title: Low Translation Fraction 4% YE


title: High Translation Fraction 4% YE-3

status: Public on Oct 02 2009

type: RNA

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

country: USA

institute: University of California San Diego

description: Expression profile of the high translation fraction on 4%YE

hyb_protocol: 12.5 micrograms of biotin-labeled cRNA was fragmented and hybridized according to the Affymetrix protocol.

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

data_processing: Data were processed using Rosetta Resolver (Rosetta Biosoftware); the Affymetrix-Rosetta – Intensity Profile and Experiment Builder pipelines were used. Data processing resulted in average expression values and associated errors as well as a statistic reporting whether the target transcript was detected above background.

label: Biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: Whole 7-8 old male

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for MessageAmp II-Biotin Enhanced kit (Ambion) starting with 100 ng total RNA.

extract_protocol: Total RNA was separated over a sucrose gradient, then RNA was isolated by Trizol extraction from the high or the low translation fractions.

tag: strain

tag: gender

value: male

tag: diet

value: 6 days on 4% YE food


title: AGS(3)

status: Public on Oct 06 2009

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 25 (unique) gastric cancer cell lines

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

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

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 500.

label: biotin

organism: Homo sapiens

source_name: gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

tag: cell line

value: AGS

tag: cell type

value: gastric cancer


title: High Translation Fraction 0.25% YE-2

description: Expression profile of the high translation fraction on 0.25%YE

value: 6 days on 0.25% YE food


title: Low Translation Fraction 4% YE-3

description: Expression profile of the low translation fraction on 4%YE


title: Low Translation Fraction 0.25% YE-3

description: Expression profile of the low translation fraction on 0.25%YE


title: High Translation Fraction 4% YE-2


title: IM95


title: High Translation Fraction 4% YE


title: High Translation Fraction 0.25% YE-3


title: ubc13A-es-rep2

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: gene expression data from transgenic arabidopsis roots under iron efficiency medium

hyb_protocol: Ten micrograms of labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 h. Washing and staining involved Fluidics Station-450 and the ATH1 Genome Array.

scan_protocol: Array was scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The results were quantified and analyzed by use of MicroArray Suite 5.0 software (Affymetrix Inc.).

organism: Arabidopsis thaliana

source_name: Arabidopsis ubc13A in iron plus medium

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis and labeled by in vitro transcription followed by fragmentation according to the manufacturer's suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: 10-day old seedlings were transferred to ES (+Fe) and ES without addition of FeEDTA (–Fe) medium, respectively. Tissues were harvested and immediately frozen in liquid nitrogen 3 days after the transfer.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit.

tag: tissue

value: root

tag: genome/variation


title: ubc13A-Fe-rep3

description: gene expression data from transgenic arabidopsis roots under iron deficiency medium

source_name: Arabidopsis ubc13A in iron minus medium

tag: environmental factor

value: iron (Fe) deficiency


title: ubc13A-es-rep3


title: ubc13A-es-rep1


title: Corticospinal_Motor_Neurons_P14_rep2_430 2.0 array

status: Public on Oct 01 2009

city: Boston

first: Bradley

last: Molyneaux

state: MA

department: MGH-HMS Center For Nervous System Repair

institute: Harvard Medical School

description: Cells purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex

hyb_protocol: Standard protocols for Affymetric protocol for 430 2.0 microarrays were used. Arrays were washed on an Affymetrix fluidics station.

scan_protocol: According to standard Affymetric protocols.

data_processing: RMA normalization was applied using Bioconductor (www.bioconductor.org).

organism: Mus musculus

source_name: corticospinal motor neurons, postnatal day 14

label_protocol: RNA was amplified according to the Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription to obtain 15-20 ug of amplified and labeled cRNA for each hybridization.

growth_protocol: All neuronal subtypes were purified from C57BL/6 mice. Neuronal subtypes were retrogradely labeled with green fluorescent microspheres injected into appropriate axonal fields: sensorimotor cortex (CSMN and CPN) or visual cortex (CTPN).

extract_protocol: RNA was extracted using the StrataPrep Total RNA Micro Kit (Stratagene).

treatment_protocol: Neurons were dissociated and microsphere-labeled CSMN, CPN, or CTPN were purified by fluorescence-activated cell sorting (FACS) directly into RNAlater.

tag: tissue type

value: neuronal

value: corticospinal motor neurons

tag: age

value: Postnatal day 14


title: Corticospinal_Motor_Neurons_P3_rep1_430 2.0 array

source_name: corticospinal motor neurons, postnatal day 3

value: Postnatal day 3


title: Corticospinal_Motor_Neurons_P6_rep1_430 2.0 array

source_name: corticospinal motor neurons, postnatal day 6

value: Postnatal day 6


title: Corticospinal_Motor_Neurons_E18_rep2_430 2.0 array

source_name: corticospinal motor neurons, embryonic day 18

value: Embryonic day 18


title: Callosal_Neurons_P6_rep2_430 2.0 array

source_name: callosal projection neurons, postnatal day 6

value: callosal projection neurons


title: Corticospinal_Motor_Neurons_P6_rep2_430 2.0 array


title: Corticotectal_Neurons_P14_rep2_430 2.0 array

source_name: corticotectal neurons, postnatal day 14

value: corticotectal neurons


title: ubc13A-Fe-rep1


title: Corticotectal_Neurons_P14_rep1_430 2.0 array


title: Corticospinal_Motor_Neurons_P3_rep2_430 2.0 array


title: Corticospinal_Motor_Neurons_P3_rep3_430 2.0 array


title: ubc13A-Fe-rep2


title: Corticospinal_Motor_Neurons_P14_rep1_430 2.0 array


title: Callosal_Neurons_P6_rep1_430 2.0 array


title: Callosal_Neurons_P14_rep2_430 2.0 array

source_name: callosal projection neurons, postnatal day 14


title: Callosal_Neurons_P3_rep2_430 2.0 array

source_name: callosal projection neurons, postnatal day 3


title: Callosal_Neurons_P14_rep1_430 2.0 array


title: Callosal_Neurons_P3_rep1_430 2.0 array


title: Callosal_Neurons_E18_rep2_430 2.0 array

source_name: callosal projection neurons, embryonic day 18


title: Corticospinal_Motor_Neurons_E18_rep1_430 2.0 array


title: anti-PECAM beads purified P16 wild type cerebellar endothelial cells replicate 1

city: Baltimore

first: Xin

last: Ye

state: MD

address: 725 N Wolfe Street, PCTB 805

institute: Johns Hopkins School of Medicine

description: contact Yanshu Wang (ywang@jhmi.edu) for details

hyb_protocol: Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/

data_processing: Raw data was processed in R2.4.1 using the affy and rma packages from the Bioconductor Project (www.bioconductor.org).

extract_protocol: Trizol and RNeasy according to manufacturer's instructions.

value: purified cerebellar endothelial cells

tag: genetic modification

value: P16 wild type

value: mixed gender

value: C57Bl6/129 mixed background


title: Callosal_Neurons_E18_rep1_430 2.0 array


title: anti-PECAM beads purified P16 Fz4-/- cerebellar endothelial cells replicate 2

scan_protocol: Johns Hopkins Microarray Core Facility http://www.microarray.jhmi.edu/


title: anti-PECAM beads purified P16 wild type cerebellar endothelial cells replicate 2

label_protocol:
Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/


title: Fz4-/- retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 1

value: retinal endothelial cells

tag: developmental stage

value: adult

tag: culture condition

value: co-cultured with norrin-expressing hek293 cells

tag: sample

value: RNA prepared from the co-culture represents a ~1:1 mixture of mouse retinal endothelial cells (REC) and human 293 RNA.


title: Fz4-/- retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 2


title: Fz4-/- retinal endothelial cells co-cultured with control HEK293 cells replicate 2

value: co-cultured with control hek293 cells


title: anti-PECAM beads purified P16 wild type cerebellar endothelial cells replicate 3


title: anti-PECAM beads purified P16 Fz4-/- cerebellar endothelial cells replicate 3


title: Fz4-/- retinal endothelial cells co-cultured with control HEK293 cells replicate 1


title: Fz4-/- retinal endothelial cells co-cultured with control HEK293 cells replicate 3


title: Fz4-/- retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 3


title: Wild type retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 3

value: wild type


title: anti-PECAM beads purified P16 Fz4-/- cerebellar endothelial cells replicate 1


title: Wild type retinal endothelial cells co-cultured with control HEK293 cells replicate 3


title: Wild type retinal endothelial cells co-cultured with control HEK293 cells replicate 2


title: Wild type retinal endothelial cells cultured on gelatin-coated plates replicate 2

value: cultured on gelatin-coated plates


title: Wild type retinal endothelial cells cultured on gelatin-coated plates replicate 3


title: Fz4-/- retinal endothelial cells cultured on gelatin-coated plates replicate 2


title: Fz4-/- retinal endothelial cells cultured on gelatin-coated plates replicate 1


title: Wild type retinal endothelial cells cultured on gelatin-coated plates replicate 1


title: Wild type retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 2


title: Fz4-/- retinal endothelial cells cultured on gelatin-coated plates replicate 3


title: Wild type retinal endothelial cells co-cultured with Norrin-expressing HEK293 cells replicate 1


title: Wild type retinal endothelial cells cultured on matrigel replicate 1

value: cultured on matrigel


title: Fz4-/- retinal endothelial cells cultured on matrigel replicate 3


title: Wild type retinal endothelial cells cultured on matrigel replicate 2


title: Wild type retinal endothelial cells co-cultured with control HEK293 cells replicate 1


title: Wild type retinal endothelial cells cultured on matrigel replicate 3


title: Fz4-/- retinal endothelial cells cultured on matrigel replicate 1


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 4

value: Acutely purified retinal endothelial cells

value: retina


title: Fz4-/- retinal endothelial cells cultured on matrigel replicate 2


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 5


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 3


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 1


title: anti-PECAM beads purified adult Norrin- retinal endothelial cells replicate 3

value: Norrin KO


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 6


title: anti-PECAM beads purified adult Lrp5-/- retinal endothelial cells replicate 2


title: anti-PECAM beads purified adult Lrp5-/- retinal endothelial cells replicate 1


title: anti-PECAM beads purified adult Norrin- retinal endothelial cells replicate 2


title: anti-PECAM beads purified adult Lrp5-/- retinal endothelial cells replicate 3


title: anti-PECAM beads purified adult Norrin- retinal endothelial cells replicate 1


title: Z/Norrin mouse yolk sac E10.5 replicate 2

description: contact Xin Ye (xye4@jhmi.edu) for details

source_name: Z/Norrin mouse yolk sac E10.5

value: ectopic Norrin expression

value: embryonic day 10.5

value: yolk sac


title: Z/Norrin mouse yolk sac E10.5 replicate 3


title: wild type mouse yolk sac E10.5 replicate 2

source_name: wild type mouse yolk sac E10.5


title: Anti-PECAM beads purified adult Fz4-/- retinal endothelial cells replicate 2

source_name: anti-PECAM beads purified adult Fz4-/- retinal endothelial cells


title: anti-PECAM beads purified adult wild type retinal endothelial cells replicate 2


title: wild type mouse yolk sac E10.5 replicate 1


title: M031 CTX +7

city: Madison

first: Dhruv

last: Sareen

state: WI

address: 1111 Highland Ave, Rm 5031 WIMR

department: Neurology

institute: University of Wisconsin Madison

description: Gene expression data from hNPCs containing a trisomy of chromosome 7

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

scan_protocol: Stained U133 Plus 2.0 arrays were scanned at 3 μM resolution using the Affymetrix GeneChip Scanner 3000

data_processing: GeneChip Operating Software v1.2 (GCOS) was used to analyze the relative abundance of each gene derived from the average difference of intensities.

source_name: Human fetal cortex

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

growth_protocol: Diploid and +7 human neural progenitor cells (hNPCs) were grown for approximately 25-30 weeks or 19-20 passages

extract_protocol: Total RNA was extracted trizol reagent. Total RNA was further extracted using a chloroform/isopropanol separation method. RNA was ethanol precipitated and allowed to briefly dry before elution in 33 ml of RNase-free water.

value: Fetal cortex

tag: genotype

value: XY, trisomy 7

value: 94 day fetus


title: Anti-PECAM beads purified adult Fz4-/- retinal endothelial cells replicate 1

value: mixed gender

value: C57Bl6/129 mixed background


title: Z/Norrin mouse yolk sac E8.5 replicate 2

source_name: Z/Norrin mouse yolk sac E8.5

value: embryonic day 8.5


title: anti-PECAM beads purified adult Fz4-/- retinal endothelial cells replicate 3

value: adult


title: Control

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: MCF7 cells transfected with CEACAM1-S double-A mutant T457A,S459A (DA)

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Bioconductor package Affy.

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol

growth_protocol: The human mammary adenocarcinoma cell line MCF7 was obtained from ATCC (HTB-22™).  MCF7 cells were cultured in MEM medium supplemented with 10% Fetal Bovine Serum, 1% penicillin/streptomycin/Am, 1% sodium pyruvate, 2% sodium bicarbonate, and 1% non-essential amino acids

extract_protocol: Total RNA was extracted from cells using the Tri-Reagent (Molecular Research Center) according to the manufacturer’s instruction

treatment_protocol: The three-dimensional Matrigel (BD Biosciences) sandwich assay has been previously described (12).  Briefly, 10 ml culture dishes were coated with 1 ml of Matrigel and incubated at 37 °C for 30 min until the Matrigel solidified, cells (1x106) in 10 ml of mammary epithelial basal medium (MEBM) plus pituitary gland extract (PGE) (Lonza Group LTD, Switzerland) were added to each well.  After 3 hr of incubation, the floating cells were removed and the bound cells were overlaid with 1ml of 50% Matrigel in MEBM plus PGE. At day 4 , the acini were recovered by adding 10 ml of dissolving solution into each dish and incubated at 4oC for 3 hrs by gentle rotation. The cells were harvested and RNA isolated for Gene chip analysis

value: MCF7 (ATCC HTB-22)

value: epithelial

tag: organ

value: mammary gland

tag: disease

value: adenocarcinoma

tag: metastatic site

value: pleural effusion


title: Z/Norrin mouse yolk sac E8.5 replicate 3

tag: gender

tag: strain


title: M031 CTX diploid

description: Gene expression data from karyotypically normal hNPCs.

value: XY, diploid


title: wild type mouse yolk sac E8.5 replicate 2

source_name: wild type mouse yolk sac E8.5


title: Z/Norrin mouse yolk sac E8.5 replicate 1


title: SW2

description: MCF7 cells transfected with CEACAM1-S wild-type (SW)

tag: cell line


title: wild type mouse yolk sac E8.5 replicate 3


title: Baylor/Oka/Li et al/12048

city: Houston

first: Kazuhiro

last: Oka

state: TX

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

description: No additional

hyb_protocol: Affymetrix Workstation

scan_protocol: Affymetrix GeneChip Scanner 3000 standard protocol

data_processing: RMA using GeneSifter (VizX Labs LLC)

label_protocol: FL-Ovation kit (NuGen)

extract_protocol: RNA extraction with an RNeasy kit (Qiagen)

treatment_protocol: Mice were fed a diet containing 0.2% (w/w) cholesterol and 10% (v/w) coconut oil to induce atherosclerosis for 30 weeks. Mice were then divided into 3 groups (n=15/group), treated with a tail vein injection of helper-dependent adenovirus expressing human apolipoprotein E3 (HDAd-gE3, 5 x 1012 viral particles/kg, n=11, vector), empty vector (HDAd-0, 5 x 1012 VP/kg, n=11, vector control) or phosphate buffered saline (PBS, vehicle) and sacrificed 10 days after. Three aortas extending sinus to arch were dissected and pooled for extraction

tag: agent

value: vector, HDAd-gE3

value: Female

value: APOE-/-

value: 8 weeks

value: C57BL/6 background


title: Baylor/Oka/Li et al/12053

description: No additional

value: vehicle, PBS


title: wild type mouse yolk sac E8.5 replicate 1

tag: tissue

value: yolk sac


title: Baylor/Oka/Li et al/12046

description: No additional


title: Baylor/Oka/Li et al/12054

description: No additional


title: Baylor/Oka/Li et al/12031

description: No additional

source_name: E4_Aorta_vector control_HDAd-0

value: vector control, HDAd-0


title: Baylor/Oka/Li et al/12051

description: No additional


title: Baylor/Oka/Li et al/12047

description: No additional


title: Baylor/Oka/Li et al/12039

description: No additional

source_name: E3_vector control


title: Baylor/Oka/Li et al/12043

description: No additional

source_name: E5_vector control


title: wild type mouse yolk sac E10.5 replicate 3

value: embryonic day 10.5

value: mixed gender

value: C57Bl6/129 mixed background


title: liver 81y, PHx T1hr, biological rep1

city: Jerusalem

first: Galit

last: Tzur

address: Kiryat Hadassah

department: Gene Therapy

country: Israel

institute: Hadassah University Hospital

description: Gene expression data from human liver tissue 81y PHx 1hr.

hyb_protocol: according to the standard Affymetrix protocol

data_processing: Data was normalized using the GCRMA algorithm, implemented in R and bioconductor.

source_name: liver 81y, PHx T1hr, biological rep1

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by phenol/chloroform purification using PLG tubes.

treatment_protocol: Liver tissues were collected from patients undergoing a PHx surgery (1.5, 42 and 81 years), and snap-frozen in liquid nitrogen and then stored at –80°C until analysis.

value: liver


title: Postnatal/Normal liver 81y, biological rep1

description: Gene expression data from post-natal, normal human liver tissue.

scan_protocol: according to the standard Affymetrix protocol

source_name: Postnatal/Normal liver 81y

treatment_protocol: After identification and separation of the liver tissue, the liver and the rest of the embryo were immediately snap-frozen in liquid nitrogen and then stored at –80°C until analysis.

value: Postnatal 81y (years)


title: liver 81y, PHx T1hr, biological rep2

source_name: liver 81y, PHx T1hr, biological rep2


title: liver 42y, PHx T1.5hr, biological rep2

description: Gene expression data from human liver tissue 42y PHx 1.5hr.

source_name: liver 42y, PHx T1.5hr, biological rep2


title: B-ALL_E2A/PBX1 1 (mRNA)

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: Gene expression data from patient with newly diagnosed ALL  (percentage of leukemic cells at least 80%)

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies)

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000Dx scanner

data_processing: Data were analyzed with R using functions ReadAffy and mas5 from package affy with default analysis settings.

source_name: Peripheral Blood

label_protocol: Total RNA (2-8 ug) was converted into double stranded cDNA using a cDNA Synthesis System kit (Roche Applied Science_Mannheim_Germany) and the Poly-A control transcripts (Affymetrix_Santa Clara_CA). cDNA was then used for in vitro transcription reaction using the Microarray RNA target synthesis kit (Roche Applied Science) and labeling nucleotide mix (Affymetrix) to synthesize biotinylated complementary RNA (cRNA)

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

value: Male

tag: phenotype

value: pre B


title: B-ALL_MLL/AF4 2 (mRNA)

source_name: Bone Marrow

value: pro B


title: Postnatal/Normal liver 1.5y, biological rep2

source_name: Postnatal/Normal liver 1.5y

value: Postnatal 1.5y (years)


title: Postnatal/Normal liver 1.5y, biological rep1


title: B-ALL_BCR/ABL 4 (mRNA)

value: B


title: B-ALL_No molecular abnormalities 3 (mRNA)

value: Female

value: B common


title: liver 42y, PHx T1.5hr, biological rep1

source_name: liver 42y, PHx T1.5hr, biological rep1


title: Postnatal/Normal liver 42y, biological rep2

source_name: Postnatal/Normal liver 42y

value: Postnatal 42y (years)


title: B-ALL_No molecular abnormalities 1 (mRNA)


title: B-ALL_No molecular abnormalities 5 (mRNA)


title: B-ALL_No molecular abnormalities 2 (mRNA)


title: B-ALL_No molecular abnormalities 6 (mRNA)


title: Postnatal/Normal liver 81y, biological rep2


title: B-ALL_BCR/ABL 2 (mRNA)


title: B-ALL_No molecular abnormalities 4 (mRNA)


title: Postnatal/Normal liver 42y, biological rep1


title: liver 1.5y, PHx T0.5hr, biological rep1

description: Gene expression data from human liver tissue 1.5y PHx 0.5hr.

source_name: liver 1.5y, PHx T0.5hr, biological rep1


title: liver 1.5y, PHx T0.5hr, biological rep2

source_name: liver 1.5y, PHx T0.5hr, biological rep2


title: B-ALL_BCR/ABL 3 (mRNA)


title: B-ALL_MLL/AF4 3 (mRNA)


title: B-ALL_BCR/ABL 1 (mRNA)


title: T-ALL_SIL/TAL 2 (mRNA)

value: T


title: B-ALL_MLL/AF4 1 (mRNA)


title: T-ALL_No molecular abnormalities 2 (mRNA)

value: mature T


title: B-ALL_E2A/PBX1 2 (mRNA)


title: T-ALL_No molecular abnormalities 1 (mRNA)

value: pre T


title: T-ALL_SIL/TAL 1 (mRNA)


title: Z/Norrin mouse yolk sac E10.5 replicate 1

source_name: Z/Norrin mouse yolk sac E10.5

value: ectopic Norrin expression

value: yolk sac


title: A375shGFP_Dox_3

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: Affymterix protocol for hyb and wash on Fludics 450

scan_protocol: Affymetrix protocol for GeneChip scanner 3000

data_processing: Data were processed using a program that implemented the recommendations of Choe, et al., Genome Biology, 2005 (PMID: 15693945). Background correction was performed as in the Affymetrix MAS 5.0 application. Probe-level normalization was performed using Quantile Normalization as in the RMA method. Perfect Match and Mismatch probes were contrasted as in the Affymetrix MAS 5.0 application. Multiple probes for each probeset were summarized using the median polish method from the RMA method. These summarized metrics were then further normalized using the Loess method.

label_protocol: Biotin labeled cRNA using an IVT kit

extract_protocol: RNA obtained using TrizolLS method.

tag: Doxycycline treatment of A375 shGFP cells. Replicate 3.


title: A375shBRaf_Dox_1

tag: Doxycycline treatment of A375 shBRAF-1 cells. Replicate 1.


title: A375sh2BRaf_Dox_1

tag: Doxycycline treatment of A375 shBRAF-2 cells. Replicate 1.


title: rosette_leaves_lcr_biological rep3

city: Cologne

first: Derry

last: Voisin

address: Carl-von-Linne weg 10

department: Saedler

country: Germany

institute: Max Planck Institute for Breeding Research

description: Gene expression data from young lcr rosette leaves

hyb_protocol: After cleaning and fragmentation, 15µg of biotinylated cRNA were hybridized on ATH1 Genome Arrays (Affymetrix, 900385). GeneChips were then washed and stained on a Fluidics Station 450 (protocol: EukGE-WS2v4; Expression Analysis Technical Manual; P/N 702232 Rev. 2/ 2005-2006).

scan_protocol: Microarrays were then scanned using a GeneChip Scanner 3000.

data_processing: The data were preprocessed using the Bioconductor packages affy and GC-RMA (fullmodel; with default settings).

source_name: lcr mutant (allele = lcr-3P77; 1,169-bp insertion in the 5' UTR from LCR gene; PNAS 98:9694-9699  (2001)

label_protocol: cRNA were prepared by in vitro translation and labelled with biotin starting from 5µg of total RNA and according to the Affymetrix Manual (Expression Analysis Technical Manual; P/N 702232 Rev. 2/ 2005-2006)

growth_protocol: Plants were grown on soil for 5,5 weeks and a half, under Short day 8 h day/ 16h night; 20°C/18°C into a growth chamber

extract_protocol: Total RNA was purified using the RNeasy Plant Mini Kit (QIAGEN) + DNase1 (QIAGEN) according to the manufacturer instructions. At the end, total RNA was eluted into 80 µl of RNase free water. Quality and concentration were evaluated on a 1,5% agarose gel by loading 0,5µl of each sample. Sample were kept frozen at -80°C until shipment.

treatment_protocol: The samples were harvested in the morning; each sample was harvested on a liquid nitrogen/ice bath and then deep-frozen in liquid nitrogen. Each sample contained tissue from 15 typical plants. A harvest round comprised a WT, a bdg, a fdh and a lcr sample; three rounds of harvesting were made sequentially. When all samples were gathered, they were transferred to a -80°C freezer until extraction.

value: Young rosette leaves 2mm to 1cm


title: A375shBRaf_Dox_2

tag: Doxycycline treatment of A375 shBRAF-1 cells. Replicate 2.


title: A375shBRaf_Dox_3

tag: Doxycycline treatment of A375 shBRAF-1 cells. Replicate 3.


title: rosette_leaves_fdh_biological rep3

description: Gene expression data from young fdh rosette leaves

source_name: fdh mutant (allele = fdh-3940; 2-bp insertion in exon-1 from FDH gene;Yephremov A. and al., The Plant Cell 11:2187-2202 (1999)


title: rosette_leaves_lcr_biological rep1


title: A375sh2BRaf_DMSO_1

tag: DMSO treatment of A375 shBRAF cells. Replicate 1.


title: A375control_DMSO_2

source_name: 2594_A375 control

tag: DMSO treatment of A375 parental cells. Replicate 2.


title: A375shBRaf_Control_2

tag: No treatment of A375 shBRAF-1 cells. Replicate 2.


title: A375shBRaf_Control_3

tag: No treatment of A375 shBRAF-1 cells. Replicate 3.


title: A375sh2BRaf_DMSO_2

tag: DMSO treatment of A375 shBRAF cells. Replicate 2.


title: A375shGFP_Dox_1

tag: Doxycycline treatment of A375 shGFP cells. Replicate 1.


title: rosette_leaves_fdh_biological rep2


title: rosette_leaves_fdh_biological rep1


title: rosette_leaves_bdg_biological rep2

description: Gene expression data from young bdg rosette leaves

source_name: bdg mutant (allele=bdg-2; 7-bp deletion in exon1 from BDG gene; Kurdyukov S. et al., The Plant Cell 18:321-339 (2006)


title: rosette_leaves_lcr_biological rep2


title: A375shGFP_Control_2

tag: No treatment of A375 shGFP cells. Replicate 2.


title: A375sh2BRaf_Dox_2

tag: Doxycycline treatment of A375 shBRAF-2 cells. Replicate 2.


title: A375sh2BRaf_Control_1

tag: No treatment of A375 shBRAF-2 cells. Replicate 1.


title: rosette_leaves_bdg_biological rep3


title: A375shGFP_Control_3

tag: No treatment of A375 shGFP cells. Replicate 3.


title: A375shBRaf_Control_1

tag: No treatment of A375 shBRAF-1 cells. Replicate 1.


title: A375sh2BRaf_Control_2

tag: No treatment of A375 shBRAF-2 cells. Replicate 2.


title: rosette_leaves_bdg_biological rep1

tag: tissue


title: rosette_leaves_WT_biological rep2

description: Gene expression data from young wild type rosette leaves

source_name: wild type Columbia-0


title: rosette_leaves_WT_biological rep3


title: A375control_DMSO_1

tag: DMSO treatment of A375 parental cells. Replicate 1.


title: A375shGFP_Dox_2

tag: Doxycycline treatment of A375 shGFP cells. Replicate 2.


title: A375sh2BRaf_1677_1

tag: RAF inhibitor #1 treatment of A375 shBRAF-2 cells. Replicate 1.


title: A375control_B439006_10uM_2

tag: BAY-43-9006 treatment of A375 parental cells. Replicate 2.


title: A375shGFP_Control_1

tag: No treatment of A375 shGFP cells. Replicate 1.


title: A375control_1677_10uM_1

tag: RAF inhibitor #1 treatment of A375 parental cells. Replicate 1.


title: rosette_leaves_WT_biological rep1


title: A375sh2BRaf_B439006_1

tag: BAY-43-9006 treatment of A375 shBRAF-2 cells. Replicate 1.


title: A375sh2BRaf_B439006_2

tag: BAY-43-9006 treatment of A375 shBRAF-2 cells. Replicate 2.


title: A375control_1677_10uM_2

tag: RAF inhibitor #1 treatment of A375 parental cells. Replicate 2.


title: A375control_B439006_10uM_1

tag: BAY-43-9006 treatment of A375 parental cells. Replicate 1.


title: A375shBRaf_AR341787

tag: RAF inhibitor #1 treatment of A375 shBRAF-1 cells. Replicate 1.


title: A375sh2BRaf_1677_2

tag: RAF inhibitor #1 treatment of A375 shBRAF-2 cells. Replicate 2.


title: NSCLC_AC_492

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

description: Gene expression data from human non-small cell lung cancer tumor tissue 492.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip« U133 Plus 2.0 in the Affymetrix GeneChip« Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip« Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned with the Affymetrix GeneChip« Scanner 3000.

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1996] were used for pre-processing of the 58 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix ROC technical manual 701021 Rev.5).

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturersÆ instructions.

treatment_protocol: tumor tissue samples from surgically treated patients were collected intraoperatively, snap-frozen and stored at -80 C. All samples underwent a careful analysis of the histopathology, estimation of tumor and stromal content and subsequent macro-dissection of the tumor regions before enrollment into the microarray experiments.

tag: disease state

value: adenocarcinoma


title: NSCLC_AC_489

description: Gene expression data from human non-small cell lung cancer tumor tissue 489.


title: NSCLC_AC_402

description: Gene expression data from human non-small cell lung cancer tumor tissue 402.


title: NSCLC_AC_434

description: Gene expression data from human non-small cell lung cancer tumor tissue 434.


title: NSCLC_AC_400

description: Gene expression data from human non-small cell lung cancer tumor tissue 400.


title: NSCLC_SCC_364

description: Gene expression data from human non-small cell lung cancer tumor tissue 364.

value: squamous cell carcinoma


title: NSCLC_AC_368

description: Gene expression data from human non-small cell lung cancer tumor tissue 368.


title: NSCLC_AC_426

description: Gene expression data from human non-small cell lung cancer tumor tissue 426.


title: NSCLC_AC_378

description: Gene expression data from human non-small cell lung cancer tumor tissue 378.


title: NSCLC_SCC_390

description: Gene expression data from human non-small cell lung cancer tumor tissue 390.


title: NSCLC_AC_445

description: Gene expression data from human non-small cell lung cancer tumor tissue 445.


title: NSCLC_SCC_412

description: Gene expression data from human non-small cell lung cancer tumor tissue 412.


title: NSCLC_AC_334

description: Gene expression data from human non-small cell lung cancer tumor tissue 334.


title: NSCLC_AC_397

description: Gene expression data from human non-small cell lung cancer tumor tissue 397.


title: NSCLC_SCC_347

description: Gene expression data from human non-small cell lung cancer tumor tissue 347.


title: NSCLC_AC_348

description: Gene expression data from human non-small cell lung cancer tumor tissue 348.


title: NSCLC_AC_342

description: Gene expression data from human non-small cell lung cancer tumor tissue 342.


title: A375shGFP_AR341787

tag: RAF inhibitor #2 treatment of A375 shGFP cells. Replicate 1.


title: NSCLC_AC_331

description: Gene expression data from human non-small cell lung cancer tumor tissue 331.


title: NSCLC_AC_276

description: Gene expression data from human non-small cell lung cancer tumor tissue 276.


title: NSCLC_SCC_248

description: Gene expression data from human non-small cell lung cancer tumor tissue 248.


title: NSCLC_SCC_301

description: Gene expression data from human non-small cell lung cancer tumor tissue 301.


title: NSCLC_AC_271

description: Gene expression data from human non-small cell lung cancer tumor tissue 271.


title: NSCLC_SCC_165

description: Gene expression data from human non-small cell lung cancer tumor tissue 165.


title: NSCLC_SCC_188

description: Gene expression data from human non-small cell lung cancer tumor tissue 188.


title: NSCLC_AC_273

description: Gene expression data from human non-small cell lung cancer tumor tissue 273.


title: NSCLC_AC_169

description: Gene expression data from human non-small cell lung cancer tumor tissue 169.


title: NSCLC_AC_282

description: Gene expression data from human non-small cell lung cancer tumor tissue 282.


title: NSCLC_AC_202

description: Gene expression data from human non-small cell lung cancer tumor tissue 202.


title: NSCLC_AC_210

description: Gene expression data from human non-small cell lung cancer tumor tissue 210.


title: NSCLC_SCC_215

description: Gene expression data from human non-small cell lung cancer tumor tissue 215.


title: NSCLC_AC_136

description: Gene expression data from human non-small cell lung cancer tumor tissue 136.


title: NSCLC_AC_147

description: Gene expression data from human non-small cell lung cancer tumor tissue 147.


title: NSCLC_AC_113

description: Gene expression data from human non-small cell lung cancer tumor tissue 113.


title: NSCLC_AC_148

description: Gene expression data from human non-small cell lung cancer tumor tissue 148.


title: NSCLC_AC_97

description: Gene expression data from human non-small cell lung cancer tumor tissue 97.


title: NSCLC_AC_161

description: Gene expression data from human non-small cell lung cancer tumor tissue 161.


title: NSCLC_SCC_95

description: Gene expression data from human non-small cell lung cancer tumor tissue 95.


title: NSCLC_AC_84

description: Gene expression data from human non-small cell lung cancer tumor tissue 84.


title: NSCLC_AC_137

description: Gene expression data from human non-small cell lung cancer tumor tissue 137.


title: NSCLC_AC_89

description: Gene expression data from human non-small cell lung cancer tumor tissue 89.


title: NSCLC_AC_88

description: Gene expression data from human non-small cell lung cancer tumor tissue 88.


title: NSCLC_SCC_77

description: Gene expression data from human non-small cell lung cancer tumor tissue 77.


title: NSCLC_SCC_75

description: Gene expression data from human non-small cell lung cancer tumor tissue 75.


title: NSCLC_AC_70

description: Gene expression data from human non-small cell lung cancer tumor tissue 70.


title: NSCLC_SCC_65

description: Gene expression data from human non-small cell lung cancer tumor tissue 65.


title: NSCLC_SCC_55

description: Gene expression data from human non-small cell lung cancer tumor tissue 55.


title: NSCLC_AC_51

description: Gene expression data from human non-small cell lung cancer tumor tissue 51.


title: NSCLC_AC_53

description: Gene expression data from human non-small cell lung cancer tumor tissue 53.


title: NSCLC_AC_40

description: Gene expression data from human non-small cell lung cancer tumor tissue 40.


title: NSCLC_SCC_25

description: Gene expression data from human non-small cell lung cancer tumor tissue 25.


title: NSCLC_SCC_37

description: Gene expression data from human non-small cell lung cancer tumor tissue 37.


title: NSCLC_AC_49

description: Gene expression data from human non-small cell lung cancer tumor tissue 49.


title: NSCLC_AC_24

description: Gene expression data from human non-small cell lung cancer tumor tissue 24.


title: NSCLC_AC_10

description: Gene expression data from human non-small cell lung cancer tumor tissue 10.


title: NSCLC_AC_233

description: Gene expression data from human non-small cell lung cancer tumor tissue 233.


title: NSCLC_SCC_30

description: Gene expression data from human non-small cell lung cancer tumor tissue 30.


title: NSCLC_SCC_22

description: Gene expression data from human non-small cell lung cancer tumor tissue 22.


title: 09-26-08_LHennighausen1_AK_Mouse430_2_CTLGMP-

status: Public on Sep 30 2009

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Gene expression of CTL_GMP-

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix Microarray Suite version 5.0

label_protocol: Affymetrix standard protocol

growth_protocol: Mice were grown in the NIDDK animal core facility with the standard protocol.

extract_protocol: Affymetrix standard protocol

treatment_protocol: Control treated with No GMP

tag: Control treated with No GMP


title: 03-25-08_Hennighausen_AK_Mouse430_2_GMPCTL-

description: Gene expression of GMP_CTL-

growth_protocol: Control

treatment_protocol: Treated with No GMP

tag: Treated with No GMP


title: 09-26-08_LHennighausen1_AK_Mouse430_2_KOGMP-C

description: Gene expression of KO_GMP-C

treatment_protocol: Stat5 KO treated with No GMP

tag: Stat5 KO treated with No GMP


title: 09-26-08_LHennighausen1_AK_Mouse430_2_CTLGMP+

description: Gene expression of CTL_GMP+

treatment_protocol: Control treated with GMP

tag: Control treated with GMP


title: 03-25-08_Hennighausen_AK_Mouse430_2_GMPCTL+

description: Gene expression of GMP_CTL+

growth_protocol: control

treatment_protocol: Treated with GMP

tag: Treated with GMP


title: 08-05-08_Hennighausen_7AK_Mouse430_2_626_CG-

description: Gene expression of 6-26_7CGwo


title: 03-25-08_Hennighausen_AK_Mouse430_2_GMPKO-

description: Gene expression of GMP_KO-


title: NSCLC_AC_16

description: Gene expression data from human non-small cell lung cancer tumor tissue 16.


title: 03-25-08_Hennighausen_AK_Mouse430_2_GMPKO+b

description: Gene expression of GMP_KO+b

treatment_protocol: Stat5 KO treated with GMP

tag: Stat5 KO treated with GMP


title: 08-05-08_Hennighausen_12AK_Mouse430_2_702_KG+

description: Gene expression of 7-2_12KGw


title: 08-05-08_Hennighausen_8AK_Mouse430_2_626_CG+

description: Gene expression of 6-26_8CGw


title: 08-05-08_Hennighausen_3AK_Mouse430_2_626_KG-

description: Gene expression of 6-26_3KGwo


title: 09-26-08_LHennighausen1_AK_Mouse430_2_KOGMP+

description: Gene expression of KO_GMP+


title: 0-30min 500µM 4sU nt-RNA Rep.9

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

description: 30 min newly transcribed RNA (nt-RNA)

hyb_protocol: Affymetrix standard

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: GCRMA

source_name: NIH-3T3 cells

label_protocol: Affymetrix one cycle target labeling protocol

growth_protocol: DMEM + 5%NCS + P/S, 37°C, 5% CO2

extract_protocol: Trizol extraction of total RNA was performed following the modified protocol described by Chomczynski et al.

treatment_protocol: NIH-3T3 cells (5th to 15th passage after thawing) were plated at 40% density 24 h before the begin of the experiment (=> 80% density at start of experiment)

tag: NIH-3T3 cells 0-30min 500µM 4sU

tag: NIH-3T3 cells split 24 h before start of experiment


title: 0-30min 500µM 4sU nt-RNA Rep. 3

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.8

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.9

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep.4

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.7

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep. 2

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.4

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep.5

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep.6

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep.8

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)


title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 2

description: 60 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h mock, 0-60min 200µM 4sU


title: 0-30min 500µM 4sU nt-RNA Rep. 1

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.5

description: total cellular RNA (tc-RNA)


title: 0-30min 500µM 4sU nt-RNA Rep.7

description: 30 min newly transcribed RNA (nt-RNA)


title: 0-30min 500µM 4sU tc-RNA Rep.6

description: total cellular RNA (tc-RNA)


title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 3

description: 60 min newly transcribed RNA (nt-RNA)


title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 1

description: 60 min newly transcribed RNA (nt-RNA)


title: 1h mock, 0-60 min 200µM 4sU p-RNA Rep. 1

description: unlabeled, preexisiting RNA (p-RNA)

tag: NIH-3T3 cells 0-60min 200µM 4sU


title: 2F_1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)


title: 1h mock, 0-60 min 200µM 4sU p-RNA Rep. 3

description: unlabeled, preexisiting RNA (p-RNA)


title: 2F_1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)


title: 2F_1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 3

description: 60 min newly transcribed RNA (nt-RNA)


title: 1h mock, 0-60 min 200µM 4sU p-RNA Rep. 2

description: unlabeled, preexisiting RNA (p-RNA)


title: 2F_1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 2

description: 60 min newly transcribed RNA (nt-RNA)


title: 2F_1h mock, 0-60 min 200µM 4sU nt-RNA Rep. 1

description: 60 min newly transcribed RNA (nt-RNA)


title: 2F_1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)


title: 2h actinomycin D, tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 2h 5µg/ml actinomycin D


title: 15min mock, 0-15 min 500µM 4sU nt-RNA Rep. 3

description: 15 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 15min mock, 0-15min 500µM 4sU


title: 1h actinomycin D, tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 1h 5µg/ml actinomycin D


title: 1h actinomycin D, tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)


title: 2h actinomycin D, tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)


title: before actinomycin D, tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells before actinomycin D treatment


title: 1h actinomycin D, tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)


title: before actinomycin D, tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)


title: 15min mock, 0-15 min 500µM 4sU nt-RNA Rep. 2

description: 15 min newly transcribed RNA (nt-RNA)


title: 2h actinomycin D, tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)


title: 15min mock, 0-15 min 500µM 4sU nt-RNA Rep. 1

description: 15 min newly transcribed RNA (nt-RNA)


title: 3h 100U/ml IFNalpha, 150-180 min 500µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)

growth_protocol: DMEM + 5%NCS + P/S, 37°C, 5% CO2,

tag: NIH-3T3 cells, 3h 100U/ml IFNalpha, 150-180 min 500µM 4sU


title: 3h mock, 150-180 min 500µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 3h mock, 150-180 min 500µM 4sU


title: 3h 100U/ml IFNgamma, 150-180 min 500µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells, 3h 100U/ml IFNgamma, 150-180 min 500µM 4sU


title: 1h mock 200µM 4sU tc-RNA Rep.4

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 30-60 min 200µM 4sU, 60 min mock


title: 3h 100U/ml IFNalpha, 150-180 min 500µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: before actinomycin D, tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)


title: 1h 100U/ml IFN gamma + 200µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 60 min 200µM 4sU + 100U/ml IFN gamma


title: 1h 100U/ml IFNalpha + 200µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 60 min 200µM 4sU + 100U/ml IFN alpha


title: 3h mock, 150-180 min 500µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: 1h 100U/ml IFN gamma + 200µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: 3h mock, 150-180 min 500µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: 3h 100U/ml IFNalpha, 150-180 min 500µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: 3h 100U/ml IFNgamma, 150-180 min 500µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: 1h 100U/ml IFNalpha + 200µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)


title: 1h 100U/ml IFNalpha 200µM 4sU tc-RNA Rep.4

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 30-60 min 200µM 4sU, 60 min 100U/ml IFN alpha


title: 1h 100U/ml IFN gamma + 200µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: 1h 100U/ml IFN gamma, 200µM 4sU tc-RNA Rep.4

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 30-60 min 200µM 4sU, 60 min 100U/ml IFN gamma


title: 1h 100U/ml IFNalpha + 200µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)


title: 3h 100U/ml IFNgamma, 150-180 min 500µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)


title: 1h mock 200µM 4sU tc-RNA Rep.1

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 60 min 200µM 4sU


title: 1h mock 200µM 4sU tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: 1h mock tc-RNA Rep.1

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells 60 min no 4sU added


title: 1h mock tc-RNA Rep.2

description: total cellular RNA (tc-RNA)

tag: NIH-3T3 cells split 24 h before start of experiment


title: 3h 100U/ml IFN alpha, 150-180 min 500µM 4sU nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)

growth_protocol: 37°C, 5% CO2, DMEM + 5%NCS + P/S

tag: NIH-3T3 cells 3h 100U/ml IFN alpha, 150-180 min 500µM 4sU


title: 1h mock 200µM 4sU tc-RNA Rep.2

description: total cellular RNA (tc-RNA)


title: 3h 100U/ml IFN gamma, 150-180 min 500µM 4sU nt-RNA Rep. 2

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 3h 100U/ml IFN gamma, 150-180 min 500µM 4sU


title: 1h 100U/ml IFNgamma, 30-60 min 500µM 4sU nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h 100U/ml IFNgamma, 30-60 min 500µM 4sU


title: 3h mock, 150-180 min 500µM 4sU nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 3h 100U/ml IFN alpha, 150-180 min 500µM 4sU nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 3h 100U/ml IFN alpha, 150-180 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFN gamma,  0-60 min 200µM 4sU nt-RNA, Rep.2

description: 60 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h 100U/ml IFNgamma, 0-60min 200µM 4sU


title: 3h mock, 150-180 min 500µM 4sU nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNalpha,  0-60 min 200µM 4sU nt-RNA, Rep.3

description: 60 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h 100U/ml IFNalpha, 0-60min 200µM 4sU


title: 3h 100U/ml IFN gamma, 150-180 min 500µM 4sU nt-RNA Rep. 3

description: 30 min newly transcribed RNA (nt-RNA)


title: 3h 100U/ml IFN gamma, 150-180 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h mock tc-RNA Rep.3

description: total cellular RNA (tc-RNA)


title: 1h mock, 30-60 min 500µM 4sU nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h mock, 30-60 min 500µM 4sU


title: 1h 100U/ml IFNalpha, 30-60 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 1h 100U/ml IFNalpha, 30-60 min 500µM 4sU


title: 3h mock, 150-180 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 3h mock, 150-180 min 500µM 4sU


title: 1h mock, 30-60 min 500µM 4sU nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNalpha, 30-60 min 500µM 4sU nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNalpha, 30-60 min 500µM 4sU nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNgamma, 30-60 min 500µM 4sU nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNgamma, 30-60 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h mock, 30-60 min 500µM 4sU nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFN gamma,  0-60 min 200µM 4sU nt-RNA, Rep.1

description: 60 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNalpha,  0-60 min 200µM 4sU nt-RNA, Rep.1

description: 60 min newly transcribed RNA (nt-RNA)


title: 30min 100U/ml IFNalpha, 0-30min 500µM 4sU, nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 30 min 500µM 4sU + 100U/ml IFN alpha


title: 30min 100U/ml IFNgamma, 0-30min 500µM 4sU, nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 30 min 500µM 4sU + 100U/ml IFN gamma


title: 30min 100U/ml IFNgamma, 0-30min 500µM 4sU, nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFN gamma,  0-60 min 200µM 4sU nt-RNA, Rep.3

description: 60 min newly transcribed RNA (nt-RNA)


title: 30min 100U/ml IFNgamma, 0-30min 500µM 4sU, nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 30min 100U/ml IFNalpha, 0-30min 500µM 4sU, nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)


title: 1h 100U/ml IFNalpha,  0-60 min 200µM 4sU nt-RNA, Rep.2

description: 60 min newly transcribed RNA (nt-RNA)


title: 30min mock, 0-30min 500µM 4sU, nt-RNA Rep.1

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells 30 min 500µM 4sU


title: 30min mock, 0-30min 500µM 4sU, nt-RNA Rep.3

description: 30 min newly transcribed RNA (nt-RNA)


title: 30min 100U/ml IFNalpha, 0-30min 500µM 4sU, nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)


title: Liver WT infected 48h replicate 3

status: Public on Sep 29 2009

city: Galveston

first: Ashok

middle: K

last: Chopra

address: 301 University Blvd.

department: Microbiology & Immunology

institute: University of Texas Medical Branch

description: Swiss-Webster female mice (Charles River Laboratories, Wilmington, MA) 5-6 weeks of age were infected intranasally with 5 LD50 of either WT or Δlpp mutant of Y. pestis CO92. Uninfected mice were used as controls. At either 12 or 48 h post infection (p.i.), 3 mice per group were euthanized and the lungs, livers, and spleens were harvested and homogenized in 1 ml of RNALater (Ambion/Applied Biosystems, Austin, TX) using 50-ml tissue homogenizers (Kendell, Mansfield, MA). RNA was isolated from the tissue homogenates and purified using RNAqueous (Ambion). After an overnight precipitation, the RNA was resuspended in 20 ul of diethylpyrocarbonate (DEPC)-treated water and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays, performed by the Molecular Genomics Core at UTMB Galveston, Texas, per manufacture protocols. The arrays had 45,000 probe sets representing more than 39,000 transcripts derived from ~34,000 well-substantiated mouse genes. The experiments were performed in triplicate (biological replicates), generating a total of 45 arrays.

hyb_protocol: Per manufacturer

scan_protocol: Per manufacturer

data_processing: Data were Robust Multichip Average (RMA) normalized and log transformed using GeneSifter software (VizX Labs, Seattle, WA).

source_name: Liver WT infected 48h

label_protocol: Per manufacturer

tag: tissue

value: Liver

tag: infection

value: wild-type Yersinia pestis CO92

tag: time point

tag: replicate

tag: strain

value: Swiss-Webster (Charles River Laboratories)

tag: gender

value: female

tag: age

value: 5-6 weeks


title: Lung WT infected 12h replicate 2

source_name: Lung WT infected 12h

extract_protocol: At either 12 or 48 h post infection (p.i.), 3 mice per group were euthanized and the lungs, livers, and spleens were harvested and homogenized in 1 ml of RNALater (Ambion/Applied Biosystems, Austin, TX) using 50-ml tissue homogenizers (Kendell, Mansfield, MA). RNA was isolated from the tissue homogenates and purified using RNAqueous (Ambion). After an overnight precipitation, the RNA was resuspended in 20 ul of diethylpyrocarbonate (DEPC)-treated water and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays, performed by the Molecular Genomics Core at UTMB Galveston, Texas, per manufacture protocols.

value: Lung


title: Lung WT infected 12h replicate 3


title: Liver WT infected 48h replicate 2


title: Liver WT infected 12h replicate 3

source_name: Liver WT infected 12h


title: Lung WT infected 48h replicate 3

source_name: Lung WT infected 48h


title: Spleen WT infected 12h replicate 3

source_name: Spleen WT infected 12h

value: Spleen


title: Liver WT infected 12h replicate 2


title: 30min mock, 0-30min 500µM 4sU, nt-RNA Rep.2

description: 30 min newly transcribed RNA (nt-RNA)

tag: NIH-3T3 cells split 24 h before start of experiment


title: Spleen WT infected 48h replicate 1

source_name: Spleen WT infected 48h


title: Spleen WT infected 48h replicate 3


title: Liver WT infected 48h replicate 1


title: Lung WT infected 48h replicate 2


title: Spleen WT infected 48h replicate 2


title: Spleen WT infected 12h replicate 2


title: Spleen WT infected 12h replicate 1


title: Lung WT infected 48h replicate 1


title: Lung WT infected 12h replicate 1


title: Spleen mutant infected 48h replicate 3

source_name: Spleen mutant infected 48h

value: Yersinia pestis CO92, Braun lipoprotein mutant


title: Liver WT infected 12h replicate 1


title: Lung mutant infected 48h replicate 1

source_name: Lung mutant infected 48h


title: Lung mutant infected 48h replicate 2


title: Spleen mutant infected 12h replicate 2

source_name: Spleen mutant infected 12h


title: Lung mutant infected 12h replicate 2

source_name: Lung mutant infected 12h


title: Spleen mutant infected 12h replicate3


title: Lung mutant infected 12h replicate 1


title: Spleen mutant infected 48h replicate 1


title: Lung mutant infected 48h replicate 3


title: Liver mutant infected 12h replicate 3

source_name: Liver mutant infected 12h


title: Lung mutant infected 12h replicate 3


title: Spleen mutant infected 48h replicate 2


title: Liver mutant infected 12h replicate 2


title: Liver mutant infected 12h replicate 1


title: Liver mutant infected 48h replicate 1

source_name: Liver mutant infected 48h


title: Liver mutant infected 48h replicate 3


title: Liver mutant infected 48h replicate 2


title: Spleen mutant infected 12h replicate 1


title: Liver uninfected replicate 3

source_name: Liver uninfected


title: Liver uninfected replicate 1


title: Liver uninfected replicate 2


title: Spleen uninfected replicate 3

source_name: Spleen uninfected


title: Lung uninfected replicate 3

source_name: Lung uninfected


title: Spleen uninfected replicate 2


title: Lung uninfected replicate 1


title: dyt1-3

status: Public on Sep 23 2009

city: State College

first: Xuan

last: Ma

state: PA

address: Life Science Building 416

department: Biology

institute: penn state university

description: Gene expression data from dyt1 mutant

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA to normalize and converted to logarithm base 2

source_name: anthers from dyt1 mutant

label_protocol: Standard Affymetrix protocol.

growth_protocol: All plants were grown at 22˚C under long day photoperiod (16 hours in light and 8 hours in darkness)

extract_protocol: RNA were extracted by using Plant RNase Mini kit (Qiagen).

treatment_protocol: The anthers at stages 4-7 were dissected and collected from the young floral buds of the plants of 3-4 weeks. Three biological replicates from each genetic background (Col., dyt1, and ams) were used for microarray analyses.

tag: genotype/variation

value: anther

tag: developmental stage

value: stages 4-7


title: Lung uninfected replicate 2


title: ams-2

description: Gene expression data from ams mutant

source_name: anthers from ams mutant

value: ams


title: Spleen uninfected replicate 1


title: dyt1-1

description: Gene expression data from dyt1 mutant


title: Wild type-3

description: Gene expression data from columbia genotype

source_name: anthers from wildtype

value: Col (wild type)


title: ams-3

description: Gene expression data from ams mutant


title: ams-1

description: Gene expression data from ams mutant


title: dyt1-2

description: Gene expression data from dyt1 mutant


title: Wild type-2


title: Cortex caudal E14 wt animal 14

status: Public on Sep 22 2009

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: 400 ng of total RNA were used for amplification

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Normalized Mas5 data

source_name: Cortex E14 (caudal) from wild type mice

label_protocol: MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion)

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment.

tag: C57Bl/6J background. wt mice crossed with Emx1::Cre knock-in mice.


title: Wild type-1


title: Cortex caudal E14 AP2gamma k.o. animal 13

scan_protocol: According to the Affymetrix expression protocol

source_name: Cortex E14 (caudal) from knock-out mice

tag: C57Bl/6J background. Mice were Ap2gamma -/- (k.o.). Exon 5 of Ap2gamma was flanked by LoxP sites. Mice were crossed with Emx1::Cre knock-in mice.


title: Cortex caudal E14 wt animal 06


title: Cortex rostral E14 AP2gamma k.o. animal 08

source_name: Cortex E14 (rostral) from knock-out mice


title: Cortex rostral E14 wt animal 12

source_name: Cortex E14 (rostral) from wild type mice


title: Cortex rostral E14 wt animal 10


title: Cortex rostral E14 wt animal 16


title: Cortex caudal E14 AP2gamma k.o. animal 02

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

tag: C57Bl/6J background. Ap2gamma -/- (k.o.). Exon 5 of Ap2gamma was flanked by LoxP sites. Mice were crossed with Emx1::Cre knock-in mice.


title: Cortex caudal E14 wt animal 04


title: Cortex rostral E14 AP2gamma k.o. animal 07


title: Cortex rostral E14 AP2gamma k.o. animal 15


title: Seed_WS_Dry_1

status: Public on Sep 20 2009

city: Rehovot

first: Ruthie

last: Ruthie

address: PO Box 26

department: Plant Science

institute: Weizmann Institute of Science

description: Dry seeds of the WT

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA- using Partek genomic suite

label: Standard Affymetrix protocol

source_name: Dry seeds of the WT

label_protocol: Standard Affymetrix protocol

growth_protocol: Long day regime (~16h of light & 8h of dark), grown in greenhouse, ~23 degree.

extract_protocol:
Total RNA was isolated as previously described  in Ruuska and Ohlrogge, 2001
and was treated with DNAase RQ-1 (Promega) then RNA was amplified using 2-cycle Affimetrix labelling using the standard Affymetrix protocol

tag: type

value: Dry seeds

tag: ecotype

value: Wassilewskija

tag: genotype

value: WT


title: Seed_WT_14DAF_1

description: Developing seeds of the WT 14DAF (days after flowering), during mid maturation-reserve accumulation.

source_name: Excised seeds

value: Excised seeds

value: 14DAF(days after flowering)


title: Seed_WT_16DAF_1

description: Developing seeds of the WT 16DAF (days after flowering), during end of maturation-reserve accumulation.

source_name: Developing seeds of the KD mutant 16DAF

value: 16DAF(days after flowering)


title: Seed_KD_16DAF_1

description: Developing seeds of the KD mutant 16DAF (days after flowering), during end of maturation-reserve accumulation

value: KD


title: Seed_KD_14DAF_2

description: Developing seeds of the KD mutant 14DAF (days after flowering), during mid maturation-reserve accumulation

label: standard Affymetrix protocol

source_name: Developing seeds of the KD mutant 14DAF


title: Seed_KD_Dry_1

description: Dry seeds of the KD mutant.


title: Seed_KD_14DAF_1


title: Cortex caudal E14 AP2gamma k.o. animal 01

tag: C57Bl/6J background. Ap2gamma -/- (k.o.). Exon 5 of AP2gamma was flanked by LoxP sites. Mice were crossed with Emx1::Cre knock-in mice.


title: Seed_WT_Dry_2

description: Dry seeds of the WT (WS ecotype).


title: DH, biological rep3

status: Public on Sep 18 2009

city: St. Paul

first: William

middle: M.

last: Gray

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Gene expression data from 7-day-old seedlings grown on 30% 2H2O media and transferred to H2O media

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized to the Affymetrix Ath121501 chip according to the protocols provided by the manufacture,GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip 3000 scanner.7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

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

growth_protocol: Seedlings were germinated on semi-solid ATS media with or without 30% 2H2O and grown under continuous light at 22±2℃.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit (Qiagen), following the manufacturer’s instructions.

treatment_protocol: Seedlings were collected and frozen in liquid nitrogen immediately.  Seedlings were ground to powder under liquid nitrogen just before total RNA isolation.

tag: tissue

value: seedling

value: Columbia


title: D2O, biological rep3

description: Gene expression data from 7-day-old seedlings grown on 30% 2H2O media


title: Seed_WT_14DAF_2

description: Developing seeds of WT-WS ecotype 14DAF (days after flowering), during mid maturation-reserve accumulation

source_name: Developing seeds of the WT - 14DAF


title: Seed_KD_16DAF_2


title: DH, biological rep2

source_name: 7-day-old seedlings grown on 30% 2H2O media and transferred to H2O media


title: Seed_WT_16DAF_2

description: Developing seeds of WT-WS ecotype 16DAF (days after flowering), during end of maturation-reserve accumulation

source_name: Developing seeds of the WT- 16DAF


title: Cbfb-deficient Treg_rep1

status: Public on Sep 19 2009

city: Kyoto

first: Akihiko

last: Kitoh

address: 53 Shogoin Kawahara-cho

department: Institute for Frontier Medical Sciences

country: Japan

institute: Kyoto University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analyses were done with the use of MeV (v4.2) (Saeed et al., 2003 Biotechniques 34, 374-378).

source_name: Cbfb-deficient Treg

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted with the RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.

tag: cell type

value: peripheral CD4+CD25hi cells

tag: mouse genotype

value: Cbfb-flox/flox, Foxp3-ires-Cre

value: male

value: 5 weeks

value: purified CD4+CD25hi cells from spleen and lymph nodes


title: HD, biological rep2

description: Gene expression data from 7-day-old seedlings grown on H2O media and transferred to 30% 2H2O media


title: Seed_KD_dry_2

description: Dry seeds of the KD mutant

source_name: Dry seeds of the KD mutant


title: HH, biological rep2

description: Gene expression data from 7-day-old seedlings grown on H2O media and transferred to H2O media


title: HH, biological rep3

source_name: 7-day-old seedlings grown on H2O media and transferred to H2O media


title: HD, biological rep1

description: Gene expression data from7-day-old seedlings grown on H2O media and transferred to 30% 2H2O media


title: Control Treg_rep1

source_name: Control Treg

value: Cbfb-flox/wt, Foxp3-ires-Cre


title: DH, biological rep1


title: D2O, biological rep2

description: Gene expression data from  7-day-old seedlings grown on 30% 2H2O media


title: HH, biological rep1


title: HD, biological rep3

source_name: 7-day-old seedlings grown on H2O media and transferred to 30% 2H2O media


title: pnp1-1_1wk_-P_rep3

status: Public on Sep 12 2009

city: Ithaca

first: Chloe

last: Marchive

state: NY

address: Tower road

institute: Boyce Thompson Institute

hyb_protocol: Labeled cRNA was hybridized on Affymetrix Arabidopsis ATH1 Genome arrays, stained and washed according to standard protocol by Affymetrix (Santa Clara, CA).

scan_protocol: GeneChips were scanned using the and scanned by GeneChip Scanner 3000.

data_processing: Raw array data were normalized at the probe level using gcRMA (Wu et al., 2004). The detection calls (present, marginal, or absent) for each probe set were obtained using the mas5calls function in the Affy package (Gautier et al., 2004). Only genes with at least one present call across all of the compared samples were used to identify differentially expressed genes. Significance of gene expression was determined using the LIMMA test (Smyth, 2004), and raw P values of multiple tests were corrected using FDR (Benjamini and Hochberg, 1995). Genes with FDR , 0.05 and fold change $ 2 were identified as differentially expressed.

source_name: 2-week old pnp1-1 rosette grown for one additional week on -P medium

label_protocol: One microgram of each total RNA sample was labeled using MessageAmp™ II-Biotin /Enhanced/ Single Round aRNA Amplification Kit from Ambion (Austin, TX), according to manufacture provided protocol.

growth_protocol: WT and pnp1-1 plants  (Columbia -0) were germinated and grown for 2 weeks on a full nutrient MS medium (+P) containing 0.6% phytagar (w/v) and 0.5% (w/v) Suc at 22˚C in a growth chamber under a 16-h photoperiod (with a fluorescent light intensity of 200 μmol m-2 s-1

extract_protocol: Total RNA was isolated from seedlings, from which roots had been removed, using the RNeasy Plant Minikit (Qiagen), including DNase treatment according to the manufacturer’s instructions.

treatment_protocol: After two weeks, they were transferred to fresh +P or -P MS medium. For the -P medium, KH2PO4 was omitted but the potassium was compensated by K2SO4. Plantlets were rinsed with distilled water before transfer and then grown for 3h or one week.

value: seedlings without roots

value: 3 weeks

tag: treatment

value: No phosphate medium


title: H2O, biological rep2

description: Gene expression data from  7-day-old seedlings grown on H2O control media

source_name: 7-day-old seedlings grown on control media


title: SAM SE agl15 agl18 double mutantL, biological rep3

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

description: Gene expression data from the shoot apical meristem somatic embryo culture of double mutant, replicate 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Arabidopsis ATH1 Genome Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.

data_processing: The data was scaled using the Affymetrix analysis software to a target intensity of 500 and log2 transformed.

source_name: 10 day SAM somatic embryo culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Arabidopsis seeds (Columbia wild type, agl15-4 agl18-1 double mutant, and 35S:AGL15) were surface sterilized and grown to complete germination in liquid MS media with 2% w/v sucrose, 10 mM MES and 4.5 micromolar 2,4-D under a 23 hour light/1 hour dark cycle on a rotary shaker.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, and the RNA was further purified using the RNeasy® plant mini kit (Qiagen, www.qiagen.com).

treatment_protocol: Tissue was collected 10 days after the start of culture and flash frozen for RNA isolation.

tag: ecotype/variety

value: columbia

tag: genome/variation

value: Insertional loss-of-function agl15-4 agl18-1


title: SAM SE agl15 agl18 double mutant, biological rep2

description: Gene expression data from the shoot apical meristem somatic embryo culture of double mutant, replicate 2


title: SAM SE 35S:AGL15, biological rep2

description: Gene expression data from the shoot apical meristem somatic embryo culture of 35S:AGL15, replicate 2


title: H2O, biological rep3

tag: age


title: pnp1-1_1wk_-P_rep2


title: pnp1-1_1wk_-P_rep1


title: SAM SE 35S:AGL15, biological rep3

description: Gene expression data from the shoot apical meristem somatic embryo culture of 35S:AGL15, replicate 3


title: SAM SE agl15 agl18 double mutant, biological rep1

description: Gene expression data from the shoot apical meristem somatic embryo culture of double mutant, replicate 1


title: pnp1-1_1wk_+P_rep3

source_name: 2-week old pnp1-1 rosette grown for one additional week on +P medium

value: Full nutrient medium (+P)


title: D2O, biological rep1

source_name: 7-day-old seedlings grown on 30% 2H2O media


title: SAM SE 35S:AGL15, biological rep1

description: Gene expression data from the shoot apical meristem somatic embryo culture of 35S:AGL15, replicate 1


title: pnp1-1_1wk_+P_rep1


title: pnp1-1_1wk_+P_rep2


title: SAM SE Col, biological rep3

description: Gene expression data from the shoot apical meristem somatic embryo culture of Col wild type, replicate 3

value: wild type


title: WT_1wk_-P_rep1

source_name: 2-week old WT rosette grown for one additional week on -P medium

value: WT Col0


title: SAM SE Col, biological rep2

description: Gene expression data from the shoot apical meristem somatic embryo culture of Col wild type, replicate 2


title: WT_1wk_-P_rep3


title: H2O, biological rep1


title: pnp1-1_3h_-P_rep2

source_name: 2-week old pnp1-1 rosette grown for 3 additional hours on -P medium

value: 2 weeks + 3h


title: WT_1wk_-P_rep2


title: pnp1-1_3h_-P_rep3


title: WT_1wk_+P_rep3

source_name: 2-week old WT rosette grown for one additional week on +P medium


title: pnp1-1_3h_-P_rep1


title: WT_3h_-P_rep2

source_name: 2-week old WT rosette grown for 3 additional hours on -P medium


title: WT_3h_+P_rep2

source_name: 2-week old WT rosette grown for 3 additional hours on +P medium


title: pnp1-1_3h_+P_rep1

source_name: 2-week old pnp1-1 rosette grown for 3 additional hours on +P medium


title: WT_1wk_+P_rep2


title: WT_3h_+P_rep3


title: pnp1-1_3h_+P_rep3


title: WT_1wk_+P_rep1


title: WT_3h_-P_rep3


title: WT_3h_+P_rep1


title: pnp1-1_3h_+P_rep2


title: WT_3h_-P_rep1


title: SAM SE Col, biological rep1

description: Gene expression data from the shoot apical meristem somatic embryo culture of Col wild type, replicate 1


title: BalbC_24h-DMSO

status: Public on Sep 04 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: BALB/cOlaHsd (inbred)

hyb_protocol: Hybridisation of 500ng cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.

source_name: Primary hepatocytes isolated from BalbC mouse strain treated with DMSO for 24h

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Mouse hepatocytes were isolated by two-step collagenase perfusion from 6 different strains of mouse; NMRI, SV129, FVB, DBA, BALB/C and C57BL/6J.

extract_protocol: Total RNA was prepared from mouse primary hepatocytes using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns.

treatment_protocol: Cells were plated on collagen-coated six-well plates. Viability was determined by Trypan Blue exclusion, and was at least 75%. Hepatocytes were suspended in William's E medium (Lonza Bioscience, Verviers, Belgium) supplemented with 10% (v/v) fetal calf serum, 20 m-units/mL insulin, 10 nM dexamethasone, 100 U/mL penicillin, 100 μg/mL of streptomycin, 0.25 μg/mL fungizone and 50 μg/mL gentamycin. After four hours the medium was discarded and replaced with fresh medium. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (10 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.

value: Primary hepatocytes

tag: strain

value: BalbC

tag: agent

value: control

tag: time

tag: gender

value: Male

value: 6 months


title: DBA_6h_DMSO

description: DBA/2OlaHsd (inbred)

source_name: Primary hepatocytes isolated from DBA mouse strain treated with DMSO for 6h

value: DBA

value: Female

value: 3 months


title: BalbC_6h_Wy

description: BALB/cOlaHsd (inbred)

source_name: Primary hepatocytes isolated from BalbC mouse strain treated with Wy14643 for 6h


title: SV129_24h_Wy

description: 129S1/SvImJ (inbred)

source_name: Primary hepatocytes isolated from SV129 mouse strain treated with Wy14643 for 24h

value: 4 months


title: DBA_6h_Wy

description: DBA/2OlaHsd (inbred)

source_name: Primary hepatocytes isolated from DBA mouse strain treated with Wy14643 for 6h


title: FVB_24h_Wy

description: FVB/NJ (inbred)

source_name: Primary hepatocytes isolated from FVB mouse strain treated with Wy14643 for 24h

value: FVB

value: 5 months


title: DBA_24h_Wy

description: DBA/2OlaHsd (inbred)

source_name: Primary hepatocytes isolated from DBA mouse strain treated with Wy14643 for 24h


title: FVB_6h_Wy

description: FVB/NJ (inbred)

source_name: Primary hepatocytes isolated from FVB mouse strain treated with Wy14643 for 6h


title: DBA_24h_DMSO

description: DBA/2OlaHsd (inbred)

source_name: Primary hepatocytes isolated from DBA mouse strain treated with DMSO for 24h


title: BalbC_24h_Wy

description: BALB/cOlaHsd (inbred)

source_name: Primary hepatocytes isolated from BalbC mouse strain treated with Wy14643 for 24h


title: BalbC_6h_DMSO

description: BALB/cOlaHsd (inbred)

source_name: Primary hepatocytes isolated from BalbC mouse strain treated with DMSO for 6h


title: FVB_6h_DMSO

description: FVB/NJ (inbred)

source_name: Primary hepatocytes isolated from FVB mouse strain treated with DMSO for 6h


title: SV129_24h_DMSO

description: 129S1/SvImJ (inbred)

source_name: Primary hepatocytes isolated from SV129 mouse strain treated with DMSO for 24h


title: SV129_6h_DMSO

description: 129S1/SvImJ (inbred)

source_name: Primary hepatocytes isolated from SV129 mouse strain treated with DMSO for 6h


title: FVB_24h_DMSO

description: FVB/NJ (inbred)

source_name: Primary hepatocytes isolated from FVB mouse strain treated with DMSO for 24h


title: NMRI_24h_Wy

description: HsdWin:NMRI (outbred)

source_name: Primary hepatocytes isolated from NMRI mouse strain treated with Wy14643 for 24h

value: NMRI


title: BL6_6h_DMSO

description: C57BL/6J (inbred)

source_name: Primary hepatocytes isolated from BL6 mouse strain treated with DMSO for 6h

value: 2 months


title: BL6_24h_DMSO

description: C57BL/6J (inbred)

source_name: Primary hepatocytes isolated from BL6 mouse strain treated with DMSO for 24h


title: NMRI_24h_DMSO

description: HsdWin:NMRI (outbred)

source_name: Primary hepatocytes isolated from NMRI mouse strain treated with DMSO for 24h


title: BL6_24h_Wy

description: C57BL/6J (inbred)

source_name: Primary hepatocytes isolated from BL6 mouse strain treated with Wy14643 for 24h


title: NMRI_6h_Wy

description: HsdWin:NMRI (outbred)

source_name: Primary hepatocytes isolated from NMRI mouse strain treated with Wy14643 for 6h


title: NMRI_6h_DMSO

description: HsdWin:NMRI (outbred)

source_name: Primary hepatocytes isolated from NMRI mouse strain treated with DMSO for 6h


title: SV129_6h_Wy

description: 129S1/SvImJ (inbred)

source_name: Primary hepatocytes isolated from SV129 mouse strain treated with Wy14643 for 6h


title: cpbh105_MCF10A-CAMK1D-noTAG

status: Public on Sep 08 2009

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72230.gif
Cell Line: CAMK1D

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5040; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 102422; Parameter Laser Power = 3.73; Parameter Scan Time = 10:51:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.02; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 102467; Parameter Laser Power = 3.38; Parameter Scan Time = 10:51:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.02; Performer: Young,,Kim

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm), default computed normalization procedure, see SMD website

source_name: human common reference_total RNA

label_protocol: not provided

extract_protocol: not provided

tag: sample type

value: human common reference_total RNA

tag: cell line background

tag: genotype/variation

tag: cell phenotype

value: mesenchymal


title: cpbh102_MCF10A

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs//72228.gif
Cell Line: vector

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5040; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 370; Parameter Laser on time = 102436; Parameter Laser Power = 3.76; Parameter Scan Time = 11:04:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.08; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 102436; Parameter Laser Power = 3.76; Parameter Scan Time = 11:04:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.08; Performer: Young,,Kim

value: epithelial


title: Normal_7

status: Public on Sep 01 2009

city: Philadelphia

first: Hiroshi

last: Nakagawa

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

description: Normal mucosa

hyb_protocol: Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: Scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 4 out of 10 for the tumor and normal tissue samples.

source_name: Normal tissue 7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy Fibrous Tissue Midi Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Surgically resected tissues were snap frozen and stored at -80ºC prior to RNA extraction

value: esophagus, normal

value: male, Japanese


title: BL6_6h_Wy

description: C57BL/6J (inbred)

source_name: Primary hepatocytes isolated from BL6 mouse strain treated with Wy14643 for 6h

value: Primary hepatocytes


title: cpbh104_MCF10A-vector

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72229.gif
Cell Line: vector

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5040; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 102453; Parameter Laser Power = 3.76; Parameter Scan Time = 11:21:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.32; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 440; Parameter Scan Power = 100; Parameter Laser on time = 102497; Parameter Laser Power = 3.37; Parameter Scan Time = 11:21:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.32; Performer: Young,,Kim


title: Normal_5

description: Normal mucosa

source_name: Normal tissue 5


title: ESCC_6

description: ESCC, TNM stage III, moderately differentiated

source_name: ESCC tumor tissue 6

value: esophagus, tumor


title: Normal_6

description: Normal mucosa

source_name: Normal tissue 6


title: ESCC_7

description: ESCC, TNM stage III, well differentiated

source_name: ESCC tumor tissue 7


title: ESCC_5

description: ESCC, TNM stage III, poorly differentiated

source_name: ESCC tumor tissue 5


title: cpbh103_MCF10A-CAMK1D

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72227.gif
Cell Line: CAMK1D

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 5040; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 102444; Parameter Laser Power = 3.76; Parameter Scan Time = 11:12:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.17; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2007-02-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 460; Parameter Scan Power = 100; Parameter Laser on time = 102488; Parameter Laser Power = 3.37; Parameter Scan Time = 11:12:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.17; Performer: Young,,Kim


title: Arabidopsis Col 10 days shoots 1

city: Columbus

first: Zidian

last: Xie

state: OH

address: 1060 Carmack Rd.

department: Dept. of Plant Cellular and Molecular Biology

institute: The Ohio State University

description: This experiment was used to look at the gene expression differences between Col wild type shoots and flp-1/myb88 double mutants.

hyb_protocol: or each array, 2.2 µg of cDNA is hybridized onto Arabidopsis ATH1 Genome GeneChips® (Affymetrix Inc., USA), designed in collaboration with TIGR, containing more than 22,500 probe sets representing approximately 24,000 genes. The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome's completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array. Hybridization is allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips are scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA) and CEL files are generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals are generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and are used to determine differential gene expression by pair-wise comparisons. The genes that are altered by two-fold either way are sorted and used for further interpretation of the microarray data.

data_processing: Affy-GUI, normalized by RMA

source_name: Arabidopsis 10 days old shoots

label_protocol: Following confirmation of RNA quality, Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) is used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA is synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA is achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA is purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content is measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Constitutive light, 22 degree

extract_protocol: RNA was extracted with Qiagen RNeasy Plant RNA extraction kit

tag: Ten-days-old Arabidopsis Columbia shoots on 1/2 MS medium


title: ESCC_3

source_name: ESCC tumor tissue 3


title: Peripheral blood monocytes, CD16 positive, rep4

status: Public on Aug 31 2009

city: Montreal

first: Petronela

last: ANCUTA

state: Quebec

address: 264, BVD Rene-Levesque East

department: Microbiology and Immunology

country: Canada

institute: Université de Montréal

description:
Gene expression data ex vivo.
042304_CD16_positive

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array (Platform ID: GPL570). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500A.

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 100.

source_name: peripheral blood monocytes, CD16+

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: ex vivo

extract_protocol: Total RNA from Mo pellets was isolated by Trizol extraction and purified using RNeasy columns (Qiagen). The quality of RNA was assessed by visualization of intact bands corresponding to 18S and 28S rRNA on formaldehyde agarose gels.

treatment_protocol: ex vivo

tag: donor health

value: healthy

value: peripheral blood

value: monocyte

value: positive


title: Peripheral blood monocytes, CD16 positive, rep2

description:
Gene expression data ex vivo.
052104_CD16_positive

tag: tissue


title: Normal_3

description: Normal mucosa

source_name: Normal tissue 3


title: Arabidopsis Col 10 days shoots 2


title: Peripheral blood monocytes, CD16 negative, rep1

description:
Gene expression data ex vivo.
042904_CD16_negative

source_name: peripheral blood monocytes, CD16-

tag: cell type

value: negative


title: Normal_2

description: Normal mucosa

source_name: Normal tissue 2


title: Peripheral blood monocytes, CD16 negative, rep4

description:
Gene expression data ex vivo.
042304_CD16_negative


title: ESCC_2

source_name: ESCC tumor tissue 2


title: Arabidopsis flp-1/myb88 10 days shoots


title: Peripheral blood monocytes, CD16 positive, rep3

description:
Gene expression data ex vivo.
021904_CD16_positive


title: Peripheral blood monocytes, CD16 positive, rep1

description:
Gene expression data ex vivo.
042904_CD16_positive


title: Peripheral blood monocytes, CD16 negative, rep2

description:
Gene expression data ex vivo.
052104_CD16_negative


title: Peripheral blood monocytes, CD16 negative, rep3

description:
Gene expression data ex vivo.
021904_CD16_negative


title: IP Tim-Dcr ZT15

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: IP sample from Tim-Dcr flies, ZT15

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hrs at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G7

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings

source_name: fly head

label_protocol: RNA was utilized to prepare cDNA and cRNA using the Affymetrix IVT labeling Kit

growth_protocol: Flies were grown under standard conditions in 12hs light and 12hs dark cycles

extract_protocol: Heads were collected and RNA extracted using TRIZOL

tag: time point

value: Tim-Dcr ZT15

value: head

tag: developmental stage

value: adult


title: L+S I BEAS2b_ML04C

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

description: Gene expression data from cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133plus2.0 chips . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Probe based analysis, background reduction, and quantile data normalization was performed in MeV 4.0 of TM4 using Robust Multi-array Average (RMA).

source_name: BEAS-2B - mechanical stretch plus LPS

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

growth_protocol: Cells were grown in DMEM with 5% FBS. Cells were seeded at 2 x 10E+5 in 6 well Flexercell plates - silicon elastic plates coated with Type I collagen (Flexercell International, McKeesport, PA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by purification of mRNA using Qiagen purification kit.

treatment_protocol: Human Bronchial Epithelial Cells (Beas-B2)  were exposed to six regiments for 4 h: 1) control (static, [control]); 2) mechanical stretch (25 PKa, 30 cycles per min, [stretch]); 3) LPS (1 mcg/ml [LPS]); 4) TNF-α (20 ng/ml; [TNF]); 5) mechanical stretch plus LPS [LPS+S], and 6) mechanical stretch plus TNF-α [TNF+S].

tag: cell line

value: Human Bronchial Epithelial Cells Beas-B2

value: Transformed Pulmonary distal (small) airway cell


title: IP ZT15, replica 2

description: IP sample, ZT15

tag: replicate


title: T+S II BEAS 2b_ML06

description: Gene expression data from cells

source_name: BEAS-2B - mechanical stretch plus TNF-α


title: IP Tim-Dcr ZT3

description: IP sample from Tim-Dcr flies, ZT3

value: Tim-Dcr ZT3


title: L+S II BEAS 2b_ML05

description: Gene expression data from cells


title: INP Tim-Dcr ZT3

description: INP sample from Tim-Dcr flies, ZT3


title: IP ZT19, replica 1

description: IP sample, ZT19


title: IP ZT23, replica 1

description: IP sample, ZT23