title: eco_0.26_0.11

status: Public on Sep 02 2010

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

description: Investigation of specific growth rate dependent gene expression changes of E. coli growing on glucose minimal medium

hyb_protocol: For hybridization standard Agilent's kits, reagents and equipment were used (See http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/Pages/default.aspx )

scan_protocol: Agilent Technologies Microarray Scanner G2565CA was used at 5 mm resolution

data_processing: Image was analized with Genepix 6 pro followed by background substration and global LOWESS normalization in R environment (KTH package). Spots with signal to noise ratio lower that 3 and/or relative standard deviation between parallel spots greater than 20% were removed.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: specific growth rate 0.26 1/h

label_protocol: cDNA was synthesized from 15 μg of total RNA at 46ºC overnight using the following reagents per reaction: 1 μg random primers (Random decamers; Invitrogen, Carlsbad, CA), 6 μL 5 x first strand buffer (Invitrogen), 3 μL 0.1 MDTT (Invitrogen), 0.9 μL dNTPs (final concentrations: dATP 0.5 mM, dCTP 0.5 mM, dGTP 0.5 mM, dTTP 0.3 mM, aminoallyl-dUTP 0.2 mM), 1 μL RNase Inhibitor (Bioron, Ludwigshafen, Germany), 2 μL Superscript III (Invitrogen). RNA strands were hydrolyzed in the samples by adding 4.5 μL 1 M NaOH and incubating at 70ºC for 10 min, after incubation the samples were neutralized with 4.5 μL 1 M HCl. cDNA was purified with MinElute PCR purification kit (QIAGEN) and labeled with Cy3 (CyTM3 Mono Reactive Dye Pack, Amersham, Buckinghamshire, UK) or Cy5 (CyTM5 Mono Reactive Dye Pack, Amersham). Staining was carried out in 10 μL of NaHCO3 (pH 9) at room temperature in dark for 1 h and the samples were purified again with MinElute PCR purification kit.

growth_protocol: Escherichia coli K12 MG1655 was cultivated using M9 minimal medium containing 4.5 g/L α-(D)-glucose, pH = 7, temperature 37 ºC, aerobic conditions

extract_protocol: Total RNA was extracted with Qiagen's Rneasy Mini Kit

treatment_protocol: RNA degradation was stopped using Qiagen's RNAprotect reagent

tag: cultivation

value: continuous cultivation, A-stat

source_name: specific growth rate 0.11 1/h

value: continuous cultivation, chemostat


title: eco_0.31_0.11

type: RNA

molecule: total RNA

source_name: specific growth rate 0.31 1/h


title: eco_0.40_0.11

source_name: specific growth rate 0.40 1/h


title: Astat_chemostat

description: Comparison of A-stat and chemostat culture to study the gene expression bias caused by continuous change of dilution rate

source_name: A-stat, specific growth rate 0.48 1/h

source_name: chemostat, specific growth rate 0.51 1/h


title: eco_0.36_0.11

source_name: specific growth rate 0.36 1/h


title: Gene expression profiles of Lkb1 KO #4 HSCs

status: Public on Dec 01 2010

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

country: USA

institute: MD Anderson Cancer Center

description: Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #4 HSCs.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: MAS5.0 was used to normalize arrays and to compute expression indices. Briefly, raw probe intensities were normalized across profiles. Expression values for each probe set were summarized. Differentially expressed probe sets were selected based on fold change as well as modified t-statistics after adjusting for multiple tests.

label: Biotin

organism: Mus musculus

source_name: LSK (Lin-, Sca-1+, c-Kit+) cells sorted from Lkb1 KO bone marrow cells

label_protocol: Approximately 10 ng of total RNA was first amplified by The RiboAmp® HS PLUS RNA Amplification Kit (Arcturus) and then processed to produce biotinylated cRNA targets.

extract_protocol: Bone marrow LSK cells were sorted from mice at 1 DPI (15,000-20,000 cells/sample). RNA from sorted LSK cells was extracted using PicoPure RNA Isolation Kit (Molecular Devices) per manufacturer's instructions, and cDNA was prepared utilizing Superscript II Rnase H-Reverse transcriptase (Invitrogen).

treatment_protocol: To achieve somatic deletion of Lkb1 in mouse, we generated Lkb1 L/L, rosa26CreERT2 mice. In this model, the treatment of adult Lkb1 L/L, rosa26CreERT2 mice with tamoxifen results in efficient deletion of Lkb1 (Lkb1 KO mice) in hematopoietic organs and cells, including HSC-enriched LSK cells. At 1 day post completing tamoxifen injection (DPI), we prepared single cell suspensions form bone marrow (from femoral and tibial bones), and stained and sorted LSK populations using FACSAria (Becton Dickinson, Mountain View, CA).

tag: strain

tag: genotype

value: Lkb1 knockout

tag: tissue

value: bone marrow from femoral and tibial bones

tag: cell type

value: LSK (Lin-, Sca-1+, c-Kit+) cells


title: eco_0.48_0.11

source_name: specific growth rate 0.48 1/h


title: eco_0.21_0.11

source_name: specific growth rate 0.21 1/h


title: Day 12, biological rep2

status: Public on Jul 21 2010

city: PITTSBURGH

first: Dongwan

middle: Don

last: Kang

state: PA

address: 130 DeSoto Street

institute: University of Pittsburgh

description: Gene expression data from infected lung at T12

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

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

data_processing: The data were analyzed with GC-RMA

label: biotin

source_name: M.tuberculosis-infected at T12

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

growth_protocol: Mice were infected with 100 CFU M.tuberculosis H37Rv  and on different time points post infections, RNA was extracted from lungs

extract_protocol: RNA was extracted using RNEasy kit (Qiagen) according to manufacturer's instrcutions

treatment_protocol: On D12, 15 and D21 RNA was extracted and proceesed

tag: time

value: Day 12

tag: infection

value: lung


title: Paneth-Cell vs Stem-Cell sort_2

status: Public on Nov 29 2010

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction Software (V.9.5.3, Agilent Technologies).

source_name: FACS sorted epithelial intestinal cells cells from Lgr5-EGFP-ires-CreERT2 mice

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Intestinal cell fractions from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations: stem cells were sorted based on high level of GFP expression (GFPhi) and Paneth cells were sorted based on high level of CD24 expression (CD24hi) and high side-scatter (SSChi).

extract_protocol: Rna was isolated using Trizol (Invitrogen)

tag: cell phenotype

value: GFPhi

value: intestinal stem cell

value: paneth cell


title: Day 21, biological rep1

description: Gene expression data from infected lung at T21

source_name: M.tuberculosis-infected at T21

value: Day 21


title: Day 15, biological rep4

description: Gene expression data from infected lung at T15

source_name: M.tuberculosis-infected at T15

value: Day 15


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547201_95709

status: Public on Sep 25 2010

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description:
Liver toxicants vs. non-toxicants based on overall necrosis score
MAQC_Distribution_Status: MAQC_T -- Training

hyb_protocol: The biotin-labeled cRNA was fragmented and hybridized to the Rat Genome 230 2.0 Array (Affymetrix, Inc.) for 17 hours, prior to washing and scanning.

scan_protocol: Data were extracted from scanned images using the Affymetrix Scanner and GeneChip Operating Software (Affymetrix, Inc.).

data_processing: Affymetrix MAS5

organism: Rattus norvegicus

source_name: Liver

label_protocol: 1 μg of total RNA from the left liver lobe of each individual rat was labeled using the GeneChip One-Cycle Target Labeling kit (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocol.

growth_protocol: F344/N male rats grow to 10-12 weeks old before exposed to one of eight hepatotoxicants

extract_protocol: Total RNA was isolated from the flash frozen portion of the left lateral liver lobe using RNeasy Midi columns (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Rats were exposed for 6, 24 or 48 hours to a low, medium or high dose of one of eight hepatotoxicants. All animals were fasted for 12-18 hours prior to exposure.

value: left lateral liver lobe

tag: gender

value: male

tag: age

value: 10-12 weeks

tag: compound

value: Diquat Dibromide

tag: hybdate

tag: route

tag: vehicle

value: PBS

tag: control

value: N

tag: dose

value: 10 mg/kg

tag: time of exposure

value: 24 hours

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: B cell  iPSC at p16 , clone 3

status: Public on Jul 20 2010

city: Boston

first: Jose

middle: Maria

last: Polo

state: MA

address: 85 Cambridge Street, CPZN 4200

department: Cancer Center

institute: MGH

hyb_protocol: Biotinylated cRNA was cleaned up, fragmented and hybridized to GeneChip HT Array Plates (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip H Scanner (Affymetrix).

data_processing: Data was analyzed uisng Genesifter. RMA was performed.

source_name: B cell derived iPSC at p16 from mouse 2, clone 3

label_protocol: Biotinylated cRNA was prepared from total RNA using the GeneChip HT IVT Labeling Kit (Affymetrix).

growth_protocol: All cells were cultured in standard ESC media (15% FBS, LIF) on irradiated MEFs.

extract_protocol: Total RNA was extracted using the QIAGEN miRNeasy kit

treatment_protocol: Cells were trypsinized and preplated for 45 minutes to remove MEFs

tag: cell type

value: iPS

tag: cell source

value: B cell

tag: clone

tag: passage


title: Day 21, biological rep2

tag: time

tag: infection

tag: tissue

value: lung


title: Day 12, biological rep1

value: Day 12


title: Day 12, biological rep4


title: B cell  iPSC at p16 , clone 1

source_name: B cell derived iPSC at p16 from mouse 2, clone 1


title: B cell  iPSC at p16 , clone 2

source_name: B cell derived iPSC at p16 from mouse 2, clone 2


title: Day 0, biological rep2

description: Gene expression data from uninfected lung

source_name: control uninfected lungs

value: Day 0

value: control uninfected


title: Day 12, biological rep3


title: Day 0, biological rep3


title: Day 15, biological rep2


title: Paneth-Cell vs Stem-Cell sort_2 swap

tag: strain

tag: cell phenotype

value: paneth cell

value: intestinal stem cell

value: GFPhigh


title: Day 15, biological rep3

value: Day 15


title: Day 0, biological rep1


title: B cell  iPSC at p4 , clone 1

source_name: B cell derived iPSC at p4 from mouse 2, clone 1


title: Day 15, biological rep1


title: B cell  iPSC at p4 , clone 2

source_name: B cell derived iPSC at p4 from mouse 2, clone 2


title: Granulocyte  iPSC at p16 , clone 3

source_name: Granulocyte derived iPSC at p16 from mouse 2, clone 3

value: Granulocytes


title: B cell  iPSC at p4 , clone 3

source_name: B cell derived iPSC at p4 from mouse 2, clone 3


title: Granulocyte  iPSC at p4 , clone 2

source_name: Granulocyte derived iPSC at p4 from mouse 2, clone 2


title: T cell  iPSC at p16 , clone 1

source_name: T cell derived iPSC at p16 from mouse 2, clone 1

value: T cell


title: T cell  iPSC at p16 , clone 3

source_name: T cell derived iPSC at p16 from mouse 2, clone 3


title: Granulocyte  iPSC at p16 , clone 1

source_name: Granulocyte derived iPSC at p16 from mouse 2, clone 1


title: Granulocyte  iPSC at p16 , clone 2

source_name: Granulocyte derived iPSC at p16 from mouse 2, clone 2


title: Granulocyte  iPSC at p4 , clone 3

source_name: Granulocyte derived iPSC at p4 from mouse 2, clone 3


title: Tail tip fibrobast  iPSC at p16 , clone 1

source_name: Tail tip fibrobast derived iPSC at p16 from mouse 2, clone 1

value: Tail tip fibrobast


title: T cell  iPSC at p16 , clone 2

source_name: T cell derived iPSC at p16 from mouse 2, clone 2


title: Tail tip fibrobast  iPSC at p4 , clone 3

source_name: Tail tip fibrobast derived iPSC at p4 from mouse 2, clone 3


title: T cell  iPSC at p4 , clone 1

source_name: T cell derived iPSC at p4 from mouse 2, clone 1


title: T cell  iPSC at p4 , clone 2

source_name: T cell derived iPSC at p4 from mouse 2, clone 2


title: SMP  iPSC at p6 , clone 2

source_name: SMP derived iPSC at p6 from mouse 1, clone 2

value: SMP


title: T cell  iPSC at p4 , clone 3

source_name: T cell derived iPSC at p4 from mouse 2, clone 3


title: Tail tip fibrobast  iPSC at p4 , clone 2

source_name: Tail tip fibrobast derived iPSC at p4 from mouse 2, clone 2


title: Tail tip fibrobast  iPSC at p16 , clone 2

source_name: Tail tip fibrobast derived iPSC at p16 from mouse 2, clone 2


title: Granulocyte  iPSC at p4 , clone 1

source_name: Granulocyte derived iPSC at p4 from mouse 2, clone 1


title: Granulocytes  iPSC at p16 , clone 1

source_name: Granulocytes derived iPSC at p16 from mouse 1, clone 1


title: Tail tip fibrobast  iPSC at p4 , clone 1

source_name: Tail tip fibrobast derived iPSC at p4 from mouse 2, clone 1


title: SMP  iPSC at p6 , clone 3

source_name: SMP derived iPSC at p6 from mouse 1, clone 3


title: B cell  iPSC at p10 , clone 3

source_name: B cell derived iPSC at p10 from mouse 2, clone 3


title: Granulocytes  iPSC at p16 ,clone 3

source_name: Granulocytes derived iPSC at p16 from mouse 1,clone 3


title: B cell  iPSC at p10 , clone 2

source_name: B cell derived iPSC at p10 from mouse 2, clone 2


title: SMP  iPSC at p6 , clone 1

source_name: SMP derived iPSC at p6 from mouse 1, clone 1


title: Tail tip fibrobast  iPSC at p16 , clone 3

source_name: Tail tip fibrobast derived iPSC at p16 from mouse 2, clone 3


title: Granulocytes  iPSC at p4 ,clone 3

source_name: Granulocytes derived iPSC at p4 from mouse 1,clone 3


title: Granulocytes  iPSC at p16 , clone 2

source_name: Granulocytes derived iPSC at p16 from mouse 1, clone 2


title: Granulocyte  iPSC at p10 , clone 1

source_name: Granulocyte derived iPSC at p10 from mouse 2, clone 1


title: Granulocytes iPSC at p4, clone 1

source_name: Granulocytes derived iPSC at p4 from mouse 1, clone 1


title: Granulocyte  iPSC at p10 , clone 3

source_name: Granulocyte derived iPSC at p10 from mouse 2, clone 3


title: Tail tip fibrobast  iPSC at p10 , clone 3

source_name: Tail tip fibrobast derived iPSC at p10 from mouse 2, clone 3


title: B cell  iPSC at p10 , clone 1

source_name: B cell derived iPSC at p10 from mouse 2, clone 1


title: Granulocyte  iPSC at p10 , clone 2

source_name: Granulocyte derived iPSC at p10 from mouse 2, clone 2


title: Tail tip fibrobast  iPSC at p10 , clone 1

source_name: Tail tip fibrobast derived iPSC at p10 from mouse 2, clone 1


title: T cell  iPSC at p10 , clone 3

source_name: T cell derived iPSC at p10 from mouse 2, clone 3


title: T cell  iPSC at p10 , clone 1

source_name: T cell derived iPSC at p10 from mouse 2, clone 1


title: T cell  iPSC at p10 , clone 2

source_name: T cell derived iPSC at p10 from mouse 2, clone 2


title: Granulocytes iPSC at p4 , clone 2

source_name: Granulocytes derived iPSC at p4 from mouse 1, clone 2


title: E13_5_MafB_3

status: Public on Jul 16 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12341

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 2.5µg The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4.

data_processing: Analysis method: Affymetrix Expression Console and GeneSpring 10.

source_name: E13.5 Podocyte Layer

label_protocol: The FL-Ovation cDNA Biotin Module V2 (NuGEN) is used to chemically modify fragments and label target sense cDNA.

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 20 embryonic Kidneys
Pooled sample: Yes
Dissection Method: Trypsinization & fluorescent activated cell sorting
MafB transgenic mice are time-mated.  Pregnant MafB transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  Embryonic kidneys are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and proceed with FACS.

tag: gene reported

value: Tg(Mafb-EGFP)79Gsat / MMRRC:011834-UCD

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Adult_Whole_Glom_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12335

hyb_protocol: Affymetrix standard protocol. Amount labeled target hybridized to array: 2.5µg The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

source_name: mature renal corpuscle

treatment_protocol:
pool size: approx 2 Adult Kidney
Pooled sample: Yes
Dissection Method: Renal corpuscles were isolated using a combination of Collagenase A digestion and sieving.
Experimental Design:  7 to 9 week old adult male mice were euthanized by standard carbon dioxide asphyxiation.  The kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300 µl of 0.5% Collagenase A for 15 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600 µl of ice-cold 10% FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 500 µl of ice-cold 2% FBS/PBS.  Mature renal corpuscles were isolated using a decreasing series of filter sizes (100µm, 70 µm, 40 µm).

value: wild-type

tag: Sex

value: Male

value: Adult


title: Tail tip fibrobast  iPSC at p10 , clone 2

source_name: Tail tip fibrobast derived iPSC at p10 from mouse 2, clone 2

value: iPS


title: CRYM_P4_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12326

hyb_protocol: Affymetrix standard protocol The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

source_name: renal vesicle

treatment_protocol:
pool size: approx 4 P4 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated.  Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Neonatal pups were fostered to new CD-1 females.  At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.

value: Tg(Crym-EGFP)82Gsat / MMRRC:012003-UCD


title: E13_5_MafB_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12340


title: E15_5_MafB_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12344

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and  Affymetrix scanning software Genechip Operating Software Version 1.4.

data_processing: Analysis method: Affymetrix Expression Console and GeneSpring 10

source_name: E15.5 Podocyte Layer


title: CRYM_P3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12321

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 2.5 µg The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

source_name: cap mesenchyme

treatment_protocol:
pool size: approx 4 P3 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated.  Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Neonatal pups were fostered to new CD-1 females.  At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.


title: Adult_MafB_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12337

source_name: visceral epithelium (syn: podocyte layer)

treatment_protocol:
pool size: approx 2 Adult Kidney
Pooled sample: Yes
Dissection Method: Podocyte cells were isolated from adult Mafb transgenic mice kidneys using a combination of Collagenase A digestion, sieving and tyrpsinization followed by FACS.
7- to 9-week-old Mafb transgenic adult male mice were euthanized by standard carbon dioxide asphyxiation.  The kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300 µl of 0.5% Collagenase A for 15 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600 µl of ice-cold 10% FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 500 µl of ice-cold 2% FBS/PBS.  Glomeruli were isolated using a decreasing series of filter sizes (100µm, 70 µm, 40 µm).  The purified glomeruli were then incubated with 0.5% trypsin-EDTA for 5-10 minutes at 37ºC.  The cells were then washed several times with 500 µl of ice-cold 2% FBS/PBS, filtered using a 70 µm  mesh.  The GFP positive podocytes were isolated using FACS.


title: E13_5_MafB_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12339

label_protocol: The FL-Ovation cDNA Biotin Module V2 (NuGEN) is used to chemically  modify fragments and label target sense cDNA.


title: CRYM_P4_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12325

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 2.5 µg The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.


title: Adult_Whole_Glom_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12334

treatment_protocol:
pool size: approx 2 Adult Kidney
Pooled sample: Yes
Dissection Method: Renal corpuscles were isolated using a combination of Collagenase A digestion and sieving.
Experimental Design: 7 to 9 week old adult male mice were euthanized by standard carbon dioxide asphyxiation.  The kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300 µl of 0.5% Collagenase A for 15 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600 µl of ice-cold 10% FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 500 µl of ice-cold 2% FBS/PBS.  Mature renal corpuscles were isolated using a decreasing series of filter sizes (100µm, 70 µm, 40 µm).


title: E15_5_MafB_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12343


title: CRYM_P3_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12323


title: Adult_Whole_Glom_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12333


title: Adult_MafB_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12338


title: CRYM_P0_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12313

treatment_protocol:
pool size: approx 4 P0 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated.  Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Neonatal pups were fostered to new CD-1 females.  At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.


title: CRYM_P0_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12314


title: CRYM_P2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12318

treatment_protocol:
pool size: approx 4 P2 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated.  Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Neonatal pups were fostered to new CD-1 females.  At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.


title: CRYM_P4

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12324


title: CRYM_P1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12315

treatment_protocol:
pool size: approx 4 P1 kidneys
Pooled sample: Yes
Dissection Method: Trypsinization and fluorescent activated cell sorting (FACS).
Crym transgenic mice were time-mated.  Pregnant Crym transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Neonatal pups were fostered to new CD-1 females.  At the appropriate time, pups were killed by decapitation with a scalpel and the kidneys were isolated and placed in ice-cold PBS.  The kidneys were minced with a razor blade and incubated in the presence of 300µl of 0.25% trypsin-EDTA for 5 minutes at 37ºC.  After incubation, the kidneys were further dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS, and then pelleted at 5000 rpm, 4ºC for 5 minutes.  The cells were resuspended in 200µl of ice-cold 2%FBS/PBS, filtered using a 70 micron mesh and isolated using FACS.


title: CRYM_P1_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12317


title: Adult_MafB_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12336


title: E15_5_MafB_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12342


title: CRYM_P3_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12322


title: CRYM_P2_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12320


title: Tie2_Glom5

status: Public on Jun 29 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13696

source_name: Glomerular Capillary System

treatment_protocol:
pool size: 1 Adult Kidney
Pooled sample: no
Dissection Method: Collagenase A treatment, differential sieving, trypsinization & fluorescent activated cell sorting
Adult Tie2-GFP transgenic mice are euthanized by standard carbon dioxide asphyxiation.  Kidneys are dissected, bisected and placed in ice-cold PBS.  The medullary region was removed, the remaining cortical region are minced into small pieces and placed into a eppendorf tube containing 500ul of 1% Collagenase A.  The kidneys are incubated  for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 2000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS. The Kidneys are filtered through 100µm mesh.  The flow through is collected and filtered using a 40µM mesh, which captures glomeruli.   The captured glomeruli are resieved through a 40µm mesh filter 2-3 times.  The glomeruli are collected, rinsed with PBS and digested with 0.5% trypsin for 5-10 minutes at 37 ºC.  The cells are rinsed twice using ice-cold 2%FBS/PBS.  The cells are filtered  using 70µm mesh and proceed with FACS.

value: Tg(TIE2GFP)287Sato / MGI:3056937

value: mixed background, primarily CD-1

value: glomerulus

value: no information provided


title: Control prednisolone 2

status: Public on Jun 15 2010

city: Nijmegen

first: Joost

last: van Galen

department: Pediatrics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description:
RS4;11_shRNA-control_prednisolone_rep2
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix cell files were imported into the Partek Genomic Suite software and normalized using the RMA algorithm with GC correction. Probeset intensities were summarized into transcript intensities by taking the mean of corresponding probesets.

organism: Homo sapiens

source_name: RS4;11 shRNA control transduced cells, 8 hours exposure to prednisolone

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were grown for 8 hours at 37ºC.

extract_protocol: Cells were harvested by centrifuging for 5 minutes at 500g. RNA was extracted using RNAeasy kit (Qiagen), including DNAse treatment (Qiagen) on the column.

treatment_protocol: Not applicable.

tag: cell line

value: acute lymphoblastic leukemia

tag: shrna

value: shRNA Control vector

tag: treatment

value: prednisolone


title: CRYM_P2_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12319


title: BTG1 prednisolone 1

description:
RS4;11_shRNA-BTG1_prednisolone_rep1
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: RS4;11 shRNA BTG1 transduced cells, 8 hours exposure to prednisolone

tag: cell type

value: shRNA BTG1 vector


title: BTG1 vehicle 1

description:
RS4;11_shRNA-BTG1_vehicle_rep1
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: RS4;11 shRNA BTG1 transduced cells, 8 hours exposure to vehicle control

value: vehicle control


title: NSC-520g-exp2-dff-1

status: Public on Jun 26 2010

city: Toronto

first: David

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description:
Experiment 2
Replicate 1
(d) 520g-r1

hyb_protocol: Hybridization is carried out in Illumina Intellihyb chambers at 58 °C (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina).

scan_protocol: Following hybridization, washing, and staining with streptavidin-Cy3, the chips were scanned using an Illumina BeadArray reader.

data_processing: Data analyses were performed with Illumina BeadStudio (v3.4.0) and Bioconductor packages (v2.3) in the R programming environment (v 2.7.1). The image data were analyzed using the BeadStudio, the output files of which were imported into the R using the lumi package (v1.8.3). Probe set signal intensities were averaged. Expression profiles were then log2 transformed and quantile normalized for ownstream analyses.

source_name: PNET cell line, miR-520g

label_protocol: Following manufacturer's instructions, 250 ng total RNA was used for cRNA in vitro transcription and labeling with the Illumina TotalPrep RNA Amplication Kit using biotinylated-UTP (Ambion, Austin, TX).

extract_protocol: Standard Trizol extraction.

value: PNET

value: neural stem cell

tag: miRNA


title: BTG1 prednisolone 2

description:
RS4;11_shRNA-BTG1_prednisolone_rep2
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: CRYM_P1_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12316

value: unknown


title: CRYM_P0

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:12312

hyb_protocol: Amount labeled  target hybridization to array: 2.5 µg Affymetrix standard protocol The arrays were washed and and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.


title: Control vehicle 1

description:
RS4;11_shRNA-control_vehicle_rep1
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: RS4;11 shRNA control transduced cells, 8 hours exposure to vehicle control


title: NSC-pcDNA-exp2-dff-1

description:
Experiment 2
Replicate 1
(d) pcDNA-r1

source_name: PNET cell line, pcDNA


title: Tie2_Glom3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13695


title: NSC-520g-exp1-dff-3

description:
Experiment 1
Replicate 3
NSC520g-r3


title: Control vehicle 2

description:
RS4;11_shRNA-control_vehicle_rep2
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: Tie2_Endo_1

status: Public on Jun 23 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13691

source_name: Renal Cortical Vasculature

treatment_protocol:
pool size: 1 Adult Kidney
Pooled sample: no
Dissection Method: Collagenase A treatment, differential sieving, trypsinization & fluorescent activated cell sorting
Adult Tie2-GFP transgenic mice are euthanized by standard carbon dioxide asphyxiation.  Kidneys are dissected, bisected and placed in ice-cold PBS.  The medullary region was removed, the remaining cortical region are minced into small pieces and placed into a eppendorf tube containing 500µl of 1% Collagenase A.  The kidneys are incubated for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 2000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS. The Kidneys are filtered through 100µm mesh.  The flow through is collected and filtered using a 40µM mesh, which removes glomeruli.   The flow through is collected, rinsed with PBS and digested with trypsin for 5 minutes at 37 ºC.  The cells are rinsed twice using ice-cold 2%FBS/PBS and the cells are filtered  using 70µm mesh and proceed with FACS.

value: mixed background primarily CD-1


title: Tie2_Glom1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13694


title: NSC-pcDNA-exp2-dff-2

description:
Experiment 2
Replicate 2
(d) pcDNA-r2


title: NSC-pcDNA-exp1-dff-1

description:
Experiment 1
Replicate 1
NSC pcDNA-r1


title: NSC-520g-exp1-dff-1

description:
Experiment 1
Replicate 1
NSC520g-r1


title: NSC-520g-exp1-dff-2

description:
Experiment 1
Replicate 2
NSC520g-r2


title: NSC-520g-exp2-dff-2

description:
Experiment 2
Replicate 2
(d) 520g-r2


title: Tie2_Endo_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13692


title: NSC-pcDNA-exp1-dff-2

description:
Experiment 1
Replicate 2
NSC pcDNA-r2


title: NSC-pcDNA-exp1-dff-3

description:
Experiment 1
Replicate 3
NSC pcDNA-r3


title: Tie2_Endo_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13693


title: Control prednisolone 1

description:
RS4;11_shRNA-control_prednisolone_rep1
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: 16HBE_sorted_positive_rep4

status: Public on Jun 04 2010

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

institute: UBC - iCAPTURE Centre

description: Gene expression in 16HBE cells interacting with A. fumigatus conidispores

hyb_protocol: Labeled cRNA (1.65μg) was fragmented for 30 minutes, hybridized to microarrays for 17 hours at 65°C in the Agilent hybridization oven, and washed with Agilent wash buffers, according to the manufacturer's protocols.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray Scanner at a resolution of 5μm and Agilent’s Feature Extraction software version 9.1 was used for quantification of signal intensities and to produce a quality control report for each microarray, using the default protocol for a one-colour array.

data_processing: Raw signals were first normalized by flooring all values smaller than 1 to 1, then dividing each value by the median intensity value of the array.

source_name: 16HBE cells incubated and directly interacting with A. fumigatus conidiospores

label_protocol: Cy3-labeled complementary RNA (cRNA) was generated following Agilent’s Low RNA Input Linear Amplification Protocol, and its quantity and specific activity assessed using a NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: 16HBE cells were maintained at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate. Cells were passaged at confluence.

extract_protocol: Following sorting, cells were lysed in 700μl buffer RLT (Qiagen, Hilden, Germany), and RNA was extracted using the RNeasy Mini Kit with QIAshredder (Qiagen), following the manufacturer’s recommendations. RNA yield from each sample was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was determined using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Confluent 16HBE monolayers were incubated with GFP-expressing A. fumigatus conidiospores at a ratio of 10 conidiospores per cell for 6 hours. Cells were brought into suspension via trypsinization and analyzed by flow cytometry. Cells were sorted based on the presence of a GFP signal, separating cells associated with conidiospores from those without direct contact with conidiospores.

value: human bronchial epithelial cell line 16HBE

tag: protocol

value: direct interaction with A. fumigatus conidispores


title: 16HBE_sorted_negative_rep4

description: Gene expression in 16HBE cells not interacting with A. fumigatus conidiospores

source_name: 16HBE cells incubated with, but not directly interacting with, A. fumigatus conidiospores

value: control


title: 16HBE_sorted_positive_rep3


title: 100Hz_LR_1h_DH3 rat

status: Public on Apr 11 2010

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42°C for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: the tissue of spinal dorsal horn of 100Hz electroacupuncture low responder (LR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and non-sensitivity on electroacupuncture analgesia was labeled with Cy3.

extract_protocol: Total RNA was prepared from DH using Trizol reagent (Invitrogen,USA), and further purified with a QIAGEN RNeasy Kit.

treatment_protocol: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's DH was then collected for transcript profiling analysis.

tag: time point

value: Sprague-Dawley

tag: tissue type

value: spinal dorsal horn

tag: frequency

tag: group

value: low responder (LR) rats

source_name: the tissue of DH of control rats

extract_protocol: Total RNA was prepared from DH of control rats using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

treatment_protocol: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of DH were collected for transcript profilinf analysis

tag: reference

value: rats sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.


title: DUCT_E10.5_3

status: Public on May 01 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13564

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 2.5µg The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

source_name: ureteric trunk

treatment_protocol:
pool size: 1 Ureteric duct
Pooled sample: No
Dissection Method: Microdissection, trypsinization & fluorescent activated cell sorting
Hoxb7-GFP transgenic mice are time-mated.  Pregnant HoxB7-GFP transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  The ureteric duct is isolated and  are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC.  The ureteric duct cells are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 3000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and proceed with FACS.

tag: gene reported

value: Tg(Hoxb7-EGFP)33Cos / MGI:3715437

tag: strain

tag: sex

tag: somite count:

tag: developmental landmark:


title: 16HBE_sorted_negative_rep1


title: BUD_E10.5_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13561

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 2.5µg. The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

source_name: ureteric tip

treatment_protocol:
pool size: 1 Ureteric bud
Pooled sample: No
Dissection Method: Microdissection, trypsinization & fluorescent activated cell sorting
HoxB7-GFP transgenic mice are time-mated.  Pregnant HoxB7-GFP transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  The ureteric bud is isolated and  are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC.  The ureteric bud cells are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 3000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and proceed with FACS.

tag: developmental stage

tag: theiler stage


title: BUD_E10.5_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13560


title: 16HBE_sorted_positive_rep1

tag: cell line


title: 96 hr doxycycline induction, biological rep1

status: Public on Apr 16 2010

first: Richard

last: Koche

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

description:
Gene expression from MEFs undergoing doxycycline-induced OSKM expression for 96 hours.
Gene expression from 96 hours of doxycycline-induced MEFs with an average of three or more cell divisions.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Robust Multi-Array (RMA) normalized.
Preprocessing, normalization, and analysis were all performed using GenePattern software (http://www.broadinstitute.org/cancer/software/genepattern/).

source_name: Doxycycline-induced MEFs

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard 10% Fetal Bovine Serum containing growth medium

extract_protocol: Extraction of total RNA was done using TRIzol (Invitrogen) followed by cleanup using the RNeasy(R) Mini column system (Qiagen).

treatment_protocol: Either 15% FBS containing medium supplemented with 2 ug/ul Doxycyline or 0.5% FBS containing Serum Starvation medium

value: secondary, inducible MEFs

value: 129/SvJ x C57/B6 hybrid

tag: agent

value: Doxycycline

tag: biological rep

tag: cell division cohort

value: average of three or more cell divisions


title: 16HBE_sorted_positive_rep2

tag: protocol


title: Ovarian Carcinoma_OC01_ARN0207 [HG-U133_Plus_2]

status: Public on Apr 14 2010

city: PARIS

first: Jean-Philippe

last: MEYNIEL

address: 26, rue d'Ulm

department: Translational Research Dept

country: France

institute: Institut Curie

description: Gene expression data from ovarian carcinoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2,0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner GCS3000

data_processing: The data were processed/analyzed with gc-RMA (Partek Genomic Suite 6.09.1008).

source_name: Ovarian Carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)_mRNA.

extract_protocol: Total RNA purification was conducted using miRNeasy kit

tag: tissue

value: Ovary

tag: histology (disease state)

value: Ovarian Carcinoma

tag: identifier

tag: histotype

value: Serous

tag: tumor/metastasis

value: T

tag: grade

tag: stade

value: IIIc


title: 100Hz_HR_1h_DH5 rat

source_name: the tissue of spinal dorsal horn of 100Hz electroacupuncture high responder (HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on electroacupuncture analgesia was labeled with Cy3.

treatment_protocol: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's DH was then collected for transcript profiling analysis.

tag: time point

tag: strain

tag: tissue type

tag: frequency

tag: group

value: high responder (HR) rats

tag: reference


title: 96 hr doxycycline induction, biological rep2

tag: cell type

tag: agent


title: 100Hz_HR_1h_DH2 rat


title: 16HBE_sorted_negative_rep2

tag: cell line

value: human bronchial epithelial cell line 16HBE


title: DUCT_E10.5_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13562

tag: gene reported

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count:

tag: developmental landmark:


title: 100Hz_HR_1h_DH4 rat

value: Sprague-Dawley


title: 100Hz_HR_1h_DH1 rat

value: spinal dorsal horn


title: BTG1 vehicle 2

description:
RS4;11_shRNA-BTG1_vehicle_rep2
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

value: acute lymphoblastic leukemia

tag: shrna

value: shRNA BTG1 vector

tag: treatment

value: vehicle control


title: BUD_E10.5_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13559

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4

value: Tg(Hoxb7-EGFP)33Cos / MGI:3715437


title: 100Hz_LR_1h_DH5 rat

tag: time point

value: low responder (LR) rats

value: rats sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.


title: Serum-starved control, biological rep1

description: Gene expression from MEFs undergoing serum starvation for 96 hours.

source_name: serum-starved, uninduced MEFs

value: secondary, inducible MEFs

tag: strain

value: 129/SvJ x C57/B6 hybrid

value: control

tag: biological rep


title: 2Hz_LR_1h_DH3 rat

source_name: the tissue of spinal dorsal horn of 2Hz electroacupuncture low responder (LR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and non-sensitivity on electroacupuncture analgesia was labeled with Cy3.

treatment_protocol: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were non-sensitivity on  EA analgesia. It's DH was then collected for transcript profiling analysis.

tag: tissue type

tag: frequency


title: Serum-starved control, biological rep2


title: 100Hz_LR_1h_DH1 rat

tag: group

tag: reference


title: 100Hz_LR_1h_DH2 rat


title: 2Hz_HR_1h_DH4 rat

source_name: the tissue of spinal dorsal horn of 2Hz electroacupuncture high responder (HR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each DH which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on electroacupuncture analgesia was labeled with Cy3.

treatment_protocol: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's DH was then collected for transcript profiling analysis.


title: 2Hz_HR_1h_DH1 rat


title: DUCT_E10.5_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13563


title: 100Hz_LR_1h_DH4 rat


title: 100Hz_HR_1h_DH3 rat


title: 2Hz_LR_1h_DH4 rat


title: Tie2_E15.5_2

status: Public on Mar 23 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13557

source_name: small blood vessels

treatment_protocol:
pool size: 4-5 Embryonic Kidneys
Pooled sample: Yes
Dissection Method: trypsinization & fluorescent activated cell sorting
Tie2-GFP transgenic mice are time-mated.  Pregnant Tie2-GFP transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  Embryonic kidneys are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes.  The media is aspirates and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and proceed with FACS.

value: Tg(TIE2GFP)287Sato / MGI:3056937


title: 2Hz_HR_1h_DH2 rat


title: Adult_Capsule_4

status: Public on Mar 06 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13520

source_name: renal capsule

treatment_protocol:
pool size: 1 Adult kidney
Pooled sample: No
Dissection Method: Microdissection
Adult CD-1 mice were euthanized by standard carbon dioxide asphyxiation.  Kidneys were removed in ice-cold PBS.  Using microforceps, the capsule of the kidney was removed and place into an eppendorf tube for RNA isolation.

value: wild-type

tag: Sex

value: male

value: Adult

tag: somite count

tag: developmental landmark

tag: cell type

value: capsule cell


title: 2Hz_HR_1h_DH5 rat

value: high responder (HR) rats


title: 2Hz_LR_1h_DH2 rat

value: Sprague-Dawley


title: 2Hz_LR_1h_DH1 rat

value: spinal dorsal horn


title: 2Hz_HR_1h_DH3 rat


title: Tie2_E15.5_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13558

tag: gene reported

tag: developmental stage


title: Tie2_Med_3

status: Public on Jan 26 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13415

source_name: renal medullary vasculature

treatment_protocol:
pool size: 2 Adult kidneys
Pooled sample: Yes
Dissection Method: Collagenase A treatment & fluorescent activated cell sorting (FACS)
Adult Tie2 trasngenic mice were euthanized by standard carbon dioxide asphyxiation.  Kidneys were removed in ice-cold PBS,  bisected and the medullary region isolated using a dissecting microscope.  The medullary region was minced into small pieces using a razor blade, placed into a 1.5ml eppendorf tube containing 500µl of 0.5% Collagenase A and incubated at 37 ºC for 10 minutes.  The tissue was then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS and pelleted at 5000 rpm, 4 ºC for 5 minutes.  The media was aspirated and the cell pellet was resuspended in 200µl of ice-cold 2%FBS/PBS.  The cells were filtered using a  70 micron mesh filter.  Proceed to FACS.

value: FVB/N

tag: sex

tag: theiler stage

tag: somite count:


title: R1E UV 2

status: Public on Jan 19 2010

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

description: R1E cells treated with UV for 8 hours.

hyb_protocol: Samples were hybridized to the Affymetrix Mouse Gene ST 1.0 GeneChip.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip scanner 3000.

data_processing:
Data were processed with Affymetrix Expression Console (version 1.1). ANOVA, p-value <0.01; fold change>1.5. Transcripts that are significantly altered in both adriamycin and Ultraviolet treatments are shown. The subsequent statistical analyses were performed using R programming language version 2.8.1.

Probe group file: MoGene-1_0-st-v1.r4.pgf
Meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: R1E cells, UV

label_protocol: Affymetrix Whole Transcript Sense Target Labeling kit per manufacturer’s protocol.

growth_protocol: R1E cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Millipore)

extract_protocol: RNAs were extracted using the RNeasy mini kit (Qiagen).

treatment_protocol: R1E cells were treated with 0.5 micromolar adriamycin or 25J/m2 UV for 8 hours in growth medium.

tag: cell line

tag: agent

value: UV


title: Tie2_E15.5_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13556

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 2.5µg The arrays were washed and and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

tag: strain


title: Adult_Meis_3

status: Public on Mar 13 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13523

source_name: glomerular mesangium & extraglomular mesangium

treatment_protocol:
pool size: 1 Adult kidney
Pooled sample: No
Dissection Method: Collagenase A treatment, trypsinization & fluorescent activated cell sorting
Adult Meis BAC transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Kidneys were removed in ice-cold PBS,  bisected and the medullary region removed using a dissecting microscope.  The cortical region was minced into small pieces using a razor blade, then placed into a 1.5ml eppendorf tube containing 500µl of 0.5% Collagenase A.   The tube  was incubated at 37°C fro 10 minutes.  Kidneys were then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The  cell suspension was filtered through a 100µM mesh to remove large cell debris.  The flow-through was collected and refiltered using a 40µM mesh filter to capture glomeruli.  The glomeruli were collected into 6cm petri dishes by overturning the 40µM mesh filter and rinsing the filter with  ice-cold PBS.  The purity of the glomeruli isolation was determined visually using a dissecting microscope.  This process was repeated  2-3 times until pure glomeruli were isolated.  The glomeruli were collected into a 1.5ml eppendorf tube and the tube was centrifuged at 2500 RPM for 5 min.  The glomeruli were washed 2-3 times in ice-cold PBS.   After the final rinse the PBS was removed and 300µl of 0.5% trypsin was added and incubated for 10-20 minutes.  Every five minutes the glomeruli were triturated and were inspected under a microscope to visualize the amount of trypsinization.  After incubation, the single-cell suspension was rinsed with 2%FBS/PBS three times. After the final wash, the cells were resuspended in 400µl of 1%FBS/PBS and refiltered through a 70µM mesh FACS tube.

value: Tg(Meis1-EGFP)FO156Gsat / MGI:3843887

value: mesangial


title: Adult_Meis_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13522

treatment_protocol:
pool size: 1 Adult kidney
Pooled sample: No
Dissection Method: Collagenase A treatment, trypsinization & fluorescent activated cell sorting
Adult Meis BAC transgenic mice were euthanized by standard carbon dioxide asphyxiation.  Kidneys were removed in ice-cold PBS,  bisected and the medullary region removed using a dissecting microscope.  The cortical region was minced into small pieces using a razor blade, then placed into a 1.5ml eppendorf tube containing 500µl of 0.5% Collagenase A.   The tube  was incubated at 37°C fro 10 minutes.  Kidneys were then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The  cell suspension was filtered through a 100µM mesh to remove large cell debris.  The flow-through was collected and refiltered using a 40µM mesh filter to capture glomeruli.  The glomeruli were collected into 6cm petri dishes by overturning the 40µM mesh filter and rinsing the filter with  ice-cold PBS.  The purity of the glomeruli isolation was determined visually using a dissecting microscope.  This process was repeated  2-3 times until pure glomerli were isolated.  The glomerli were collected into a 1.5ml eppendorf tube and the tube was centrifuged at 2500 RPM for 5 min.  The glomerui were washed 2-3 times in ice-cold PBS.   After the final rinse the PBS was removed and 300µl of 0.5% trypsin was added and incubated for 10-20 minutes.  Every five minutes the glomeruli were triturated and were inspected under a microscope to visualize the amount of trypsinization.  After incubation, the single-cell suspension was rinsed with 2%FBS/PBS three times. After the final wash, the cells were resuspended in 400µl of 1%FBS/PBS and refiltered through a 70µM mesh FACS tube.


title: Adult_Capsule_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13519


title: R1E Adriamycin 2

description: R1E cells treated with adriamycin for 8 hours.

source_name: R1E cells, Adriamycin

value: adriamycin


title: Adult_Capsule_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13518

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 2.5µg The arrays were washed and stained using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.


title: R1E Adriamycin 1


title: Adult_Meis_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13521

source_name: glomerular mesangium & extraglomerular mesangium


title: uroplakin2+ve

status: Public on Jan 22 2010

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13411

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: postnatal day 7 bladder epithelial DsRed +ve cells

treatment_protocol:
pool size: n/a
Pooled sample: no
Dissection Method: Bladder microdissected into rings and treated with 1 mg/ml trypsin in Tyrode's solution to dissociate the epithelium as a layer. This was then further digested with Blendzymes 1 & 4.
At postnatal day 7 mice were euthanized by CO2 asphyxiation and the bladders were removed and cut at the bladder neck. The bladder was cut into rings and treated with 1 mg/ml trypsin in Tyrode’s solution for 30 minutes at 37 °C. The layers were separated by gentle micro-dissection and the epithelial layer was further digested in a mixture of Blendzymes 1 & 4 at 37 °C until a single cell suspension was obtained. The samples were placed in RLT and stored at -80 °C. RNA was prepared and the Epicentre 2-round amplification scheme described on the GUDMAP web site was performed.  Affymetrix GeneChip Mouse Genome 430 2.0 Array chips were used to interrogate the amplified RNA.

value: FVB/N x C57BL/6

value: Male

value: bladder epithelial cell


title: Tie2_Med_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13413

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 2.5µg The arrays were washed and and stained  using a Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

tag: developmental landmark:


title: Tie2_Med_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: WT-Ovation Pico RNA Amplification System (NuGEN)
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13414


title: uroplakin1+ve

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13410


title: uroplakin5-ve

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13409

source_name: postnatal day 7 bladder epithelial DsRed -ve cells


title: R1E Mock 1

description: R1E cells mock treated.

source_name: R1E cells, mock

value: mock


title: R1E UV 4

description: R1E cells treated with UV for 8 hours.


title: R1E UV 3

description: R1E cells treated with UV for 8 hours.


title: uroplakin1-ve

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13407


title: Phen_L_11-2

status: Public on Jan 05 2010

city: Vicksburg

first: Xin

last: Guan

address: 3909 Halls Ferry Rd

department: EPP

institute: USACE-ERDC

description: Gene Expression after 24h exposed to Phen_L_11-2 in rat liver cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned at PMT levels 350 using GenePix 4200AL scanner (Molecular Device Inc.),

data_processing: The Feature extraction software (V. 9.5.1) from Agilent was used to automatically find and place microarray grids, reject outlier pixels, accurately determine feature intensities and ratios, flag outlier pixels, and calculate statistical confidences. First normalize be median perchip, then by median per gene, which means normalization by median value across all samples, then transformed to log2 based value.

label_protocol: Rat whole genome oligo arrays in the format of 4X44K were purchased from Agilent. Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 1.0). 1ug of total RNA was used. The Agilent One-Color Spike-Mix (part number 5188-5282) was diluted 5000-fold and 5 μL of the diluted spike-in mix was added to 1000 ng of each of the total RNA samples prior to labeling reactions. The labeling reactions were performed using the Agilent Low RNA Input Linear Amplification Kit in the presence of cyanine 3-CTP.

growth_protocol: The primary rat hepatocytes, rtNHeps (AC-2630), isolated from male Sprague Dawley and its hepatocyte culture medium (HCM), and supplements and growth factors (CC-3198) were purchased from Cambrex BioScience (Walkersville, MD).  Freshly isolated hepatocytes were shipped overnight on ice and processed immediately upon receipt.  These cells were seeded on BioCoat Type 1 Collagen-coated T-25 (BD356484) or T-75 (BD356485) flasks, or clear, flat-bottom, 96-well plates (BD356407) that were purchased from BD Biosciences (Palo Alto, CA).  Phosphate buffered saline (PBS, 21600-010), Trypsin-EDTA (15400-054), Trypan Blue stain (15250-061), Leibovitz medium (12448-015) were obtained from GIBCO-InVitrogen (Grand Island, NY).

extract_protocol: Total RNA was extracted from primary rat hepatocytes cell pellet.  Cell pellet were homogenized in the lysis buffer with FAST Prep-24 from MP at speed 6.0/s twice, each last 30s before using RNeasy kits (Qiagen). Total RNA concentrations were measured using NanoDrop® ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity and quality of total RNA was checked on an Agilent 2100 Bioanalyzer (Palo Alto, CA). The gel-like images generated by the Bioanalyzer show that total RNAs have two bands, represent 18S and 26S RNA of mammalian RNA . Nuclease-free water (Ambion) was used to elute total RNA.

treatment_protocol: The chemicals for the entire OMICS study were purchased from various sources:  Energetics from Chem Service (West Chester, PA) and SRI International (Menlo Park, CA); remaining chemicals from Sigma-Aldrich (St. Louis, MO) and Fisher Scientific (Fair Lawn, NJ).  The purity of all these compounds was equal or greater than 98%.  Prior to testing, the compounds were made up and serially diluted in dimethyl sulfoxide, DMSO (Fisher Scientific, Fair Lawn, NJ).  Metal compounds were made up and serially diluted in 0.1Fm-filtered, ultra-pure water before testing.  The 24-h toxicity of each OMICS compound was first determined in the human hepatocyte cell line HepG2 using the Neutral Red cytotoxicity kit (In Vitro Toxicology Kit Tox-4) obtained from Sigma-Aldrich.Primary rtNHeps cells collected at the end of the 24h chemical exposure were immediately stored in RNA Later (7021) purchased from Ambion (Austin, TX).  The primary rtN Heps cells were reconstituted in HCM supplemented with ascorbic acid, fatty acid-free bovine serum albumin, transferrin, insulin, recombinant human epidermal growth factor, hydrocortisone 21 hemisuccinate, Gentamicin sulfate, and Amphotericin B immediately upon receipt.  An aliquot of the cell suspension was stained in a 0.05% Trypan Blue solution and counted under an inverted microscope.  The cells were then seeded at 3 x 106 cells per (Type 1 collagen-coated) T-75 flask.   The flasks were left in a 37C, 5% CO2 incubator overnight to allow for cell attachment.    The cells were replenished with fresh HCM and dosed in triplicate flasks with the non-toxic concentration of each compound (pre-determined in the HepG2 cells) at 1% DMSO (v/v) or with solution at 1% water (v/v).  Another set of triplicate flasks were dosed with the appropriate solvent control.  Hence, for every 3 chemicals and a solvent control, a total of 12 flasks were used.After dosing, the flasks were returned to the incubator and incubated for 24 hours. The cells were washed with 1x PBS and detached with 1x trypsin-EDTA.  The cells were left in tryspin-EDTA no longer than 5 minutes.  Freshly warmed HCM was then added to neutralize the trypsin.  The cells were then transferred into a tube and centrifuged.  RNA Later was added the cell pellet and stored at –20C until genomic analysis

tag: treatment

tag: dose

value: 30 uM

tag: time

value: primary rat hepatocytes, rtNHeps

tag: gender


title: Phen_L_11-2_R


title: uroplakin5+ve

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13412

tag: Sex


title: Phen_M_11-2_R

description: Gene Expression after 24h exposed to Phen_M_11-2 in rat liver cell

value: Phenytoin, 100 uM_2


title: R1E UV 1

description: R1E cells treated with UV for 8 hours.


title: uroplakin2-ve

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13408

tag: somite count


title: R1E Adriamycin 3


title: Phen_C_11-2_R

description: Gene Expression after 24h exposed to Phen_control set_11-2 in rat liver cell


title: R1E Mock 4

description: R1E cells mock treated.


title: R1E Adriamycin 4


title: Phen_H_11-1

description: Gene Expression after 24h exposed to Phen_H_11-1 in rat liver cell


title: Phen_C_11-1

description: Gene Expression after 24h exposed to Phen_control set_11-1 in rat liver cell


title: MTX_M_11-2_R1

description: Gene Expression after 24h exposed to MTX_M_11-2 in rat liver cell

value: Methotrexate (MTX), 10 uM_3

value: 10 uM


title: R1E Mock 2

description: R1E cells mock treated.


title: Phen_C_11-2


title: Phen_M_11-2_R1

value: Phenytoin, 100 uM_3


title: Phen_M_11-2

value: Phenytoin, 100 uM_1


title: R1E Mock 3

description: R1E cells mock treated.


title: MTX_M_11-2_R

value: Methotrexate (MTX), 10 uM_2


title: 16HBE_sorted_negative_rep3

description: Gene expression in 16HBE cells not interacting with A. fumigatus conidiospores

source_name: 16HBE cells incubated with, but not directly interacting with, A. fumigatus conidiospores

treatment_protocol: Confluent 16HBE monolayers were incubated with GFP-expressing A. fumigatus conidiospores at a ratio of 10 conidiospores per cell for 6 hours. Cells were brought into suspension via trypsinization and analyzed by flow cytometry. Cells were sorted based on the presence of a GFP signal, separating cells associated with conidiospores from those without direct contact with conidiospores.

value: human bronchial epithelial cell line 16HBE

tag: protocol

value: control


title: Phen_L_11-1

description: Gene Expression after 24h exposed to Phen_L_11-1 in rat liver cell

tag: cell type


title: MTX_H_11-2_R

description: Gene Expression after 24h exposed to MTX_H_11-2 in rat liver cell


title: Phen_H_11-2

description: Gene Expression after 24h exposed to Phen_H_11-2 in rat liver cell


title: Phen_H_11-2_R


title: MTX_M_11-2

value: Methotrexate (MTX), 10 uM_1


title: MTX_L_11-2

description: Gene Expression after 24h exposed to MTX_L_11-2 in rat liver cell

value: 3 uM


title: MTX_L_11-1

description: Gene Expression after 24h exposed to MTX_L_11-1 in rat liver cell


title: MTX_H_11-2


title: MTX_C_11-1

description: Gene Expression after 24h exposed to MTX_control set_11-1 in rat liver cell


title: MTX_H_11-1

description: Gene Expression after 24h exposed to MTX_H_11-1 in rat liver cell


title: MethylCaproate_L_11-2_R

description: Gene Expression after 24h exposed to MethylCaproate_L_11-2 in rat liver cell

value: Methyl Caproate_1-2

value: 1 ppm


title: MethylCaproate_M_11-2_R

description: Gene Expression after 24h exposed to MethylCaproate_M_11-2 in rat liver cell

value: Methyl Caproate, 3 ppm_2

value: 3 ppm

value: Male


title: MethylCaproate_M_11-2_R1

value: Methyl Caproate, 3 ppm_3


title: MethylCaproate_L_11-1_R

description: Gene Expression after 24h exposed to MethylCaproate_L_11-1 in rat liver cell

value: Methyl Caproate_1-3

value: primary rat hepatocytes, rtNHeps


title: MethylCaproate_L_11-2


title: MethylCaproate_M_11-2

value: Methyl Caproate, 3 ppm_1


title: MTX_C_11-2

description: Gene Expression after 24h exposed to MTX_control set_11-2 in rat liver cell


title: MethylCaproate_L_11-1

value: Methyl Caproate_1-1


title: MTX_C_11-2_R


title: MethylCaproate_H_11-1

description: Gene Expression after 24h exposed to MethylCaproate_H_11-1 in rat liver cell

value: Methyl Caproate_10-2

value: 10 ppm


title: MethylCaproate_H_11-2_R

description: Gene Expression after 24h exposed to MethylCaproate_H_11-2 in rat liver cell

value: Methyl Caproate_10-3


title: MethylCaproate_C_11-2_R

description: Gene Expression after 24h exposed to MethylCaproate_control set_11-2 in rat liver cell

value: Methyl Caproate_Con-2


title: MethylCaproate_C_11-1

description: Gene Expression after 24h exposed to MethylCaproate_control set_11-1 in rat liver cell

value: Methyl Caproate_Con-3


title: Glucagon_M_11-2_R1

description: Gene Expression after 24h exposed to Glucagon_M_11-2 in rat liver cell

value: Glucagon, 0.3 ppm_3

value: 0.3 ppm


title: Glucagon_H_11-1

description: Gene Expression after 24h exposed to Glucagon_H_11-1 in rat liver cell


title: MethylCaproate_C_11-2

value: Methyl Caproate_Con-1


title: MethylCaproate_C_11-1_R


title: MethylCaproate_H_11-2

value: Methyl Caproate_10-1


title: Glucagon_L_11-2_R

description: Gene Expression after 24h exposed to Glucagon_L_11-2 in rat liver cell

value: 0.1 ppm


title: DIMP_M_11-2_R1

description: Gene Expression after 24h exposed to DIMP_M_11-2 in rat liver cell

value: Diisopropyl methylphosphonate (DIMP), 300 ppm_3

value: 300 ppm


title: Glucagon_H_11-2

description: Gene Expression after 24h exposed to Glucagon_H_11-2 in rat liver cell

value: 1 ppm

value: Male


title: Glucagon_M_11-2_R

value: Glucagon, 0.3 ppm_2

value: primary rat hepatocytes, rtNHeps


title: Glucagon_L_11-1

description: Gene Expression after 24h exposed to Glucagon_L_11-1 in rat liver cell


title: Glucagon_C_11-1

description: Gene Expression after 24h exposed to Glucagon_control set_11-1 in rat liver cell


title: DIMP_L_11-2_R

description: Gene Expression after 24h exposed to DIMP_L_11-2 in rat liver cell

value: 100 ppm


title: Glucagon_C_11-2_R

description: Gene Expression after 24h exposed to Glucagon_control set_11-2 in rat liver cell


title: DIMP_L_11-2


title: DIMP_H_11-1

description: Gene Expression after 24h exposed to DIMP_H_11-1 in rat liver cell


title: DIMP_H_11-2_R

description: Gene Expression after 24h exposed to DIMP_H_11-2 in rat liver cell


title: DIMP_M_11-2_R

value: Diisopropyl methylphosphonate (DIMP), 300 ppm_2


title: Glucagon_C_11-2


title: DIMP_L_11-1

description: Gene Expression after 24h exposed to DIMP_L_11-1 in rat liver cell


title: MethylCaproate_H_11-1_R

value: 10 ppm


title: DIMP_C_11-2_R

description: Gene Expression after 24h exposed to DIMP_control set_11-2 in rat liver cell


title: DIMP_H_11-2


title: Glucagon_H_11-2_R


title: DIMP_M_11-2

value: Diisopropyl methylphosphonate (DIMP), 300 ppm_1


title: Glucagon_M_11-2

value: Glucagon, 0.3 ppm_1


title: DIMP_C_11-1

description: Gene Expression after 24h exposed to DIMP_control set_11-1 in rat liver cell


title: Cr_M_11-2

description: Gene Expression after 24h exposed to Cr_M_11-2 in rat liver cell

value: Chromium [Potassium Dichromate (VI)], 0.1 ppm_1


title: Glucagon_L_11-2


title: Cr_M_11-2_R1

value: Chromium [Potassium Dichromate (VI)], 0.1 ppm_3


title: Cr_L_11-2_R

description: Gene Expression after 24h exposed to Cr_L_11-2 in rat liver cell

value: Chromium (sodium chromate)_0.03-3


title: Cr_M_11-2_R

value: Chromium [Potassium Dichromate (VI)], 0.1 ppm_2


title: Cr_L_11-1

description: Gene Expression after 24h exposed to Cr_L_11-1 in rat liver cell

value: Chromium (sodium chromate)_0.03-1


title: Cr_H_11-2

description: Gene Expression after 24h exposed to Cr_H_11-2 in rat liver cell

value: Chromium (sodium chromate)_0.3-1

value: 0.3 ppm


title: Cr_H_11-1

description: Gene Expression after 24h exposed to Cr_H_11-1 in rat liver cell

value: Chromium (sodium chromate)_0.3-3


title: DIMP_C_11-2


title: Cr_H_11-2_R

value: Chromium (sodium chromate)_0.3-2


title: Cr_C_11-2_R

description: Gene Expression after 24h exposed to Cr_control set_11-2 in rat liver cell

value: Chromium (sodium chromate)_Con-3

value: Male


title: Cr_C_11-2

value: Chromium (sodium chromate)_Con-2

value: primary rat hepatocytes, rtNHeps


title: CCl4_L_11-2

description: Gene Expression after 24h exposed to CCl4_L_11-2 in rat liver cell

value: Carbon tetrachloride_1-1

value: 1 ppm


title: CCl4_M_11-2

description: Gene Expression after 24h exposed to CCl4_M_11-2 in rat liver cell

value: Carbon Tetrachloride, 3 ppm_1

value: 3 ppm


title: CCl4_M_11-2_R

value: Carbon Tetrachloride, 3 ppm_2


title: CCl4_C_11-2_R

description: Gene Expression after 24h exposed to CCl4_control set_11-2 in rat liver cell

value: Carbon tetrachloride_Con-2


title: CCl4_H_11-1

description: Gene Expression after 24h exposed to CCl4_H_11-1 in rat liver cell

value: Carbon tetrachloride_10-3

value: 10 ppm


title: Cr_C_11-1

description: Gene Expression after 24h exposed to Cr_control set_11-1 in rat liver cell

value: Chromium (sodium chromate)_Con-1


title: CCl4_L_11-1

description: Gene Expression after 24h exposed to CCl4_L_11-1 in rat liver cell

value: Carbon tetrachloride_1-3


title: CCl4_L_11-2_R

value: Carbon tetrachloride_1-2


title: CCl4_H_11-2

description: Gene Expression after 24h exposed to CCl4_H_11-2 in rat liver cell

value: Carbon tetrachloride_10-1


title: BNF_M_11-2_R1

description: Gene Expression after 24h exposed to BNF_M_11-2 in rat liver cell

value: Beta-Naphthoflavone (BNF), 3 uM_3

value: 3 uM


title: CCl4_H_11-2_R

value: Carbon tetrachloride_10-2

value: Male


title: CCl4_C_11-2

value: Carbon tetrachloride_Con-1

value: primary rat hepatocytes, rtNHeps


title: BNF_L_11-2

description: Gene Expression after 24h exposed to BNF_L_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_1-1

value: 1 uM


title: BNF_M_11-2

value: Beta-Naphthoflavone (BNF), 3 uM_1


title: BNF_H_11-2_R

description: Gene Expression after 24h exposed to BNF_H_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_10-3

value: 10 uM


title: BNF_L_11-1

description: Gene Expression after 24h exposed to BNF_L_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_1-2


title: BNF_C_11-2_R

description: Gene Expression after 24h exposed to BNF_control set_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_Con3


title: Bap_M_11-2_R

description: Gene Expression after 24h exposed to Bap_M_11-2 in rat liver cell

value: Benzo(a)pyrene (BaP), 1 uM_3


title: BNF_H_11-1

description: Gene Expression after 24h exposed to BNF_H_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_10-1


title: BNF_M_11-2_R

value: Beta-Naphthoflavone (BNF), 3 uM_2


title: CCl4_M_11-2_R1

value: Carbon Tetrachloride, 3 ppm_3

value: 3 ppm


title: BNF_L_11-2_R

value: BaP (benzo(a)pyrene)_1-3


title: CCl4_C_11-1

description: Gene Expression after 24h exposed to CCl4_control set_11-1 in rat liver cell

value: Carbon tetrachloride_Con-3


title: BNF_C_11-1

description: Gene Expression after 24h exposed to BNF_control set_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_Con1

value: Male


title: Bap_L_11-2_R

description: Gene Expression after 24h exposed to Bap_L_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_0.3uM3

value: primary rat hepatocytes, rtNHeps


title: Bap_H_11-2

description: Gene Expression after 24h exposed to Bap_H_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_3uM2

value: 3 uM


title: Bap_M_11-2

value: Benzo(a)pyrene (BaP), 1 uM_1


title: Bap_C_11-2_R

description: Gene Expression after 24h exposed to Bap_control set_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_Con2


title: Bap_H_11-2_R

value: BaP (benzo(a)pyrene)_3uM3


title: Bap_L_11-1

description: Gene Expression after 24h exposed to Bap_L_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_0.3uM2


title: BNF_C_11-2


title: AS_M_11-2_R

description: Gene Expression after 24h exposed to AS_M_11-2 in rat liver cell

value: Arsenic [Sodium(meta)Arsenite], 0.3 ppm_3


title: MTX_L_11-2_R

description: Gene Expression after 24h exposed to MTX_L_11-2 in rat liver cell


title: Bap_L_11-2

value: BaP (benzo(a)pyrene)_0.3uM1


title: AS_M_11-2_R1

value: Arsenic [Sodium(meta)Arsenite], 0.3 ppm_2


title: Bap_H_11-1

description: Gene Expression after 24h exposed to Bap_H_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_3uM1


title: Bap_C_11-1

description: Gene Expression after 24h exposed to Bap_control set_11-1 in rat liver cell

value: BaP (benzo(a)pyrene)_Con3


title: BNF_H_11-2

value: BaP (benzo(a)pyrene)_10-2

value: 10 uM


title: AS_L_11-2

description: Gene Expression after 24h exposed to AS_L_11-2 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_0.1-1

value: 0.1 ppm


title: AS_M_11-2

value: Arsenic [Sodium(meta)Arsenite], 0.3 ppm_1

value: Male


title: AS_L_11-1

description: Gene Expression after 24h exposed to AS_L_11-1 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_0.1-3

value: primary rat hepatocytes, rtNHeps


title: AS_H_11-2_R

description: Gene Expression after 24h exposed to AS_H_11-2 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_1-3

value: 1 ppm


title: Bap_M_11-2_R1

value: Benzo(a)pyrene (BaP), 1 uM_2


title: AS_L_11-2_R

value: Arsenic (sodium (meta) arsenite)_0.1-2


title: AS_H_11-1

description: Gene Expression after 24h exposed to AS_H_11-1 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_1-1


title: AS_C_11-2_R

description: Gene Expression after 24h exposed to AS_control set_11-2 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_Con3


title: Aceto_M_11-2_R1

description: Gene Expression after 24h exposed to Aceto_M_11-2 in rat liver cell

value: Acetominophen, 3 mM_3


title: AS_C_11-1

description: Gene Expression after 24h exposed to AS_control set_11-1 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_Con1


title: AS_C_11-2

value: Arsenic (sodium (meta) arsenite)_Con2


title: Aceto_M_11-2

value: Acetominophen, 3 mM_1


title: Aceto_M_11-2_R

value: Acetominophen, 3 mM_2


title: Aceto_H_11-2_R

description: Gene Expression after 24h exposed to Aceto_H_11-2 in rat liver cell


title: Aceto_C_11-2_R

description: Gene Expression after 24h exposed to Aceto_control set_11-2 in rat liver cell


title: Aceto_H_11-1

description: Gene Expression after 24h exposed to Aceto_H_11-1 in rat liver cell


title: 9_Ketoconazole_90-2_R

description: Gene Expression after 24h exposed to 9_Ketoconazole_90-2 in rat liver cell


title: 9_Ketoconazole_90-2


title: Aceto_L_11-2

description: Gene Expression after 24h exposed to Aceto_L_11-2 in rat liver cell

value: 1 mM


title: Aceto_H_11-2


title: Aceto_C_11-1

description: Gene Expression after 24h exposed to Aceto_control set_11-1 in rat liver cell


title: 9_Ketoconazole_90-1

description: Gene Expression after 24h exposed to 9_Ketoconazole_90-1 in rat liver cell


title: 9_Dexamethasone_90-2_R

description: Gene Expression after 24h exposed to 9_Dexamethasone_90-2 in rat liver cell

value: 1 0 ppm


title: 9_Dexamethasone_90-1

description: Gene Expression after 24h exposed to 9_Dexamethasone_90-1 in rat liver cell


title: Aceto_L_11-2_R


title: Bap_C_11-2

description: Gene Expression after 24h exposed to Bap_control set_11-2 in rat liver cell

value: BaP (benzo(a)pyrene)_Con1


title: 9_Dexamethasone_90-2

value: Male


title: 9_DEHP_90-2_R

description: Gene Expression after 24h exposed to 9_DEHP_90-2 in rat liver cell

value: DEHP (di-(2-ethylhexyl)phthalate)_3


title: 8_Zinc_90-2_R

description: Gene Expression after 24h exposed to 8_Zinc_90-2 in rat liver cell

value: Zinc (zinc sulfate heptahydrate, ZnSO4.7H2O)_3

value: 10  ppm

value: primary rat hepatocytes, rtNHeps


title: 9_c_90-2

description: Gene Expression after 24h exposed to 9_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_2


title: 8_Zinc_90-2

value: Zinc (zinc sulfate heptahydrate, ZnSO4.7H2O)_1


title: 9_c_90-2_R

value: Solvent Control (DMSO)_3


title: 8_Selenium_90-1

description: Gene Expression after 24h exposed to 8_Selenium_90-1 in rat liver cell

value: Selenium (sodium selenite, Na2SeO3)_1

value: 0.1 ppm


title: 9_DEHP_90-2

value: DEHP (di-(2-ethylhexyl)phthalate)_2

value: 1 ppm