title: 14178766 - col3 vs de3

hyb_protocol: de3 Cy5 / col3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178761 - de1 vs col1

status: Public on Mar 20 2012

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: difference in global transcript in mutants with an affected cell cycle progression

hyb_protocol: col1 Cy5 / de1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - media : 1/2 MS 0.5% Sucrose  temperature : 20 degrees C

treatment_protocol: no treatment

tag: ecotype

tag: genotype/variation

value: wild type

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


title: 14178756 - cdk1 vs col1

hyb_protocol: col1 Cy5 / cdk1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178757 - col1 vs d1

hyb_protocol: d1 Cy5 / col1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178759 - col1 vs de1

hyb_protocol: de1 Cy5 / col1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: A-253

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

country: USA

institute: Broad Institute

description: Gene expression data from the CCLE

hyb_protocol: Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.

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

data_processing: The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.

label: Biotin

organism: Homo sapiens

source_name: ATCC

label_protocol: The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.

tag: primary site

tag: histology

value: carcinoma

tag: histology subtype1


title: A4/Fuk

description: Gene expression data from the CCLE

source_name: HSRRB


title: A3/KAW

description: Gene expression data from the CCLE


title: 697

description: Gene expression data from the CCLE

source_name: DSMZ


title: 14178755 - col1 vs cdk1

hyb_protocol: cdk1 Cy5 / col1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C. elegans: X. nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 1 of 4.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans young adults, fed Xenorhabdus nematophila, 4 hours

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Xenorhabdus nematophila plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

tag: strain

value: N2 Bristol

tag: treatment

value: exposed to Xenorhabdus nematophila

tag: timepoint

value: 4 hour feeding / exposure

tag: hybridization

value: Test sample

source_name: C. elegans young adults, fed E.coli OP50, 4 hours

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto control E. coli OP50 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to E. coli OP50

value: Reference sample


title: 14178767 - d3 vs col3

hyb_protocol: col3 Cy5 / d3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C. elegans: S. marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 3

description: Biological replicate 3 of 4.

source_name: C. elegans young adults, fed Serratia marcescens, 4 hours

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Serratia marcescens plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to Serratia marcescens


title: C. elegans: X. nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye swap)

description: Biological replicate 3 of 4. It is also a dye-swap.


title: H181 (passage 74) with bFGF

city: Seville

first: Rafael

middle: A.

last: Tapia Limonchi

state: Seville

address: Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93

department: Department of Cell Therapy and Regenerative Medicine

country: Spain

institute: Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings form GeneChip Operating System 1.4.0.036 and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Human embryonic stem cells H181 undifferentiated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.

growth_protocol: hESCs were cultured on Matrigel-coated tissue culture plates at 37ºC, 5% CO2 in Dulbecco’s modified Eagle’s  Medium/KO supplemented with 20% knock-out serum replacement (Gibco), 2mM L-glutamine (Gibco),  0.1mM 2-mercaptoethanol (Gibco), 1% nonessential aminoacids (Gibco) and 100U/ml per 100mg/ml penicillin/streptomycin  (Gibco). Cells were subcultured every 6 days by mechanical splitting.

extract_protocol: Cells were recovered with accutase by 3 min at 37C. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) and Chloroform, centrifuged at 13000rpm for 10 min, then precipitated with isopropanol and centrifuged at 13000rpm for 10 min. The pellet was dried and resuspended in 10uL of DNAse and RNAse free water. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer

treatment_protocol: For experiments, undifferentiated cells were maintained by adding 8ng/ml of bovine fibrolblast growth factor (bFGF (Gibco)) to the culture medium. Treatment with nitric oxide (NO) was carried out adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to cells cultured in medium without bFGF. Differentiated cells control were cultures in absence of bFGF. All the cultures were mantained for 6 days.

tag: cell line

tag: cell passage


title: C. elegans: S. marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 2 (Dye-swap)

description: Biological replicate 2 of 4. This is also a dye-swap.


title: 14178696 - col3 vs d3

hyb_protocol: d3 Cy5 / col3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C. elegans: S. marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 1 (Dye-swap)

description: Biological replicate 1 of 4. This is also a dye-swap.


title: C. elegans: X. nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 4.


title: C. elegans: S. marcescens vs. E. coli OP50 exposure; 4hours, Biological Replicate 4

description: Biological replicate 4 of 4.


title: H181 (passage 73) without bFGF plus NO

source_name: Human embryonic stem cells H181 differentiated by bFGF withdrawal and treated with 2uM DETA-NO


title: C. elegans: X. nematophila vs. E. coli OP50 exposure; 4hours, Biological Replicate 4 (Dye swap)

description: Biological replicate 4 of 4. It is also a dye-swap.


title: H181 (passage 74) without bFGF

source_name: Human embryonic stem cells H181 differentiated by bFGF withdrawal


title: H181 (passage 74) without bFGF plus NO


title: H181 (passage 73) without bFGF


title: H181 (passage 72) without bFGF plus NO


title: Cells derived from GTML tumor

city: San Francisco

first: William

last: Weiss

state: CA

address: 1450 3rd Street, HD-220

department: Neurology

institute: University of California, San Francisco

hyb_protocol: Samples were hybridized using the Affymetrix Hybridization Kit according to the manufacturer's instructions.  Samples washed using Affymetrix Fluidics FS450

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing:
Data were processed using the Bioconductor R Package XPS (1.6.2) at the Core level.  RMA was followed by DABG.
MoEx-1_0-st-v1.na30.mm9.transcript.csv

organism: Mus musculus

source_name: Cells derived from GTML tumor

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix) after the Affymetrix ST Labeling Protocol (GTML MB and P7 Cerebella) or the Ambion WT Expression Protocol (Transplanted Tumors/Cells)

extract_protocol: Total RNA was extracted using Trizol and purified using the Rneasy Mini Kit

tag: somatic or tumor

tag: tissue or cells

value: cells

tag: origin

value: GTML

tag: cell type

value: Cells derived from GTML tumor

tag: genetic background

value: FVB/N


title: Cells derived from P0 Glioma 1 Tumor

source_name: Cells derived from P0 Forebrain Tumor

value: P0 Forebrain

value: Cells derived from P0 Glioma 1 Tumor

tag: age


title: H181 (passage 72) with bFGF


title: H181 (passage 73) with bFGF


title: Orthotopic P0 Forebrain Tumor Biological Rep 2

source_name: Orthotopic P0 Forebrain Tumor

value: tumor

value: tissue

tag: tissue

value: Orthotopic P0 Forebrain Tumor


title: C. elegans: S. aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 3 (Dye-swap)

description: Biological replicate 3 of 4. This is also a dye-swap.

value: young adults

source_name: C. elegans young adults, fed Staphylococcus aureus, 4 hours

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Staphylococcus aureus plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: exposed to Staphylococcus aureus


title: GFP-transduced P0 Cerebellar NSCs, unsorted

source_name: P0C NSCs + GFP (unsorted)

value: P0 Cerebellum


title: Orthotopic P0 Forebrain Tumor Biological Rep 1


title: C. elegans: S. aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

description: Biological replicate 1 of 4.

value: N2 Bristol

value: 4 hour feeding / exposure


title: C. elegans: S. aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 4.

value: Test sample

value: exposed to E. coli OP50


title: GFP-transduced P0 Forebrain NSCs

source_name: P0F NSCs + GFP

value: GFP-transduced P0 Forebrain NSCs


title: C. elegans: S. aureus vs. E. coli OP50 exposure; 4hours, Biological Replicate 4 (Dye-swap)

description: Biological replicate 4 of 4. This is also a dye-swap.

value: Reference sample


title: H181 (passage 72) without bFGF


title: GFP-transduced P0 Cerebellar NSCs, GFP Sorted

source_name: P0C NSCs + GFP (sorted)

value: cells


title: Orthotopic P0 Cerebellar Tumor Biological Rep 2

source_name: Orthotopic P0 Cerebellar Tumor

value: Orthotopic P0 Cerebellar Tumor


title: Cells derived from P0 MB 1 Tumor

source_name: Cells derived from P0 Cerebellar Tumor

value: Cells derived from P0 MB 1 Tumor

value: FVB/N


title: Orthotopic P0 Cerebellar Tumor Biological Rep 3


title: GFP-transduced E16 Cerebellar NSCs

source_name: E16C NSCs + GFP

value: E16 Cerebellum


title: N-myc(T58A)-transduced P0 Cerebellar NSCs

source_name: P0C NSCs + N-myc (T58A)


title: Orthotopic E16 Cerebellar Tumor Biological Rep 2

source_name: Orthotopic E16 Cerebellar Tumor

value: tumor

value: Orthotopic E16 Cerebellar Tumor


title: N-myc(T58A)-transduced E16 Cerebellar NSCs

source_name: E16C NSCs + N-myc (T58A)

value: GFP-transduced E16 Cerebellar NSCs


title: GTML Medulloblastoma Tumor Biological Rep 30

source_name: Tumor harvested from GTML mouse

value: tissue

value: GTML

value: GTML Medulloblastoma Tumor


title: Orthotopic E16 Cerebellar Tumor Biological Rep 1


title: GTML Medulloblastoma Tumor Biological Rep 32


title: GTML Medulloblastoma Tumor Biological Rep 31


title: GTML Medulloblastoma Tumor Biological Rep 26


title: Orthotopic P0 Forebrain Tumor Biological Rep 3

value: P0 Forebrain

value: Orthotopic P0 Forebrain Tumor


title: GTML Medulloblastoma Tumor Biological Rep 27


title: Orthotopic P0 Cerebellar Tumor Biological Rep 1

value: P0 Cerebellum


title: Orthotopic E16 Cerebellar Tumor Biological Rep 3

value: Cells derived from E16 MB 1 tumor


title: Cells derived from E16 MB 1 tumor

source_name: Cells derived from E16 Cerebellar Tumor

value: N-myc(T58A)-transduced E16 Cerebellar NSCs


title: GTML Medulloblastoma Tumor Biological Rep 20


title: GTML Medulloblastoma Tumor Biological Rep 24


title: GTML Medulloblastoma Tumor Biological Rep 28


title: GTML Medulloblastoma Tumor Biological Rep 21


title: GTML Medulloblastoma Tumor Biological Rep 23


title: GTML Medulloblastoma Tumor Biological Rep 16


title: GTML Medulloblastoma Tumor Biological Rep 17


title: GTML Medulloblastoma Tumor Biological Rep 18


title: GTML Medulloblastoma Tumor Biological Rep 22


title: GTML Medulloblastoma Tumor Biological Rep 15


title: GTML Medulloblastoma Tumor Biological Rep 29


title: GTML Medulloblastoma Tumor Biological Rep 25


title: GTML Medulloblastoma Tumor Biological Rep 14


title: GTML Medulloblastoma Tumor Biological Rep 13


title: GTML Medulloblastoma Tumor Biological Rep 11


title: GTML Medulloblastoma Tumor Biological Rep 6


title: GTML Medulloblastoma Tumor Biological Rep 10


title: GTML Medulloblastoma Tumor Biological Rep 7


title: GTML Medulloblastoma Tumor Biological Rep 8


title: GTML Medulloblastoma Tumor Biological Rep 19


title: GTML Medulloblastoma Tumor Biological Rep 9


title: GTML Medulloblastoma Tumor Biological Rep 1


title: GTML Medulloblastoma Tumor Biological Rep 5


title: Normal P7 Cerebellum, Biological Rep 4

source_name: P7 GTML Cerebellum, + Dox

value: somatic

value: P7 Cerebellum

value: Normal P7 Cerebellum


title: Normal P7 Cerebellum, Biological Rep 3


title: Normal P7 Cerebellum, Biological Rep 5


title: GTML Medulloblastoma Tumor Biological Rep 3


title: Normal P7 Cerebellum, Biological Rep 1


title: GTML Medulloblastoma Tumor Biological Rep 4


title: CJKO MEF control, rep3

city: Parkville

first: Geoff

last: Macintyre

state: Victoria

address: University of Melbourne

department: Department of Computer Science and Software Engineering

country: Australia

institute: University of Melbourne

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Arrays were processed using the aroma package in R using RMA background correction with quantile normalisation
probe group file: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
meta-probeset file: MoEx-1_0-st-v1.na29.mm9.transcript.csv

source_name: C-JUN -/- mouse embryonic fibroblasts

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were cultured in DMEM supplemented with 5% foetal bovine serum (JRH Biosciences, Lenexa, KS, USA) and 2 mM L-Glutamine (JRH Biosciences, Lenexa, KS, USA)

extract_protocol: Cells were harvested in Trireagent (Invitrogen) and followed by extraction on RNeasy midi kits (Qiagen).

treatment_protocol: 107 C-JUN / and wild type MEFs cells were plated in T175 flasks and allowed to adhere for 24 hours. Media was replaced with fresh media with or without a combination of IFNg (1,000 IU/mL) and cycloheximide and cultured for additional three hours.

value: embryonic fibroblast

tag: genotype/variation

value: CJUN-/-

tag: agent

value: control


title: CJKO MEF IFNg+CHX treated, rep3

value: IFNg+CHX


title: CJKO MEF CHX treated, rep1

value: CHX


title: GTML Medulloblastoma Tumor Biological Rep 2

value: tumor

value: FVB/N


title: Normal P7 Cerebellum, Biological Rep 2

value: tissue


title: CJKO MEF IFNg treated, rep1

value: IFNg


title: CJKO MEF CHX treated, rep3


title: CJKO MEF control, rep2


title: CJKO MEF IFNg treated, rep2


title: CJKO MEF IFNg+CHX treated, rep2


title: CJKO MEF IFNg treated, rep3


title: WT MEF CHX treated, rep1

source_name: Wild-type mouse embryonic fibroblasts

value: WT


title: WT MEF CHX treated, rep3


title: WT MEF IFNg+CHX treated, rep3


title: WT MEF IFNg treated, rep2


title: WT MEF IFNg+CHX treated, rep2


title: WT MEF IFNg treated, rep3


title: WT MEF IFNg treated, rep1


title: WT MEF control, rep1


title: CJKO MEF IFNg+CHX treated, rep1


title: WT MEF control, rep2


title: CJKO MEF CHX treated, rep2


title: WT MEF IFNg+CHX treated, rep1


title: GTML Medulloblastoma Tumor Biological Rep 12

value: GTML

value: GTML Medulloblastoma Tumor


title: WT MEF CHX treated, rep2


title: Genotype_737_25dpa_fiber_rep3

city: Lucknow

first: Samir

middle: V

last: Sawant

address: Sikandrabad

department: Centre for Plant and Molecular Breeding

country: India

institute: National Botanical Research Institute

description:
737 inferior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum

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

scan_protocol: GeneChips were scanned using the Gene chip scanner 3000.

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.

organism: Gossypium hirsutum

source_name: Fiber 25day post anthesis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All five Genotype of G. hirsutum were sown in the open field at National Botanical Research Institute, Lucknow, India and grown in natural condition.

extract_protocol: Total RNA  was isolated from Spectrum plant total RNA Kit (Sigma-Aldrich) according to the manufacturer’s instructions.

treatment_protocol: During the flowering season flowers were tagged on anthesis and harvested at six different developmental time points: 0, 6, 9, 12, 19 & 25 days post anthesis (dpa). For RNA isolation whole ovule was taken as 0dpa sample whereas for rest of the stages only fibers were the starting material.

tag: genotype

value: JKC 737

tag: development stage

value: 25 dpa fiber


title: Genotype_737_19dpa_fiber_rep1

description:
737 inferior traits of fiber quality
Gene expression data from 19DPA fiber from Gossypium hirsutum

source_name: Fiber 19day post anthesis

value: 19 dpa fiber


title: Genotype_737_19dpa_fiber_rep3


title: Genotype_737_19dpa_fiber_rep2


title: Genotype_737_9dpa_fiber_rep3

description:
737 inferior traits of fiber quality
Gene expression data from 9DPA fiber from Gossypium hirsutum

source_name: Fiber 9day post anthesis

value: 9 dpa fiber


title: Genotype_737_9dpa_fiber_rep1


title: Genotype_737_25dpa_fiber_rep2


title: Genotype_737_0dpa_fiber_rep1

description:
737 inferior traits of fiber quality
Gene expression data from 0DPA fiber from Gossypium hirsutum

source_name: Fiber 0day post anthesis

value: 0 dpa fiber


title: Genotype_737_12dpa_fiber_rep3

description:
737 inferior traits of fiber quality
Gene expression data from 12DPA fiber from Gossypium hirsutum

source_name: Fiber 12day post anthesis

value: 12 dpa fiber


title: Genotype_737_0dpa_fiber_rep2


title: Genotype_737_6dpa_fiber_rep1

description:
737 inferior traits of fiber quality
Gene expression data from 6DPA fiber from Gossypium hirsutum

source_name: Fiber 6day post anthesis

value: 6 dpa fiber


title: Genotype_783_12dpa_fiber_rep3

description:
783 inferior traits of fiber quality
Gene expression data from 12DPA fiber from Gossypium hirsutum

value: JKC 783


title: Genotype_737_0dpa_fiber_rep3


title: Genotype_737_6dpa_fiber_rep2


title: Genotype_783_25dpa_fiber_rep2

description:
783 inferior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum


title: Genotype_783_12dpa_fiber_rep2


title: Genotype_783_19dpa_fiber_rep2

description:
783 inferior traits of fiber quality
Gene expression data from 19DPA fiber from Gossypium hirsutum


title: Genotype_737_12dpa_fiber_rep2


title: Genotype_783_12dpa_fiber_rep1


title: Genotype_737_9dpa_fiber_rep2


title: Genotype_737_12dpa_fiber_rep1


title: Genotype_783_19dpa_fiber_rep1


title: Genotype_737_6dpa_fiber_rep3


title: Genotype_783_25dpa_fiber_rep1


title: Genotype_783_9dpa_fiber_rep2

description:
783 inferior traits of fiber quality
Gene expression data from 9DPA fiber from Gossypium hirsutum


title: Genotype_783_6dpa_fiber_rep2

description:
783 inferior traits of fiber quality
Gene expression data from 6DPA fiber from Gossypium hirsutum


title: delta-efg1 vs wild type / Geldanamycin-treated 1

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: wt + GdA

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was isolated from quadruplicate independent biological samples using the RNeasy mini kit (Qiagen). Briefly, frozen cells were thawed out in RNeasy buffer RLT at a ratio of 3:1 [vol/vol] buffer/pellet. Resuspended cells were divided into 1 ml aliquots in 2 ml screw cap microcentrifuge tubes containing 0.6 ml of 0.5 mm diameter acid-washed glass beads. Samples were homogenized 6 times, for 5 minutes each, in a BeadBeater set at maximum speed.

treatment_protocol: Cells were grown overnight in YPD at 30°C, diluted to OD600 of 0.2, and grown overnight again with or without 10 µM geldanamycin, as indicated in above. Cells were again diluted to OD600 of 0.2 in the same conditions and grown to mid-log phase.

value: wt

value: GdA

source_name: delta-efg1 + GdA


title: delta-efg1 vs wild type / Geldanamycin-treated 3


title: delta-efg1 vs wild type 4

source_name: wt


title: Genotype_783_6dpa_fiber_rep3


title: delta-efg1 vs wild type / Geldanamycin-treated 2


title: Genotype_783_9dpa_fiber_rep1


title: Genotype_783_9dpa_fiber_rep3


title: Genotype_783_19dpa_fiber_rep3


title: Genotype_783_0dpa_fiber_rep1

description:
783 inferior traits of fiber quality
Gene expression data from 0DPA fiber from Gossypium hirsutum


title: delta-efg1 vs wild type / Geldanamycin-treated 4


title: Genotype_783_0dpa_fiber_rep2


title: delta-efg1 vs wild type 3


title: Genotype_777_25dpa_fiber_rep3

description:
777 superior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum

value: JKC 777


title: Genotype_783_6dpa_fiber_rep1


title: Genotype_783_0dpa_fiber_rep3


title: SW480 cell line, control

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of cell lines

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using Gene Expression Console (Affymetrix)

source_name: SW480 cell line

label_protocol: cRNA was prepared using one-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were used.  Five cell lines were treated with 5-aza-2'-deoxycytidine.

tag: metastasis

tag: Stage

value: SW480 cell line


title: CJKO MEF control, rep1

value: embryonic fibroblast

value: CJUN-/-

value: control


title: delta-efg1 vs wild type 2


title: Genotype_777_19dpa_fiber_rep3

description:
777 superior traits of fiber quality
Gene expression data from 19DPA fiber from Gossypium hirsutum


title: Genotype_777_25dpa_fiber_rep1


title: Ctrl ChIP-chip GldA Replicate 1

type: genomic

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done in an Advalytix SlideBooster. The slides were washed twice with 1X SSC-0.2% SDS and 3 times with 0.1X SSC.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 5-µm resolution.

data_processing: Signal intensity was quantified with ImaGene software (BioDiscovery), background corrected, and normalized for signal intensity (using Lowess normalization).

molecule: genomic DNA

source_name: Control strain, 10 uM GldA

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. Chromatin immunoprecipitation was performed by following the protocol available at http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html with the following exceptions: chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with anti-FLAG agarose beads.

treatment_protocol: Cells were grown overnight in YPD at 30°C, diluted to OD600 of 0.2, and grown overnight again with or without 10 µM geldanamycin. Cells were again diluted to OD600 of 0.2 in the same conditions and grown to mid-log phase.

value: GldA

tag: chip antibody

source_name: Flag-Hms1 strain, 10 uM GldA

value: anti-FLAG


title: RKO cell line, control

description: Gene expression profile of cell lines

source_name: RKO cell line

value: RKO cell line


title: SW480 cell line, 5aza treated

description: Gene expression profile of cell lines


title: Geldanamycin in delta-efg1 mutants 3

tag: treatment


title: RKO cell line, 5aza treated

description: Gene expression profile of cell lines


title: Geldanamycin in delta-efg1 mutants 4


title: Geldanamycin in delta-efg1 mutants 2


title: Ctrl ChIP-chip GldA Replicate 2


title: Genotype_777_19dpa_fiber_rep1


title: Geldanamycin in delta-efg1 mutants 1


title: Genotype_777_19dpa_fiber_rep2


title: Genotype_777_12dpa_fiber_rep3

description:
777 superior traits of fiber quality
Gene expression data from 12DPA fiber from Gossypium hirsutum


title: HT29 cell line, 5aza treated 2

description: Gene expression profile of cell lines

source_name: HT29 cell line

value: HT29 cell line


title: HCT116 cell line, control

description: Gene expression profile of cell lines

source_name: HCT116 cell line

value: HCT116 cell line


title: Geldanamycin in wild type 4


title: Genotype_777_25dpa_fiber_rep2

value: 25 dpa fiber


title: Genotype_777_9dpa_fiber_rep3

description:
777 superior traits of fiber quality
Gene expression data from 9DPA fiber from Gossypium hirsutum

value: 9 dpa fiber


title: Geldanamycin in wild type 3


title: Ctrl ChIP-chip Replicate 1

source_name: Control strain, no GldA

value: no GldA

source_name: Flag-Hms1 strain, no GldA


title: Genotype_777_12dpa_fiber_rep2

value: 12 dpa fiber


title: COLO320 cell line, 5aza treated

description: Gene expression profile of cell lines

source_name: COLO320 cell line

value: COLO320 cell line


title: HCT116 cell line, 5aza treated

description: Gene expression profile of cell lines


title: Geldanamycin in wild type 2

value: wt


title: patient 047b, cancer, homogenized

description: Gene expression profile of surgically resected material

source_name: surgically resected material

value: cancer, homogenized


title: Genotype_777_9dpa_fiber_rep2

source_name: Fiber 9day post anthesis

value: JKC 777


title: Geldanamycin in wild type 1

value: GdA


title: Genotype_777_12dpa_fiber_rep1


title: COLO320 cell line, control

description: Gene expression profile of cell lines


title: Genotype_777_9dpa_fiber_rep1


title: patient 044b, cancer, homogenized


title: patient 045b, cancer, homogenized

value: metastatic recurrence


title: Genotype_777_0dpa_fiber_rep3

description:
777 superior traits of fiber quality
Gene expression data from 0DPA fiber from Gossypium hirsutum

source_name: Fiber 0day post anthesis

value: 0 dpa fiber


title: WT MEF control, rep3

source_name: Wild-type mouse embryonic fibroblasts

value: embryonic fibroblast

value: WT

value: control


title: Genotype_777_6dpa_fiber_rep1

description:
777 superior traits of fiber quality
Gene expression data from 6DPA fiber from Gossypium hirsutum

source_name: Fiber 6day post anthesis

value: 6 dpa fiber


title: Genotype_777_6dpa_fiber_rep3


title: Genotype_737_25dpa_fiber_rep1

description:
737 inferior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum

source_name: Fiber 25day post anthesis

value: JKC 737


title: patient 038b, cancer, homogenized


title: Genotype_777_6dpa_fiber_rep2


title: patient 035b, cancer, homogenized

value: metastasis


title: patient 036b, cancer, homogenized


title: Genotype_703_25dpa_fiber_rep1

description:
703 inferior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum

value: JKC 703

value: 25 dpa fiber


title: Genotype_777_0dpa_fiber_rep1


title: patient 041b, cancer, homogenized


title: patient 033b, cancer, homogenized


title: Genotype_777_0dpa_fiber_rep2


title: patient 032b, cancer, homogenized


title: Genotype_703_25dpa_fiber_rep2


title: patient 031b, cancer, homogenized


title: Genotype_703_25dpa_fiber_rep3


title: patient 030b, cancer, homogenized


title: patient 028b, cancer, homogenized


title: Genotype_703_19dpa_fiber_rep1

description:
703 inferior traits of fiber quality
Gene expression data from 19DPA fiber from Gossypium hirsutum

source_name: Fiber 19day post anthesis

value: 19 dpa fiber


title: Genotype_703_19dpa_fiber_rep3


title: MUC4-KD3

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.5).

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction and LOWESS normalization.

label_protocol: standard Agailent protocol

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Human pancreatic cancer cell lines were invalidated for the ErbB2 or MUC4 genes.

value: Muc4 knockdown

value: human pancreatic cell line

tag: cell line

source_name: mock

value: mock


title: Genotype_703_19dpa_fiber_rep2


title: patient 042b, cancer, homogenized

value: cancer, homogenized


title: delta-efg1 vs wild type 1

source_name: wt

value: wt


title: Genotype_703_12dpa_fiber_rep3

description:
703 inferior traits of fiber quality
Gene expression data from 12DPA fiber from Gossypium hirsutum

source_name: Fiber 12day post anthesis

value: 12 dpa fiber


title: patient 027b, cancer, homogenized


title: patient 006b, cancer, homogenized

value: metastatic recurrence


title: MUC4-KD2


title: patient 024b, cancer, homogenized


title: Genotype_703_12dpa_fiber_rep1


title: HT29 cell line, control 2

description: Gene expression profile of cell lines

value: HT29 cell line


title: MUC4-KD1


title: patient 011b, cancer, homogenized


title: MUC4-KD4


title: ErbB2-KD4

source_name: pool NT

value: untreated

value: ErbB2 knockdown


title: ErbB2-KD3


title: ErbB2-KD2


title: patient 045b, normal, homogenized

value: normal, homogenized


title: patient 047b, normal, homogenized


title: Genotype_703_6dpa_fiber_rep1

description:
703 inferior traits of fiber quality
Gene expression data from 6DPA fiber from Gossypium hirsutum

value: 6 dpa fiber


title: Genotype_703_6dpa_fiber_rep3


title: patient 044b, normal, homogenized


title: patient 042b, normal, homogenized


title: Hippocampus from adult exercise female SAMP8 mice, biological replicate 5

city: Barcelona

first: Perla

last: Kaliman

address: Corsega 176 bajos

institute: IDIBAPS

description: Mice strains used were SAMP8 (senescence-accelerated mouse P8) and SAMR1 (SAM resistant mice) [Takeda et al., Senescence-accelerated mouse (SAM): A novel murine model of accelerated senescence. J Am Geriatr Soc, 1991]

hyb_protocol: Total RNA (500 ng) was labeled with Cy3 dye using the Quick Amp Labeling Kit, One-Color from Agilent. Fluorescently labeled samples were hybridized to the microarray slide with 60-mer probes. Hybridization and wash processes were performed according to the manufacturer’s instructions.

scan_protocol: Hybridized microarrays were scanned using an Axon 4000B scanner.

data_processing: GenPix Pro 6.0 extraction software was used for the detection of signals. Background correction and normalization were done with Bioconductor's package limma using method's "minimum" and "quantile" respectively.

source_name: Whole hippocampus exercised

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana™ RNA Isolation Kit (Applied Biosystems) following the manufacturer's recommendations. The yield, purity and quality of RNA were determined spectrophotometrically (NanoDrop, USA) and using the Bioanalyzer 2100 capillary electrophoresis (Agilent Technologies).

treatment_protocol: Hippocampus were rapidly frozen after the sacrifice of the animals.

tag: strain

value: SAMP8 (senescence-accelerated mouse P8)

tag: intervention

value: exercised


title: HCT116 +/+ 5FU Replicate 1

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: Gene expression data of HCT116 with 5FU

hyb_protocol: Fragmented and biotin-labeled targets were hybridized to Human Exon ST 1.0 (Affymetrix) gene chips for analysis of over 6,553,000 probe sets.

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

data_processing:
The data were analyzed with R-Bioconductor (RMA) using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-param-apt-opt-pgf-file=HuEx-1_0-st-v2.r2.pgf
affymetrix-algorithm-param-apt-opt-clf-file=HuEx-1_0-st-v2.r2.clf
affymetrix-algorithm-param-apt-opt-bgp-file=HuEx-1_0-st-v2.r2.antigenomic.bgp
affymetrix-algorithm-param-apt-opt-analysis-name=rma-sketch
affymetrix-algorithm-param-apt-opt-analysis-spec=rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true.target=0.doavg=fa
lse.subsetmd5=c4b91fa323b1ba2869ed604f831a2c4f,pm-only,med-polish.FixFeatureEffect=false.UseInputModel=false.FitFeatureResponse=true.exp
on=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.allele-a=false
affymetrix-algorithm-param-apt-opt-do-residuals=false
affymetrix-algorithm-param-apt-opt-do-feature-effects=false
affymetrix-algorithm-param-apt-opt-write-sketch=false
affymetrix-algorithm-param-quantification-name=med-polish
affymetrix-algorithm-param-quantification-version=1.0
affymetrix-algorithm-param-quantification-scale=log2
affymetrix-algorithm-param-quantification-type=signal

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated using the PicoPure RNA isolation Kit (Arcturus) according to the manufacturers instructions.


title: Genotype_703_9dpa_fiber_rep2

description:
703 inferior traits of fiber quality
Gene expression data from 9DPA fiber from Gossypium hirsutum

value: JKC 703

value: 9 dpa fiber


title: Genotype_703_6dpa_fiber_rep2


title: Hippocampus from adult exercise female SAMP8 mice, biological replicate 4


title: Hippocampus from adult exercise female SAMP8 mice, biological replicate 3


title: patient 038b, normal, homogenized


title: patient 041b, normal, homogenized


title: ErbB2-KD1


title: Genotype_703_9dpa_fiber_rep1


title: Genotype_703_0dpa_fiber_rep3

description:
703 inferior traits of fiber quality
Gene expression data from 0DPA fiber from Gossypium hirsutum

value: 0 dpa fiber


title: Hippocampus from adult exercise female SAMP8 mice, biological replicate 2


title: HCT116 +/+ None Replicate 2

description: Gene expression data of control HCT116


title: patient 035b, normal, homogenized

value: metastasis


title: patient 036b, normal, homogenized


title: Genotype_703_0dpa_fiber_rep1


title: HCT116 +/+ 5FU Replicate 2

description: Gene expression data of HCT116 with 5FU


title: HCT116 +/+ Nutlin 3R Replicate 2

description: Gene expression data of HCT116 with Nutlin 3

source_name: Nutlin 3R

value: Nutlin 3R


title: zdp meDIP rep1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: meDIP-chip zdp mutant

hyb_protocol: The hybridization to tiling array chip was performed by NimbleGen (http://www.nimblegen.com/)

scan_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

data_processing: The updated chromosome locations of Nimblegen array probes were found by remapping probes to the TAIR9 genome assembly using SOAP2 (Li et al., 2009, Bioinformatics 25:1966-1967.). Probe intensities were normalized using the Tukey-biweight scaling procedure implemented in Ringo (method= “nimblegen”) (Toedling et al., 2007, BMC Bioinformatics. 8:221.).

source_name: pull-down meDIP from zdp mutant seedling cell extract

label_protocol: 2 mg of genomic DNA were used for 5-Methylcytosine immunoprecipitation (meDIP) analysis. The meDIP and amplification of immunoprecipitated products were performed according to published protocols (Zilberman et al., 2007, Nat Genet 39:61-69)

growth_protocol: Arabidopsis seedlings were grown on Murashige-Skoog (MS) nutrient agar plates at 23ºC with 16 h of light and 8 h of darkness for 2 weeks

extract_protocol: Genomic DNA was extracted from two-week seedlings using DNeasy Plant Maxi kit (Qiagen)

tag: ecotype

value: zdp mutant

value: seedling

value: 2 wk

tag: sample type

value: MeDIP

source_name: input DNA  from zdp mutant seedling cell extract

value: input


title: HCT116 +/+ Nutlin 3R Replicate 1


title: Genotype_703_9dpa_fiber_rep3


title: Genotype_725_25dpa_fiber_rep3

description:
725 superior traits of fiber quality
Gene expression data from 25DPA fiber from Gossypium hirsutum

value: JKC 725

value: 25 dpa fiber


title: Hippocampus from adult sedentary female SAMP8 mice, biological replicate 4

source_name: Whole hippocampus sedentary

value: sedentary


title: Hippocampus from adult exercise female SAMP8 mice, biological replicate 1


title: patient 032b, normal, homogenized

value: normal, homogenized


title: Hippocampus from adult sedentary female SAMP8 mice, biological replicate 5


title: Hippocampus from adult sedentary female SAMP8 mice, biological replicate 3


title: WT meDIP rep1

description: meDIP-chip WT

source_name: pull-down meDIP from Col-0 WT seedling cell extract

value: wild type

source_name: input DNA  from Col-0 WT seedling cell extract


title: Genotype_725_19dpa_fiber_rep3

description:
725 superior traits of fiber quality
Gene expression data from 19DPA fiber from Gossypium hirsutum

value: 19 dpa fiber


title: patient 030b, normal, homogenized

source_name: surgically resected material


title: Genotype_725_25dpa_fiber_rep1


title: Genotype_725_25dpa_fiber_rep2


title: HCT116 +/+ None Replicate 1

description: Gene expression data of control HCT116


title: Hippocampus from adult sedentary female SAMP8 mice, biological replicate 2

value: SAMP8 (senescence-accelerated mouse P8)


title: Hippocampus from adult sedentary female SAMP8 mice, biological replicate 1


title: patient 027b, normal, homogenized


title: patient 028b, normal, homogenized

value: metastatic recurrence


title: Genotype_725_19dpa_fiber_rep2


title: Genotype_703_12dpa_fiber_rep2

value: JKC 703

value: 12 dpa fiber


title: Hippocampus from adult sedentary female SAMR1 mice, biological replicate 5

value: SAMR1 (SAM resistant mice)


title: zdp meDIP rep2

description: meDIP-chip zdp mutant


title: WT meDIP rep2

description: meDIP-chip WT


title: patient 033b, normal, homogenized


title: patient 011b, normal, homogenized

value: metastasis


title: Genotype_725_19dpa_fiber_rep1


title: Hippocampus from adult sedentary female SAMR1 mice, biological replicate 2


title: Hippocampus from adult sedentary female SAMR1 mice, biological replicate 3


title: Hippocampus from adult sedentary female SAMR1 mice, biological replicate 4


title: Genotype_725_12dpa_fiber_rep2

description:
725 superior traits of fiber quality
Gene expression data from 12DPA fiber from Gossypium hirsutum


title: 293_siDBC1_r2

city: Liegge

first: pierre

last: close

address: Avenue de l'hopital

department: GIGA-Institute

country: Belgium

institute: University of Liege

hyb_protocol: Hybridization was performed for 16 hours using the FS450_0001 fluidics protocol.

scan_protocol: Genechip scanner 3000 7G

data_processing:
Quantile normalised probe level and core level signal estimates were generated using RMA implemented in APT (apt-1.10.0, Affymetrix). Detection p-values (dabg) were also calculated using apt. Antigenomic probes were used for background.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HEK293 cells transfected with Dbc1 siRNA

label_protocol: Whole transcript (WT) sene target labeling protocol V1.0 from Affymetrix. GeneChip® Poly-A RNA Control Kit, human RiboMinus transcriptome isolation kit from Invitrogen were used in the protocol.

growth_protocol: HEK293 cells grown in DMEM supplemented with 10% FBS_1% Pen/Strep_1% Lglutamine

extract_protocol: RNA was extracted using Rneasy Mini kit (Qiagen). Total RNAs were DNAse-treated on the column.

tag: sirna

value: Dbc1 siRNA knockdown


title: 293_siZNF326_r2

source_name: HEK293 cells transfected with znf326 siRNA

value: znf326 siRNA knockdown


title: Genotype_725_9dpa_fiber_rep2

description:
725 superior traits of fiber quality
Gene expression data from 9DPA fiber from Gossypium hirsutum

source_name: Fiber 9day post anthesis

value: 9 dpa fiber


title: Genotype_725_12dpa_fiber_rep3


title: patient 006b, normal, homogenized


title: Genotype_725_9dpa_fiber_rep3


title: patient 024b, normal, homogenized


title: Genotype_725_12dpa_fiber_rep1


title: 293_siDBC1_r3


title: 293_siZNF326_r1


title: 293_siZNF326_r3


title: 293_siDBC1_r1


title: Genotype_725_9dpa_fiber_rep1


title: Hippocampus from adult sedentary female SAMR1 mice, biological replicate 1


title: EKLF, replicate 3

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

description:
The EKLF knock out mice were referenced in our manuscript
(#34)  Perkins, A. C., A. H. Sharpe, and S. H. Orkin. 1995. Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF.
Nature 375:318 322.
From this paper:
The EKLF genomic clones were isolated from a lambdaFiXII mouse strain 129 library.......and targeting clones were injected into C57BL/6 blastocysts, which were transferred to the uterus in pseudopregnant BALB/c Swiss mice.

hyb_protocol: Hybridization of samples to  Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affymerix manual instructions

data_processing: MAS 5.0 data was performed in the Affymetrix GeneChip Expression Console

source_name: EKLF -/- fetal liver 3

label_protocol: Prepared samples using the Affymetrix GeneChip ENZO labeling kit

extract_protocol: RNA was prepared from early erythroid progenitor cells sorted from day 13.5 wild type and Eklf -/- fetal liver cells using  TRIzol reagent. RNA quality was verified with an Agilent 2100 Bioanalyzer. GeneChip target probes from 3 independent Eklf -/- and 3 wild type RNA samples were prepared according to Affymetrix’ instructions starting with 10μg of total RNA.

treatment_protocol: Fetal livers from day 13.5 wild type and Eklf -/- embryos were dissociated to a single cell suspension and stained with 7AAD, anti-CD71 and Ter119 antibodies. Early erythroid progenitor cell populations were isolated using a FACSAria flow cytometer running FACSDiva software.

value: 13.5 day old fetus

value: EKLF knock out

value: liver

tag: cell type

value: early erythroid progenitors


title: Genotype_725_6dpa_fiber_rep2

description:
725 superior traits of fiber quality
Gene expression data from 6DPA fiber from Gossypium hirsutum

source_name: Fiber 6day post anthesis

value: JKC 725

value: 6 dpa fiber


title: EKLF, replicate 2

source_name: EKLF -/- fetal liver 2

tag: age


title: Genotype_725_6dpa_fiber_rep1


title: EKLF, replicate 1

source_name: EKLF -/- fetal liver 1

tag: tissue


title: Genotype_725_6dpa_fiber_rep3


title: 293_siCTR_r3

source_name: HEK293 cells transfected with control siRNA vector

value: CTR siRNA knockdown


title: Dam-Dcr1_H2O2

status: Public on Mar 19 2012

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Cells grown in YES with 0.5 mM H2O2

hyb_protocol: hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R
additional results files: DamID_results.tab
results file descriptions: DamID_results.tab is a table containing all 8014 features for which DamID enrichment was calculated with a separate column for each of the 64 contrasts.

organism: Schizosaccharomyces pombe

label_protocol: The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.4 (unless otherwise stated)

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)

treatment_protocol: Harvested cells were spheroplasted to remove cell wall

tag: expression


title: Dam-Dcr1_normal

value: normal


title: Dam-Dcr1_sorbitol

description: Cells grown in YES with 1 M sorbitol

value: sorbitol


title: Dam-Nup85_ago1D_1

tag: genotype/variation


title: Dam-Nup85_heatshock_2

description: Cells grown at 36°C

value: heatshock


title: Dam-Nup85_wt_2

value: wt


title: Dam-Nup85_ago1D_2


title: Dam-Nup85_heatshock_1

description: Cells grown at 36°C


title: Dam-Nup85_wt_3


title: Dam-Nup85_wt_1


title: Dam-Dcr1_550_wt_2


title: Dam-Dcr1_550_wt_1


title: patient 031b, normal, homogenized

description: Gene expression profile of surgically resected material

value: normal, homogenized


title: Dam-Dcr1_550_wt_3


title: Wild type, replicate 2

source_name: Normal fetal liver 2

value: wild-type


title: 293_siCTR_r1


title: Wild type, replicate 3

source_name: Normal fetal liver 3


title: Amo1-Dam_wt_3


title: Genotype_725_0dpa_fiber_rep3

description:
725 superior traits of fiber quality
Gene expression data from 0DPA fiber from Gossypium hirsutum

source_name: Fiber 0day post anthesis

tag: genotype

value: 0 dpa fiber


title: Wild type, replicate 1

source_name: Normal fetal liver 1


title: Amo1-Dam_wt_2


title: Amo1-Dam_wt_1


title: Genotype_725_0dpa_fiber_rep1

tag: development stage


title: Dam-Dcr1_clr4D_ago1D_3


title: Dam-Dcr1_528_wt_3


title: 293_siCTR_r2


title: Dam-Dcr1_528_wt_1


title: Genotype_725_0dpa_fiber_rep2


title: Genotype_703_0dpa_fiber_rep2

value: JKC 703


title: Dam-Dcr1_rdp1D_3


title: Dam-Dcr1_ago1D_1


title: Dam-Dcr1_ago1D_2


title: Dam-Dcr1_clr4D_rdp1D_1


title: Dam-Dcr1_clr4D_ago1D_1


title: Dam-Dcr1_clr4D_rdp1D_2


title: Dam-Dcr1_ago1D_3


title: Dam-Dcr1_528_wt_2


title: Dam-Dcr1_clr4D_ago1D_2


title: Dam-Dcr1_rdp1D_2


title: Dam-Rdp1_clr4D_ago1D_3


title: Dam-Rdp1_clr4D_ago1D_2


title: Dam-Rdp1_clr4D_ago1D_1


title: Dam-Rdp1_clr4D_dcr1D_2


title: Dam-Rdp1_ago1D_3


title: Dam-Rdp1_clr4D_dcr1D_1


title: Dam-Rdp1_ago1D_2


title: Dam-Dcr1_rdp1D_1


title: Dam-Rdp1_dcr1D_1


title: Dam-Rdp1_dcr1D_3


title: Dam-Rdp1_ago1D_1


title: Dam-Rdp1_dcr1D_2


title: Dam-Cid14_wt_1


title: Dam-Ago1_wt_3


title: Arb1-Dam_wt_1


title: Dam-Rrp6_wt_2


title: Arb1-Dam_wt_3


title: Dam-Cid14_wt_2


title: Arb1-Dam_wt_2


title: Dam-Ago1_wt_1


title: Dam-Ago1_wt_2


title: Dam-Dcr1_clr4D_rdp1D_3


title: Dam-Rdp1_clr4D_3


title: Dam-Dcr1_clr4D_2


title: Dam-Dcr1_clr4D_1


title: Dam-Rrp6_wt_1


title: Dam-Rdp1_clr4D_2


title: Dam-Swi6_wt_3


title: Dam-Rdp1_clr4D_1


title: Dam-Rdp1_wt_1


title: Dam-Swi6_wt_1


title: Dam-Swi6_wt_2


title: Kc cells, GFP control, rep 2

city: Boston

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: H4K16ac, Kc cells, GFP control, rep 2

hyb_protocol: [Supplied by Nimblegen] DNA Microarray Hybridization. In a new Eppendorf tube, 2.5 ug of Cy5-labeled chromatin immunoprecipitation (ChIP) DNA is mixed with 2.5 ug of Cy3-labeled genomic DNA and 36 ug of human Cot-1 DNA (Invitrogen; catalogue no. 15279-011). Sodium acetate(1/10 vol of 3 M) is added to the tube along with 2 vol of ethanol. After ethanol precipitation, the DNA is dissolved in 22.4 ul of hybridization buffer 1 (2.2× SSC/0.22% SDS). The mixture can be heated for 10 min at 37°C to facilitate the DNA to dissolve. Then 20 ul of hybridization buffer 2 (70% formamide/3× SSC/14.3% dextran sulfate) is added to the mixture, and the tube is first heated at 95°C for 5 min to denature DNA, then incubated at 42°C for 2 min. At this step, 4 ul of yeast tRNA (Sigma; catalogue no. R9001 at 10 ug/ul) and 3 ul of 2% BSA are added to the mixture, which is then spotted to a DNA microarray slide that has been incubated with the prehybridization solution for 40 min at 42°C. A 25-mm × 60-mm cover slip is then gently placed on top of the sample, and the hybridization is carried on in a hybridization chamber (Corning; catalogue no. 07-200-271) at 60°C overnight in a water bath. After the hybridization, the microarray slide is washed once with washing buffer 1 (2× SSC/0.1% SDS) at 60°C for 5 min in a glass slide staining dish. This is followed by a wash with buffer 2 (0.2× SSC/0.1% SDS) for 10 min at room temperature and three times with buffer 3 (0.2× SSC) at room temperature. The slide is then dried by a brief spinning at 1,000 × g in a table-top centrifuge.

scan_protocol: [Supplied by Nimblegen] Microarray Scanning and Initial Analysis. The microarray slides are scanned using GenePix 4000B scanner from Axon Instruments (Foster City, CA), and each microarray image is first analyzed with the image analysis software GENEPIX PRO 3.0 to derive the Cy3 and Cy5 fluorescent intensity and background noise for all the spots on the array. The intensities for both Cy3 and Cy5 channels are first adjusted by subtracting the background intensity of each spot by using the formula channel channel I - B , where channel represents either Cy5 or Cy3. The intensities are further adjusted by subtracting the median intensity of all the blank spots on the array. If any of these values was lower than 10, it was then raised to 10. Intensity Normalization: The normalization factor is calculated based on the intensities of spots that are considered good (more than 65% of pixels have intensities higher than the background intensity plus 1 SD). The median of the intensity ratios, I635/I532 is then used to adjust the Cy3 channel intensity to the same level as that of the Cy5 channel.

data_processing: Dye-specific bias was identified from the average intensity vs. log-ratio plot (i.e. MA plot) and a combination of rotation and a robust curve-fitting is used to correct the problem (Peng et al., 2007).

organism: Drosophila melanogaster

source_name: Kc GFP K16 EL

label_protocol: [Supplied by Nimblegen] Labeling of Amplified DNA. In a colored Eppendorf tube, 200 ng of DNA from the previous step is mixed with 20 ul of 2.5× random primer solution (BioPrime kit, Invitrogen; catalogue no. 18094-011) and dH2O in a final volume of 42.5 ul. The mixture is boiled for 5 min and then cooled on ice for 5 min. Subsequently, 5 ul of 10× low dCTP mixture (2.5 mM each for dATP, dTTP, and dGTP, and 0.6 mM for dCTP), 1.5 ul of Cy5-dCTP (Amersham; catalogue no. PA55021) or Cy3-dCTP (Amersham; catalogue no. PA53021), and 40 units of Klenow DNA polymerase are added to tube. The tube is incubated at 37°C for 2 h. After the reaction, the labeled DNA is purified using the Qiagen PCR kit (Qiagen; catalogue no. 28106).

extract_protocol: The immunoprecipitated material was eluted from the beads by adding 10 μL (100 U) of AcTEV protease into 450 μL of TEV buffer followed by incubation at 25°C for 1 h. To reverse the cross-links, samples were brought to 0.3M NaCl and 1% SDS and incubated at 65°C for 12 h. The samples were then extracted with phenol/chloroform/isoamyl alcohol followed by chloroform, and precipitated by ethanol in the presence of glycogen. The resulting precipitated DNA and the input DNA were amplified using a DNA linker as described (Strutt et al., 1997). LM-PCR (25 cycles) was performed using Platinum Pfu (Invitrogen). The resulting DNA was labeled and hybridized to arrays by NimbleGen Systems, Inc. Two-channel tiling arrays containing 388,000 probes were designed based on FlyBase 3.2. Chromosomes X and 19.6Mb of 2L were covered. The ChIP sample of interest was hybridized on one channel and genomic DNA was used as the reference on the other channel. Each ChIP-chip experiment was performed in duplicate.

tag: knockdown

value: GFP control

value: Kc cells

source_name: Kc GFP IN EL

value: input DNA


title: Dam-Rdp1_wt_2


title: Dam-Dcr1_clr4D_3


title: Dam-Rdp1_wt_3


title: wt_391_2

data_processing: oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R

label_protocol: 200ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.5

extract_protocol: Total RNA was isolated using the hot phenol method

value: wild type


title: wt_391_3


title: swi6D_1


title: swi6D_3


title: swi6D_2


title: EA0703_03

city: Niigata

first: yohei

last: Tsuchida

address: 1-757 Asahimachi-dori

institute: Niigata University Graduate School of Medical and Dental Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: cardio-renal syndrome mice

label_protocol: Biotinylated cRNA were prepared by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.

growth_protocol: Mice were maintained in our animal facility. Animal care was in accordance with the guidelines of Niigata University.

extract_protocol: Each remaining kidney in uninephrectomy alone mice or cardio-renal syndrome mice was removed to purify total RNA 6 weeks after the uninephrectomy. Total RNA was extracted by using RNAiso (Takara Bio, Japan) which use AGPC(acid guanidinium thiocyanate-phenol-chloroform extraction) method.

treatment_protocol: Cardio-renal syndrome mice were established by the combination of abdominal aortic banding and uninephrectomy. Abdominal aortic banding was conducted by constricting the abdominal aorta under the divergence of bilateral renal arteries. Unilateral nephrectomy was conducted 2 weeks after the aortic banding.

value: kidney removed 6week after the uninephrectomy

tag: gender

value: Male

value: C57BL/6J mice

value: 16 weeks old


title: Kc cells, H4K16, Sxl RNAi KD, 21490, rep 2

description: H4K16ac, Kc cells, Sxl RNAi KD, 21490, rep 2

source_name: Kc Sxl 21490 K16 EL

value: Sxl RNAi KD, 21490

tag: chip antibody

source_name: Kc Sxl 21490 IN EL


title: EA0703_02


title: mVSG

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Gene expression data from DCs from C57Bl/6 mice, treated with mVSG

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and quantile-quantile as normalization method

source_name: DCs from C57Bl/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Fresh bone marrow precursors were isolated from Tibia and Femur of 6-8 weeks old C57Bl/6 mice, depleted of CD90 and CD19 positive cells and cultivated for 8 days  at 37° and 5% CO2 at 3e6 cells/well in 10 ml complete RPMI medium supplemented with 10% GM-CSF supernatant

extract_protocol: Cells were lysed in Trizol reagent and complete RNA was isolated according to manufacturers instructions.

treatment_protocol: 8 days old DCs were treated with appropriate stimuli for 24 hours at 37° and 5% CO2.

tag: treatment

value: treated with mVSG

value: Dendritic cells


title: EA0703_01

source_name: uninephrectomy alone mice


title: Kc cells, H4K16, Sxl RNAi KD, 28896, rep 2

description: H4K16ac, Kc cells, Sxl RNAi KD, 28896, rep 2

source_name: Kc Sxl 28896 K16 EL

value: Sxl RNAi KD, 28896

tag: cell line

source_name: Kc Sxl 28896 IN EL


title: Kc cells, H4K16, Sxl RNAi KD, 21490, rep 1

description: H4K16ac, Kc cells, Sxl RNAi KD, 21490, rep 1

source_name: Kc Sxl 21490 IN MG

source_name: Kc Sxl 21490 K16 MG


title: wt_391_1

tag: strain


title: Kc cells, H4K16, Sxl RNAi KD, 28896, rep 1

description: H4K16ac, Kc cells, Sxl RNAi KD, 28896, rep 1

source_name: Kc Sxl 28896 IN MG

source_name: Kc Sxl 28896 K16 MG


title: Mitat

description: Gene expression data from DCs from C57Bl/6 mice, treated with Mitat

value: treated with Mitat


title: Kc cells, GFP control, rep 1

description: H4K16ac, Kc cells, GFP control, rep 1

source_name: Kc GFP IN MG

source_name: Kc GFP K16 MG


title: ago1D_2


title: ago1D_1


title: rdp1D_2


title: ctrl

description: Gene expression data from DCs from BALB/C mice, untreated

value: untreated


title: LPS

description: Gene expression data from DCs from C57Bl/6 mice, treated with LPS

value: treated with LPS


title: rdp1D_1


title: wt_597_2


title: OH1 biological rep3

city: TAIPEI

first: PRASHANT

last: SINGH

state: TAIPEI

address: Rm 1150, Life Science Building, No. 1, Sec. 4, Roosevelt Road

department: INSTITUTE OF PLANT BIOLOGY

country: Taiwan

institute: NATIONAL TAIWAN UNIVERSITY

description: Gene expression data from 5-week-old transgenics over expressing LecRKVI.2 (OH1)

hyb_protocol: Eleven µg of labelled samples were hybridised to the GeneChip Arabidopsis ATHI at 45°C for 16.5 hours. Washing and staining were performed using the Fluidic Station-450.

scan_protocol: GeneChip were scanned with Affymetrix GeneChip Scanner 7G.

data_processing: The data were analysed using GeneSpring GX11 software and alogrithm RMA as normalisation method.

source_name: OH1  rosette

label_protocol: Ten µg of total RNA were used for cDNA synthesis, labeled by in vitro transcription followed by fragmentation according to the manufacturer’s suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: Arabidopsis thaliana (L. Heyhn.) Columbia (Col-0) were grown in commercial potting soil/perlite (3:2) at 22-24°C day, 17-19°C night temperature under a 15-h-light/9-h-dark photoperiod.

extract_protocol: Total RNA was isolated using TRIZOL reagent according to the manufacturers instructions.

value: leaves

tag: genetic background


title: wt_597_1


title: Female Titanium 16

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

scan_protocol: Arrays were washed and scanned on an Agilent G2505B scanner at 5 m resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing:
A reference design (Kerr 2003; Kerr and Churchill 2007) was used to analyse gene expression microarray data. The background fluorescence was measured using the (-)3xSLv1 probes; probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent (within the background signal). Data were normalized using LOWESS in R (2004).
RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls.) Log.Ratio is calculated as log2(NormCy5/NormCy3)

source_name: Liver tissue

label_protocol: Individual total RNA (200 ng) samples and universal reference total RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine labelled cRNA according to the manufacturer’s instructions (Agilent Linear Amplification Kits, Agilent Technologies, Mississauga, ON, Canada). Experimental samples were labelled with Cyanine 5-CTP, and reference RNA with Cyanine 3-CTP (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada). Cyanine-labelled cRNA targets were in vitro transcribed using T7 RNA polymerase and purified by RNeasy Mini Kit (Qiagen). Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies, Mississauga, ON, Canada) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 µm resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

extract_protocol:
ch1: Total RNA was isolated from random sections of the liver tissue using TRIzol reagent (Invitrogen) and purified using RNeasy Mini Kit (Qiagen). All RNA samples showing A260/280 ratios between 2.0 and 2.1 were further analysed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). Only high quality RNA (28S/18S > 1.8) was used for analysis. Was quantified using UV spectrophotometer and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).
ch2: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

value: Time-mated mice C57BL/6BomTac mice

value: liver

value: Female

value: Titanium


title: Male Control 33

hyb_protocol: Labelled cRNA was hybridized to Agilent mouse 4 x 44 oligonucleotide microarrays (Agilent Technologies, Mississauga, ON, Canada) at 60ºC overnight. Arrays were washed and scanned on an Agilent G2505B scanner at 5 µm resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

value: Control

source_name: universal mouse reference total RNA (Stratagene, CA, USA)


title: Female Control 25

value: universal mouse reference total RNA (Stratagene, CA, USA)


title: Female Control 40


title: FF15

city: College Station

first: Jennifer

last: Goldsby

state: TX

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

institute: Texas A&M University

description: Raw data file: T00346131_FF15_1.TXT

hyb_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from Codelink Expression Analysis Version 5.0

molecule: polyA RNA

source_name: stool RNA formula fed

label_protocol: Ambion MessageAmp II aRNA Amplification and Biotin Enhanced kits:  Manual Labelled cRNA Target preparation following manufacturer's instructions http://www.ambion.com/techlib/prot/fm_1751.pdf and http://www.ambion.com/techlib/prot/fm_1791.pdf

extract_protocol: PolyA RNA was extracted from stool samples following the protocol published in Biomarkers, 2003, Jan-Feb;8(1):51-61.

value: Male

value: 3 months


title: OH1 biological rep2

value: transgenics over expressing LecRKVI.2 (OH1)


title: OH1 biological rep1


title: dcr1D_3


title: FF13

description: Raw data file: T00346128_FF13_1.TXT


title: Male Titanium 17


title: Female Titanium 10


title: Male Titanium 3


title: Male Control 43


title: FF5

description: Raw data file: T00346118_FF5_1.TXT


title: Col-0 biological rep3

description: Gene expression data from 5-week-old wild type arabidopsis

source_name: Col-0  rosette

value: wild type


title: FF3

description: Raw data file: T00346125_FF3_1.TXT


title: FF2

description: Raw data file: T00346121_FF2_1.TXT


title: FF7

description: Raw data file: T00346135_FF7_1.TXT


title: Col-0 biological rep1


title: App1_NE_rep3

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description: biological replicate 3 of 3 for norepinephrine treated Actinobacillus pleuropneumoniae

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). After fragmentation, 300ng of Cy5 labeled cRNA and Cy3 labeled cRNA were hybridized with the same array at 65°C, 10 rpm rotation for 17 hours. Then, the arrays were washed twice using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent Microarray Scanner System (G2565BA) (Agilent) with resolution of 5μm. The scanner uses 100% and 10% PTM respectively and combines the two data automatically.

data_processing: We used and submitted only one probe signal (the probe that near the 3 end of the gene) for each gene in this study. The 2477 rows in the sample data table represented 2477 ORFs on the array. The data were analyzed using Feature Extraction Software (Agilent). The signal intensities were normalized using Feature Extraction Software (Agilent) and transformed into log2 values.

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

source_name: Actinobacillus pleuropneumoniae 4074

label_protocol: 2μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After purified, 4μg cRNA from control sample was labeled with Cy5 NHS ester and 4μg cRNA of Epi or NE treated sample was labeled with Cy3 NHS ester (GE healthcare) respectively and purified.

growth_protocol: A. pleuropneumoniae was cultured in Tryptic Soy Broth (TSB) or on Tryptic Soy Agar (TSA) (Difco Laboratories) supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C.

extract_protocol: Total RNA was extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions, then purified using QIAGEN RNeasy Mini Kit (QIAGEN).

treatment_protocol: For catecholamines treated A. pleuropneumoniae samples, epinephrine (Epi) and norepinephrine (NE) were added respectively into the medium at 50μM.

tag: culture condition

value: cultured in TSB medium to middle exponential phase

value: control

organism: Actinobacillus pleuropneumoniae

source_name: Norepinephrine (NE) treated Actinobacillus pleuropneumoniae

value: cultured in TSB medium with 50 μM norepinephrine to middle exponential phase

value: Norepinephrine


title: Col-0 biological rep2


title: BF6

description: Raw data file: T00346134_BF6_1.TXT

source_name: stool RNA breast fed


title: Male Control31

tag: sample type


title: dcr1D_1


title: BF4

description: Raw data file: T00346119_BF4_1.TXT


title: Female Titanium 21


title: Female Titanium 8


title: Male  Titanium 5


title: wt_561_3


title: dcr1D_2


title: wt_561_2


title: wt_561_1


title: App1_NE_rep1

description: biological replicate 1 of 3 for norepinephrine treated Actinobacillus pleuropneumoniae


title: App1_NE_rep2

description: biological replicate 2 of 3 for norepinephrine treated Actinobacillus pleuropneumoniae


title: App1_Epi_rep3

description: biological replicate 3 of 3 for epinephrine treated Actinobacillus pleuropneumoniae

source_name: Epinephrine (Epi) treated Actinobacillus pleuropneumoniae

value: cultured in TSB medium with 50 μM epinephrine to middle exponential phase

value: Epinephrine


title: BMS16

description: Raw data file: T00346117_BMS16_1.TXT


title: BF3

description: Raw data file: T00346127_BF3_1.TXT


title: App1_Epi_rep2

description: biological replicate 2 of 3 for epinephrine treated Actinobacillus pleuropneumoniae


title: Female Control 35


title: BMS10

description: Raw data file: T00346136_BMS10_1.TXT


title: Male Titanium 4


title: Female Titanium 2


title: Male Control 41


title: App1_Epi_rep1

description: biological replicate 1 of 3 for epinephrine treated Actinobacillus pleuropneumoniae


title: BMS8

description: Raw data file: T00346122_BMS8_1.TXT


title: TNF

description: Gene expression data from DCs from C57Bl/6 mice, treated with TNF alpha

source_name: DCs from C57Bl/6 mice

value: treated with TNF alpha

value: Dendritic cells


title: F.207 father NspI

status: Public on Mar 18 2012

city: Valencia

first: Joaquín

last: Dopazo

state: Valencia

address: c/ Eduardo Primo Yufera, 3

department: Computational Genomics

institute: Centro de Investigación Príncipe Felipe (CIPF)

description: Hybridized to 250K_Nsp

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and images were obtained using an Affymetrix GeneChip® Scanner 3000.

data_processing:
CEL files were processed using Affymetrix Power Tools (APT v1.10.2) using BRLMM calling algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: phenotype

value: unaffected

tag: family

tag: family member

value: father

value: male

value: peripheral blood

tag: disease state


title: F.207 mother NspI

description: Hybridized to 250K_Nsp

value: mother

value: female

tag: tissue


title: F.205 mother NspI

description: Hybridized to 250K_Nsp


title: F.205 father NspI

description: Hybridized to 250K_Nsp


title: F.201 father NspI

description: Hybridized to 250K_Nsp


title: F.205 child NspI

description: Hybridized to 250K_Nsp

value: affected

value: child

value: Hirschsprung's disease


title: F.206 mother NspI

description: Hybridized to 250K_Nsp


title: F.202 father NspI

description: Hybridized to 250K_Nsp


title: F.206 child NspI

description: Hybridized to 250K_Nsp


title: F.202 child NspI

description: Hybridized to 250K_Nsp


title: F.153 child NspI

description: Hybridized to 250K_Nsp


title: F.153 mother NspI

description: Hybridized to 250K_Nsp


title: F.201 mother NspI

description: Hybridized to 250K_Nsp


title: F.202 mother NspI

description: Hybridized to 250K_Nsp


title: F.195 mother NspI

description: Hybridized to 250K_Nsp


title: F.207 child NspI

description: Hybridized to 250K_Nsp


title: F.201 child NspI

description: Hybridized to 250K_Nsp


title: F.195 father NspI

description: Hybridized to 250K_Nsp


title: F.152 child NspI

description: Hybridized to 250K_Nsp


title: F.146 mother NspI

description: Hybridized to 250K_Nsp


title: F.152 mother NspI

description: Hybridized to 250K_Nsp


title: F.152 father NspI

description: Hybridized to 250K_Nsp


title: F.195 child NspI

description: Hybridized to 250K_Nsp


title: F.206 father NspI

description: Hybridized to 250K_Nsp


title: F.146 child NspI

description: Hybridized to 250K_Nsp


title: F.153 father NspI

description: Hybridized to 250K_Nsp


title: F.151 mother NspI

description: Hybridized to 250K_Nsp


title: F.146 father NspI

description: Hybridized to 250K_Nsp


title: F.151 child NspI

description: Hybridized to 250K_Nsp


title: F.151 father NspI

description: Hybridized to 250K_Nsp


title: F.207 mother StyI

description: Hybridized to 250K_Sty


title: F.139 father NspI

description: Hybridized to 250K_Nsp


title: F.207 father Sty

description: Hybridized to 250K_Sty


title: F.139 child NspI

description: Hybridized to 250K_Nsp


title: F.205 mother Sty

description: Hybridized to 250K_Sty


title: F.205 father Sty

description: Hybridized to 250K_Sty


title: F.207 child StyI

description: Hybridized to 250K_Sty


title: F.130 father NspI

description: Hybridized to 250K_Nsp


title: F.130 mother NspI

description: Hybridized to 250K_Nsp


title: F.202 father Sty

description: Hybridized to 250K_Sty


title: F.139 mother NspI

description: Hybridized to 250K_Nsp


title: F.202 mother Sty

description: Hybridized to 250K_Sty


title: F.206 child Sty

description: Hybridized to 250K_Sty


title: F.120 mother NspI

description: Hybridized to 250K_Nsp


title: F.115 father NspI

description: Hybridized to 250K_Nsp


title: F.202 child Sty

description: Hybridized to 250K_Sty


title: F.106 father NspI

description: Hybridized to 250K_Nsp


title: F.115 child NspI

description: Hybridized to 250K_Nsp


title: F.206 father Sty

description: Hybridized to 250K_Sty


title: F.115 mother NspI

description: Hybridized to 250K_Nsp


title: F.106 mother NspI

description: Hybridized to 250K_Nsp


title: F.120 child NspI

description: Hybridized to 250K_Nsp


title: F.130 child NspI

description: Hybridized to 250K_Nsp


title: F.201 father Sty

description: Hybridized to 250K_Sty


title: F.195 mother StyI

description: Hybridized to 250K_Sty


title: F.201 child Sty

description: Hybridized to 250K_Sty


title: F.195 child Sty

description: Hybridized to 250K_Sty


title: F.201 mother Sty

description: Hybridized to 250K_Sty


title: F.105 father NspI

description: Hybridized to 250K_Nsp


title: F.205 child Sty

description: Hybridized to 250K_Sty


title: F.153 father Sty

description: Hybridized to 250K_Sty


title: F.120 father NspI

description: Hybridized to 250K_Nsp


title: F.102 mother NspI

description: Hybridized to 250K_Nsp


title: F.153 mother Sty

description: Hybridized to 250K_Sty


title: F.153 child Sty

description: Hybridized to 250K_Sty


title: F.152 mother Sty

description: Hybridized to 250K_Sty


title: F.206 mother Sty

description: Hybridized to 250K_Sty


title: F.152 father Sty

description: Hybridized to 250K_Sty


title: F.98B father NspI

description: Hybridized to 250K_Nsp


title: F.98B mother NspI

description: Hybridized to 250K_Nsp


title: F.105 mother NspI

description: Hybridized to 250K_Nsp


title: F.151 mother Sty

description: Hybridized to 250K_Sty


title: F.111 child NspI

description: Hybridized to 250K_Nsp


title: F.152 child Sty

description: Hybridized to 250K_Sty


title: F.98 mother NspI

description: Hybridized to 250K_Nsp


title: F.98 father NspI

description: Hybridized to 250K_Nsp


title: F.98 child NspI

description: Hybridized to 250K_Nsp


title: F.98B child NspI

description: Hybridized to 250K_Nsp


title: F.146 father Sty

description: Hybridized to 250K_Sty


title: F.102 child NspI

description: Hybridized to 250K_Nsp

tag: comment

value: Consanguineous


title: F.151 father Sty

description: Hybridized to 250K_Sty


title: F.146 mother Sty

description: Hybridized to 250K_Sty


title: F.95 mother NspI

description: Hybridized to 250K_Nsp


title: F.106 child NspI

description: Hybridized to 250K_Nsp


title: F.95 father NspI

description: Hybridized to 250K_Nsp


title: F.195 father Sty

description: Hybridized to 250K_Sty


title: F.95 child NspI

description: Hybridized to 250K_Nsp


title: F.139 father Sty

description: Hybridized to 250K_Sty


title: F.89 mother NspI

description: Hybridized to 250K_Nsp


title: F.102 father NspI

description: Hybridized to 250K_Nsp


title: F.146 child Sty

description: Hybridized to 250K_Sty


title: F.130 father Sty

description: Hybridized to 250K_Sty


title: F.89 child NspI

description: Hybridized to 250K_Nsp


title: F.81 mother NspI

description: Hybridized to 250K_Nsp


title: F.139 child Sty

description: Hybridized to 250K_Sty


title: F.89 father NspI

description: Hybridized to 250K_Nsp


title: F.80 mother NspI

description: Hybridized to 250K_Nsp


title: F.120 mother Sty

description: Hybridized to 250K_Sty


title: F.130 mother Sty

description: Hybridized to 250K_Sty


title: F.120 father Sty

description: Hybridized to 250K_Sty


title: F.69 father NspI

description: Hybridized to 250K_Nsp


title: F.81 father NspI

description: Hybridized to 250K_Nsp


title: F.151 child Sty

description: Hybridized to 250K_Sty


title: F.81 child NspI

description: Hybridized to 250K_Nsp

value: Down syndrome


title: F.115 mother Sty

description: Hybridized to 250K_Sty


title: F.115 father Sty

description: Hybridized to 250K_Sty


title: F.69 mother NspI

description: Hybridized to 250K_Nsp


title: F.68 mother NspI

description: Hybridized to 250K_Nsp


title: F.80 child NspI

description: Hybridized to 250K_Nsp


title: F.69 child NspI

description: Hybridized to 250K_Nsp


title: F.120 child Sty

description: Hybridized to 250K_Sty


title: F.115 child Sty

description: Hybridized to 250K_Sty


title: F.31 father NspI

description: Hybridized to 250K_Nsp


title: F.80 father NspI

description: Hybridized to 250K_Nsp


title: F.102 father Sty

description: Hybridized to 250K_Sty


title: F.106 father Sty

description: Hybridized to 250K_Sty


title: F.106 mother Sty

description: Hybridized to 250K_Sty


title: F.105 father Sty

description: Hybridized to 250K_Sty


title: F.106 child Sty

description: Hybridized to 250K_Sty


title: F.102 mother Sty

description: Hybridized to 250K_Sty


title: F.105 mother Sty

description: Hybridized to 250K_Sty


title: F.68 father NspI

description: Hybridized to 250K_Nsp


title: F.111 child Sty

description: Hybridized to 250K_Sty


title: F.65 mother NspI

description: Hybridized to 250K_Nsp


title: F.64 father NspI

description: Hybridized to 250K_Nsp


title: F.102 child Sty

description: Hybridized to 250K_Sty


title: F.98B child Sty

description: Hybridized to 250K_Sty


title: F.64 mother NspI

description: Hybridized to 250K_Nsp


title: F.65 father NspI

description: Hybridized to 250K_Nsp


title: F.98 mother Sty

description: Hybridized to 250K_Sty


title: F.98B mother Sty

description: Hybridized to 250K_Sty


title: F.63 child NspI

description: Hybridized to 250K_Nsp


title: F.61 father NspI

description: Hybridized to 250K_Nsp


title: F.98 father StyI

description: Hybridized to 250K_Sty


title: F.65 child NspI

description: Hybridized to 250K_Nsp


title: F.63 father NspI

description: Hybridized to 250K_Nsp


title: F.61 child NspI

description: Hybridized to 250K_Nsp


title: F.98B father Sty

description: Hybridized to 250K_Sty


title: F.95 mother Sty

description: Hybridized to 250K_Sty


title: F.98 child Sty

description: Hybridized to 250K_Sty


title: F.61 mother NspI

description: Hybridized to 250K_Nsp


title: F.64 child NspI

description: Hybridized to 250K_Nsp


title: F.68 child NspI

description: Hybridized to 250K_Nsp


title: F.130 child Sty

description: Hybridized to 250K_Sty


title: F.139 mother Sty

description: Hybridized to 250K_Sty


title: F.95 child Sty

description: Hybridized to 250K_Sty


title: F.58 father NspI

description: Hybridized to 250K_Nsp


title: F.58 mother NspI

description: Hybridized to 250K_Nsp


title: F.89 mother StyI

description: Hybridized to 250K_Sty


title: F.57 father NspI

description: Hybridized to 250K_Nsp


title: F.89 child Sty

description: Hybridized to 250K_Sty


title: F.57 child NspI

description: Hybridized to 250K_Nsp


title: F.80 father Sty

description: Hybridized to 250K_Sty


title: F.95 father Sty

description: Hybridized to 250K_Sty