title: Stem tissue at 5 days NAA treatment, biological rep3

city: Wien

first: Javier

last: Agusti

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Gene expression data from stem tissue treated with NAA for 5 days in vitro not containing starch sheath or vascular bundles
5dNAA-C3_Rep3

hyb_protocol: Following fragmentation, the aRNAs were hybridized for 16 hr at 45C on GeneChip ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the RMA method using limma and affy libraries in the Bioconductor statiscal package (R2.9.0).

source_name: Arabidopsis stem tissue except the starch sheath and the vascular bundles after 5 days of NAA in vitro treatment

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown for 3 weeks on short days (8 hours light 16 hours dark)under standard conditions and then switched to lond days (16 hours light 8 hours dark)

extract_protocol: Total RNA extraction was performed using the RNeasy Plus Micro Kit (QIAGEN) following the manufacturer´s instructions.Two RNA amplification rounds were performed using the TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit (EPICENTRE Biotechnologies, Madison, WI, USA) following the manufacturer’s instructions.

treatment_protocol: Stem fragments of 1.5 cm in length located 2.5 cm apically from the base were excised with a scalpel and transferred to MS split-plates considering the original apical to basal orientation. After 2 or 5 days incubation, the central area (3 mm) of these samples, which had no direct contact with the media, was collected for snap-frozen embeding in OCT.Transversal 5 µm sections were cut with a cryostat and mounted in slides that were used to capture the appropriate tissue utilizing Laser Capture Microdissection.

value: stem tissue

tag: tissue collection method

value: laser capture microdissection

tag: genotype

value: wild type

tag: treatment

value: NAA treatment

tag: time

value: 5 days

tag: biological rep

tag: protocol

value: Stem tissue with NAA treatment


title: Cambium at 5 days NAA treatment, biological rep3

status: Public on Dec 31 2010

type: RNA

description:
Gene expression data from induced cambium after 5 days NAA in vitro treatment
5dNAA-CAM3_Rep3

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis established interfascicular cambium after 5 daysNAA in vitro treatment

tag: tissue

value: cambium

value: Interfascicular cambium induced after 5 days NAA in vitro treatment


title: Schizophrenia and Epilepsy-140

type: genomic

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

tag: cell type

value: lymphoblast cell line

tag: disease state

value: Schizophrenia and epilepsy

tag: id (rutgers)

tag: nimh identifier

tag: sex

value: M

source_name: blood

tag: sample type

value: blood

value: control


title: Stem tissue at 5 days NAA treatment, biological rep2

description:
Gene expression data from stem tissue treated with NAA for 5 days in vitro not containing starch sheath or vascular bundles
5dNAA-C2_Rep2


title: Starch sheath at 5 days MS incubation, biological rep3

description:
Gene expression data from stem starch sheath incubated for 5 days in MS media in-vitro
5dMS-SS3_Rep3

source_name: Arabidopsis stem starch sheath after 5 days MS incubation

value: starch sheath

value: MS incubation

value: Stem starch sheath incubated in MS media in vitro


title: Schizophrenia and Epilepsy-142


title: Schizophrenia and Epilepsy-146

value: F


title: Schizophrenia and Epilepsy-141


title: Schizophrenia and Epilepsy-143


title: Starch sheath at 5 days MS incubation, biological rep1

description:
Gene expression data from stem starch sheath incubated for 5 days in MS media in-vitro
5dMS-SS1_Rep1


title: Stem tissue at 5 days NAA treatment, biological rep1

description:
Gene expression data from stem tissue treated with NAA for 5 days in vitro not containing starch sheath or vascular bundles
5dNAA-C1_Rep1

value: stem tissue


title: Schizophrenia and Epilepsy-138


title: Cambium at 5 days NAA treatment, biological rep1

description:
Gene expression data from induced cambium after 5 days NAA in vitro treatment
5dNAA-CAM1_Rep1

value: laser capture microdissection


title: Schizophrenia and Epilepsy-145


title: Daphnia_LC25_ZnO_exp4,rep1

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: 9.0 mg/L ZnO NP

hyb_protocol: The labeled cDNA for the unexposed and exposed D. magna was mixed and hybridized to the D. magna cDNA microarray (protocols available at http://cmgm.stanford.edu/pbrown/mguide).

scan_protocol: Axon GenePix 4000B scanner

data_processing: Microarray images acquired from the scanner were analyzed using GenePix Pro 6.1 (Molecular Devices/MDS Analytical Technologies, Sunnyvale, CA).  Resulting GenePix result files were converted into a format compatible with The Institute for Genomic Research (TIGR) microarray software suite (TM4) using Express Converter (available through TIGR, www.tm4.org).  All downstream data analysis was performed using TIGR TM4 (available at www.tm4.org) (21).  Background subtracted signal intensities were normalized by total intensity and also underwent lowess normalization, standard deviation normalization using Microarray Data Analysis System ver. 2.19 (MIDAS).   In addition, MIDAS was used to check the consistency of dye flipped pairs and to detect outlier genes using slice analysis (22).  Normalized signal intensities were then analyzed using MultiExperiment Viewer ver. 4.3 (MeV) to detect differentially expressed genes using both a one-class T-test (23) and Statistical Analysis for Microarrays (SAM) (24) (user guide available at www-stat.stanford.edu/~tibs/SAM/).  The three resulting gene lists from MIDAS slice analysis, T-test, and SAM were compared and any genes not reproduced in at least two gene lists were eliminated.  The remaining genes were selected as candidate differentially expressed genes and were sequenced.

organism: Daphnia magna

source_name: unexposed 24h

label_protocol: RNA was reverse transcribed with M-MuLV Reverse Transcriptase (New England Biolabs, Ipswich, MA) in the presence of  aminoallyl-labeled dUTP (Applied Biosystems/Ambion, Austin, TX).  Flourescence labeling proceeded by incubating the aminoallyl-labeled cDNA with Cy5 or Cy3 fluorescent dyes (GE Healthcare, Piscataway, NJ).

growth_protocol: Daphnia magna were cultured at the US EPA culture facility in Cincinnati OH in Moderately Hard Reconstituted water at 25 degrees C.  They were fed 3 times weekly a combination of Pseudokirchneriella subcapitata and alfalfa extract.

extract_protocol: D. magna were removed from the exposure vessels with a pipet and immersed immediately in Tri Reagent (Molecular Research Center, Cincinnati, OH).  Whole organism daphnid tissue was homogenized for 5 min. at 30 vibrations/s using a Retsch MM 300 mixer mill (Retsch, Newtown, PA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK).  Following homogenization, RNA was isolated using Tri Reagent according to the manufacturer’s methods (Molecular Research Center, Cincinnati, OH) and treated with DNAse I using Ambion's DNAfree kit (Ambion, Austin, TX).

treatment_protocol: All exposures to the nanoparticles or Zn salt were conducted on adult female daphnids 10 days old and occurred at 25.0 C for 24 hours

value: 16 pooled daphnids

tag: age

value: 10d old

value: female

source_name: LC25 ZnO NP exposed 24 h


title: Schizophrenia and Epilepsy-139


title: Schizophrenia and Epilepsy-135


title: Schizophrenia and Epilepsy-144


title: Schizophrenia and Epilepsy-137


title: Starch sheath at 2 days MS incubation, biological rep3

description:
Gene expression data from stem starch sheath incubated for 2 days in MS media in-vitro
2dMS-SS3_Rep3

source_name: Arabidopsis stem starch sheath after 2 days MS incubation

value: wild type

value: 2 days


title: Schizophrenia and Epilepsy-134


title: Schizophrenia and Epilepsy-133


title: Schizophrenia and Epilepsy-136


title: Schizophrenia and Epilepsy-132


title: Schizophrenia and Epilepsy-131


title: Schizophrenia and Epilepsy-130


title: Starch sheath at 2 days MS incubation, biological rep2

description:
Gene expression data from stem starch sheath incubated for 2 days in MS media in-vitro
2dMS-SS2_Rep2


title: Starch sheath at 2 days MS incubation, biological rep1

description:
Gene expression data from stem starch sheath incubated for 2 days in MS media in-vitro
2dMS-SS1_Rep1


title: Starch sheath at 2 days NAA treatment, biological rep1

description:
Gene expression data from stem starch sheath treated for 2 days with NAA in-vitro
2dNAA-SS1_Rep1

source_name: Arabidopsis stem starch sheath after 2 days NAA in vitro treatment

value: NAA treatment

value: Stem starch sheath under NAA in vitro treatment before cell divission


title: Schizophrenia and Epilepsy-128

value: lymphoblast cell line

value: Schizophrenia and epilepsy


title: Stem tissue at 2 days NAA treatment, biological rep1

description:
Gene expression data from stem tissue treated with NAA for 2 days in vitro not containing starch sheath or vascular bundles
2dNAA-C1_Rep1

source_name: Arabidopsis stem tissue except the starch sheath and the vascular bundles after 2 days of NAA in vitro treatment

value: Stem tissue with NAA treatment


title: Stem tissue at T0, biological rep1

description:
Gene expression data from stem tissue not containing starch sheath or vascular bundles
0dC1_Rep1

source_name: Arabidopsis stem tissue except the starch sheath and the vascular bundles

value: untreated

value: control

value: Stem tissue with no treatment


title: Stem tissue at 2 days NAA treatment, biological rep2

description:
Gene expression data from stem tissue treated with NAA for 2 days in vitro not containing starch sheath or vascular bundles
2dNAA-C2_Rep2


title: Stem tissue at T0, biological rep3

description:
Gene expression data from stem tissue not containing starch sheath or vascular bundles
0dC3_Rep3


title: Stem tissue at T0, biological rep2

description:
Gene expression data from stem tissue not containing starch sheath or vascular bundles
0dC2_Rep2


title: Starch sheath at T0, biological rep1

description:
Gene expression data from stem starch sheath
0dSS1_Rep1

source_name: Arabidopsis stem starch sheath

value: starch sheath

value: Stem starch sheath with no treatment before cell divission


title: Schizophrenia and Epilepsy-127

value: M

value: blood


title: Schizophrenia and Epilepsy-124


title: Schizophrenia and Epilepsy-126

value: F


title: Schizophrenia and Epilepsy-121


title: Starch sheath at T0, biological rep3

description:
Gene expression data from stem starch sheath
0dSS3_Rep3

value: laser capture microdissection


title: Starch sheath at T0, biological rep2

description:
Gene expression data from stem starch sheath
0dSS2_Rep2


title: Schizophrenia and Epilepsy-115


title: Schizophrenia and Epilepsy-120


title: rpp4_Emwa1_2dpi_rep1+rep2

city: Durham

first: Jinyoung

middle: Yang

last: Barnaby

state: NC

address: 4204 FFSC Bldg (Box 90338)

department: Biology

institute: Duke Univeristy

description: 2-week-old soil grown plants with no treatment used as 0 day reference.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm. .

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing:
Mixed-model ANOVA used to globally normalize all arrays and to identify differentially expressed probe sets is described in (Ref. 1 and 2).
Ref. 1: Brady, S. M. et al. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318, 801-806 (2007).
Ref. 2: Levesque, M. P. et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS biology 4, 1284-1284 (2006).

label_protocol: RNA probes were labelled using the GeneChip® Eukaryotic Small Sample Target Labelling Assay Version II.

growth_protocol: Arabidopsis seedlings were grown for 10 days at 16-18°C, 12-hr day length, 80-100% relative humidity

extract_protocol: Total RNA was isolated from the frozen material using the Qiagen RNeasy kit

treatment_protocol: 2-week old Col-0 wild-type plants and rpp4 mutants were infected with spores (500,000 spores / 1ml in dH2O) from 10-day old H. arabidopsidis EMWA1. Leaves were harvested at 0, 0.5, 2, 4, 6 days post-inoculation. Replicates are derived from two independent biological experiments, with no overlap in growing periods.

value: seedling

tag: genotype/variation

tag: pathogen

value: Hyaloperonospora arabidopsidis Emwa1

value: 2 dpi


title: Schizophrenia and Epilepsy-118


title: Schizophrenia and Epilepsy-125


title: rpp4_Emwa1_6dpi_rep1+rep2


title: Schizophrenia and Epilepsy-119


title: Schizophrenia and Epilepsy-122


title: rpp4_Emwa1_4dpi_rep1+rep2

value: 4 dpi


title: Schizophrenia and Epilepsy-116


title: WT_Emwa1_6dpi_rep1+rep2

value: WT


title: Schizophrenia and Epilepsy-123

value: lymphoblast cell line


title: Schizophrenia and Epilepsy-129

value: Schizophrenia and epilepsy


title: Schizophrenia and Epilepsy-117


title: rpp4_Emwa1_0.5dpi_rep1+rep2

value: 0.5 dpi


title: Schizophrenia and Epilepsy-114


title: Schizophrenia and Epilepsy-113


title: WT_Emwa1_4dpi_rep1+rep2


title: Schizophrenia and Epilepsy-111


title: Schizophrenia and Epilepsy-112


title: Schizophrenia and Epilepsy-110


title: Schizophrenia and Epilepsy-107


title: Schizophrenia and Epilepsy-109


title: Schizophrenia and Epilepsy-108


title: rpp4_Emwa1_0dpi_rep1+rep2

value: 0 dpi


title: WT_Emwa1_0dpi_rep1+rep2


title: Schizophrenia and Epilepsy-106

value: control


title: AP-2300_well_watered_predawn_rep3

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

description: Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073

data_processing: GC-RMA in BioConductor

organism: Populus balsamifera

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay

growth_protocol: All trees were grown in a climate-controlled growth chamber in 1m tall pots with a 0.1m diameter. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C.

extract_protocol: Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-11

treatment_protocol: After 9 weeks of growth without water limitation. No further input of water was given to 50% of plants. The other 50% were watered as before.

value: Mature leaf, including petiole

value: Clonally-propagated, 11-week-old P. balsamifera

tag: time of day

value: Leaves collected in the hour before lights were turned on (Pre-dawn)

tag: water status

value: Well-watered ie. 11 weeks without water limitation

tag: tissue provider

value: Alberta-Pacific, Alberta, CANADA


title: Schizophrenia and Epilepsy-100

value: M

value: blood


title: WT_Emwa1_2dpi_rep1+rep2

value: seedling


title: WT_Emwa1_0.5dpi_rep1+rep2

value: Hyaloperonospora arabidopsidis Emwa1


title: AP-2300_water_limited_predawn_rep3

tag: genotype

value: Water-limited ie. 9 weeks without water limitation followed by 15 days without further input of water


title: AP-2300_water_limited_midday_rep3

value: Leaves collected in the hour in the middle of the photoperiod (Mid-day)


title: Schizophrenia and Epilepsy-104

value: F


title: AP-2300_water_limited_midday_rep2


title: Schizophrenia and Epilepsy-103

value: lymphoblast cell line


title: AP-2300_water_limited_predawn_rep1


title: AP-2300_well_watered_midday_rep1


title: AP-2300_water_limited_midday_rep1


title: AP-2300_well_watered_predawn_rep2


title: AP-2300_well_watered_predawn_rep1


title: Schizophrenia and Epilepsy-97

value: Schizophrenia and epilepsy


title: AP-2300_water_limited_predawn_rep2


title: AP-2300_well_watered_midday_rep2


title: AP-2300_well_watered_midday_rep3


title: Schizophrenia and Epilepsy-95


title: Schizophrenia and Epilepsy-105


title: Schizophrenia and Epilepsy-96


title: Schizophrenia and Epilepsy-98


title: Schizophrenia and Epilepsy-101


title: AP-2298_water_limited_midday_rep3


title: AP-2298_water_limited_midday_rep2


title: Schizophrenia and Epilepsy-99


title: Schizophrenia and Epilepsy-102


title: Schizophrenia and Epilepsy-94


title: AP-2298_water_limited_predawn_rep3


title: Schizophrenia and Epilepsy-93


title: Schizophrenia and Epilepsy-92


title: AP-2298_well_watered_midday_rep2


title: AP-2298_well_watered_midday_rep1


title: Schizophrenia and Epilepsy-91


title: AP-2298_water_limited_predawn_rep2


title: AP-2298_water_limited_predawn_rep1


title: AP-2298_well_watered_predawn_rep3


title: AP-2298_well_watered_midday_rep3


title: AP-2278_water_limited_midday_rep3


title: AP-2298_well_watered_predawn_rep1


title: Schizophrenia and Epilepsy-84


title: Schizophrenia and Epilepsy-83


title: Schizophrenia and Epilepsy-85


title: Schizophrenia and Epilepsy-82


title: Schizophrenia and Epilepsy-90


title: Schizophrenia and Epilepsy-87


title: Schizophrenia and Epilepsy-86


title: AP-2298_water_limited_midday_rep1


title: AP-2298_well_watered_predawn_rep2


title: Schizophrenia and Epilepsy-89


title: AP-2278_water_limited_midday_rep1


title: Schizophrenia and Epilepsy-81


title: AP-2278_well_watered_midday_rep3


title: AP-2278_water_limited_midday_rep2


title: Schizophrenia and Epilepsy-88


title: Schizophrenia and Epilepsy-78


title: Schizophrenia and Epilepsy-80


title: AP-2278_well_watered_midday_rep1


title: Schizophrenia and Epilepsy-77


title: AP-2278_water_limited_predawn_rep3


title: Schizophrenia and Epilepsy-76


title: AP-2278_well_watered_midday_rep2


title: Schizophrenia and Epilepsy-74


title: Schizophrenia and Epilepsy-79


title: AP-2278_well_watered_predawn_rep2


title: AP-2278_water_limited_predawn_rep1


title: AP-1006_water_limited_midday_rep1


title: AP-1006_water_limited_midday_rep3


title: Schizophrenia and Epilepsy-75


title: Schizophrenia and Epilepsy-72


title: AP-2278_well_watered_predawn_rep3


title: AP-2278_well_watered_predawn_rep1


title: AP-1006_water_limited_midday_rep2


title: AP-2278_water_limited_predawn_rep2


title: Schizophrenia and Epilepsy-71


title: AP-1006_well_watered_midday_rep3


title: Schizophrenia and Epilepsy-69


title: Schizophrenia and Epilepsy-68


title: Schizophrenia and Epilepsy-70


title: Schizophrenia and Epilepsy-67


title: AP-1006_water_limited_predawn_rep3


title: AP-1006_well_watered_midday_rep2


title: Schizophrenia and Epilepsy-66


title: AP-1006_well_watered_midday_rep1


title: Schizophrenia and Epilepsy-64


title: Schizophrenia and Epilepsy-63


title: Schizophrenia and Epilepsy-62


title: Schizophrenia and Epilepsy-65


title: Schizophrenia and Epilepsy-73


title: Schizophrenia and Epilepsy-61


title: AP-1006_well_watered_predawn_rep3


title: AP-1006_water_limited_predawn_rep1


title: AP-1006_well_watered_predawn_rep2


title: AP-1005_well_watered_midday_rep2


title: AP-1005_water_limited_midday_rep2


title: Schizophrenia and Epilepsy-57


title: Schizophrenia and Epilepsy-60


title: Schizophrenia and Epilepsy-58


title: AP-1005_water_limited_midday_rep3


title: AP-1005_well_watered_midday_rep1


title: AP-1005_well_watered_midday_rep3


title: Schizophrenia and Epilepsy-59


title: Schizophrenia and Epilepsy-55


title: AP-1005_water_limited_midday_rep1


title: Schizophrenia and Epilepsy-52


title: AP-1005_water_limited_predawn_rep1


title: Schizophrenia and Epilepsy-53


title: AP-1005_water_limited_predawn_rep2


title: AP-1005_well_watered_predawn_rep3


title: Schizophrenia and Epilepsy-56


title: Schizophrenia and Epilepsy-54


title: AP-1006_well_watered_predawn_rep1


title: AP-1005_water_limited_predawn_rep3


title: Schizophrenia and Epilepsy-48


title: Schizophrenia and Epilepsy-50


title: Schizophrenia and Epilepsy-49


title: Schizophrenia and Epilepsy-51


title: AP-1005_well_watered_predawn_rep1


title: AP-1006_water_limited_predawn_rep2


title: AP-1005_well_watered_predawn_rep2


title: Schizophrenia and Epilepsy-46


title: Schizophrenia and Epilepsy-47


title: AP-947_water_limited_midday_rep3


title: Schizophrenia and Epilepsy-45


title: Schizophrenia and Epilepsy-44


title: AP-947_water_limited_midday_rep1


title: AP-947_well_watered_predawn_rep3


title: AP-947_water_limited_midday_rep2


title: AP-947_well_watered_midday_rep1


title: AP-947_well_watered_midday_rep3


title: AP-947_water_limited_predawn_rep3


title: AP-947_water_limited_predawn_rep1


title: Schizophrenia and Epilepsy-43


title: Schizophrenia and Epilepsy-40


title: Schizophrenia and Epilepsy-38


title: AP-947_well_watered_midday_rep2


title: Schizophrenia and Epilepsy-41


title: Schizophrenia and Epilepsy-37


title: AP-947_water_limited_predawn_rep2


title: Schizophrenia and Epilepsy-39


title: Schizophrenia and Epilepsy-36


title: Schizophrenia and Epilepsy-35


title: AP-947_well_watered_predawn_rep1


title: AP-947_well_watered_predawn_rep2


title: Schizophrenia and Epilepsy-31


title: Schizophrenia and Epilepsy-26


title: Schizophrenia and Epilepsy-30


title: Schizophrenia and Epilepsy-27


title: Schizophrenia and Epilepsy-42


title: Schizophrenia and Epilepsy-33


title: Schizophrenia and Epilepsy-20


title: Schizophrenia and Epilepsy-23


title: Schizophrenia and Epilepsy-25


title: Schizophrenia and Epilepsy-24


title: Schizophrenia and Epilepsy-29


title: Schizophrenia and Epilepsy-18


title: Schizophrenia and Epilepsy-32


title: Schizophrenia and Epilepsy-19


title: Schizophrenia and Epilepsy-28


title: Schizophrenia and Epilepsy-34


title: Schizophrenia and Epilepsy-15


title: Schizophrenia and Epilepsy-11


title: Schizophrenia and Epilepsy-21


title: Schizophrenia and Epilepsy-22


title: Schizophrenia and Epilepsy-13


title: Schizophrenia and Epilepsy-17


title: Schizophrenia and Epilepsy-14


title: Schizophrenia and Epilepsy-6


title: Schizophrenia and Epilepsy-16


title: Schizophrenia and Epilepsy-9


title: Schizophrenia and Epilepsy-10


title: Schizophrenia and Epilepsy-12


title: Control-191


title: Schizophrenia and Epilepsy-7


title: Schizophrenia and Epilepsy-8


title: Schizophrenia and Epilepsy-5


title: Control-189


title: Schizophrenia and Epilepsy-4


title: Schizophrenia and Epilepsy-1


title: Control-187


title: Control-180


title: Control-181


title: Control-190


title: Control-179


title: Control-184


title: Control-188


title: Shoots of root-wounded seedling  after 360 min replicate 2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Biological replicate 2 of 2. Shoots,  wounding of roots vs unwounding of roots, harvested after 360 min of wounding

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) containing fragmented Cydye-labeled cRNA labeled were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Wash Buffer 1 (6× SSPE, 0.005% N-lauroylsarcosine) and Wash Buffer 2 (0.06× SSPE, 0.005% N-lauroylsarcosine) for 1 min at room temperture.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.1.1).

data_processing: Agilent Feature Extraction Software (v 7.1.1) was used for background subtraction and LOWESS normalization.

source_name: Shoots, wounding of roots, 360min

label_protocol: Total RNA samples (400 ng) from untreated and treated shoots were used to prepare Cy3- or Cy5-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer's instructions

growth_protocol: Sterilised seeds (ecotype Columbia-0) were sown on Murashige and Skoog (MS) agar medium supplemented with 3% (w/v) sucrose and 0.25% (w/v) gelrite. After vernalization, plants were grown at 22ºC under long day conditions (16 h light/8 h dark) for 13days.

extract_protocol: Total RNA extracted using Agilent Plant RNA isolation Mini Kit (Agilent Technologies) following manufacturer's instructions

treatment_protocol: For wounding of roots, primary roots of Arabidopsis seedlings were wounded 5 mm from the shoot base using a razor blade. Shoots were then incubated in the growth chamber at the time indicated.

value: Shoots

tag: ecotype

tag: treatment

value: wounding of roots

tag: time after treatment

value: 360 min

source_name: Shoots, unwounding of roots, 360min

value: unwounding of roots


title: Shoots of root-wounded seedling  after 360 min replicate 2 (Dye Swap)

description: Dyeswap of Shoots of root-wounded seedling after 360 min replicate 2

tag: tissue


title: Control-186

tag: cell type

value: control


title: Shoots of root-wounded seedling after 30 min  replicate 1 (Dye Swap)

description: DyeSwap of shoots of root-wounded seedling after 30 min replicate 1

source_name: Shoots, unwounding of roots, 30min

value: 30 min

source_name: Shoots, wounding of roots, 30min


title: Shoots of root-wounded seedling after 360 min replicate 1

description: Biological replicate 1 of 2. Shoots,  wounding of roots vs unwounding of roots, harvested after 360 min of wounding


title: Control-182

tag: disease state


title: Shoots of root-wounded seedling  after 30 min replicate 2 (Dye Swap)

description: DyeSwap of shoots of root-wounded seedling after 30 min replicate 2


title: Control-178

tag: id (rutgers)


title: Shoots of root-wounded seedling  after 30 min replicate 2

description: Biological replicate 2 of 2. Shoots,  wounding of roots vs unwounding of roots, harvested after 30 min of wounding


title: Shoots of root-wounded seedling after 30 min replicate 1

description: Biological replicate 1 of 2. Shoots,  wounding of roots vs unwounding of roots, harvested after 30 min of wounding


title: Control-177

tag: nimh identifier


title: Control-185

tag: sex


title: Control-183

tag: sample type


title: Control-176


title: Schizophrenia and Epilepsy-2


title: Schizophrenia and Epilepsy-3


title: MEK5/CA transduced, cell line 10a, biological replicate 6

city: Ridgefield

first: Adedayo

last: Hanidu

address: 175 Briar Ridge Rd

description: Gene expression data from MEK5/CA Transduced HDMEC.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCOS 3000 7G Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 750. After exporting the .chp files and before data analsysis, probesets that were flagged as Absent in all the samples were eliminated from further data analysis.

source_name: MEK5/CA Transduced HDMEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Cells were grown to confluence in EGM2-MV growth medium on 75cm2 cultureware

extract_protocol: Rneasy kit (Qiagen) used to extract total RNA according to the manufacturer's instructions (DNAse treatment also performed)

treatment_protocol: Human endothelial cells were transduced with either MEK5/CA or LacZ control

value: Dermal Microvascular Endothelial Cells

tag: cell line

tag: transfectant

value: MEK5/CA transduced


title: MEK5/CA transduced, cell line 10, biological replicate 5


title: MEK5/CA transduced, cell line 11a, biological replicate 8


title: MEK5/CA transduced, cell line 6, biological replicate 1


title: Control-171

value: M


title: LacZ transduced, cell line 11a, biological replicate 8

description: Gene expression data from LacZ Transduced HDMEC.

source_name: LacZ Transduced HDMEC

value: LacZ transduced


title: MEK5/CA transduced, cell line 11, biological replicate 7


title: Control-172

value: blood


title: Control-170


title: MEK5/CA transduced, cell line 6a, biological replicate 2


title: MEK5/CA transduced, cell line 8d, biological replicate 3


title: Shoots of root-wounded seedling after 360 min  replicate 1 (Dye Swap)

description: DyeSwap of shoots of root-wounded seedling after 360 min replicate 1

tag: age


title: Control-173


title: Control-168


title: LacZ transduced, cell line 10, biological replicate 5


title: LacZ transduced, cell line 11, biological replicate 7


title: LacZ transduced, cell line 6a, biological replicate 2


title: Control-175


title: Control-167


title: LacZ transduced, cell line 10a, biological replicate 6


title: LacZ transduced, cell line 6, biological replicate 1


title: LacZ transduced, cell line 9a, biological replicate 4


title: LacZ transduced, cell line 8d, biological replicate 3


title: Control-165


title: Control-169


title: Control-174


title: Control-166


title: Control-164


title: T-regs from cord blood_SCO9

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

description: Gene expression data from cord blood T-regs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0

scan_protocol: GeneChips were scanned using the 7G Scanner

data_processing: The data were analyzed with dChip software. For normalization, model based expressions were computed for each array and probe set, using the PM-only model

source_name: T-regs from  cord blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Highly purified T-regs were cultured for 6 days in complete RPMI medium with IL-2, coated on a plate with anti-CD3 and anti- CD28

extract_protocol: Highly purified T-regs from either peripheral blood or cord blood were homogenized, and total RNA was extracted using Trizol.

treatment_protocol: MACS separation

value: cord blood

value: Regulatory T Cell (T-reg)


title: Control-163

source_name: lymphobast cell lines


title: T-regs from cord blood_SCO16


title: Oestrogen-deprieved T47D Tamoxifen Resistant cells

city: London

last: Hurst

address: Charterhouse Square

department: Centre for Tumour Biology

country: United Kingdom

institute: Institute of Cancer

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridised for 16 hours at 45C on HU133plus2.0 Human chip. Gene chip were washed and stained in Fluid Station 400.

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

data_processing: The data were analyzed with R/Bioconductor using RMA as normalization method.

source_name: Breast cancer cell line T47D grown in oestrogen deprieved and tamoxifen containing media.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol for 6ug total RNA (Protocol manual version 6)

growth_protocol: T47D and ZR75-1 were grown in their respective media according to ATCC protocol. The Oestrogen-deprieved (OD) T47D and OD ZR75-1 were grown using charcoal-stripped serum in phenol red free mediafor 6 months.

extract_protocol: RNAeasy Mini kit from Qiagen as per manufacturer protocol.

treatment_protocol: Tamoxifen Resistant cells were labelled as T47D TR, ZR TR, OD T47D TR and OD ZR TR respectively when the cells were grown in tamoxifen-containing media for at least 6 months.

tag: growth condition

value: This is a hypotriploid human breast cell

tag: biomaterial provider

value: ATCC


title: T-regs from cord blood_SCO6


title: T-regs from peripheral blood_BC8

description: Gene expression data from peripheral blood T-regs

source_name: T-regs from  peripheral blood

value: peripheral blood


title: ZR75-1 Tamoxifen resistant

description: ZRTR

source_name: Breast cancer cell line ZR75-1 grown in tamoxifen containing media.

value: grown in tamoxifen containing media


title: Control-160

value: lymphoblast cell line

source_name: blood


title: T-regs from peripheral blood_BC7


title: T-regs from peripheral blood_BC10


title: T-regs from cord blood_SCO15


title: T47D Tamoxifen resistant

source_name: Breast cancer cell line T47D grown in tamoxifen containing media.


title: Control-158


title: T-regs from peripheral blood_BC6


title: Oestrogen-deprieved ZR75-1 Tamoxifen Resistant cells

description: ODZRTR

source_name: Breast cancer cell line ZR75-1 grown in oestrogen deprieved and tamoxifen containing media.


title: Control-159


title: Control-162


title: T-regs from peripheral blood_BC9


title: recurrent miscarriage, 8 weeks

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000

data_processing: The raw intensity data (cel files) were analyzed with dChip2005 using invariant-set normalization and the PM-MM model

source_name: recurrent miscarriage, 8 weeks

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

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

tag: tissue type

value: placenta


title: Control-157


title: Control-156


title: recurrent miscarriage, 6.6 weeks, 1

source_name: recurrent miscarriage, 6.6 weeks


title: recurrent miscarriage, 6.6 weeks, 2


title: elective termination, 13 weeks

source_name: elective termination, 13 weeks


title: Control-155


title: elective termination, 8 weeks, 2

source_name: elective termination, 8 weeks


title: recurrent miscarriage, 14.6 weeks

source_name: recurrent miscarriage, 14.6 weeks


title: T-regs from peripheral blood_BC1


title: elective termination, 8 weeks, 3


title: MB231 transfected with Dmimic, biological rep3

city: Bethesda

first: Mark

last: Mackiewicz

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

description: Gene expression data of total RNA extracted from MB231 cells 48hrs post-transfection

hyb_protocol: cRNA was hybridized for 16 hrs at 45C (60 rpm).  GeneChips were washed and stained in the Affymetrix FS450 fluidics station.

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip 3000 Scanner.  Data was collected using Affymetrix GCOS software.

data_processing: Expression values were normalized using Robust Multichip Averaging (RMA).  Analyses were performed with Bioconductor packages AFFYGUI and LIMMA on a R environment.

source_name: MDA-MB-231 cells grown in 6 well dishes 48 hrs post-transfection

label_protocol: RNA quality ws assessed on an Agilent Bioanalyzer.  Total RNA (1 ug) was reverse transcribed with T7-oligo(dT) primer and labeled with biotin using Affymetrix One Cycle Target Labeling kit following the manufacturer's protocol.

growth_protocol: MDA-MB-231 cells were grown in T75 flasks containing RPMI 1640 basal medium + 10% Fetal Bovine Serum at 37C with 5% CO2.  Cells at 80-90% confluency were used in transfections.

extract_protocol: At 48 hrs post-transfection, total RNA was extracted from each well using Qiagen's miRNeasy extraction kit according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231 cells (600,000 cells/well) were reverse transfected in 6 well dishes with either AllStar negative control, Qmimic, or Dmimic at 10 nM final concentration using Lipofectamine 2000 (10.5 ul/well),


title: elective termination, 11 weeks

source_name: elective termination, 11 weeks


title: Control-154


title: Control-153


title: Control-151


title: elective termination, 4 weeks

source_name: elective termination, 4 weeks


title: Control-146


title: MB231 transfected with Dmimic, biological rep1


title: elective termination, 8 weeks, 1


title: MB231 transfected with Dmimic, biological rep2


title: Control-142


title: MB231 transfected with Qmimic, biological rep1


title: MB231 transfected with Qmimic, biological rep3


title: MB231 transfected with AllStar, biological rep3


title: Control-140


title: Control-141


title: oligodendrogliomas at T2, biological rep5

city: Luoyang

first: Zhiqiang

last: Yao

state: Henan

address: No.288, Zhongzhou Road

department: Neurosurgery

country: China

institute: No.150 Military Central Hospital

description: gene expression data from WHO grade Ⅱ oligodendrogliomas pathological resected tissues

hyb_protocol: Carry out the hybridization process in a affymetrix hybridazaiton Oven 640, P/N28320.

scan_protocol: Use Affymetrix GeneChip Scaner 3000 controlled by Affymetrix Microarray Suit or GCOS to aquire the hybridization image.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Oligodendrogliomas(WHO grade Ⅱ)

label_protocol: Use One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493 to label the 3' termini of the fragmentation products.

value: glioma tumor

tag: tumor type

value: oligodendroglioma

tag: tumor grade

value: WHO grade II


title: MB231 transfected with Qmimic, biological rep2


title: Control-161

value: control


title: Control-139


title: MB231 transfected with AllStar, biological rep1


title: MEK5/CA transduced, cell line 9a, biological replicate 4

source_name: MEK5/CA Transduced HDMEC

value: Dermal Microvascular Endothelial Cells


title: Control-138

source_name: lymphobast cell lines


title: MB231 transfected with AllStar, biological rep2


title: oligodendrogliomas at T2, biological rep2


title: Control-137


title: Control-135


title: Control-136


title: oligodendrogliomas at T2, biological rep1


title: oligodendrogliomas at T2, biological rep4


title: ependymomas at T2, biological rep4

description: gene expression data from WHO grade Ⅱ ependymomas pathological resected tissues

source_name: Ependymomas (WHO grade Ⅱ)

value: ependymoma


title: ependymomas at T2, biological rep3


title: ependymomas at T2, biological rep2


title: Control-134

value: M


title: normal tissue,biological rep4

description: gene expression data from normal brain tissue

hyb_protocol: Carry out the hybridization process in a affymetrix  hybridazaiton Oven 640 ,P/N28320.

scan_protocol: Use Affymetrix GeneChip  Scaner 3000 controlled by Affymetrix Microarray Suit or GCOS to aquire the hybridization image.

source_name: normal brain tissue

value: normal brain sample


title: ependymomas at T2, biological rep1


title: Control-133

value: blood


title: normal tissue,biological rep3

value: F


title: Control-129


title: normal tissue,biological rep2

label_protocol: Use One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493 to label the 3' termini of the fragmentation products


title: Control-128


title: choroid-cellline-2

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

description: Eyes 5.CEL

hyb_protocol: The cRNA samples were then fragmented and hybridised onto Affymetrix GeneChip ® Human Genome U133 Plus 2.0 arrays (Affymetrix, High Wycombe, Bucks, UK) by incubating at 45°C for 16 hours. Washing and staining of the arrays were carried out following Affymetrix GeneChip ® protocols using a Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000. GCOS software (Affymetrix) was used to monitor scanning and to convert the raw image files into cell intensity files (‘.CEL’).

data_processing: CEL files were processed with the BioConductor gcrma function from the simpleaffy package.

source_name: vascular endothelial choroid cells

label_protocol: Biotinylated cRNA probes were prepared from the total RNA samples (1µg) using the microarray target amplification kit and the microarray target RNA synthesis kit (both Roche Applied Sciences) following the manufacturer’s instructions.

growth_protocol: Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: The total RNA was extracted from primary cultures of unpassaged endothelial cells when they had reached approximately 80% confluence, using the Qiagen  RNeasy minikit as directed (Qiagen, Crawley, UK). Approximately 5μg of total RNA was obtained from each 35mm culture plate. RNA integrity and quality was assessed using an Agilent 2100 Bioanalyser and RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: Matched human ocular MVEC were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of human macular inner choroidal endothelial cells utilising anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK) was used with the substitution of macular choroidal tissue with isolated iris, retinal and choroidal tissues (PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129).

value: choroid

value: vascular endothelial cells


title: huvec-cellline-1

description: Eyes 7.CEL

source_name: umbilical vein endothelial cells

value: umbilical vein

value: umbilical vein endothelial cells (HUVEC)


title: retina-cellline-3

description: Eyes 20.CEL

source_name: vascular endothelial retina cells

value: retina


title: retina-cellline-2

description: Eyes 12.CEL


title: choroid-cellline-3

description: Eyes 6.CEL


title: iris-cellline-2

description: Eyes 2.CEL

source_name: vascular endothelial iris cells

value: iris


title: Control-127

value: lymphoblast cell line

source_name: blood


title: Control-121


title: iris-cellline-3

description: Eyes 3.CEL


title: retina-cellline-1

description: Eyes 11.CEL


title: iris-cellline-1

description: Eyes 1.CEL


title: Control-120


title: huvec-cellline-3

description: Eyes 9.CEL


title: Control-112


title: IND3PED DChip

city: Toledo

first: Manuel

last: Nieto-Diaz

state: Toledo

address: Finca La Peraleda s/n

department: Unidad de Neurología Experimental

country: Spain

institute: Hospital Nacional de Parapléjicos (SESCAM)

hyb_protocol: Affymetrix standard protocols

scan_protocol: Affymetrix standard protocols

data_processing: CEL files were processed using R. Processing following MAS5, GCRMA, RMA, and Dchip methodologies

organism: Cervus elaphus

source_name: PEDICLE SKIN

label_protocol: Affymetrix standard protocols and reactives

extract_protocol: samples from pedicle and frontal skin were extracted using 4mm biopsy punches while samples from velvet and mesenchyme were extracted after section of the antler tip. Animals were in all cases anesthetized

treatment_protocol: no treatments

tag: individual

tag: sampling method

value: PUNCH

value: pedicle skin


title: choroid-cellline-1

description: Eyes 4.CEL

tag: tissue


title: IND3FRNT DChip

source_name: FRONTAL SKIN

value: frontal skin


title: huvec-cellline-2

description: Eyes 8.CEL

tag: cell type


title: oligodendrogliomas at T2, biological rep3

value: glioma tumor

value: oligodendroglioma

value: WHO grade II


title: Control-110

tag: disease state

value: control

value: M


title: IND3MSCH DChip

source_name: MESEMCHYME

value: SURGERY

value: mesemchyme


title: Control-118

tag: id (rutgers)

value: blood


title: IND2MSCH DChip


title: IND2FRNT DChip


title: IND2VLVT DChip

source_name: VELVET

value: antler velvet


title: IND3VLVT DChip


title: Control-109

tag: nimh identifier


title: IND1PED DChip


title: IND2PED DChip


title: IND1FRNT DChip


title: Control-107

tag: sex


title: IND1MSCH DChip


title: Control-108

tag: sample type


title: IND1VLVT DChip


title: Control-106


title: Control-105


title: Control-104


title: IND3FRNT GCRMA


title: IND2FRNT GCRMA


title: IND3PED GCRMA


title: IND1PED GCRMA


title: IND3MSCH GCRMA


title: IND2PED GCRMA


title: IND1VLVT GCRMA


title: Control-103


title: IND3VLVT GCRMA


title: IND2PED RMA


title: IND3FRNT RMA


title: IND1MSCH GCRMA


title: IND2MSCH GCRMA


title: IND3MSCH RMA


title: IND3PED RMA


title: IND2VLVT GCRMA


title: Control-115


title: IND1FRNT GCRMA


title: IND2FRNT RMA


title: Control-100


title: Control-102


title: Control-95


title: Control-113


title: Control-99


title: IND3VLVT RMA


title: IND2VLVT RMA


title: Control-96


title: IND2MSCH RMA


title: Control-101


title: IND3VLVT MAS5


title: IND3MSCH MAS5


title: IND1MSCH RMA


title: IND1PED RMA


title: IND1FRNT RMA


title: IND1PED MAS5


title: IND2FRNT MAS5


title: IND2VLVT MAS5


title: IND3FRNT MAS5


title: IND3PED MAS5


title: IND2MSCH MAS5


title: IND1VLVT RMA


title: IND1MSCH MAS5


title: Control-91

value: F


title: IND1VLVT MAS5


title: Control-88


title: Control-93


title: IND2PED MAS5


title: Control-87


title: Control-92


title: Multiple sclerosis CD8+T cells 16-US

first: Viviana

last: Annibali

address: Via di Grottarossa,1035

institute: University of Rome "Sapienza"

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.

label: Biotin

source_name: CD8+T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).

value: Multiple sclerosis

tag: twin

value: U


title: Control-94


title: Healthy CD8+T cells 14-UD

value: Healthy


title: Control-89

value: lymphoblast cell line


title: Healthy CD8+T cells 12-RP

value: R


title: IND1FRNT MAS5

value: PUNCH


title: Control-90


title: Healthy CD8+T cells 6-PS

value: P


title: Control-83


title: Multiple sclerosis CD8+T cells 8-PM


title: Control-86


title: Healthy CD4+T cells 11-RP

source_name: CD4+T cells


title: Healthy CD8+T cells 2-TP

value: T


title: Control-85


title: Multiple sclerosis CD4+T cells 15-US


title: Multiple sclerosis CD8+T cells 10-RS


title: Multiple sclerosis CD4+T cells 9-RS


title: Multiple sclerosis CD8+T cells 4-TE


title: Healthy CD4+T cells 13-UD


title: Multiple sclerosis CD4+T cells 7-PM


title: Healthy CD4+T cells 5-PS


title: Control-82


title: Control-80


title: Control-78


title: Multiple sclerosis CD4+T cells 3-TE


title: NO_Kidney_Ref_SNP_Xba

city: Grand Rapids

first: Bin

middle: Tean

last: Teh

state: MI

address: 330 Bostwick Av

department: Cancer Genetics

institute: Van Andel Institute

description:
Ref
Hybridized to 50K Xba

hyb_protocol: Following fragmentation, 40 ug of genomic DNA was hybridized for 16 hr at 48C on Affymetrix GeneChip Human Mapping 50K chip, either Xba Array or Hind array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing:
Starting from the CEL files, we used the R package oligo (48) to read the raw SNP data set. The result is an object containing the summarized signals of either A or B allele, of sense or antisense strand for each SNP on the array. The SNP's A or B allele signal was averaged by its sense and antisense signals respectively. To obtain SNP raw copy numbers, we used a total of 56 normal references either downloaded from Affymetrix (n = 48) or obtained by our own scan on normal kidney tissues (n = 8) to calculate the reference signals for each SNP's A and B alleles. The overall signal for the SNP was the sum of its A and B signals. The raw copy number for a SNP of a target sample was its overall signal subtracted by the averaged overall signals from the normal references (as all signals are in logarithm scale). We then used a divide-and-conquer algorithm to partition the raw copy numbers into segments based on the maximum likelihood estimate of the break points. It is a top-down algorithm to speed up the segmentation process. The raw copy numbers of SNPs within any identified segment will be regarded identical. The (one-sided t-) test score (to test location=0) would replace the raw copy numbers within the identified segment and was reported thereafter. A segment identified in an individual sample would be declared either a gain or a loss if the score for the segment was larger or smaller than a preselected cutoff value (e.g., 10). The actual segmentation algorithm was a two round algorithm. In the first round, the algorithm identifies segments with unusual large or small test scores (e.g., 5 standard deviations away from the mean), will mark the segment as outliers. The reported scores were actually the output from the second round of segmentation based on the raw copy numbers after removal of the outliers identified from the first round.
Table containing t-test scores of identified segmental gains or losses is provided as a supplementary file on the Series record.

label: R-Phycoerythrin Streptavidin (SAPE)

source_name: Normal kidney tissue

label_protocol: 40 ug per Xba1 chip and 40 ug per HindIII chip. Purified pooled 3 Xba1 PCRs with 3 pooled HindIII PCRs. R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml (we use 6ul per reaction).

extract_protocol: extraction of total Genomic DNA was performed using Genomed JETquick tissue DNA Maxi Kit (part # 452050), according to manufacturers instructions.

value: Normal kidney tissue


title: NO_Kidney_057_SNP_Xba

description:
GR057N
Hybridized to 50K Xba

tag: gender


title: NO_Kidney_061_SNP_Xba

description:
GR061N
Hybridized to 50K Xba


title: Nr1_neg

city: Wuerzburg

first: Claudia

last: Beyrich

address: Grombuehlstr. 12

department: IKBZ

country: Germany

institute: University of Wuerzburg

description: Gene expression data from HCAEC, treated with LB-medium

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG U 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method using perfect match only.

source_name: HCAEC

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

growth_protocol: HCAEC were grown in EBM2-medium to subconfluency

extract_protocol: total RNA was isolated using the Rneasy Mini Kit from Quiagen (including Dnase digest)

treatment_protocol: cells were treated with LB medium only

tag: cells

value: Clonetics® HCAEC-Human Coronary Artery Endothelial Cells


title: Control-81

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

value: control


title: NO_Kidney_049_SNP_Xba

description:
GR049N
Hybridized to 50K Xba

value: M

tag: ethnicity

value: W


title: NO_Kidney_201_SNP_Xba

description:
GR201N
Hybridized to 50K Xba


title: Control-84


title: Nr2_6h

description: Gene expression data from HCAEC, treated with GBS in LB medium

treatment_protocol: GBS (ATCC®13813 strain, serotype V, septic), diluted in LB medium, were added in multiplicity of infection (MOI) of 20 to HCAEC


title: NO_Kidney_116_SNP_Xba

description:
GR116N
Hybridized to 50K Xba


title: Healthy CD4+T cells 1-TP


title: NO_Kidney_066_SNP_Xba

description:
GR066N
Hybridized to 50K Xba


title: NO_Kidney_111_SNP_Xba

description:
GR111N
Hybridized to 50K Xba


title: Control-73


title: Control-79


title: Control-74


title: Control-75


title: CC_Kidney_202_SNP_Xba

description:
GR202T
Hybridized to 50K Xba

source_name: Clear cell renal cell caricinoma

value: Clear cell renal cell caricinoma

tag: tumor size(cm)


title: CC_Kidney_201_SNP_Xba

description:
GR201T
Hybridized to 50K Xba


title: CC_Kidney_207_SNP_Xba

description:
GR207T
Hybridized to 50K Xba


title: Control-71

source_name: lymphobast cell lines

value: blood


title: CC_Kidney_T057_SNP_Xba

description:
GT057T
Hybridized to 50K Xba


title: Control-72


title: Control-66


title: CC_Kidney_179_SNP_Xba

description:
GR179T
Hybridized to 50K Xba


title: Control-76


title: CC_Kidney_156_SNP_Xba

description:
GR156T
Hybridized to 50K Xba


title: Control-70


title: CC_Kidney_153_SNP_Xba

description:
GR153T
Hybridized to 50K Xba


title: Control-67


title: Control-77


title: CC_Kidney_138_SNP_Xba

description:
GR138T
Hybridized to 50K Xba


title: CC_Kidney_127_SNP_Xba

description:
GR127T
Hybridized to 50K Xba


title: CC_Kidney_124_SNP_Xba

description:
GR124T
Hybridized to 50K Xba


title: Control-61


title: CC_Kidney_198_SNP_Xba

description:
GR198T
Hybridized to 50K Xba


title: CC_Kidney_113_SNP_Xba

description:
GR113T
Hybridized to 50K Xba


title: Control-69


title: Control-64


title: Control-65


title: Control-60


title: CC_Kidney_116_SNP_Xba

description:
GR116T
Hybridized to 50K Xba


title: Control-68


title: CC_Kidney_111_SNP_Xba

description:
GR111T
Hybridized to 50K Xba


title: Control-57


title: Control-62


title: Control-58


title: Control-63


title: Tg(krt4:myrAkt1)_rep2

city: Chung-Li

first: Chung-Der

last: Hsiao

address: 200, Chung-Pei Rd.

department: Bioscience Technology

country: Taiwan

institute: Chung Yuan Christian University

description:
the ab strain of zebrafish (danio rerio) were obtained from zirc (http: //zebrafish.org/zirc/home/guide.php), and kept in the stock of Chung Yuan Christian University.
The commercial Zebrafish 14K oligo microarray chip was obtained from Institute of Cellular and Organismic Biology at Academia Sinica and contained 14067 oligonucleotides represent 9666 unique genes with a redundancy of 31%. The detail oligonucleotide description can be obtained from Ocimun Biosolution (http://www.ocimumbio.com/web/default.asp).

hyb_protocol: Before hybridization, the Zebrafish microarray chips were pretreated with 1% bovine serum albumin, 4X SCC, and 1% sodium dodecylsulfate (SDS) for 45min at 42℃, and then hybridized in SlideHybTM buffer (Ambion) for overnight at 42℃.

scan_protocol: After hybridization, chips were washed with 2X SSC and 0.5% SDS for 15min at 25℃ and finally with 0.5X SSC and 0.5% SDS for 15min at 25℃. The fluorescence intensities of Alexa Fluor 555 and Alexa Fluor 647 targets were scanned by Genepix scanner (Molecular Devices, Sunnyvale, CA, USA) and the acquired date were analyzed by Genepix and Genespring software (Aglient Technologies, Foster City, CA, USA).

data_processing: The measurements of spots were filtered by flags, and Lowess normalization was performed after subtraction of the median background. The VALUE indicated the transformation algorithm of Cy5/Cy3 normalized log2 ratio, which was used to identify the 247 genes which were selected from those with at least 2 of 3 significant signals (ratio > 1.75 or < 0.5).

organism: Danio rerio

source_name: Tg(krt4:myrAkt1) tail tissue

label_protocol: We used SuperScriptTM Indirect cDNA Labeling System kit (Invitrogen) to generate the fluorescently labeled probes. Total RNA isolated from WT and Tg(krt4:myrAkt1)cy18 were reversed transcribed into cDNA and coupling for Alexa Fluor 555 and Alexa Fluor 647 fluorescent dyes (Invitrogen), respectively.

extract_protocol: We dissected two tail tissues (as a pooled sample) from six month-old wild-type and Tg(krt4:myrAkt1)cy18 (n=5), and homogenized in Trizol reagent (Ambion) to isolate total RNA according to the manufacture instruction. The RNA was treated with DNase I at 25℃ for 10 minutes to remove DNA contamination and then cleanup by RNase-free spin columns (Qiagen). The total RNA concentration was determined by spectrophotometry (ND-1000 ; NanoDrop Technol, Wilmington, DE), and the RNA quality was checked by running electrophoresis in RNA-denatured gels. All total RNA were stored at -20℃.

tag: genetic background

value: AB

tag: genotype

value: tail

source_name: Wild-type tail tissues

value: wild type


title: Tg(krt4:myrAkt1)_rep1


title: Tg(krt4:myrAkt1)_rep3


title: CC_Kidney_106_SNP_Xba

description:
GR106T
Hybridized to 50K Xba

value: F


title: Control-56

last: Hall

address: One Baylor Plaza

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)


title: Control-59


title: CC_Kidney_091_SNP_Xba

description:
GR091T
Hybridized to 50K Xba


title: Control-53


title: Control-54


title: CC_Kidney_078_SNP_Xba

description:
GR078T
Hybridized to 50K Xba


title: Control-51


title: Control-55


title: CC_Kidney_066_SNP_Xba

description:
GR066T
Hybridized to 50K Xba

tag: tumor grade

value: II~III

tag: tumor stage


title: Control-48

value: lymphoblast cell line


title: Control-49


title: Control-50


title: NFAT5 siRNA transfected HUVEC biological replicate 4

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: HUVECs were isolated from normal-term umbilical cord veins and maintained in M 199 medium containing 20% FCS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1)

source_name: HUVEC

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: FLS: refer to [PMID:16888030], HUVEC: maintained in M 199 medium containing 20% FCS

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: HUVEC

value: Human umbilical vascular endothelial cells (HUVEC)

tag: transfection

value: NFAT5 siRNA


title: Control-52

city: Houston

first: April

institute: Baylor College of Medicine

tag: cell type

tag: tissue


title: CC_Kidney_076_SNP_Xba

description:
GR076T
Hybridized to 50K Xba

value: H

value: IV


title: Non-transfected HUVEC biological replicate 4


title: Control siRNA transfected HUVEC biological replicate 4

value: control siRNA


title: Control-46

tag: disease state

value: control

tag: id (rutgers)


title: Control-47

tag: nimh identifier

tag: sex

value: M


title: Non-transfected HUVEC biological replicate 3


title: Control siRNA transfected HUVEC biological replicate 2


title: NFAT5 siRNA transfected HUVEC biological replicate 3


title: CC_Kidney_061_SNP_Xba

description:
GR061T
Hybridized to 50K Xba

value: II


title: CC_Kidney_057_SNP_Xba

description:
GR057T
Hybridized to 50K Xba

value: Clear cell renal cell caricinoma


title: Non-transfected HUVEC biological replicate 2


title: tumor cells from bladder bU29

description: tumor cells from bladder

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used. Data were then rma normalized using R and the bioconductor suite of analysis tools (eset <- rma(ab))

source_name: urothelial cell carcinoma from bladder

label_protocol: 10 ug of Qiagen-purified total RNA was labeled with 6ul of 1mg/ml R-Phycoerythrin Streptavidin (SAPE)

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's protocol

value: urothelial cell carcinoma

tag: tissues

value: Stroma Admixed


title: tumor cells from bladder bU12

description: tumor cells from bladder


title: NFAT5 siRNA transfected HUVEC biological replicate 1


title: tumor cells from bladder bU28

description: tumor cells from bladder

value: Extensive Stroma admixed


title: tumor cells from bladder bU31

description: tumor cells from bladder


title: NFAT5 siRNA transfected HUVEC biological replicate 2


title: CC_Kidney_055_SNP_Xba

description:
GR055T
Hybridized to 50K Xba

tag: gender

value: W


title: Control siRNA transfected HUVEC biological replicate 1


title: CC_Kidney_059_SNP_Xba

description:
GR059T
Hybridized to 50K Xba

value: F

value: (IV)


title: Control-44

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

value: lymphoblast cell line

tag: sample type

value: blood


title: CC_Kidney_049_SNP_Xba

description:
GR049T
Hybridized to 50K Xba

tag: ethnicity

value: III


title: Control-43


title: Control-45


title: Non-transfected HUVEC biological replicate 1

value: HUVEC

value: Primary fibroblast-like synoviocytes drived from patients with rheumatoid arthritis


title: Control-42


title: Control-41


title: Meibomian Glands Female Diseased Replicate 6

city: Boston

first: David

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: The eyelids used in this study were obtained from tissues removed during surgeries. Immediately after removal the eyelids were placed in RNAlater (Ambion, Austin, TX) and stored at 4º C overnight.  The tissues were then store at -80º C until needed. Prior to the surgeries, the meibomian gland disease state of the patient was evaluated by an opthamologist using the meibum quality criteria described by Bron et al., 1991

hyb_protocol: Labeled cRNA was used to probe HumanHT-12 v3 Expression BeadChips.  Hybridization, washing, and scanning of the Illumina arrays were carried out according to the manufacturer’s instructions.  Briefly, cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.  BeadChips were washed and stained in the following steps:  1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer.  BeadArrays were dried in a centrifuge for 4 minutes.

scan_protocol: BeadArrays were scanned with a BeadArray scanner.  Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 12 arrays.  Raw data were extracted using Illumina BeadStudio software v 3.

data_processing:
Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report containing the project description (sample key), gene identifiers and corresponding probe IDs, table of detection p-values, tables of normalized data with and without background subtraction, array quality control metrics, and array quality control metric cut-offs and definitions.
Cubic spline normalizaed data produced by BeadStudio software were selected for use in this study.  In Excel,  the cubic spline data were further processed by setting  negative values to zero and then adding 16 to all intensities.
The raw data provided has no background subtraction.

source_name: Sections of eye lids removed during surgeries

label_protocol: Samples for mRNA profiling studies were processed by Asuragen, Inc., according to the company’s standard operating procedures.  The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer.  The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis.  Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using a MessageAmp™ II-based protocol (Ambion Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: Total RNA was isolated from the lid tissues using a RNAqueous Kit (Ambion). After thawing, the tarsal plates, containing the meibomian glands, were trimmed of excessive skin and connective tissues.  The tarsal plates were weighed to ensure that the tissue did not exceed the 75 mg capacity of the RNAqueous spin columns and then cut into small pieces using a fresh razor blade.  The tissues were then place in a microfuge tube containing RNAqueous Lysis Buffer and homogenized using Pellet Pestle Cordless Motor (Kimble Chase, Vineland, NJ).  Total RNA was then bound to the spin columns following the procedure Ambion provide with the RNAqueous Kit. To elute the RNA each column was washed twice with 85°C nuclease free water, an initial elution of 30µl followed by 20 µl. The RNA concentration and 260/280 nm ratio of each sample was determined using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham MA) and the integrity of the RNA assayed on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with RNA Nano 6000 Series II Chips (Agilent Technologies).

value: Female

tag: age

tag: meibomian gland secretion grade

tag: meibomian gland disease state

value: Moderate

value: tarsal plate of the eyelid


title: CC_Kidney_034_SNP_Xba

description:
GR034T
Hybridized to 50K Xba

tag: tumor grade

tag: tumor size(cm)


title: Control siRNA transfected HUVEC biological replicate 3

tag: cell line

value: Human umbilical vascular endothelial cells (HUVEC)

value: control siRNA


title: CC_Kidney_040_SNP_Xba

description:
GR040T
Hybridized to 50K Xba

value: Clear cell renal cell caricinoma

value: B

value: II

tag: tumor stage


title: tumor cells from bladder bU09

description: tumor cells from bladder

value: urothelial cell carcinoma


title: CC_Kidney_015_SNP_Xba

description:
GR015T
Hybridized to 50K Xba

value: II~III


title: Control-40

tag: cell type

value: control

value: F

value: M


title: tumor cells from bladder bU10

description: tumor cells from bladder


title: Control-39

value: lymphoblast cell line

tag: tissue

value: blood


title: tumor cells from bladder bU07

description: tumor cells from bladder

tag: disease state


title: Meibomian Glands Male Diseased Replicate 4

value: Male

value: Severe


title: CC_Kidney_025_SNP_Xba

description:
GR025T
Hybridized to 50K Xba

value: W


title: CC_Kidney_018_SNP_Xba

description:
GR018T
Hybridized to 50K Xba

value: III


title: tumor cells from bladder bU02

description: tumor cells from bladder


title: Meibomian Glands Female Diseased Replicate 3

value: Female

value: Moderate

value: tarsal plate of the eyelid


title: CC_Kidney_011_SNP_Xba

description:
GR011T
Hybridized to 50K Xba

value: Clear cell renal cell caricinoma


title: Meibomian Glands Female Diseased  Replicate 5


title: tumor cells from bladder bU01

description: tumor cells from bladder


title: Control-38

tag: id (rutgers)


title: CC_Kidney_010_SNP_Xba

description:
GR010T
Hybridized to 50K Xba


title: Control-36

tag: nimh identifier


title: Control-37

tag: sex


title: CC_Kidney_060_SNP_Xba

description:
CHTN060
Hybridized to 50K Xba


title: Meibomian Glands Female Diseased Replicate 2


title: normal tissues from bladder bN26

description: normal tissues from bladder

source_name: normal from bladder


title: normal tissues from bladder bN16

description: normal tissues from bladder


title: Meibomian Glands Male Diseased  Replicate 1


title: normal tissues from bladder bN15

description: normal tissues from bladder


title: normal tissues from bladder bN27

description: normal tissues from bladder


title: CC_Kidney_012_SNP_Xba

description:
CHTN012T
Hybridized to 50K Xba


title: Control-35

source_name: blood


title: CC_Kidney_035_SNP_Xba

description:
CHTN035
Hybridized to 50K Xba


title: normal tissues from bladder bN23

description: normal tissues from bladder


title: CC_Kidney_009_SNP_Xba

description:
CHTN009T
Hybridized to 50K Xba


title: normal tissues from bladder bN24

description: normal tissues from bladder


title: normal tissues from bladder bN25

description: normal tissues from bladder


title: Control-34


title: Control-33


title: tumor cells from bladder bU30

description: tumor cells from bladder


title: NO_Kidney_Ref_SNP_Hind

description:
Ref
Hybridized to 50K Hind

value: Normal kidney tissue


title: P2KB2

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

description: Gene expression data from DC3000 PSPTO_2222 mutant strains when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.

hyb_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.

data_processing: For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor projec(http://www.bioconductor.org), and gene calls were generated by using the RMA algorithm (Robust Multichip Average) (Irizarry et al., 2003). The relative fluorescent intensities of each ORF were scaled by assuming a constant mean signal intensity of 1,000 signal units for each array.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Pseudomonas syringae pv. tomato DC3000.

growth_protocol: Grown in KB (King et al., 1954) to ~0.7x109 cfu/mL and then harvested for RNA extraction.

extract_protocol: Total RNA was extracted using a modified hot phenol procedure (Aiba et al. 1981), then purified by using RNeasy Midi kit following the manufacture instruction (Qiagen, Valencia, CA).

tag: strain

tag: mutant

tag: media

value: KB


title: NO_Kidney_201_SNP_Hind

description:
GR201N
Hybridized to 50K Hind

tag: gender

tag: ethnicity


title: 3/2 MM2

description: Gene expression data from DC3000 PSPTO_2222-2223 deletion mutant strains when grown in MM at 6hr(King et al., 1954).

scan_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.

growth_protocol: Grown in KB (King et al., 1954) to ~0.7x109 cfu/mL. The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.

value: PSPTO_2222-2223 deletion

value: MM


title: P2KB1

description: Gene expression data from DC3000 PSPTO_2222 mutant when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.

label_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.


title: Control-28

value: control

tag: sample type


title: Control-29

value: F


title: CC_Kidney_005_SNP_Xba

description:
CHTN005
Hybridized to 50K Xba


title: 3-2 kb2

description: Gene expression data from DC3000 PSPTO_2222-2223 deletion mutant when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.


title: 3-2 kb1


title: Control-31

value: M


title: NO_Kidney_116_SNP_Hind

description:
GR116N
Hybridized to 50K Hind


title: Heart-TAC3d_KO-2

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

description:
TAC3d_KO2
3 day pressure overload
KO2_061609_Mouse430_2.CEL

hyb_protocol: The Affymetrix arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method.

organism: Mus musculus

source_name: left ventricle,Hsp22 KO,TAC surgery

label_protocol: cDNA synthesis (SuperScript, Invitrogen) was performed from 10 μg total RNA with a T7-oligo(24)dT primer. The DNA was transcribed into biotin-labeled RNA (Bioarray RNA Labeling Kit, ENZO)

growth_protocol: No growth protocol. Samples were taken from animals in vivo.

treatment_protocol: No treatment prior to experiment was applied.

value: heart, left ventricle

value: male

tag: genotype/variation

value: Hsp22 KO

tag: stress

value: pressure overload


title: Control-27

value: lymphoblast cell line

value: blood


title: Control-26


title: Control-32


title: Heart-TAC3d_KO-1

description:
TAC3d_KO1
3 day pressure overload
KO1_061609_Mouse430_2.CEL


title: NO_Kidney_111_SNP_Hind

description:
GR111N
Hybridized to 50K Hind


title: 3/2 MM2-2


title: NO_Kidney_066_SNP_Hind

description:
GR066N
Hybridized to 50K Hind

value: W


title: Control-24


title: Control-25


title: Heart-TAC3d_KO-3

description:
TAC3d_KO3
3 day pressure overload
KO3_061609_Mouse430_2.CEL


title: NO_Kidney_057_SNP_Hind

description:
GR057N
Hybridized to 50K Hind


title: Control-30


title: NO_Kidney_061_SNP_Hind

description:
GR061N
Hybridized to 50K Hind


title: Heart-TAC3d_KO-4

description:
TAC3d_KO4
3 day pressure overload
KO4_061609_Mouse430_2.CEL


title: Heart-TAC3d_WT-4

description:
TAC3d_WT4
3 day pressure overload
WT4_061609_Mouse430_2.CEL

source_name: left ventricle,Hsp22 WT,TAC surgery

value: Hsp22 WT


title: 2222MM1

description: Gene expression data from DC3000 PSPTO_2222 mutant strains when grown in MM at 6hr(King et al., 1954).


title: 2222-MM


title: Control-23


title: NO_Kidney_049_SNP_Hind

description:
GR049N
Hybridized to 50K Hind


title: CC_Kidney_T057_SNP_Hind

description:
GT057T
Hybridized to 50K Hind


title: 293T Ras and hTERT

city: Singapore

first: Tan

last: Wei Han

address: 21 Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

scan_protocol: Scanner used: Illumina BeadArray Reader  Scanning protocol: Scan factor of 1, PMT525  Software: Illumina Beadscan version 3.0

data_processing: Data is extracted using Illumina Genomestudio version 2010.2, Expression Module version 1.7.0  No normalization applied on the data exported. Data were RMA normalized and log2 transformed using Partek GS6.4 Ver 6.09.0922 software. Statistical analysis was performed using ANOVA.

source_name: Embryonic Kidney

label_protocol: Standard Illumina label protocol

growth_protocol: Cell were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum (HIFBS) (Gibco, Invitrogen), 2mM L-glutamine (Gibco, Invitrogen) and 100U/ml penicillin and streptomycin (Gibco, Invitrogen).

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) with modifications. Cells were first washed with PBS twice and then lysed in TRIzol (Invitrogen) before purification using RNA extraction columns and buffers provided in the kit. The RNA concentration was quantified using Nanodrop (Thermo Scientific). 500ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion). Steps were carried out by following the instructional manual in the kit.

treatment_protocol: IMR90 and BJ culture cells were infected with DMEM-diluted virus supernatant with 8µg/ml of polybrene for 24 hours. Cell infected with control vector were selected using puromycin (1µg/ml) (InvivoGen) and cells infected with Ras, SV40 Large-T and hTERT combination were selected using both puromycin (1µg/ml) and hygromycin (1µg/ml) (Invitrogen) for 5 days.

tag: commerical source

value: Fibroblast

tag: oncogenic factors

value: Ras, hTERT


title: Heart-TAC3d_WT-3

description:
TAC3d_WT3
3 day pressure overload
WT3_061609_Mouse430_2.CEL


title: BJ Ras, SV40 and hTERT

source_name: Skin; Foreskin

value: ATCC:BJ (CCL-186)

value: Ras, SV40, hTERT


title: CC_Kidney_207_SNP_Hind

description:
GR207T
Hybridized to 50K Hind

value: Clear cell renal cell caricinoma

tag: tumor size(cm)


title: CC_Kidney_202_SNP_Hind

description:
GR202T
Hybridized to 50K Hind


title: Heart-Base_KO-3

description:
Base_KO3
no pressure overload
HQIU_430-2_HIIK-KO3_092507.CEL

source_name: left ventricle,Hsp22 KO,basal condition


title: CC_Kidney_201_SNP_Hind

description:
GR201T
Hybridized to 50K Hind


title: Heart-TAC3d_WT-1

description:
TAC3d_WT1
3 day pressure overload
WT1_061609_Mouse430_2.CEL


title: Heart-TAC3d_WT-2

description:
TAC3d_WT2
3 day pressure overload
WT2_061609_Mouse430_2.CEL


title: Control-21

tag: cell type


title: Heart-Base_WT-3

description:
Base_WT3
no pressure overload
HQIU_430-2_HIIK-WT3_092607.CEL

source_name: left ventricle,Hsp22 WT,basal condition

tag: tissue


title: Control-20

tag: disease state


title: IMR90 GFP

source_name: Lung

value: ATCC:IMR90 (CCL-186)


title: Heart-Base_WT-1

description:
Base_WT1
no pressure overload
HQIU_430-2_HIIK-WT1_092607.CEL

value: control


title: CC_Kidney_198_SNP_Hind

description:
GR198T
Hybridized to 50K Hind

source_name: Clear cell renal cell caricinoma

value: F


title: Heart-Base_WT-2

description:
Base_WT2
no pressure overload
HQIU_430-2_HIIK-WT2_092607.CEL


title: Heart-Base_KO-2

description:
Base_KO2
no pressure overload
HQIU_430-2_HIIK-KO2_092607.CEL


title: Heart-Base_KO-1

description:
Base_KO1
no pressure overload
HQIU_430-2_HIIK-KO1_092607.CEL


title: Control-19

source_name: lymphobast cell lines

tag: id (rutgers)

value: M


title: IMR90 SV40


title: CC_Kidney_179_SNP_Hind

description:
GR179T
Hybridized to 50K Hind


title: Control-22

tag: nimh identifier


title: Control-17

tag: sex


title: CC_Kidney_156_SNP_Hind

description:
GR156T
Hybridized to 50K Hind


title: BJ Lenti


title: Control-18


title: IMR90 hTERT

value: hTERT


title: IMR90 Ras, SV40 and hTERT


title: CC_Kidney_138_SNP_Hind

description:
GR138T
Hybridized to 50K Hind


title: Control-14


title: CC_Kidney_153_SNP_Hind

description:
GR153T
Hybridized to 50K Hind


title: Control-16


title: CC_Kidney_124_SNP_Hind

description:
GR124T
Hybridized to 50K Hind


title: 293 Lenti

value: Epithelial


title: CC_Kidney_127_SNP_Hind

description:
GR127T
Hybridized to 50K Hind


title: Granulosa cells from wild type ovary, eCG-treated 48h,  hCG 24h

first: JoAnne

last: Richards

department: Molecular and Cellular Biology

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

value: ovarian granulosa cells

value: wild type

tag: age

value: 24 days


title: Granulosa cells from wild type ovary, eCG-treated 48h, hCG 8h

value: 23 days


title: Control-13

department: Molecular and Human Genetics

value: lymphoblast cell line

value: blood


title: Control-15


title: Control-12


title: Granulosa cells from CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 4h

value: CEBPα/β fl/fl fl/fl;Cyp19-cre


title: Gene expression between liver, 2

city: College Station

first: Huaijun

last: Zhou

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide.

hyb_protocol: 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each array in Agilent 4x44K microarrays. Arrays were incubated at 65℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R 2.9.0 (Yang et al, 2002).

organism: Gallus gallus

source_name: Liver

label_protocol: A 400 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

extract_protocol: Tissue sample was homogenized within lysis buffer (Qiagen RNeasy mini RNA extraction kit, Qiagen Inc., Valencia, CA). Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 30 µl RNase-free water and stored at -80°C.

tag: type

value: broiler

value: 4 weeks

value: liver

tag: biological replicate


title: Gene expression between liver, 4

description: Four arrays are included in one slide.


title: CC_Kidney_116_SNP_Hind

description:
GR116T
Hybridized to 50K Hind

value: Clear cell renal cell caricinoma

tag: gender

value: W


title: Gene expression between liver, 1

description: Four arrays are included in one slide.


title: Control-10

value: control


title: Stroke Infiltrated_6

city: Shreveport

first: Jonathan

middle: S

last: Alexander

state: LA

address: 1501 Kings Highway

department: Physiology

institute: LSUHSC-Shreveport

description: Gene expression data from stroke brain recovered cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as normalization method.

source_name: Cultured ImmortomouseTM stem cells recovered from ischemic infarcts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow derived stem cells cultured from ImmortomouseTM mice. Passaged 3X before characterization and freeze down.

extract_protocol: RNA was extracted from cells using QIAshredder (Qiagen, Hilden, GmbH) and Qiagen RNeasy column (Qiagen, Maryland), according to manufacturer?s directions.

treatment_protocol: Bone marrow derived stem cells injected in mouse with middle cerebral artery occlusion. Cells recovered from infarct and cultured 3X before characterization and freeze down.

tag: strain

value: transgenic Immortomouse strain (SC, infiltrating)

value: C57BL/6 (ischemic stroke subject)

tag: phenotype

tag: protocol

value: stroke brain recovered cells


title: Parent Line_5

description: Gene expression data from parent cells

source_name: ImmortomouseTM-derived bone marrow cells

value: transgenic Immortomouse strain (SC, naïve)

value: parent cells


title: Granulosa cells from CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 8h

value: ovarian granulosa cells

tag: genotype/variation


title: Gene expression between liver, 3

description: Four arrays are included in one slide.


title: Gene expression between kidney, 3

description: Four arrays are included in one slide.

source_name: Kidney

value: kidney


title: Control-9

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

value: F

value: M

tag: sample type


title: Gene expression between kidney, 4

description: Four arrays are included in one slide.


title: Control-8

value: lymphoblast cell line

value: blood


title: CC_Kidney_106_SNP_Hind

description:
GR106T
Hybridized to 50K Hind

tag: ethnicity


title: Control-11


title: CC_Kidney_091_SNP_Hind

description:
GR091T
Hybridized to 50K Hind


title: 2222MM2

tag: mutant

tag: media

value: MM


title: CC_Kidney_111_SNP_Hind

description:
GR111T
Hybridized to 50K Hind

tag: tissue

tag: tumor size(cm)


title: Control-7

tag: cell type

tag: disease state

tag: id (rutgers)


title: CC_Kidney_113_SNP_Hind

description:
GR113T
Hybridized to 50K Hind


title: Parent Line_3

description: Gene expression data from parent cells


title: Stroke Infiltrated_4


title: Control-6

tag: nimh identifier

tag: sex


title: Parent Line_1

description: Gene expression data from parent cells


title: Control-5


title: Gene expression between kidney, 1

description: Four arrays are included in one slide.

tag: type

value: broiler

tag: age

value: 4 weeks

tag: biological replicate


title: Stroke Infiltrated_2

tag: strain

tag: phenotype


title: Control-4


title: CC_Kidney_066_SNP_Hind

description:
GR066T
Hybridized to 50K Hind

value: Clear cell renal cell caricinoma

tag: gender

tag: tumor grade

value: II~III

tag: tumor stage


title: CC_Kidney_076_SNP_Hind

description:
GR076T
Hybridized to 50K Hind

tag: ethnicity

value: H

value: IV


title: HGF WT Mouse Tumor #2 (40wks) Cancer

city: Pittsburgh

first: Jill

middle: M

last: Siegfried

state: PA

address: The Hillman Cancer Center, UPCI Research Pavilion Suite 2.18, 5117 Centre Avenue

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

description: Positive and negative controls are included within the array. Final images were saved in either .tiff or .jpg, and uploaded for further analysis as described below.

hyb_protocol: Hybridization was completed following the GEArray® protocol (SABiosciences) for HybTube. In brief: prehybridization was carried out 60°C for 2 hours followed by an overnight hybridization with labeled cDNA probe (4μg). On the second day two 15 minute washes at 60°C were completed before blocking and detection of spot signal. http://www.sabiosciences.com/support_manual.php

scan_protocol: X-ray film, exposed to the chemiluminescent array, was scanned on a flatbed scanner to obtain a digital image.

data_processing: Data analysis was conducted using online with GEArray Expression Analysis Suite at www.SuperArray.com. Absolute and comparison analyses were conducted using the following settings: average density, clover off, and no background correction. Data in the Value column are presented as relative induction of each gene normalized to the housekeeping gene GAPDH.

source_name: isolated tumors from lung

label_protocol:
cDNA template was reverse-transcribed from total RNA followed by amplification and biotin-16-labeling using the Oligo GEArray TrueLabeling-AMP™ 2.0 Kit (SABiosciences) according to the manufacturers protocol. Resulting cDNA was further purified using cRNA clean-up kit (SABiosciences) following the manufacturers procedure.
http://www.sabiosciences.com/support_manual.php

extract_protocol:
Total RNA was isolated from whole lung tissue in TRIzol (Invitrogen) following the manufacturers instructions. RNA was resuspended in RNase-free water and further purified using the RT² qPCR-Grade RNA Isolation Kit (SABiosciences) by following the manufacturers protocol.
http://www.sabiosciences.com/support_manual.php

treatment_protocol: Twice weekly nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) injections over 2 weeks

value: Male/Female (equal numbers)

value: 40 weeks

value: Isolated tumors from lung tissue


title: CC_Kidney_078_SNP_Hind

description:
GR078T
Hybridized to 50K Hind


title: HGF TG Mouse Tumor #1 (40wks) Cancer

tag: genome/variation

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways


title: Gene expression between bone marrow, 3

description: Four arrays are included in one slide.

source_name: Bone marrow

tag: tissue

value: bone marrow


title: CC_Kidney_061_SNP_Hind

description:
GR061T
Hybridized to 50K Hind

value: II

tag: tumor size(cm)


title: HGF TG Mouse Tumor #2 (40wks) Cancer


title: HGF WT Mouse Tumor #1 (40wks) Cancer


title: Control-3

tag: cell type

value: control

source_name: blood

tag: sample type


title: CC_Kidney_059_SNP_Hind

description:
GR059T
Hybridized to 50K Hind

value: F

value: W

value: (IV)


title: CC_Kidney_057_SNP_Hind

description:
GR057T
Hybridized to 50K Hind

value: M


title: Th2 KO

city: Shanghai

first: Yuan

last: Zhang

address: Yueyang St. 320#

institute: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

description: gene expression data from liver of ECM1 Ko mice

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.Eukaryotic Target Hybridization,Lot no.900720, is used for the experiment.

scan_protocol: The chips were scanned withthe affymetrix genechip 7G plus and GCOS v1.0 is used for the image processing.

data_processing: genespring 10.0, is used for automatic normalizing the chip data and analysis the fold change.

source_name: Th2 cell from ECM1 Ko mice

label_protocol: Start with 3μg total RNA and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, One-Cycle Eukaryotic Target Labeling Assay(Lot no. 900493) is used in the experiment.

growth_protocol: Female C57BL6 is grown in SPF condition until 6 weeks, KO mice is confirmed by Realtime RT-PCR and western-blot.

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

treatment_protocol: Spleen of the mice is treated with RBC lysis buffer for 5 minutes, 10μg anti-CD4 antibody is added for each spleen. After incubating for 30 minutes, we washed cell 2 times and add 25ul Goat-anti-rat IgG(miltenyi biotec) for each spleen. Finally, CD4+ cell is separated with MACS separation column, counted and cultured with 3 μg/ml plate-bound anti-CD3 and 2 μg/ml soluble anti-CD28 under the Th2 conditions for 4 days (10 ng/mIL-4, 10μg/ml anti-IFN-γ and 10μg/ml anti-IL-12).


title: Gene expression between bone marrow, 4

description: Four arrays are included in one slide.

value: broiler


title: HGF WT Mouse Whole Lung #2 (40wks) Cancer

source_name: whole lung

value: Whole Lung


title: Granulosa cells from CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 24h

value: ovarian granulosa cells

tag: genotype/variation

value: CEBPα/β fl/fl fl/fl;Cyp19-cre

value: 24 days


title: Control-2

value: lymphoblast cell line

tag: disease state

tag: id (rutgers)

tag: nimh identifier

value: blood


title: HGF WT Mouse Whole Lung #1 (40wks) Cancer

value: Male/Female (equal numbers)

tag: age

value: 40 weeks


title: Gene expression between kidney, 2

description: Four arrays are included in one slide.

tag: type

value: 4 weeks

value: kidney

tag: biological replicate


title: Th2 WT

description: gene expression data from liver of wildtype mice

source_name: Th2 cell from WT mice

tag: strain


title: Gene expression between bone marrow, 1

description: Four arrays are included in one slide.

value: bone marrow


title: CC_Kidney_040_SNP_Hind

description:
GR040T
Hybridized to 50K Hind

value: Clear cell renal cell caricinoma

tag: gender

value: B

value: II