title: CantonS at 22 vs 29 degrees replicate 3

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

description: CantonS wild type at 22 vs 29 degrees on slide 28_032102

hyb_protocol: Microarray hybridization   The hybridization protocol described here is to be used with microarrays printed with double-stranded DNA.  (For arrays with single-stranded DNA, the amplification and labeling method should be modified) Sample array hybridization.  The hybridization procedure here is for microarrays to be covered with 22mm x 40mm cover slip.  If other sizes of arrays are used, the hybridization volume should be adjusted accordingly.  DieTech hybridization chambers were used here, however the procedure is very similar for other chambers. 1.	Add the following to the 21.9 ul labeled sample (to a 28.6 ul final volume) a.	4.05 ul 20x SSC (final concentration to be ~ 2.83x SSC) b.	1.64 ul 5mg/ml yeast tRNA or 10mg/ml polyA (0.22 um filtered) c.	(Mix now by gently tapping the tube before adding SDS) d.	 0.99 ul 5% SDS (0.22 um filtered) (Mix well by gently tapping the tube) 2.	Denature sample in boiling water for 2 min. 3.	Centrifuge at ~ 12,000 g for 10 min, cool at room temperature for ~ 2 min.  Measure volume.  If the volume is less than 27 ul, adjust it to 28.6 ul with H2O.  It is OK if it is only ~ 1 ul short of 28.6 ul. 4.	 Add 10-15 ul of 2.83x SSC in the each of the two reservoirs of a Die-Tech hybridization chamber.  Set a 100 ul pipette at 28 ul and apply to array. Place and adjust the position of the cover slip on the array using a pipette tip to squarely cover the DNA area.  Put 3-4 droplets of 2.83x SSC on each ends of the slide outside of the Parafilm strips, total ~28 ul.  Put on the chamber over and tighten it with the provided screws.  Incubate in a water bath at ~42°C for 10 min. to adjust temperature.  Then move to another water bath at 64 °C, incubate for 15-18 hours. Washing and scanning microarrays. Prepare Washing Solution in 4 staining dishes (6cmH x 7.5cmW x 9.5cmL, Wheaton Cat. No.: 900200).  Put a slide rack (the matching glass rack for the staining dishes) in the Wash 1A dish and the Wash 2 dish.  Note 1: All washes are done at room temperature.  (do not add SDS into Wash Solution 1A until just prior to the initial use)  All the procedures here need be done swiftly.  After washing, microarrays are to be dried using a centrifuge with swing bucket rotor that takes slide racks.   Microarray Wash Solutions done in sequence of solution numbers: 1A = 1.14 x SSC, 0.0285% SDS; 1B = 1.14 x SSC; 2 = 0.228 x SSC; 3 = 0.057 x SSC

scan_protocol: Array Scanning The scanning method here uses a GenePix 4000 scanner (Axon Instrument) as an example. Scan per manufacturer’s instruction.  Usually the intensity where the histogram curve intersecting the X (intensity) axis is best kept at approximately 35,000, which should keep most features within dynamic range.  Keep the histogram curves from both channels as close a possible, which usually correlated to an intensity ratio of 1.  The resulting image is then analyzed using the GenePix Pro software provided by Axon Instruments per manufacturer’s instructions.

data_processing:
Statistical analysis of microarray data
 Data filtering, normalization and extraction from GenePix Pro.
1.	During the image analysis, GenePix Pro software recognizes the spots representing genes (called features) on an array.  Then the intensity of the red and green channel (pseudo-colors representing the Cy5 channel (635 nm wavelength) and Cy3 channel (532 nm wavelength), respectively) in each feature is quantified and registered as the expression reading of the gene represented.  The ratio of the intensities between two channels is registered as the relative ratio of expression level of this gene in the two samples that hybridized on the array.  The identity of the gene represented by a spot is determined by tracing back to the identity of the original DNA sample used to make the microarray.
2.	In the case of using GenePix Pro software, there is an automatic flagging process in which the software identifies the spots that are of poor quality and flags them as bad (flag value less than 0).
3.	We also apply another data filter to eliminate features whose quality is doubtful.  In the formula of this filter, for a spot to pass quality control, 3 conditions need to be met: (1) There is no negative automatic or manual flags during image processing using GenePix Pro software.  (2) For this spot, in at least 1 channel, the intensities of at least 75% of the pixels are one standard deviation above background.  (3) The net signal-to-noise ratio should be at least 1 in at least one channel.  For a channel, the net signal-to-noise ratio is: [(Feature Intensity) – (Background Intensity)]/ (Background Intensity).  The Feature Intensity is the median signal intensity reading of a spot (feature).  The Background Intensity is the bigger value of two: the median of median background intensity of all the spots on the whole array, and median background intensity of this particular spot.
4.	After data filtering, the intensity ratios (“Ratio of Medians” in the GenePix Pro result file) of every spots are then normalized using the normalization method (calculation based on “Ratio of Medians”) from GenePix Pro software.  This normalization method is based on removal of all spots whose “Ratio of Medians” value is >10-fold and then calculation of the average ratio of medians and multiplication of each value by the resulting correction factor (“Normalization Factor-Medians”) such that the average of the corrected “ratios of medians” equals 1.0.  The normalized Ratio of Medians is the product of Ratio of Medians and the Normalization Factor-Medians.  All subsequent analyses use the normalized Ratio of Medians as the value of gene expression.  A log base 2 transformation of the ratios was performed before further analysis.
Statistical analysis of extracted array data.
1.	At least 3 biological repeats are required to provide statistical power. The models used for significant genelists includes: t-test, t-test combined with fold-cutoff, ANOVA, ANOVA combined with fold-cutoff were used to define significant gene lists.  The formulas for these tests are available in many statistical books, such as Biometry by Sokal and Rohlf (1995).
2.	In the case of comparison of samples from two experimental conditions (for example, normal vs. mutant), t-test or fold-cutoff was used.  In the method a gene is considered significant if it passes a t-test with a certain p-value score, and its expression level is different between the 2 samples by certain fold.  One such example a t-test score of p-value 0.05, plus a 2- fold change in expression level.  Examples of this method could be found in Li and White (2003).
3.	For a time-course experiment (or comparisons between 3 or more timepoints or developmental stages) with at least 3 repeats per time point, one-way ANOVA was the suitable statistical model utilized to it test whether a gene is changed significantly along the time.  Examples of this method could be found in White et al. (2002) and Li and White (2003).

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: CantonS at 22 degrees (REF)

label_protocol:
Labeling of poly-A selected RNA
1.	labeling reactions were set up on ice in two 0.2 ml PCR tubes (two samples for one microarray):
a.	Mix 4.5 ug mRNA and 2.5 ul Random hexamer (3 ug/ul).
b.	Adjust volume to 15.4 ul (either by adding nuclease-free H2O or by partially drying (heating at 70°C with cap open), mix well by pipetting.
c.	Transfer to a preheated PCR machine to denature at 70°C for 10 min.  Then cool on ice for 2 min.
d.	Add 9.6 ul ice-cold Labeling Mixture (6 ul 5x SuperScript II first strand buffer + 3 ul  0.1M DTT +  0.6 ul  Labeling dNTP mix (25mM dATP, dCTP, dGTP, and 10mM dTTP))
2.	Add 3 ul Cy3-dUTP (1 mM) or 3 ul Cy5-dUTP (1 mM) (ice-cold) to the corresponding samples.  Then add 2 ul SuperScript II (200 U/ul) to each sample.  Mix well by pipeting while on ice.  Incubate the complete mixture for 3 min. at room temperature.  Then transfer to a preheated PCR machine to incubate at 42° C for 120 min.
3.	Cool the reaction to room temperature then add 15 ul RNA Degradation Solution (0.1 M NaOH, 2 mM EDTA), immediately mix well by pipetting 3-4 times, transfer to a preheated PCR machine to incubate at 65°C for 9 min. to degrade RNA and stop the reaction.
4.	Prepare a new 1.5 ml microcentrifuge tube with 10 ul H2O and 10 ul 3M NaAcetate (pH ~5). Transfer both the cy3 reaction and the cy5 reaction to the 1.5 ml microcentrifuge tube already.  Note: Cy5 is not stable at basic condition so this neutralization needs to be done quickly after the RNA degradation.
5.	Purify labeled cDNA using QIAquick PCR Purification Kit (follow manufacturer product insert protocol).

extract_protocol:
RNA extraction
1.	Samples were collected and frozen in TRIzol and homogenized by pestle (Kontes disposable pellet pestle, Fisher Cat. No. K749521-0590).  Then incubate for 5 min. at room temperature.  After this step the sample can be stored at -80°C for at least 3 month.  TRIzol disables RNases.
2.	Add 5 µg linear polyacrylamide (LPA, GenElute from Sigma) as carrier to the sample tube. (If the number of animals in a given collection allowed RNA yield more than 5 ug, LPA was not added.)  Vortex for 10 seconds.  Then transfer the sample to the pre-spun Phase Lock Gel tubes (pre-spin to ensure gel is pelleted at the bottom).
3.	Add 60 ul chloroform and shake vigorously for 15 seconds by hands.  Note: Do not vortex.  Then centrifuge samples at 11,000 to 12,000 g (no more than 12,000 g) for 10 min. at 2–8.  Transfer the aqueous phase (~ 200 ul) to a clean nuclease-free tube.
4.	Add 0.7-0.8 volumes of isopropanol (~160 µl), mix well by shaking and vortexing.  Precipitate overnight at -20ºC.
5.	Centrifuge at 12,000 ~ 14,000 g for 30 min. at 4ºC.  Carefully remove the supernatant by pipette.  Add 500 µl 75% ethanol (room temperature) to wash the pellet by shaking.   Centrifuge at 12,000 ~ 14,000 g for 5 min. at room temperature.  Carefully remove the supernatant by pipette then spin at 12,000 ~ 14,000 g for 15 seconds to collect all residual liquid at the bottom.  Carefully remove the supernatant with a 10 ul pipette tip.  Air-dry (sitting the tubes on bench) the pellet for 1-1.5 min.
6.	Redissolve the pellet in 5 µl (4 ul if it is clear that 20% of the yield isn’t enough for a spectrometer measurement.) nuclease-free water.  (optionally:  Heat the tube in a heat block at 55°C for 30 seconds if the pellet does not disappear immediately.
7.	1 ul of the solution  was used for nanodrop spectrometer measurement.  The sample’s OD260nm/OD280nm ratio is usually > 1.8.
8.	When extracting RNA from whole animal samples and the RNA yield is expected to be > 5 ug, resuspend the pellet in 105 ul of nuclease- free water and clean up the RNA using an RNeasy column from Qaigen using the manufacturer’s protocol as described in the product insert.

value: wpp

tag: wild type

value: CantonS

tag: temperature

value: 22 Celsius

source_name: CantonS at 29 degrees (EXP)

value: 29 Celsius


title: CantonS at 22 vs 29 degrees replicate 2

status: Public on Feb 01 2011

type: RNA

country: USA

description: CantonS wild type at 22 vs 29 degrees on slide 72_031902

tag: developmental stage


title: GFPminus 2

city: Braunschweig

first: Andre

last: Lemme

address: Inhoffenstr. 7

department: Cell Biology

country: Germany

institute: Helmholtz Centre for Infection Research

description: Biological replicate 2 of 2: FACS population GFPminus compared to non-induced cells.

hyb_protocol: 450 ng of each Cy3- and Cy5-labeled RNA was fragmented and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner. Raw data were extracted using the Agilent Feature Extraction software.

data_processing: The algorithm of the Agilent software was used for background correction and normalization. Afterwards, the p-values for differential expression were adjusted for false-discovery rate using the method by Benjamini and Hochberg (BH).

molecule: total RNA

organism: Streptococcus mutans

source_name: FACS GFPminus with CSP

label_protocol: RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: S. mutans were grown in THBY medium at 37°C aerobical (5% CO2 enriched).

extract_protocol: RNA extraction was performed using the Rneasy micro kit (Qiagen).

treatment_protocol: Induction of competence by adding peptide CSP and separation of cells with FACS.

tag: strain

tag: genotype

value: wildtype

tag: induction

value: competence-stimulating peptide (CSP)

tag: cell population

value: incompetent

source_name: Cells not induced with CSP


city: Kansas City

first: Olivier

last: Pourquie

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for RA treatment, biological rep3

hyb_protocol: Each chip was hybridized to 13 μg fragmented cRNA. Arrays were hybridized according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned with a Affymetrix GeneChip Scanner 3000 7G at the Microarray Core Facility of the Stowers Institute for Medical Research

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

organism: Danio rerio

source_name: Zebrafish embryos paraxial mesoderm

label_protocol: Biotinylated cRNA were prepared by using Affymetrix GeneChip Expression 3'-Amplification Reagents for IVT Labeling kit.

growth_protocol: Embryos from AB line were grown at 24C° untill 12-somite stage.

extract_protocol: Trizol extraction of total RNA was performed.

treatment_protocol: Embryos are either incubated in drugs (RA, DMSO, DAPT) at room temperature (24C°) or heat-shocked at 37C° then transfered to 24C°. Embryos were manually dechorionated at 24C°. Selected embryos were transferred to a basket in L15 media. Embryos were manually dissected and the tissue sections were placed in the Trizol solution (Invitrogen) and frozen immediately on dry ice and stored at -80C°.

tag: protocol

value: 1.5 hour DMSO treatment

tag: tissue

value: posterior PSM

value: wild-type AB

tag: age

value: 12-somite stage


title: GFPplus 1

description: Biological replicate 1 of 2: FACS population GFPplus compared to non-induced cells.

source_name: FACS GFPplus with CSP

value: competent


title: Slide 188595

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description: rok-comK vs comK replicate 4

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus subtilis

source_name: Macrocolonies from comK

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Macrocolonies were grown on 2xSG plate and harveseted for RNA preparation after 3 days

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: comK

source_name: Macrocolonies from rok-comK

value: rok-comK


title: GFPminus 1

description: Biological replicate 1 of 2: FACS population GFPminus compared to non-induced cells.


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for RA treatment, biological rep1


title: GFPplus 2

description: Biological replicate 2 of 2: FACS population GFPplus compared to non-induced cells.


title: Slide 188594

description: rok-comK vs comK replicate 3


title: Slide 188694

description: rok vs wt replicate 4

source_name: Macrocolonies from rok

value: rok

source_name: Macrocolonies from wt

value: wt


title: CantonS vs ecdysoneless 22 degrees replicate 4

description: CantonS wild type vs ecdysoneless mutant on slide 73 _031902

source_name: ecdysonelss mutant at 22 degrees (EXP)

tag: mutant

value: ecdysoneless


title: CantonS at 22 vs 29 degrees replicate 1

description: CantonS wild type at 22 vs 29 degrees on slide70_031902

value: wpp


title: CantonS vs ecdysoneless 22 degrees replicate 2

description: CantonS wild type vs ecdysoneless mutant on slide 74_031902 print

value: CantonS


title: ecdysonelss mutant at 22 degrees vs 29 degrees replicate 2

description: mRNA hyb with slide 27 _021802 print

source_name: ecdysonelss mutant at 22 degrees (REF)

value: 22 Celsius

source_name: ecdysonelss mutant at 29 degrees (EXP)


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for RA treatment, biological rep2


title: Slide 188692

description: rok vs wt replicate 2


title: Slide 188691

description: rok vs wt replicate 1

source_name: Macrocoloniesfrom rok


title: Slide 188693

description: rok vs wt replicate 3


title: CantonS vs ecdysoneless 29 degrees replicate 3

description: CantonS wild type vs ecdysoneless mutant on slide 28_021802 print

source_name: CantonS at 29 degrees (REF)

value: 29 Celsius


title: Slide 188171

description: rok-comK vs comK replicate 1


title: CantonS vs ecdysoneless 29 degrees replicate 2

description: CantonS wild type vs ecdysoneless mutant on slide29_021802 print


title: INHA-HCG3

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Affymetrix protocols at Baylor Microarray Core, BCM

data_processing: GCRMA (Genespring 10.0.2, default parameters, baseline transformed to median of all samples)

organism: Mus musculus

source_name: Granulosa Cell, 44-46hr PMSG, 6hr hCG

growth_protocol: 21-day mice were injected with 5IU PMSG for 44-46 hours or 44-46 hours PMSG followed by 6 hr 5IU hCG

extract_protocol: RNA extracted using Qiagen RNeasy Kit

treatment_protocol: Granulosa cells collected by puncture of antral follicles; cells processed immediately, no further treatment

tag: genome/variation

value: Inha-/-

tag: cell type

value: granulosa cell

tag: treatment group

value: 44-46hr PMSG, 6hr hCG


title: INHA-HCG2

scan_protocol: Affymetrix protocols at Baylor Microarray Core, BCM


title: ecdysonelss mutant at 22 degrees vs 29 degrees replicate 1

description: mRNA hyb with slide 27 _021802 print


title: Slide 188593

description: rok-comK vs comK replicate 2


title: INHA-HCG1

label_protocol: Affymetrix protocols at Baylor Microarray Core, BCM


title: WT-HCG3

value: wild type


title: CantonS vs ecdysoneless 29 degrees replicate 1

description: CantonS wild type vs ecdysoneless mutant on slide 60_021802 print


title: INHA1

source_name: Granulosa Cell, 44-46hr PMSG

value: 44-46hr PMSG


title: WT-HCG1


title: ecdysonelss mutant at 22 degrees vs 29 degrees replicate 3

description: ecdysoneless 22 vs ecdysoneless 29

source_name: ecdysonelss mutant at 29 degrees (REF)


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 4

status: Public on Jan 31 2011

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: NKI-AVL

description:
replicate:  F266F8
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel at 10 um resolution using a suitable scan area.

data_processing: Images of the expression arrays were quantified using Imagene software. We used the LIMMA package (R package for statistical computing; http://www.r-project.org) to obtain loess normalized log2-transformed In(3LR)sep over wild type ratios.

source_name: 3rd instar larval brain, In(3LR)sep

label_protocol: 1 µg of amplified mRNA was labeled with 0.3 µl of ULS-Cy5 or 1 µl of ULS-Cy3 label using the ULS labeling system from Kreatech. Details can be found at the website of the NKI Central Microarray Facility (http://cmfdb.nki.nl/process/protocolView).

growth_protocol: Flies were raised at 25 ˚C on standard cornmeal/molasses/agar medium until 3rd instar stage

extract_protocol: For a single microarray experiment, we used isolated central brains from 20 3rd instar larvae. Central brain tissue was collected in TriZol to extract total RNA following manufacturer's instructions. Subsequently, 1 µg of total RNA was amplified using the Superscript RNA amplification system (Invitrogen) following manufacturers’s instructions. This system specifically amplifies mRNA molecules.

treatment_protocol: 3rd instar wandering larvae were collected and dissected.

tag: genotype/variation

value: In(3LR)sep, vvl[sep] kni[ri-1] p[p]

value: central brain

value: 3rd instar larvae

source_name: 3rd instar larval brain, wild type


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 2, dye swap

description:
replicate:  F266F5
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 4, dye swap

description:
replicate:  F266F9
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 3

description:
replicate:  F266F6
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: WT3


title: In(3LR)sep 4C map of Antp, biological replicate 1

type: genomic

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Antennapedia P1 promoter region (Antp) as bait. Samples are derived from In(3LR)sep larval brain tissue. Fly strain In(3LR)sep carries a chromosomal inversion, which rearranges the centromere-proximal ~5.8 Mbp of chromosome 3R to the left arm and approximately 17 Mbp of chromosome 3L to the right arm. We used this strain to demonstrate that long-range chromatin interactions are constrained by chromosome architecture. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (IN_Antp_rep1, and IN_Antp_rep2).

hyb_protocol: Differentially labeled 4C and reference samples were combined in a total volume of 120 µl, containing: blocking solution (1 µg human COT-1 DNA, 1 µg poly d(A), 0.4 µg yeast tRNA) and F buffer (50% v/v Formamide, 10x SSC, 0.2% v/v SDS). Prior to hybridization, the mixture was heated at 95 ˚C for 3 minutes. Mixture was hybridized at 42 ˚C for more than 16 hours using a DNA microarray hybridization chamber (SureHyb, Agilent) in a DNA microarray hybridization oven (Agilent). Next, we performed a series of stringency washes to remove non- and aspecifically annealed material. First, we washed 30 seconds in 5xSSC, 0.1% (v/v) SDS at 42 ˚C. Second, we washed 30 seconds in 2xSSC, 0.1% (v/v) SDS at 42 ˚C. Third, we washed 5 minutes in 1xSSC at 42 ˚C. Finally, we washed 2 minutes in 0.2xSSC at room temperature. Washed slides were quickly dried using Nitrogen gas.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version GE2-v4.9.1).

data_processing: LOWESS normalized data obtained from log2 of processed Red signal/processed Green signal. R statistical programming language was used. Note: the “background filter” (to correct for linear proximity) was not applied to raw and normalized data that is presented here.

molecule: genomic DNA

source_name: Antp 4C DNA from In(3LR)sep larval brain tissue

label_protocol: The 4C and reference samples were differentially labeled with the ULS aRNA labeling kit (EA-006, Kreatech), using Cy3 and Cy5 dyes (Amersham). Briefly, 1 µg of material was incubated for 1h at 85 ˚C in 1x Labeling Buffer (Kreatech) and in the presence 1 µl of either Cy3-ULS or Cy5-ULS. Afterwards, samples were cooled on ice and non-reacted ULS was removed using KREApure columns (Kreatech).

growth_protocol: Flies were raised at 25 ˚C on standard cornmeal/molasses/agar medium

extract_protocol: We dissected and pooled 40 pairs of central brain hemispheres. With gentle forceps manipulation we quickly removed the central nervous system from each larva, while leaving the mouth hook and imaginal discs attached, and placed it in PBS on ice. After 40 dissections, we replaced the PBS with 2% formaldehyde in PBS and fixed the samples for 15 minutes at room temperature while tumbling. The reaction was quenched for 5 minutes by adding 125 mM glycin final concentration, followed by three quick washes with cold PBS. Next, we removed the mouth hook, imaginal discs, and ventral nerve cord with gentle forceps manipulation. The remaining central brain hemispheres were placed into ice cold cell lysis buffer (10 mM Tris – pH 8.0; 10 mM NaCl; 0.2% Nonidet P40; 1x Complete protease inhibitors – Roche). Finally, the nuclei were centrifuged for 15 minutes with 2700g at 4˚C and supernatant was removed afterwards. On this nuclei pellet, we applied the 3C procedure as described (Tolhuis et al. 2002 Mol. Cell 10, 1453-1465), yielding ligation products between EcoRI fragments. We used the original 4C protocol to obtain circularized DNA templates for the 4C PCR (Simonis et al., 2006 Nat. Genet. 38, 1348-1354), and either DpnII or NlaIII as frequently cutting restriction enzymes. We supplemented our reverse 4C PCR primers with a T7 promoter sequence overhang. 4C PCR reactions were performed directly on the circularized 4C templates using Taq polymerase (Invitrogen) and conditions were as follows: 94 ˚C for 2 min; 30 cycles of 94 ˚C for 15s, 60 ˚C for 1 min and 72 ˚C for 1 min; and a final elongation step of 72 ˚C for 5 min. We purified the PCR products using the Qiaquick PCR purification kit (Qiagen). We further amplified the 4C PCR products in a strictly linear fashion using a T7 RNA amplification step. For this we used the Superscript RNA amplification system (Invitrogen) according to the manufacturer’s guidelines. As a reference, we digested genomic DNA from w1118 third instar larvae with DpnII. To each restriction end, we added adaptors containing the T7 promoter sequence by means of ligation. We amplified 1 µg of this DNA using the Superscript RNA amplification system.

value: 3rd instar larva

tag: sample type

source_name: genomic DNA reference

value: Whole larva

value: genomic DNA reference


title: INHA2


title: WT2


title: WT-HCG2


title: In(3LR)sep 4C map of Abd-B, biological replicate 2, technical replicate b

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait. Samples are derived from In(3LR)sep larval brain tissue. Fly strain In(3LR)sep carries a chromosomal inversion, which rearranges the centromere-proximal ~5.8 Mbp of chromosome 3R to the left arm and approximately 17 Mbp of chromosome 3L to the right arm. We used this strain to demonstrate that long-range chromatin interactions are constrained by chromosome architecture. Each biological replicate was hybridized twice using technical replicates. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 4 samples (IN_Abd-B_rep1a, IN_Abd-B_rep1b, IN_Abd-B_rep2a, and IN_Abd-B_rep2b).

source_name: Abd-B 4C DNA from In(3LR)sep larval brain tissue


title: INHA3


title: WT1


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 3, dye swap

description:
replicate:  F266F7
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 1, dye swap

description:
replicate:  F266D6
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: Non-hairpin shRNA, RA-differentiated

city: New York

first: Hao

last: Jiang

state: NY

address: 1230 York Ave

institute: Rockefeller University

description:
Non-hairpin shRNA, RA-differentiated
4639127062_E.txt

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Results were analyzed by GeneSpring GX 10.0.2. Genes were filtered on Flags Present or Marginal. Signals were normalized against the median in each sample.

source_name: E14 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: E14 cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium supplemented with LIF

extract_protocol: Total RNAs were extracted using the RNeasy kit (Qiagen).

treatment_protocol: Cells stably infected with viruses expressing indicated shRNAs were either untreated or treated with retinoic acid (RA) for differentiation (four days depletion of LIF followed by four days of 1 µM all-trans RA on monolayer culture.

tag: shRNA

value: control

tag: differentiation status

value: RA-differentiated


title: RbBP5 shRNA, undifferentiated

description:
RbBP5 shRNA, undifferentiated
4639127062_C.txt

value: RbBP5 knockdown

value: undifferentiated


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 1

description:
replicate:  F266D3
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: 3rd instar larval brain cells, mRNA changes in In(3LR)sep compared to wild type strains, rep 2,

description:
replicate:  F266F4
Data from all replicate samples (i.e. F266D3, F266D6,  F266F4, F266F5, F266F6, F266F7, F266F8, and F266F9) was averaged; see supplementary file on Series record.


title: Scramble shRNA, undifferentiated

description:
Scramble shRNA, undifferentiated
4639127062_B.txt


title: Dpy-30 shRNA, undifferentiated

description:
Dpy-30 shRNA, undifferentiated
4639127062_D.txt

value: Dpy-30 knockdown


title: Scramble shRNA, RA-differentiated

description:
Scramble shRNA, RA-differentiated
4639127062_F.txt


title: Non-hairpin shRNA, undifferentiated

description:
Non-hairpin shRNA, undifferentiated
4639127062_A.txt


title: In(3LR)sep 4C map of Antp, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Antennapedia P1 promoter region (Antp) as bait. Samples are derived from In(3LR)sep larval brain tissue. Fly strain In(3LR)sep carries a chromosomal inversion, which rearranges the centromere-proximal ~5.8 Mbp of chromosome 3R to the left arm and approximately 17 Mbp of chromosome 3L to the right arm. We used this strain to demonstrate that long-range chromatin interactions are constrained by chromosome architecture. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (IN_Antp_rep1, and IN_Antp_rep2).


title: RbBP5 shRNA, RA-differentiated

description:
RbBP5 shRNA, RA-differentiated
4639127062_G.txt


title: Dpy-30 shRNA, RA-differentiated

description:
Dpy-30 shRNA, RA-differentiated
4639127062_H.txt


title: In(3LR)sep 4C map of Abd-B, biological replicate 2, technical replicate a

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait. Samples are derived from In(3LR)sep larval brain tissue. Fly strain In(3LR)sep carries a chromosomal inversion, which rearranges the centromere-proximal ~5.8 Mbp of chromosome 3R to the left arm and approximately 17 Mbp of chromosome 3L to the right arm. We used this strain to demonstrate that long-range chromatin interactions are constrained by chromosome architecture. Each biological replicate was hybridized twice using technical replicates. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 4 samples (IN_Abd-B_rep1a, IN_Abd-B_rep1b, IN_Abd-B_rep2a, and IN_Abd-B_rep2b).


title: Wild type 4C map of Crc, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Calreticulin  (Crc) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_Crc_rep1, and WT_Crc_rep2).

source_name: Crc 4C DNA from w[1118] larval brain tissue


title: Wild type 4C map of RpII140, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using RNA polymerase II 140 kD subunit  (RpII140) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_ RpII140_rep1, and WT_ RpII140_rep2).

source_name: RpII140 4C DNA from w[1118] larval brain tissue


title: In(3LR)sep 4C map of Abd-B, biological replicate 1, technical replicate a

value: long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait


title: Wild type 4C map of Crc, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Calreticulin  (Crc) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_Crc_rep1, and WT_Crc_rep2).


title: Wild type 4C map of wntD, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Wnt inhibitor of Dorsal  (wntD) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_wntD_rep1, and WT_wntD_rep2).

source_name: wntD 4C DNA from w[1118] larval brain tissue


title: Wild type 4C map of CG5107, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using CG5107 as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_CG5107_rep1, and WT_ CG5107_rep2).

source_name: CG5107 4C DNA from w[1118] larval brain tissue


title: bone metastasis 6#

city: guangzhou

first: David

last: Guo

address: zhongshan 2 road

country: China

institute: SYSU

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 303 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).

hyb_protocol: Standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: The miRNA arrays were scanned with a confocal LuxScan 10K/A scanner at CapitalBio Corp.

data_processing:
Image intensities were measured as a function of the median of foreground minus the background.
Raw data were normalized and analyzed in GenePix Pro 4.0 software (Axon Instruments). We processed data with linear normalization, which calculates the global mean.

organism: Homo sapiens

source_name: bone metastatic tissue of prostate cancer

label_protocol: MiRNAs was labeled with Fluorescein, as described as (Thomson JM, 2004).About 2μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, USA), then miRNA was separated from 30-50 mg total RNA using the Ambion miRNA Isolation Kit.

treatment_protocol: All the samples were formalin-fixed and paraffin-embedded (FFPE).

tag: disease state


title: bone metastasis 4#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 301 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).

value: bone metastatic tissue of prostate cancer


title: bone metastasis 5#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 302 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: bone metastasis 7#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 304 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: Wild type 4C map of Ptx1, biological replicate 2, technical replicate b

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Ptx1 as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was hybridized twice using technical replicates. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 4 samples (WT_Ptx1_rep1a, WT_ Ptx1_rep1b, WT_ Ptx1_rep2a, and WT_ Ptx1_rep2b).

source_name: Ptx1 4C DNA from w[1118] larval brain tissue

tag: developmental stage


title: Wild type 4C map of Ptx1, biological replicate 1, technical replicate b

value: long-range chromatin interactions using Ptx1 as bait


title: Wild type 4C map of trh, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using trachealess (trh) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_trh_rep1, and WT_trh_rep2).

source_name: trh 4C DNA from w[1118] larval brain tissue


title: Wild type 4C map of Antp, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Antennapedia P1 promoter region (Antp) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_Antp_rep1, and WT_Antp_rep2).

source_name: Antp 4C DNA from w[1118] larval brain tissue


title: bone metastasis 3#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 300 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: Wild type 4C map of wntD, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Wnt inhibitor of Dorsal  (wntD) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_wntD_rep1, and WT_wntD_rep2).


title: P1-A vs P1-B

description: compare miRNA profile of primary prostate cancer and bone metastasis

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

data_processing: The raw data were normalized with Lowess program in R package.  The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: primary prostate cancer specimen

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) or '-phosphate-cytidyl-uridyl-cy5-3' with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

extract_protocol: Total RNA was isolated using trizol reagent (invitrogen, USA) according to manufacturer's directions.

value: primary prostate cancer


title: Wild type 4C map of RpII140, biological replicate 1

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using RNA polymerase II 140 kD subunit  (RpII140) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 2 samples (WT_RpII140_rep1, and WT_ RpII140_rep2).


title: In(3LR)sep 4C map of Abd-B, biological replicate 1, technical replicate b

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait. Samples are derived from In(3LR)sep larval brain tissue. Fly strain In(3LR)sep carries a chromosomal inversion, which rearranges the centromere-proximal ~5.8 Mbp of chromosome 3R to the left arm and approximately 17 Mbp of chromosome 3L to the right arm. We used this strain to demonstrate that long-range chromatin interactions are constrained by chromosome architecture. Each biological replicate was hybridized twice using technical replicates. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 4 samples (IN_Abd-B_rep1a, IN_Abd-B_rep1b, IN_Abd-B_rep2a, and IN_Abd-B_rep2b).


title: Wild type 4C map of CG5107, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using CG5107 as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_ CG5107_rep1, and WT_ CG5107_rep2).


title: Wild type 4C map of Abd-B, biological replicate 2, technical replicate a

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was hybridized twice using technical replicates. The represented final value is an average of 4 hybridizations/raw data files: 1) WT_Abd-B_rep1a.txt is a straight hybridization (Cy5 = 4C, and Cy3 = reference); 2) WT_Abd-B_rep1b.txt sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference); 3)  WT_Abd-B_rep2a.txt is a straight hybridization (Cy5 = 4C, and Cy3 = reference); and 4) WT_Abd-B_rep2b.txt is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference).

source_name: Abd-B 4C DNA from w[1118] larval brain tissue


title: Wild type 4C map of trh, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using trachealess (trh) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_trh_rep1, and WT_trh_rep2).


title: Wild type 4C map of Ptx1, biological replicate 2, technical replicate a

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Ptx1 as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was hybridized twice using technical replicates. This sample is a straight hybridization (Cy5 = 4C, and Cy3 = reference). The final value is an average of 4 samples (WT_ Ptx1_rep1a, WT_ Ptx1_rep1b, WT_ Ptx1_rep2a, and WT_ Ptx1_rep2b).


title: Wild type 4C map of Abd-B, biological replicate 1, technical replicate b

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Abdominal-B promoter region (Abd-B) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was hybridized twice using technical replicates. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 4 samples (WT_Abd-B_rep1a, WT_Abd-B_rep1b, WT_Abd-B_rep2a, and WT_Abd-B_rep2b).


title: Wild type 4C map of Antp, biological replicate 2

description: We analyzed two biological replicates of 4C products to our custom microarray to capture long-range chromatin interactions using Antennapedia P1 promoter region (Antp) as bait. Samples are derived from wild type (i.e. fly strain w[1118]) larval brain tissue. Each biological replicate was differentially labeled. This sample is a dye swap hybridization (Cy3 = 4C, and Cy5 = reference). The final value is an average of 2 samples (WT_Antp_rep1, and WT_Antp_rep2).


title: Wild type 4C map of Abd-B, biological replicate 2, technical replicate b


title: bone metastasis 2#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 299 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 6#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 297 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 5#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 296 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: bone metastasis 1#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 298 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 2#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 293 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 3#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 294 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 4#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 295 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: primary PCa 1#

description: Sample was used for hybridization on each miRNA microarray chip containing 924 probes in triplicate, corresponding to 677 human (including 122 predicted miRNAs), 461 mouse, and 292 rat miRNAs found in the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 10.0, 2007).


title: Wild type 4C map of Abd-B, biological replicate 1, technical replicate a


title: SV40 immortalized MEF Tdg heterozygous rep1

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

hyb_protocol: 15 µg of fragmented cRNA were hybridized to Mouse Genome 430A 2.0 Arrays (Affymetrix) according to the manufacturers protocol.

scan_protocol: Arrays were scanned with a Affymetrix Scanner 3000 7G using the Microarray Suite software

data_processing: Scanned images were processed with the Microarray Suite software. Data was normalized by robust multi-array average (RMA) expression measure 'rma()' and detection calls and p-values were calculated by 'mas5calls()'. Statistical analysis were performed with R / Bioconductor using the package affy and libraries contained therein, in particular limma.

label: biotin-streptavidin R-phycoerythrin

source_name: Mouse embryonic fibroblasts - TDG heterozygotes, SV40 immortalized

label_protocol: 13 µg of total RNA were used to generate cDNA with the SuperScript double-Stranded cDNA Synthesis kit (Invitrogen) followed by in vitro transcription and labelling reactions performed with the MEGA Script T7 Kit (Ambion) supplemented with 1.5 mM Bio-11-CTP and Bio-16-UTP (Enzo Life Sciences).

growth_protocol: Cells were grown in DMEM 10% FCS 1x Penicillin/Streptomycin

extract_protocol: Total RNA was extracted from cell pellets stored in RNA later using the RNeasy Mini Kit (Qiagen)

tag: clone

value: Tdg+/-

value: embryonic fibroblast


title: SV40 immortalized MEF Tdg heterozygous rep2

tag: genotype


title: SV40 immortalized MEF Tdg knockout rep2

source_name: Mouse embryonic fibroblasts - TDG knock-out, SV40 immortalized

value: Tdg-/-


title: SV40 immortalized MEF Tdg knockout rep3


title: Liver tissue from chimeric mouse 3

status: Public on Jan 25 2011

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).

source_name: Liver tissue from untreated chimeric mouse 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

growth_protocol: uPA/SCID mice were transplanted with human hepatocytes derived from a Caucasian 9-month-old male infant and an African American 6-year-old girl. Around 60 days after transplantation the mouse livers were replated with human hepatocytes.

extract_protocol:
Total RNA was extracted from cells or liver tissues with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
The purified total RNAs of white and red regions from 3 uPA/SCID mouse livers were pooled and used for the analysis.

treatment_protocol:
A half of the chimeric mice were continuously infused with  2.5 mg/kg b.w./day h-growth hormone through an s.c.-implanted Alzet micro-osmotic pump for 2 weeks berore sactifice. h-Hepatocytes were isolated from h-GH-treated and untreated chimeric mice by collagenase perfusion method.  h-Hepatocyte-repopulated regions were dissected from liver tissue of h-GH-treated and untreated chimeric mice.
White and red regions were dissected from liver tissue of 3 uPA/SCID mice to investigate cross-reactivity of the mouse genes to the microarrays. White regions are originated from an uPA-derived diseased liver, and red regions are uPA gene-deleted recovered ares of the liver.

tag: donor of hepatocytes

value: African American 6-year-old girl

tag: gender of mice

value: female

tag: age of mice (wk)

tag: days post-transplantation

tag: human albumin level in mouse blood (mg/ml)

value: Liver tissue

tag: host genetic background

value: uPA/SCID


title: Liver tissue from chimeric mouse 1

source_name: Liver tissue from untreated  chimeric mouse 1

tag: tissue


title: SV40 immortalized MEF Tdg heterozygous rep3

tag: cell type


title: Liver tissue from chimeric mouse 2

source_name: Liver tissue from untreated chimeric mouse 2


title: Liver tissue from h-GH-treated chimeric mouse 2


title: SV40 immortalized MEF Tdg knockout rep1


title: Liver tissue from h-GH-treated chimeric mouse 3


title: Liver tissue from h-GH-treated chimeric mouse 1

value: male


title: Wild type 4C map of Ptx1, biological replicate 1, technical replicate a

value: central brain

value: 3rd instar larva

source_name: genomic DNA reference

value: Whole larva

value: genomic DNA reference


title: OvCLMixRefC1(3) vs. TOV21G

status: Public on Jan 22 2011

city: Santa Monica

first: Charles

middle: L

last: Ginther

state: CA

address: 2825 Santa Monica Blvd, #200

department: Hem-Onc

institute: UCLA

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization;: (1) local background used, (2) special detrend Off, (3) adjust background globally Off, (4) red autoestimate Off, and (5) green autoestimate Off.
normalized log10 ratio (Cy5/Cy3) representing test/reference
Rosetta Resolver (v.7.2.2.0) was used for subsequent analysis of the array data

source_name: OvCLMixRefC1(41 cell lines)

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

growth_protocol:
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.  The growth media for the various lines were as follows:
All cell lines were characterized using mtDNA sequence prior to use
A2780: RPMI1640 Medium (ATCC) plus 10% FBS and 0.25 U.ml insulin.
CAOV3: DMEM Medium plus 10% FBS and 4.5 g.L glucose
COLO704, HEY, OV2008, C90:  RPMI1640 medium plus 10% FBS
DOV13, MCAS: Eagle's Minimal Essential Medium (ATCC) plus 15% FBS
EFO21, EFO27: RPMI1640 Medium 20% FBS and 1% MEM Non-Essential Amino Acid Solution (ATCC)
ES-2: McCoy's 5A Medium (ATCC) plus 10% FBS
HEY-C2: DMEM/F12 (ATCC) plus 10% FBS
KK, KOC-7c, KURAMOCHI: RPMI1640 Medium plus 10% FBS and 1% MEM Non-Essential Amino Acid Solutioin and 0.25 U/ml insulin
OAW28, OAW42: DMEM (ATCC) plus 10% FBS
OV167, OV177, OV207: MEM (Fisher Sci.) plus 20% FBS
OVCA420, OVCA429: MEM plus 10%FBS
OVCA432: Eagle's Minimal Essential Medium
All cultures were supplimented with !% penicillin-streptomycin and 1% l-glutamine

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol

value: OvCLMixRefC1(41 cell lines)

value: 41 ovarian cell lines

tag: pd-0332991 ic50 in umol

tag: pd-0332991 sensitivity

value: Sensitive

tag: cell line

value: Ovarian cell line


title: OvCLMixRefC1(3) vs. PEO14

tag: sample type


title: OvCLMixRefC1(3) vs. RMUGS

source_name: RMUGS

value: RMUGS


title: Polycomb in larval brain, replicate 2

description: Polycomb DamID in untreated larval brain tissue

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 13 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in an Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 5 µm per pixel resolution. Images were quantified using NimbleScan Software (version 2.5).

data_processing: Values of all reporters except NimbleGen control reporters were extracted from pair files, represented as log2-ratios and normalized using the the lowess() function in R.

source_name: Larval brain tissue expressing PC-Dam

label_protocol: 1 µg DamID DNA was directly labeled by Klenow random priming with Cy5/Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: For a single DamID experiment, we used 10 M{UAS-Pc::Dam}ZH51C/CyO, P{Dfd-EYFP} and 10 M{UAS-Dam}ZH51C/CyO central brains from 3rd instar larvae. Isolation and amplification of DamID DNA fragments were performed as described (Greil et al. 2003, Genes Dev. 17, 2825-2838).

treatment_protocol: 3rd instar wandering larvae were collected and dissected. PC-Dam expression depended solely on leakiness of the uninduced pUAST promoter in the absence of a Gal4 driver.

value: M{UAS-Pc::Dam}ZH51C/CyO, P{Dfd-EYFP}

value: 3rd instar larvae

source_name: Larval brain tissue expressing Dam

treatment_protocol: 3rd instar wandering larvae were collected and dissected. Dam expression depended solely on leakiness of the uninduced pUAST promoter in the absence of a Gal4 driver.


title: OvCLMixRefC1(3) vs. RMG1


title: OvCLMixRefC1(3) vs. OVTOKO

source_name: OVTOKO

value: OVTOKO


title: OvCLMixRefC1(3) vs. SKOV3


title: OvCLMixRefC1(3) vs. SW626


title: OvCLMixRefC1(3) vs. OVCAR5


title: OvCLMixRefC1(3) vs. PEA2

value: Resistant


title: OvCLMixRefC1(3) vs. OVSAHO

source_name: OVSAHO

value: OVSAHO


title: OvCLMixRefC1(3) vs. TYK-nu

source_name: TYK-nu

value: TYK-nu


title: Polycomb in larval brain, replicate 1


title: OvCLMixRefC1(3) vs. PE06


title: OvCLMixRefC1(3) vs. OVMANA

source_name: OVMANA

value: OVMANA


title: OvCLMixRefC1(3) vs. OVKATE

source_name: OVKATE

value: OVKATE


title: OvCLMixRefC1(3) vs. TOV112D


title: H3K27me3 in larval brain, replicate 2

description: Comparison of H3K27me3 and non-specific control (IgG) in larval brain tissue.

source_name: Larval brain tissue

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow random priming with Cy5/Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: We used the Red ChIP kit according the manufacturers guidelines (www.diagenode.com). For each ChIP reaction, we used 1 µg of either one of the following antibodies, anti-H3K27me3 (07-449, Upstate), and anti-IgG (ab17890, Abcam). We dissected central brains from 50 3rd instar larvae for a single ChIP experiment. Amplification of ChIP isolated DNA fragments and microarray analysis were performed as described (Tolhuis et al. 2006. Nat. Genet. 38, 694-699).

value: central brain

tag: chip antibody

value: H3k27me3 (07-449 – Upstate)

value: IgG (ab17890 – Abcam)


title: H3K27me3 in larval brain, replicate 1


title: OvCLMixRefC1(3) vs. OVISE

source_name: OVISE

value: OVISE


title: OvCLMixRefC1(3) vs. OVCA432

value: OvCLMixRefC1(41 cell lines)


title: OvCLMixRefC1(3) vs. OVCAR3 (2)

value: 41 ovarian cell lines


title: OvCLMixRefC1(3) vs. OVCA420

value: Sensitive


title: OvCLMixRefC1(3) vs. OV207

value: Ovarian cell line


title: OvCLMixRefC1(3) vs. OVCA429


title: OvCLMixRefC1(3) vs. OV177


title: OvCLMixRefC1(3) vs. OV90


title: OvCLMixRefC1(3) vs. OV167


title: OvCLMixRefC1(3) vs. OV2008


title: OvCLMixRefC1(3) vs. KK

source_name: KK

value: KK


title: OvCLMixRefC1(3) vs. KOC-7C


title: OvCLMixRefC1(3) vs. MCAS

source_name: MCAS

value: MCAS


title: OvCLMixRefC1(3) vs. ES2


title: OvCLMixRefC1(3) vs. OAW28


title: OvCLMixRefC1(3) vs. OAW42


title: Scap_ko2

status: Public on Jan 08 2011

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: data processed/normalized by algorithm:RMA

source_name: E18.5 total lung RNA, knockout

label_protocol: based on Affymetrix protocols

extract_protocol: Whole lung total RNA was purified by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

value: lung

tag: strain

value: mixed background issued from the FVB/N strain and B6

tag: genotype/variation

value: SREBP cleavage-activating protein gene(Scap) was deleted from respiratory epithelial cells (Scap d/d) in vivo. / knockout


title: OvCLMixRefC1(3) vs. HEY

source_name: HEY

value: HEY


title: OvCLMixRefC1(3) vs. HEYC2


title: OvCLMixRefC1(3) vs. EFO21

value: Resistant


title: OvCLMixRefC1(3) vs. Kuramochi

source_name: Kuramochi

value: Kuramochi


title: OvCLMixRefC1(3) vs. DOV13


title: OvCLMixRefC1(3) vs. A2780


title: Scap_control3

source_name: E18.5 total lung RNA, control

value: SREBP cleavage-activating protein gene(Scap) was deleted from respiratory epithelial cells (Scap d/d) in vivo. / control


title: Scap_ko1


title: OvCLMixRefC1(3) vs. CaOV3

source_name: OvCLMixRefC1(41 cell lines)


title: OvCLMixRefC1(3) vs. COLO704


title: OvCLMixRefC1(3) vs. EFO27


title: Scap_control1


title: Scap_ko3


title: Whole plant_rep2

status: Public on Dec 01 2010

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression in the rice whole plant

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 - 1400ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

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

data_processing:
Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). We slightly modified manufacturer's default extraction protocol called 'GE1-v5_95_Feb07' as follows: 'Background Subtraction Method' was set to 'Average of Negative Control Features', and 'Use Surrogates' was set to 'False'. Then 'gBGSubSignal' columns were extracted from the text data files produced by FeatureExtraction, and introduced into GeneSpring 7.3.1 (Agilent). Positive and negative control features (such as spike-in or dark corner) were removed before data introduction into GeneSpring. Introduced signal intensities were scaled to the 75th percentile per chip (scaled the 75th percentile value was set to 10), and the lowest value of scaled signal intensity was set to 0.01. Microarray intensity values were also normalized per chip by Z score transformation using R software (http://www.r-project.org/).
A scaled data set with the 75th percentile scaling (VALUE) was used in the scatter plot analysis, correlation plot analysis, and to make the lists of the top 10 highly expressed probes. Z-score transformed (per chip) data sets (VALUE2) were also used in the cluster analysis and heat map analysis.

organism: Oryza sativa

source_name: Whole plant, replicate 2

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

growth_protocol: Wild-type rice plants (Oryza sativa L. cv. Nipponbare) were grown in pots under natural conditions.

extract_protocol: Total RNA was extracted from each cell type and tissue with a PicoPure™ RNA isolation kit (Molecular Devices, Ontario, Canada) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To check influences in gene expression of the isolated cells caused by the transient storage in mannitol solution, we prepared RNA samples derived from ovaries with mannitol treatment and another kind of RNA samples derived from ovaries without mannitol treatment, to look for differences in expression between them. Mannitol treatment consisted of soaking five ovaries in mannitol solution for 8 h.

tag: subspecies

value: japonica

tag: cultivars

value: Nipponbare

value: Whole plant


title: Whole plant_rep3

description: Gene expression in the rice whole plant

source_name: Whole plant, replicate 3


title: Whole plant_rep1

description: Gene expression in the rice whole plant

source_name: Whole plant, replicate 1


title: Ovary_M-_rep2

description: Gene expression in the rice ovary without mannitol treatment

source_name: Ovary without mannitol treatment, replicate 2

value: Ovary

tag: treatment group

value: without mannitol treatment


title: Scap_control2


title: Synergid cell_rep1

description: Gene expression in the rice synergid cell

source_name: Synergid cell, replicate 1

value: Synergid cell


title: Egg cell_rep3

description: Gene expression in the rice egg cell

source_name: Egg cell, replicate 3

value: Egg cell


title: Ovary_M+_rep2

description: Gene expression in the rice ovary with mannitol treatment

source_name: Ovary with mannitol treatment, replicate 2

value: with mannitol treatment


title: Egg cell_rep1

description: Gene expression in the rice egg cell

source_name: Egg cell, replicate 1


title: Synergid cell_rep3

source_name: Synergid cell, replicate 3


title: Ovary_M+_rep3

source_name: Ovary with mannitol treatment, replicate 3


title: Anther at P1, biological rep2

status: Public on Nov 11 2010

description: Gene expression data from developing anther.

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 ng of labeled and fragmented cRNA was hybridized to microarray using  hybridization oven G2545A (Agilent), and wash step was performed with  Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). We slightly modified manufacturer's default extraction protocol called 'GE1-v5_95_Feb07' as follows: 'Background Subtraction Method' was set to 'Average of Negative Control Features', and 'Use Surrogates' was set to 'False'. Then 'gBGSubSignal' columns were extracted from the text data files produced by FeatureExtraction, and introduced into GeneSpring 7.3.1 (Agilent). Positive and negative control features (such as spike-in or dark corner) were removed before data introduction into GeneSpring. Introduced signal intensities were scaled to median per chip, and the lowest value of scaled signal intensity was set to 0.01. Normalized signal intensities of some probes locating multiple positions on a array were average values of all corresponding probes.

source_name: Anther, uni-nucleated gametopyte stage

label_protocol: Cy3-labeled cRNA were prepared from 100 ng total RNA using Low RNA Input Linear Amp Kit (Agilent) according to manufacturer's protocol .

growth_protocol: Plants were grown in paddy fields under normal condition at Mishima, Japan.

extract_protocol: Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Tissue samples were collected on July - October. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.

tag: cultivar


title: Ovary_M-_rep3

source_name: Ovary without mannitol treatment, replicate 3


title: Anther at P3, biological rep2

source_name: Anther, tri-cellular mature pollen stage


title: Ovary_M+_rep1

source_name: Ovary with mannitol treatment, replicate 1


title: Synergid cell_rep2

source_name: Synergid cell, replicate 2


title: Ovary_M-_rep1

source_name: Ovary without mannitol treatment, replicate 1


title: Anther at P2, biological rep2

source_name: Anther, bi-cellular gametopyte stage


title: Egg cell_rep2

description: Gene expression in the rice egg cell

source_name: Egg cell, replicate 2


title: Anther at P3, biological rep3


title: Anther at M2, biological rep1

source_name: Anther, pollen mother cells at meiotic zygotene-pachytene stage


title: Anther at P2, biological rep3


title: Anther at M1, biological rep2

source_name: Anther, pollen mother cells at meiotic leptotene stage


title: Anther at M3, biological rep2

source_name: Anther, pollen mother cells at meiotic diplotene-tetrad stage


title: Anther at M2, biological rep3


title: Anther at P1, biological rep1


title: WT MEFs without IFNa treatment

status: Public on Nov 04 2010

city: Taipei

first: Chien-Kuo

last: Lee

address: No. 1, Jen-Ai Road, Section 1, Rm 513

department: Graduate Institute of Immunology

country: Taiwan

institute: National Taiwan University College of Medicine

data_processing: The data were normalised using Illumina Inc. BeadStudio version 3.2.3, normalization = cubic spline.

source_name: WT Mouse Embryonic Fibroblasts (MEFs) without IFNa treatment

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.

value: MEF cell line

value: WT

tag: agent

value: no IFNa treatment


title: Anther at An1, biological rep1

source_name: Anther, hypodermal archesporial cells forming stage


title: WA BC anther rep 3

status: Public on Aug 22 2010

city: Sendai

first: Kinya

last: Toriyama

state: Miyagi

address: Tsutsumidori^Amamiyamachi, Aobaku

department: Graduate School of Agricultural Science

institute: Tohoku University

description: Gene expression in bicellular pollen stage anthers of the WA-CMS line

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.3.1 (Agilent). Quantile normalization was done using normalizeQuantile function included in limma library of R v 2.9.1 software (R development Core team 2009).

source_name: WA-CMS line, bicellular pollen stage anther, rep_3

label_protocol: Cy3-labeled cRNA were prepared from 100 ng of total RNA using Low RNA Linear Amplification Kit (Agilent) according to manufacturer's protocol.

growth_protocol: Plants are grown in a glasshouse under natural conditions at Tohoku University, Sendai, Japan.

extract_protocol: Total RNA was extracted from 180 anthers at the uninucleate microspore or bicellular pollen stages using RNeasy Plant Mini Kit (Qiagen) .

treatment_protocol: Six distinct rice lines derived from cytoplasmic substitution.

tag: phenotype

value: male-sterile

value: WA-CMS line

value: anther

tag: developmental stage

value: bicellular pollen stage


title: Anther at Mei1, biological rep3

source_name: Anther, pollen mother cells at pre-meiotic S/G2 stage


title: Anther at Mei1, biological rep2


title: Anther at An1, biological rep2


title: WA BC anther rep 1

source_name: WA-CMS line, bicellular pollen stage anther, rep_1


title: W11 BC anther rep 1

description: Gene expression in bicellular pollen stage anthers of the W11-CMS line

source_name: W11-CMS line, bicellular pollen stage anther, rep_1

value: W11-CMS line


title: WA BC anther rep 2

source_name: WA-CMS line, bicellular pollen stage anther, rep_2


title: W11 BC anther rep 2

source_name: W11-CMS line, bicellular pollen stage anther, rep_2


title: T65 BC anther rep 2

description: Gene expression in bicellular pollen stage anthers of the T65 line

source_name: T65, bicellular pollen stage anther, rep_2

value: male-fertile

value: Taichung 65


title: LD BC anther rep 2

description: Gene expression in bicellular pollen stage anthers of the LD-CMS line

source_name: LD-CMS line, bicellular pollen stage anther, rep_2

value: LD-CMS line


title: T65 BC anther rep 3

source_name: T65, bicellular pollen stage anther, rep_3


title: T65 BC anther rep 1

source_name: T65, bicellular pollen stage anther, rep_1


title: W11 BC anther rep 3

source_name: W11-CMS line, bicellular pollen stage anther, rep_3


title: Anther at M1, biological rep1

value: Nipponbare


title: LD BC anther rep 3

source_name: LD-CMS line, bicellular pollen stage anther, rep_3


title: LD BC anther rep 1

source_name: LD-CMS line, bicellular pollen stage anther, rep_1


title: CW BC anther rep 3

description: Gene expression in bicellular pollen stage anthers of the CW-CMS line

source_name: CW-CMS line, bicellular pollen stage anther, rep_3

value: CW-CMS line


title: WA UN anther rep 3

description: Gene expression in uninucleate microspore stage anthers of the WA-CMS line

source_name: WA-CMS line, uninucleate microspore stage anther, rep_3

value: uninucleate microspore stage


title: BT BC anther rep 1

description: Gene expression in bicellular pollen stage anthers of the BT-CMS line

source_name: BT-CMS line, bicellular pollen stage anther, rep_1

value: BT-CMS line


title: CW BC anther rep 2

source_name: CW-CMS line, bicellular pollen stage anther, rep_2


title: BT BC anther rep 2

source_name: BT-CMS line, bicellular pollen stage anther, rep_2


title: CW BC anther rep 1

source_name: CW-CMS line, bicellular pollen stage anther, rep_1


title: BT BC anther rep 3

source_name: BT-CMS line, bicellular pollen stage anther, rep_3


title: WA UN anther rep 2

source_name: WA-CMS line, uninucleate microspore stage anther, rep_2


title: W11 UN anther rep 3

description: Gene expression in uninucleate microspore stage anthers of the W11-CMS line

source_name: W11-CMS line, uninucleate microspore stage anther, rep_3


title: WA UN anther rep 1

source_name: WA-CMS line, uninucleate microspore stage anther, rep_1


title: W11 UN anther rep 1

source_name: W11-CMS line, uninucleate microspore stage anther, rep_1


title: M82, biological rep 6, 2008, low pmt

status: Public on Aug 16 2010

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

description: M82_6 low

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C.  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as the following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST wash solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing:
Data extraction was carried out using CombiMatrix Microarray Imager software, and a median normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the two-factor ANOVA module in the TIGR Multiple Experiment Viewer Software v4.0 (http://www.tigr.org/software/tm4/).

Hybridization signals with a variability coefficient higher than 0.5 were filtered out. A 10% cut off was applied to remove the lower tail from the low PMT distribution. Also, a 5% cut off on both tails was applied to the high PMT distribution.

label: Alexa Fluor 647

organism: Solanum lycopersicum

source_name: Red ripe fruit from tomato M82 variety, trial 2008

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions.

growth_protocol: The introgression line 12-4 (IL 12-4) and its parental genotype (cv. M82) were cultivated over consecutive years in a greenhouse at the Department of Soil, Plant, Environmental and Animal Production Sciences at the University of Naples (Portici, Italy). Six plants from IL 12-4 and the parental cv. M82 were transferred into 20-cm pots containing a 1:1 mixture of medium sandy soil and compost at the beginning of March. Pots were distributed randomly 15 cm apart in rows 1 separated by a 50-cm 2 channel, and were supplemented with Nitrophoska Blu Spezial 12-12-17 (+2+20) (Compu) slow release fertilizer (5 g). Plants were watered twice daily using an automated irrigation device with 4 individual drip lines. Prior to flowering, the plants were supplied every two weeks with 30-10-10 liquid fertilizer (Grow More, USA). Fruits were collected at red-ripe stage.

extract_protocol: Total RNA was extracted from frozen, homogenized and powdered tomato fruit tissue using the CTAB (hexadecyltrimethylammonium bromide) method (Griffiths et al. J Exp Bot 50: 793–798 1999). Samples were taken from IL 12-4 and M82 using three plants per genotype in the 2007 and 2008 growing trials.

treatment_protocol: Fruits were collected from IL 12-4 and its cultivated parent when 75% were full sized and red-ripe, softening had increased and the inside of the columella was completely red. Samples were generated by pooling ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Samples were frozen under liquid nitrogen and stored at –80°C prior to homogenization in a Waring blender and processing for the extraction of ascorbic acid and total RNA.

tag: genotype

value: var. M82

value: epicarp and mesocarp

tag: trial

tag: plant replica

tag: scan pmt

value: low


title: T65 UN anther rep 1

description: Gene expression in uninucleate microspore stage anthers of the T65 line

source_name: T65, uninucleate microspore stage anther, rep_1

tag: tissue


title: LD UN anther rep 3

description: Gene expression in uninucleate microspore stage anthers of the LD-CMS line

source_name: LD-CMS line, uninucleate microspore stage anther, rep_3


title: T65 UN anther rep 3

source_name: T65, uninucleate microspore stage anther, rep_3


title: M82, biological rep 6, 2008, high pmt

description: M82_6 high

value: high


title: T65 UN anther rep 2

source_name: T65, uninucleate microspore stage anther, rep_2


title: M82, biological rep 4, 2008, low pmt

description: M82_4 low


title: M82, biological rep 5, 2008, low pmt

description: M82_5 low


title: M82, biological rep 5, 2008, high pmt

description: M82_5 high


title: CW UN anther rep 3

description: Gene expression in uninucleate microspore stage anthers of the CW-CMS line

source_name: CW-CMS line, uninucleate microspore stage anther, rep_3


title: LD UN anther rep 1

source_name: LD-CMS line, uninucleate microspore stage anther, rep_1


title: M82, biological rep 3, 2007, low pmt

description: M82_3 low

source_name: Red ripe fruit from tomato M82 variety, trial 2007


title: M82, biological rep 3, 2007, high pmt

description: M82_3 high


title: LD UN anther rep 2

source_name: LD-CMS line, uninucleate microspore stage anther, rep_2


title: BT UN anther rep 2

description: Gene expression in uninucleate microspore stage anthers of the BT-CMS line

source_name: BT-CMS line, uninucleate microspore stage anther, rep_2


title: CW UN anther rep 2

source_name: CW-CMS line, uninucleate microspore stage anther, rep_2


title: BT UN anther rep 3

source_name: BT-CMS line, uninucleate microspore stage anther, rep_3


title: BT UN anther rep 1

source_name: BT-CMS line, uninucleate microspore stage anther, rep_1


title: CW UN anther rep 1

source_name: CW-CMS line, uninucleate microspore stage anther, rep_1


title: M82, biological rep 4, 2008, high pmt

description: M82_4 high


title: M82, biological rep 1, 2007, low pmt

description: M82_1 low


title: Anther at M3, biological rep3

source_name: Anther, pollen mother cells at meiotic diplotene-tetrad stage


title: M82, biological rep 2, 2007, high pmt

description: M82_2 high


title: M82, biological rep 1, 2007, high pmt

description: M82_1 high


title: M82, biological rep 2, 2007, low pmt

description: M82_2 low


title: chitin treatment swap (OsCERK1 RNAi)

status: Public on Jun 24 2010

city: Kawasaki

first: Hanae

last: Kaku

state: Kanagawa

address: 1-1-1, Higashi-Mita, Tama-ku

department: Life Sciences

institute: Meiji University

description: Rice suspension cultured cells (Oryza sativa L. cv. Nipponnbare) used for total RNA extraction were maintained using a modified N-6 medium and incubated on a rotary shaker at 25 C and 120 rpm in a dark. Cells were transferred to a fresh medium every week. Those cells 4 or 5 days after transfer to the new medium were used experiment.40mg of cultured rice cells were transferred to 1 ml of the fresh medium in a 2 ml centrifuge tube and pre-incubated for 30 min at 25 C on a thermomixer shaken at 750 rpm. N-acetylchitooctaose elicitor (100nM) was added to the culture medium and incubated for 2hr.Total RNA was extracted from rice cells by RNeasy Plant Mini Kit (QIAGEN Inc., Valencia, CA, USA).

hyb_protocol: The microarrays were hybridized according to the Agilent manufacture’s protocol.

scan_protocol: The slides were scanned by an Agilent scanner.

data_processing: Data was analyzed by Fearure Extraction software

source_name: chitin treatment rice cells (OsCERK1 RNAi)

label_protocol: Fluorescence labeled according to the Agilent manufacture’s protocol.

extract_protocol: RNeasy plant Mini Kit (QIAGEN)

treatment_protocol: treated with chitin for 2hr

tag: cell type

value: OsCERK1 knock-down mutant (RNAi)

source_name: water treatment rice cells (OsCERK1 RNAi)

treatment_protocol: treated with water for 2hr


title: chitin treatment swap (vector control)

source_name: chitin treatment rice cells

value: vector control

source_name: water treatment rice cells


title: breast tumor sample 3371

status: Public on Oct 07 2008

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: breast tumor tissue

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from cell samples using the Trizol Kit.

tag: breast cancer


title: breast tumor sample 3366


title: chitin treatment (OsCERK1 RNAi)


title: breast tumor sample 3367


title: breast tumor sample 42


title: breast tumor sample 3363


title: breast tumor sample 77


title: breast tumor sample 3369


title: breast tumor sample 3368


title: breast tumor sample 9


title: breast tumor sample 3356


title: breast tumor sample 3364


title: NF4050 replicate 2

status: Public on Mar 31 2010

city: Lubbock

first: Kameswara Rao

last: Kottapalli

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = rice
Keyword = lesion mimics

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Agilent Microarray Scanner

data_processing: Feature Extraction software Version 9.5 from Agilent Technologies

source_name: Nipponbare control

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were raised in the green house and tissue samples were harvested on 50 DAS.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Mini Kit according to manufacturer’s protocol.

treatment_protocol: No treatment

value: leaf

source_name: NF4050-8 mutant

treatment_protocol: Plants were raised in green house for 50days after sowing and samples were collected when the appearance of lesion mimic symptom in NF4050-8 was conspicuous and in progressive stage.


title: breast tumor sample 3370


title: NF4050 replicate 1

description:
Keyword = rice
Keyword = lesion mimics


title: breast tumor sample 3360


title: breast tumor sample 3357


title: breast tumor sample 3365


title: breast tumor sample 3362


title: breast tumor sample 3353


title: breast tumor sample 3354


title: chitin treatment (vector control)

extract_protocol: RNeasy Plant Mini Kit (Qiagen)


title: breast tumor sample 3352


title: breast tumor sample 3355


title: breast tumor sample 3350


title: breast tumor sample 3349


title: W11 UN anther rep 2

source_name: W11-CMS line, uninucleate microspore stage anther, rep_2

value: male-sterile

value: anther


title: breast tumor sample 3351


title: breast tumor sample 3348


title: breast tumor sample 3347


title: breast tumor sample 3344


title: breast tumor sample 2160


title: breast tumor sample 2309


title: breast tumor sample 87


title: breast tumor sample 3346


title: breast tumor sample 88


title: breast tumor sample 2392


title: breast tumor sample 46


title: breast tumor sample 2377


title: breast tumor sample 2297


title: breast tumor sample 38


title: breast tumor sample 2354


title: breast tumor sample 8


title: breast tumor sample 21279


title: breast tumor sample 2455


title: breast tumor sample 92


title: breast tumor sample 2237


title: breast tumor sample 21276


title: breast tumor sample 2056


title: breast tumor sample 2342


title: breast tumor sample 2386


title: breast tumor sample 19


title: breast tumor sample 2492


title: breast tumor sample 21148


title: breast tumor sample 37


title: breast tumor sample 33


title: breast tumor sample 2548


title: breast tumor sample 2420


title: breast tumor sample 21790


title: breast tumor sample 9442


title: breast tumor sample 21514


title: breast tumor sample 2647


title: breast tumor sample 2872


title: breast tumor sample 2639


title: breast tumor sample 9191


title: breast tumor sample 2534


title: breast tumor sample 21590


title: breast tumor sample 2494


title: breast tumor sample 71


title: breast tumor sample 2143


title: breast tumor sample 129


title: breast tumor sample 2308


title: breast tumor sample 65


title: breast tumor sample 21815


title: breast tumor sample 2556


title: breast tumor sample 2236


title: breast tumor sample 2536


title: breast tumor sample 21604


title: breast tumor sample 172


title: breast tumor sample 21572


title: breast tumor sample 2048


title: breast tumor sample 41826


title: breast tumor sample 2588


title: breast tumor sample 9253


title: breast tumor sample 123


title: breast tumor sample 2733


title: breast tumor sample 108


title: breast tumor sample 57


title: breast tumor sample 2162


title: breast tumor sample 3280


title: breast tumor sample 100


title: breast tumor sample 3273


title: breast tumor sample 3272


title: breast tumor sample 3262


title: breast tumor sample 3274


title: breast tumor sample 3261


title: breast tumor sample 3265


title: breast tumor sample 3256


title: breast tumor sample 3271


title: breast tumor sample 3279


title: breast tumor sample 3254


title: breast tumor sample 3338


title: breast tumor sample 3278


title: breast tumor sample 3252


title: breast tumor sample 3275


title: breast tumor sample 3337


title: breast tumor sample 3266


title: breast tumor sample 3336


title: breast tumor sample 3257


title: breast tumor sample 3260


title: breast tumor sample 3340


title: breast tumor sample 3277


title: breast tumor sample 3270


title: breast tumor sample 3267


title: breast tumor sample 3251


title: breast tumor sample 3259


title: breast tumor sample 3258


title: breast tumor sample 3343


title: breast tumor sample 3250


title: breast tumor sample 3335


title: breast tumor sample 3012


title: breast tumor sample 3329


title: breast tumor sample 3013


title: breast tumor sample 3005


title: breast tumor sample 3009


title: breast tumor sample 3003


title: breast tumor sample 3007


title: breast tumor sample 3331


title: breast tumor sample 3015


title: breast tumor sample 3333


title: breast tumor sample 3004


title: breast tumor sample 3006


title: breast tumor sample 3014


title: breast tumor sample 3001


title: breast tumor sample 3002


title: 100-WT_2

status: Public on Jan 01 2005

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

description: Comparison of the Arabidopsis toc90 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT. P. Jarvis, unpublished

organism: Arabidopsis thaliana

source_name: WT, ecotype Columbia 0


title: 100-WT_3


title: 100-toc90_2

source_name: toc90 mutant, ecotype Columbia 0


title: 100-toc90_5


title: 100-toc90_6


title: 100-WT_6


title: 100-WT_5


title: 100-WT_4


title: 100-toc90_4


title: 100-toc90_3


title: 100-WT_1


title: 100-toc90_1