title: small airways, COPD 136

value: COPD, GOLD-I, 119 pack-years


title: C. crescentus mixed population in M2 60 min, biological replicate 1

status: Public on Apr 20 2011

type: RNA

city: Stanford

first: Leticia

last: Britos

state: CA

address: 279 Campus Dr.

country: USA

institute: Stanford University

description: Gene expression datas for C. crescentus cells incubated in the absence of glucose for 60 min

hyb_protocol: Following fragmentation, 2.9 ug (for biological replicates 1) and 3.6 ug (for biological replicates 2) of cDNA were hybridized overnight at 50 deg C on GeneChip CauloHi1, using the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol ProkGE_WS2v3_450.

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

data_processing: The RMA statistical algorithm [78], available under the Bioconductor software package of R, was used for background noise removal, normalization and summarization of the microarray data corresponding to two independent experiments for each condition (cells starved for carbon for 30 and 60 min, and the respective controls). A Significance Analysis of Microarrays (SAM) [76] was applied to the dataset, with the following parameters: unpaired, logged, median centered, T statistic. A 2-fold minimum change was selected as cutoff, and a delta value yielding a false discovery rate lower than 1%.

label: biotin

molecule: total RNA

organism: Caulobacter vibrioides

label_protocol: cDNA was synthesized using Super Script II (Invitrogen) with random hexamers, according to the manufacturer’s instructions. After reverse transcription, RNA was removed by 30 min NaOH incubation at 65 °C and cDNA was purified using MinElute columns (Qiagen). Purified cDNA was fragmented by a 5 min incubation with DNAseI (Invitrogen; 0.6U/μg cDNA) in a thermocycler, followed by 15 min enzyme inactivation at 98 °C. DNAseI activity was previously titrated, and the same batch of enzyme and thermocycler were used across all experiments to obtain reproducible fragmentation. RNA 6000 Nano kit (Agilent) on a Agilent 2100 Bioanalyzer was used to control for homogeneous fragmentation (50-200 bp range) of samples. Fragmented cDNA was biotinylated at the 3’ termini with GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: Cells were grown overnight in small cultures in M2G medium (never reaching OD600nm greater than 0.4) . These cultures were used to inoculate 1200 ml cultures, which were incubated at 28 °C until they had reached an OD600 nm of 0.3-0.4.

extract_protocol: Total RNA was extracted from cells using the Purelink Mini Total RNA Purification System (Invitrogen), according to the manufacturer’s instructions for on-column DNAse treatment to remove contaminating DNA

treatment_protocol: Cells were collected by centrifugation (5 min at 9,000xg) and washed twice with a large volume of ice-cold M2 medium, resuspending by gentle pipetting. Control cells were mock-washed with ice-cold M2 with 0.2% glucose. Washed cells were resuspended in pre-warmed M2 or M2G media and incubated at 28 °C in a water bath with shaking. Samples were collected at 30 and 60 minutes, frozen in liquid nitrogen and stored at -80 °C.

tag: strain

tag: growth media

tag: time

value: 60 min

tag: treatment

value: carbon starvation


title: C. crescentus mixed population in M2G 30 min, biological replicate 2

description: Gene expression datas for C. crescentus cells incubated in complete media for 30 min

value: 30 min

value: mock


title: wt_vestibule_3

city: Tel Aviv

first: Tal

last: Elkan-Miller

address: P.O.B. 39040, Ramat Aviv

country: Israel

institute: Tel Aviv University

description: Gene expression data from inner ear vestibular sensory epithelia

hyb_protocol: According to the Affymetrix expression protocol.

data_processing: Expression levels were computed using the robust multiarray average (RMA) method (implemented in the BioConductor package). To remove systematic biases among the chips, they were normalized using the stringent quantile normalization scheme. To filter out probe sets whose corresponding genes are not expressed in the analyzed samples, Presence flags were computed according to Affymetrix MAS5 method. Probe sets that got 10 or more 'Absent' calls (out of the 12 calls) were filtered out.

organism: Mus musculus

source_name: C3H wt saccule, utricle and lateral and anterior sensory epithelia replicate 3

label_protocol: Affymetrix 2-Cycle Amplification Kit labeled with biotin.

extract_protocol:
Cochlear and vestibular sensory epithelia were dissected from wild type C3H mice and collected separately. The vestibular epithelia consisted of the saccule, utricle and the lateral and anterior cristae. Both the cochlear and vestibular sensory epithelia were dissected with their underlying mesenchyma.
Total RNA was extracted using a standard Trizol protocol. RNA was DNAseI treated (Qiagen), resuspended and quality assessed using a nano-range bioanalyzer (Agilent Technologies).

tag: tissue

tag: genotype/variation

value: wild type

tag: age

value: postnatal day 2


title: Cen3 tel 1034 doublings

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 8.1. Output files were then treated with the Limma (linear models for microarray data) package (Smyth 2005) available within Bioconductor (http://www.bioconductor.org/). Linear models were fitted to the normalised data to compare cen3tel cells at each population doubling with control cen3 fibroblasts. The empirical Bayes method was used to compute moderated t-statistic and F-statistic (Smyth, 2004). P-values were adjusted for multiple testing by using the Benjamini-Hochberg approach (Benjamini 1995). To select differentially expressed transcripts, a cut-off of 0.01 was applied to the adjusted p-value. To look for significant enrichment of Gene Ontology terms or of cellular pathways within the lists of differentially expressed sequences, the Agilent sequences were annotated using Bioc Web Annotation Tool (http://sourceforge.net/projects/annotweb-bioc/) and then the corresponding Entrez Gene IDs were loaded into DAVID Functional Annotation tool (http://david.abcc.ncifcrf.gov/).

label: Cy5, Cy3

organism: Homo sapiens

source_name: Cen3 tel 1034

label_protocol: Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns (Amino Allyl MessageAmp II aRNA Kit Ambion)

extract_protocol: Total RNA was extracted from actively dividing cells using the Trizol reagent (Invitrogen) and quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer. Total RNA was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit.

tag: cell line

value: cen3 tel

tag: cell density

value: 1034 population doubling

source_name: Cen3 15

value: 15 population doubling


title: small airways, smoker 314

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: no additional information

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: sex

value: F

tag: ethnic group

value: black

tag: smoking status

value: smoker,  1 pack-years


title: C. crescentus mixed population in M2G 60 min, biological replicate 1

description: Gene expression datas for C. crescentus cells incubated in complete media for 60 min


title: small airways, COPD 094_2

description: no additional information

value: COPD, GOLD-III, 53 pack-years


title: Cen3 tel 1042 doublings

source_name: Cen3 tel 1042

value: 1042 population doubling


title: Gene expression profiling of NtPT1-trasngenic rice (PT 1-7-8) treated with low phosphorus_1st

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

description: This experiment was performed with three independent biological replicates (1st, 2nd and 3rd ). The whole genome microarray consisting of a total of 64,896 oligonucleotides was printed on two separate slides (Slides A and B).

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 5X SSC, 0.1% SDS, 0.2 mg/ml of yeast tRNA, 0.2 mg/ml of polyadenylic acid and 25% super-pure formamide. Hybridization was performed by applying the labeled mixture of control and transgenic rice samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified hybridization chamber (Genomictree). The chamber was submerged into 42C water from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

scan_protocol: The microarray was scanned with ArrayWoRx Biochip Reader-Standard (AppliedPrecision, USA).

data_processing: Quality flagging was performed on the microarray scans using Imagene 5.0 (BioDiscovery, USA) and Genesight 3.2 (BioDiscovery, USA). A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatics analysis of the gene expression data. Gene expression data in each image was normalized globally (see VALUE below) prior to high level analysis.

organism: Oryza sativa

source_name: Control NtPT1-trasngenic rice (PT 1-7-8) seedlings

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy3 fluorescent dye.

extract_protocol: Total RNA was isolated from NtPT1-trasngenic rice (PT 1-7-8) seedlings treated with normal P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

tag: genotype

value: NtPT1-trasngenic rice (PT 1-7-8)

value: normal P (320μM Pi)

tag: developmental stage

value: seedling

source_name: Treated NtPT1-trasngenic rice (PT 1-7-8) seedlings

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy5 fluorescent dye.

extract_protocol: Total RNA was isolated from NtPT1-trasngenic rice (PT 1-7-8) seedlings treated with low P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

value: low P (32μM Pi)


title: C. crescentus stalked cells in M2G media

description: Gene expression data for a population enriched in stalked cells in M2G medium

hyb_protocol: Following fragmentation, 1.9 ug of cDNA were hybridized overnight at 50 deg C on GeneChip CauloHi1, using the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol ProkGE_WS2v3_450.

growth_protocol: Cells were grown in M2G medium (never reaching OD600nm greater than 0.4). Cultures were cooled on ice, pelleted at 9,000 x g at 4°C, and resuspended in 300 μl of ice-cold M2G. After adjusting the volume to 1ml, one volume of ice-cold Percoll was added and mixed thoroughly. The suspension was centrifuged at 11,000 x g for 20 min at 4°C, to separate the swarmer cells (lower band) from the rest of the population (top band). To obtain the stalked cells samples, the synchronization procedure was performed as described above, swarmers were resuspended in M2G , and allowed to differentiate for 60 min at 28°C. At that point, loss of motility of the majority of the population was confirmed by microscopy.

treatment_protocol: Cells were collected by centrifugation (5 min at 9,000xg) and washed twice with a large volume of ice-cold M2 medium, resuspending by gentle pipetting. Control cells were mock-washed with ice-cold M2 with 0.2% glucose. Washed cells were resuspended in pre-warmed M2 or M2G media and incubated at 28 °C in a water bath with shaking. Samples were collected after 15 minutes, frozen in liquid nitrogen and stored at -80 °C.

value: stalked cells


title: wt_vestibule_2

scan_protocol: According to the Affymetrix expression protocol.

source_name: C3H wt saccule, utricle and lateral and anterior sensory epithelia replicate 2


title: Gene expression profiling of control rice variety (Dongjin-byeo) treated with low phosphorus_3rd

source_name: Control  rice (Oryza sativa, spp. japonica cv. Dongjin-byeo) seedlings

extract_protocol: Total RNA was isolated from Dongjin-byeo seedlings treated with normal P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

tag: cultivar

value: Dongjin-byeo

source_name: Treated rice (Oryza sativa, spp. japonica cv. Dongjin-byeo) seedlings

extract_protocol: Total RNA was isolated from Dongjin-byeo seedlings treated with low P using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.


title: Cen3 tel 618 doublings

source_name: Cen3 tel 618

value: 618 population doubling


title: wt_cochlea_3

description: Gene expression data from inner ear cochlear sensory epithelia

source_name: C3H wt cochlea sensory epithelia replicate 3

value: cochlear sensory epithelia

value: wild type


title: Tet1_shRNA2863

status: Public on Apr 21 2011

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

description: Gene expression data from E14 ES cells treated with Tet1 shRNA2863 and selected with puromycin.

hyb_protocol: Hybridization was performed according to the manufacturer's instructions at Expression Analysis, Inc. (http://www.expressionanalysis.com)

scan_protocol: Scanning was performed at Expression Analysis, Inc. (http://www.expressionanalysis.com)

data_processing: The data were analyzed with the MATLAB (R2009b) Bioinformatics toolbox affygcrma function with default analysis settings.

source_name: mouse embryonic stem cells, Tet1 shRNA2863

label_protocol: Biotinylated cRNA were prepared using the Affymetrix One Cycle kit according to the standard Affymetrix protocol at Expression Analysis, Inc. (http://www.expressionanalysis.com)

growth_protocol: E14 ES cells were feeder-free cultured.

extract_protocol: Total RNA was extracted by Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse-free DNAse I.

treatment_protocol: E14 ES cells were infected with Scr shRNA, Tet1 shRNA2863 or Tet1 shRNA3387 containing lentivirus and harvested after 4-days selection with puromycin.

tag: cell type

value: mouse embryonic stem (MES) cells

value: Tet1 shRNA2863


title: Cen3 tel 97 doublings

source_name: Cen3 tel 97

value: cen3 tel

value: 97 population doubling

value: 15 population doubling


title: Cen3 tel 167 doublings

source_name: Cen3 tel 167

value: 167 population doubling


title: wt_vestibule_1

source_name: C3H wt saccule, utricle and lateral and anterior sensory epithelia replicate 1

value: postnatal day 2


title: wt_cochlea_1

source_name: C3H wt cochlea sensory epithelia replicate 1


title: wt_cochlea_2

source_name: C3H wt cochlea sensory epithelia replicate 2


title: CC8

status: Public on Apr 19 2011

city: Berkeley

first: Don

last: Pham

address: 238 Morgan Hall

institute: University of California, Berkeley

description:
Control
WetlandIndicators_09

hyb_protocol: 0.8 ug Cy3-labeled cRNA samples (with specific activity >8.0 pmol Cy3/ug cRNA) were hybridized onto custom-made 15k Agilent arrays following Agilent's standard hybridization protocol.  Slides were incubated at 65 degrees C for >17 hours and then washed with Agilent's wash buffers 1 and 2 and stabilization solution, following Agilent's standard washing protocol.

scan_protocol: Post-washed slides were immediately scanned on a GenePix 4000B Microarray Scanner.

data_processing: Data were analyzed using GenePix Pro v.6.0. Foreground intensities in each single slide were subtracted with local background and all positive values were log(base-2)-transformed (negative values, if any, were labeled as NAs). Relative intensity values (log(base-2)-transformed ratios known as 'M-values') were then corrected for non-linear trend(if any) with loess global normalization. Please see "Preprocessing_for_GEO.txt" file on the Series record for additional details.

organism: Gillichthys mirabilis

label_protocol: Total RNA samples were labeled with Cyanine-3 (Cy3) dye using Agilent's Low Input Quick Amp, Single Color kit and following its standard protocol.  Concentration and dye incorporatin of cRNA were checked using Nano-drop spectrophotometry.

growth_protocol: Fish were collected from natural estuarine wetlands (runoff was not quantified).

extract_protocol: Total RNA was prepared using standard Trizol-based protocol (Invitrogen).  Concentration of RNA was determined using UV-Vis spectrophotometry (BioRad), and RNA integrity was checked on a 1.2% agarose gel.

value: Liver tissue

tag: gender

value: Female

tag: sampling source (geographic)

value: Lab controls


title: CC2

description:
Control
WetlandIndicators_09


title: CC3

description:
Control
WetlandIndicators_09


title: CC1

description:
Control
WetlandIndicators_09

value: Male


title: TE3

description:
TE
WetlandIndicators_09

value: Tijuana River Estuary


title: TE5

description:
TE
WetlandIndicators_09


title: TE4

description:
TE
WetlandIndicators_09


title: Gene expression profiling of control rice variety (Dongjin-byeo) treated with low phosphorus_1st

value: normal P (320μM Pi)

value: seedling

value: low P (32μM Pi)


title: TE7

description:
TE
WetlandIndicators_09


title: TE1

description:
TE
WetlandIndicators_09


title: CC7

description:
Control
WetlandIndicators_09


title: TE2

description:
TE
WetlandIndicators_09


title: CC5

description:
Control
WetlandIndicators_09


title: TE6

description:
TE
WetlandIndicators_09


title: CC4

description:
Control
WetlandIndicators_09


title: CC6

description:
Control
WetlandIndicators_09


title: Cen3 tel 37 doublings

source_name: Cen3 tel 37

value: 37 population doubling


title: SB21

description:
SB
WetlandIndicators_09

value: Seal Beach National Wildlife Refuge


title: SB10

description:
SB
WetlandIndicators_09


title: SB13

description:
SB
WetlandIndicators_09


title: SB17

description:
SB
WetlandIndicators_09


title: SB19

description:
SB
WetlandIndicators_09


title: SB18

description:
SB
WetlandIndicators_09


title: SB6

description:
SB
WetlandIndicators_09


title: SB7

description:
SB
WetlandIndicators_09


title: SB11

description:
SB
WetlandIndicators_09


title: SB9

description:
SB
WetlandIndicators_09


title: SB4

description:
SB
WetlandIndicators_09


title: SB5

description:
SB
WetlandIndicators_09


title: SB1

description:
SB
WetlandIndicators_09


title: SB2

description:
SB
WetlandIndicators_09


title: CR14

description:
CR
WetlandIndicators_09

value: Carpinteria Reference


title: SB3

description:
SB
WetlandIndicators_09


title: CR15

description:
CR
WetlandIndicators_09


title: CR8

description:
CR
WetlandIndicators_09


title: TE8

description:
TE
WetlandIndicators_09


title: CR6

description:
CR
WetlandIndicators_09


title: CR9

description:
CR
WetlandIndicators_09


title: CR10

description:
CR
WetlandIndicators_09


title: CR4

description:
CR
WetlandIndicators_09


title: CR3

description:
CR
WetlandIndicators_09


title: CR12

description:
CR
WetlandIndicators_09


title: CR7

description:
CR
WetlandIndicators_09


title: CR13

description:
CR
WetlandIndicators_09


title: CR2

description:
CR
WetlandIndicators_09


title: CR1

description:
CR
WetlandIndicators_09


title: CM14

description:
CM
WetlandIndicators_09

value: Carpinteria Marsch


title: CM15

description:
CM
WetlandIndicators_09


title: CM10

description:
CM
WetlandIndicators_09


title: CM12

description:
CM
WetlandIndicators_09


title: CM11

description:
CM
WetlandIndicators_09


title: CM8

description:
CM
WetlandIndicators_09


title: CR5

description:
CR
WetlandIndicators_09


title: CM5

description:
CM
WetlandIndicators_09


title: CM9

description:
CM
WetlandIndicators_09


title: CM7

description:
CM
WetlandIndicators_09


title: CM2

description:
CM
WetlandIndicators_09


title: CM3

description:
CM
WetlandIndicators_09


title: CM6

description:
CM
WetlandIndicators_09


title: CM4

description:
CM
WetlandIndicators_09


title: CM1

description:
CM
WetlandIndicators_09


title: stage_01_Unf_Cy5_80

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

hyb_protocol: Labeled aRNA samples (2 pmol dye/ul) were hybridized to slides in 10 ul of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNAse free poly(A) RNA (Sigma)] for 44 hours at 42º C.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of gene expression were normalized using a linear mixed model in JMP Genomics 3.2 (SAS, Cary, NC, USA) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA version 0.98.8 for R to account for both intensity and spatial bias.  The model was of the form yij = μ  + Ai + Dj + (AxD)ij + εij where, yij is the signal from the ith array with dye j, μ is the sample mean, Ai and Dj are the overall variation in arrays (arrays 1-80) and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and εij is the stochastic error.

organism: Fundulus heteroclitus

source_name: stage 0 embryo

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX, USA) to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Eggs from multiple females were fertilized by sperm from multiple males, and excess sperm were removed.  Fertilized embryos were maintained in Petri dishes half submerged in 15 ppt filtered seawater in a 25°C environmental chamber under light during the first two stages of development (2-cell stage).  Embryos that successfully reached the 2-cell stage within 3 hours were incubated under a 16 hour light: 8 hour dark photoperiod at 25°C in the environmental chamber (818 Low Temperature Illuminated Incubator, Precision Scientific, USA).

extract_protocol: Embryo RNA was extracted using a Trizol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: Pools of frozen embryos collected at each developmental stage were used for RNA isolation, labeling, and microarray hybridization.  Four pools of 25 embryos were used for stages 1-10, four pools of 15 embryos were used for stages 11-15, and 4 pools of 10 embryos were used for stages 16-40.

tag: source

value: wild population

value: stage 0 embryo


title: stage_38_Cy5_86

source_name: stage 38 embryo

value: stage 38 embryo


title: stage_39_Cy5_84

source_name: stage 39 embryo

value: stage 39 embryo


title: stage_38_Cy5_74


title: stage_35_Cy5_92

source_name: stage 35 embryo

value: stage 35 embryo


title: CM13

description:
CM
WetlandIndicators_09

value: Liver tissue


title: stage_36_Cy5_70

source_name: stage 36 embryo

value: stage 36 embryo


title: stage_36_Cy5_90


title: stage_37_Cy5_88

source_name: stage 37 embryo

value: stage 37 embryo


title: stage_37_Cy5_72


title: stage_35_Cy5_68


title: stage_34_Cy5_94

source_name: stage 34 embryo

value: stage 34 embryo


title: stage_40_Cy5_78

source_name: stage 40 embryo

value: stage 40 embryo


title: stage_31_Cy5_60

source_name: stage 31 embryo

value: stage 31 embryo


title: stage_40_Cy5_82


title: stage_32_Cy5_98

source_name: stage 32 embryo

value: stage 32 embryo


title: stage_31_Cy5_100


title: stage_33_Cy5_64

source_name: stage 33 embryo

value: stage 33 embryo


title: stage_33_Cy5_96


title: stage_32_Cy5_62


title: stage_39_Cy5_76


title: stage_34_Cy5_66


title: stage_28_Cy5_106

source_name: stage 28 embryo

value: stage 28 embryo


title: stage_28_Cy5_54


title: stage_30_Cy5_58

source_name: stage 30 embryo

value: stage 30 embryo


title: stage_30_Cy5_102


title: stage_29_Cy5_104

source_name: stage 29 embryo

value: stage 29 embryo


title: stage_29_Cy5_56


title: stage_27_Cy5_52

source_name: stage 27 embryo

value: stage 27 embryo


title: stage_24_Cy5_46

source_name: stage 24 embryo

value: wild population

value: stage 24 embryo


title: stage_26_Cy5_42

source_name: stage 26 embryo

value: stage 26 embryo


title: stage_26_Cy5_118


title: stage_27_Cy5_108


title: stage_23_Cy5_44

source_name: stage 23 embryo

value: stage 23 embryo


title: stage_23_Cy5_116


title: stage_21_Cy5_40

source_name: stage 21 embryo

value: stage 21 embryo


title: stage_20_Cy5_122

source_name: stage 20 embryo

value: stage 20 embryo


title: stage_20_Cy5_38


title: stage_18_Cy5_34

source_name: stage 18 embryo

value: stage 18 embryo


title: stage_22_Cy5_110

source_name: stage 22 embryo

value: stage 22 embryo


title: stage_17_Cy5_128

source_name: stage 17 embryo

value: stage 17 embryo


title: stage_24_Cy5_114


title: stage_19_Cy5_36

source_name: stage 19 embryo

value: stage 19 embryo


title: stage_16_Cy5_30

source_name: stage 16 embryo

value: stage 16 embryo


title: stage_19_Cy5_124


title: stage_21_Cy5_120


title: Gene expression profiling of control rice variety (Dongjin-byeo) treated with low phosphorus_2nd

source_name: Control  rice (Oryza sativa, spp. japonica cv. Dongjin-byeo) seedlings

value: Dongjin-byeo

value: normal P (320μM Pi)

value: seedling

source_name: Treated rice (Oryza sativa, spp. japonica cv. Dongjin-byeo) seedlings

value: low P (32μM Pi)


title: stage_16_Cy5_130


title: stage_13_Cy5_136

source_name: stage 13 embryo

value: stage 13 embryo


title: stage_25_Cy5_112

source_name: stage 25 embryo

value: stage 25 embryo


title: stage_14_Cy5_26

source_name: stage 14 embryo

value: wild population

value: stage 14 embryo


title: stage_17_Cy5_32


title: stage_14_Cy5_134


title: stage_13_Cy5_24


title: stage_12_Cy5_138

source_name: stage 12 embryo

value: stage 12 embryo


title: stage_12_Cy5_22


title: stage_15_Cy5_132

source_name: stage 15 embryo

value: stage 15 embryo


title: stage_15_Cy5_28


title: stage_18_Cy5_126


title: stage_11_Cy5_140

source_name: stage 11 embryo

value: stage 11 embryo


title: stage_10_Cy5_18

source_name: stage 10 embryo

value: stage 10 embryo


title: stage_11_Cy5_20


title: stage_07_Cy5_12

source_name: stage 7 embryo

value: stage 7 embryo


title: stage_08_Cy5_146

source_name: stage 8 embryo

value: stage 8 embryo


title: stage_06_Cy5_150

source_name: stage 6 embryo

value: stage 6 embryo


title: stage_09_Cy5_144

source_name: stage 9 embryo

value: stage 9 embryo


title: stage_06_Cy5_10


title: stage_09_Cy5_16


title: stage_04_Cy5_154

source_name: stage 4 embryo

value: stage 4 embryo


title: stage_05_Cy5_152

source_name: stage 5 embryo

value: stage 5 embryo


title: stage_04_Cy5_6


title: stage_08_Cy5_14


title: stage_03_Cy5_4

source_name: stage 3 embryo

value: stage 3 embryo


title: stage_07_Cy5_148


title: stage_40_Cy3_83

source_name: stage 40 embryo

value: stage 40 embryo


title: stage_02_Cy5_158

source_name: stage 2 embryo

value: stage 2 embryo


title: stage_05_Cy5_8


title: stage_40_Cy3_79


title: stage_10_Cy5_142


title: stage_02_Cy5_2


title: stage_01_Unf_Cy5_160

source_name: stage 0 embryo

value: stage 0 embryo


title: stage_01_Unf_Cy3_81


title: stage_03_Cy5_156


title: stage_38_Cy3_87

source_name: stage 38 embryo

value: stage 38 embryo


title: stage_37_Cy3_89

source_name: stage 37 embryo

value: wild population

value: stage 37 embryo


title: stage_39_Cy3_77

source_name: stage 39 embryo

value: stage 39 embryo


title: stage_38_Cy3_75


title: stage_39_Cy3_85


title: stage_36_Cy3_71

source_name: stage 36 embryo

value: stage 36 embryo


title: stage_37_Cy3_73


title: stage_36_Cy3_91


title: stage_34_Cy3_67

source_name: stage 34 embryo

value: stage 34 embryo


title: stage_34_Cy3_95


title: stage_35_Cy3_69

source_name: stage 35 embryo

value: stage 35 embryo


title: stage_35_Cy3_93


title: stage_33_Cy3_97

source_name: stage 33 embryo

value: stage 33 embryo


title: stage_32_Cy3_99

source_name: stage 32 embryo

value: stage 32 embryo


title: stage_33_Cy3_65


title: Pre-Symptomatic Sample_P1

city: Leiden

first: Seyed Yahya

last: Anvar

address: Einthovenweg 20

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocols

scan_protocol: According to Illumina protocols

data_processing: Microarray measurements were normalized using the quantile method. The quality of the data was assessed by principal component analysis (PCA). Human subjects were grouped into controls, pre-symptomatic, and symptomatic subjects. P-value cut-off of 0.05 were used due to high inter-individual variation. Probe annotation was done using the illuminaHumanv3BeadID package in R.

source_name: Quadricept

growth_protocol: Human quadriceps muscle samples were collected with the needle or by an open surgical procedure from OPMD patients and family members as well as from anonymous age-matching healthy individuals that gave informed consent. The presence of expansion mutation in PABPN1 in OPMD patients and pre-symptomatic was determined with sequencing. Bergstrom needle biopsies from the (pre)symptomatic patients were approved by the ethical committee.

extract_protocol: Total RNA was extracted from skeletal muscles using RNA Bee (Amsbio) according to the manufacturer's instructions. RNA integration number (RIN) was determined with RNA 6000 Nano (Agilent Technologies). RNA with RIN >7 were used for subsequent steps. RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

tag: disease state

value: Pre-Symptomatic

value: 31 Year-old

value: Female


title: Symptomatic Sample_O2

label_protocol: RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

value: Symptomatic

value: 57 Year-old


title: Healthy Sample_W6

value: Healthy

value: 42 Year-old

value: Male


title: stage_32_Cy3_63


title: Symptomatic Sample_O3

value: 59 Year-old


title: stage_30_Cy3_59

source_name: stage 30 embryo

value: wild population

value: stage 30 embryo


title: stage_29_Cy3_105

source_name: stage 29 embryo

value: stage 29 embryo


title: stage_31_Cy3_101

source_name: stage 31 embryo

value: stage 31 embryo


title: stage_28_Cy3_55

source_name: stage 28 embryo

value: stage 28 embryo


title: stage_29_Cy3_57


title: Symptomatic Sample_O4

value: 60 Year-old


title: Healthy Sample_W10

value: 66 Year-old


title: Healthy Sample_W9


title: Healthy Sample_W8


title: Healthy Sample_W11

value: 67 Year-old


title: stage_27_Cy3_53

source_name: stage 27 embryo

value: stage 27 embryo


title: stage_27_Cy3_109


title: stage_31_Cy3_61


title: Pre-Symptomatic Sample_P2

value: Pre-Symptomatic

value: 37 Year-old


title: stage_30_Cy3_103


title: stage_26_Cy3_119

source_name: stage 26 embryo

value: stage 26 embryo


title: Healthy Sample_W12

value: 85 Year-old

value: Female


title: stage_24_Cy3_115

source_name: stage 24 embryo

value: stage 24 embryo


title: Healthy Sample_W7

value: Healthy

value: 58 Year-old


title: stage_24_Cy3_47

value: wild population


title: stage_28_Cy3_107


title: stage_25_Cy3_113

source_name: stage 25 embryo

value: stage 25 embryo


title: stage_23_Cy3_117

source_name: stage 23 embryo

value: stage 23 embryo


title: stage_23_Cy3_45


title: stage_26_Cy3_43


title: stage_22_Cy3_111

source_name: stage 22 embryo

value: stage 22 embryo


title: stage_21_Cy3_41

source_name: stage 21 embryo

value: stage 21 embryo


title: stage_21_Cy3_121


title: stage_20_Cy3_123

source_name: stage 20 embryo

value: stage 20 embryo


title: stage_19_Cy3_37

source_name: stage 19 embryo

value: stage 19 embryo


title: Healthy Sample_W14

value: 89 Year-old


title: stage_18_Cy3_127

source_name: stage 18 embryo

value: stage 18 embryo


title: stage_18_Cy3_35


title: stage_22_Cy3_51


title: stage_17_Cy3_33

source_name: stage 17 embryo

value: stage 17 embryo


title: Healthy Sample_W1

value: 38 Year-old


title: Healthy Sample_W2

value: 39 Year-old

value: Male


title: Healthy Sample_W4

value: 40 Year-old


title: Healthy Sample_W13

value: 87 Year-old

value: Female


title: stage_22_Cy5_50


title: stage_20_Cy3_39


title: stage_16_Cy3_131

source_name: stage 16 embryo

value: stage 16 embryo


title: stage_16_Cy3_31

value: wild population


title: Pre-Symptomatic Sample_P3

source_name: Quadricept

value: Pre-Symptomatic

value: 37 Year-old


title: Symptomatic Sample_O1

value: Symptomatic

value: 49 Year-old


title: Pre-Symptomatic Sample_P4


title: stage_15_Cy3_29

source_name: stage 15 embryo

value: stage 15 embryo


title: stage_19_Cy3_125

value: stage 19 embryo


title: stage_14_Cy3_27

source_name: stage 14 embryo

value: stage 14 embryo


title: stage_25_Cy5_48

value: stage 25 embryo


title: stage_17_Cy3_129

value: stage 17 embryo


title: Healthy Sample_W3

value: Healthy


title: stage_14_Cy3_135


title: stage_15_Cy3_133


title: Healthy Sample_C4

value: 20 Year-old


title: Healthy Sample_C5

value: 21 Year-old


title: stage_13_Cy3_25

source_name: stage 13 embryo

value: stage 13 embryo


title: Healthy Sample_C3


title: Healthy Sample_C2

value: 19 Year-old


title: stage_12_Cy3_23

source_name: stage 12 embryo

value: stage 12 embryo


title: stage_12_Cy3_139


title: stage_11_Cy3_21

source_name: stage 11 embryo

value: stage 11 embryo


title: stage_13_Cy3_137

value: wild population


title: stage_11_Cy3_141


title: stage_09_Cy3_145

source_name: stage 9 embryo

value: stage 9 embryo


title: stage_08_Cy3_15

source_name: stage 8 embryo

value: stage 8 embryo


title: stage_10_Cy3_143

source_name: stage 10 embryo

value: stage 10 embryo


title: stage_07_Cy3_149

source_name: stage 7 embryo

value: stage 7 embryo


title: stage_09_Cy3_17


title: stage_06_Cy3_11

source_name: stage 6 embryo

value: stage 6 embryo


title: stage_08_Cy3_147


title: Healthy Sample_C1

value: 17 Year-old

value: Female


title: stage_06_Cy3_151


title: stage_07_Cy3_13


title: stage_04_Cy3_7

source_name: stage 4 embryo

value: stage 4 embryo


title: stage_05_Cy3_9

source_name: stage 5 embryo

value: stage 5 embryo


title: stage_03_Cy3_157

source_name: stage 3 embryo

value: stage 3 embryo


title: stage_03_Cy3_5


title: stage_04_Cy3_155


title: stage_01_Unf_Cy3_1

source_name: stage 0 embryo

value: stage 0 embryo


title: stage_10_Cy3_19


title: stage_02_Cy3_3

source_name: stage 2 embryo

value: stage 2 embryo


title: stage_02_Cy3_159


title: V5-L3-F7 gDNA

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Filter V5-L3-F7 hybridization with labeled yeast genomic DNA.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml.The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization background subtracted using in-house software (Our database is at http://vydbase.uv.es/)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: In vitro genomic DNA labelling with 33P-dCTP in the W303-1a yeast strain exponentially growing in YPD

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol).The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

growth_protocol: Exponential growth in YPD

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267-272

tag: sample type

value: normalization control (in vitro genomic dna labelling:with 33P-dCTP in a yeast strain exponentially growing in YPD)


title: V5-L3-F3 gDNA

description: Filter V5-L3-F3 hybridization with labeled yeast genomic DNA.


title: V5-L3-F5 gDNA

description: Filter V5-L3-F5 hybridization with labeled yeast genomic DNA.


title: V5-L3-F2 gDNA

description: Filter V5-L3-F2 hybridization with labeled yeast genomic DNA.


title: V5-L3-F6 gDNA

description: Filter V5-L3-F6 hybridization with labeled yeast genomic DNA.


title: stage_05_Cy3_153


title: V5-L3-F4 gDNA

description: Filter V5-L3-F4 hybridization with labeled yeast genomic DNA.


title: TR-heat shock t26 rep 2

description: Run-on labelling from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F7

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t26

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 Ci/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t26: 26 min after heat shock.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

value: run-on sample

tag: strain

tag: stress

value: heat shock

tag: time

value: t26 (26 min after heat shock)

tag: hyb protocol

value: Hybridization on macrochip V5-L3-F7


title: TR-heat shock t26 rep 1

description: Run-on labelling from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F6

value: Hybridization on macrochip V5-L3-F6


title: TR-heat shock t40 rep 2

description: Run-on labelling from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F2

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t40

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t40: 40 min after heat shock.

value: t40 (40 min after heat shock)

value: Hybridization on macrochip V5-L3-F2


title: TR-heat shock t26 rep 3

description: Run-on labelling from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F2


title: TR-heat shock t40 rep 1

description: Run-on labelling from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F7


title: TR-heat shock t16 rep 2

description: Run-on labelling from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F6

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t16

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t16: 16 min after heat shock.

value: t16 (16 min after heat shock)


title: TR-heat shock t4 rep 2

description: Run-on labelling from W303-1a yeast strain. t4: 4 min after heat stress. Hybridization on macrochip V5-L3-F4

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t4

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t4: 4 min after heat shock.

value: t4 (4 min after heat shock)

value: Hybridization on macrochip V5-L3-F4


title: TR-heat shock t4 rep 3

description: Run-on labelling from W303-1a yeast strain. t4: 4 min after heat stress. Hybridization on macrochip V5-L3-F5

value: Hybridization on macrochip V5-L3-F5


title: TR-heat shock t0 rep 1

description: Run-on labelling from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F2

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t0

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t0: before heat shock.

value: control

value: t0 (before heat shock)


title: TR-heat shock t40 rep 3

description: Run-on labelling from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F3

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t40: 40 min after heat shock

value: Hybridization on macrochip V5-L3-F3


title: NA_pos103a

city: Baltimore

first: Scott

last: Devine

state: MD

address: 801 W. Baltimore Street

institute: Institute for Genome Sciences

hyb_protocol: Standard Affymetrix 6.0 kits and protocols were used.

data_processing: Affymetrix APT software with BRLMM-P.  The APT select_probes routine was used to identify probes with AIC values <325 and FLDAB >3.  INDELs with >60 no calls also were eliminated.

source_name: control

extract_protocol: Genomic DNA was purchased from Coriell.


title: RA-heat shock t40 rep 3

description: Total RNA from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F3

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t40

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 ÂµL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL  dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

value: total RNA


title: TR-heat shock t16 rep 1

description: Run-on labelling from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F5


title: TR-heat shock t11 rep 3

description: Run-on labelling from W303-1a yeast strain. t11: 11 min after heat stress. Hybridization on macrochip V5-L3-F6

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. TR t11

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t11: 11 min after heat shock.

value: t11 (11 min after heat shock)


title: TR-heat shock t0 rep 2

description: Run-on labelling from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F3


title: NA_A12

scan_protocol: Standard Affymetrix 6.0 kits and protocols were used.


title: TR-heat shock t11 rep 2

description: Run-on labelling from W303-1a yeast strain. t11: 11 min after heat stress. Hybridization on macrochip V5-L3-F5


title: TR-heat shock t16 rep 3

description: Run-on labelling from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F7


title: TR-heat shock t11 rep 1

description: Run-on labelling from W303-1a yeast strain. t11: 11 min after heat stress. Hybridization on macrochip V5-L3-F4


title: TR-heat shock t4 rep 1

description: Run-on labelling from W303-1a yeast strain. t4: 4 min after heat stress. Hybridization on macrochip V5-L3-F3


title: RA-heat shock t40 rep 1

description: Total RNA from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F7


title: RA-heat shock t26 rep 3

description: Total RNA from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F2

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t26


title: RA-heat shock t26 rep 2

description: Total RNA from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F7


title: RA-heat shock t16 rep 1

description: Total RNA from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F5

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t16


title: RA-heat shock t26 rep 1

description: Total RNA from W303-1a yeast strain. t26: 26 min after heat stress. Hybridization on macrochip V5-L3-F6


title: TR-heat shock t0 rep 3

description: Run-on labelling from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F4


title: stage_25_Cy3_49

source_name: stage 25 embryo

value: wild population

value: stage 25 embryo


title: RA-heat shock t11 rep 3

description: Total RNA from W303-1a yeast strain. t11: 11 minutes after heat stress. Hybridization on macrochip V5-L3-F6

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t11

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 ÂµL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t11: 11 minutes after heat shock.

value: heat shock


title: RA-heat shock t4 rep 2

description: Total RNA from W303-1a yeast strain. t4: 4 min after heat stress. Hybridization on macrochip V5-L3-F4

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t4

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t4: 4 min after  heat shock.


title: RA-heat shock t16 rep 3

description: Total RNA from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F7


title: RA-heat shock t4 rep 3

description: Total RNA from W303-1a yeast strain. t4: 4 min after heat stress. Hybridization on macrochip V5-L3-F5


title: RA-heat shock t11 rep 2

description: Total RNA from W303-1a yeast strain. t11: 11 min after heat stress. Hybridization on macrochip V5-L3-F5

growth_protocol: Heat stress conditions were created by addition of pre-heated fresh YPD medium to 49ºC to the 25 ºC yeast cells in order to get 37 ºC instantaneously. Experiments were initiated on exponential cultures growing in YPD at 0.5 OD600. t1: 11 min after heat shock.


title: RA-heat shock t11 rep 1

description: Total RNA from W303-1a yeast strain. t11: 11 min after heat stress. Hybridization on macrochip V5-L3-F4


title: RA-heat shock t0 rep 3

description: Total RNA from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F4

source_name: Saccharomyces cerevisiae W303-1a. Heat stress 37 ºC. RA t0


title: RA-heat shock t4 rep 1

description: Total RNA from W303-1a yeast strain. t4: 4 minafter heat stress. Hybridization on macrochip V5-L3-F3


title: RA-heat shock t0 rep 2

description: Total RNA from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F3


title: Crimean-Congo hemorrhagic fever virus-555

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

description: hybridization of infected culture for use in testing the performance of VIPR

hyb_protocol: 70 degree incubation for 12 hours

scan_protocol: scanned using GenePix 4000B scanner

data_processing: The data was produced with the intention of being analyzed by several different diagnostic algorithms, each of which employs its own normalization method. Because there is no standard normalization procedure between the different software diagnosis tools, we decided to submit raw intensities that can be used as input to any of the various available programs and independently processed by each.

organism: Orthonairovirus haemorrhagiae

source_name: infected culture

label_protocol: amino-allyl Cy3 dye coupled to cDNA

extract_protocol: RNA extracted using Trizol extraction protocol

tag: culture

value: Vero or C6/36

tag: causes hf

value: Yes


title: RA-heat shock t0 rep 1

description: Total RNA from W303-1a yeast strain. t0: before heat stress. Hybridization on macrochip V5-L3-F2


title: Crimean-Congo hemorrhagic fever virus-554


title: RA-heat shock t40 rep 2

description: Total RNA from W303-1a yeast strain. t40: 40 min after heat stress. Hybridization on macrochip V5-L3-F2


title: Crimean-Congo hemorrhagic fever virus-546


title: Tumor_Notch-inactivated_Rep1

city: Seoul

first: Young-Yun

last: Kong

address: San56-1, Silim-dong, Gwanak-gu

department: Department of Biological Sciences, College of Natural Sciences

institute: Seoul National University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using quantile method

source_name: Tumor tissue from Notch-inactivated Apcmin mice

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy columns (QIAGEN).

value: Apcmin mice

tag: genotype variation


title: Crimean-Congo hemorrhagic fever virus-552


title: Tumor_WT_Rep2

source_name: Tumor tissue from wild type Apcmin mice

value: wt


title: Tumor_Notch-activated_Rep1

source_name: Tumor tissue from Notch-activated Apcmin mice


title: Tumor_Notch-inactivated_Rep2


title: Crimean-Congo hemorrhagic fever virus-553


title: Tumor_Notch-activated_Rep2


title: Crimean-Congo hemorrhagic fever virus-547


title: Tumor_WT_Rep1


title: Normal_Notch-activated_Rep2

source_name: Normal tissue from Notch-activated Apcmin mice


title: Normal_Notch-inactivated_Rep1

source_name: Normal tissue from Notch-inactivated Apcmin mice


title: Crimean-Congo hemorrhagic fever virus-544


title: Normal_Notch-inactivated_Rep2


title: Crimean-Congo hemorrhagic fever virus-545


title: Omsk hemorrhagic fever virus-541

organism: Omsk hemorrhagic fever virus


title: Normal_Notch-activated_Rep1


title: Omsk hemorrhagic fever virus-540


title: 13192028 - H3_I_INPUT vs H3_I_IP

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

description: Epigenomic mapping

hyb_protocol: H3_I_IP Cy5 / H3_I_INPUT Cy3 : 120pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%

data_processing: Data were normalized as ChIP-chip data in Turck e al.(2007). This method is based on the properties of dye-swaps to remove technical biases. To be specific, let Yij be the signal of the sample labeled with the dye j on the array i. Given that the second array is a technical replicate of the first one, the distribution of Y21 (respectively Y22) should be close to that of Y12 (respectively Y11). In practice, the relationship between Y21 and Y12 is linear but it is not the identity function. The parameters of the two linear models are estimated by Y21=a+bY12+N(0,sigma2) and Y22=c+dY11+N(0,sigma2),and these estimates are used to define the normalized IP and INPUT values of the second array relative to the first one: Y21=(Y21-a)/b and Y22=(Y22-c)/d.For each sample and for each tile, the values of the two arrays of the dye-swap are then averaged.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, DNA  .

growth_protocol: seedling - 10-11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

treatment_protocol: no treatment

tag: ecotype

tag: age

value: 10 day

tag: antibody

tag: vendor


title: Normal_WT_Rep2

source_name: Normal tissue from wild type Apcmin mice


title: 13192484 - H3_I_IP vs H3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3_I_INPUT Cy5 / H3_I_IP Cy3 : 120pmol.


title: 13189665 - H3_II_IP vs H3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3_II_INPUT Cy5 / H3_II_IP Cy3 : 120pmol.


title: 13189664 - H3_II_INPUT vs H3_II_IP

description: Epigenomic mapping

hyb_protocol: H3_II_IP Cy5 / H3_II_INPUT Cy3 : 120pmol.


title: Normal_WT_Rep1


title: Omsk hemorrhagic fever virus-539


title: Primary Prostate Epithelial Culture (DNMT3A2 overexpressed)

first: Yuya

last: Kobayashi

address: 259 Campus Dr

department: Genetics

description: primary prostate culture

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: Each raw intensity values were background subtracted and beta scores were calculated manually. Values were normalized using ComBat.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA were isolated from prostate tissue samples using Qiagen Allprep kit according to standard instructions

value: Male

value: primary prostate culture

value: Normal


title: Primary Prostate Epithelial Culture (DNMT3B3 overexpressed)

description: primary prostate culture


title: 13189677 - H4K20me1_I_IP vs H4K20me1_I_INPUT

description: Epigenomic mapping

hyb_protocol: H4K20me1_I_INPUT Cy5 / H4K20me1_I_IP Cy3 : 120pmol.


title: Omsk hemorrhagic fever virus-538


title: Primary Prostate Epithelial Culture (EZH2 overexpressed)

description: primary prostate culture


title: 13192467 - H4K20me1_I_INPUT vs H4K20me1_I_IP

description: Epigenomic mapping

hyb_protocol: H4K20me1_I_IP Cy5 / H4K20me1_I_INPUT Cy3 : 120pmol.


title: Primary Prostate Epithelial Culture (DNMT3A2 and EZH2 overexpressed)

description: primary prostate culture


title: Primary Prostate Epithelial Culture (DNMT3B2 overexpressed)

description: primary prostate culture


title: Omsk hemorrhagic fever virus-533


title: Primary Prostate Epithelial Culture (DNMT3B1 overexpressed)

description: primary prostate culture


title: 13189655 - H4K20me1_II_INPUT vs H4K20me1_II_IP

description: Epigenomic mapping

hyb_protocol: H4K20me1_II_IP Cy5 / H4K20me1_II_INPUT Cy3 : 120pmol.


title: Omsk hemorrhagic fever virus-532


title: Omsk hemorrhagic fever virus-531


title: Primary Prostate Epithelial Culture (DNMT3A and EZH2 overexpressed)

description: primary prostate culture


title: Primary Prostate Epithelial Culture (DNMT3B1 and EZH2 overexpressed)

description: primary prostate culture


title: Primary Prostate Epithelial Culture (DNMT3A overexpressed)

description: primary prostate culture


title: 13189609 - H4K20me1_II_IP vs H4K20me1_II_INPUT

description: Epigenomic mapping

hyb_protocol: H4K20me1_II_INPUT Cy5 / H4K20me1_II_IP Cy3 : 120pmol.


title: Primary Prostate Epithelial Culture (DNMT3B3 and EZH2 overexpressed)

description: primary prostate culture


title: Primary Prostate Epithelial Culture (mock transfection)

description: primary prostate culture


title: 13603545 - H3K56Ac_II_IP vs H3K56Ac_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K56Ac_II_INPUT Cy5 / H3K56Ac_II_IP Cy3 : 120pmol.


title: Prostate Tissue PC180 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC180

value: prostate tissue

value: Tumor


title: Prostate Tissue PC148 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC148


title: Omsk hemorrhagic fever virus-530


title: Prostate Tissue PC180 Normal

description: Normal Prostate Tissue


title: Prostate Tissue PC148 Tumor

description: Prostate Tumor


title: Primary Prostate Epithelial Culture (DNMT3B2 and EZH2 overexpressed)

description: primary prostate culture


title: 13603542 - H3K56Ac_I_IP vs H3K56Ac_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K56Ac_I_INPUT Cy5 / H3K56Ac_I_IP Cy3 : 120pmol.


title: 13603548 - H3K56Ac_II_INPUT vs H3K56Ac_II_IP

description: Epigenomic mapping

hyb_protocol: H3K56Ac_II_IP Cy5 / H3K56Ac_II_INPUT Cy3 : 120pmol.


title: C6/36-499

description: hybridization of uninfected culture for use in testing the performance of VIPR

organism: unidentified

source_name: uninfected culture


title: Prostate Tissue PC153 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC153


title: RA-heat shock t16 rep 2

description: Total RNA from W303-1a yeast strain. t16: 16 min after heat stress. Hybridization on macrochip V5-L3-F6

value: t16 (16 min after heat shock)

value: Hybridization on macrochip V5-L3-F6


title: C6/36-497


title: C6/36-498


title: C6/36-496


title: Prostate Tissue PC112 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC112


title: 13584970 - H3K27me2_I_IP vs H3K27me2_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me2_I_INPUT Cy5 / H3K27me2_I_IP Cy3 : 120pmol.


title: Prostate Tissue PC92 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC92

tag: pre-treatment psa

tag: path gr (gleason)

tag: months followed-up

tag: recurrence

tag: days to recurrence


title: Prostate Tissue PC103 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC103

tag: gender

tag: sample type

tag: disease state

value: Biochemical


title: Prostate Tissue PC83 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC83


title: Prostate Tissue PC153 Tumor

description: Prostate Tumor


title: 13584979 - H3K56Ac_I_INPUT vs H3K56Ac_I_IP

description: Epigenomic mapping

hyb_protocol: H3K56Ac_I_IP Cy5 / H3K56Ac_I_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC83 Normal

description: Normal Prostate Tissue


title: Prostate Tissue PC37 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC37


title: 13584956 - H3K27me2_II_INPUT vs H3K27me2_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me2_II_IP Cy5 / H3K27me2_II_INPUT Cy3 : 120pmol.


title: 13584968 - H3K27me2_I_INPUT vs H3K27me2_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me2_I_IP Cy5 / H3K27me2_I_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC100 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC100


title: Prostate Tissue PC112 Normal

description: Normal Prostate Tissue


title: Prostate Tissue PC92 Tumor

description: Prostate Tumor


title: Vero-489

hyb_protocol: 70 degree incubation for 12 hours

value: Vero


title: Prostate Tissue PC37 Tumor

description: Prostate Tumor


title: 13584957 - H3K27me2_II_IP vs H3K27me2_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me2_II_INPUT Cy5 / H3K27me2_II_IP Cy3 : 120pmol.


title: 13190041 - H3K27me3_II_IP vs H3K27me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_II_INPUT Cy5 / H3K27me3_II_IP Cy3 : 120pmol.

value: Upstate 07-449


title: Vero-488


title: Prostate Tissue PC84 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC84


title: Prostate Tissue PC111 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC111


title: Vero-487


title: Vero-486


title: Lymphocytic choriomeningitis virus-474

organism: Mammarenavirus choriomeningitidis

source_name: infected culture

value: No


title: Prostate Tissue PC233 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC233


title: 13190040 - H3K27me3_II_INPUT vs H3K27me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_II_IP Cy5 / H3K27me3_II_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC 2337 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC 2337


title: Prostate Tissue PC111 Tumor

description: Prostate Tumor


title: Prostate Tissue PC233 Normal

description: Normal Prostate Tissue


title: Amapari virus-473

organism: Mammarenavirus amapariense


title: Prostate Tissue PC482 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC482


title: 13189670 - H3K27me3_I_IP vs H3K27me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_I_INPUT Cy5 / H3K27me3_I_IP Cy3 : 120pmol.


title: Prostate Tissue PC470 Tumor

description: Prostate Tumor

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

source_name: Prostate Tissue PC470


title: Prostate Tissue PC335 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC335


title: Dengue virus 1-470

organism: dengue virus type 1


title: Prostate Tissue PC491 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC491


title: 13190026 - H3K9me3_II_IP vs H3K9me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K9me3_II_INPUT Cy5 / H3K9me3_II_IP Cy3 : 120pmol.


title: Kyasanur Forest disease virus-465

organism: Kyasanur Forest disease virus


title: Prostate Tissue PC299 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC299


title: 13192082 - H3K9me3_II_INPUT vs H3K9me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K9me3_II_IP Cy5 / H3K9me3_II_INPUT Cy3 : 120pmol.


title: 13190028 - H3K27me3_I_INPUT vs H3K27me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K27me3_I_IP Cy5 / H3K27me3_I_INPUT Cy3 : 120pmol.


title: 13192087 - H3K9me3_I_IP vs H3K9me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K9me3_I_INPUT Cy5 / H3K9me3_I_IP Cy3 : 120pmol.


title: Kyasanur Forest disease virus-464


title: Kyasanur Forest disease virus-462


title: Prostate Tissue PC393 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC393


title: Prostate Tissue PC335 Tumor

description: Prostate Tumor


title: 13192025 - H3K4me3_II_IP vs H3K4me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_II_INPUT Cy5 / H3K4me3_II_IP Cy3 : 120pmol.


title: Prostate Tissue PC86 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC86


title: Prostate Tissue PC501 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC501


title: Prostate Tissue PC S07 8980 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC S07 8980


title: Kyasanur Forest disease virus-463


title: 13190017 - H3K9me3_I_INPUT vs H3K9me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K9me3_I_IP Cy5 / H3K9me3_I_INPUT Cy3 : 120pmol.


title: Lymphocytic choriomeningitis virus-452


title: Prostate Tissue PC S07 9957 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC S07 9957


title: Prostate Tissue PC482 Tumor

description: Prostate Tumor


title: Prostate Tissue PC470 Normal

description: Normal Prostate Tissue


title: 13189676 - H3K4me3_II_INPUT vs H3K4me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_II_IP Cy5 / H3K4me3_II_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC205 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC205


title: Prostate Tissue PC501 Tumor

description: Prostate Tumor


title: Prostate Tissue PC348 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC348


title: Prostate Tissue PC362 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC362


title: 13189673 - H3K4me3_I_INPUT vs H3K4me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_I_IP Cy5 / H3K4me3_I_INPUT Cy3 : 120pmol.


title: Amapari virus-451


title: 13189680 - H3K4me2_I_IP vs H3K4me2_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_I_INPUT Cy5 / H3K4me2_I_IP Cy3 : 120pmol.

growth_protocol: seedling - whole seedling - 10-11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

tag: dev.stage (boyes et al. plant cell 2001)

value: seedling


title: 13189675 - H3K4me3_I_IP vs H3K4me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_I_INPUT Cy5 / H3K4me3_I_IP Cy3 : 120pmol.


title: Lassa virus-292

organism: Mammarenavirus lassaense

value: Vero or C6/36


title: Prostate Tissue PC157 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC157


title: Prostate Tissue PC229 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC229


title: Prostate Tissue PC398 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC398


title: Dengue virus 1-448

source_name: infected culture

value: Yes


title: Guanarito virus-291

organism: Mammarenavirus guanaritoense


title: Prostate Tissue PC452 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC452


title: 13192029 - H3K4me2_I_INPUT vs H3K4me2_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me2_I_IP Cy5 / H3K4me2_I_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC88 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC88


title: Prostate Tissue PC455 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC455


title: Guanarito virus-290

hyb_protocol: 70 degree incubation for 12 hours


title: Prostate Tissue PC450 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC450


title: 13190030 - H3K9me2_I_INPUT vs H3K9me2_I_IP

description: Epigenomic mapping

hyb_protocol: H3K9me2_I_IP Cy5 / H3K9me2_I_INPUT Cy3 : 120pmol.

growth_protocol: whole plant - 11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

value: 11 day


title: Dengue virus 1-287


title: Guanarito virus-289


title: Guanarito virus-288


title: Prostate Tissue PC455 Tumor

description: Prostate Tumor


title: 13189659 - H3K4me2_II_INPUT vs H3K4me2_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me2_II_IP Cy5 / H3K4me2_II_INPUT Cy3 : 120pmol.


title: 13189669 - H3K9me2_I_IP vs H3K9me2_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K9me2_I_INPUT Cy5 / H3K9me2_I_IP Cy3 : 140pmol.


title: 13189658 - H3K4me2_II_IP vs H3K4me2_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_II_INPUT Cy5 / H3K4me2_II_IP Cy3 : 120pmol.


title: Dengue virus 4-285

organism: dengue virus type 4


title: Prostate Tissue PC398 Tumor

description: Prostate Tumor

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


title: Prostate Tissue PC645 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC645


title: Prostate Tissue PC485 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC485


title: Prostate Tissue PC555 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC555


title: 13189661 - H3K9me2_II_IP vs H3K9me2_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K9me2_II_INPUT Cy5 / H3K9me2_II_IP Cy3 : 140pmol.


title: Prostate Tissue PC646 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC646


title: Prostate Tissue PC477 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC477


title: Prostate Tissue PC S07 8392 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC S07 8392


title: Prostate Tissue PC452 Tumor

description: Prostate Tumor


title: 13189663 - H3K9me2_II_INPUT vs H3K9me2_II_IP

description: Epigenomic mapping

hyb_protocol: H3K9me2_II_IP Cy5 / H3K9me2_II_INPUT Cy3 : 100pmol.


title: Dengue virus 3-284

organism: dengue virus type 3


title: Dengue virus 2-283

organism: dengue virus type 2


title: Lassa virus-282


title: Prostate Tissue PC205 Tumor

description: Prostate Tumor

organism: Homo sapiens

source_name: Prostate Tissue PC205


title: Prostate Tissue PC2364 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC2364


title: 13603533 - H3K36me3_II_INPUT vs H3K36me3_II_IP

description: Epigenomic mapping

hyb_protocol: H3K36me3_II_IP Cy5 / H3K36me3_II_INPUT Cy3 : 120pmol.


title: Prostate Tissue PC477 Tumor

description: Prostate Tumor


title: Guanarito virus-281


title: Guanarito virus-280


title: Guanarito virus-279


title: Prostate Tissue PC248 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC248


title: Prostate Tissue PC448 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC448


title: Prostate Tissue PC457 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC457


title: Prostate Tissue PC191 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC191


title: Prostate Tissue PC485 Tumor

description: Prostate Tumor


title: Prostate Tissue PC 2337 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC 2337


title: Prostate Tissue PC265 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC265


title: Prostate Tissue PC498 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC498


title: Dengue virus 4-275

source_name: infected culture


title: Dengue virus 1-277


title: 13603546 - H3K36me3_I_INPUT vs H3K36me3_I_IP

description: Epigenomic mapping

hyb_protocol: H3K36me3_I_IP Cy5 / H3K36me3_I_INPUT Cy3 : 120pmol.


title: Guanarito virus-278


title: 13603532 - H3K36me3_I_IP vs H3K36me3_I_INPUT

description: Epigenomic mapping

hyb_protocol: H3K36me3_I_INPUT Cy5 / H3K36me3_I_IP Cy3 : 120pmol.


title: Prostate Tissue PC430 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC430


title: Prostate Tissue PC634 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC634


title: Prostate Tissue PC490 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC490


title: Prostate Tissue PC190 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC190


title: Prostate Tissue PC636 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC636


title: Prostate Tissue PC99 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC99


title: Prostate Tissue PC480 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC480


title: Prostate Tissue PC473 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC473


title: 13603534 - H3K36me3_II_IP vs H3K36me3_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K36me3_II_INPUT Cy5 / H3K36me3_II_IP Cy3 : 120pmol.


title: Sabia virus-270

organism: Mammarenavirus brazilense


title: Machupo virus-271

organism: Mammarenavirus machupoense


title: La Crosse virus-269

organism: La Crosse virus


title: Dengue virus 2-273


title: Dengue virus 3-274


title: Prostate Tissue PC363 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC363


title: Lassa virus-272


title: Yellow fever virus-266

organism: Yellow fever virus


title: Prostate Tissue PC474 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC474


title: Prostate Tissue PC527 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC527


title: Machupo virus-261


title: Tacaribe virus-265

organism: Mammarenavirus tacaribeense


title: Prostate Tissue PC629 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC629


title: Prostate Tissue PC274 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC274


title: Prostate Tissue PC97 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC97


title: Prostate Tissue PC538 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC538


title: Lassa virus-262


title: Prostate Tissue PC625 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC625


title: Prostate Tissue PC499 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC499


title: Prostate Tissue PC252 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC252


title: Prostate Tissue PC453 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC453


title: Prostate Tissue PC604 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC604


title: Prostate Tissue PC627 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC627


title: Prostate Tissue PC621 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC621


title: Prostate Tissue PC537 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC537


title: Prostate Tissue PC343 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC343


title: Prostate Tissue PC423 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC423


title: Prostate Tissue PC187 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC187


title: Prostate Tissue PC540 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC540


title: Sabia virus-260

source_name: infected culture


title: La Crosse virus-259


title: Tacaribe virus-255


title: Yellow fever virus-256


title: FX-IPS2

city: Los Angeles

first: ANYOU

last: WANG

address: Gonda BLDG

department: Human Genetics

institute: UCLA

description:
Replicate 2
FX-iPS2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio (version 3.1.3.0).

source_name: induced pluripotent stem cell (iPSC) line carrying the fragile X mutation

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: induced pluripotent stem cell (iPSC)

tag: genotype/variation

value: fragile X mutant


title: Dengue virus 2-250

tag: culture

tag: causes hf


title: Prostate Tissue PC599 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC599

value: Male


title: Dengue virus 2-249


title: BJ-IPS

description:
replicate 1
BJ-IPS

source_name: induced pluripotent stem cell (iPSC) line, control

value: control


title: Prostate Tissue PC594 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC594

value: Normal


title: Seoul virus-248

organism: Orthohantavirus seoulense


title: Prostate Tissue PC237 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC237

value: prostate tissue

tag: pre-treatment psa:

value: Unknown

tag: days to recurrence:


title: CCD-1079Sk-4f-4 iPS new rep1

description: replicate 1

source_name: CCD-1079Sk-4f-4 iPS

label_protocol: CY3-cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol


title: Prostate Tissue PC47 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC47

tag: age


title: CCD-1079Sk-4f-4 iPS new rep2

description: replicate 2


title: Prostate Tissue PC634 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC634

value: Tumor


title: Prostate Tissue PC375 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC375


title: Prostate Tissue PC19 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC19


title: Prostate Tissue PC579 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC579


title: Prostate Tissue PC370 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC370


title: FX-IPS1

description:
replicate 1
FX-iPS1


title: Prostate Tissue PC185 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC185


title: CCD-1079Sk-91 new rep1

description: replicate 1

value: somatic cell


title: CCD-1079Sk-91 new rep2

description: replicate 2


title: HSF1 P34 rep1

description: replicate 1

source_name: HSF1 P34

value: stem cell


title: Prostate Tissue PC582 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC582


title: Mopeia virus-244

organism: Mammarenavirus mopeiaense


title: Ippy virus-245

organism: Mammarenavirus ippyense


title: HSF6 P44_1 K27+

description: replicate 1


title: Prostate Tissue PC593 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC593


title: Prostate Tissue PC575 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC575


title: Mobala virus-243

organism: Mammarenavirus praomyidis

source_name: infected culture


title: Prostate Tissue PC184 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC184


title: Angola marburgvirus-242

organism: Lake Victoria marburgvirus - Angola2005


title: Prostate Tissue PC367 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC367


title: Prostate Tissue PC188 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC188


title: H9 P27 rep1

description: replicate 1


title: Prostate Tissue PC405 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC405

value: Biochemical


title: Gabon ebolavirus-240

organism: Ebola virus - Gabon (1994-1997)


title: Prostate Tissue PC563 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC563


title: Prostate Tissue PC643 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC643


title: Prostate Tissue PC166 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC166


title: Zaire ebolavirus-241

organism: Zaire ebolavirus


title: H9 P27 rep2

description: replicate 2


title: hNPC iPS #8 P3 rep2

description: replicate 2

source_name: hNPC iPS #8 P3


title: hNPC iPS #9 P3

description: replicate 1

source_name: hNPC iPS #9 P3


title: Prostate Tissue PC366 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC366


title: Prostate Tissue PC457 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC457


title: Zaire ebolavirus-239


title: Prostate Tissue PC498 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC498


title: Prostate Tissue PC14 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC14


title: hNPC iPS #10 P3

description: replicate 1

source_name: hNPC iPS #10 P3


title: Prostate Tissue PC191 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC191


title: Prostate Tissue PC242 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC242


title: Rift Valley fever virus-238

organism: Rift Valley fever virus

source_name: infected culture


title: Prostate Tissue PC159 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC159


title: Prostate Tissue PC551 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC551


title: H1 P31

description: replicate 1


title: Prostate Tissue PC448 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC448


title: Hantaan virus-236

organism: Orthohantavirus hantanense


title: Yellow fever virus-235


title: Prostate Tissue PC430 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC430


title: Prostate Tissue PC45 Normal

description: Normal Prostate Tissue

source_name: Prostate Tissue PC45


title: Prostate Tissue PC2364 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC2364


title: IMR90 iPS P24

description: replicate 1

source_name: IMR90 iPS P24


title: Junin virus-233

organism: Mammarenavirus juninense


title: IMR90 P5 rep1

description: replicate 1

source_name: IMR90 P5


title: hNPC P6

description: replicate 1

source_name: hNPC P6


title: ILD_23

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: ILD patient

hyb_protocol: The purified labeled miRNA probes were hybridized for 20 h at 55 °C.

scan_protocol: The arrays were washed and scanned at 5-micron resolution with a PerkinElmer ScanArray Express array scanner.

data_processing: The resulting images were quantified by using Agilent’s Feature Extraction software. Further, expression data was consolidated to make representative expression profile for each probe and then normalized using quantile method (MATLAB R2009b).

source_name: Lung tissue sample from the patient with ILD

label_protocol: T4 ligase was used to join cyanine 3-cytidine bisphosphate to the termini of all single-stranded RNA (including miRNA) and the labeled RNA was purified from these reactions by gel filtration on MicroBioSpin 6 columns (Bio-Rad).

extract_protocol: 100 ng of total RNA was dephosphorylated with calf intestinal alkaline phosphatase, followed by denaturation in dimethyl sulfoxide.

tag: tissue

value: lung

tag: disease status

value: ILD patient

tag: diagnosis

value: UIP/IPF

tag: fvc-group


title: Rift Valley fever virus-232

value: Vero or C6/36


title: Prostate Tissue PC473 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC473

tag: pre-treatment psa

tag: path gr (gleason)

tag: months followed-up

tag: recurrence


title: Prostate Tissue PC480 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC480

tag: gender

tag: sample type

tag: disease state

tag: days to recurrence


title: ILD_22

description: ILD patient


title: Dengue virus 3-231

organism: dengue virus type 3

tag: culture

value: Yes


title: IMR90 P5 rep2

description: replicate 2

organism: Homo sapiens

tag: cell type


title: Dengue virus 4-234

organism: dengue virus type 4

tag: causes hf


title: Prostate Tissue PC99 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC99


title: Prostate Tissue PC187 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC187


title: Prostate Tissue PC648 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC648


title: Prostate Tissue PC21 Tumor (2)

description: Prostate Tumor

source_name: Prostate Tissue PC21


title: Prostate Tissue PC TB2682 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC TB2682


title: hNPC iPS #8 P3 rep1

description: replicate 1

source_name: hNPC iPS #8 P3


title: Prostate Tissue PC474 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC474


title: ILD_21

description: ILD patient

value: HP


title: ILD_20

description: ILD patient

value: NSIP


title: Prostate Tissue PC423 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC423


title: Rocio virus-229

organism: Rocio virus

source_name: infected culture

value: No


title: ILD_16

description: ILD patient

value: RB-ILD


title: Toscana virus-230

organism: Toscana virus


title: ILD_17

description: ILD patient

value: COP


title: Puumala virus-228

organism: Orthohantavirus puumalaense


title: ILD_19

description: ILD patient


title: Prostate Tissue PC97 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC97

value: Male


title: Prostate Tissue PC453 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC453

value: prostate tissue


title: ILD_14

description: ILD patient


title: Prostate Tissue PC616 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC616


title: ILD_15

description: ILD patient


title: Prostate Tissue PC343 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC343


title: Ngari virus-226

organism: Ngari virus


title: Prostate Tissue PC86 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC86


title: Prostate Tissue PC625 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC625


title: California encephalitis virus-225

organism: California encephalitis virus


title: Prostate Tissue PC538 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC538


title: ILD_12

description: ILD patient

source_name: Lung tissue sample from the patient with ILD


title: Prostate Tissue PC621 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC621


title: Prostate Tissue PC540 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC540


title: Prostate Tissue PC85 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC85


title: ILD_11

description: ILD patient


title: Ippy virus-221


title: ILD_10

description: ILD patient


title: ILD_9

description: ILD patient


title: Prostate Tissue PC619 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC619


title: Angola marburgvirus-218


title: ILD_8

description: ILD patient


title: Prostate Tissue PC274 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC274


title: Mopeia virus-220

organism: Mammarenavirus mopeiaense


title: Gabon ebolavirus-217


title: Seoul virus-224

organism: Orthohantavirus seoulense


title: Prostate Tissue PC494 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC494


title: ILD_6

description: ILD patient


title: ILD_5

description: ILD patient


title: Prostate Tissue PC252 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC252


title: Zaire ebolavirus-215


title: Mobala virus-219

organism: Mammarenavirus praomyidis


title: Prostate Tissue PC228 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC228


title: Rift Valley fever virus-237

source_name: infected culture


title: Prostate Tissue PC646 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC646


title: Prostate Tissue PC190 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC190


title: Rift Valley fever virus-213


title: ILD_3

description: ILD patient

value: FU


title: Hantaan virus-212


title: ILD_2

description: ILD patient


title: 6302402 - H3K4me2_WT_II_IP vs H3K4me2_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_II_INPUT Cy5 / H3K4me2_WT_II_IP Cy3 : 80pmol.

scan_protocol: NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%

data_processing: For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf  is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA  .

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.

tag: ecotype

value: 10 day

tag: dev.stage (boyes et al. plant cell 2001)

value: seedling

tag: antibody

tag: vendor


title: Prostate Tissue PC47 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC47

value: Tumor

tag: age


title: 16408402 - H3K4me2_WT_II_INPUT vs H3K4me2_WT_II_IP

description: Epigenomic mapping

hyb_protocol: H3K4me2_WT_II_IP Cy5 / H3K4me2_WT_II_INPUT Cy3 : 80pmol.


title: Rift Valley fever virus-214


title: 11994902 - H3K4me3_WT_I_INPUT vs H3K4me3_WT_I_IP

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_I_IP Cy5 / H3K4me3_WT_I_INPUT Cy3 : 80pmol.


title: Prostate Tissue PC19 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC19

value: Biochemical


title: Prostate Tissue PC645 Tumor

description: Prostate Tumor

source_name: Prostate Tissue PC645


title: Reston ebolavirus-227

hyb_protocol: 70 degree incubation for 12 hours

organism: Reston ebolavirus


title: 15202202 - H3K27me3_WT_II_IP vs H3K27me3_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K27me3_WT_II_INPUT Cy5 / H3K27me3_WT_II_IP Cy3 : 80pmol.

growth_protocol: seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hours photoperiod.

value: Upstate 07-449


title: 18026002 - H3K4me3_WT_II_IP vs H3K4me3_WT_II_INPUT

description: Epigenomic mapping

hyb_protocol: H3K4me3_WT_II_INPUT Cy5 / H3K4me3_WT_II_IP Cy3 : 80pmol.