title: Kidney_5wk_female_rep2

description: whole ground tissue homogenized


title: Kidney_6wk_female_rep4

status: Public on Jul 31 2013

type: RNA

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

country: USA

institute: US FDA National Center for Toxicological Research

description: whole ground tissue homogenized

hyb_protocol: Hybridizations were conducted accourding to manufacturer's protocol (65 degrees for 17 hours).

scan_protocol: Arrays were scanned using the Agilent High Resolution C Scanner according to manufacturer's protocols.

data_processing: Array data was normalized using 75th percentile normalization (TargetValue=1000) within USFDA's ArrayTrack.

molecule: total RNA

organism: Rattus norvegicus

source_name: whole kidney,female,totalRNA,6weeks

label_protocol: Single color (Cy3) Agilent Whole Rat Genome 4x44k microarrays and reagents were used according to manufacturer’s protocols using 500 nanograms of total RNA. An Agilent one-color spike-in kit was used as a positive control.

growth_protocol: Female Fischer 344 rats were obtained and housed under AAALAC-approved conditions with a 12-hr light/dark cycle (0600-1800).  Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%

extract_protocol: Total RNA was isolated from ~30 mg of whole, homogenized, kidney tissue of independent animals using Qiagen RNeasy Mini Kit according to manufacturer’s protocol.  The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.5 for all samples.

treatment_protocol: No treatments

tag: strain

value: Fischer 344

tag: Sex

value: female

tag: age


title: Kidney_21wk_female_rep6

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,21weeks


title: Kidney_2wk_female_rep5

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,2weeks


title: Kidney_2wk_female_rep2

description: whole ground tissue homogenized


title: Kidney_21wk_female_rep5

description: whole ground tissue homogenized


title: Kidney_2wk_female_rep4

description: whole ground tissue homogenized


title: Kidney_21wk_female_rep1

description: whole ground tissue homogenized


title: Untreated WT-R plants, biological rep1

status: Public on Aug 09 2013

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description:
Arabidopsis WT-1R
Gene expression data from untreated Arabidopsis WT plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization. The intensities of (PM-MM) were used in all subsequent data analyses.

label: biotin

organism: Arabidopsis thaliana

source_name: Untreated Arabidopsis WT plants

label_protocol: Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.85%) medium supplemented with 1% sucrose for 15 days under 16-h-light/8-h-dark (40-80 mmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: ISOGEN (Nippon Gene Co., Toyama, Japan) extraction of total RNA from untreated seedling samples was performed according to the manufacturer's instructions.

treatment_protocol: None.

tag: ecotype

value: Columbia

tag: genotype

value: WT

tag: tissue

value: seedling

value: 15 days

tag: treatment


title: Kidney_21wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_15wk_female_rep6

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,15weeks


title: Kidney_78wk_female_rep5

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,78weeks


title: Kidney_5wk_female_rep3

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,5weeks


title: Kidney_15wk_female_rep2

description: whole ground tissue homogenized


title: Kidney_104wk_female_rep5

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,104weeks


title: Kidney_15wk_female_rep4

description: whole ground tissue homogenized


title: Kidney_15wk_female_rep5

description: whole ground tissue homogenized


title: Kidney_104wk_female_rep6

description: whole ground tissue homogenized


title: Kidney_15wk_female_rep1

description: whole ground tissue homogenized


title: Kidney_104wk_female_rep1

description: whole ground tissue homogenized


title: Kidney_104wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_104wk_female_rep2

description: whole ground tissue homogenized


title: Kidney_78wk_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,78weeks

growth_protocol: Male Fischer 344 rats were obtained and housed under AAALAC-approved conditions with a 12-hr light/dark cycle (0600-1800).  Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%

value: male


title: Kidney_78wk_male_rep3

description: whole ground tissue homogenized


title: Kidney_8wk_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,8weeks


title: Kidney_21wk_female_rep4

description: whole ground tissue homogenized


title: Kidney_8wk_male_rep6

description: whole ground tissue homogenized


title: Kidney_8wk_male_rep5

description: whole ground tissue homogenized


title: Kidney_78wk_male_rep8

description: whole ground tissue homogenized


title: Kidney_78wk_male_rep4

description: whole ground tissue homogenized


title: Kidney_6wk_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,6weeks


title: Kidney_78wk_male_rep6

description: whole ground tissue homogenized


title: Kidney_8wk_male_rep2

description: whole ground tissue homogenized


title: Kidney_6wk_male_rep4

description: whole ground tissue homogenized


title: Kidney_2wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_6wk_male_rep5

description: whole ground tissue homogenized


title: Kidney_6wk_male_rep6

description: whole ground tissue homogenized


title: Kidney_5wk_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,5weeks


title: Kidney_21wk_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,21weeks


title: Kidney_5wk_male_rep2

description: whole ground tissue homogenized


title: Kidney_2wk_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,2weeks


title: Kidney_5wk_male_rep5

description: whole ground tissue homogenized


title: Kidney_21wk_male_rep6

description: whole ground tissue homogenized


title: Kidney_5wk_male_rep4

description: whole ground tissue homogenized


title: Kidney_2wk_male_rep5

description: whole ground tissue homogenized


title: Kidney_2wk_male_rep1

description: whole ground tissue homogenized


title: Kidney_21wk_male_rep3

description: whole ground tissue homogenized


title: Untreated Arabidopsis Col plants array F biological rep1

status: Public on May 16 2011

description:
15-day-old plants grown on the agar plates
Gene expression data from untreated Arabidopsis plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 45 hr  at 18°C  using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses.

source_name: Untreated Arabidopsis Col plants

label_protocol:
Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).

tag: genetic background

value: whole seedling

value: wild type


title: Untreated Arabidopsis Col plants array F biological rep2


title: Kidney_21wk_male_rep4

description: whole ground tissue homogenized


title: Kidney_2wk_male_rep6

description: whole ground tissue homogenized


title: Untreated Arabidopsis met1-3 plants array F biological rep3

description:
15-day-old plants grown on the agar plates
Gene expression data from  untreated met1-3 plants

source_name: Untreated Arabidopsis met1-3 plants


title: Kidney_21wk_male_rep2

description: whole ground tissue homogenized


title: Untreated Arabidopsis Col plants array F biological rep3


title: Kidney_104wk_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,104weeks


title: Kidney_104wk_male_rep2

description: whole ground tissue homogenized


title: Kidney_15wk_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,male,totalRNA,15weeks


title: Kidney_104wk_male_rep1

description: whole ground tissue homogenized


title: Kidney_15wk_male_rep4

description: whole ground tissue homogenized


title: Kidney_15wk_male_rep6

description: whole ground tissue homogenized


title: Kidney_15wk_male_rep5

description: whole ground tissue homogenized


title: Untreated Arabidopsis DR5 plants array F biological rep3

description:
15-day-old plants grown on the agar plates
Gene expression data from untreated DR5 plants

source_name: Untreated Arabidopsis DR5 plants

value: parental DR5


title: Untreated Arabidopsis Col plants array R biological rep3


title: Duke_DnaseSeq_HSMM

status: Public on Oct 14 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: genomic

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

Raw data witheld due to privacy concerns.

molecule: genomic DNA

organism: Homo sapiens

source_name: HSMM

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

value: primary cell

value: skeletal muscle myoblast

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell description

value: skeletal muscle myoblasts

tag: controlid

tag: labversion

value: private-noSequence p-value cutoff:0.05,private-noSequence baseAlignCounts.pl v 1,private-noSequence fseq v 1.84, iff_generic_male

tag: cell organism

value: human

value: Normal Human Skeletal Muscle Myoblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: treatment description

value: No special treatment or protocol applies

value: align_on_cluster_bwa.pl v 1

tag: replicate

tag: replicate description

value: tier 1


title: Kidney_104wk_male_rep3

description: whole ground tissue homogenized

tag: strain

value: Fischer 344

tag: Sex

value: male

tag: age


title: Untreated Arabidopsis Col plants array R biological rep1

tag: tissue

value: whole seedling

tag: genotype

value: wild type


title: Untreated Arabidopsis Col plants array R biological rep2

tag: genetic background


title: Kidney_15wk_male_rep2

description: whole ground tissue homogenized


title: Untreated Arabidopsis met1-3 plants array R biological rep3


title: Untreated Arabidopsis axe1-5 plants array R biological rep3

description:
15-day-old plants grown on the agar plates
Gene expression data from  untreated axe1-5 plants

source_name: Untreated Arabidopsis axe1-5 plants


title: Untreated Arabidopsis met1-3 plants array R biological rep1


title: Untreated Arabidopsis axe1-5 plants array F biological rep3


title: Untreated Arabidopsis met1-3 plants array F biological rep1


title: Untreated Arabidopsis axe1-5 plants array F biological rep2


title: Untreated Arabidopsis axe1-5 plants array R biological rep1

description:
15-day-old plants grown on the agar plates
Gene expression data from untreated axe1-5 plants


title: Untreated Arabidopsis axe1-5 plants array R biological rep2


title: Untreated Arabidopsis met1-3 plants array F biological rep2


title: Untreated Arabidopsis DR5 plants array R biological rep3

value: parental DR5


title: Untreated Arabidopsis DR5 plants array R biological rep1


title: Untreated Arabidopsis axe1-5 plants array F biological rep1


title: Untreated Arabidopsis DR5 plants array F biological rep2


title: Untreated Arabidopsis DR5 plants array F biological rep1


title: Untreated Arabidopsis met1-3 plants array R biological rep2


title: Middle silique, biological rep3_F

status: Public on Dec 22 2010

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-3F

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400(O.K. Check).

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization (using home-made software).
The intensities of (PM-MM) were used in all subsequent data analyses.

source_name: Arabidopsis WT middle silique

growth_protocol: The wild-type (WT) plants used in this study were Columbia accession of Arabidopsis (Arabidopsis thaliana). To obtain approximately 3-week-old leaf and root, plants were grown on a 0.5% gelangum (Wako) containing 0.5% sucrose and 1/2 MS at 22℃ under the continuous light condition. In case of sampling for other tissues (stem, flower, early silique, middle silique, and late silique), plants were grown on soil in pots at 22℃ under 16-h light/8-h dark cycle.

extract_protocol: Total RNA was isolated using ISOGEN (Nippon gene) or RNAqueous Kit (Qiagen) according to manufacturer’s protocol.

value: Middle silique


title: Late silique, biological rep2_F

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-2F

source_name: Arabidopsis WT late silique

value: Late silique


title: Late silique, biological rep3_F

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-3F


title: Middle silique, biological rep2_F

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-2F


title: Late silique, biological rep1_F

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-1F


title: Untreated Arabidopsis DR5 plants array R biological rep2


title: Early silique, biological rep3_F

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-3F

source_name: Arabidopsis WT early silique

value: Early silique


title: Middle silique, biological rep1_F

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-1F


title: Early silique, biological rep2_F

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-2F


title: Flower, biological rep3_F

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-3F

source_name: Arabidopsis WT flower

value: Flower


title: Flower, biological rep2_F

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-2F


title: Stem, biological rep2_F

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-2F

source_name: Arabidopsis WT stem

value: Stem


title: Stem, biological rep3_F

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-3F


title: Flower, biological rep1_F

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-1F


title: DR5, Untreated plants, biological rep1

status: Public on Jan 27 2011

description: Gene expression data from untreated DR5 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring ver.7 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing MS agar (0.85%) medium supplemented with 1% sucrose for 14 days under 16-h-light/8-h-dark (40-80 μmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: The total RNA was extracted from the plants before or after cold treatment (at 2°C for 3days) using Plant RNA Purification Reagent (Invitrogen) according to manufacture’s instruction.

treatment_protocol: The plants were treated with or without 3 days of cold treatment ( at 2°C, 12 h light / 12 h dark).

tag: ecotype

value: Columbia

tag: genotype/variation

value: parental line DR5

value: Whole plants

value: 14 day old seedlings


title: Stem, biological rep1_F

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-1F


title: axe1-5, Cold-treated plants, biological rep2

description: Gene expression data from cold-treated axe1-5 plants

source_name: Cold-treated Arabidopsis axe1-5 plants

value: hda6 mutant axe1-5


title: DR5, Cold-treated plants, biological rep3

description: Gene expression data from cold-treated DR5 plants

source_name: Cold-treated Arabidopsis DR5 plants


title: axe1-5, Cold-treated plants, biological rep3


title: axe1-5, Untreated plants, biological rep2

description: Gene expression data from untreated axe1-5 plants


title: DR5, Untreated plants, biological rep2


title: axe1-5, Untreated plants, biological rep1


title: Leaf, biological rep3_F

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-3F

source_name: Arabidopsis WT leaf

value: Leaf


title: Root, biological rep1_F

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-1F

source_name: Arabidopsis WT root

value: Root


title: Root, biological rep3_F

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-3F


title: DR5, Cold-treated plants, biological rep2


title: DR5, Cold-treated plants, biological rep1


title: Leaf, biological rep2_F

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-2F


title: Early silique, biological rep1_F

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-1F


title: axe1-5, Cold-treated plants, biological rep1


title: axe1-5, Untreated plants, biological rep3


title: DR5, Untreated plants, biological rep3


title: Middle silique, biological rep3_R

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-3R


title: Late silique, biological rep1_R

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-1R


title: Late silique, biological rep2_R

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-2R


title: Middle silique, biological rep1_R

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-1R


title: Root, biological rep2_F

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-2F


title: Middle silique, biological rep2_R

description:
Gene expression data from Arabidopsis WT middle silique
Arabidopsis WT middle silique-2R


title: Early silique, biological rep3_R

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-3R


title: Early silique, biological rep2_R

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-2R


title: Late silique, biological rep3_R

description:
Gene expression data from Arabidopsis WT late silique
Arabidopsis WT late silique-3R


title: Leaf, biological rep1_F

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-1F


title: Rlower, biological rep3_R

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-3R


title: Stem, biological rep2_R

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-2R


title: Rlower, biological rep1_R

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-1R


title: Root, biological rep2_R

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-2R


title: Rlower, biological rep2_R

description:
Gene expression data from Arabidopsis WT flower
Arabidopsis WT flower-2R


title: LeaR, biological rep2_R

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-2R


title: Root, biological rep1_R

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-1R


title: LeaR, biological rep1_R

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-1R


title: LeaR, biological rep3_R

description:
Gene expression data from Arabidopsis WT leaf
Arabidopsis WT leaf-3R


title: UW_AffyExonArray_H7-hESC_diffProtA_2d_1

status: Public on Nov 08 2012

value: in vitro differentiated cells

value: cardiac mesoderm

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: AffyExonArray

tag: datatype description

value: Affymetrix Exon Microarray

tag: cell

value: human

tag: cell description

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

tag: treatment

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm

tag: labexpid


title: Early silique, biological rep1_R

description:
Gene expression data from Arabidopsis WT early silique
Arabidopsis WT early silique-1R

value: wild type

value: Early silique


title: mom1-2, biological rep1

status: Public on Sep 27 2010

description: Gene expression data from the mom-1-2 plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 18 hr  at 45°C  using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: The mom1-2 mutant plants

label_protocol:
Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vitro transcription using the GeneChIP IVT Labeling Kit (Affymetrix).

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia-0 and the mom1-2 mutant) were grown on soil for 3 weeks under 16-h-light/8-h-dark.

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

tag: Three-week-old plants grown on soil


title: mom1-2, biological rep2


title: Col-0, biological rep1

description: Gene expression data from the wild type Col-0 plants

source_name: The wild type Col-0 plants


title: Stem, biological rep3_R

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-3R

value: Stem


title: mom1-2, biological rep3


title: Root, biological rep3_R

description:
Gene expression data from Arabidopsis WT root
Arabidopsis WT root-3R


title: Col-0, biological rep3


title: Stem, biological rep1_R

description:
Gene expression data from Arabidopsis WT stem
Arabidopsis WT stem-1R


title: Col-0, biological rep2


title: UW_AffyExonArray_H7-hESC_diffProtA_9d_2

tag: cell organism

tag: cell lineage

tag: cell sex

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm

tag: replicate


title: SK-N-MC-DS14413

status: Public on Nov 01 2011

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing:
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

source_name: Neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

value: immortalized cell line

tag: line

value: SK-N-MC

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: cell karyotype

value: cancer

value: ectoderm

value: F


title: Liver_104wk_Male_rep2

status: Public on Jun 24 2010

description: rat lifecycle liver gene expression

hyb_protocol: Accourding to manufacturer's (Agilent) protocol

scan_protocol: Arrays were scanned for fluorescent signal intensities using a GenePix 4000B microarray scanner (Molecular Devices, Union City, CA) at 10micron.

data_processing: Microarray intensity data were uploaded to the ArrayTrack database and normalized using 75th-percentile scaling without background subtraction.

label_protocol: Agilent Whole Rat Genome 4x44k microarrays and reagents according to manufacturer’s protocols (Agilent Technologies, Santa Clara, CA) for cRNA labeling and hybridization using 500 nanograms of total RNA. An Agilent one-color spike-in kit was used as positive control and monitor of labeling efficiency across all experiments.

growth_protocol: Rrats obtained from NCTR animal breeding colony, fed the NIH-31 diet (ad libitum) and 12-hr light/dark cycle (0600-1800).  Rats housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of 50%.

extract_protocol: Total RNA was isolated from approximately 30 mg liver sections using Qiagen RNeasy Mini Kit according to manufacturer’s protocol.  Purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used.

treatment_protocol: No treatment

tag: strain

tag: sex

value: male

tag: tissue

value: liver

tag: age


title: Liver_104wk_Fem_rep1

description: rat lifecycle liver gene expression

value: female


title: Liver_78wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_104wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_104wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_78wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_104wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_104wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_52wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_104wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_78wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_104wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_78wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_78wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_104wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_104wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_78wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_52wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_78wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_78wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_52wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_52wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_52wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_52wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_78wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_52wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_78wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_52wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_21wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_15wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_15wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_21wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_21wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_8wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_21wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_15wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_8wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_15wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_21wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_8wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_52wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_15wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_52wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_8wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_8wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_15wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_21wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_21wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_21wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_15wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_15wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_15wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_8wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_21wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_15wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_21wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_8wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_6wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_8wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_6wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_6wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_5wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_5wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_8wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_6wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_2wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_2wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_2wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_6wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_5wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_5wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_5wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_8wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_6wk_Male_rep1

description: rat lifecycle liver gene expression


title: Liver_5wk_Male_rep5

description: rat lifecycle liver gene expression


title: Liver_5wk_Male_rep3

description: rat lifecycle liver gene expression


title: Liver_6wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_5wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_6wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_5wk_Fem_rep3

description: rat lifecycle liver gene expression


title: Liver_6wk_Fem_rep2

description: rat lifecycle liver gene expression


title: Liver_2wk_Male_rep4

description: rat lifecycle liver gene expression


title: Liver_6wk_Fem_rep4

description: rat lifecycle liver gene expression


title: Liver_2wk_Fem_rep5

description: rat lifecycle liver gene expression


title: Liver_2wk_Male_rep2

description: rat lifecycle liver gene expression


title: Liver_5wk_Fem_rep2

description: rat lifecycle liver gene expression


title: WT endosperm at 24 h after seed imbibition-3F biological rep3

status: Public on Apr 16 2010

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis WT endosperm at 24 h after seed imbibition

growth_protocol: Plants were grown for 2 weeks on 1% agar plates containing 1/2MS and 0.5% sucrose, transferred to soil in 200 ml pots, and grown in a growth chamber at 22°C and 50-60% humidity under 16-h light/8-h dark cycle. Freshly harvested seeds were imbibed in 8.5 cm petri dishes containing two filter papers (approximately 7 cm diameter) and 2 mL of water under continuous light and harvested after 24 h. Dissection of embryo and testa/endosperm from 24-h-imbibed seeds was carried out under a stereoscopic microscope.

extract_protocol: Total RNA from dry seed and imbibied seeds was isolated using an RNA aqueous column with plant RNA isolation aid (Ambion) according to manufacturer’s protocol.

value: endosperm

tag: genotype


title: WT endosperm at 24 h after seed imbibition-1F biological rep1

source_name: Arabidopsis WT endosperm at 24 h after seed imbibition


title: WT endosperm at 24 h after seed imbibition-2F biological rep2


title: WT embryo at 24 h after seed imbibition-1F biological rep1

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis WT embryo at 24 h after seed imbibition

value: embryo


title: HEK293-DS13691

status: Public on Aug 16 2010

data_processing:
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf

source_name: embryonic kidney

tag: cell type

value: embryonic kidney

tag: term


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-3F biological rep3

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis cyp707a1-1a2-1a3-1 mutant 24-h-imbibed seeds

value: seed


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-1F biological rep1

source_name: Arabidopsis cyp707a1-1a2-1a3-1 mutant 24-h-imbibed seeds


title: WT 24-h-imbibed seeds-3F biological rep3

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis WT 24-h-imbibed seeds

source_name: Arabidopsis WT 24-h-imbibed seeds

value: wild type


title: aba2-1 mutant 24-h-imbibed seeds-2F biological rep2

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis aba2-1 mutant 24-h-imbibed seeds


title: WT 24-h-imbibed seeds-1F biological rep1


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-2F biological rep2

description:
Freshly harvested dry seeds
Gene expression data from Arabidopsis cyp707a1-1a2-1a3-1 dry seeds


title: aba2-1 mutant 24-h-imbibed seeds-1F biological rep1

source_name: Arabidopsis aba2-1 mutant 24-h-imbibed seeds


title: aba2-1 mutant dry seeds-2F biological rep2

description:
Freshly harvested dry seeds
Gene expression data from Arabidopsis aba2-1 dry seeds

source_name: Arabidopsis aba2-1 dry seeds


title: aba2-1 mutant dry seeds-1F biological rep1


title: aba2-1 mutant dry seeds-3F biological rep3


title: WT embryo at 24 h after seed imbibition-2F biological rep2

source_name: Arabidopsis WT embryo at 24 h after seed imbibition


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-1F biological rep1

source_name: Arabidopsis cyp707a1-1a2-1a3-1 dry seeds


title: WT dry seeds-2F biological rep2

description:
Freshly harvested dry seeds
Gene expression data from Arabidopsis WT dry seeds

source_name: Arabidopsis WT dry seeds


title: aba2-1 mutant 24-h-imbibed seeds-3F biological rep3


title: Liver_2wk_Fem_rep1

description: rat lifecycle liver gene expression


title: Liver_2wk_Fem_rep3

description: rat lifecycle liver gene expression


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-3F biological rep3


title: WT 24-h-imbibed seeds-2F biological rep2


title: WT dry seeds-3F biological rep3


title: Liver_2wk_Fem_rep2

description: rat lifecycle liver gene expression


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-2F biological rep2


title: WT dry seeds-1F biological rep1


title: WT endosperm at 24 h after seed imbibition-2R biological rep2


title: WT embryo at 24 h after seed imbibition-3R biological rep3


title: WT endosperm at 24 h after seed imbibition-1R biological rep1


title: WT embryo at 24 h after seed imbibition-2R biological rep2


title: WT embryo at 24 h after seed imbibition-1R biological rep1


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-3R biological rep3


title: aba2-1 mutant 24-h-imbibed seeds-2R biological rep2


title: aba2-1 mutant 24-h-imbibed seeds-3R biological rep3


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-1R biological rep1


title: aba2-1 mutant 24-h-imbibed seeds-1R biological rep1


title: cyp707a1-1a2-1a3-1 triple mutant 24-h-imbibed seeds-2R biological rep2


title: Liver_2wk_Fem_rep4

description: rat lifecycle liver gene expression


title: WT 24-h-imbibed seeds-3R biological rep3


title: WT 24-h-imbibed seeds-2R biological rep2


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-3R biological rep3


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-1R biological rep1


title: WT endosperm at 24 h after seed imbibition-3R biological rep3


title: WT 24-h-imbibed seeds-1R biological rep1


title: aba2-1 mutant dry seeds-2R biological rep2


title: cyp707a1-1a2-1a3-1 triple mutant dry seeds-2R biological rep2


title: aba2-1 mutant dry seeds-1R biological rep1


title: WT dry seeds-3R biological rep3


title: WT dry seeds-2R biological rep2


title: hyl1-2-1F biological rep1

status: Public on Dec 02 2009

description: Gene expression data from  untreated hyl1-2 plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for ? hr  at ?°C  using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400(O.K. Check).

source_name: Untreated Arabidopsis hyl1-2 plants


title: hyl1-2-2F biological rep2


title: WT dry seeds-1R biological rep1


title: hyl1-2-3F biological rep3


title: ago1-25-1F biological rep1

description: Gene expression data from untreated ago1-25 plants

source_name: Untreated Arabidopsis ago1-25 plants


title: ago1-25-2F biological rep2

description: Gene expression data from  untreated ago1-25 plants


title: ago1-25-3F biological rep3


title: WT-2F biological rep2

description: Gene expression data from untreated Arabidopsis plants

source_name: Untreated Arabidopsis WT plants


title: WT-3F biological rep3


title: WT-1F biological rep1


title: aba2-1 mutant dry seeds-3R biological rep3


title: hyl1-2-1R biological rep1


title: hyl1-2-2R biological rep2


title: ago1-25-3R biological rep3


title: ago1-25-2R biological rep2


title: ago1-25-1R biological rep1


title: WT-3R biological rep3


title: WT-2R biological rep2


title: upf1-1-2F_Untreated plants, biological rep2

status: Public on Jan 14 2009

description: Gene expression data from untreated upf1-1 plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 18hr at 45C using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses. Files contain data of X, Y, and intensity in order. The order is same between raw data and normalized data. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.

source_name: Untreated Arabidopsis upf1-1 plants

tag: 15-day-old plants grown on the agar plates


title: upf3-1-2F_Untreated plants, biological rep2

description: Gene expression data from untreated upf3-1 plants

source_name: Untreated Arabidopsis upf3-1 plants


title: upf1-1-3F_Untreated plants, biological rep3


title: upf1-1-1F_Untreated plants, biological rep1


title: upf3-1-3F_Untreated plants, biological rep3


title: WT-1F_Untreated plants, biological rep1


title: upf3-1-1F_Untreated plants, biological rep1


title: upf3-1-3R_Untreated plants, biological rep3


title: WT-3F_Untreated plants, biological rep3


title: upf3-1-1R_Untreated plants, biological rep1


title: upf1-1-3R_Untreated plants, biological rep3


title: WT-2F_Untreated plants, biological rep2


title: upf1-1-2R_Untreated plants, biological rep2


title: hyl1-2-3R biological rep3


title: upf3-1-2R_Untreated plants, biological rep2


title: upf1-1-1R_Untreated plants, biological rep1


title: WT-2R_Untreated plants, biological rep2


title: WT-1R_Untreated plants, biological rep1


title: WT-3R_Untreated plants, biological rep3


title: WT-1R biological rep1


title: 2-h high-salinity-treated plants, biological rep3-F

status: Public on Nov 19 2008

description: Gene expression data from 2-h high-salinity-treated Arabidopsis plants

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.85%) medium supplemented with 1% sucrose for 2 weeks under 16-h-light/8-h-dark (40-80 μmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: ISOGEN (Nippon Gene Co., Toyama, Japan) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol:
For drought treatments, the plants were removed from the agar and dehydrated in plastic dishes for 2 and 10 h at 22°C under dim light (0.9-1.2 μmol photons m-2 sec-1) essentially as reported previously (Seki et al., 2002, Plant J. 31:279-292).
For cold treatments, the covered plastic dishes with the plants were transferred directly from 22°C to 4°C  and kept for 2 and 10 h under dim light (0.4-0.8 μmol photons m-2 sec-1) as reported previously (Oono et al., 2006, Functional & Integrative Genomics, 6: 212-234).
For high-salinity stress treatments, the plants were transferred to plastic dishes containing 250 mM NaCl solution  and kept for 2 and 10 h under dim light  (0.9-1.2 μmol photons m-2 sec-1) essentially as reported previously (Seki et al., 2002, Plant J. 31:279-292).
For ABA treatments, the plants were transferred to plastic dishes containing 100μM ABA solution and kept for 2 and 10 h under dim light  (0.9-1.2 μmol photons m-2 sec-1) essentially as reported previously (Seki et al., 2002, Plant J. 31:279-292).

tag: Two-week-old plants grown on the agar plates


title: 10-h high-salinity-treated plants, biological rep1-F

description: Gene expression data from 10-h high-salinity-treated Arabidopsis plants


title: 2-h high-salinity-treated plants, biological rep2-F

source_name: 2-h high-salinity-treated Arabidopsis plants


title: 10-h drought-treated plants, biological rep3-F

description: Gene expression data from 10-h drought-treated Arabidopsis plants

source_name: 10-h drought-treated Arabidopsis plants


title: 10-h high-salinity-treated plants, biological rep2-F

source_name: 10-h high-salinity-treated Arabidopsis plants


title: 10-h high-salinity-treated plants, biological rep3-F


title: 10-h drought-treated plants, biological rep1-F


title: 2-h high-salinity-treated plants, biological rep1-F


title: 10-h drought-treated plants, biological rep2-F


title: 2-h drought-treated plants, biological rep1-F

description: Gene expression data from 2-h drought-treated Arabidopsis plants

source_name: 2-h drought-treated Arabidopsis plants


title: 10-h cold-treated plants, biological rep3-F

description: Gene expression data from 10-h cold-treated Arabidopsis plants

source_name: 10-h cold-treated Arabidopsis plants


title: 10-h cold-treated plants, biological rep2-F


title: 2-h drought-treated plants, biological rep3-F


title: 2-h drought-treated plants, biological rep2-F


title: 2-h cold-treated plants, biological rep3-F

description: Gene expression data from 2-h cold-treated Arabidopsis plants

source_name: 2-h cold-treated Arabidopsis plants


title: 10-h cold-treated plants, biological rep1-F


title: 2-h cold-treated plants, biological rep1-F


title: 10-h ABA-treated plants, biological rep1-F

description: Gene expression data from 10-h ABA-treated Arabidopsis plants

source_name: 10-h ABA-treated Arabidopsis plants


title: 10-h ABA-treated plants, biological rep3-F


title: 2-h cold-treated plants, biological rep2-F


title: 2-h ABA-treated plants, biological rep2-F

description: Gene expression data from 2-h ABA-treated Arabidopsis plants

source_name: 2-h ABA-treated Arabidopsis plants


title: 10-h ABA-treated plants, biological rep2-F


title: Untreated plants, biological rep2-F

source_name: Untreated Arabidopsis plants


title: 10-h high-salinity-treated plants, biological rep1-R


title: 2-h high-salinity-treated plants, biological rep3-R


title: 2-h high-salinity-treated plants, biological rep2-R


title: 10-h high-salinity-treated plants, biological rep3-R


title: 10-h high-salinity-treated plants, biological rep2-R


title: 2-h ABA-treated plants, biological rep1-F


title: Untreated plants, biological rep3-F


title: 10-h drought-treated plants, biological rep2-R


title: 10-h drought-treated plants, biological rep1-R


title: 2-h drought-treated plants, biological rep3-R


title: 10-h drought-treated plants, biological rep3-R


title: 2-h ABA-treated plants, biological rep3-F


title: Untreated plants, biological rep1-F


title: Untreated plants, biological rep4-F


title: 2-h drought-treated plants, biological rep2-R


title: 2-h high-salinity-treated plants, biological rep1-R


title: 10-h cold-treated plants, biological rep3-R


title: 10-h cold-treated plants, biological rep1-R


title: 2-h cold-treated plants, biological rep3-R


title: 10-h ABA-treated plants, biological rep3-R


title: 2-h cold-treated plants, biological rep1-R


title: 2-h ABA-treated plants, biological rep3-R


title: 10-h cold-treated plants, biological rep2-R


title: 10-h ABA-treated plants, biological rep1-R


title: 10-h ABA-treated plants, biological rep2-R


title: 2-h ABA-treated plants, biological rep1-R


title: 2-h ABA-treated plants, biological rep2-R


title: Untreated plants, biological rep2-R


title: Untreated plants, biological rep1-R


title: Untreated plants, biological rep4-R


title: Untreated plants, biological rep3-R


title: Arabidopsis ddc-2F_Untreated plants, biological rep2

status: Public on Oct 23 2008

description: Gene expression data from untreated ddc plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 18 hr at 45°C using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 6.4 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 3.2 millions PM and 3.2 millions MM probes, of individual replicates for all treated and untreated samples were normalized at the same time via quantile normalization (Bolstad et al. 2003). After this normalization, intensities of all replicates representing different samples reach a common median. Files contain data of X, Y, and intensity in order. The order is same between raw data and normalized data. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
The intensities of (PM-MM) were used in all subsequent data analyses.

source_name: Untreated Arabidopsis ddc plants

label_protocol:
Eight mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).


title: Arabidopsis ddc-1F_Untreated plants, biological rep1


title: Arabidopsis ddc-3F_Untreated plants, biological rep3


title: Arabidopsis rdr2-1-2F_Untreated plants, biological rep2

description: Gene expression data from untreated rdr2-1 plants

source_name: Untreated Arabidopsis rdr2-1 plants


title: Arabidopsis rdr2-1-3F_Untreated plants, biological rep3


title: Arabidopsis rdr2-1-1F_Untreated plants, biological rep1


title: Arabidopsis WT-3F_Untreated plants, biological rep3


title: Arabidopsis WT-2F_Untreated plants, biological rep2


title: 2-h drought-treated plants, biological rep1-R


title: Arabidopsis ddc-3R_Untreated plants, biological rep3


title: Arabidopsis ddc-2R_Untreated plants, biological rep2


title: Arabidopsis WT-1F_Untreated plants, biological rep1


title: Arabidopsis WT-3R_Untreated plants, biological rep3


title: Arabidopsis rdr2-1-3R_Untreated plants, biological rep3


title: Arabidopsis WT-2R_Untreated plants, biological rep2


title: 2-h cold-treated plants, biological rep2-R


title: Arabidopsis WT-1R_Untreated plants, biological rep1


title: WT embryo at 24 h after seed imbibition-3F biological rep3

description:
24-h-imbibed seeds
Gene expression data from Arabidopsis WT embryo at 24 h after seed imbibition


title: Arabidopsis rdr2-1-2R_Untreated plants, biological rep2


title: Arabidopsis rdr2-1-1R_Untreated plants, biological rep1


title: Arabidopsis ddc-1R_Untreated plants, biological rep1


title: sdg4 open flowers replicate 2

status: Public on Oct 27 2008

description: Biological replicate 1 of 2

hyb_protocol: The hybridization experiment was performed according to the manufacturer's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol Ver. 5.0.1).

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: LOWESS normalized data obtained from log10 of processed Red signal /processed Green signal. Agilent software was used.

source_name: Total RNA from wild type open flowers

label_protocol: The labeling experiment was performed according to the manufacturer's protocol (Agilent technologies, Low RNA Input Fluorescent Linear Amplification Kit Protocol, Ver. 5.0.1).

growth_protocol: Seeds were germinated in Murashige and Skoog (MS) medium (MS salts, 1% sucrose, 0.8% agar, 0.05% MES-KOH pH 5.7, and B5 vitamins: 1 mg nicotinic acid, 1 mg pyridoxine-HCl, 10 mg thiamine-HCl, and 100 mg myo-inositol) and the plants were grown at 22°C.

extract_protocol: Total RNA extracted using the Trizol reagent (Invitrogen) according to manufacturer's instructions

tag: Columbia ecotype

source_name: Total RNA from sdg4 open flowers

tag: SALK T-DNA line_128444


title: sdg4 open flowers replicate 1

description: Biological replicate 1 of 2


title: NHGRI_SRS-5

status: Public on Jan 24 2001

city: Bethesda

first: Michael

last: Bittner

state: MD

department: Cancer Genetics Branch

institute: NHGRI, NIH

description:
See http://www.nhgri.nih.gov/DIR/Microarray/Nature_paper.pdf
and http://www.nhgri.nih.gov/DIR/Microarray/Melanoma_Supplement/index.html

source_name: unknown