title: LCMV-Clone 13 spleen day 9, rep2

description:
5219
Gene expression data from spleens harvested at day 9, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Clone 13-infected_spleen harvested on day 9

value: day 9


title: LCMV-Clone 13 spleen day 9, rep3

status: Public on Feb 15 2013

type: RNA

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
5220
Gene expression data from spleens harvested at day 9, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks

hyb_protocol: Affymetrix Mouse Genes ST 1.0 microarray

scan_protocol: Affymetrix Expression Console

data_processing:
Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.
Relative expression levels for each probeset were calculated by normalization to the median value for all uninfected samples

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Ambion WT labeling kit

growth_protocol: Six-ten week old mice were used for all experiments, and were housed under pathogen-free conditions.

extract_protocol: Harvested spleens were frozen in RNA Later (Qiagen) at 1 mg/ml tissue.  Whole spleens were homogenized, and RNA from homogenates were isolated with Rneasy extraction kit (Qiagen).

treatment_protocol: Mice were infected intravenously via the retro-orbital sinus with 2x10^6 plaque forming unites of LCMV-Armstrong or LCMV-Clone 13.

tag: strain

tag: age

value: 6-10 weeks

tag: infected with

value: LCMV clone 13

tag: tissue

value: spleen

tag: harvest time point


title: LCMV-Clone 13 spleen day 9, rep4

description:
5221
Gene expression data from spleens harvested at day 9, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: LCMV-Clone 13 spleen day 30, rep1

description:
5234
Gene expression data from spleens harvested at day 30, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Clone 13-infected_spleen harvested on day 30

value: day 30


title: LCMV-Clone 13 spleen day 9, rep1

description:
5218
Gene expression data from spleens harvested at day 9, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: WT RNA pooled from embryonic murine limb tissue

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from murine wildtype pooled fore- and hindlimbs at stage E12.5.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of mouse430_2 -type from Affymetrix. A Custom CDF Version 11 with UniGene-based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: E12.5 pooled fore- and hindlimb tissue, WT

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

growth_protocol: Murine embryonic fore- and hindlimb tissue was dissected at stage E12.5.

extract_protocol: For total RNA isolation by TRIzol® (Invitrogen), samples from embryonic limbs (E12.5) of the same genotype (wildtype and Shox2-/-) were pooled. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue was stored at -80°C until RNA preparation.

tag: genotype/variation

value: WT

value: forelimbs and hindlimbs


title: 4177L1_resistant

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: SAMPLE 3

hyb_protocol: 1650ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 4x180K Custom Microarray (Design ID 032034 )

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour GEand 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.5.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities

organism: Homo sapiens

source_name: LNCaP derived xenograft_resistant

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: Cell Culture. Cultured LNCaP cells (derived from the lymph node metastasis of a prostate cancer patient), passage 35–45, were maintained in RPMI 1640 with 5% FCS at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated using the mirVana™ miRNA Isolation Kit (Ambion AM1560)

tag: cell type origin

value: Cultured LNCaP cells

value: LNCaP derived xenograft

tag: harvest time point (along the psa curve)

value: resistant


title: 21.5Mxmau12M

city: Bloomington

first: Colin

middle: D

last: Meiklejohn

state: IN

address: Jordan Hall, 1001 E. 3rd St.

department: Biology Department

institute: Indiana University

hyb_protocol: Hybridization was done using the 3DNA Array50 kit following the manufacturer's protocols

scan_protocol: Slides were scanned in an Axon 4000B scanner and microarray images were processed with GenePix v5.0

data_processing: Spots were filtered using the following quality control criteria: 70% of the foreground pixels within a spot were required to have a signal intensity higher than two standard deviations above the median background signal intensity in at least one of the two channels (Cy3 or Cy5); the median foreground signal intensity was required to be at least three times as great as the median background signal intensity in at least one of the two channels; a spot must have more than 30 foreground pixels.  Spot-wise log2 ratios were normalized over overall spot signal intensity by loess smoothing using a span of 0.3.  To account for spatial variation in signal across arrays, spot-wise log2 ratios were subsequently normalized by a second loess smoothing over the physical location of the spots on the slide, using a span of 0.002, which corresponds to an effective neighborhood of ~ 250 spots.

molecule: polyA RNA

organism: Drosophila simulans

source_name: whole adult flies

label_protocol: At least 20μg total RNA was used as a template for cDNA synthesis and incorporation of fluorescent dyes was done using the 3DNA Array50 kit following the manufacturer’s protocols

growth_protocol: Flies were reared in three independent cohorts on standard media  at 25C on a 12:12 light:dark cycle.  Culture density was controlled by combining 15 parental males with 15 females per vial for homozygous introgression genotypes, and 10 males with 10 females for the simB, mau12, and heterozygous introgression genotypes.

extract_protocol: RNA was extracted from frozen flies using TRIzol, chloroform and phase-lock gel tubes

treatment_protocol: Adults were collected as virgins and the sexes were aged separately for 1-2 days before flash-freezing in liquid nitrogen and storage at -80C at the same time of day

tag: Sex

value: male

value: whole organism


title: 15.6Mxs21.5M


title: S.Erasmo_April_DigestiveGland_POOL3

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Pool consisting of 5 digestive gland

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Ruditapes philippinarum

source_name: Pool of Ruditapes philippinarum digestive gland sampled in S.Erasmo (Venice Lagoon) in April

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: digestive gland


title: S.Erasmo_April_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: cAMP-treated NCI-H295A cells, sample 1

city: San Francisco

last: Tee

address: HSE1401, 513 Parnassus Ave

institute: UCSF

description: NCI-H295A cells treated with 1 mM cAMP.

hyb_protocol: The chips were stained and washed using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using a GCS 3000 scanner with auto-loader in the Genomics Core laboratory.

data_processing: Hybridization intensity signals from the scanned images were analyzed using Affymetrix GeneChip Operating Software (GCOS, version 1.3) to provide qualitative detection calls and quantitative estimates of gene expression levels (signal values).

source_name: cell line

label_protocol: 4 μg RNA was used to synthesize double-stranded cDNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX) with oligo-dT primer [5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24] to incorporate a T7 RNA polymerase promoter. Antisense cRNA was labeled with biotin-UTP using T7 RNA polymerase (Ambion), and the cRNA was fragmented to 35–200 nucleotides (nt) at 94 C for 35 min in 40 μl 40 mm Tris-acetate (pH 8.1), 100 mm KOAc, 30 mm MgOAc. The integrities of total RNAs, cRNAs, and fragmented cRNAs were assessed on a Bio-Rad (Hercules, CA) Experion BioAnalyzer.

growth_protocol: NCI-H295A adrenocortical cells were grown on 10-cm plates in RPMI 1640 with 2% fetal calf serum, gentamicin, insulin, and selenium. Three nearly confluent plates were incubated in the presence and absence of 1 mm 8-Br-cAMP for 18 h; the cells were washed with PBS and lysed with 1 ml Trizol (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was purified further using RNeasy columns (QIAGEN, Valencia, CA).

treatment_protocol: NCI-H295A cells were treated with 1 mM 8-Br-cAMP for 18 h.

tag: treatment

value: 1 mM cAMP

tag: cell line


title: LCMV-Clone 13 spleen day 5, rep3

description:
5213A
Gene expression data from spleens harvested at day 5, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Clone 13-infected_spleen harvested on day 5

value: day 5


title: LCMV-Clone 13 spleen day 5, rep2

description:
5212A
Gene expression data from spleens harvested at day 5, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: LCMV-Armstrong spleen day 30, rep4

description:
5233
Gene expression data from spleens harvested at day 30, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Armstrong-infected_spleen harvested on day 30

value: LCMV Armstrong


title: LCMV-Armstrong spleen day 30, rep2

description:
5231
Gene expression data from spleens harvested at day 30, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: LCMV-Clone 13 spleen day 5, rep1

description:
5211A
Gene expression data from spleens harvested at day 5, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: S.Erasmo_April_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: S.Erasmo_April_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: LCMV-Armstrong spleen day 9, rep2

description:
5215
Gene expression data from spleens harvested at day 9, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Armstrong-infected_spleen harvested on day 9


title: Chioggia_December_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Chioggia (Venice Lagoon) in December


title: Chioggia_December_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: s16.25Mx21.10M


title: 15.6MxsimBM

value: simB


title: LCMV-Armstrong spleen day 9, rep1

description:
5214
Gene expression data from spleens harvested at day 9, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks

value: day 9


title: LCMV-Armstrong spleen day 5, rep3

description:
5210A
Gene expression data from spleens harvested at day 5, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks

source_name: LCMV-Armstrong-infected_spleen harvested on day 5

value: 6-10 weeks


title: LCMV-Armstrong spleen day 30, rep3

description:
5232
Gene expression data from spleens harvested at day 30, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: Chioggia_December_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Chioggia_September_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Chioggia (Venice Lagoon) in September


title: Chioggia_December_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: LCMV-Armstrong spleen day 9, rep4

description:
5217
Gene expression data from spleens harvested at day 9, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: 16.25Mx18.19M


title: LCMV-Armstrong spleen day 30, rep1

description:
5230
Gene expression data from spleens harvested at day 30, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: LCMV-Armstrong spleen day 9, rep3

description:
5216
Gene expression data from spleens harvested at day 9, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: LCMV-Armstrong spleen day 5, rep2

description:
5209A
Gene expression data from spleens harvested at day 5, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: s16.12Mx16.12M


title: s18.19Mxs16.25M


title: 21.5Mx20.9M


title: LCMV-Armstrong spleen day 5, rep1

description:
5208A
Gene expression data from spleens harvested at day 5, from LCMV-Armstrong infected C57BL7 mice aged 6-10 weeks


title: Uninfected spleen, day 0, rep3

description:
N3A
Gene expression data from spleens harvested at day 0, from uninfected C57BL7 mice aged 6-10 weeks

source_name: uninfected_spleen harvested on day 0

value: none (uninfected control)

value: day 0


title: Uninfected spleen, day 0, rep4

description:
N4A
Gene expression data from spleens harvested at day 0, from uninfected C57BL7 mice aged 6-10 weeks

value: spleen


title: mau12Mx16.12M

organism: Drosophila mauritiana


title: Chioggia_September_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: Chioggia_September_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Uninfected spleen, day 0, rep1

description:
N1A
Gene expression data from spleens harvested at day 0, from uninfected C57BL7 mice aged 6-10 weeks


title: Uninfected spleen, day 0, rep2

description:
N2A
Gene expression data from spleens harvested at day 0, from uninfected C57BL7 mice aged 6-10 weeks


title: s21.5Mx21.5M


title: Chioggia_September_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Chioggia_June_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Chioggia (Venice Lagoon) in June


title: s21.10Mxs20.9M


title: s20.9Mxs21.5M


title: simBMxmau12M


title: Chioggia_June_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: PGK12.1_MOF&MSL1 RNAi_E

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: Single-RNAi experiment 8 in PGK12.1.

hyb_protocol: Hybridization and washing were performed according to the standard Affymetrix protocol.

scan_protocol: Array hybridizations were done at the Microarray Facility at CHDD (University of Washington, Seattle WA).

data_processing: Raw data files from paired RNAi experiments were analyzed with Affymetrix® Expression Console™ Software using the RMA gene default.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of MOF and MSL1 siRNAs.

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

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for RNAi experiments and cell collection.

extract_protocol: Total RNA was prepared by the Qiagen RNeasy kit with on-column DNaseI digestion

treatment_protocol: 100pmol of gene-specific siRNAs or negative control siRNAs (Invitrogen Stealth or Silencer control) were transfected into 2x105 ES or MEF cells in six-well plates using a standard reverse transfection protocol with Lipofectamine RNAiMax (Invitrogen). For co-transfection, 100pmol of Mof siRNAs and 50 pmol of Msl1 siRNAs were used. Cells were harvested after 48h of RNAi treatment. For the double RNAi knockdown of MOF, after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest.

value: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: cell type

value: PGK12.1 ES cell line

tag: passage


title: WD44_control RNAi-2

description: Single-RNAi experiment 2 in WD44. MOF RNAi experiment-2 in WD44.

source_name: Mouse male ES cells WD44 after single RNAi treatment of negative control siRNAs.

value: Derived from BL6 blastcysts.

value: WD44 ES cell line


title: E14_MOF RNAi-2

description: Single-RNAi experiment 2 in E14. MOF RNAi experiment-2 in E14.

source_name: Mouse male ES cells E14 after single RNAi treatment of MOF siRNAs.

value: Derived from blastcysts from a BL6 female crossed to a Cast. male.

value: E14 hybrid ES cell line (Cast/BL6)

value: single RNAi treatment of MOF siRNA


title: Chioggia_June_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland

value: digestive gland


title: 20.9Mxs20.9M

value: male

value: whole organism


title: WD44_MOF RNAi-1

description: Single-RNAi experiment 1 in WD44. MOF RNAi experiment-1 in WD44.

source_name: Mouse male ES cells WD44 after single RNAi treatment of MOF siRNAs.


title: E14_control RNAi-2

source_name: Mouse male ES cells E14 after single RNAi treatment of negative control siRNAs.


title: Chioggia_June_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: WD44_MOF RNAi-2


title: E14_MOF RNAi-1

description: Single-RNAi experiment 1 in E14. MOF RNAi experiment-1 in E14.


title: WD44_control RNAi-1

value: single RNAi treatment of negative control siRNA


title: E14_control RNAi-1


title: PGK12.1_NSL1 RNAi_E

description: Single-RNAi experiment 8 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of NSL1 siRNAs.

value: single RNAi treatment of NSL1 siRNA


title: 21.10Mxs21.10M

source_name: whole adult flies


title: s16.25Mxs21.10M


title: Chioggia_April_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Chioggia (Venice Lagoon) in April


title: Chioggia_April_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: s15.6Mx15.6M


title: PGK12.1_NSL1 RNAi_D

description: Single-RNAi experiment 7 in PGK12.1.


title: PGK12.1_MOF&MSL1 RNAi_D

description: Single-RNAi experiment 7 in PGK12.1.

value: single RNAi treatment of MOF and MSL1 siRNAs


title: PGK12.1_Control-E

description: Single-RNAi experiment 8 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of negative control siRNAs.


title: 16.12Mx15.6M


title: PGK12.1_NSL1 RNAi_C

description: Single-RNAi experiment 6 in PGK12.1.


title: Chioggia_April_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: PGK12.1_MSL1 RNAi_C

description: Single-RNAi experiment 6 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of MSL1 siRNAs.

value: single RNAi treatment of MSL1 siRNA


title: PGK12.1_Control-A

description: Single-RNAi experiment 4 in PGK12.1.


title: s21.10Mx20.9M


title: s16.12Mxs18.19M


title: PGK12.1_MSL1 RNAi_A

description: Single-RNAi experiment 4 in PGK12.1.


title: PGK12.1_MSL1 RNAi_B

description: Single-RNAi experiment 5 in PGK12.1.


title: PGK12.1_Control-B

description: Single-RNAi experiment 5 in PGK12.1.


title: Alberoni_December_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Alberoni (Venice Lagoon) in December


title: PGK12.1_Control-C

description: Single-RNAi experiment 6 in PGK12.1.


title: Alberoni_December_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: PGK12.1_Control-D

description: Single-RNAi experiment 7 in PGK12.1.


title: PGK12.1_control RNAi-3

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). MOF single-RNAi experiment 3 in PGK12.1.


title: s21.5Mxs15.6M


title: 16.25Mxs16.25M


title: PGK12.1_MOF RNAi-2

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of MOF siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. MOF double-RNAi experiment-2 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of MOF siRNAs.

value: double RNAi treatment of MOF siRNA


title: PGK12.1_MOF RNAi-3

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of MOF siRNAs. MOF single-RNAi experiment 3 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after single RNAi treatment of MOF siRNAs.


title: 21.10MxsimB

value: simB


title: s20.9Mx21.5M


title: Alberoni_September_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Alberoni (Venice Lagoon) in September


title: Alberoni_December_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: PGK12.1_control RNAi-1

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. MOF double-RNAi experiment-1 in PGK12.1.

source_name: Mouse female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs.


title: PGK12.1_MOF RNAi-1

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of MOF siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. MOF double-RNAi experiment-1 in PGK12.1.


title: Alberoni_December_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: s15.6Mxs16.12M


title: PGK12.1_control RNAi-2

description: Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. MOF double-RNAi experiment-2 in PGK12.1.


title: CD4+ T cells of Donor # 56 at day6

city: Bethesda

first: Luciano

last: Castiello

state: Maryland

address: 10 Center Drive

department: DTM

institute: NIH/CC

description: CD4+ T cells of Donor # 56 at day6

hyb_protocol: Samples were hybridized according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used with dafault settings for processed signals

source_name: CD4+ T cells of Donor # 56 at day6

label_protocol: Test RNA and Universal Reference RNA (Stratagene Catalog #740000) were amplified and labeled according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

growth_protocol: Thawed CD4+ cells were cultured in in X-VIVO 20 media with 5% heat inactivated human AB plasma, IL-4 (1,000 IU/ mL), IL-2 (20 IU/mL), Rapamycin (1 uM) and tosylactivated paramagnetic M-450 beads coated with anti-CD3 (OKT3) and anti-CD28 (clone 9.3) at a ratio of 3 beads per cell for 6 days

extract_protocol: Total RNA extracted using miRNeasy kit from Qiagen

value: CD4+ T cells

tag: donor

tag: day

source_name: Universal Human Reference RNA

tag: origin

value: Stratagene Catalog #740000


title: 20.9Mx21.10M


title: CD4+ T cells of Donor # 51 at day6

description: CD4+ T cells of Donor # 51 at day6

source_name: CD4+ T cells of Donor # 51 at day6


title: Alberoni_September_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Alberoni_September_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: s18.19Mx16.25M


title: CD4+ T cells of Donor # 51 at day12

description:
Raw data file:
US45103062_251485059428_S01_GE2-v5_95_Feb07_1_2.txt.txt
CD4+ T cells of Donor # 51 at day12

source_name: CD4+ T cells of Donor # 51 at day 12

label_protocol: Test RNA and Universal Reference RNA were amplified and labeled according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

growth_protocol: Thawed CD4+ cells were cultured in in X-VIVO 20 media with 5% heat inactivated human AB plasma, IL-4 (1,000 IU/ mL), IL-2 (20 IU/mL), Rapamycin (1 uM) and tosylactivated paramagnetic M-450 beads coated with anti-CD3 (OKT3) and anti-CD28 (clone 9.3) at a ratio of 3 beads per cell for 12 days

tag: culture protocol

value: IL-2, IL-4, Rapamycin

tag: time

value: day 12

tag: reference


title: 16.12Mxs15.6M

tag: strain


title: CD4+ T cells of Donor # 55 at day6

description: CD4+ T cells of Donor # 55 at day6

source_name: CD4+ T cells of Donor # 55 at day6


title: CD4+ T cells of Donor # 56 at day12

description:
Raw data file:
US45103062_251485060054_S01_GE2-v5_95_Feb07_1_3.txt.txt
CD4+ T cells of Donor # 56 at day12

source_name: CD4+ T cells of Donor # 56 at day 12


title: CD4+ T cells of Donor # 50 at day6

description: CD4+ T cells of Donor # 50 at day6

source_name: CD4+ T cells of Donor # 50 at day6


title: Alberoni_September_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

tag: tissue


title: Alberoni_June_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Alberoni (Venice Lagoon) in June


title: CD4+ T cells of Donor # 57 at day6

description: CD4+ T cells of Donor # 57 at day6

source_name: CD4+ T cells of Donor # 57 at day6


title: CD4+ T cells of Donor # 59 at day12

description:
Raw data file:
US45103062_251485060054_S01_GE2-v5_95_Feb07_1_4.txt.txt
CD4+ T cells of Donor # 59 at day12

source_name: CD4+ T cells of Donor # 59 at day 12


title: 15.6FxsimBF

source_name: whole adult flies

value: female


title: simBFx18.19F


title: CD4+ T cells of Donor # 55 at day12

description:
Raw data file:
US45103062_251485060054_S01_GE2-v5_95_Feb07_1_2.txt.txt
CD4+ T cells of Donor # 55 at day12

source_name: CD4+ T cells of Donor # 55 at day 12


title: CD4+ T cells of Donor # 51 at day0

description:
Raw data file:
US45103062_251485055220_S01_GE2-v5_95_Feb07_1_3.txt.txt
CD4+ T cells of Donor # 51 at day0

source_name: CD4+ T cells of Donor # 51 at day 0

value: control

value: day 0


title: CD4+ T cells of Donor # 49 at day6

description: CD4+ T cells of Donor # 49 at day6

source_name: CD4+ T cells of Donor # 49 at day6


title: CD4+ T cells of Donor # 49 at day12

description:
Raw data file:
US45103062_251485060051_S01_GE2-v5_95_Feb07_1_1.txt.txt
CD4+ T cells of Donor # 49 at day12

source_name: CD4+ T cells of Donor # 49 at day 12


title: Alberoni_June_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Alberoni_June_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: CD4+ T cells of Donor # 50 at day12

description:
Raw data file:
US45103062_251485060051_S01_GE2-v5_95_Feb07_1_2.txt.txt
CD4+ T cells of Donor # 50 at day12

source_name: CD4+ T cells of Donor # 50 at day 12


title: CD4+ T cells of Donor # 50 at day0

description:
Raw data file:
US45103062_251485055220_S01_GE2-v5_95_Feb07_1_2.txt.txt
CD4+ T cells of Donor # 50 at day0

source_name: CD4+ T cells of Donor # 50 at day 0


title: Alberoni_June_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: Alberoni_April_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Alberoni (Venice Lagoon) in April


title: CD4+ T cells of Donor # 55 at day0

description:
Raw data file:
US45103062_251485060055_S01_GE2-v5_95_Feb07_1_1.txt.txt
CD4+ T cells of Donor # 55 at day0

source_name: CD4+ T cells of Donor # 55 at day 0

source_name: Universal Human Reference RNA


title: Alberoni_April_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: 20.9Fx21.10F


title: simBFxmau12F


title: mau12Fx16.25F


title: CD4+ T cells of Donor # 56 at day0

description:
Raw data file:
US45103062_251485060055_S01_GE2-v5_95_Feb07_1_2.txt.txt
CD4+ T cells of Donor # 56 at day0

source_name: CD4+ T cells of Donor # 56 at day 0


title: s21.10Fx20.9F


title: CD4+ T cells of Donor # 57 at day0

description:
Raw data file:
US45103062_251485060051_S01_GE2-v5_95_Feb07_1_4.txt.txt
CD4+ T cells of Donor # 57 at day0

source_name: CD4+ T cells of Donor # 57 at day 0


title: Alberoni_April_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Alberoni_April_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Rice ovule stage E6 rep4

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

country: Japan

institute: National Institute of Genetics

description: Gene expression data in developing rice ovule

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 600 - 800 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent) using manufacturer's default extraction protocol named 'GE1-v5_95_Feb07'. The text data files produced by FeatureExtraction were introduced into GeneSpring 7.3.1, then the introduced signal intensities (gProcessedSignal) were scaled to the 75th percentile per chip (scaled the 75th percentile value was set to 10), and the lowest value of scaled signal intensity was set to 0.01.

organism: Oryza sativa

source_name: Rice ovule, mature stage

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Quick Amp Labeling Kit (Agilent) in accordance with the manufacturer's protocol with slight modification. The cDNA synthesis reaction time was extended to 6 hrs.

growth_protocol: Wild-type rice plants (Oryza sativa L. cv. Nipponbare) were grown in paddy field under natural conditions at Mishima, Japan in the summer of 2009.

extract_protocol: Total RNA was extracted from 50 - 150 pieces of microdissected ovules with a PicoPure™ RNA isolation kit (Life Technologies) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA quantity was determined by the Quant-iT™ RiboGreen® RNA Assay Kit (Life Technologies).

treatment_protocol: Collected pistil samples were fixed in acetone overnight at 4 degree. Sections of 10 µm thickness were cut from paraffin-embedded samples and mounted on PEN membrane class slides (Life Technologies, Carlsbad, CA), then ovules were isolated using the Veritas Laser Microdissection System LCC1704 (Molecular Devices, Ontario, Canada).

tag: subspecies

value: japonica

tag: cultivar

value: Nipponbare

tag: developmental stage

value: mature

value: ovule


title: CD4+ T cells of Donor # 49 at day0

description:
Raw data file:
US45103062_251485055220_S01_GE2-v5_95_Feb07_1_1.txt.txt
CD4+ T cells of Donor # 49 at day0

source_name: CD4+ T cells of Donor # 49 at day 0


title: Rice ovule stage E6 rep3


title: Rice ovule stage E6 rep1


title: 21.5Fx20.9F

value: whole organism


title: Rice ovule stage E6 rep2


title: s21.10Fxs20.9F


title: 21.10FxsimBF


title: Rice ovule stage E5 rep3

source_name: Rice ovule, bi - eightnuclear cell stage

value: bi - eightnuclear


title: 16.25Fx18.19F


title: 16.12Fx15.6F


title: s16.12Fxs18.19F


title: 18.19Mxs16.12M

value: male


title: mau12Fx16.12F


title: 16.25Fxs16.25F


title: Rice ovule stage E5 rep2


title: s21.5Fx21.5F


title: s21.5Fxs15.6F


title: Rice ovule stage E3 rep3

source_name: Rice ovule, diplotene - tetrad stages

value: diplotene - tetrad


title: Rice ovule stage E5 rep1


title: Rice ovule stage E4 rep3

source_name: Rice ovule, mononuclear cell stage

value: mononuclear


title: Chioggia_April_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Chioggia (Venice Lagoon) in April

value: digestive gland


title: Rice ovule stage E4 rep2


title: Rice ovule stage E4 rep1


title: 21.5Fxmau12F

source_name: whole adult flies


title: Rice ovule stage E3 rep1


title: Rice ovule stage E3 rep2


title: Cultured adipocytes, Day 4, bio rep 1

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: Gene expresssion data from differentiated mouse pre-adipocytes

hyb_protocol: Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization on a custom designed GeneChip® Mouse 430 2.0 (PN 900496). The washing and staining were performed on the GeneChip® Fluidics Station

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays.

data_processing: R/Bioconductor, MAS5.0 background corrected, quantile normalized, pmonly & avgdiff probset summarization

source_name: Cultured adipocytes, Day 4

label_protocol: In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate.

growth_protocol: White pre-adipocytes are isolated from subcutaneous fat pat from young mice (2 weeks old). After collagenase digestion and fractionation, pre-adipocytes,enriched in bottom stromal vascular fraction (VSC)s, are resuspended and cultured to confluence in DMEM supplemented with 10% New-born Bovine Serum.  The cells arethen exposed to differentiation medium: 10%FBS DMEM, Insulin 850nM (Sigma), Dexamethasone 0.5uM (Sigma), IBMX 250uM (Sigma), Rosiglitazone 1uM (Cayman Chemical). After 2 days, cells are incubated in culture medium containing insulin 160nM for another 2 days, and then are switched to 10% FBS DMEM.

extract_protocol: Total RNA from the samples was extracted via the MiRNeasy kit (Qiagen) according to manufacturer's instructions and normalized to 50 ng/ul. The GeneChip® 3’ IVT Express Protocol was used for amplification in a semi automated process. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription.

tag: sample type

value: Cultured white pre-adipocytes+differentiation medium

value: differentiated cultured white pre-adipocytes


title: Cultured adipocytes, Day 4, bio rep 2


title: Rice ovule stage E2 rep3

source_name: Rice ovule, zygotene - pachytene stages

value: zygotene - pachytene


title: s18.19Fxs16.25F

tag: Sex


title: 21.10Fxs21.10F


title: Pre-adipocytes, bio rep3

description: Gene expresssion data from mouse pre-adipocytes

source_name: Pre-adipocytes

value: Cultured white pre-adipocytes

value: cultured white pre-adipocytes


title: Rice ovule stage E2 rep1


title: Cultured adipocytes, Day 4, bio rep 3


title: s20.9Fxs21.5F

value: female


title: Pre-adipocytes, bio rep2


title: s16.12Fx16.12F


title: Rice ovule stage E2 rep2


title: Pre-adipocytes, bio rep1


title: Rice ovule stage E1 rep3

source_name: Rice ovule, premeiotic S/G2 - leptotene stages

value: premeiotic S/G2 - leptotene


title: Rice ovule stage E1 rep2

value: japonica


title: s15.6Fx15.6F


title: Scramble siRNA knockdown, bio rep1

source_name: Scramble siRNA knockdown


title: Scramble siRNA knockdown, bio rep2


title: s20.9Fx21.5F


title: 20.9Fxs20.9F


title: s18.19Fx16.25F


title: 16.12Fxs15.6F


title: Rice ovule stage E1 rep1

value: Nipponbare


title: siRNA knockdown of AK136742, bio rep1

source_name: siRNA knockdown of AK136742

tag: knockdown


title: siRNA knockdown of AK161599, bio rep1

source_name: siRNA knockdown of AK161599


title: 18.19Fxs16.12F


title: s16.25Fxs21.10F


title: siRNA knockdown of AK136742, bio rep2


title: ahp2,3,5, well-watered, replicate 1

city: Yokohama

first: Rie

last: Nishiyama

state: Kanagawa

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

department: Plant Science Center

institute: RIKEN

description: Gene expression data from well-watered ahp2,3,5

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

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

data_processing: The scanned images were analyzed with GeneSpring GX11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: ahp2,3,5, well-watered, replicate 1

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

growth_protocol: Two-week-old WT and ahk2,3,5 mutant plants (Columbia ecotype) were transferred from GM plates to soil and grown for an additional week (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The three week-old plants were exposed to drought stress for 10 days or grown under well-watered condition in parallel.

tag: ecotype

value: Columbia

tag: genotype

value: rosette leaves

tag: age

value: 31 day-old

tag: treatment

value: well-watered


title: siRNA knockdown of AK045415, bio rep1

source_name: siRNA knockdown of AK045415

tag: cell type


title: siRNA knockdown of AK045415, bio rep2


title: siRNA knockdown of AK041310, bio rep2

source_name: siRNA knockdown of AK041310


title: 18.19Fxs18.19F

value: whole organism


title: WT, well-watered, replicate 2

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 2

value: wild type


title: s15.6Fxs16.12F


title: WT, well-watered, replicate 3

source_name: WT, well-watered, replicate 3


title: WT, well-watered, replicate 1

source_name: WT, well-watered, replicate 1


title: ahp2,3,5, well-watered, replicate 3

source_name: ahp2,3,5, well-watered, replicate 3


title: siRNA knockdown of AK041310, bio rep1


title: 15.6Fxs21.5F


title: ahp2,3,5, droughted, replicate 3

description: Gene expression data from droughted ahp2,3,5

source_name: ahp2,3,5, droughted, replicate 3

value: droughted


title: ahp2,3,5, well-watered, replicate 2

source_name: ahp2,3,5, well-watered, replicate 2


title: siRNA knockdown of AK040954, bio rep2

source_name: siRNA knockdown of AK040954


title: s16.25Fx21.10F

source_name: whole adult flies


title: siRNA knockdown of AK040027, bio rep2

source_name: siRNA knockdown of AK040027


title: ahp2,3,5, droughted, replicate 2

source_name: ahp2,3,5, droughted, replicate 2


title: siRNA knockdown of AK030946, bio rep1

source_name: siRNA knockdown of AK030946


title: WT, droughted, replicate 3

description: Gene expression data from droughted WT

source_name: WT, droughted, replicate 3


title: iMyc B-lymphoma, biological replicate 6

city: Iowa City

first: Siegfried

last: Janz

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

hyb_protocol: Human:  arrays were washed and stained using the Affymetrix Model 450 Fluidics Station.  Mouse:  biotin-labeled cDNA was mixed with Affymetrix hybridization buffer, added to the array and incubated at 45º C for 18 hrs (60 rpm rotation) in an Affymetrix Model 640 Genechip Hybridization Oven.  Arrays were then washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR) and signal-amplified with anti-streptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Affymetrix Model 3000 scanner

data_processing: Expression values were generated using the Micro Array Suite (MAS) v. 5.0 software within the GeneChip operating software (GCOS) v 1.4.  Array data were imported into Partek GS (v6.3) and normalized as separate batches using default settings for robust multi-averaging (RMA).  Normal and tumor samples were compared using ANOVA.  False discovery rate (FDR) correction relied on default settings for the step-up method in Partek.

source_name: iMyc B-lymphoma

label_protocol: Human:  5 ug total RNA was biotin-labelled using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA).  Mouse:  50 ng total RNA was converted to cDNA, amplified by SPIA using the Ovation RNA Amplification System v2, and purified using a QIAGEN MinElute Reaction Cleanup column according to modifications from NuGEN.  SPIA-amplified cDNA (3.75 ug) was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2.

growth_protocol: Isolated B cells from both mouse and human were flash frozen immediately in liquid nitrogen following magnetic bead separation and prior to RNA extraction.  Mouse tumor samples were collected upon necropsy and immediately flash frozen in liquid nitrogen.  Human tumor samples were OCT-embedded and frozen.  Storage was at -80°C until processed for RNA.

extract_protocol: Tumor tissues were ground in liquid nitrogen with a mortar and pestle just prior to RNA extraction.  RNA extraction for human tissues was done using the PerfectPure RNA Tissue Kit (5 PRIME, Hannover, Germany) according to the manufacturer's instructions, whereas RNA from mouse tissues was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.  Isolated cells were immediately subjected to RNA extraction reagent (respective to isolation method) upon removal from storage.

value: iMyc B-lymphoma

tag: substrain

value: iMycDEm

tag: gender

tag: origin tissue

value: lymph node


title: siRNA knockdown of AK030946, bio rep2

value: Cultured white pre-adipocytes+differentiation medium

value: differentiated cultured white pre-adipocytes


title: ahp2,3,5, droughted, replicate 1

source_name: ahp2,3,5, droughted, replicate 1


title: siRNA knockdown of AK017076, bio rep2

source_name: siRNA knockdown of AK017076


title: iMyc B-lymphoma, biological replicate 5

value: iMycCa


title: iMyc B-lymphoma, biological replicate 3

value: female


title: siRNA knockdown of AK040027, bio rep1


title: JUND_UM_HK_8-mer

type: protein

first: Ishminder

last: Mann

state: MD

address: 9000 Rockville pike

institute: National Cancer Institute, NIH

hyb_protocol: We used 150 ng of plasmid DNA in a 16 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor. After a 2-h incubation at 37oC, 15 ml of the mix was added to 135 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20 and once with PBS/0.01% Triton-X 100. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20 and once with PBS.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

source_name: JUND, HK design

label_protocol: DBD sequences along with 15 amino acid residues on either side of the DBD in the native protein were cloned as NcoI-SacI fragments into a  T7-driven C-terminal GST expression vector (Sharrocks 1994, Gene:138, 105-108).

treatment_protocol: The double stranded arrays were either methylated (M) or unmethylated (UM). The methylation of the double stranded microarray were performed using 10 μl of  M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: dbd

value: BZIP

tag: protein

value: JUND

tag: probe state

value: unmethylated


title: iMyc B-lymphoma, biological replicate 4

tag: strain

value: iMycEm

value: peripheral lymph node


title: iMyc B-lymphoma, biological replicate 7

value: cervical lymph node


title: WT, droughted, replicate 1

description: Gene expression data from droughted WT

source_name: WT, droughted, replicate 1

value: Columbia

tag: tissue

value: rosette leaves

value: 31 day-old


title: iMyc B-lymphoma, biological replicate 2


title: WT, droughted, replicate 2

description: Gene expression data from droughted WT

source_name: WT, droughted, replicate 2

value: wild type

value: droughted


title: donor 5 (AT13)_passage 5

type: genomic

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

description: hybridized to SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: GeneChip Operating Software (GCOS), Genotyping Console v3.0.1, Chromosome Analysis Suite Software (ChAS)

molecule: genomic DNA

source_name: mesenchymal stem cells

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: MSC from adipose tissue (MSC-AT) were isolated from lipoaspirates after written consent according to the guidelines of the Ethics Committee of the University of Aachen (Permit number 163/07). Lipoaspirates were washed in 9 g/L NaCl, digested with 2 g/L collagenase type I (PAA, Pasching, Austria) and passed through a 100 µm cell strainer as described before (Cholewa et al., 2011). Culture medium consisted of Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG; PAA) with 2 mM L-glutamine (Sigma Aldrich, St. Louis, MO, USA), 100 U/mL penicillin/streptomycin (pen/strep; Lonza, Basel, Switzerland) and 10% human platelet lysate (HPL) which was pooled from five platelet units of healthy donors as described before (Horn et al., 2010). Cells were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice per week.

extract_protocol: Genomic DNA of 10(6) MSC was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

treatment_protocol: MSC were always harvested by trypsinisation upon 80% confluent growth, counted with a Neubauer counting chamber (Brand, Wertheim, Germany) and additionally with a CASY cell counter (Schärfe System, Reutlingen, Germany) and re-seeded in a density of 10,000 cells/cm2 in culture flasks (Nunc Thermo Fisher Scientific, Langenselbold, Germany). Different passages were compared as indicated in sample title.

tag: passage


title: donor 10 (AT22)_passage 10

description: hybridized to SNP 6.0


title: donor 8 (AT27)_passage 5

description: hybridized to SNP 6.0


title: JUND_M_HK_8-mer

extract_protocol: We used 150 ng of plasmid DNA in a 16 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor.

value: methylated


title: iMyc B-lymphoma, biological replicate 1

value: iMyc B-lymphoma

value: mesentyric lymph node


title: siRNA knockdown of AK017076, bio rep1

tag: sample type

value: Cultured white pre-adipocytes+differentiation medium

value: differentiated cultured white pre-adipocytes


title: donor 11 (AT26)_passage 5

description: hybridized to SNP 6.0


title: siRNA knockdown of AK016444, bio rep2

source_name: siRNA knockdown of AK016444


title: donor 5 (AT13)_passage 32

description: hybridized to SNP 6.0


title: donor 11 (AT26)_passage 10

description: hybridized to SNP 6.0


title: JUN_UM_HK_8-mer

source_name: JUN, HK design

value: JUN


title: siRNA knockdown of AK016444, bio rep1


title: donor 4 (AT25)_passage 10

description: hybridized to SNP 6.0


title: siRNA knockdown of AK005218, bio rep2

source_name: siRNA knockdown of AK005218


title: donor 8 (AT27)_passage 10

description: hybridized to SNP 6.0


title: DLBCL, biological replicate 9

source_name: DLBCL

value: human diffuse large B cell (DLBCL)


title: CREB1_UM_HK_8-mer

source_name: CREB1, HK design

value: BZIP


title: whole zebrafish 36hpf, glucose treated, biological replicate 2

city: Boston

first: Trista

last: North

address: 3 Blackfan Circle

institute: BIDMC

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GC-RMA was performed in R for normalization and background correction.

organism: Danio rerio

source_name: glucose treated

label_protocol: Affymetrix protocol

growth_protocol: Incubated at 28C

extract_protocol: RNA was extracted with Trizol and submitted to the Microarray Core Facility at the Molecular Genetics Department at Children's Hospital Boston/ Harvard Medical School

treatment_protocol: Embroys grown in 1% glucose in E3 media from 12-36hpf

value: 1% glucose


title: isolated mouse B220+ splenic B cells, biological replicate 3

description: MACS®-isolated

source_name: isolated mouse B220+ splenic B cells

value: isolated mouse B220+ splenic B cells

value: female


title: CREB1_M_HK_8-mer


title: siRNA knockdown of AK040954, bio rep1

source_name: siRNA knockdown of AK040954


title: siRNA knockdown of AK005218, bio rep1


title: DLBCL, biological replicate 7


title: DLBCL, biological replicate 8


title: undifferentiated_PGK12.1

scan_protocol: GeneChips were scanned and processed by the University of Washington Microarray Center.

data_processing: The data were analyzed with the Affymetrix GCOS1.1 software.

source_name: undifferentiated (day0) mouse female ES cells PGK12.1

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection. After depletion of MEF feeders, mouse female ES cells were differentiated for 15 days by the EB (embryoid body) differentiation protocol.

value: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: PGK12.1 ES cell line


title: CEBPG_UM_HK_8-mer

source_name: CEBPG, HK design

value: CEBPG

value: unmethylated


title: isolated mouse B220+ splenic B cells, biological replicate 1

description: MACS®-isolated


title: 15-day-differentiated_PGK12.1

source_name: 15-day-differentiated PGK12.1 cells

value: differentiated PGK12.1 cells


title: isolated mouse B220+ splenic B cells, biological replicate 2

description: MACS®-isolated


title: donor 4 (AT25)_passage 5

description: hybridized to SNP 6.0


title: donor 10 (AT22)_passage 5

description: hybridized to SNP 6.0


title: CEBPG_M_HK_8-mer


title: CEBPD_UM_HK_8-mer

source_name: CEBPD, HK design

value: CEBPD


title: DLBCL, biological replicate 4


title: CEBPD_M_HK_8-mer

value: methylated


title: CEBPB_UM_HK_8-mer

source_name: CEBPB, HK design

value: CEBPB


title: JUN_M_HK_8-mer


title: whole zebrafish 36hpf, control, biological replicate 1

source_name: control

value: control


title: DLBCL, biological replicate 3


title: CEBPB-GST_ATF4_M_HK_8-mer

source_name: CEBPB and ATF4, HK design

value: CEBPB and ATF4


title: isolated human peripheral blood B-cells, biological replicate 3

description: MACS®-isolated

source_name: isolated human peripheral blood B-cells

value: isolated human peripheral blood B-cells


title: CEBPB_ATF4-GST_UM_MA_8-mer

hyb_protocol: We used 250 ng of plasmid DNA in a 25 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor. After a 2-h incubation at 37oC, 15 ml of the mix was added to 135 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20 and once with PBS/0.01% Triton-X 100. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20 and once with PBS.

data_processing: We provide median intensity each 8-mer in each experiment. Please see the supplementary files on the platform record to match the raw data files with the array probes.

source_name: CEBPB and ATF4, MA design


title: DLBCL, biological replicate 5


title: DLBCL, biological replicate 1


title: DLBCL, biological replicate 2


title: whole zebrafish 36hpf, control, biological replicate 2


title: CEBPB-GST_ATF4_M_MA_8-mer


title: whole zebrafish 36hpf, glucose treated, biological replicate 1


title: CEBPB_M_MA_8-mer

source_name: CEBPB, MA design


title: CEBPB_M_HK_8-mer


title: isolated human peripheral blood B-cells, biological replicate 2

description: MACS®-isolated


title: CEBPB_UM_MA_8-mer


title: CEBPB_ATF4-GST_M_MA_8-mer


title: CEBPB-GST_ATF4_UM_HK_8-mer


title: DLBCL, biological replicate 6


title: CEBPB-GST_ATF4_UM_MA_8-mer


title: CEBPB_ATF4-GST_UM_HK_8-mer


title: CEBPB-GST_ATF4-GST_UM_MA_8-mer


title: THP1 BRG1

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: ChIP-chip THP1 BRG1

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: mean-centered log2(Cy5/Cy3) in gff format. The gff files are combined to generate matrix dataset in R.

source_name: BRG1 ChIP DNA from THP1

label_protocol: According to standard NimbleGen Protocol

growth_protocol: RPMI 1640 medium

extract_protocol: THP1 cells were crosslinked in 1% formaldehyde, sonicated to shear DNA, and IPs performed with antibodies. IP with no antibody was used as the Input control.

treatment_protocol: No Treatment

source_name: THP1 IgG control

growth_protocol: RPMI medium


title: isolated human peripheral blood B-cells, biological replicate 1

description: MACS®-isolated


title: CEBPB_ATF4-GST_M_HK_8-mer


title: CEBPA_UM_HK_8-mer

source_name: CEBPA, HK design

value: CEBPA


title: THP1 JHDM2A

description: ChIP-chip THP1 JHDM2A

source_name: JHDM2A ChIP DNA from THP1


title: CEBPB-GST_ATF4-GST_M_MA_8-mer


title: THP1 SIN3A

description: ChIP-chip THP1 SIN3A

source_name: SIN3A ChIP DNA from THP1


title: CEBPA_M_HK_8-mer


title: ATF4_UM_HK_8-mer

source_name: ATF4, HK design


title: CEBPA_M_MA_8-mer

source_name: CEBPA, MA design


title: ATF4_M_HK_8-mer


title: 4 h_starvation_culture_rep1

status: Public on Feb 14 2013

city: Heverle

first: Tekle Tafese

last: Fida

address: Kastelpark Arenberg 220

department: Earth and environmental Science

country: Belgium

institute: KU Leuven

hyb_protocol: Sixty nanograms of labeled cDNA with an incorporation efficiency of cyanine-3-labeled dCTP between 4-5% were used for microarray analysis. The cDNA was hybridized with the array for 17 h at 65oC, washed, and scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

scan_protocol: The Agilent Feature Extraction software package (version 9.5.3; Agilent Technologies) was used to extract the hybridization signal intensities from the images scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

data_processing: Normalization of the signal intensities (Quantile normalization) and analysis of the data were done using the Genespring GX software package (version 11, Agilent technologies). To test for significantly differentially expressed genes, Welch’s t- test with unequal variances was first used to calculate p-values. The Benjamini and Hochberg procedure was then used to correct the p-vales for multiple hypothesis testing and convert the p-vales into false discovery rates (FDRs)

organism: Sphingomonas sp. LH128

source_name: 4h stravation

label_protocol: The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer  The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer    The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer

growth_protocol: Cells were pregrown in phosphate buffered minimal medium containg 2 g per liter glucos

extract_protocol: RNA was immediately extracted from 1 ml of the cell suspensions from triplicate tubes of each condition using the RNeasy Protect Bacteria Mini Kit (Qiagen, Benelux, BV) according to the manufacturer’s instructions. RNA was further purified and precipitated by using sodium acetate and ethanol precipitation method.

treatment_protocol: Cells were pregrown to exponential phase (OD600 of 0.5) in triplicate of 50 ml MM containing 2 g l-1 glucose. Five ml of the cells each corresponding to about 1.4 x 109 CFU per ml, was centrifuged at 5000 x g for 10 min in a Becton Dickinson centrifuge (Benelux, NV), washed twice with 0.01M MgSO4 and finally resuspended in 5 ml of MgSO4 and  kept at 20°C for 4 h after which the tubes were sacrificed for physiological analysis and RNA extraction. As a control, freshly prepared non-starved cells washed in 0.01M MgSO4 were similarly treated.

tag: growth condition

value: 4 h starvation culture


title: 4 h_starvation_culture_rep3


title: 4 h_starvation_culture_rep2


title: CEBPA_UM_MA_8-mer

value: BZIP


title: ATF4_UM_MA_8-mer

source_name: ATF4, MA design


title: ATF4_M_MA_8-mer


title: THP1 JHDM3A

description: ChIP-chip THP1 JHDM3A

source_name: JHDM3A ChIP DNA from THP1


title: nonstarved_culture_rep2

source_name: control nonstarved culture

value: nonstarved culture


title: nonstarved_culture_rep1


title: THP1 JHDM1A

description: ChIP-chip THP1 JHDM1A

source_name: JHDM1A ChIP DNA from THP1


title: nonstarved_culture_rep3


title: THP1 SNF2H

description: ChIP-chip THP1 SNF2H

source_name: SNF2H ChIP DNA from THP1


title: THP1 JARIDIA

description: ChIP-chip THP1 JARIDIA

source_name: JARIDIA ChIP DNA from THP1


title: THP1 H3K9Me2

description: ChIP-chip THP1 H3K9Me2

source_name: H3K9Me2 ChIP DNA from THP1


title: RNA from primary UM 60

city: Cleveland

first: Li

last: Zhang

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with background subtraction.

source_name: primary uveal melanoma cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with mirVana kit (Ambion), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: primary uveal melanoma cells

value: M

tag: survival (days)

tag: death with metastasis

tag: metastasis


title: RNA from primary UM 51

value: F


title: RNA from primary UM 55


title: RNA from primary UM 54


title: RNA from primary UM 63


title: RNA from primary UM 57


title: RNA from primary UM 46


title: RNA from primary UM 47


title: RNA from primary UM 56


title: RNA from primary UM 50


title: RNA from primary UM 58


title: THP1 H3K27Me3

description: ChIP-chip THP1 H3K27Me3

source_name: H3K27Me3 ChIP DNA from THP1


title: RNA from primary UM 45


title: RNA from primary UM 52


title: THP1 H3K4Me3

description: ChIP-chip THP1 H3K4Me3

source_name: H3K4Me3 ChIP DNA from THP1


title: THP1 H3K56Ac

description: ChIP-chip THP1 H3K56Ac

source_name: H3K56Ac ChIP DNA from THP1 cells

source_name: THP1 IgG control

value: THP1 cell line


title: RNA from primary UM 44


title: RNA from primary UM 53


title: THP1 LSD1

description: ChIP-chip THP1 LSD1

source_name: LSD1 ChIP DNA from THP1


title: RNA from primary UM 42


title: RNA from primary UM 41


title: RNA from primary UM 61


title: RNA from primary UM 48


title: RNA from primary UM 59


title: RNA from primary UM 38


title: RNA from primary UM 40


title: RNA from primary UM 43


title: RNA from primary UM 39


title: RNA from primary UM 32


title: RNA from primary UM 36


title: RNA from primary UM 37


title: RNA from primary UM 34


title: RNA from primary UM 33


title: RNA from primary UM 29


title: RNA from primary UM 25


title: RNA from NUM 35

source_name: Normal Uveal Melanocytes

value: Normal Uveal Melanocytes

value: unknown


title: RNA from primary UM 28


title: RNA from primary UM 31


title: RNA from primary UM 27


title: RNA from primary UM 26


title: RNA from primary UM 30


title: RNA from primary UM 22


title: RNA from primary UM 18


title: RNA from primary UM 19


title: RNA from ESC 23

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells


title: RNA from primary UM 17


title: RNA from primary UM 13


title: RNA from primary UM 12


title: RNA from primary UM 15


title: RNA from primary UM 21


title: RNA from primary UM 16


title: RNA from primary UM 24


title: RNA from primary UM 20


title: RNA from primary UM 11


title: RNA from NCSC 14

source_name: neural crest stem cells

value: neural crest stem cells


title: RNA from primary UM 9


title: RNA from primary UM 10


title: RNA from primary UM 7


title: RNA from primary UM 8


title: RNA from primary UM 62


title: RNA from primary UM 4


title: RNA from primary UM 6


title: RNA from OCM1A 5

source_name: OCM1A uveal melanoma cell line

tag: cell line

value: OCM1A uveal melanoma cell line


title: RNA from primary UM 64


title: RNA from primary UM 3


title: RNA from MUM2B 2

source_name: MUM2B uveal melanoma cell line

value: MUM2B uveal melanoma cell line


title: RNA from primary UM 1


title: genomic DNA from primary UM 125M

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software Methylation Module

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from primary UM, neural crest stem cell and embryonic stem cells using Qiagen DNeasy Kit according to standard instructions


title: 1 seizures_hippocampal_CA_region_Rep_2

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: Determine and compare the transcriptomic alteration induced by 1 and 3 seizures episodes induced by injection with kainic acid.

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 Operon Rat 27k V3.0 printed oligonucleotide array V3.0 (GPL9207). Hybridization design ("multiple yellow" strategy) is described in Iacobas et al. Biochem Biophys Res Commun. 2006 (PMID 16934745).

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 GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005 (PMID 15585606). This experiment used the "multiple yellow strategy" in which each channel is normalized separately.

label: Alexa Fluor® 555

organism: Rattus norvegicus

source_name: Hippocampal CA1 region of 1 seizure rat

label_protocol: 30ug total RNA extracted from the hippocampal CA1 region was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor® 555–aha-dUTP using the SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

extract_protocol: Total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). 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). The extractions from two rats subjected to the same condition were pooled to ensure the necessary amount of RNA, so that finally we obtained 8/2 = 4 biological replicas of each condition.

treatment_protocol: Lactating female Sprague Dawley rats with 10 male pups obtained from Charles River Laboratories, Wilmington, MA, USA were first received and maintained under quarantine for 2 weeks at room temperature (55% humidity) in accordance with NIH guidelines and approval by the Institutional Animal Care and Use animal Committee (IACUC) at NYCOM. Rats were given food and water ad libitum on a 12-hr light/dark cycle and the healthy male litters were kept with their lactating mother for the duration of the experiments. To induce seizures, we used our previously established protocol of multiple early-life seizures with kainic acid (KA) (Ascent Scientific, Princeton, NJ, USA) as described (Liu et al., 2006 (PMID 16309925)). Neonate (P6 and P9) and juvenile (P20) rats were injected with KA once (1×KA) or three times (3×KA) (P20: i.p. 9-10 mg/mg vs. P6 or P9, s.c., 2 mg/kg, n=8 per condition) and sacrificed at 72 hrs after the last harmful seizure. Equal numbers of age-matched control littermates (n=8) were injected with equivalent volumes of phosphate-buffered saline (PBS) (0.1M, pH7.4). After KA injection, rats were placed into a clean and comfortable cage and their epileptic behavior was continuously monitored and scored every five minutes for two hours.

value: Sprague Dawley

tag: Sex

value: male

tag: age

value: 23 days

value: hippocampal CA1 region

tag: treatment

value: 1 seizure induced by kainic acid injection


title: 1 seizures_hippocampal_CA_region_Rep_4


title: genomic DNA from primary UM 113M

tag: cell type

tag: gender


title: genomic DNA from primary UM 122M


title: 3 seizures_hippocampal_CA_region_Rep_3

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 Operon Rat 27k V3.0 printed oligonucleotide array V3.0 (GPL9207). Hybridization design ("multiple yellow" strategy) is described in Iacobas et al. Biochem Biophys Res Commun. 2006 (PMID 16934745).

label: Alexa Fluor® 647

source_name: Hippocampal CA1 region of 3 seizures rat

label_protocol: 30ug total RNA extracted from the hippocampal CA1 region was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor® 647–aha-dUTP using the SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

value: 3 seizures induced by kainic acid injection


title: genomic DNA from primary UM 115


title: Control_hippocampal_CA_region_Rep_3

source_name: Hippocampal CA1 region of control rat

value: control


title: 3 seizures_hippocampal_CA_region_Rep_1


title: genomic DNA from primary UM 121

value: primary uveal melanoma cells


title: 3 seizures_hippocampal_CA_region_Rep_4


title: genomic DNA from primary UM 114


title: genomic DNA from primary UM 120M

value: M


title: genomic DNA from primary UM 123M


title: 1 seizures_hippocampal_CA_region_Rep_3


title: Control_hippocampal_CA_region_Rep_2


title: genomic DNA from primary UM 109


title: genomic DNA from primary UM 112


title: Control_hippocampal_CA_region_Rep_4


title: 3 seizures_hippocampal_CA_region_Rep_2


title: 1 seizures_hippocampal_CA_region_Rep_1


title: genomic DNA from primary UM 110M

value: F


title: genomic DNA from primary UM 108M


title: BOEC_Replicate3_swap2

city: jouy en josas

first: barbara

last: schmaltz-barbara

address: domaine de vilvert

country: France

institute: INRA

description: Biological replicate 3_swap2

hyb_protocol: Slides (lot 218) were prehybridised in 3.5 X SSC, 0.1% SDS, and 1% BSA, for 30 minutes at 50°C and washed with water. 500 ng of each Cy3- and Cy5-labelled sample were hybridized on microarray. Hybridisation was performed at 60°C for 20 hours using Agilent’s DNA Microarray Hybridisation Oven and buffers (Agilent Technologies). Slides were washed all at room temperature for 5 minutes under orbital agitation as follows: twice in [2× SSC, 0.1% SDS] solution, twice in [0.5× SSC, 0.1% SDS] solution, twice in [0.1× SSC, 0.1% SDS] solution, 3 times in [0.1X SSC] solution and finally 1 minute in ultra pure water. After the post-hybridisation washes slides were finally dried under neutral gas before scan

scan_protocol: Microarrays were scanned at 10 µm pixel resolution using an Agilent scanner (Agilent Technologies).

data_processing: Quantitative data acquisition was realized using Feature extraction 9.1 computer software (Agilent Technologies) .

organism: Bos taurus

source_name: Boec control

label_protocol: 500 ng of each RNA samples were labelled with Cy3 or Cy5 dyes (GE Healthcare Europe) using the SuperScript Indirect cDNA Amplification System (Invitrogen Life Technologies, France). Labelled aRNA yield and frequencies of dye incorporation were estimated by measuring the absorbance at 260 nm, 550 nm and 650 nm on a Nanodrop spectrophotometer (Nyxor Biotech).

growth_protocol: Bovine oviducts were collected from a local slaughterhouse without regard to oestrus cycle status of the donor and transported to the laboratory at room temperature in 50 mL tubes. All the following procedures took place within 2 to 3 h post-mortem. The cellular suspension was diluted 100 times in TCM-199 supplemented with 10% FCS and 80µg/mL gentamycin for seeding in four-well culture plates (NUNC, Roskilde, Denmark) in a humidified atmosphere of 20% O2, 5% CO2 and 90% N2 at 38.5°C. The medium was completely renewed after 48h with the same medium as previously described. From then, half of the medium was removed every 48h and replaced by TCM-199 supplemented with 10% heat-treated FCS + 60 µg/mL gentamycin until the day preceding the embryo co-culture. Actually, bovine oviduct epithelial cells (Boec) cultures were established six days prior to their use for embryo co-culture so that the cells reached confluence at that time. Twenty four hours before introducing the presumptive zygotes (five days after seeding), the medium was changed with SOF supplemented with 5% FCS

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Bovine in vitro produced embryos were co-cultured with bovine oviduct epithelial cells (Boec) monolayer at day five of boec culture for eight days.

value: Oviductal cells without stimulation

tag: culture time

value: 13 days

tag: media

value: SOF

source_name: Boec+Embryos

value: Oviductal cells stimulated by the presence of embryos


title: genomic DNA from primary UM 111


title: Control_hippocampal_CA_region_Rep_1


title: genomic DNA from primary UM 103


title: genomic DNA from primary UM 105D


title: BOEC_Replicate3_swap1

description: Biological replicate 3_swap1

source_name: Boec Control


title: BOEC_Replicate2_swap1

description: Biological replicate 2_swap1


title: genomic DNA from primary UM 106M

source_name: primary uveal melanoma cells


title: genomic DNA from primary UM 44M


title: genomic DNA from primary UM 102M


title: genomic DNA from primary UM 47


title: genomic DNA from primary UM 50


title: genomic DNA from primary UM 101M


title: genomic DNA from primary UM 45M


title: genomic DNA from primary UM 46M


title: BOEC_Replicate2_swap2

description: Biological replicate 2_swap2


title: genomic DNA from primary UM 48


title: genomic DNA from primary UM 104M


title: BOEC_Replicate1_swap1

description: Biological replicate 1_swap1


title: BOEC_Replicate1_swap2

description: Biological replicate 1_swap2


title: genomic DNA from primary UM 42


title: Monocytes_CD163lo_3

city: München

first: Lynsey

last: Fairbairn

address: Troger str. 1

institute: Technical University Munich

hyb_protocol: The fragmented and biotin labelled cDNA was hybridised to the Snowball arrays, using the Affymetrix HybWashStain Kit and Affymetrix standard protocols.

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

data_processing: A total of 6 Affymetrix SNOWBALLs520824F_v1 arrays were QC analysed using the arrayQualityMetrics Bioconductor  package to identify sub-standard and/or outlier arrays.  Normalisation of the 47845 features across all arrays was achieved using the robust multi-array average (RMA) expression measure.  Statistical anlysis was performed by Fios Genomics and using Biolayout Express 3D.   Comparisons, manually chosen to explore the data, were undertaken using linear modelling. Subsequently, empirical Bayesian analysis was applied (including vertical (within a given comparison) p value adjustment for multiple testing, which controls for false discovery rate). For each comparison, the null hypothesis was that there was no difference between the groups being compared. The Bioconductor package limma was used (Smyth (2005))

organism: Sus scrofa

source_name: porcine monocytes expressing CD14 and lower levels of CD163

label_protocol: 500 ng of total RNA was amplified using the Ambion WT Expression Kit (Affymetrix).  5.5 µg of the resulting cDNA was fragmented and labelled using the Affymetrix Terminal Labelling Kit.

growth_protocol: PBMC used for micro-arrays were isolated from 3 Large White Landrace F1 cross piglets (8 weeks old). The pigs were sedated with ketamine and euthanized using a captive bolt.  Blood was collected by intra-cardiac puncture into a vacuum sealed glass bottle containing 100mLs Acid Citrate Dextrose (ACD) buffer.  Whole blood was centrifuged at 1200g for 15 minutes with no brake.  The buffy coat layer was removed and mix with a same volume of RPMI (Sigma).  30 mls of the buffy coat/RPMI mix was layered on top of 15mLs of Lymphoprep (Axis-Shield, Norway) and centrifuged at 1200g for 25 minutes with no brake.  PBMCs separate out into a distinct layer which can be easily removed.  This was washed twice with RPMI 1640 and centrifuged at 600g for 10 minutes then 400g for 10 minutes. Red cells were lysed using 5mL of erythrocyte lysis buffer (10mM KHCO3, 155mM NH4Cl, 0.1M EDTA, sterile 0.2uM filtered) for 5 minutes then the cells washed and centrifuged at 400g for 10 minutes. The pellet was resuspended in a freezing medium (90%FCS-10%DMSO) before being slow frozen at -80°C in an isopropanol box. Vials were moved to -155°C for long term storage the next day.   PBMC used for micro-arrays were isolated from 3 Large White Landrace F1 cross piglets (8 weeks old). The pigs were sedated with ketamine and euthanized using a captive bolt.  Blood was collected by intra-cardiac puncture into a vacuum sealed glass bottle containing 100mLs Acid Citrate Dextrose (ACD) buffer.  Whole blood was centrifuged at 1200g for 15 minutes with no brake.  The buffy coat layer was removed and mix with a same volume of RPMI (Sigma).  30 mls of the buffy coat/RPMI mix was layered on top of 15mLs of Lymphoprep (Axis-Shield, Norway) and centrifuged at 1200g for 25 minutes with no brake.  PBMCs separate out into a distinct layer which can be easily removed.  This was washed twice with RPMI 1640 and centrifuged at 600g for 10 minutes then 400g for 10 minutes. Red cells were lysed using 5mL of erythrocyte lysis buffer (10mM KHCO3, 155mM NH4Cl, 0.1M EDTA, sterile 0.2uM filtered) for 5 minutes then the cells washed and centrifuged at 400g for 10 minutes. The pellet was resuspended in a freezing medium (90%FCS-10%DMSO) before being slow frozen at -80°C in an isopropanol box. Vials were moved to -155°C for long term storage the next day.

extract_protocol: RNA extraction was carried out using RNA-Bee (Fischer) and RNA quantified using a Nanodrop (Nanodrop, USA).  RNA quality was assessed using Agilent nanochip (Agilent)

treatment_protocol: Cells for FACS analysis were prepared using pre-chilled solutions and all centrifugation steps were carried out at 4˚C. PBMC were recovered from cryopreservation as previously described (Kapetanovic et al., 2012), washed and incubated 5M cells/mL in high-block (1x PBS, 0.1% NaN3, 2% heat inactivated FCS, 0.1% BSA) with 2% heat inactivated normal mouse serum on ice for 15 minutes. PBMC were stained with anti-CD14 (MCA1218F) and anti-CD163 (MCA2311PE) antibodies or their corresponding isotype and sorted into CD14high-CD163low and CD14low-CD163high monocyte populations using cell sorting flow cytometer (BD FACSAria Illu, BD BIosciences).

value: monocytes expressing CD14

tag: cd163 expression

value: low


title: genomic DNA from primary UM 41M


title: genomic DNA from primary UM Asingh-660w_D08

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA was genotyped using Infinium HumanHap66W-Quad v1.0 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.


title: genomic DNA from primary UM Asingh-660w_G08


title: Normal colon tissue, NBRCCC041

city: Seodaemun-gu

first: Park

last: Chan Hee

state: Seoul

address: Shinchondong 134

country: South Korea

institute: Cancer Metastasis Research Center

hyb_protocol: The labeled DNA was denatured and pre-annealed with Cot-1 DNA and Agilent blocking reagent and hybridized for 40 hours at 20 rpm in an Agilent hybridization oven.

scan_protocol: The arrays were scanned at 5-㎛ resolution using an Agilent scanner (Agilent), and the image was analyzed with Feature Extraction Software 9.1.1.1. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Normal colon tissue, recurrence-free group

label_protocol: Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.

growth_protocol: Tissues were obtained and immediately snap-frozen in liquid nitrogen and stored.

extract_protocol: Genomic DNA (gDNA) was prepared using the phenol/chloroform/isoamyl alcohol method.

value: normal colon adjacent to colon cancer

value: 52 yr

tag: relapse status

value: recurrence-free

source_name: Commerical gDNA

extract_protocol: Control DNA: Promega #G1471 (male) and #G1521 (female).

value: reference


title: genomic DNA from primary UM Asingh-660W_H08


title: genomic DNA from primary UM Asingh-660w_B08


title: genomic DNA from primary UM 40M


title: genomic DNA from primary UM Asingh-660w_F08


title: Monocytes_CD163hi_3

source_name: porcine monocytes expressing CD14 and higher levels of CD163

value: high


title: genomic DNA from primary UM 39M


title: genomic DNA from primary UM 38


title: genomic DNA from primary UM Asingh-660w_E08


title: Normal colon tissue, NBRCCC039

tag: tissue

value: 58 yr


title: Normal colon tissue, NBRCCC040

source_name: Normal colon tissue, relapse group

value: 53 yr

value: relapse


title: Monocytes_CD163lo_2


title: Monocytes_CD163hi_1


title: Normal colon tissue, NBRCCC036

value: 57 yr


title: Normal colon tissue, NBRCCC038

value: 71 yr


title: Monocytes_CD163lo_1


title: Normal colon tissue, NBRCCC037

value: 65 yr


title: genomic DNA from NUM NUM

source_name: Normal Uveal Melanocytes

value: Normal Uveal Melanocytes

value: unknown


title: Monocytes_CD163hi_2


title: genomic DNA from primary UM Asingh-660w_A08

value: primary uveal melanoma cells

value: F


title: genomic DNA from primary UM 37M


title: 70 days after BCCAo

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

description: Twelve-week-old Male Wistar rat

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Rat whole genome 44K, Agilent Technologies, USA) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: 70 days after BCCAo

label_protocol: The pooled RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification kit PLUS (Agilent Technologies, USA).

growth_protocol: The rats were housed in a room with the temperature controlled at 24±1 °C at a relative humidity of 50±10%, with a 12h dark/light cycle. Food and water were provided ad libitum throughout the experiment.

extract_protocol: Total RNA were isolated with TriPure Isolation Reagent in accordance with the manufacturer's instructions (Roche Applied Science, Indianapolis, USA).

treatment_protocol: Rats were anesthetized using 5% isoflurane and the bilateral common carotid arteries were tightly double ligated with silk sutures.

tag: background strain

value: Wister

value: hippocampus

value: male

value: 17 weeks


title: 55 days after BCCAo

description: Twelve-week-old Male Wistar rat

source_name: 55 days after BCCAo

value: 16 weeks


title: genomic DNA from primary UM Asingh-660w_C08

value: M


title: genomic DNA from primary UM 36M


title: genomic DNA from primary UM Asingh-660w_G07


title: genomic DNA from primary UM Asingh-660w_H07


title: genomic DNA from primary UM Asingh-660w_D07


title: 45 days after BCCAo

description: Twelve-week-old Male Wistar rat

source_name: 45 days after BCCAo

value: 15 weeks


title: Control

description: Twelve-week-old Male Wistar rat

source_name: Control

value: 12 weeks


title: 35 days after BCCAo

description: Twelve-week-old Male Wistar rat

source_name: 35 days after BCCAo

value: 14 weeks


title: Normal colon tissue, NBRCCC032

value: normal colon adjacent to colon cancer

value: 39 yr

value: recurrence-free

tag: sample type

value: reference


title: Normal colon tissue, NBRCCC033

value: 70 yr

value: relapse


title: genomic DNA from primary UM Asingh-660w_C07

value: primary uveal melanoma cells


title: genomic DNA from primary UM 33M

value: F


title: genomic DNA from primary UM 35M


title: genomic DNA from primary UM 32M


title: genomic DNA from primary UM 34M


title: 21 days after BCCAo

description: Twelve-week-old Male Wistar rat

source_name: 21 days after BCCAo

value: Wister

value: 13 weeks


title: genomic DNA from primary UM Asingh-660w_E07


title: Normal colon tissue, NBRCCC035

value: 73 yr


title: genomic DNA from primary UM 31M


title: Normal colon tissue, NBRCCC031

value: 64 yr


title: genomic DNA from primary UM Asingh-660w_B07


title: Normal colon tissue, NBRCCC028

value: 54 yr


title: genomic DNA from primary UM 30M

value: M


title: genomic DNA from primary UM Asingh-660w_H06


title: genomic DNA from primary UM 29M


title: genomic DNA from primary UM Asingh-660w_F07


title: genomic DNA from primary UM Asingh-660w_F06


title: Normal colon tissue, NBRCCC029

value: 59 yr


title: Normal colon tissue, NBRCCC030


title: genomic DNA from primary UM Asingh-660w_G06


title: Normal colon tissue, NBRCCC023

value: 71 yr


title: genomic DNA from primary UM Asingh-660w_D06


title: Normal colon tissue, NBRCCC024

value: 68 yr


title: genomic DNA from primary UM 28


title: Normal colon tissue, NBRCCC027

value: normal colon adjacent to colon cancer

value: 50 yr


title: Normal colon tissue, NBRCCC026

value: 52 yr


title: Oryzias latipes 7day 200ng/L rep2

city: Tsukuba

first: Katsuyuki

last: Kadota

state: Ibaraki

address: Tokodai 5-13-11

department: Research

institute: Japan pulp & Research Institute, Inc.

description: Gene expression after 7 day in 200 ng/L TB treated whole medaka

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Medaka Genome Oligo Microarrays (G2514F) for 17 hours at 65oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37oC GE Wash buffer 2 (Agilent), then dried immediately by N2 gas.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryzias latipes

source_name: Oryzias latipes, 7 day, 200 ng/L, replicate 2

label_protocol: cRNA was prepared from the total RNA using the Quick Amp Labeling Kit (Agilent Technologies) following procedures recommended by the manufacturer. Briefly, 500 ng of the total RNA was reverse transcribed to cDNA followed by synthesis of cRNA incorporated with cyanine 3 (Cy3)-labeled nucleotide. cRNA was then purified using RNeasy mini columns (QIAGEN GmbH). The quality of the cRNA samples was verified by total yield of the cRNA and the incorporation rates of Cy3 calculated based on the spectrophotometric measurement using a NanoDrop ND 1000 spectrophotometer (Thermo Fisher Scientific Co., Ltd.).

growth_protocol: The experiment was performed in a climate chamber at 24±1oC and with 16 h light-8 h dark photoperiod. Each aquarium contained 90 medaka.

extract_protocol: Each frozen sample was ground with a mortar and pestle in liquid nitrogen. Total RNA was isolated from the homogeneous powder using the Qiagen RNeasy Lipid Tissue Midi Kit (QIAGEN GmbH) following procedures recommended by the manufacture. The quantity and purity of the total RNA were examined photometrically by 260nm/280nm and 260nm/230nm ratios using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific Co., Ltd., Wilmington, USA) and electrophoretically with RNA 6000 Nano LabChip Kit using Agilent Bioanalyzer 2100 (Agilent Technologies). Only RNA samples with RNA Integrity Number (RIN) values above 9.0 were used for further cRNA preparations.

treatment_protocol: Exposures of TB were carried out by a continuous flowthrough system, designed to maintain constant concentrations of TB throughout the exposure experiments. Briefly, the TB stock solution was delivered to a mixing glass chamber by a mini-chemical pump unit (Oriental Mortar Co., Ltd., Tokyo, Japan) and diluted with carbon-filtered tap water continuously delivered at a flow rate of 100 mL/min. The TB test solution overflowed the mixing chamber to enter each test glass aquaria containing 23L of the test solution. Larvae were exposed to TB for 7 days by the continuous flow-through system as for the chronic exposures except in 1L test chambers.   TB concentrations used were 0 (control), 2, 6, 20, 60, 100 and 200 ng/L for 7 days of exposure (dimethyl sulfoxide with a final concentration of 1:2,500 v/v water). Each TB treatment had 90 larvae for each chamber. At day 7 of the exposures, triplicate samples (30 larvae/sample) from each chamber respectively were collected, flash-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction. All experiments were conducted with a 16 h light-8 h dark photoperiod and at 24±1oC. The fish were fed Artemia nauplii (<24 h after hatching) twice a day.

value: whole body

value: 7 day

tag: dose


title: genomic DNA from primary UM 26

tag: survival (days)


title: genomic DNA from ES ES

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells

value: unknown

tag: death with metastasis


title: genomic DNA from primary UM 27

value: primary uveal melanoma cells

value: F

tag: metastasis


title: Normal colon tissue, NBRCCC022

value: relapse

value: reference


title: genomic DNA from primary UM Asingh-660w_E06


title: Normal colon tissue, NBRCCC025

value: 53 yr

value: recurrence-free


title: genomic DNA from primary UM 25


title: Oryzias latipes 7day 200ng/L rep3

source_name: Oryzias latipes, 7 day, 200 ng/L, replicate 3


title: genomic DNA from primary UM 23

value: M


title: Oryzias latipes 7day 200ng/L rep1

source_name: Oryzias latipes, 7 day, 200 ng/L, replicate 1


title: genomic DNA from primary UM Asingh-660w_G05

source_name: primary uveal melanoma cells


title: Normal colon tissue, NBRCCC018

value: 59 yr


title: genomic DNA from primary UM 19M


title: Normal colon tissue, NBRCCC021

value: 62 yr


title: Normal colon tissue, NBRCCC034

value: 42 yr


title: Oryzias latipes 7day 100ng/L rep1

description: Gene expression after 7 day in 100 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 1


title: genomic DNA from primary UM Asingh-660w_F05


title: genomic DNA from primary UM 16


title: Normal colon tissue, NBRCCC019

source_name: Normal colon tissue, recurrence-free group

value: normal colon adjacent to colon cancer

value: 54 yr


title: genomic DNA from primary UM 21M


title: Oryzias latipes 7day 60ng/L rep3

description: Gene expression after 7 day in 60 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 60 ng/L, replicate 3

value: 60 ng/L


title: genomic DNA from primary UM Asingh-660w_B06


title: Normal colon tissue, NBRCCC017

value: 71 yr

source_name: Commerical gDNA


title: Normal colon tissue, NBRCCC020

source_name: Normal colon tissue, relapse group

value: 63 yr


title: genomic DNA from primary UM Asingh-660w_H05


title: genomic DNA from NCSC NCSC

source_name: Neural Crest Stem Cells

value: neural crest stem cells


title: Oryzias latipes 7day 100ng/L rep2

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 2

value: whole body

value: 7 day


title: genomic DNA from primary UM Asingh-660w_C06

value: primary uveal melanoma cells

value: F


title: genomic DNA from primary UM Asingh-660w_A06


title: Oryzias latipes 7day 100ng/L rep3

source_name: Oryzias latipes, 7 day, 100 ng/L, replicate 3


title: Oryzias latipes 7day 60ng/L rep2

source_name: Oryzias latipes, 7 day, 60 ng/L, replicate 2


title: genomic DNA from primary UM 15M


title: genomic DNA from primary UM 13M


title: Oryzias latipes 7day 20ng/L rep3

description: Gene expression after 7 day in 20 ng/L TB treated whole medaka

source_name: Oryzias latipes, 7 day, 20 ng/L, replicate 3

value: 20 ng/L


title: genomic DNA from primary UM Asingh-660w_A05


title: Normal colon tissue, NBRCCC013

value: 77 yr

value: relapse

value: reference


title: Oryzias latipes 7day 60ng/L rep1

source_name: Oryzias latipes, 7 day, 60 ng/L, replicate 1


title: Oryzias latipes 7day 20ng/L rep1

source_name: Oryzias latipes, 7 day, 20 ng/L, replicate 1


title: genomic DNA from primary UM Asingh-660w_B05

value: M


title: Normal colon tissue, NBRCCC014

value: 67 yr


title: genomic DNA from primary UM 14