol/Chloroform extraction of quick-frozen leaves

treatment_protocol: Plants were sprayed with 0.01% Silwet and 1 mM salicylic acid 2 hours before harvesting of leaves

tag: Columbia ecotype, 3- to 4-week old plants, greenhouse-grown in 16-hour days, leaves treated with 0.01% Silwet and 1 mM SA 2 hours before harvest


title: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 1

description: salicylic-treated plants, replicate 1 of 3


title: LS-65

description: lung squamous carcinoma


title: LS-63

description: lung squamous carcinoma


title: leaf material harvested 2 hours after spraying of 1 mM salicylic acid biological replicate 2

description: salicylic-treated plants, replicate 2 of 3

tag: Columbia ecotype, 3 to 4-week old plants, greenhouse-grown in 16-hour days, leaves treated with 0.01% Silwet and 1 mM SA 2 hours before harvest


title: 2-hour mock-treated leaf material biological replicate 3

description: control for salicylic-treated plants, replicate 3 of 3

source_name: leaf tissue of 3- to 4-week old plants, treated with 0.01% Silwet 2 hours before harvest

treatment_protocol: Plants were sprayed with 0.01% Silwet 2 hours before harvesting of leaves

tag: Columbia ecotype, 3- 4-week old plants, greenhouse-grown in 16-hour days, leaves treated with 0.01% Silwet 2 hours before harvest


title: LS-71

description: lung squamous carcinoma


title: 2-hour mock-treated leaf material biological replicate 2

description: control for salicylic-treated plants, replicate 2 of 3

source_name: leaf tissue of 3-4 week old plants, treated with 0.01% Silwet 2 hours before harvest

tag: Columbia ecotype, 3- to 4-week old plants, greenhouse-grown in 16-hour days, leaves treated with 0.01% Silwet 2 hours before harvest


title: LS-61

description: lung squamous carcinoma


title: HVB_71_F2_A: F2 mouse # 71 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: mouse whole lung gene expression, 21 days post-Sendai virus infection, CB6F2/J extreme cohorts

data_processing: Gene expression levels were assessed using oligonucleotide microarrays (Affymetrix gene chip MG U74v2) hybridized to labeled cRNA as described previously (Rozzo S et al, 2001). Differential expression was analyzed by GeneChip 3.1 software (Affymetrix) and was assessed by pairwise comparisons of samples from the 4 extreme cohorts of CB6F2/J mice. Criteria for differential expression required increases or decreases in 12 of the 16 possible pairwise comparisons. Subsequently microarrays were normalized using the GC-RMA algorithm as implemented in Bioconductor (Wu Z et al, 2004, Gentleman RC et al, 2004).

source_name: whole lung

label_protocol: Second-strand cDNA synthesis, was performed using a T7-promoter coupled oligo(d)T primer (GeneChip T7-Oligo(d)T Promoter Primer Kit, Affymetrix, Santa Clara, CA), after which an in vitro transcription (IVT) reaction was performed using an Enzo BioArray High Yield RNA transcript labeling kit (Affymetrix).

growth_protocol: Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.

extract_protocol: Mice were sacrificed 21 days post-infection with Sendai virus. Lungs were flash frozen liquid nitrogen, and subsequently, total RNA was isolated by the acid guanidinium thiocyanate-phenol-chloroform extraction method (Trizol®, Invitrogen, Carlsbad, CA).

treatment_protocol: F1-hybrid CB6F1/J mice were obtained from Jackson Laboratory. F1-hybrid mice were bred to generate an F2 intercross population (CB6F2/J).  Mice were inoculated intranasally with Sendai virus (2e5 PFU), and airway hyperreactivity was assessed 21 days post infection as previously described (Walter et al, 2002), after which mice were sacrificed and lungs were harvested, right for RNA, left for histology and analysis of goblet cell metaplasia.

tag: whole lung, 21 days post-Sendai infection, CB6F2/J


title: HVB_67_F2_A: F2 mouse # 67 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_69_F2_A: F2 mouse # 69 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-55

description: lung squamous carcinoma


title: LS-59

description: lung squamous carcinoma


title: LS-57

description: lung squamous carcinoma


title: LS-52

description: lung squamous carcinoma


title: LS-119

description: lung squamous carcinoma


title: LS-53

description: lung squamous carcinoma


title: 2-hour mock-treated leaf material biological replicate 1

description: control for salicylic-treated plants, replicate 1 of 3

tag: Columbia ecotype, 3-4 week old plants, greenhouse-grown in 16-hour days, leaves treated with 0.01% Silwet 2 hours before harvest


title: HVB_54_F2_A: F2 mouse # 54 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-51

description: lung squamous carcinoma


title: HVB_56_F2_A: F2 mouse # 56 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-47

description: lung squamous carcinoma


title: HVB_3_F2_A: F2 mouse # 3 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: LS-49

description: lung squamous carcinoma


title: LS-43

description: lung squamous carcinoma


title: LS-45

description: lung squamous carcinoma


title: HVB_44_F2_A: F2 mouse # 44 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: LS-41

description: lung squamous carcinoma


title: LS-83

description: lung squamous carcinoma


title: LS-39

description: lung squamous carcinoma


title: HVB_71_F2_B: F2 mouse # 71 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-37

description: lung squamous carcinoma


title: HVB_69_F2_B: F2 mouse # 69 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_75_F2_A: F2 mouse # 75 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_253_F2_A: F2 mouse # 253 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_221_F2_A: F2 mouse # 221 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: LS-33

description: lung squamous carcinoma


title: HVB_1_F2_A: F2 mouse # 1 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_75_F2_B: F2 mouse # 75 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_51_F2_A: F2 mouse # 51 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: LS-35

description: lung squamous carcinoma


title: HVB_67_F2_B: F2 mouse # 67 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-31

description: lung squamous carcinoma


title: LS-29

description: lung squamous carcinoma


title: LS-27

description: lung squamous carcinoma


title: HVB_56_F2_B: F2 mouse # 56 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-25

description: lung squamous carcinoma


title: HVB_51_F2_B: F2 mouse # 51 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_44_F2_B: F2 mouse # 44 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_54_F2_B: F2 mouse # 54 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-23

description: lung squamous carcinoma


title: HVB_3_F2_B: F2 mouse # 3 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: LS-21

description: lung squamous carcinoma


title: LS-17

description: lung squamous carcinoma


title: LS-19

description: lung squamous carcinoma


title: LS-13

description: lung squamous carcinoma


title: HVB_253_F2_B: F2 mouse # 253 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_56_F2_C: F2 mouse # 56 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_1_F2_B: F2 mouse # 1 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_221_F2_B: F2 mouse # 221 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_44_F2_C: F2 mouse # 44 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_54_F2_C: F2 mouse # 54 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_69_F2_C: F2 mouse # 69 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: LS-15

description: lung squamous carcinoma


title: LS-9

description: lung squamous carcinoma


title: HVB_67_F2_C: F2 mouse # 67 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: HVB_253_F2_C: F2 mouse # 253 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_3_F2_C: F2 mouse # 3 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_51_F2_C: F2 mouse # 51 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: NM2

description: Culture made from normal human infant foreskin.


title: NM1


title: LS-1

description: lung squamous carcinoma


title: HVB_221_F2_C: F2 mouse # 221 , Low Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_75_F2_C: F2 mouse # 75 , High Goblet Cell Metaplasia, High Airway Hyperreactivity


title: HVB_1_F2_C: F2 mouse # 1 , High Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: YUSIT1

description: Culture was made from a metastatic melanoma of unknown origin.


title: MNT1

description: Culture was made from a lymph node metastasis of melanoma.


title: HVB_71_F2_C: F2 mouse # 71 , Low Goblet Cell Metaplasia, Low Airway Hyperreactivity


title: YUMAC

description: Culture was made from a recurrent metastasis at the site of excision.


title: LS-5

description: lung squamous carcinoma


title: YUHEIK

description: Culture was made from a maxillary gingiva, lymph node metastasis of melanoma.

value: metastatic melanoma


title: MDAMB231_DHA treated 6hr

status: Public on Mar 29 2006

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: Human Breast cancer cells, nameley MDA-MB231, MDA-MB435, MCF-7 and HCC2218 were seeded in lab. Samples were treated by 10uM fatty acids (arachidonic acid (AA) or linoleic Acid (LA) or eicosapentaenoic acid (EPA) or docosahexanoic acid (DHA)) for 6hr and 24hr respectively. The treated and control cells of each time point were colleced at same time. The total RNA for Ch1 and Ch2 was Reverse Transcribed and Hybridized using The MicromaxÔ Tyramide Signal Amplification (TSA)Ô Labeling and Detection Kit (PerkinElmer, Inc., MA). The Hybridization time and temperature was 16hr and 55c respectively.

data_processing: Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.0 (Agilent Tech., CA).

source_name: Commercially available Breast Cancer cells (Control or treated by different fatty acids)

tag: RNA isolation was accomplished by Trizol isolation method (Invitrogen, CA)

source_name: Reference RNA

tag: Reference RNA bought from Strategen, Inc, CA


title: MDAMB231_Control 6hr


title: MDAMB231_EPA treated 24hr


title: MDAMB231_LA treated 6hr


title: MDAMB231_DHA treated 24hr


title: WW165

description: Culture was made from a 2.25 mm lesion removed from the back.

value: primary melanoma


title: MDAMB231_Control 24hr


title: YUCAL

description: Culture was made from a soft tissue metastasis of melanoma.

source_name: metastatic melanoma culture


title: MDAMB435_LA treated 6hr


title: MDAMB231_EPA treated 6hr


title: MDAMB231_LA treated 24hr


title: MDAMB435_EPA treated 6hr


title: MCF-7_LA treated 6hr

description: Human brest cancer cells, nameley MDA-MB231, MDA-MB435, MCF-7 and HCC2218 were seeded in lab. Samples were treated by 10uM fatty acids (arachidonic acid (AA) or linoleic Acid (LA) or eicosapentaenoic acid (EPA) or docosahexanoic acid (DHA)) for 6hr and 24hr respectively. The treated and control cells of each time point were colleced at same time. The total RNA for Ch1 and Ch2 was Reverse Transcribed and Hybridized using The MicromaxÔ Tyramide Signal Amplification (TSA)Ô Labeling and Detection Kit (PerkinElmer, Inc., MA). The Hybridization time and temperature was 16hr and 55c respectively.


title: MDAMB435_AA treated 24hr


title: MDAMB435_Control 24hr


title: MDAMB435_DHA treated 6hr


title: MDAMB435_AA treated 6hr


title: MDAMB231_AA treated 24hr


title: MDAMB435_EPA treated 24hr


title: MDAMB435_LA treated 24hr


title: MCF-7_EPA treated 6hr


title: MCF-7_DHA treated 6hr


title: MDAMB231_AA treated 6hr


title: MCF-7_LA treated 24hr


title: MCF-7_EPA treated 24hr


title: MCF-7_DHA treated 24hr


title: MDAMB435_Control 6hr


title: HCC-2218_DHA treated 24hr


title: HCC-2218_LA treated 24hr


title: MCF-7_AA treated 6hr


title: HCC-2218_EPA treated 6hr


title: MCF-7_Control 6hr


title: HCC-2218_EPA treated 24hr


title: HCC-2218_AA treated 6hr


title: MDAMB435_DHA treated 24hr


title: HCC-2218_LA treated 6hr


title: HCC-2218_Control 24hr


title: MCF-7_AA treated 24hr


title: MCF-7_Control 24hr


title: HCC-2218_Control 6hr


title: wild-type glia vehicle-treated 4hrs replicate 2

status: Public on Mar 25 2006

city: Manchester

first: Ralph

last: Andre

address: Michael Smith Building, Oxford Road

department: Faculty of Life Sciences

country: United Kingdom

institute: University of Manchester

hyb_protocol: Church hybridization

scan_protocol: ArrayVision 5.1 (Molecular Dynamics) phospho-image analysis

data_processing: intensity, normalized against average intensity of control spots

source_name: primary mixed glial cells

label_protocol: reverse transcription of DNAse-treated RNA to incorporate radio-labelled dCTP

growth_protocol: cells maintained post-isolation for 10-12 days prior to treatment

extract_protocol: TRIzol (Invitrogen)

treatment_protocol: vehicle for 4 hrs prior to RNA extraction

tag: C57/BL6 x 129sv, 0-2 days old


title: HCC-2218_AA treated 24hr


title: HCC-2218_DHA treated 6hr


title: HepG2-S-G2_Day 8

status: Public on Mar 28 2006

city: Shanghai

first: Xiaochen

last: Tian

address: No.138 Yixueyuan Road

department: Shanghai Medical college

country: China

institute: Fudan University

description: Plasmid pCMV-S was transfected into HepG2 cells. After screened by G418, stable cell clones were selected and used for array.

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Affymetrix

source_name: pCMV-S transfected HepG2 cell, cultured for 8 days

label_protocol: Standard Affymetrix labelling protocol

growth_protocol: Maintained in Dulbeccco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 250µg/ml G418, 100U/ml penicillin, 100µg/ml streptomycin, 2mM glutamine, 25mM HEPES solution, and 1mM sodium pyruvate at 37℃ under 5% CO2.

extract_protocol: Standard extraction protocol according to the TRIzol reagent manual.

tag: Plasmid pCMV-S transfected HepG2 cells, cultured for 8 days before array assay.


title: wild-type glia vehicle-treated 4hrs replicate 3


title: HepG2-Neo-F4_Day 8

description: Plasmid pCMV was transfected into HepG2 cells. After screened by G418, stable cell clones were selected and used for array.

source_name: pCMV transfected HepG2 cell, cultured for 8 days

tag: Plasmid pCMV transfected HepG2 cells, cultured for 8 days before array assay.


title: HepG2-Neo-F4_Day 4

description: Plasmid pCMV was transfected into the HepG2 cells. After screened by G418, stable cell clones were selected and used for array.

data_processing: Affymetrix "Statistical Algorithms Reference Guide" describes the details of data processing

source_name: pCMV transfected HepG2 cell, cultured for 4 days

tag: Plasmid pCMV transfected HepG2 cells, cultured for 4 days before array assay.


title: wild-type glia vehicle-treated 4hrs replicate 1


title: HepG2-S-G2_Day 4

source_name: pCMV-S transfected HepG2 cell, cultured for 4 days

tag: Plasmid pCMV-S transfected HepG2 cells, cultured for 4 days before array assay.


title: wild-type glia IL-1β-treated 4hrs replicate 1

treatment_protocol: 10 ng/ml rrIL-1β for 4 hrs prior to RNA extraction


title: IL-1R1-/- glia IL-1β-treated 4hrs replicate 3

tag: IL-1R1-/-, 0-2 days old


title: wild-type glia IL-1β-treated 4hrs replicate 3


title: IL-1R1-/- glia vehicle-treated 4hrs replicate 2

tag: IL-1R-/-, 0-2 days old


title: IL-1R1-/- glia IL-1β-treated 4hrs replicate 2

treatment_protocol: 10 ng/ml IL-1β for 4 hrs prior to RNA extraction


title: Grown under 300 μM initial iron condition

status: Public on Mar 24 2006

city: Koganei

first: Tadashi

last: Matsunaga

state: Tokyo

department: Biotechnology

institute: Tokyo University of Agriculture and Technology

description: Five micrograms of purified RNA was reverse transcribed using random 6-mer primers and the fluorochromes Cy3 dUTP and Cy5 dUTP. Cy3–labeled cDNAs (from mRNA of cells grown under several iron condition) and Cy5–labeled cDNAs (from mRNA of cells grown under 0.1 μM iron: reference condition). Deatails of the sample and experiment can be found in the publications Suzuki et al., The Journal of Bacteriology “Global gene expression analysis of iron-inducible genes in Magnetospirillum magneticum AMB-1”.

data_processing: Mean ratios of normalized intensities defined as ch1 divided by ch2.

organism: Paramagnetospirillum magneticum AMB-1

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 300 μM initial iron condition.

source_name: Grown under 0.1 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 0.1 μM initial iron condition.


title: Grown under 150 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 150 μM initial iron condition.


title: Grown under 200 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 200 μM initial iron condition.


title: Grown under 100 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 100 μM initial iron condition.


title: Grown under 80 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 80 μM initial iron condition.


title: plus 100nM RA treatment, 24h, replicate 1 (affy)

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Stem Cell and Developmental Biology

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: All Chip hybridization, processing and scanning was done according to standard Affymetrix protocols.

data_processing: Raw data from a scanner consist of probe level data. A probe set contains 15 probe pairs and each probe pair consists of a perfect match and a mismatch probe. Affymetrix MAS version 5 was used to produce signal and signal detection calls. The resulting signals were log-transformed with base 2. A linear normalization with trimmed mean was employed to normalize signals across different experimental conditions. Mean signals of duplicate chips in each group were used for fold change computation. One-way analysis of variance was conducted and planned pairwise comparisons were performed for each miRNA with respect to Day 0. All the statistical computations were conducted using SAS« and S-Plus«. Data extraction and processing protocols were done on the Agilent scanner for Affymetrix(www.affymetrix.com). All Normalizations, transformations and data selection procedures and parameters were done using Affymetrix MAS.5 and GECOS software and algorithm (www.affymetrix.com)

source_name: E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)

label_protocol: 10 micrograms of total RNA was dephosphorylated with shrimp alkaline phosphatase (SAP, Invitrogen; 37degrees C, 40 min), followed by SAP inactivation (65degrees C, 40 min). The dephosphorylated RNA was biotin end-labeled (NEN biotin-N4 û CTP, NEL-510) with T4 RNA ligase (100 U/ml) in the presence of 40% polyethylene glycol (PEG) (37degrees C, 2 h).

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 24h  were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).

tag: mouse embryonic stem cell


title: plus 100nM RA treatment, 24h, replicate 2 (affy)

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 24h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: IL-1R1-/- glia IL-1β-treated 4hrs replicate 1


title: Grown under 250 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 250 μM initial iron condition.


title: minus RA treatment replicate 1 (affy)

description: minus RA treatment replicate 1

extract_protocol: Total RNA from Mouse embryonic stem cells without all-trans retinoic acid induction were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: minus RA treatment replicate 2 (affy)

description: minus RA treatment replicate 2


title: plus 100nM RA treatment, 96h, replicate 1 (affy)

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 96h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: plus 100nM RA treatment, 96h, replicate 2 (affy)


title: wild-type glia IL-1β-treated 4hrs replicate 2


title: Grown under 20 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 20 μM initial iron condition.


title: IL-1R1-/- glia vehicle-treated 4hrs replicate 3


title: KO_1A

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: mCftr-|-

data_processing: raw data from experiment is provided

label: biotinylate

tag: Strain

value: Mixture of FVB/N and C57BL/6


title: Grown under 40 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) grown under 40 μM initial iron condition.


title: WT_1A

description: mCftr+|+


title: IL-1R1-/- glia vehicle-treated 4hrs replicate 1


title: Thalamus_Reverse

city: Urbana

first: Mark

middle: Robert

last: Band

address: 1201 W. Gregory Dr

institute: University of Illinois

description: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized overnight at 42C

data_processing: Value = log2 ratio of background corrected 632 median/background corrected 532 median

organism: Bos taurus

source_name: Universal Control 635

tag: Total RNA from bovine cell cultures of :

tag: Brain

tag: EBTR (tracheal cell line)

tag: MDBK (kidney cell line)

tag: BL-30 (lymphocyte line)

source_name: Thalamus 532

tag: Male, 2 week old Jersey calf


title: Thymus_Reverse

source_name: Thymus 532


title: Thymus_Forward

source_name: Thymus 635

source_name: Universal Control 532


title: Skin_Forward

source_name: Skin 635


title: Testis_Reverse

source_name: Testis 635


title: Spleen_Reverse

source_name: Spleen 532


title: Placentome_Forward

source_name: Placentome 635

tag: IVF male holstein cow at term. Delivery by ceasarian section.


title: Lymph_Node_Reverse

source_name: Lymph Node 532


title: Kidney_Reverse2

source_name: Kidney 532


title: Drosophila heads_Chronic group_biological rep6_RD01D024

city: Houston

first: Zhiyong

last: Yang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Gene expression data from whole heads of flies treated with humidified air for 50 min followed by 5 exposures of 50% ethanol vapor for 40 min

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

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

data_processing: The raw data of the 18 microarray were imported to dChip program (version 1.3). The arrays were normalized to a common baseline array that has the median overall brightness. The expression value for each probe set on each chip was then calculated as model-based expression index (MBEI) by Perfect Match-only model.

organism: Drosophila melanogaster

source_name: Heads of Drosophila received humidified air for 50 min followed by 5 exposures of 50% ethanol vapor for 40 min

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

growth_protocol: Flies were maintained on a 12 hr dark/12 hr light cycle on standard Drosophila medium at 25°C and 60% relative humidity.

extract_protocol: Whole heads of Canton-S flie were seperated from bodies using liquid nitrogen freezing and sieve (0.710 mm) seperation. About 60 seperated whole fly heads were homoginized in 0.5 ml Trizol (Invitrogen). Then 0.1 ml chloroform was added. After vigorous vortexing and centrifugation at 12,000 g for 15 minuntes, 0.28 ml of the aquous phase sample was transfered to a new tube, mixed with 0.25 ml 2-isopropanol, then loaded on a RNeasy column (Qiagen), the RNA sample was further purified by the RNeasy kit.

treatment_protocol: Drosophila was treated with humidified air for 50 min followed by 5 exposures of 50% ethanol vapor for 40 min.

tag: Genotype

value: Canton-S

tag: Age

value: 2-5 days


title: Drosophila heads_Chronic group_biological rep4_RD01D022


title: Drosophila heads_Chronic group_biological rep5_RD01D023


title: Vts1 IP (slide 0713)

type: mixed

city: Toronto

first: Tzvi

last: Aviv

state: Ontario

address: 600 University

country: Canada

institute: Lunenfeld institute

description: Coimmunoprecipitated RNA and 30 mg of total RNA was reverse transcribed to cDNA with SuperScript II (Invitrogen) using random primers and directly labeled with dCTP conjugated to either Cy3 or Cy5. Differentially labeled cDNA preparations were pooled, heated to 65°C for 2 min, then cooled to 50°C. Hybridization to cDNA microarrays (University of Toronto Microarray Center) was performed overnight at 37°C in a 20:1:1 ratio of DIG-Easy Hybe solution (Roche) : yeast tRNA(10 mg ml–1) : ssDNA (10 mg ml–1). Arrays were rinsed three times in wash buffer (2xSSC, 0.2% (w/v) SDS) for 10 minutes at 37° followed by a rinse in 0.1xSSC at room temperature and a gentle spin. Scanning was performed with a GenePix 4000B instrument (Axon Instruments).

data_processing: Abnormally shaped spots were deleted from our analysis. Spot intensities were quantitated and backgrounds subtracted with the Quantarray 1.0 software package (GSI Lumonics). Enrichment ratios were calculated from normalized intensities in the IP channel over the intensities in the total RNA channel

molecule: other

organism: Saccharomyces cerevisiae

source_name: Vts1-FLAG IP

tag: Yeast cells (vts1Δ) bearing pGAL1-VTS1-FLAG expression plasmids were grown in SC–Leu medium containing 2% (w/v) raffinose to an OD600 of 0.6. Expression was induced with 0.2% (w/v) galactose (added directly) for 2 hours. Cells were then harvested by centrifugation, washed and resuspended in lysis buffer containing 50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM MgCl2, 50 mM β-glycerophosphate, 20 mM NaF, 2 mM benzamidine, 0.5% (v/v) Triton X-100, 0.5mM DTT, 10 µg ml–1 leupeptin, 2 µg ml–1 aprotinin, 0.2mM AEBSF, 1mM PMSF, 1 µg ml–1 pepstatin A, 20 mM Vandyl complexes (Sigma R3380), 0.2 mg ml–1 heparin (sigma H4784), and 200 u ml–1 Rnasin (Promega N2111). Cell pellets were lysed by the glass bead method 53. Cell extracts were clarified by centrifugation at 14,000 rpm for 30 minutes and incubated with 100 µl of anti-FLAG- sepharose resin (Sigma-Aldrich) for 2 h at 4 ºC. Resin was then washed three times with wash buffer (50mM HEPES pH 7.5, 150mM NaCl, 1mM EDTA, 10mM MgCl2, 50mM β-glycerophosphate, 5% (v/v) glycerol, 0.1% (v/v) Triton X-100, 0.5mM DTT, 0.2mM AEBSF) and twice with wash buffer without Triton X-100. FLAG-tagged protein complexes were eluted twice by 15 min incubations at room temperature with 200 µg ml–1 FLAG peptide (DYKDDDDK, Sigma). RNA was extracted from the affinity purified FLAG-tagged protein complexes using phenol/chloroform and precipitated with ethanol and the addition of glycogen.

source_name: Total RNA

tag: Yeast cells (vts1Δ) bearing pGAL1-VTS1-FLAG expression plasmids were grown in SC–Leu medium containing 2% (w/v) raffinose to an OD600 of 0.6. Expression was induced with 0.2% (w/v) galactose (added directly) for 2 hours. Cells were then harvested by centrifugation, washed and resuspended and lysed by the glass bead. Total RNA was extracted by phenol/chloroform.


title: Small_Intestine_Reverse

source_name: Small Intestine 532


title: Muscle_Forward

source_name: Muscle 635


title: Liver_Forward

source_name: Liver 635


title: Testis_Forward


title: Skin_Reverse

source_name: Universal Control 635

source_name: Skin 532


title: Placentome_Reverse

source_name: Placentome 532

tag: IVF male holstein at term delivered by cesearian section.


title: Vts1 IP (slide 0744)

description: Coimmunoprecipitated RNA and 30 mg of total RNA was reverse transcribed to cDNA with SuperScript II (Invitrogen) using random primers and directly labeled with dCTP conjugated to either Cy3 or Cy5.  Differentially labeled cDNA preparations were pooled, heated to 65°C for 2 min, then cooled to 50°C. Hybridization to cDNA microarrays (University of Toronto Microarray Center) was performed overnight at 37°C in a 20:1:1 ratio of DIG-Easy Hybe solution (Roche) : yeast tRNA(10 mg ml–1) : ssDNA (10 mg ml–1).  Arrays were rinsed three times in wash buffer (2xSSC, 0.2% (w/v) SDS) for 10 minutes at 37° followed by a rinse in 0.1xSSC at room temperature and a gentle spin.  Scanning was performed with a GenePix 4000B instrument (Axon Instruments).

data_processing: Abnormally shaped spots were deleted from our analysis. Spot intensities were quantitated and backgrounds subtracted with the Quantarray 1.0 software package (GSI Lumonics).  Enrichment ratios were calculated from normalized intensities in the IP channel over the intensities in the total RNA channel

tag: Yeast cells (vts1Δ) bearing pGAL1-VTS1-FLAG expression plasmids were grown in SC–Leu medium containing 2% (w/v) raffinose to an OD600 of 0.6. Expression was induced with 0.2% (w/v) galactose (added directly) for 2 hours.  Cells were then harvested by centrifugation, washed and resuspended in lysis buffer containing 50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM MgCl2, 50 mM β-glycerophosphate, 20 mM NaF, 2 mM benzamidine, 0.5% (v/v) Triton X-100, 0.5mM DTT, 10 µg ml–1 leupeptin, 2 µg ml–1 aprotinin, 0.2mM AEBSF, 1mM PMSF, 1 µg ml–1 pepstatin A, 20 mM Vandyl complexes (Sigma R3380), 0.2 mg ml–1 heparin (sigma H4784), and 200 u ml–1 Rnasin (Promega N2111). Cell pellets were lysed by the glass bead method 53. Cell extracts were clarified by centrifugation at 14,000 rpm for 30 minutes and incubated with 100 µl of anti-FLAG- sepharose resin (Sigma-Aldrich) for 2 h at 4 ºC. Resin was then washed three times with wash buffer (50mM HEPES pH 7.5, 150mM NaCl, 1mM EDTA, 10mM MgCl2, 50mM β-glycerophosphate, 5% (v/v) glycerol, 0.1% (v/v) Triton X-100, 0.5mM DTT, 0.2mM AEBSF) and twice with wash buffer without Triton X-100. FLAG-tagged protein complexes were eluted twice by 15 min incubations at room temperature with 200 µg ml–1 FLAG peptide (DYKDDDDK, Sigma). RNA was extracted from the affinity purified FLAG-tagged protein complexes using phenol/chloroform and precipitated with ethanol and the addition of glycogen.

tag: Yeast cells (vts1Δ) bearing pGAL1-VTS1-FLAG expression plasmids were grown in SC–Leu medium containing 2% (w/v) raffinose to an OD600 of 0.6. Expression was induced with 0.2% (w/v) galactose (added directly) for 2 hours.  Cells were then harvested by centrifugation, washed and resuspended and lysed by the glass bead. Total RNA was extracted by phenol/chloroform.


title: Small_Intestine_Forward

source_name: Small Intestine 635


title: Kidney_Reverse


title: Lung_Reverse

source_name: Lung 635

source_name: Universal Control 532


title: Rumen_Reverse

source_name: Rumen 532


title: Lung_Forward


title: Muscle_Reverse

source_name: Muscle 532


title: Liver_Reverse

source_name: Liver 532


title: Lymph_Node_Forward

source_name: Lymph_Node 635


title: Large_Intestine_Forward

source_name: Large_Intestine 635


title: Large_Intestine_Reverse

source_name: Large_Intestine 532


title: Drosophila heads_Chronic group_biological rep2_RD01D020

source_name: Heads of Drosophila received humidified air for 50 min followed by 5 exposures of 50% ethanol vapor for 40 min


title: Drosophila heads_Fast group_biological rep5_RD01D017

description: Gene expression data from whole heads of flies treated with humidified air for 50 min followed by a single exposure of 50% ethanol vapor for 40 min

source_name: Heads of Drosophila received humidified air for 50 min followed by a single exposure of 50% ethanol vapor for 40 min.

treatment_protocol: Drosophila was treated with humidified air for 50 min followed by a single exposure of 50% ethanol vapor for 40 min, then flash frozen in liquid nitrogen.


title: Drosophila heads_Chronic group_biological rep1_RD01D019


title: Drosophila heads_Fast group_biological rep6_RD01D018


title: Drosophila heads_Naïve group_biological rep4_RD01D010

description: Gene expression data from whole heads of flies treated with humidified ari (30 ml/min) for 50 min

source_name: Heads of Drosophila received humidified air (30 ml/min) for 50 min

treatment_protocol: Drosophila was treated with humidified air (30ml/min) for 50 min, then flash frozen in liquid nitrogen.


title: Drosophila heads_Chronic group_biological rep3_RD01D021


title: Drosophila heads_Fast group_biological rep2_RD01D014


title: Drosophila heads_Naïve group_biological rep3_RD01D009


title: Drosophila heads_Fast group_biological rep4_RD01D016


title: Drosophila heads_Fast group_biological rep3_RD01D015


title: Cerebrum_Reverse

source_name: Cerebrum 532


title: Kidney_Forward

source_name: Kidney 635


title: Heart_Reverse

source_name: Universal Control 635


title: Drosophila heads_Naïve group_biological rep2_RD01D008


title: Cerebrum_Forward

source_name: Cerebrum 635


title: Drosophila heads_Naïve group_biological rep5_RD01D011


title: Cerebellum_Reverse

source_name: Cerebellum 532


title: Heart_Forward

source_name: Heart 635


title: Drosophila heads_Fast group_biological rep1_RD01D013


title: Drosophila heads_Naïve group_biological rep1_RD01D007


title: Drosophila heads_Naïve group_biological rep6_RD01D012


title: Cerebellum_Forward

source_name: Cerebellum 635


title: Adrenal_Reverse

source_name: Adrenal gland 532


title: HE_3

description: Heteozygous SP-C-hCFTR+|-

value: FVB/N

value: SP-C-hCFTR+|-/mCftr+|+


title: Blood_Forward

source_name: Blood 635

source_name: Universal Control 532


title: Adrenal_Forward

source_name: Adrenal gland 635


title: WT_4A

description: FABP-hCFTR+|-/mCftr+|+


title: HO_2

description: Homozygous SP-C-hCFTR+|-

value: SP-C-hCFTR+|+/mCftr+|+


title: HE_2

description: Heteozygous SP-C-hCFTR+|-


title: Rumen_Forward

source_name: Rumen 635


title: WT_3B

description: FABP-hCFTR+|-/mCftr+|+


title: WT_2b

description: mCftr+|+


title: HE_1

description: Heteozygous SP-C-hCFTR+|-


title: KO_3A

description: FABP-hCFTR+|-/mCftr-|-


title: KO_4A

description: FABP-hCFTR+|-/mCftr-|-


title: KO_3B

description: FABP-hCFTR+|-/mCftr-|-


title: WT2

description: WT

value: mCftr+|+


title: HO_3

description: Homozygous SP-C-hCFTR+|+


title: HO_1

description: Homozygous SP-C-hCFTR+|+


title: 2d-sham-71

city: Columbus

first: Sashwati

last: Roy

institute: Ohio State University

description: Rat underwent sham surgery for LAD occlusion/reperfusion. sample collected 2d after surgery to control for 2d IR.

source_name: rat heart

tag: rat heart ventricle


title: WT1

description: WT

tag: Strain


title: WT3

description: WT


title: 2d-sham-72


title: 7d-sham-82

description: Rat underwent sham surgery for LAD occlusion/reperfusion. sample collected 7d after surgery to control for 7d IR.


title: 7d-Sham-81

source_name: Rat Heart

tag: Rat heart ventricle


title: 2d-sham-74


title: WT_3A

description: FABP-hCFTR+|-/mCftr+|+


title: 7d-sham-80

description: sham surgery was performed - LAD was not ligated. sample collected after 7d surgery to control for the 7d - IR rats.


title: 2d-IR-76

description: LAD was ligated for 30 min followed by repefusion. sample collected after 2d of reperfusion.


title: KO_2b

description: mCftr-|-


title: Spleen_Forward

source_name: Spleen 635

tag: Total RNA from bovine cell cultures of :


title: 2d-IR-73


title: WT_2

description: mCftr+|+


title: 7d-IR-48

description: LAD was ligated for 30 min followed by repefusion. sample collected after 7d of reperfusion.

source_name: Rat heart


title: 2d-IR-69


title: Aorta_untreated_20hr_rep3b

status: Public on Mar 23 2006

city: Seattle

first: Alfred

middle: C

last: Aplin

state: WA

address: Box 357470 HSB-UW

department: Pathology

institute: University of Washington

description: RNA labeling, array hybridization, scanning, and initial data transformation done at the Center for Expression Arrays at the Univesity of Washington.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label: Phycoerythrin

source_name: thoracic aorta, untreated, 20hr

label_protocol: Standard Affymetrix

growth_protocol: Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 14 days in serum free-EBM, changing medium every third day.

extract_protocol: Four to Six individual rings combined, snap frozen in liquid nitrogen, crushed and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment. Total RNA eluted into DEPC water.

value: Fisher 344

tag: Gender

value: Male

value: 5 weeks

tag: Tissue

value: Thoracic aorta


title: Aorta_VEGF_20hr_rep3b

source_name: thoracic aorta, VEGF treated, 20hr

growth_protocol:
Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 13 days in serum free-EBM, changing medium every third day.

On day 13 , recombinant human VEGF protein (R&D Systems #293-VE) added to the culture at a final concentration of 10ng/ml in 0.5ml EBM

extract_protocol: 20 hours after treatment with VEGF, four to six individual rings were combined, snap frozen in liquid nitrogen, crushed, and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment. Total RNA eluted into DEPC water.


title: Aorta_VEGF_20hr_rep1a


title: ungerminated vs germinated lily pollen

city: Siena

first: Cecilia

last: Del Casino

address: Via Mattioli 4

department: Scienze Ambientali "G.Sarfatti"

country: Italy

institute: Università di Siena

description: ungerminated vs germinated pollen of Lilium longiflorum L.

organism: Lilium longiflorum

source_name: ungerminated pollen

source_name: germinated pollen


title: Aorta_VEGF_20hr_rep1b


title: 7d-IR-44

description: LAD was occluded for 30 min followed by reperfusion. Ventricle was collected after 7d of reperfusion.


title: Aorta_VEGF_20hr_rep2b

growth_protocol:
Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 13 days in serum free-EBM, changing medium every third day.

On day 13 , recombinant human VEGF protein (R&D Systems #293-VE) added to the culture at a final concentration of 10ng/ml in 0.5ml EBM.


title: Aorta_Ang1_20hr_rep1a

source_name: thoracic aorta, Ang1 treated, 20hr

growth_protocol:
Thoracic aorta dissected, cut into 2mm rings, washed 12 times in serum free EBM (Cambrex BioScience) and cultured for 13 days in serum free-EBM, changing medium every third day.

On day 13 , recombinant human angiopoietin-1 protein (R&D Systems #923-AN) added to the culture at a final concentration of 100ng/ml in 0.5ml EBM containing 5ug/ml poly-His antibody (R&D Systems #MAB050).

extract_protocol: 20 hours after treatment with Ang-1, four to six individual rings were combined, snap frozen in liquid nitrogen, crushed, and extracted with Trizol reagent (Invitrogen) followed by RNAEasy Micro kit (Qiagen) purification with DNAse I treatment. Total RNA eluted into DEPC water.


title: KO_2

description: FABP-hCFTR+|-/mCftr-|-

value: FABP-hCFTR+|-/mCftr-|-


title: Aorta_Ang1_20hr_rep3a


title: 7d-IR-47


title: Aorta_untreated_20hr_rep2b


title: Aorta_untreated_20hr_rep1b

label_protocol: Standard Affymetrix "two-cycle" target labeling


title: Vts1 IP (slide 4976)

data_processing: Abnormally shaped spots are flagged. Spot intensities were quantitated and backgrounds subtracted with the Quantarray 1.0 software package (GSI Lumonics). Enrichment ratios were calculated from unnormalized and unaveraged intensities in the IP channel over the intensities in the total RNA channel

source_name: Vts1 IP

source_name: Total RNA


title: Vts1 IP (slide 4798)


title: Aorta_VEGF_20hr_rep2a


title: Aorta_Ang1_20hr_rep1b

source_name: thoracic aorta, ang-1 treated, 20hr


title: Aorta_VEGF_20hr_rep3a


title: Aorta_Ang1_20hr_rep2a


title: Aorta_Ang1_20hr_rep2b