title: 13484552 - sdg26-1 vs wt-1

hyb_protocol: wt-1 Cy5 / sdg26-1 Cy3 : 30pmol. 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: 13561077 - wt-3 vs sdg26-3

status: Public on Jul 20 2007

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Differential transcriptome in mutant plants

hyb_protocol: sdg26-3 Cy5 / wt-3 Cy3 : 30pmol. 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 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,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 indirect, amplification=yes, DNA 5 ug. 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: whole plant - Media : MS 0255, 1% sucrose, 0,9% agar hygrometry : ? Temperature : 21degreeC/ 17degreeC Light : 16h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: wild type 0min after HU blockage vs. wild type 120min after HU blockage

status: Public on Jul 25 2007

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

description: Wild type strain was incubated in 50mM of hydroxyrurea (HU) to cause transient S-phase arest and allowed to grow for additional 0, 60, 90 and 120 minutes after HU was withdrawn from the culture medium. Harvested conidia from each time point were DAPI stained and microscopically analyzed in terms of nucelar division kinetics  and polar growth before RNA extraction. This procedure validated the phenotipic traits of the wild type strain.

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2 X SSC 0,5% SDS, 0,5 X SSC and 0.05X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation

scan_protocol: Slides were dried by centrifugation and subjected to fluorescent detection with a GMS 418 Array Scanner (Affymetrix Inc., Santa Clara, CA).

data_processing: TIFF images generated were analyzed using TIGR Spotfinder (http://www.tigr.org/software/) to obtain relative transcript levels. Spotfinder uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels. This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio). Spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses. Data was normalized using a local regression technique LOWESS (LOcally WEighted Scatterplot Smoothing) for hybridizations with RNA-based samples and SD regularization of the Cy5/Cy3 ratio across all sectors (blocks) of the array using a software tool MIDAS (http://www.tigr.org/softlab). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS and the union of all genes identified at each time point were considered significant in this experiment. The resulting data were organized and visualized based on similar expression vectors in genes using Euclidean distance and hierarchical clustering with average linkage clustering method to view the whole data set and k-means to group the genes in 60 clusters with TIGR MEV (multi experiment viewer), also available at http://www.tigr.org/software.

organism: Aspergillus nidulans

source_name: wild type conidia grown for 0 minutes after hydroxyurea blockage

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out™ (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.

extract_protocol: At each time point the germlings were harvested by centrifugation and quickly frozen in liquid nitrogen. For total RNA isolation, the germlings were disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 2.2 M formaldehyde, 1.2% agarose gel, stained with ethidium bromide, and then visualized with UV-light. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

tag: For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) strain were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks containing 50 mM of hydroxyurea (HU) and allow to grow for 5 hours in a reciprocal shaker (250 rpm) at 37°C to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. Hybridization experiments were competitive using probes derived from wild type and delta atmA strain grown for zero, 60, 90 and 120 minutes after HU blockage release using timepoint zero as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: wild type conidia grown for 120 minutes after hydroxyurea blockage

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy5-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out™ (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy5-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.


title: 13420445 - wt-2 vs sdg25-2

hyb_protocol: sdg25-2 Cy5 / wt-2 Cy3 : 30pmol. 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: rat_hepatocytes_WY24h_pooled

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: primary hepatocytes, rat, treatment with WY14643 for 24h

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, empirical Bayes

label: biotin

organism: Rattus norvegicus

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions.

tag: Material

value: primary hepatocytes, rat


title: 13561078 - sdg26-3 vs wt-3

hyb_protocol: wt-3 Cy5 / sdg26-3 Cy3 : 30pmol. 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: 13484550 - wt-1 vs sdg26-1

hyb_protocol: sdg26-1 Cy5 / wt-1 Cy3 : 30pmol. 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: wild type 0min after HU blockage vs.  wild type 60min after HU blockage

source_name: wild type conidia grown for 60 minutes after hydroxyurea blockage


title: 13561075 - sdg25-3 vs wt-3

hyb_protocol: wt-3 Cy5 / sdg25-3 Cy3 : 30pmol. 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: 13484546 - sdg25-1 vs wt-1

hyb_protocol: wt-1 Cy5 / sdg25-1 Cy3 : 30pmol. 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: 13561074 - wt-3 vs sdg25-3

hyb_protocol: sdg25-3 Cy5 / wt-3 Cy3 : 30pmol. 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: rat_hepatocytes_control_pooled

description: primary hepatocytes, rat, control condition

scan_protocol: According to standard Affymetrix protocols.

tag: primary hepatocytes, rat


title: 13484545 - wt-1 vs sdg25-1

hyb_protocol: sdg25-1 Cy5 / wt-1 Cy3 : 30pmol. 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: 13420179 - wt-2 vs sdg26-2

hyb_protocol: sdg26-2 Cy5 / wt-2 Cy3 : 30pmol. 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: 13371090 - sdg8-2 vs wt-2

hyb_protocol: wt-2 Cy5 / sdg8-2 Cy3 : 30pmol. 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

growth_protocol: whole plant - Media : MS 0255, 1% sucrose, 0,9% agar Temperature : 21degreeC/ 17degreeC Light : 16h

tag: Arabidopsis thaliana (columbia)  mutant (At1g77300 t-DNA col0 mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13602843 - wt-4 vs sdg8-4

hyb_protocol: sdg8-4 Cy5 / wt-4 Cy3 : 30pmol. 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: 13302367 - vip4-1 vs wt-1

hyb_protocol: wt-1 Cy5 / vip4-1 Cy3 : 30pmol. 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.

growth_protocol: whole plant - Media : MS 0255, 1% sucrose, 0,9% agar hygrometry : ? temperature : 21degreeC/ 17degreeC Light : 16h

tag: Arabidopsis thaliana (columbia)  mutant (At5g61150 t-DNA col0 mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13561073 - sdg8-4 vs wt-4

hyb_protocol: wt-4 Cy5 / sdg8-4 Cy3 : 30pmol. 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: 13602842 - sdg8-3 vs wt-3

hyb_protocol: wt-3 Cy5 / sdg8-3 Cy3 : 30pmol. 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: 13366297 - wt-2 vs vip4-2

hyb_protocol: vip4-2 Cy5 / wt-2 Cy3 : 30pmol. 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: 13366298 - vip4-2 vs wt-2

hyb_protocol: wt-2 Cy5 / vip4-2 Cy3 : 30pmol. 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: 13365202 - wt-1 vs m2

hyb_protocol: m2 Cy5 / wt-1 Cy3 : 30pmol. 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.

tag: Arabidopsis thaliana (columbia)  mutant (At4g26110 t-DNA col0 mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13300951 - wt-1 vs vip4-1

hyb_protocol: vip4-1 Cy5 / wt-1 Cy3 : 30pmol. 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: 13365205 - sdg8-1 vs wt-1

hyb_protocol: wt-1 Cy5 / sdg8-1 Cy3 : 30pmol. 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: 13365198 - wt-1 vs X123

hyb_protocol: X123 Cy5 / wt-1 Cy3 : 30pmol. 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.

tag: Arabidopsis thaliana (columbia)  mutant ( At2g19480, At4g26110 and At5g56950 triple t-DNA mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13371087 - wt-2 vs clf1

hyb_protocol: clf1 Cy5 / wt-2 Cy3 : 30pmol. 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.

tag: Arabidopsis thaliana (columbia)  mutant (clf1) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13365194 - m3 vs wt-1

hyb_protocol: wt-1 Cy5 / m3 Cy3 : 30pmol. 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.

tag: Arabidopsis thaliana (columbia)  mutant (At5g56950 t-DNA col0 mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: trophozoite timepoint 15 with actD

status: Public on Jul 19 2007

city: San Francisco

first: Joseph

middle: L

last: DeRisi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: University of California San Francisco

description: trophozoite timepoint 15 with actD

hyb_protocol: Labeled cDNA from both the sample and reference pool are mixed in 3x SSC and 0.2% SDS and pipetted underneath a coverslip.  Arrays are placed in hyb chambers and are hybridized at 65 degrees for 24 hours.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner.  The control yeast RNA spots were used for scanning and normalization so that the intensity of Cy5 and Cy3 is equal for each of those spots.

data_processing: Spot analysis was performed with GenePix v3.0 and stored in a relational database (NOMAD). Extracted values are directly as calculated by GenePix and not normalized.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum strain 3D7

label_protocol: 8 µg of total RNA were primed with oligo(dT) and random nonamers, then reversed transcribed at 42¡C for 2 h in the presence of dNTPs and amino-allyl dUTP. Labeled cDNAs were resuspended in 0.1M sodium bicarbonate and then coupled to Cy5 (GE Healthcare).

extract_protocol: Trizol extraction

tag: Plasmodium falciparum strain 3D7

source_name: Plasmodium falciparum 3D7 reference

label_protocol: 8 µg of total RNA were primed with oligo(dT) and random nonamers, then reversed transcribed at 42¡C for 2 h in the presence of dNTPs and amino-allyl dUTP. Labeled cDNAs were resuspended in 0.1M sodium bicarbonate and then coupled to Cy3 (GE Healthcare).

tag: Plasmodium falciparum strain 3D7 total RNA reference pool


title: 13365197 - wt-1 vs m1

hyb_protocol: m1 Cy5 / wt-1 Cy3 : 30pmol. 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.

tag: Arabidopsis thaliana (columbia)  mutant (At2g19480 t-DNA col0 mutant) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13365200 - X123 vs wt-1

hyb_protocol: wt-1 Cy5 / X123 Cy3 : 30pmol. 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: 13365204 - wt-1 vs sdg8-1

hyb_protocol: sdg8-1 Cy5 / wt-1 Cy3 : 30pmol. 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: 13365193 - wt-1 vs m3

hyb_protocol: m3 Cy5 / wt-1 Cy3 : 30pmol. 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: 13602841 - wt-3 vs sdg8-3

hyb_protocol: sdg8-3 Cy5 / wt-3 Cy3 : 30pmol. 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: wild type 0min after HU blockage vs.  wild type 90min after HU blockage

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2 X SSC 0,5% SDS, 0,5 X SSC and 0.05X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation

source_name: wild type conidia grown for 90 minutes after hydroxyurea blockage


title: 13371089 - wt-2 vs sdg8-2

hyb_protocol: sdg8-2 Cy5 / wt-2 Cy3 : 30pmol. 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: 13371088 - clf1 vs wt-2

hyb_protocol: wt-2 Cy5 / clf1 Cy3 : 30pmol. 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: 13365203 - m2 vs wt-1

hyb_protocol: wt-1 Cy5 / m2 Cy3 : 30pmol. 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: trophozoite timepoint 10 with actD

description: trophozoite timepoint 10 with actD


title: 13365199 - m1 vs wt-1

hyb_protocol: wt-1 Cy5 / m1 Cy3 : 30pmol. 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: schizont timepoint 30 with actD

description: schizont timepoint 30 with actD


title: schizont timepoint 120 with actD

description: schizont timepoint 120 with actD


title: trophozoite timepoint 0 repeat

description: trophozoite timepoint 0 repeat


title: trophozoite timepoint 0 with actD

description: trophozoite timepoint 0 with actD


title: schizont timepoint 60 with actD

description: schizont timepoint 60 with actD


title: trophozoite timepoint 5 with actD

description: trophozoite timepoint 5 with actD


title: schizont timepoint 10 with actD

description: schizont timepoint 10 with actD


title: ring replicate 2 timepoint 240 with actD


title: schizont timepoint 15 with actD

description: schizont timepoint 15 with actD


title: trophozoite timepoint 0

description: trophozoite timepoint 0


title: schizont timepoint 5 with actD

description: schizont timepoint 5 with actD


title: trophozoite replicate 3 timepoint 0

description: trophozoite replicate 3 timepoint 0


title: trophozoite replicate 3 timepoint 0 with actD


title: trophozoite replicate 3 timepoint 0 repeat


title: schizont timepoint  0 repeat

description: schizont timepoint  0 repeat


title: schizont timepoint 240 with actD

description: schizont timepoint 240 with actD


title: trophozoite replicate 3 timepoint 10 with actD


title: late schizont timepoint 240 with actD

description: late schizont timepoint 240 with actD


title: trophozoite replicate 3 timepoint 15 with actD


title: trophozoite replicate 3 timepoint 5 with actD


title: schizont timepoint 0

description: schizont timepoint 0


title: schizont replicate 2 timepoint 10 with actD


title: schizont replicate 3 timepoint 120 with actD


title: schizont timepoint 0 with actD

description: schizont timepoint 0 with actD


title: schizont replicate 3 timepoint 60 with actD


title: schizont replicate 2 timepoint 5 with actD


title: schizont replicate 2 timepoint 15 with actD


title: schizont replicate 3 timepoint 240 with actD


title: schizont replicate 2 timepoint 0 repeat

description: schizont replicate 2 timepoint 0 repeat


title: schizont replicate 3 timepoint 30 with actD


title: schizont replicate 2 timepoint 0

description: schizont replicate 2 timepoint 0


title: late schizont replicate 2 timepoint 30 with actD


title: late schizont replicate 2 timepoint 240 with actD


title: late schizont replicate 2 timepoint 60 with actD


title: late schizont replicate 2 timepoint 120 with actD


title: ring replicate 2 timepoint 0

description: ring replicate 2 timepoint 0


title: trophozoite timepoint 30 with actD

description: trophozoite timepoint 30 with actD


title: ring replicate 2 timepoint 15 with actD

description: ring replicate 2 timepoint 15 with actD


title: ring replicate 2 timepoint 10 with actD

description: ring replicate 2 timepoint 10 with actD


title: ring replicate 2 timepoint 0 with actD

description: ring replicate 2 timepoint 0 with actD


title: trophozoite replicate 3 timepoint 120 with actD


title: ring replicate 2 timepoint 0 repeat

description: ring replicate 2 timepoint 0 repeat


title: trophozoite timepoint 120 with actD

description: trophozoite timepoint 120 with actD


title: trophozoite timepoint 240 with actD

description: trophozoite timepoint 240 with actD


title: trophozoite replicate 3 timepoint 30 with actD


title: ring replicate 2 timepoint 5 with actD

description: ring replicate 2 timepoint 5 with actD


title: late schizont replicate 2 timepoint 0 repeat


title: trophozoite replicate 3 timepoint 60 with actD


title: late schizont replicate 2 timepoint 0

description: late schizont replicate 2 timepoint 0


title: late schizont replicate 2 timepoint 0 with actD


title: late schizont replicate 2 timepoint 10 with actD


title: late schizont replicate 2 timepoint 15 with actD


title: k562-mock_Human Tiling 2.0R G Array

type: genomic

city: Stanford

first: David

middle: Scott

last: Johnson

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description: reverse crosslinked chromatin

hyb_protocol: Hybridization was performed according to manufacturer's instructions.

data_processing: We used MAT (Johnson et al., 2006) to process the raw CEL files.  The following settings were used: BandWidth = 300, MaxGap = 300, MinProbe = 10, Trim = 0.1, pvalue=1e-5.

molecule: genomic DNA

organism: Homo sapiens

source_name: k562 - erythroblastoid cell line

label_protocol: Each individual ChIP was amplified using a random primer amplification protocol (Cooper et al., 2007), except 2mM dUTP was added to the 10mM dNTP mix.  Four ChIPs were pooled for each replicate array set.  Two positive QPCR primers were used to QC each pool of IPs.  Labeling thereafter was according to standard Affymetrix protocols.

growth_protocol: We used a single growth of formaldehyde crosslinked k562cells, which were pelleted and sent to Stanford on dry ice by the ENCODE common cell culture source (National Cell Culture Center) to produce chromatin according to standard procedures (after Johnson et al., 2007).  2x10^7 cells were used for each chromatin IP.

extract_protocol: Chromatin extracted according to standard procedures (after Johnson et al., 2007).

treatment_protocol: The background model was created using reverse crosslinked chromatin, instead of a ChIP, which was amplified and hybed to arrays with the same protocol as the ChIP samples.  For their respective ChIPs, 5ug of antibody was used.  Each of the three antibodies from Santa Cruz biotechnology: mAb TAFIIp250 (sc-735), mAb GABPa G1 (sc-28312), and rabbit polyclonal SRF G20 (sc-335).  Antibody specificity had been previously validated by Western blot to demonstrate that the correct size protein was identified.

tag: reverse crosslinked chromatin


title: trophozoite timepoint 60 with actD

description: trophozoite timepoint 60 with actD


title: k562-TAF_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor TAF in k562 cells (ChIP)


title: trophozoite replicate 3 timepoint 240 with actD


title: k562-SRF_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in k562 cells (ChIP)


title: ring timpoint 5 with actD

description: ring timpoint 5 with actD


title: k562-GABP_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in k562 cells (ChIP)


title: ring timepoint 0

description: ring timepoint 0


title: trophozoite replicate 2 timepoint 240 with actD


title: k562-mock_Human Tiling 2.0R D Array

description: reverse crosslinked chromatin


title: trophozoite replicate 2 timepoint 60 with actD


title: trophozoite replicate 2 timepoint 120 with actD


title: trophozoite replicate 2 timepoint 30 with actD


title: late schizont replicate 3 timepoint 120 with actD


title: late schizont replicate 3 timepoint 60 with actD


title: schizont replicate 3 timepoint 10 with actD


title: ring timpoint 0 with actD

description: ring timpoint 0 with actD


title: ring timepoint 10 with actD

description: ring timepoint 10 with actD


title: k562-TAF_Human Tiling 2.0R D Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor TAF in k562 cells (ChIP)


title: ring timepoint 15 with actD

description: ring timepoint 15 with actD


title: k562-SRF_Human Tiling 2.0R D Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in k562 cells (ChIP)


title: Jurkat-mock_Human Tiling 2.0R G Array

description: reverse crosslinked chromatin

source_name: Jurkat - T cell leukaemia derived cell line

growth_protocol: We used a several growths of Jurkat cells to produce chromatin according to standard procedures (after Johnson et al., 2007).  4x10^7 cells were used for each chromatin IP.

treatment_protocol: The background model was created using reverse crosslinked chromatin, instead of a ChIP, which was amplified and hybed to arrays with the same protocol as the ChIP samples.  Two different antibodies were used: a custom mAb (Mortazavi et al., 2006) and a polyclonal Ab from Upstate (catalog 07-579).


title: Jurkat-NRSF-mAb_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for NRSF/REST using two different antibodies in Jurkat cells


title: Jurkat-NRSF-pAb_Human Tiling 2.0R G Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for NRSF/REST using two different antibodies in Jurkat cells


title: Jurkat-mock_Human Tiling 2.0R D Array

description: reverse crosslinked chromatin


title: Jurkat-NRSF-pAb_Human Tiling 2.0R D Array


title: late schizont replicate 3 timepoint 30 with actD


title: HepG2-mock_Human Tiling 2.0R G Array

description: reverse crosslinked chromatin

source_name: HepG2 - hepatocarcinoma cell line

growth_protocol: We used a single growth of formaldehyde crosslinked HepG2 cells, which were pelleted and sent to Stanford on dry ice by the ENCODE common cell culture source (National Cell Culture Center) to produce chromatin according to standard procedures (after Johnson et al., 2007).  2x10^7 cells were used for each chromatin IP.

treatment_protocol: The background model was created using reverse crosslinked chromatin, instead of a ChIP, which was amplified and hybed to arrays with the same protocol as the ChIP samples.  For their respective ChIPs, 5ug of antibody was used.  Each of the three antibodies from Santa Cruz biotechnology: GABPa G1 (sc-28312), and rabbit polyclonal SRF G20 (sc-335).  Antibody specificity had been previously validated by Western blot to demonstrate that the correct size protein was identified.


title: Jurkat-NRSF-mAb_Human Tiling 2.0R D Array


title: late schizont replicate 3 timepoint 240 with actD


title: schizont replicate 3 timepoint 15 with actD


title: HepG2-mock_Human Tiling 2.0R D Array

description: reverse crosslinked chromatin


title: HepG2-SRF_Human Tiling 2.0R D Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in HepG2 cells (ChIP)


title: HepG2-SRF_Human Tiling 2.0R G Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in HepG2 cells (ChIP)


title: schizont replicate 3 timepoint 5 with actD


title: schizont replicate 3 timepoint 0 with actD


title: HepG2-GABP_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in HepG2 cells (ChIP)


title: HepG2-GABP_Human Tiling 2.0R D Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in HepG2 cells (ChIP)


title: Hela-mock_Human Tiling 2.0R D Array

description: reverse crosslinked chromatin

source_name: HeLa - cervical epithelial carcinoma

growth_protocol: We used a single growth of formaldehyde crosslinked HeLa S3 cells, which were pelleted and sent to Stanford on dry ice by the ENCODE common cell culture source (National Cell Culture Center) to produce chromatin according to standard procedures (after Johnson et al., 2007).  4x10^7 cells were used for each chromatin IP.


title: Hela-mock_Human Tiling 2.0R G Array

description: reverse crosslinked chromatin


title: Hela-TAF_Human Tiling 2.0R D Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor TAF in HeLa cells (ChIP)


title: schizont replicate 3 timepoint 0

description: schizont replicate 3 timepoint 0


title: Hela-TAF_Human Tiling 2.0R G Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor TAF in HeLa cells (ChIP)


title: GMO-mock_Human Tiling 2.0R D Array

description: reverse crosslinked chromatin

source_name: GMO6990 lymphoblastoid cells

growth_protocol: We used a single growth of formaldehyde crosslinked GMO6690 cells, which were pelleted and sent to Stanford on dry ice by the ENCODE common cell culture source (National Cell Culture Center) to produce chromatin according to standard procedures (after Johnson et al., 2007).  8x10^7 cells were used for each chromatin IP.


title: trophozoite replicate 2 timepoint 5 with actD


title: Hela-SRF_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in HeLa cells (ChIP)


title: Hela-SRF_Human Tiling 2.0R D Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in HeLa cells (ChIP)


title: Hela-GABP_Human Tiling 2.0R D Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in HeLa cells (ChIP)


title: Hela-GABP_Human Tiling 2.0R G Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in HeLa cells (ChIP)


title: trophozoite replicate 2 timepoint 0 with actD


title: GMO-SRF_Human Tiling 2.0R D Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in GMO6990 cells (ChIP)


title: k562-mock_Human Tiling 2.0R C Array

description: reverse crosslinked chromatin


title: GMO-mock_Human Tiling 2.0R G Array

description: reverse crosslinked chromatin


title: trophozoite replicate 2 timepoint 0

description: trophozoite replicate 2 timepoint 0


title: k562-TAF_Human Tiling 2.0R C Array


title: schizont replicate 2 timepoint 120 with actD


title: schizont replicate 3 timepoint 0 repeat

description: schizont replicate 3 timepoint 0 repeat


title: k562-SRF_Human Tiling 2.0R C Array


title: GMO-SRF_Human Tiling 2.0R G Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor SRF in GMO6990 cells (ChIP)


title: k562-GABP_Human Tiling 2.0R C Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in k562 cells (ChIP)


title: Jurkat-mock_Human Tiling 2.0R C Array

description: reverse crosslinked chromatin


title: schizont replicate 2 timepoint 240 with actD


title: trophozoite replicate 2 timepoint 0 repeat


title: Jurkat-NRSF-pAb_Human Tiling 2.0R C Array


title: schizont replicate 2 timepoint 30 with actD


title: k562-mock_Human Tiling 2.0R E Array

description: reverse crosslinked chromatin


title: HepG2-mock_Human Tiling 2.0R C Array

description: reverse crosslinked chromatin


title: GMO-GABP_Human Tiling 2.0R G Array

description: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in GMO6990 cells (ChIP)


title: Jurkat-NRSF-mAb_Human Tiling 2.0R C Array


title: HepG2-SRF_Human Tiling 2.0R C Array


title: k562-TAF_Human Tiling 2.0R E Array


title: trophozoite replicate 2 timepoint 10 with actD


title: Hela-mock_Human Tiling 2.0R C Array

description: reverse crosslinked chromatin


title: GMO-GABP_Human Tiling 2.0R D Array

tag: chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R (chip-chip) for transcription factor GABP in GMO6990 cells (ChIP)


title: HepG2-GABP_Human Tiling 2.0R C Array


title: k562-SRF_Human Tiling 2.0R E Array


title: Hela-TAF_Human Tiling 2.0R C Array


title: k562-GABP_Human Tiling 2.0R E Array


title: Hela-SRF_Human Tiling 2.0R C Array


title: Hela-GABP_Human Tiling 2.0R C Array


title: GMO-mock_Human Tiling 2.0R C Array

description: reverse crosslinked chromatin


title: Jurkat-mock_Human Tiling 2.0R E Array

description: reverse crosslinked chromatin


title: GMO-SRF_Human Tiling 2.0R C Array


title: Jurkat-NRSF-mAb_Human Tiling 2.0R E Array


title: Jurkat-NRSF-pAb_Human Tiling 2.0R E Array


title: HepG2-mock_Human Tiling 2.0R E Array

description: reverse crosslinked chromatin


title: GMO-GABP_Human Tiling 2.0R C Array


title: k562-mock_Human Tiling 2.0R A Array

description: reverse crosslinked chromatin


title: k562-TAF_Human Tiling 2.0R A Array


title: ring replicate 2 timepoint 30 with actD

description: ring replicate 2 timepoint 30 with actD


title: k562-SRF_Human Tiling 2.0R A Array


title: late schizont replicate 3 timepoint 15 with actD


title: trophozoite replicate 2 timepoint 15 with actD


title: HepG2-SRF_Human Tiling 2.0R E Array


title: ring replicate 2 timepoint 60 with actD

description: ring replicate 2 timepoint 60 with actD


title: schizont replicate 2 timepoint 60 with actD


title: k562-GABP_Human Tiling 2.0R A Array


title: Jurkat-mock_Human Tiling 2.0R A Array

description: reverse crosslinked chromatin


title: HepG2-GABP_Human Tiling 2.0R E Array


title: Hela-mock_Human Tiling 2.0R E Array

description: reverse crosslinked chromatin


title: late schizont replicate 3 timepoint 0

description: late schizont replicate 3 timepoint 0


title: late schizont replicate 3 timepoint 10 with actD


title: HepG2-mock_Human Tiling 2.0R A Array

description: reverse crosslinked chromatin


title: HepG2-SRF_Human Tiling 2.0R A Array


title: HepG2-GABP_Human Tiling 2.0R A Array


title: late schizont replicate 3 timepoint 0 with actD


title: Hela-TAF_Human Tiling 2.0R E Array


title: late schizont replicate 3 timepoint 0 repeat


title: Hela-mock_Human Tiling 2.0R A Array

description: reverse crosslinked chromatin


title: Hela-SRF_Human Tiling 2.0R E Array


title: Hela-TAF_Human Tiling 2.0R A Array


title: Hela-GABP_Human Tiling 2.0R E Array


title: Jurkat-NRSF-pAb_Human Tiling 2.0R A Array


title: Hela-SRF_Human Tiling 2.0R A Array


title: GMO-mock_Human Tiling 2.0R E Array

description: reverse crosslinked chromatin


title: Jurkat-NRSF-mAb_Human Tiling 2.0R A Array


title: ring timepoint 30 with actD

description: ring timepoint 30 with actD


title: late schizont timepoint 0 with actD

description: late schizont timepoint 0 with actD


title: Hela-GABP_Human Tiling 2.0R A Array


title: GMO-SRF_Human Tiling 2.0R E Array


title: GMO-mock_Human Tiling 2.0R A Array

description: reverse crosslinked chromatin


title: late schizont timepoint 0 repeat

description: late schizont timepoint 0 repeat


title: GMO-SRF_Human Tiling 2.0R A Array


title: late schizont timepoint 0

description: late schizont timepoint 0


title: GMO-GABP_Human Tiling 2.0R E Array


title: k562-mock_Human Tiling 2.0R F Array

description: reverse crosslinked chromatin


title: k562-mock_Human Tiling 2.0R B Array

description: reverse crosslinked chromatin


title: k562-TAF_Human Tiling 2.0R B Array


title: GMO-GABP_Human Tiling 2.0R A Array


title: k562-SRF_Human Tiling 2.0R F Array


title: k562-TAF_Human Tiling 2.0R F Array


title: k562-SRF_Human Tiling 2.0R B Array


title: k562-GABP_Human Tiling 2.0R F Array


title: Jurkat-mock_Human Tiling 2.0R F Array

description: reverse crosslinked chromatin


title: k562-GABP_Human Tiling 2.0R B Array


title: ring timepoint 60 with actD

description: ring timepoint 60 with actD


title: late schizont timepoint 120 with actD

description: late schizont timepoint 120 with actD


title: Jurkat-mock_Human Tiling 2.0R B Array

description: reverse crosslinked chromatin


title: late schizont timepoint 15 with actD

description: late schizont timepoint 15 with actD


title: ring timepoint 120 with actD

description: ring timepoint 120 with actD


title: late schizont timepoint 30 with actD

description: late schizont timepoint 30 with actD


title: Jurkat-NRSF-pAb_Human Tiling 2.0R F Array


title: ring timepoint 240 with actD

description: ring timepoint 240 with actD


title: Jurkat-NRSF-mAb_Human Tiling 2.0R F Array


title: k562-GABP_Human Tiling 2.0R D Array


title: Jurkat-NRSF-mAb_Human Tiling 2.0R B Array


title: HepG2-SRF_Human Tiling 2.0R F Array


title: HepG2-mock_Human Tiling 2.0R B Array

description: reverse crosslinked chromatin


title: HepG2-mock_Human Tiling 2.0R F Array

description: reverse crosslinked chromatin


title: HepG2-GABP_Human Tiling 2.0R F Array


title: HepG2-SRF_Human Tiling 2.0R B Array


title: HepG2-GABP_Human Tiling 2.0R B Array


title: Hela-TAF_Human Tiling 2.0R F Array


title: Hela-mock_Human Tiling 2.0R B Array

description: reverse crosslinked chromatin


title: Hela-SRF_Human Tiling 2.0R F Array


title: Hela-GABP_Human Tiling 2.0R F Array


title: Hela-SRF_Human Tiling 2.0R B Array


title: Jurkat-NRSF-pAb_Human Tiling 2.0R B Array


title: GMO-SRF_Human Tiling 2.0R F Array


title: Hela-GABP_Human Tiling 2.0R B Array


title: GMO-mock_Human Tiling 2.0R B Array

description: reverse crosslinked chromatin


title: GMO-GABP_Human Tiling 2.0R F Array


title: Hela-TAF_Human Tiling 2.0R B Array


title: GMO-GABP_Human Tiling 2.0R B Array


title: late schizont timepoint 10 with actD

description: late schizont timepoint 10 with actD


title: GMO-mock_Human Tiling 2.0R F Array

description: reverse crosslinked chromatin


title: Hela-mock_Human Tiling 2.0R F Array

description: reverse crosslinked chromatin


title: late schizont timepoint 60 with actD

description: late schizont timepoint 60 with actD


title: GMO-SRF_Human Tiling 2.0R B Array


title: Menstruation blood, primary E6

status: Public on Jul 17 2007

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Menstruation blood, primary E6.

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16 h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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 100.

source_name: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates, according to the manufacturer’s protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy (QIAGEN), according to manufacture’s instructions.

tag: Menstruation blood-derived mesenchymal cell, primary


title: MP vs JUV Replicate3

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

description: Biological replicate 3 of 4. Mid pubertal vs juvenile monkey hypothalamus gene expression

hyb_protocol: Paired cDNAs were hybridized in Hybridization Buffer (PerkinElmer MICROMAX TSA Labeling and Detection Kit) under Erie Scientific M-series LifterSlips.  Hybridizations were performed overnight in TeleChem Hybridization Cassettes in a 65C waterbath.

scan_protocol: Arrays were scanned on a PerkinElmer ScanArray 4000XL.  Images were quantified using ImaGene from BioDiscovery with 5% trimming of highest and lowest values for each feature.

data_processing: Data preprocessing was performed in GeneSight using linear spline regression normalization, background subtracted Data obtained from log of processed red signal / processed green signal.

organism: Macaca mulatta

source_name: Total RNA from juvenile female monkey hypothalamus labeled with Cyanine-5 (red).

label_protocol: Total RNA samples were labeled using the PerkinElmer MICROMAX TSA Labeling and Detection Kit, as modified by the OHSU Spotted Microarray Core.  The complete protocol and modifications are available at this link:http://www.ohsu.edu/gmsr/smc/downloads/TSA_Processing_protocol.pdf.Fluorescein-modified (for Cy3) or biotin-modified (for Cy5) dCTP was incorporated into a cDNA generated from 5 micrograms of total RNA sample.  RNA template was removed by base hydrolysis at 65 C for 30 minutes.  cDNA was separated from free nucleotides by spinning in Millipore YM-100 spin cups and washing the samples twice in the cups with 200 microliters of 10 mM Tris, pH 7.5.  At the end of the second wash, samples were reduced to approximately 20 microliters by centrifugation at 500xG, then the cups were inverted into another tube and the cDNA recovered by centrifugation.  Samples were reduced to approximately 5 microliters in a LabConCo CentriVap concentrator without heating.  After the final concentrating step, the samples were combined for hybridization. For each labeling, three solutions were prepared: TN - 0.1M Tris HCl pH 7.5 / 0.15 M NaCl; TNT - TN with added 0.05% Tween-20; and TNB - TN with added blocking reagent. At the end of the hybridization, slides were placed in 0.5X SSC / 0.1% SDS.  The coverslips were removed while the slides were submerged.  The slides were then washed for five minutes in 0.5X SSC / 0.1% SDS, for five minutes in 0.06X SSC / 0.1% SDS, and for five minutes in 0.06X SSC.  Slides were blocked in TNB with 10% goat serum.  Blocking was done in 11 milliliters of blocking solution in five-slide holders for 10 minutes in the dark.  Following blocking, slides were washed in TNT for 2 minutes. Ninety-eight microliters of streptavidin-horseradish peroxidase (HRP) were combined with 11 milliliters of TNB with 10% goat serum.  Up to five slides were incubated in this solution in the dark for 10 minutes in a five-slide holder.  Slides were washed twice for three minutes each in TNT.  Forty microliters of Cy5-tyramine in DMSO was combined with 11 milliliters of amplification diluent (from the kit).  Up to five slides were incubated in this solution in a five-slide holder in the dark for 15 minutes.  The slides were then incubated for 15 minutes in the dark in HRP Inactivation Solution (from the kit).  Slides were then washed three times for three minutes each in TNT. Ninety-eight microliters of anti-fluorescein antibody conjugated to HRP was combined with 11 mls of TNB with 10% goat serum.  Up to five slides were incubated in this solution in the dark for 10 minutes in a five-slide holder.  The slides were washed twice for three minutes each in TNT.  Forty microliters of Cy3-tyramine in DMSO were combined with 11 milliliters of amplification diluent (from the kit).  Up to five slides were incubated in this solution for 10 minutes in the dark.  The slides were then washed three times for three minutes each in TNT, followed by 3 minutes in 0.06X SSC.  The slides were spun for 10 minutes at 1000 rpm in a Sorvall RT7plus tabletop centrifuge in conical 50 ml tubes and stored in the dark until scanning was performed.

extract_protocol: Total RNA was extracted using TriReagent (MRC Inc., Cincinnati, OH), as follows: The tissues were homogenized in 1 ml (<100mg of tissue/ml) of TriReagent solution, and the aqueous and organic phases were separated by the addition of 0.1 vol bromo-chloropropane (BCP, Sigma Chemicals, St. Louis, MO) followed by centrifugation at 4C. RNA was precipitated from the aqueous phase with 1 volume of isopropanol followed by centrifugation at 13,000 rpm for 15 min at 4C.  The pellets were resuspended in DEPC-treated H2O, and the suspension incubated with Ambion’s DNA-free DNAse I (2U per reaction) for 30 min at 37C. RNA concentrations were determined by spectrometry at UV 260nm, and RNA integrity was verified by RNA Nano Chip profiling using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: 341 days old

source_name: Total RNA from mid pubertal female monkey hypothalamus labeled with Cyanine-3 (green).

tag: 3 years 143 days old


title: MP vs JUV Replicate4

description: Biological replicate 4 of 4. Mid pubertal vs juvenile monkey hypothalamus gene expression

tag: 1 year 95 days old

tag: 3 years 254 days old


title: Menstruation blood, primary

description: Menstruation blood, primary


title: Rat Angiotensin II sample

status: Public on Jul 18 2007

city: Augusta

first: Edson

middle: da Fonseca

last: Nogueira

state: GA

department: Physiology

institute: Medical College of Georgia

description:
Quality control steps taken:
Sample from treated cells were compared to untreated (control) using different arrays. No dye-swap was used in any experiment.

hyb_protocol: HYBRIDIZATION Sample + Fragmented cRNA 		40	40 Control oligo B2		3.9	3.9 Control cRNA from Affy	12	12 Herring Sperm DNA		2.4	2.4 Acetylated BSA		2.4	2.4 2XMES Hybrid buffer	120	120 Water to final volume 	59.3	59.3 The control RNA must be heated at 65o C for 5 minutes before adding to mix (use Affymetrix kit)   Warm chips to room temperature Set up the experiment in GCOS Experiment name Project- name of the PI Sample name could be same as experiment. Read the bar code on chip and all the other information is filled up. Add 1X MES to chip and incubate at 45o C for 10 minutes Heat hybridization cocktail to 99o C for 5 min and then 45o C for 5 minutes Spin for 5 min Remove buffer solution from the chip and add 200ul of hybridization cocktail. Hybridize for 16 hours Prepare buffer A and B Non-stringent Wash Buffer A For 1000 mL 300 ml of 20X SSPE 1.0 mL of 10% Tween-20 698 water Filter through 0.2um filter Stringent Wash Buffer B For 1000 ml 83.3 mL of 12X MES stock buffer (refer chapter 5 of the manual to prepare 12X MES) 5.2 mL of 5M NaCl 1.0ml of 10%tween 20 910.5 mL of water Filter through 0.2um filter Next day Prepare the stains and antibody solution for x number of samples according to the chart on the desk. Switch on fuidics and scanner and then click on GCOS. Change water bottles on fuidics to buffer A and B at the designated places. Prime fuidics by choosing Prime_450 in the protocol dropdown list Remove cocktail from the chip and fill with buffer A. In the Fluidics Station dialog box on the workstation, select the correct experiment in the dropdown Experiment list. In the protocol dropdown list, select the specific satin protocol which is in most cases FlexGE WS3. Choose run in the fluidics Station dialog box to begin the washing and staining and follow the instruction on the LCD window of the fuidics. When the wash is complete the LCD window will display EJECT CARTIDGE. Remove the cartridge and follow the instruction on LCD window again. Run the shutdown protocol replacing water bottles with buffer. There should not be any air bubble in the chip.

scan_protocol: The scanner is also controlled by GCOS.  Put the chips in the scanner.  You can scan as many as 48 chips at the same time.  Click the start icon in GCOS and the follow the direction there on.  After all the chips are scanned, data can be analyzed. Analysis Open the data files.  Check the grid corners by pressing F5, F6, F7 and F8.  Then press the analyze icon.  Choose target signal 150 then proceed for analysis.  Analyzed data is presented as excel spreadsheet and present as .CHP file.  Check for GAPDH5’/3’ signal intensity.  The ratio should be less then 4.

data_processing:
Software: GeneSpring (Agilent)
Data (.chip files) were inserted into the program and RMA normalization was selected. Then we used a protocol on GeneSpring to create an experiment. The parameters were: Basal versus Angiotensin II
Normalization order: Data Transformation: set measurements less than 0.01 to 0.01; Normalization to the 50th percentile
Error model for one-color data was selected
Base error model on deviation from one selected
Experiment interpretation:
Analysis mode: ration (signal/control); Use measurements flagged: flags present in both arrays.

label: ENZO LABELING KIT

source_name: The rat glomerulosa cells were obtained from adrenal glands of female Long Evans rats weighing 200-250 grams.

label_protocol: Mix 20ul of cDNA from above (from 5ug of RNA), Xul Water (Final volume should be 40 ul), 3ul of 10X HY, 3ul Labeled ribonucleotides, 3ul 10XDTT, 3ul 10XRNase Inhibitor, 1.5ul	20X T7 RNA polymerase. Add above at RT to tube in order listed. Mix by centrifugation 5 sec. Place at 37 oC for 5hrs. Remove and mix about every 30-45 minutes.Place in freezer at –20 overnight.

growth_protocol: The rat glomerulosa cells were obtained from adrenal glands of female Long Evans rats weighing 200-250 grams and isolated according to the method previously described in detail. All protocols were approved by the Animal Care and Ethics Committee of the Université de Sherbrooke. Isolation and cell dissociation of the zona glomerulosa was performed in MEM medium, supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin. After a 20-min incubation at 37°C with collagenase (2 mg/ml) and deoxyribonuclease (25 µg/ml), cells were disrupted by gentle aspiration with a sterile 10 ml pipette, filtered and centrifuged for 10 min at 1200 x g. The cell pellet was then resuspended in OPTI-MEM medium supplemented with 2 % FBS (fetal bovine serum), 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol: Total RNA was extracted from cells plates using Trizol (Invitrogen) according to the manufacturer’s directions.

treatment_protocol: Glomerulosa cells were plated at density of 6 x 105 cells/Petri dish and were cultured at 37°C in a humidified atmosphere composed of 95 % air / 5 % CO2. Glomerulosa cells were incubated without or with 10 nM Ang-II for 1h.

tag: File represents rat adrenal glomerulosa cells treated with 10 nM angiotensin II for 1 hour. Attached supplementary table lists the top 50 genes up-regulated by angiotensin II in rat adrenal glomerulosa cells (1 hour treatment, 10 nM angiotensin II).


title: Menstruation blood, primary E5

description: Menstruation blood, primary E5


title: Bovine Angiotensin II

description:
Quality control steps taken:
Sample from treated cells were compared to untreated (control) using different arrays. 3 replicates were used for human array. No dye-swap was used in any experiment.

organism: Bos taurus

source_name: The bovine adrenal glomerulosa cells were isolated from male and female near term fetal bovine calves.

label_protocol: Mix 20ul of cDNA from above (from 5ug of RNA), Xul Water (Final volume should be 40 ul), 3ul of 10X HY, 3ul Labeled ribonucleotides, 3ul 10XDTT, 3ul 10XRNase Inhibitor, 1.5ul	20X T7 RNA polymerase. Add above at RT to tube in order listed. Mix by centrifugation 5 sec. Place at 37 oC for 5hrs. Remove and mix about every 30-45 minutes.Place in freezer at –20 overnight

growth_protocol: The bovine adrenal glomerulosa cells were isolated from male and female near term fetal bovine calves and cultured overnight in Falcon Primaria dishes (Becton Dickinson labware, Lincoln Park, NJ) in a DMEM/Ham’s F12 medium (1:1) containing: 10 % horse serum (vol/vol), 2 % fetal bovine serum (vol/vol), 100 μM ascorbate, 1.2 µM alpha-tocopherol, 0.05 μM Na2SeO3, 50 µM butylated hydroxyanisole, 5 µM metyrapone, 100 U/mL penicillin, 100 µg/ml streptomycin, and 0.25 µg/ml amphotericin B.

treatment_protocol: Cells were then rinsed with bicarbonate-buffered Kreb's Ringer solution containing 2.5 mM sodium acetate (KRB+) and incubated for 30 min (in 5 % CO2) in KRB+ before addition of KRB+ without or with 10 nM AngII. After 1 hour incubation medium was aspirated and cells were frozen until processing to obtain RNA.

tag: File represents data from bovine adrenal glomerulosa cells treated with 10 nM angiotensin II for 1 hour. Attached supplementary table lists the top 50 genes up-regulated by angiotensin II in bovine adrenal glomerulosa cells (1 hour treatment, 10 nM angiotensin II).


title: EP vs JUV Replicate4

description: Biological replicate 4 of 4. Early pubertal vs juvenile monkey hypothalamus gene expression

source_name: Total RNA from early pubertal female monkey hypothalamus labeled with Cyanine-3 (green).

tag: 2 years 344 days old


title: Menstruation blood, HRF treatment, primary E6HRF


title: MP vs JUV Replicate2

description: Biological replicate 2 of 4. Mid pubertal vs juvenile monkey hypothalamus gene expression

tag: 3 years 70 days old


title: Menstruation blood, HRF treatment, primary E5HRF


title: Hst5-Cy5 vs CAI4-Cy3-2

city: Buffalo

first: Wansheng

last: Li

state: NY

address: 3435 main st.

department: Oral Biology

institute: University at Buffalo

description: Candida albicans Hst5 treated wild-type strain compared to wild-type strain CAI4

hyb_protocol: The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before application to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and scanned.

scan_protocol: As described in the the manufacturer's instructions of GenePix 4200A scanner (Axon Instruments).

data_processing: Slides have been scanned by Axon scanner 4200A and image analysis analyzed by GenePix Version 6.0. Post analysis was performed using TIGR microarray software suite(http://www.tm4.org). ExprConverter v1.7 to transform GPR format to Mev file, Midias 2.19 to normalize the data, and Mev4.0 to do statistical analysis. The VALUE column is the log2 based expression level after background correction, total intensity normaliztion,Lowess normalization. if VALUE=null, then this spot was bad.

organism: Candida albicans

source_name: wild-type strain CAI4

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy3 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

extract_protocol: cDNA was synthesized from total RNA samples using Superscript II RT (Invitrogen) in reaction mixtures containing 0.5 mM deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates). After cDNA synthesis, RNA was hydrolyzed with 1 M NaOH and 0.5 M EDTA, followed by neutralization with 1 M HCl. The cDNA was purified using the Qiagen QIAquick PCR purification kit and dried by SpeedVac.

tag: Candida albicans wild-type strain CAI4

source_name: Hst5 treated wild-type strain

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy5 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

growth_protocol: Cells were grown overnight in 10 ml of YNB medium, 2% glucose with the addition of uridine when required. AFTER this, the cells were treated using Hst5.

treatment_protocol: wild-type CAI4 cells were harvested, washed twice with 10 mM NaPB, pH 7.4 and reconstituted in the same buffer. About 3x10^8 cells were incubated with 500uM Hst 5 (an LD40 dose) for 60 min.

tag: wild-type strain CAI4 treated 60min. with Hst5.


title: E6, E7, hTERT, endometrial cell	+2

description: E6, E7, hTERT, endometrial cell +2

tag: Endometrial cell


title: Menstruation blood, HRF treatment, primary E4HRF


title: E6, E7, hTERT, endometrial cell EPC214

description: E6, E7, hTERT, endometrial cell EPC214


title: Bone marrow cell, primary Yub10F

description: Bone marrow cell, primary Yub10F

source_name: Bone marrow

tag: Bone marrow cell, primary


title: Bovine Control Sample # 1

tag: The file represents the control sample used for this experiment.


title: Fetal fibroblast, primary

description: Fetal fibroblast, primary

tag: Fetal fibroblast, primary


title: EP vs JUV Replicate3

description: Biological replicate 3 of 4. Early pubertal vs juvenile monkey hypothalamus gene expression

tag: 1 year 348 days old

tag: 2 years 171 days old


title: E6, E7, hTERT, endometrial cell, control


title: E7, hTERT, cord blood

description: E7, hTERT, cord blood

tag: Cord blood, primary


title: Placenta, primary PL112

description: Placenta, primary PL112


title: E7, hTERT, bone marrow cell UET9

description: E7, hTERT, bone marrow cell UET9


title: E6, E7, hTERT, endometrial cell	EPC100

description: E6, E7, hTERT, endometrial cell EPC100


title: Rat Control Sample

tag: File represents control sample from rat adrenal glomerulosa cells.


title: Normal follicular dermal papillar cell, primary


title: MP vs JUV Replicate1

description: Biological replicate 1 of 4. Mid pubertal vs juvenile monkey hypothalamus gene expression

tag: 351 days old

tag: 3 years 345 days old


title: EP vs JUV Replicate2

description: Biological replicate 2 of 4. Early pubertal vs juvenile monkey hypothalamus gene expression

tag: 341 days old

tag: 2 years 83 days old


title: Hst5-Cy3 vs CAI4-Cy5-2

growth_protocol: Cells were grown overnight in 10 ml of YNB medium, 2% glucose with the addition of uridine when required.


title: hTERT, cord blood

description: hTERT, cord blood


title: Cord blood, primary UCB302-D7

description: Cord blood, primary UCB302-D7


title: EP vs JUV Replicate1

description: Biological replicate 1 of 4. Early pubertal vs juvenile monkey hypothalamus gene expression

tag: 2 years 43 days old


title: Cord blood, primary

description: Cord blood, primary

tag: Cord blood-derived cells


title: E6, E7, hTERT, bone marrow cell

description: E6, E7, hTERT, bone marrow cell

tag: Marrow mesenchymal cell, primary


title: HAdpc1E6E7TERT28

tag: Adipocyte cell, primary


title: E6, E7, umbilical cord blood

description: E6, E7, umbilical cord blood


title: E7, hTERT, neural differentiation, bone marrow cell 1

tag: Nerural differentiated marrow stromal cell


title: E6, E7, hTERT, dedifferentiated chondrocyte

tag: Dedifferentiated chondrocyte


title: E6, E7, bone marrow cell

description: E6, E7, bone marrow cell


title: E7, hTERT, neural differentiation, bone marrow cell 4


title: Cord blood, primary UCB302

description: Cord blood, primary UCB302


title: Bmi-1, bone marrow cell

description: Bmi-1, bone marrow cell

tag: Marrow stromal cells


title: Placenta, primary

description: Placenta, primary

tag: Placenta, primary


title: Vector, bone marrow cell

description: Vector, bone marrow cell


title: EWSR1-POU5F1 chimera, Undifferentiated bone tumor GST6-extra

source_name: Pelvic tumor

tag: Undifferentiated sarcoma from pelvic bone


title: Bmi-1, E6, hTERT, bone marrow cell

description: Bmi-1, E6, hTERT, bone marrow cell

tag: Bone marrow cell, primary


title: Ewing, ETV4, Cancer

description: Ewing, ETV4, Cancer

tag: Ewing, cancer


title: E7, hTERT, neural differentiation, bone marrow cell 5


title: hTERT, bone marrow cell

description: hTERT, bone marrow cell


title: Bmi-1, hTERT, bone marrow cell

description: Bmi-1, hTERT, bone marrow cell


title: E7, hTERT, neural differentiation, bone marrow cell


title: EWSR1-POU5F1 chimera, 5azaC, Undifferentiated bone tumor - extra


title: E7, hTERT, bone marrow cell UET13

description: E7, hTERT, bone marrow cell UET13


title: U937+HRF

tag: Myelomonocytic leukemia


title: Ewing, Cancer

description: Ewing, Cancer


title: Embryonal carcinoma, NCR-G3, adherent

description: Embryonal carcinoma, NCR-G3, adherent

source_name: Germ cell tumor

tag: Embryonal carcinoma, cancer


title: U937+HRF+antibody


title: Embryonal carcinoma, NCR-G2, non adherent


title: Ligament, primary

description: Ligament, primary

tag: Ligament-derived cells


title: Pulmonary epithelial cell line

description: Pulmonary epithelial cell line

tag: Pulmonary epithelial cell line


title: Bronchial epithelial cell line

description: Bronchial epithelial cell line


title: Intraabdominal stromo vascular fraction, rep3

city: Boston

first: Stephane

last: Gesta

state: MA

address: One Joslin Place

institute: Joslin Diabetes Center

description: Stromo vascular fraction from intraabdominal adipose tissue

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74Av2  . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 G7

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 1500.

label: Biotin

organism: Mus musculus

label_protocol: Double-stranded cDNA synthesis was reverse-transcribed from 15 µg of isolated mRNA by using the SuperScript Choice system (Invitrogen) with an oligo(dT) primer containing a T7 RNA polymerase promoter site. Double-stranded cDNA was purified with Phase Lock Gel (Eppendorf). Biotin-labeled cRNA was transcribed by using a BioArray RNA transcript labeling kit (Enzo).

growth_protocol: To obtain purified cell fractions, ten 6- to 7-week-old C57BL/6 males were killed, and epididymal and flank subcutaneous adipose tissue was removed under sterile conditions. Tissues from each depot were pooled, minced, and digested with 1 mg/ml collagenase for 45 min at 37°C in DMEM/Ham’s F-12 1:1 (DMEM/F12) containing 1% BSA and antibiotics (100 units/ml penicillin, 0.1 mg/ml streptomycin, 2.5 mg/ml fungizone, and 50 mg/ml gentamicin). Digested tissues were filtered through sterile 150-µm nylon mesh and centrifuged at 250 × g for 5 min. The floating fraction consisting of pure isolated adipocytes was then removed and washed two more times before proceeding to RNA extraction. The pellet, representing the SVF containing preadipocytes and other cell types, was resuspended in erythrocyte lysis buffer consisting of 154 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA for 10 min. The cell suspension was centrifuged at 500 × g for 5 min and then resuspended in a culture medium consisting of DMEM/F12, 10% FCS, and antibiotics. This cell suspension was filtered through a 25-µm sterile nylon mesh before being plated on a 10-cm plate at 60,000 cells per cm². Sixteen hours after plating, cells were extensively washed with PBS and then subjected to RNA extraction

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: Strain

tag: Gender

value: male

tag: Age

value: 42 to 49 days

tag: Tissue

value: epididymal adipose tissue


title: Normal epidermal keratinocyte, neonate, primary

tag: Normal epithelial cell,primary