title: SMAD4 binding targets in murine R1 ES cells (1/2)

status: Public on Oct 21 2009

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565BA scanner and probe features were extracted using Feature Extraction Software (version 10.0)

data_processing: Log ratios were calculated by limma (Bioconductor package) and underwent Lowess normalization.

source_name: murine R1 ES cells, immuno-enriched DNA

label_protocol: DNA was labeled with CGH labeling kits (Invitrogen)

extract_protocol:
Murine R1 ES cells were cultured under typical feeder free ES cell conditions (DMEM supplemented with Knockout serum replacement (Invitrogen Gibco), leukemia inhibitory factor (LIF), non-essential amino acids, GlutaMax-I (Invitrogen Gibco), β-mercaptoethanol and penicillin/streptomycin.
R1 ES cells (5x107 – 1x108 cells) were chemically cross-linked by addition of one tenth volume of freshly-prepared 11% formaldehyde solution to cell media for 15 min at room temperature.  Cells were rinsed twice with 1xPBS, harvested using a silicon scraper, frozen in liquid nitrogen and stored at -80°C prior to use.  Cells were resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to obtain DNA fragments of about 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and pre-absorbed by 50 ul protein A beads (Zymed) and then incubated with 10 ug antibodies (anti-Smad4) overnight at 4°C. The immunocomplex was collected with 100 ul protein A beads by 3 hour co-incubation and then washed sequentially with TSE I (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors), TSE II (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, proteinase inhibitors), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 mM LiCl, 0.1% NP-40, 1% deoxycholate sodium) and TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0). The bound immunocomplex was eluted with 400 ul fresh elution buffer (25 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) by heating at 65°C with occasional vortex for 15 min and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract (WCE) DNA (Input fraction reserved from the sonication step) was also treated for crosslinking reversal. Immunoprecipitated DNA and WCE DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl alcohol extraction.

treatment_protocol: Undifferentiated ES cells under normal culture conditions

tag: sample type

value: Elute from a Smad4 chromatin immunoprecipitation

value: R1 ES cell

source_name: murine R1 ES cells, WCE DNA

value: Input for Smad4 chromatin immunoprecipitation


title: BiMP epi01 BS+

status: Public on Apr 23 2009

type: genomic

city: Genève

first: Jon

last: Reinders

state: Genève

address: 30 quai Ernest-Ansermet

department: Department of Plant Biology

country: Switzerland

institute: Universite de Geneve

hyb_protocol: Each hybridization was performed by transferring 200µl of sample to a prehybridized GeneChip® Arabidopsis Tiling 1.0R array (Affymetrix) for 16 hours at 45°C, as recommended by the manufacturer. A GeneChip Fluidics Station 450/250 was used with protocol FS4500_0001.

scan_protocol: A GeneChip Scanner 3000 was used.

data_processing: The analysis was performed with the inclusion of the BiMP data for the parental lines, which are available as GEO accession 9051. For this analysis, the 15 CEL files were quantile normalized together using the method previously published by Zheng et al (PLoS Genet 4(3): e1000032; see also http://naturalvariation.org/ccggMethylome for further analysis details). Resulting from this analysis, the normalized signal intensity values for 1,683,620 unique features are provided per sample within the attached processed data file (see attached matrix file). The sample headers per column describe the entry, where: Col-0 (col) is the wild-type parent; met1-3 (met) is the mutant parent; epi01 is the first profiled epiRIL entry; epi12 is the second profiled epiRIL entry; and epi28 is the third profiled epiRIL entry. The replicates are indicated by an underscore (“_”) followed by the replicate number (1 to 3). For this analysis, the “limma” package (http://www.bioconductor.org) within R (http://www.R-project.org) was used with the empirical Bayes method to calculate a F-test statistic per comparison. The tests were corrected for multiple comparisons using the Benjamini Hochberg method. The number of statistically significant comparisons at the 95% confidence level was determined for each entry.

label: biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: epiRIL01; DNA isolated from leaf tissue sampled from approx 10 plants

label_protocol: A DNA-labeling reaction contained 12µl of 5X terminal deoxynucleotidyl transferase (TdT) buffer, 2µl of terminal deoxynucleotidyl transferase, 1µl DNA-labeling reagent (5mM) and the DNA sample (total volume 60µl). Labeling was performed at 37°C for 60 minutes, terminated by heating to 70°C for 10 minutes, and cooled to 4°C for at least 2 minutes. To the 60µl of fragmented and labeled DNA, 4µl of 3nM B2 control oligonucleotides (Affymetrix), 12.5µl of 20X RNA hybridization spike controls, 120µl of 2X hybridization buffer, 16.8µl of DMSO and 36.7µl of water were added and samples were heat denatured at 99°C for 5 minutes, cooled to 45°C for 5 minutes and centrifuged at 13,000 rpm for 5 minutes.

extract_protocol: genomic DNA was extracted 0.8g leaf tissue using the Qiagen MaxiPrep kit (Qiagen), essentially as recommended by the manufacturer (with the RNAse treatment), but with the following modifications. After washing the spin column with ethanol, the column was transferred to a new cartridge and spun a second time for 15 minutes at 4000 rpm in an Eppendorf 5810R centrifuge to remove all ethanol. Additionally, the column was dried at 37ºC for 45 minutes prior to two elution steps with the pre-warmed (55ºC) Qiagen elution buffer. DNA samples (4μg) were DraI-digested followed by extraction with phenol/chloroform/isoamyl alcohol and ethanol precipitation. After two 70% ethanol washes, the pellet was resuspended with water to 100ng/μl. Each DNA sample in 20µl (2μg) was bisulfite modified using the EpiTect Bisulfite Modification Kit (Qiagen).


title: BiMP epi28 BS+

tag: epiRIL01; DNA isolated from leaf tissue sampled from approx 10 plants


title: BiMP epi12 BS+


title: 2x At x 2x Aa hybird, biological rep2

status: Public on Oct 01 2009

type: RNA

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

country: USA

institute: University of Nebraska

description: incompatible interspecies hybrid seed

hyb_protocol: Standard Affymetrix protocol for Tiling Array platform

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

data_processing: The data were analyzed with TAS (from Affymetrix) and TileMap software. Normalization was performed using the quantile normalization approach.

molecule: total RNA

organism: Arabidopsis arenosa x Arabidopsis thaliana

source_name: incompatible hybrid silques

label_protocol: Labeled cDNA was obtaine dusing the Affymetrix whole genome transcriptome protocol using 7 ug total RNA

growth_protocol: Plant grown in 16 h light and 8 h dark in growth chamber conditions.

extract_protocol: Qiagen total RNA extraction kit was used according to the manufacturer's instructions.

treatment_protocol: Flowers were emasculated and then pollinated with A. arenosa pollen next morning

tag: seed lethality

tag: 5 DAP


title: gra2-D

status: Public on Jun 02 2009

city: Gent

first: Nathalie

last: Gonzalez

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: VIB

description: grandifolia2-D DNA tiling array

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing:
The algorithm MAT (Model based Analysis of Tiling-arrays (http://liulab.dfci.harvard.edu/MAT/) was used in order to detect duplicated or deleted genomic regions.
bar-file:  binary file containing the MAT score for each probe.  bed-file:  text file containing the enriched genomics regions

source_name: gra2-D DNA tiling

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: DNeasy plant mini kit (Qiagen) , according to manufacturer protocol

tag: tissue

value: rosette

source_name: WT


title: SMAD4 binding targets in murine R1 ES cells (2/2)

city: Beijing

country: China

organism: Mus musculus

growth_protocol: Murine R1 ES cells were cultured under typical feeder free ES cell conditions (DMEM supplemented with Knockout serum replacement (Invitrogen Gibco), leukemia inhibitory factor (LIF), non-essential amino acids, GlutaMax-I (Invitrogen Gibco), β-mercaptoethanol and penicillin/streptomycin.

extract_protocol: R1 ES cells (5x107 – 1x108 cells) were chemically cross-linked by addition of one tenth volume of freshly-prepared 11% formaldehyde solution to cell media for 15 min at room temperature.  Cells were rinsed twice with 1xPBS, harvested using a silicon scraper, frozen in liquid nitrogen and stored at -80°C prior to use.  Cells were resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to obtain DNA fragments of about 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and pre-absorbed by 50 ul protein A beads (Zymed) and then incubated with 10 ug antibodies (anti-Smad4) overnight at 4°C. The immunocomplex was collected with 100 ul protein A beads by 3 hour co-incubation and then washed sequentially with TSE I (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors), TSE II (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, proteinase inhibitors), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 mM LiCl, 0.1% NP-40, 1% deoxycholate sodium) and TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0). The bound immunocomplex was eluted with 400 ul fresh elution buffer (25 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) by heating at 65°C with occasional vortex for 15 min and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract (WCE) DNA (Input fraction reserved from the sonication step) was also treated for crosslinking reversal. Immunoprecipitated DNA and WCE DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl alcohol extraction.

tag: cell type


title: Col-0_tiling

status: Public on Apr 14 2009

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: This is a Col-0 sample hybed for comparison with the mutant on the Tiling array.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: age

value: ~6 weeks

value: Leaves


title: 14501_tiling

description: This is a esb1-1 (aka 14501) sample hybed to the Tiling array to identify deletions.


title: SMAD1/5 binding targets in murine R1 ES cells (2/2)

extract_protocol: R1 ES cells (5x107 – 1x108 cells) were chemically cross-linked by addition of one tenth volume of freshly-prepared 11% formaldehyde solution to cell media for 15 min at room temperature.  Cells were rinsed twice with 1xPBS, harvested using a silicon scraper, frozen in liquid nitrogen and stored at -80°C prior to use.  Cells were resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to obtain DNA fragments of about 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and pre-absorbed by 50 ul protein A beads (Zymed) and then incubated with 10 ug antibodies (anti-Smad1/5) overnight at 4°C. The immunocomplex was collected with 100 ul protein A beads by 3 hour co-incubation and then washed sequentially with TSE I (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors), TSE II (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, proteinase inhibitors), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 mM LiCl, 0.1% NP-40, 1% deoxycholate sodium) and TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0). The bound immunocomplex was eluted with 400 ul fresh elution buffer (25 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) by heating at 65°C with occasional vortex for 15 min and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract (WCE) DNA (Input fraction reserved from the sonication step) was also treated for crosslinking reversal. Immunoprecipitated DNA and WCE DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl alcohol extraction.

value: Elute from a Smad1/5 chromatin immunoprecipitation

value: Input for Smad1/5 chromatin immunoprecipitation


title: SMAD1/5 binding targets in murine R1 ES cells (1/2)


title: Control heart rep2

status: Public on Aug 07 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: control

hyb_protocol: Alexa Fluor®_555-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-labeled biological replica overnight at 50°C on a Duke MO30N mouse oligonucleotide array spotted with 30k Operon 70-mer oligonucleotides V3.0.1. Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed iterative algorithm, alternating within-array normalization with interarray normalization, until the average corrected ratio differed by <5% from the previous one (Iacobas et al. Physiol Genomics 2005, PMID: 15585606).

label: Alexa Fluor®_555

source_name: Control heart

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: All animals were raised and maintained at the Gonçalo Moniz Research Center/FIOCRUZ and provided with rodent diet and water ad libitum. Animals were handled according to the NIH guidelines for animal experimentation. All procedures had prior approval from the local animal ethics committee.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Age-matched non-infected C57Bl/6 mice were sacrificed and hearts removed and quickly frozen in liquid nitrogen for five minutes.

tag: strain

value: heart

tag: infection

value: control


title: Control heart rep3

description: control

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a Duke MO30N mouse oligonucleotide array spotted with 30k Operon 70-mer oligonucleotides V3.0.1. Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_647

label_protocol: 20ug total RNA extracted from each heart were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: Chagasic heart rep3

description: Determine the transcriptomic alteration induced by infection with the parasite T. cruzi

source_name: Chagasic heart

treatment_protocol: C57Bl/6 mice were infected by intraperitoneal injection with Colombian Trypanosoma cruzi trypomastigotes obtained from culture supernatants of infected LCC-MK2 cells. Parasitemia of infected mice was evaluated at various times after infection by counting the number of trypomastigotes in peripheral blood aliquots. Mice were sacrificed after 8 months of infection and hearts removed and quickly frozen in liquid nitrogen for five minutes.

value: T. cruzi

tag: disease state

value: chronic chagasic cardiomyopathy


title: Chagasic heart rep1


title: Chagasic heart rep4


title: Chagasic heart rep2


title: Bacteroids two weeks

status: Public on Nov 17 2009

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

institute: KULeuven

description: Common bean plants (Phaseolus vulgaris cv. Limburgse vroege) were cultivated and inoculated with wildtype R. etli CFN42. Nodules were harvested 2 weeks after inoculation and the bacteroids were purified by differential centrifugation.

hyb_protocol: The Cy3-labeled cDNA was hybridized to the custom R. etli tiling expression array at 42°C for 16 hour using the NimbleGen Hybridization System and kit.

scan_protocol: GenePix 4000B.

data_processing: Data preprocessing was done by performing a nonlinear intensity dependent rescaling on non-background corrected data. To this end, a loess fit normalization with a span of 25% was performed for each array compared against an artificial reference array, consisting of the median intensity values of each probe across all arrays. To ensure that the artificial reference itself was not altered by this rescaling, the artificial reference expression levels were chosen for the average log intensity in the loess fit (instead of the mean expression levels of the respective array and the artificial reference). A robust median-polish procedure was used to combine measurements from multiple probes into a single value. Results are linked as supplementary GFF files in standard format with columns: seqname (chromosome name); source (article); feature (RNA); start; end; score (normalized sRNA value); strand (forward (1) or reverse (-1)); frame (empty for RNA); attribute (ID for sRNA).

organism: Rhizobium etli CFN 42

source_name: Wildtype R. etli CFN42 bacteroids harvested 2 weeks after inoculation

label_protocol: cDNA, median≥400bp, was synthesized using random decamers (Ambion) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s protocol. All cDNA samples were labeled with Cy3 by Nimblegen using the NimbleGen One- Color DNA Labeling Kit (05223555001).

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Bacteroid pellets were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). To increase RNA yields and account for experimental variation, RNA from 6 different cultures or 4 batches of bacteroids was pooled. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. The ncRNA peak could be detected in each sample. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.

tag: genetic background

value: CFN 42

tag: genotype

value: wild type


title: Control heart rep1

description: control


title: totRNA_UV_2

status: Public on Aug 18 2009

city: Oslo

first: Gard

last: Thomassen

state: Oslo

address: Rikshospitalet University Hospital

department: Molecular microbiology

country: Norway

institute: Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology

description: single colony and culture parallell to totRNA_MOCK_2 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)

hyb_protocol: Fragmented and labelled cDNA were hybridized to arrays overnight at 45°C according to the Affymetrix 'Prokaryotic sample and array processing' protocol version 701029 Rev. 4.

scan_protocol: The arrays were scanned using GeneChip Skanner 3000 7G with settings appropriate to the array type.

data_processing:
Details on the analysis methods applied is found in the connected paper: Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. Thomassen GO, Rowe AD, Lagesen K, Lindvall JM, Rognes T. PLoS One. 2009 Jun 17;4(6):e5943. PMID: 19536279
Results of analysis of the reference dataset (the 5 MOCK E. coli arrays,) and the treated dataset (the 5 UV treated E. coli arrays) are provided in the "MOCKvsUVresults.tar" supplementary file available on the Series record.

label: Biotin

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

source_name: total RNA extracted 20 min after induction of the SOS response by UV irradiation (50 J/m2)

label_protocol: Fragmented cDNA was terminal labelled with Biotin according to the Affymetrix 'Prokaryotic sample and array processing' protocol version 701029 Rev. 4.

growth_protocol: Escherichia coli K-12 MG1655 single colony from overnight cultures were diluted 1:500 in 100 ml K-medium (1xM9, 1.2% glucose, 1.25% casamino acids (dCAA), 1 mM MgSO4, 0.1 mM CaCl2) and grown at 37°C with aeration by rotary shaking until OD600=0.5.

extract_protocol: 1 ml trizol was added pr 106 cells and incubated at room temperature for 5 minutes. 0.2 ml chloroform was added pr ml Trizol and the sample was mixed for 15 seconds before 15 minutes centrifutgation (12000 g 4°C). The aqueous phase was slowly added 1:1(vol) to 70% EtOH and further loaded to a RNeasy column (QIAGEN), washed and DNase treated according to RNeasy protocol (QIAGEN).

treatment_protocol: 50 ml culture of Escherichia coli K-12 MG1655 was irradiated by UV 50 J/m2 OD600 = 0.5. The culture was further harvested by centrifugation 20 minutes after exposure to UV. (Samples 6-10)

tag: cell culture

value: mid-log phase


title: Control heart rep4

description: control


title: E6.5 retina RCAS control rep2

status: Public on Mar 27 2009

city: Wako

first: Shinichi

last: Nakagawa

state: Saitama

address: Hirosawa 2-1

country: Japan

institute: RIKEN ASI

description:
E1.5 retinas were electroporated with RCAS c-hairy1. Retinas were recovered at E6.5.
RCAS provirus vector with no insert was used as a control.

hyb_protocol: Hybridization was carried out following the manufacturer's instruction.

scan_protocol: Scan was carried out following the manufacturer's instruction.

data_processing: Affymetrix GCOS 1.4

label: 3' amplification Reagents for IVT

molecule: polyA RNA

organism: Gallus gallus

source_name: E6.5 retina control (2)

label_protocol: Labeling reaction was carried out following the manufacturer's instruction.

extract_protocol:
Tissues were homogenized with Trizol reagents.
Total RNA was purified following the manufacturer's instruction.
polyA RNA was purified on Oligo-dT column.

tag: protocol

value: retina


title: E6.5 retina RCAS Delta rep2

description:
E1.5 retinas were electroporated with RCAS Delta-1. Retinas were recovered at E6.5.
Delta-1 inhibits neuronal differentiation

source_name: E6.5 retina expressing Delta (2)

value: expression of Delta


title: E6.5 retina RCAS Wnt2b rep1

description:
E1.5 retinas were electroporated with RCAS Wnt2b. Retinas were recovered at E6.5.
Wnt2b inhibits neuronal differentiation

source_name: E6.5 retina expressing Wnt2b (1)

value: expression of Wnt2b


title: E6.5 retina RCAS Delta rep1

source_name: E6.5 retina Delta (1)


title: E6.5 retina RCAS Wnt2b rep2

source_name: E6.5 retina expressing Wnt2b (2)


title: totRNA_UV_4

description: single colony and culture parallell to totRNA_MOCK_4 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: E6.5 retina RCAS c-hairy1 rep2

description:
E1.5 retinas were electroporated with RCAS c-hairy1. Retinas were recovered at E6.5.
c-hairy1 inhibits neuronal differentiation

source_name: E6.5 retina expressing c-hairy1 (2)

value: expression of c-hairy1


title: E6.5 retina RCAS c-hairy1 rep1

description:
E1.5 retinas were electroporated with RCAS c-hairy1
Retinas were recovered at E6.5
c-hairy1 inhibits neuronal differentiation

source_name: E6.5 retina expressing c-hairy1 (1)


title: totRNA_MOCK_4

description: single colony and culture parallell to totRNA_UV_4 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)

source_name: total RNA extracted 20 min after mock treatment parallel to induction of the SOS response, unirradiated

treatment_protocol: 50 ml culture of Escherichia coli K-12 MG1655 was treated as to be irradiated by UV 0 J/m2 OD600 = 0.5. The culture was further harvested by centrifugation 20 minutes after non-exposure to UV.(Samples 1-5)


title: totRNA_MOCK_3

description: single colony and culture parallell to totRNA_UV_3 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: totRNA_MOCK_1

description: single colony and culture parallell to totRNA_UV_1 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: totRNA_UV_3

description: single colony and culture parallell to totRNA_MOCK_3 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: totRNA_MOCK_5

description: single colony and culture parallell to totRNA_UV_5 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: E6.5 retina RCAS control rep1

description:
E1.5 retinas were electroporated with RCAS. Retinas were recovered at E6.5.
RCAS provirus vector with no insert was used as a control.

source_name: E6.5 retina control (1)


title: totRNA_UV_5

description: single colony and culture parallell to totRNA_MOCK_5 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: totRNA_MOCK_2

description: single colony and culture parallell to totRNA_UV_2 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: Embryo - Plumule - Dry Seed Replicate 1

status: Public on Oct 16 2008

city: New Haven

first: Timothy

last: Nelson

state: CT

department: MCDB

institute: Yale University

description: Biological replicate 1 of 4. We printed our oligos onto two slides and the same sample was hybridized onto both slides. The Sample data tables contain merged normalized data from both slides.

hyb_protocol: Hybridization were carried out as described previously (Jiao et al., Plant Cell 17:3239).

scan_protocol: Scanned on a GenePix 4200A Images were quantified using GenePix 5.0

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

organism: Oryza sativa

source_name: Amplified RNA from rice suspension cultured cells (red).

label_protocol: A two-round T7 polymerase-based linear amplification systems, RiboAmp (Arcturus Engineering), was used according to the manufacturer to amplify and label RNA. For details, see http://bioinformatics.med.yale.edu/riceatlas/protocols.jspx.

extract_protocol: Arcturus Picopure RNA isolation Kit

tag: cultivar

value: Nipponbare

value: Undifferentiated rice suspension cultured cells

source_name: Amplified RNA from rice Embryo - Plumule - Dry Seed (green)

value: Embryo Plumule from Dry Seeds.


title: Embryo - Epiblast - Dry Seed Replicate 3

description: Biological replicate 3 of 4. We printed our oligos onto two slides and the same sample was hybridized onto both slides. The Sample data tables contain merged normalized data from both slides.

source_name: Amplified RNA from rice suspension cultured cells (green).

source_name: Amplified RNA from rice Embryo - Epiblast - Dry Seed (red)

value: Embryo Epiblast from Dry Seeds.


title: Embryo - Epiblast - Dry Seed Replicate 4

description: Biological replicate 4 of 4. We printed our oligos onto two slides and the same sample was hybridized onto both slides. The Sample data tables contain merged normalized data from both slides.


title: Embryo - Plumule - Dry Seed Replicate 2

description: Biological replicate 2 of 4. We printed our oligos onto two slides and the same sample was hybridized onto both slides. The Sample data tables contain merged normalized data from both slides.


title: Embryo - Radicle - Dry Seed Replicate 2

source_name: Amplified RNA from rice Embryo - Radicle - Dry Seed (green)

value: embryo radicle from dry seeds..


title: Embryo - Plumule - Dry Seed Replicate 3

source_name: Amplified RNA from rice Embryo - Plumule - Dry Seed (red)


title: totRNA_UV_1

description: single colony and culture parallell to totRNA_MOCK_1 (the culture was split in two, half induced by UV irradiation the other half as reference was not induced)


title: Embryo - Coleoptile - Dry Seed Replicate 3

source_name: Amplified RNA from rice Embryo - Coleoptile - Dry Seed (red)

value: Embryo Coleoptile from Dry Seeds from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Embryo - Epiblast - Dry Seed Replicate 1

source_name: Amplified RNA from rice Embryo - Epiblast - Dry Seed (green)

value: Embryo Epiblast from Dry Seeds from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Embryo - Radicle - Dry Seed Replicate 1

value: Embryo Radicle from Dry Seeds.


title: Embryo - Coleoptile - Dry Seed Replicate 2

source_name: Amplified RNA from rice Embryo - Coleoptile - Dry Seed (green)

value: embryo coleoptile from dry seeds.


title: Embryo - Plumule - Dry Seed Replicate 4


title: Tissue - Whole leaf blade (fresh) Replicate 3

source_name: Amplified RNA from rice Tissue - Whole leaf blade (fresh) (red)

value: Whole leaf blade (fresh) from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Embryo - Coleoptile - Dry Seed Replicate 1

value: embryo Coleoptile from dry seeds


title: Tissue - Whole root (fresh) Replicate 4

source_name: Amplified RNA from rice Tissue - Whole root (fresh) (red)

value: Whole root (fresh) from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Tissue - Whole leaf blade (fresh) Replicate 2

source_name: Amplified RNA from rice Tissue - Whole leaf blade (fresh) (green)


title: Tissue - Whole leaf blade (fresh) Replicate 1


title: Seedling - Leaf blade (2nd leaf) - Stomata Replicate 2

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Stomata (green)

value: Seedling - Leaf blade (2nd leaf) - Stomata from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Stomata Replicate 4

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Stomata (red)


title: Seedling - Leaf blade (2nd leaf) - Stomata Replicate 3


title: Seedling - Leaf blade (2nd leaf) - Bulliform Replicate 1

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Bulliform (green)

value: Seedling - Leaf blade (2nd leaf) - Bulliform from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell Replicate 3

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell (red)

value: Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Tissue - Whole root (fresh) Replicate 1

source_name: Amplified RNA from rice Tissue - Whole root (fresh) (green)


title: Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell Replicate 4


title: Seedling - Leaf blade (2nd leaf) - Stomata Replicate 1

source_name: Amplified RNA from rice suspension cultured cells (red).


title: Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell Replicate 1

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell (green)


title: Embryo - Coleoptile - Dry Seed Replicate 4

source_name: Amplified RNA from rice suspension cultured cells (green).

value: Embryo Coleoptile from Dry Seeds.


title: Seedling - Leaf blade (2nd leaf) - Epidermal Long Cell Replicate 2


title: Seedling - Leaf blade (2nd leaf) - Bulliform Replicate 4

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Bulliform (red)


title: Tissue - Whole leaf blade (fresh) Replicate 4


title: Seedling - Leaf blade (2nd leaf) - Bulliform Replicate 2


title: Tissue - Whole root (fresh) Replicate 2


title: Tissue - Whole root (fresh) Replicate 3


title: Embryo - Radicle - Dry Seed Replicate 3

source_name: Amplified RNA from rice Embryo - Radicle - Dry Seed (red)


title: Seedling - Leaf blade (2nd leaf) - Vein Replicate 3

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Vein (red)

value: Seedling - Leaf blade (2nd leaf) - Vein from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Vein Replicate 4

value: Nipponbare


title: Seedling - Leaf blade (2nd leaf) - Bulliform Replicate 3

value: Undifferentiated rice suspension cultured cells


title: Seedling - Leaf blade (2nd leaf) - Vein Replicate 2

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Vein (green)


title: Seedling - Leaf blade (2nd leaf) - Bundle sheath Replicate 3

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Bundle sheath (red)

value: Seedling - Leaf blade (2nd leaf) - Bundle sheath from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Bundle sheath Replicate 4


title: Seedling - Leaf blade (2nd leaf) - Vein Replicate 1


title: Seedling - Leaf blade (2nd leaf) - Mesophyll Replicate 4

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Mesophyll (red)

value: Seedling - Leaf blade (2nd leaf) - Mesophyll from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Bundle sheath Replicate 2

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Bundle sheath (green)


title: Seedling - Leaf blade (2nd leaf) - Mesophyll Replicate 2

source_name: Amplified RNA from rice Seedling - Leaf blade (2nd leaf) - Mesophyll (green)


title: Seedling - Leaf blade (2nd leaf) - Mesophyll Replicate 3


title: Seedling - Shoot - Axillary meristem Replicate 2

source_name: Amplified RNA from rice Seedling - Shoot - Axillary meristem (green)

value: Seedling - Shoot - Axillary meristem from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - Axillary primordium Replicate 4

source_name: Amplified RNA from rice Seedling - Shoot - Axillary primordium (red)

value: Seedling - Shoot - Axillary primordium from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Leaf blade (2nd leaf) - Bundle sheath Replicate 1


title: Seedling - Shoot - Axillary primordium Replicate 3


title: Seedling - Shoot - Axillary primordium Replicate 2

source_name: Amplified RNA from rice Seedling - Shoot - Axillary primordium (green)


title: Seedling - Leaf blade (2nd leaf) - Mesophyll Replicate 1


title: Seedling - Shoot - P3 Replicate 3

source_name: Amplified RNA from rice Seedling - Shoot - P3 (red)

value: Seedling - Shoot - leaf primordia P3 from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - Axillary meristem Replicate 1


title: Seedling - Shoot - Axillary meristem Replicate 3

source_name: Amplified RNA from rice Seedling - Shoot - Axillary meristem (red)


title: Seedling - Shoot - Axillary meristem Replicate 4


title: Seedling - Shoot - P3 Replicate 1

source_name: Amplified RNA from rice Seedling - Shoot - P3 (green)


title: Seedling - Shoot - P3 Replicate 4


title: Seedling - Shoot - P2 Replicate 2

source_name: Amplified RNA from rice suspension cultured cells (red).

source_name: Amplified RNA from rice Seedling - Shoot - P2 (green)

value: Seedling - Shoot - leaf primordia P2 from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - P2 Replicate 1


title: Seedling - Shoot - P2 Replicate 4

source_name: Amplified RNA from rice suspension cultured cells (green).

source_name: Amplified RNA from rice Seedling - Shoot - P2 (red)


title: Seedling - Shoot - P1 Replicate 2

source_name: Amplified RNA from rice Seedling - Shoot - P1 (green)

value: Seedling - Shoot - leaf primordia P1 from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - P1 Replicate 3

source_name: Amplified RNA from rice Seedling - Shoot - P1 (red)


title: Seedling - Shoot - P3 Replicate 2


title: Seedling - Shoot - P2 Replicate 3


title: Seedling - Shoot - Apical meristem Replicate 4

source_name: Amplified RNA from rice Seedling - Shoot - Apical meristem (red)

value: Seedling - Shoot - Apical meristem from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - P1 Replicate 4


title: Seedling - Root maturation zone - Epidermis Replicate 4

source_name: Amplified RNA from rice Seedling - Root maturation zone - Epidermis (red)

value: Seedling - Root maturation zone - Epidermis from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Shoot - Apical meristem Replicate 1

source_name: Amplified RNA from rice Seedling - Shoot - Apical meristem (green)


title: Seedling - Shoot - Apical meristem Replicate 3


title: Seedling - Root maturation zone - Epidermis Replicate 2

source_name: Amplified RNA from rice Seedling - Root maturation zone - Epidermis (green)


title: Seedling - Root maturation zone - Epidermis Replicate 1


title: Seedling - Root maturation zone - Epidermis Replicate 3


title: Seedling - Root maturation zone - Endodermis Replicate 2

source_name: Amplified RNA from rice Seedling - Root maturation zone - Endodermis (green)

value: Seedling - Root maturation zone - Endodermis from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root maturation zone - Stele/Vascular bundle Replicate 4

source_name: Amplified RNA from rice Seedling - Root maturation zone - Stele/Vascular bundle (red)

value: Seedling - Root maturation zone - Stele/Vascular bundle from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root maturation zone - Cortex Replicate 1

source_name: Amplified RNA from rice Seedling - Root maturation zone - Cortex (green)

value: Seedling - Root maturation zone - Cortex from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root maturation zone - Endodermis Replicate 1


title: Seedling - Root maturation zone - Endodermis Replicate 4

source_name: Amplified RNA from rice Seedling - Root maturation zone - Endodermis (red)


title: Seedling - Root maturation zone - Cortex Replicate 4

source_name: Amplified RNA from rice Seedling - Root maturation zone - Cortex (red)


title: Seedling - Root maturation zone - Stele/Vascular bundle Replicate 2

source_name: Amplified RNA from rice Seedling - Root maturation zone - Stele/Vascular bundle (green)


title: Seedling - Shoot - P1 Replicate 1


title: Embryo - Epiblast - Dry Seed Replicate 2

source_name: Amplified RNA from rice Embryo - Epiblast - Dry Seed (green)

value: Embryo Epiblast from Dry Seeds from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root maturation zone - Cortex Replicate 2

source_name: Amplified RNA from rice suspension cultured cells (red).


title: Seedling - Root maturation zone - Stele/Vascular bundle Replicate 1


title: Seedling - Root maturation zone - Cortex Replicate 3


title: Seedling - Root elongation zone - Epidermis Replicate 4

source_name: Amplified RNA from rice Seedling - Root elongation zone - Epidermis (red)

value: Seedling - Root elongation zone - Epidermis from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root maturation zone - Endodermis Replicate 3

source_name: Amplified RNA from rice suspension cultured cells (green).


title: Seedling - Root elongation zone - Epidermis Replicate 3


title: Seedling - Root elongation zone - Endodermis Replicate 4

source_name: Amplified RNA from rice Seedling - Root elongation zone - Endodermis (red)

value: Seedling - Root elongation zone - Endodermis from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root elongation zone - Epidermis Replicate 2

value: Nipponbare

source_name: Amplified RNA from rice Seedling - Root elongation zone - Epidermis (green)


title: Seedling - Root maturation zone - Stele/Vascular bundle Replicate 3

value: Undifferentiated rice suspension cultured cells


title: Seedling - Root elongation zone - Endodermis Replicate 2

source_name: Amplified RNA from rice Seedling - Root elongation zone - Endodermis (green)


title: Seedling - Root elongation zone - Endodermis Replicate 1


title: Seedling - Root elongation zone - Cortex Replicate 1

source_name: Amplified RNA from rice Seedling - Root elongation zone - Cortex (green)

value: Seedling - Root elongation zone - Cortex from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root elongation zone - Cortex Replicate 4

source_name: Amplified RNA from rice Seedling - Root elongation zone - Cortex (red)


title: Seedling - Root elongation zone - Endodermis Replicate 3


title: Seedling - Root elongation zone - Cortex Replicate 3


title: Seedling - Root elongation zone - Epidermis Replicate 1


title: Seedling - Root elongation zone - Central metaxylem Replicate 4

source_name: Amplified RNA from rice Seedling - Root elongation zone - Central metaxylem (red)

value: Seedling - Root elongation zone - Central metaxylem from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root elongation zone - Cortex Replicate 2


title: Seedling - Root elongation zone - Central metaxylem Replicate 3


title: Seedling - Root elongation zone - Stele/Vascular bundle Replicate 1

source_name: Amplified RNA from rice Seedling - Root elongation zone - Stele/Vascular bundle (green)

value: Seedling - Root elongation zone - Stele/Vascular bundle from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root elongation zone - Stele/Vascular bundle Replicate 4

source_name: Amplified RNA from rice Seedling - Root elongation zone - Stele/Vascular bundle (red)


title: Seedling - Root elongation zone - Stele/Vascular bundle Replicate 2


title: Seedling - Root elongation zone - Stele/Vascular bundle Replicate 3


title: Seedling - Root tip - Central metaxylem precursor Replicate 4

source_name: Amplified RNA from rice Seedling - Root tip - Central metaxylem precursor (red)

value: Seedling - Root tip - Central metaxylem precursor from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root tip - Vascular bundle Replicate 4

source_name: Amplified RNA from rice Seedling - Root tip - Vascular bundle (red)

value: Seedling - Root tip - Vascular bundle from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root elongation zone - Central metaxylem Replicate 2

source_name: Amplified RNA from rice Seedling - Root elongation zone - Central metaxylem (green)


title: Seedling - Root elongation zone - Central metaxylem Replicate 1


title: Seedling - Root tip - Central metaxylem precursor Replicate 3


title: Seedling - Root tip - Central metaxylem precursor Replicate 1

source_name: Amplified RNA from rice Seedling - Root tip - Central metaxylem precursor (green)


title: Seedling - Root tip - Vascular bundle Replicate 3


title: Seedling - Root tip - Central metaxylem precursor Replicate 2


title: Seedling - Root tip - Cortex Replicate 3

source_name: Amplified RNA from rice Seedling - Root tip - Cortex (red)

value: Seedling - Root tip - Cortex from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root tip - Vascular bundle Replicate 2

source_name: Amplified RNA from rice Seedling - Root tip - Vascular bundle (green)


title: Seedling - Shoot - Axillary primordium Replicate 1

source_name: Amplified RNA from rice suspension cultured cells (red).

source_name: Amplified RNA from rice Seedling - Shoot - Axillary primordium (green)

value: Seedling - Shoot - Axillary primordium from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root tip - Cortex Replicate 1

source_name: Amplified RNA from rice Seedling - Root tip - Cortex (green)


title: Embryo - Scutellum - 24hr post imbibition Replicate 1

source_name: Amplified RNA from rice Embryo - Scutellum - 24hr post imbibition (green)

value: embryo scutellum from germinated seeds (24h post-imbibition).


title: Seedling - Root tip - Lateral root cap Replicate 1

source_name: Amplified RNA from rice Seedling - Root tip - Lateral root cap (green)

value: Seedling - Root tip - Lateral root cap from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Seedling - Root tip - Vascular bundle Replicate 1


title: Seedling - Root tip - Cortex Replicate 4

source_name: Amplified RNA from rice suspension cultured cells (green).


title: Embryo - Scutellum - 24hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Scutellum - 24hr post imbibition (red)


title: Embryo - Radicle - 24hr post imbibition Replicate 2

source_name: Amplified RNA from rice Embryo - Radicle - 24hr post imbibition (green)

value: embryo radicle from germinated seeds (24h post-imbibition).


title: Seedling - Root tip - Cortex Replicate 2


title: Embryo - Scutellum - 24hr post imbibition Replicate 2


title: Embryo - Radicle - 24hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Radicle - 24hr post imbibition (red)


title: Seedling - Root tip - Lateral root cap Replicate 2


title: Embryo - Scutellum - 24hr post imbibition Replicate 4


title: Embryo - Radicle - 24hr post imbibition Replicate 4


title: Seedling - Root tip - Lateral root cap Replicate 3

source_name: Amplified RNA from rice Seedling - Root tip - Lateral root cap (red)


title: Embryo - Radicle - 24hr post imbibition Replicate 1


title: Seedling - Root tip - Lateral root cap Replicate 4


title: Embryo - Epiblast - 24hr post imbibition Replicate 2

source_name: Amplified RNA from rice Embryo - Epiblast - 24hr post imbibition (green)

value: embryo epiblast from germinated seeds (24h post-imbibition).


title: Embryo - Epiblast - 24hr post imbibition Replicate 4

source_name: Amplified RNA from rice Embryo - Epiblast - 24hr post imbibition (red)


title: Embryo - Coleoptile - 24hr post imbibition Replicate 4

source_name: Amplified RNA from rice Embryo - Coleoptile - 24hr post imbibition (red)

value: embryo coleoptile from germinated seeds (24h post-imbibition).


title: Embryo - Plumule - 24hr post imbibition Replicate 4

source_name: Amplified RNA from rice Embryo - Plumule - 24hr post imbibition (red)

value: embryo plumule from germinated seeds (24h post-imbibition).


title: Embryo - Plumule - 24hr post imbibition Replicate 2

source_name: Amplified RNA from rice Embryo - Plumule - 24hr post imbibition (green)


title: Embryo - Plumule - 24hr post imbibition Replicate 3


title: Embryo - Scutellum - 12hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Scutellum - 12hr post imbibition (red)

value: embryo scutellum from germinated seeds (12h post-imbibition).


title: Embryo - Scutellum - 12hr post imbibition Replicate 4


title: Embryo - Epiblast - 24hr post imbibition Replicate 1


title: Embryo - Plumule - 24hr post imbibition Replicate 1


title: Embryo - Coleoptile - 24hr post imbibition Replicate 1

source_name: Amplified RNA from rice Embryo - Coleoptile - 24hr post imbibition (green)


title: Embryo - Plumule - 12hr post imbibition Replicate 2

source_name: Amplified RNA from rice suspension cultured cells (red).

source_name: Amplified RNA from rice Embryo - Plumule - 12hr post imbibition (green)

value: embryo plumule from germinated seeds (12h post-imbibition).


title: Embryo - Epiblast - 24hr post imbibition Replicate 3

value: Nipponbare


title: Embryo - Radicle - 12hr post imbibition Replicate 4

value: Undifferentiated rice suspension cultured cells

source_name: Amplified RNA from rice Embryo - Radicle - 12hr post imbibition (red)

value: embryo radicle from germinated seeds (12h post-imbibition).


title: Embryo - Scutellum - 12hr post imbibition Replicate 1

source_name: Amplified RNA from rice Embryo - Scutellum - 12hr post imbibition (green)


title: Seedling - Shoot - Apical meristem Replicate 2

source_name: Amplified RNA from rice Seedling - Shoot - Apical meristem (green)

value: Seedling - Shoot - Apical meristem from 5 day old seedlings grown in an environmental chamber in a short day cycle of 10hr light of 120µE/m^2/sec at 30°C and 14hr darkness at 24°C.


title: Embryo - Coleoptile - 24hr post imbibition Replicate 2


title: Embryo - Radicle - 12hr post imbibition Replicate 3

source_name: Amplified RNA from rice suspension cultured cells (green).


title: Embryo - Radicle - 12hr post imbibition Replicate 1

source_name: Amplified RNA from rice Embryo - Radicle - 12hr post imbibition (green)


title: Embryo - Radicle - 12hr post imbibition Replicate 2


title: Embryo - Epiblast - 12hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Epiblast - 12hr post imbibition (red)

value: embryo epiblast from germinated seeds (12h post-imbibition).


title: Embryo - Scutellum - 12hr post imbibition Replicate 2


title: Embryo - Epiblast - 12hr post imbibition Replicate 4


title: ein5-6Xabh1-1_bud_totalRNA_R_2

status: Public on May 15 2008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: ein5-6Xabh1-1 flower bud total RNA Reverse replicate 2

hyb_protocol: The Arabidopsis Tiling 1.0R whole genome tiling array was hybridized for 16 h, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix Scanner G7

data_processing: Gene chip data files were processed using TileMap to identify regions of significant changes in gene expression, with a cutoff of 0.6 pp.

source_name: Immature floral tissue, unopened buds

label_protocol: Fifteen micrograms of total RNA was used to synthesize double-stranded cDNA using the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was generated by in vitro transcription using the GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23C under a 16-hour light/8-hour dark cycle.

extract_protocol: total RNA was isolated from immature floral tissue following instructions from the manufacturer (Qiagen, RNeasy Plant Mini Kit).

treatment_protocol: no treatment


title: ein5-6_bud_totalRNA_R_1

description: ein5-6 flower bud total RNA Reverse replicate 1


title: Embryo - Plumule - 12hr post imbibition Replicate 1


title: Embryo - Plumule - 12hr post imbibition Replicate 4

source_name: Amplified RNA from rice Embryo - Plumule - 12hr post imbibition (red)


title: Embryo - Coleoptile - 12hr post imbibition Replicate 2

source_name: Amplified RNA from rice Embryo - Coleoptile - 12hr post imbibition (green)

value: embryo coleoptile from germinated seeds (12h post-imbibition)..


title: Embryo - Coleoptile - 12hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Coleoptile - 12hr post imbibition (red)


title: abh1-1_bud_totalRNA_R_1

description: abh1-1 flower bud total RNA Reverse replicate 1


title: abh1-1_bud_totalRNA_R_2

description: abh1-1 flower bud total RNA Reverse replicate 2


title: col-0_no_antibody_1

status: Public on Apr 21 2008

description: Col-0 control (no antibody) replicate 1

hyb_protocol: The Arabidopsis Tiling 1.0R whole genome tiling array was hybridized for 16 h, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 accordingto the standard Affymetrix protocol.

data_processing: Gene chip data files were processed using TileMap. This array was one of two control samples that were used to identify methylated regions in the methylcytosine immunoprecipitation reactions.

label_protocol: Genomic DNA from the "no antibody" control was amplified using the Sigma GenomePlex WGA1 kit as per manufacturer's instructions to yield 15 µg, fragmented by incubation with DNaseI (0.05 U/µg DNA) for 10 min at room temperature, then denatured. DNA was labeled by incubating the fragmented DNA with biotin-16-dUTP, biotin-16-ddUTP and terminal transferase for 90 min at 37˚C.

growth_protocol: All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23˚C under a 16-hour light/8-hour dark cycle.

extract_protocol: Genomic DNA was isolated from the immature floral tissue following instructions from the manufacturer (Qiagen, DNeasy Plant mini kit). 2 µg of fragmented genomic DNA was incubated under the same conditions as the methylcytosine immunoprecipitation samples, except no antibody was added.


title: Embryo - Coleoptile - 12hr post imbibition Replicate 4


title: col-0_no_antibody_2

description: Col-0 control (no antibody) replicate 2


title: Embryo - Scutellum - Dry Seed Replicate 3

source_name: Amplified RNA from rice Embryo - Scutellum - Dry Seed (red)

value: embryo scutellum from dry seeds.


title: ein5-6_bud_totalRNA_R_2

description: ein5-6 flower bud total RNA Reverse replicate 2


title: Embryo - Epiblast - 12hr post imbibition Replicate 2

source_name: Amplified RNA from rice Embryo - Epiblast - 12hr post imbibition (green)


title: Embryo - Coleoptile - 24hr post imbibition Replicate 3

source_name: Amplified RNA from rice Embryo - Coleoptile - 24hr post imbibition (red)


title: Col-0_bud_totalRNA_R_2

description: Col-0 flower bud total RNA Reverse replicate 2


title: Col-0_bud_totalRNA_R_1

description: Col-0 flower bud total RNA Reverse replicate 1


title: col-0_mcip_2

description: Col-0 methylcytosine immunoprecipitation replicate 2

data_processing: Gene chip data files were processed using TileMap to identify methylated regions, with a cutoff of 0.5 pp. The no antibody arrays were used as controls for identification of methylated regions.

label_protocol: Immunoprecipitated genomic DNA was amplified using the Sigma GenomePlex WGA1 kit as per manufacturer's instructions to yield 15 µg, fragmented by incubation with DNaseI (0.05 U/µg DNA) for 10 min at room temperature, then denatured. DNA was labeled by incubating the fragmented DNA with biotin-16-dUTP, biotin-16-ddUTP and terminal transferase for 90 min at 37˚C.

extract_protocol: Genomic DNA was isolated from the immature floral tissue following instructions from the manufacturer (Qiagen, DNeasy Plant mini kit). Genomic DNA containing methylcytosines was immunoprecipitated with anti-5-methylcytosine antibody from 2 µg of fragmented genomic DNA.


title: Embryo - Scutellum - Dry Seed Replicate 1

source_name: Amplified RNA from rice Embryo - Scutellum - Dry Seed (green)


title: Embryo - Coleoptile - 12hr post imbibition Replicate 1


title: Embryo - Scutellum - Dry Seed Replicate 2


title: col-0_mcip_1

description: Col-0 methylcytosine immunoprecipitation replicate 1


title: ein5-6Xabh1-1_bud_totalRNA_R_1

description: ein5-6Xabh1-1 flower bud total RNA Reverse replicate 1


title: Embryo - Epiblast - 12hr post imbibition Replicate 1


title: Embryo - Scutellum - Dry Seed Replicate 4


title: Embryo - Radicle - Dry Seed Replicate 4

source_name: Amplified RNA from rice Embryo - Radicle - Dry Seed (red)

value: embryo radicle from dry seeds..


title: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep2_85756

status: Public on Jun 23 2007

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 85756
treated sample for experiment (RepID) 6082
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM205110: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep1_85734
Replicate experimental sample: GSM205112: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep3_85773
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

organism: Rattus norvegicus

source_name: LIVER, VALPROIC ACID, 1500mg/kg, 5 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

value: 6 to 8 weeks

tag: sex

value: male

value: LIVER

tag: treatment compound

value: VALPROIC ACID

tag: dose

tag: solvent

value: WATER

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 5 days

tag: experiment date


title: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep2_88543

description:
HybID: 88543
treated sample for experiment (RepID) 6885
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM205109: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep3_88542
Replicate experimental sample: GSM205107: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep1_88544
Matched control sample: GSM204754: LIVER_vehicle_NA_3days_control_NA_87504
Matched control sample: GSM204694: LIVER_vehicle_NA_1days_control_NA_87505
Matched control sample: GSM204807: LIVER_vehicle_NA_5days_control_NA_87510
Matched control sample: GSM204654: LIVER_vehicle_NA_1days_control_NA_87511
Matched control sample: GSM204596: LIVER_vehicle_NA_.25days_control_NA_87569
Matched control sample: GSM204789: LIVER_vehicle_NA_3days_control_NA_87570
Matched control sample: GSM204804: LIVER_vehicle_NA_5days_control_NA_87575
Matched control sample: GSM204650: LIVER_vehicle_NA_1days_control_NA_87638
Matched control sample: GSM204632: LIVER_vehicle_NA_.25days_control_NA_87642
Matched control sample: GSM204728: LIVER_vehicle_NA_3days_control_NA_87780
Matched control sample: GSM204623: LIVER_vehicle_NA_.25days_control_NA_87869
Matched control sample: GSM204633: LIVER_vehicle_NA_.25days_control_NA_87871
Matched control sample: GSM204639: LIVER_vehicle_NA_1days_control_NA_88484
Matched control sample: GSM204711: LIVER_vehicle_NA_1days_control_NA_88486
Matched control sample: GSM204765: LIVER_vehicle_NA_3days_control_NA_88488
Matched control sample: GSM204821: LIVER_vehicle_NA_5days_control_NA_88490
Matched control sample: GSM204607: LIVER_vehicle_NA_.25days_control_NA_88604
Matched control sample: GSM204649: LIVER_vehicle_NA_1days_control_NA_88607
Matched control sample: GSM204833: LIVER_vehicle_NA_5days_control_NA_88609
Matched control sample: GSM204867: LIVER_vehicle_NA_5days_control_NA_88611
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, TROGLITAZONE, 1200mg/kg, 5 days

tag: age

tag: tissue

value: TROGLITAZONE

value: CORN OIL


title: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep1_87173

description:
HybID: 87173
treated sample for experiment (RepID) 6493
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM205132: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep2_87172
Replicate experimental sample: GSM205133: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep3_87276
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, VINORELBINE, 1.5mg/kg, 5 days

value: VINORELBINE

value: 1.5 mg/kg

value: SALINE

value: INTRAVENOUS


title: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep3_87276

description:
HybID: 87276
treated sample for experiment (RepID) 6493
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM205132: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep2_87172
Replicate experimental sample: GSM205131: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep1_87173
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep2_87172

description:
HybID: 87172
treated sample for experiment (RepID) 6493
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM205131: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep1_87173
Replicate experimental sample: GSM205133: LIVER_VINORELBINE_1.5mg/kg_5days_exp6493_rep3_87276
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep1_85929

description:
HybID: 85929
treated sample for experiment (RepID) 6143
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM205124: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep3_85927
Replicate experimental sample: GSM205123: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep2_85928
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, VINBLASTINE, .3mg/kg, 5 days

value: VINBLASTINE

value: .3 mg/kg


title: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep3_85773

description:
HybID: 85773
treated sample for experiment (RepID) 6082
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM205110: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep1_85734
Replicate experimental sample: GSM205111: LIVER_VALPROIC_ACID_1500mg/kg_5days_exp6082_rep2_85756
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep3_85927

description:
HybID: 85927
treated sample for experiment (RepID) 6143
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM205123: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep2_85928
Replicate experimental sample: GSM205122: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep1_85929
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep3_83952

description:
HybID: 83952
treated sample for experiment (RepID) 5568
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM205104: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep1_83950
Replicate experimental sample: GSM205105: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep2_83951
Matched control sample: GSM204850: LIVER_vehicle_NA_5days_control_NA_83512
Matched control sample: GSM204828: LIVER_vehicle_NA_5days_control_NA_83673
Matched control sample: GSM204674: LIVER_vehicle_NA_1days_control_NA_83735
Matched control sample: GSM204784: LIVER_vehicle_NA_3days_control_NA_83737
Matched control sample: GSM204724: LIVER_vehicle_NA_3days_control_NA_83739
Matched control sample: GSM204843: LIVER_vehicle_NA_5days_control_NA_83741
Matched control sample: GSM204700: LIVER_vehicle_NA_1days_control_NA_83831
Matched control sample: GSM204660: LIVER_vehicle_NA_1days_control_NA_83833
Matched control sample: GSM204766: LIVER_vehicle_NA_3days_control_NA_83835
Matched control sample: GSM204844: LIVER_vehicle_NA_5days_control_NA_83838
Matched control sample: GSM204659: LIVER_vehicle_NA_1days_control_NA_83978
Matched control sample: GSM204781: LIVER_vehicle_NA_3days_control_NA_83980
Matched control sample: GSM204741: LIVER_vehicle_NA_3days_control_NA_83982
Matched control sample: GSM204806: LIVER_vehicle_NA_5days_control_NA_83983
Matched control sample: GSM204852: LIVER_vehicle_NA_5days_control_NA_83985
Matched control sample: GSM204873: LIVER_vehicle_NA_5days_control_NA_84149
Matched control sample: GSM204648: LIVER_vehicle_NA_1days_control_NA_84194
Matched control sample: GSM204703: LIVER_vehicle_NA_1days_control_NA_84196
Matched control sample: GSM204758: LIVER_vehicle_NA_3days_control_NA_84198
Matched control sample: GSM204836: LIVER_vehicle_NA_5days_control_NA_84201
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, TRICHLOROACETIC ACID, 474mg/kg, 5 days

value: TRICHLOROACETIC ACID

value: 474 mg/kg

value: SUBCUTANEOUS


title: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep3_88542

description:
HybID: 88542
treated sample for experiment (RepID) 6885
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM205108: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep2_88543
Replicate experimental sample: GSM205107: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep1_88544
Matched control sample: GSM204754: LIVER_vehicle_NA_3days_control_NA_87504
Matched control sample: GSM204694: LIVER_vehicle_NA_1days_control_NA_87505
Matched control sample: GSM204807: LIVER_vehicle_NA_5days_control_NA_87510
Matched control sample: GSM204654: LIVER_vehicle_NA_1days_control_NA_87511
Matched control sample: GSM204596: LIVER_vehicle_NA_.25days_control_NA_87569
Matched control sample: GSM204789: LIVER_vehicle_NA_3days_control_NA_87570
Matched control sample: GSM204804: LIVER_vehicle_NA_5days_control_NA_87575
Matched control sample: GSM204650: LIVER_vehicle_NA_1days_control_NA_87638
Matched control sample: GSM204632: LIVER_vehicle_NA_.25days_control_NA_87642
Matched control sample: GSM204728: LIVER_vehicle_NA_3days_control_NA_87780
Matched control sample: GSM204623: LIVER_vehicle_NA_.25days_control_NA_87869
Matched control sample: GSM204633: LIVER_vehicle_NA_.25days_control_NA_87871
Matched control sample: GSM204639: LIVER_vehicle_NA_1days_control_NA_88484
Matched control sample: GSM204711: LIVER_vehicle_NA_1days_control_NA_88486
Matched control sample: GSM204765: LIVER_vehicle_NA_3days_control_NA_88488
Matched control sample: GSM204821: LIVER_vehicle_NA_5days_control_NA_88490
Matched control sample: GSM204607: LIVER_vehicle_NA_.25days_control_NA_88604
Matched control sample: GSM204649: LIVER_vehicle_NA_1days_control_NA_88607
Matched control sample: GSM204833: LIVER_vehicle_NA_5days_control_NA_88609
Matched control sample: GSM204867: LIVER_vehicle_NA_5days_control_NA_88611
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: 6 to 8 weeks

value: male

value: LIVER


title: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep1_88544

description:
HybID: 88544
treated sample for experiment (RepID) 6885
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM205109: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep3_88542
Replicate experimental sample: GSM205108: LIVER_TROGLITAZONE_1200mg/kg_5days_exp6885_rep2_88543
Matched control sample: GSM204754: LIVER_vehicle_NA_3days_control_NA_87504
Matched control sample: GSM204694: LIVER_vehicle_NA_1days_control_NA_87505
Matched control sample: GSM204807: LIVER_vehicle_NA_5days_control_NA_87510
Matched control sample: GSM204654: LIVER_vehicle_NA_1days_control_NA_87511
Matched control sample: GSM204596: LIVER_vehicle_NA_.25days_control_NA_87569
Matched control sample: GSM204789: LIVER_vehicle_NA_3days_control_NA_87570
Matched control sample: GSM204804: LIVER_vehicle_NA_5days_control_NA_87575
Matched control sample: GSM204650: LIVER_vehicle_NA_1days_control_NA_87638
Matched control sample: GSM204632: LIVER_vehicle_NA_.25days_control_NA_87642
Matched control sample: GSM204728: LIVER_vehicle_NA_3days_control_NA_87780
Matched control sample: GSM204623: LIVER_vehicle_NA_.25days_control_NA_87869
Matched control sample: GSM204633: LIVER_vehicle_NA_.25days_control_NA_87871
Matched control sample: GSM204639: LIVER_vehicle_NA_1days_control_NA_88484
Matched control sample: GSM204711: LIVER_vehicle_NA_1days_control_NA_88486
Matched control sample: GSM204765: LIVER_vehicle_NA_3days_control_NA_88488
Matched control sample: GSM204821: LIVER_vehicle_NA_5days_control_NA_88490
Matched control sample: GSM204607: LIVER_vehicle_NA_.25days_control_NA_88604
Matched control sample: GSM204649: LIVER_vehicle_NA_1days_control_NA_88607
Matched control sample: GSM204833: LIVER_vehicle_NA_5days_control_NA_88609
Matched control sample: GSM204867: LIVER_vehicle_NA_5days_control_NA_88611
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: ORAL GAVAGE


title: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep2_85928

description:
HybID: 85928
treated sample for experiment (RepID) 6143
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM205124: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep3_85927
Replicate experimental sample: GSM205122: LIVER_VINBLASTINE_.3mg/kg_5days_exp6143_rep1_85929
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: DAILY


title: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep1_83950

description:
HybID: 83950
treated sample for experiment (RepID) 5568
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM205105: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep2_83951
Replicate experimental sample: GSM205106: LIVER_TRICHLOROACETIC_ACID_474mg/kg_5days_exp5568_rep3_83952
Matched control sample: GSM204850: LIVER_vehicle_NA_5days_control_NA_83512
Matched control sample: GSM204828: LIVER_vehicle_NA_5days_control_NA_83673
Matched control sample: GSM204674: LIVER_vehicle_NA_1days_control_NA_83735
Matched control sample: GSM204784: LIVER_vehicle_NA_3days_control_NA_83737
Matched control sample: GSM204724: LIVER_vehicle_NA_3days_control_NA_83739
Matched control sample: GSM204843: LIVER_vehicle_NA_5days_control_NA_83741
Matched control sample: GSM204700: LIVER_vehicle_NA_1days_control_NA_83831
Matched control sample: GSM204660: LIVER_vehicle_NA_1days_control_NA_83833
Matched control sample: GSM204766: LIVER_vehicle_NA_3days_control_NA_83835
Matched control sample: GSM204844: LIVER_vehicle_NA_5days_control_NA_83838
Matched control sample: GSM204659: LIVER_vehicle_NA_1days_control_NA_83978
Matched control sample: GSM204781: LIVER_vehicle_NA_3days_control_NA_83980
Matched control sample: GSM204741: LIVER_vehicle_NA_3days_control_NA_83982
Matched control sample: GSM204806: LIVER_vehicle_NA_5days_control_NA_83983
Matched control sample: GSM204852: LIVER_vehicle_NA_5days_control_NA_83985
Matched control sample: GSM204873: LIVER_vehicle_NA_5days_control_NA_84149
Matched control sample: GSM204648: LIVER_vehicle_NA_1days_control_NA_84194
Matched control sample: GSM204703: LIVER_vehicle_NA_1days_control_NA_84196
Matched control sample: GSM204758: LIVER_vehicle_NA_3days_control_NA_84198
Matched control sample: GSM204836: LIVER_vehicle_NA_5days_control_NA_84201
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: 5 days


title: LIVER_THIOACETAMIDE_200mg/kg_5days_exp6941_rep1_88745

description:
HybID: 88745
treated sample for experiment (RepID) 6941
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM205084: LIVER_THIOACETAMIDE_200mg/kg_5days_exp6941_rep2_88744
Replicate experimental sample: GSM205085: LIVER_THIOACETAMIDE_200mg/kg_5days_exp6941_rep3_88755
Matched control sample: GSM204686: LIVER_vehicle_NA_1days_control_NA_88722
Matched control sample: GSM204845: LIVER_vehicle_NA_5days_control_NA_88763
Matched control sample: GSM204696: LIVER_vehicle_NA_1days_control_NA_89140
Matched control sample: GSM204651: LIVER_vehicle_NA_1days_control_NA_89142
Matched control sample: GSM204800: LIVER_vehicle_NA_4days_control_NA_89144
Matched control sample: GSM204797: LIVER_vehicle_NA_4days_control_NA_89146
Matched control sample: GSM204635: LIVER_vehicle_NA_0days_control_NA_89148
Matched control sample: GSM204634: LIVER_vehicle_NA_0days_control_NA_89150
Matched control sample: GSM204722: LIVER_vehicle_NA_30days_control_NA_89231
Matched control sample: GSM204798: LIVER_vehicle_NA_4days_control_NA_89446
Matched control sample: GSM204875: LIVER_vehicle_NA_6days_control_NA_89484
Matched control sample: GSM204876: LIVER_vehicle_NA_6days_control_NA_89516
Matched control sample: GSM204799: LIVER_vehicle_NA_4days_control_NA_89522
Matched control sample: GSM204707: LIVER_vehicle_NA_1days_control_NA_89555
Matched control sample: GSM204670: LIVER_vehicle_NA_1days_control_NA_89557
Matched control sample: GSM204667: LIVER_vehicle_NA_1days_control_NA_89706
Matched control sample: GSM204769: LIVER_vehicle_NA_3days_control_NA_89709
Matched control sample: GSM204824: LIVER_vehicle_NA_5days_control_NA_89713
Matched control sample: GSM204879: LIVER_vehicle_NA_7days_control_NA_89818
Matched control sample: GSM204764: LIVER_vehicle_NA_3days_control_NA_89852
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, THIOACETAMIDE, 200mg/kg, 5 days

value: THIOACETAMIDE

value: 200 mg/kg

value: INTRAPERITONEAL


title: Embryo - Plumule - 12hr post imbibition Replicate 3

description: Biological replicate 3 of 4. We printed our oligos onto two slides and the same sample was hybridized onto both slides. The Sample data tables contain merged normalized data from both slides.

source_name: Amplified RNA from rice suspension cultured cells (green).

value: Nipponbare

tag: cell type

value: Undifferentiated rice suspension cultured cells

value: embryo plumule from germinated seeds (12h post-imbibition).