title: XX_WT-E_090707_A

status: Public on Mar 01 2009

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip C. ElegansGenome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Consol software (Irizarry et al. 2003).    Data were analyzed by ArrayStar.  Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

organism: Caenorhabditis elegans

source_name: embryo from worms grown on egg plates

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: sdc-2(-) XX animals were prepared by growing sdc-2(y93) XX animals on Ahringer feeding library bacteria (Kamath et al. 2003) bearing an sdc-2 plasmid.  The wild-type control for the sdc-2 RNAi was N2 worms fed Ahringer library feeding bacteria bearing a plasmid lacking an insert.  Feeding bacteria was prepared by seeding 1L LB cultures with a single colony, growing overnight at 37∞C, inducing for 2hr with 5 mM IPTG, pelleting, and resuspending in 1 volume (w/v) of LB with 20% glycerol.

extract_protocol: Gravid adults were bleached and embryos harvested as described (Portman, D.S, Wombook, Profiling C. elegans gene expression with DNA microarrays) and 100 µl aliquots snap frozen in liquid nitrogen and stored at -80∞C.  An aliquot was thawed at 65∞C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes.  Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

treatment_protocol: Embryos used for microarray analysis were obtained from bleached gravid adults.

tag: Wild Type controls for XO_TY2222-E


title: XX_WT-E_090707_C

type: RNA

state: CA

country: USA

label: biotin

molecule: total RNA


title: XX_WT-E_090707_B


title: H1299 cancer cell line sample

status: Public on Mar 03 2009

city: New Haven

first: Pedro

middle: P

last: Medina-Vico

state: CT

address: 266 Whitney Ave, 938 KBT

institute: Yale University

description: The goal of this analysis is to see the genes differential expressed in the lung cancer cell line in relation with a control (universal RNA Stratagene).

hyb_protocol: 3.- Hybridization: the probe (mix Cy3-labeled and Cy5-labeled cDNAs) was centrifuged at full speed for 5min at room temperature. Then it was applied (approx. 44µl, leave 2µl from the bottom of the tube behind in order to avoid transferring any sediment to the slide) to a clean cover-slip and place on the pre-hybridized microarray. The slide was placed in a hybridization chamber with the printed area and the cover-slip at the top, and was incubated overnight (15-20h) at 55ºC in an oven.

scan_protocol: 1.- Place each slide in a cassette as follows: orient the slide so that it is array-side down and to the left; take cassette flat side down, place on flat surface and push down on the two buttons; with the buttons pressed, insert the slide (keeping everything flat); release buttons when slide has been fully inserted. 2.- Place cassettes into carousel. The etched side should now face to the left, and you should be looking at the back of the slide. Note: the cassette must start with the first slot. The scanner recognizes an empty slot as a sign to stop scanning. Close the scanner top. 3.- Double-click on the Agilent Scanner icon. When it opens, the scanner will go through some initialization steps. Also, if the lasers are not fully warm, there will be a warning sign that will give an approximate time that the lasers will be ready. 4.- Enter your name under Operator and check to see that the controls are set for the following: output directory is D:\niehs; both Red and Green channels are checked and are set to 100%; the size is 10 microns. 5.- Click on Options: choose to scan default slide area under Scan Region Options; specify slide area to largest area under Default Scan Region; click on Instrument serial number under Automatic File Naming (it will then be highlighted). Choose and type in your identifier for that day. Leave the Slot Number as is. 6.- Fill out log in the Scanner Cassette Log with your name, date and the order you put your slides into the carousel. This is important to assure proper renaming after scanning is complete. Click on OK to close the Options window. 7.- Double check that all the settings are properly set and click on Scan. 8.- After scan is complete, you will need to change the names to format pxxsxx. To do this: with the right mouse button, click on the Start menu and choose Explorer. Navigate your way through the files by clicking on the D drive on the far left hand side of the screen. Double click on D drive then double click onniehs. This folder contains all of the scanned files. Locate your slides by looking for the identifier you used for the scan. Click once to highlight name and click once more to get a cursor in the file name. Type in the proper name using the log you filled out earlier. Once all of the names have been changed, highlight the newest slides and move them into the appropriate boxes on Witchfire. 9.- Once you are done, log out of the computer, take the cassettes out of the carousel and your slides out of the cassettes. Turn off scanner.

data_processing: Cy3 and Cy5 fluorescent signals were quantified using GenePix Pro 5.0 (Axon Instruments Inc.). Substandard spots were manually flagged and discarded for further analysis. The Cy5/Cy3 ratios were normalized to the median ratio value using the DNMAD tool, based on a print-tip loess method. The conditions for the normalization were: 1) use negative flags, that means that the flagged spots are not used for the normalization and are turned into missing values; 2) do not use background correction. The normalized and semi-logarithmic transformed data were preprocessing using GEPAS software. Conditions for data pre-processing were: 1) merge replicates (the Cy5/Cy3 ratios of replicated spots were averaged); 2) filter missing values in order to exclude for further analysis any gene with data missing in more than 10% of the samples.

organism: Homo sapiens

source_name: RNA from H1299 labeled with Cy5

label_protocol:
1.- RNA from each sample were primed with 3µl of random hexamers d(N)6 0.5mg/ml (Promega) at 70ºC for 10min. For each labeling reaction, a master mix was prepared: 5µl First Strand buffer 5x, 2.5µl DTT 0.1M, 0.5µl unlabeled dNTPs 50x (dATP/dCTP/dGTP:dTTP 25:5), 1.5µl Cy5-dUTP 10mM or Cy3-dUTP 10mM (for Universal Human Reference RNA), 0.63µl RNasin Inhibitor and 1.25µl SuperScript II (200U/µl). The labeling reaction was incubated at room temperature for 10min and then incubated at 42ºC for 2h. Tubes were protected from direct light.
2.- Each fluorescent labeled cDNA was purified with CyScribe GFX Purification kit (Amersham) following manufacturer's instructions.
3.- The Cy3-labeled and Cy5-labeled cDNAs for each hybridization were combined into a single tube. 10µg of Human Cot-1 DNA (Invitrogen) were added.
4.- To precipitate each hybridization probe, 0.1 volumes of sodium acetate 0.1M and 2.5 volumes of absolute ethanol were added.
5.- Each probe was resuspended in 4µl of filtered EDTA 10mM ph 8 and denatured at 95ºC for 10min. 40µl of SlideHyb buffer 1x (Ambion), prewarmed at 65ºC, and blocking agents (mix of polyA and yeast tRNA, 10µg and 4µg in 2µl of final volume) were added.

growth_protocol: DMEM Glutamax, 10% FBS, Antibiotics (Peneciline, Streptomicine, Fungizone).

extract_protocol: Total RNA from lung tumors and normal lung tissues was isolated with  RNeasy mini kit (QIAGEN) and digestion with RNase-free DNase I (QIAGEN)  following the manufacturer's instructions. Universal Human Reference RNA  (Stratagene), the reference used in all the hybridizations, is provided in a  solution of 70% ethanol and 0.1M sodium acetate; it was prepared by centrifugation and washing with 70% ethanol.

tag: Lung cancer cell line

source_name: RNA from Stratagene's Universal Human Reference RNA labeled with Cy3

extract_protocol: Commercial sample already extracted.

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Equal quantities of DNase-treated total RNA from each cell line (adenocarcinoma, mammary  gland; melanoma; hepatoblastoma, liver; liposarcoma; adenocarcinoma,  cervix; histiocytic lymphoma; macrophage; embryonal carcinoma, testis;  lymphoblastic leukemia, T lymphoblast; glioblastoma, brain; plasmacytoma;  myeloma; B lymphocyte) were pooled to make the Universal Human  Reference RNA.


title: H2126 cancer cell line sample

scan_protocol: Slides were scanned for Cy3 and Cy5 following the steps: 1.- Place each slide in a cassette as follows: orient the slide so that it is array-side down and to the left; take cassette flat side down, place on flat surface and push down on the two buttons; with the buttons pressed, insert the slide (keeping everything flat); release buttons when slide has been fully inserted. 2.- Place cassettes into carousel. The etched side should now face to the left, and you should be looking at the back of the slide. Note: the cassette must start with the first slot. The scanner recognizes an empty slot as a sign to stop scanning. Close the scanner top. 3.- Double-click on the Agilent Scanner icon. When it opens, the scanner will go through some initialization steps. Also, if the lasers are not fully warm, there will be a warning sign that will give an approximate time that the lasers will be ready. 4.- Enter your name under Operator and check to see that the controls are set for the following: output directory is D:\niehs; both Red and Green channels are checked and are set to 100%; the size is 10 microns. 5.- Click on Options: choose to scan default slide area under Scan Region Options; specify slide area to largest area under Default Scan Region; click on Instrument serial number under Automatic File Naming (it will then be highlighted). Choose and type in your identifier for that day. Leave the Slot Number as is. 6.- Fill out log in the Scanner Cassette Log with your name, date and the order you put your slides into the carousel. This is important to assure proper renaming after scanning is complete. Click on OK to close the Options window. 7.- Double check that all the settings are properly set and click on Scan. 8.- After scan is complete, you will need to change the names to format pxxsxx. To do this: with the right mouse button, click on the Start menu and choose Explorer. Navigate your way through the files by clicking on the D drive on the far left hand side of the screen. Double click on D drive then double click onniehs. This folder contains all of the scanned files. Locate your slides by looking for the identifier you used for the scan. Click once to highlight name and click once more to get a cursor in the file name. Type in the proper name using the log you filled out earlier. Once all of the names have been changed, highlight the newest slides and move them into the appropriate boxes on Witchfire. 9.- Once you are done, log out of the computer, take the cassettes out of the carousel and your slides out of the cassettes. Turn off scanner.

source_name: RNA from H2126 labeled with Cy5

label_protocol:
1.- RNA from each sample were primed with 3µl of random hexamers d(N)6 0.5mg/ml (Promega) at 70ºC for 10min. For each labeling reaction, a master mix was prepared: 5µl First Strand buffer 5x, 2.5µl DTT 0.1M, 0.5µl unlabeled dNTPs 50x (dATP/dCTP/dGTP:dTTP 25:5), 1.5µl Cy5-dUTP 10mM  or Cy3-dUTP 10mM (for Universal Human Reference RNA), 0.63µl RNasin Inhibitor and 1.25µl SuperScript II (200U/µl). The labeling reaction was incubated at room temperature for 10min and then incubated at 42ºC for 2h. Tubes were protected from direct light.
2.- Each fluorescent labeled cDNA was purified with CyScribe GFX Purification kit (Amersham) following manufacturer's instructions.
3.- The Cy3-labeled and Cy5-labeled cDNAs for each hybridization were combined into a single tube. 10µg of Human Cot-1 DNA (Invitrogen) were added.
4.- To precipitate each hybridization probe, 0.1 volumes of sodium acetate 0.1M and 2.5 volumes of absolute ethanol were added.
5.- Each probe was resuspended in 4µl of filtered EDTA 10mM ph 8 and denatured at 95ºC for 10min. 40µl of SlideHyb buffer 1x (Ambion), prewarmed at 65ºC, and blocking agents (mix of polyA and yeast tRNA, 10µg and 4µg in 2µl of final volume) were added.


title: Calu3 cancer cell line sample CGH

type: genomic

description: The goal of this analysis is to see the copy number genes differential changed in lung cancer cell lines in relation with a control (normal females).

molecule: genomic DNA

source_name: DNA from Calu3 labeled with Cy5

label_protocol:
1.- DNA from each sample were primed with 3µl of random hexamers d(N)6 0.5mg/ml (Promega) at 70ºC for 10min. For each labeling reaction, a master mix was prepared: 5µl First Strand buffer 5x, 2.5µl DTT 0.1M, 0.5µl unlabeled dNTPs 50x (dATP/dCTP/dGTP:dTTP 25:5), 1.5µl Cy5-dUTP 10mM or Cy3-dUTP 10mM (for Universal Human Reference RNA), 0.63µl RNasin Inhibitor and 1.25µl SuperScript II (200U/µl). The labeling reaction was incubated at room temperature for 10min and then incubated at 42ºC for 2h. Tubes were protected from direct light.
2.- Each fluorescent labeled cDNA was purified with CyScribe GFX Purification kit (Amersham) following manufacturer's instructions.
3.- The Cy3-labeled and Cy5-labeled cDNAs for each hybridization were combined into a single tube. 10µg of Human Cot-1 DNA (Invitrogen) were added.
4.- To precipitate each hybridization probe, 0.1 volumes of sodium acetate 0.1M and 2.5 volumes of absolute ethanol were added.
5.- Each probe was resuspended in 4µl of filtered EDTA 10mM ph 8 and denatured at 95ºC for 10min. 40µl of SlideHyb buffer 1x (Ambion), prewarmed at 65ºC, and blocking agents (mix of polyA and yeast tRNA, 10µg and 4µg in 2µl of final volume) were added.

extract_protocol: Total DNA was extracted following conventional DNA extraction methods.

source_name: Genomic DNA extracted from 5 females

extract_protocol: Genomic DNA extracted from blood using conventional protocols for DNA extraction.

tag: Genomic DNA extracted from blood


title: XX_WT-E_080307_B


title: XX_WT-E_080307_A


title: XX_WT-E_080307_C


title: H441 cancer cell line sample

source_name: RNA from H441 labeled with Cy5


title: XO_TY2222-E-022208_D

tag: her-1(hv1y101); xol-1(y9) sdc-2(y74) unc-9(e101) XO embryos


title: H522 Lung cancer cell line

data_processing: Cy3 and Cy5 fluorescent signals were quantified using GenePix Pro 5.0 (Axon Instruments Inc.). Substandard spots were manually flagged and discarded for further analysis. The Cy5/Cy3 ratios were normalized to the median ratio value using the DNMAD tool, based on a print-tip loess method. The conditions for the normalization were: 1) use negative flags, that means that the flagged spots are not used for the normalization and are turned into missing values; 2) do not use background correction. The normalized and semi-logarithmic transformed data were preprocessing using GEPAS software. Conditions for data pre-processing were: 1) merge replicates (the Cy5/Cy3 ratios of replicated spots were averaged); 2) filter missing values in order to exclude for further analysis any gene with data  missing in more than 10% of the samples.

source_name: RNA from NSCLC H522 cell line labeled with Cy5

growth_protocol: Commercial

extract_protocol: Commercial sample already extracted

treatment_protocol: Commercial


title: XO_TY2222-E-022208_C


title: XO_TY2222-E-022208_B


title: H2126 cancer cell line sample CGH

source_name: DNA from H2126 labeled with Cy5


title: XO_TY2222-E-022208_A


title: XO_TY2222-E-022208_E


title: XO_TY2222-E_080307_C


title: A427 cancer cell line sample

source_name: RNA from A427 labeled with Cy5


title: XO_TY2222-E_080307_A


title: XO_TY2222-E_080307_B


title: 13852077 - Hypocotyls 5d 3 vs Hypocotyls 11d 3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Fine regulation of genes specifically expressed during cell elongation.

hyb_protocol: Hypocotyls 11d 3 Cy5 / Hypocotyls 5d 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 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Hypocotyls 11d 3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 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: hypocotyl - Media=Murashige and Skoog+2%sucrose+1.2% agar hygrometry=in vitro Temperature=23°C Light=dark

extract_protocol: Hypocotyls 11d3:72.56ug.

treatment_protocol: no treatment

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

source_name: Hypocotyls 5d 3

extract_protocol: Hypocotyls 5d 3:31.78ug.


title: 13368662 - Hypocotyls 11d 2 vs Hypocotyls 5d 2

hyb_protocol: Hypocotyls 5d 2 Cy5 / Hypocotyls 11d 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%

source_name: Hypocotyls 5d 2

growth_protocol: hypocotyl - Media = Murashige and Skoog + 2% sucrose + 1.2% agar	 hygrometry = in vitro	 Temperature = 23°C	 Light = dark

extract_protocol: Hypocotyls 5d 2:7.38ug.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.0

source_name: Hypocotyls 11d 2

extract_protocol: Hypocotyls 11d 2:9.98ug.


title: 13852081 - Hypocotyls 11d 3 vs Hypocotyls 5d 3

hyb_protocol: Hypocotyls 5d 3 Cy5 / Hypocotyls 11d 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: 13368660 - Hypocotyls 11d 1 vs Hypocotyls 5d 1

hyb_protocol: Hypocotyls 5d 1 Cy5 / Hypocotyls 11d 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.

source_name: Hypocotyls 5d 1

extract_protocol: Hypocotyls 5d 1:5.98ug.

source_name: Hypocotyls 11d 1

extract_protocol: Hypocotyls 11d 1:4.97ug.


title: 13368659 - Hypocotyls 5d 1 vs Hypocotyls 11d 1

hyb_protocol: Hypocotyls 11d 1 Cy5 / Hypocotyls 5d 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: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 28 of 38

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description: Chromatin immunoprecipitation was performed using antibodies against STAT1 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from HeLa cells using STAT1 antibody

label_protocol: Cy5 input Cy3 ChIP sample

extract_protocol: NimbleGen

tag: cells

value: HeLa

source_name: Input DNA from HeLa cells


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 10 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 12 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 01 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 26 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 25 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 14 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 11 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 16 of 38


title: 13368661 - Hypocotyls 5d 2 vs Hypocotyls 11d 2

hyb_protocol: Hypocotyls 11d 2 Cy5 / Hypocotyls 5d 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: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 08 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 18 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 02 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 27 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 17 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 09 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 21 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 23 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 30 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 19 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 37 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 35 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 34 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 32 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 20 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 33 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 36 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 06 of 38


title: Control 1 follow-up

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description:
Total cellular RNA extracted from individual enriched monocytes
C01.B2

hyb_protocol: Wistar Microarray Facility Protocol for Nylon based Custom Human Arrays

scan_protocol: Arrays were exposed to PhosphorImage screens (Packard Instruments) for 7-10 days, scanned in a Storm 820 PhosphorImager and visualized using ImageQuant (Molecular Dynamics)

data_processing: Image Analysis was performed using Imagene 4.0 (Biodiscovery, Inc.), Probes for which median signal instensity was less than the local background, had final normalized intensity values imputed to 0.002

source_name: circulating monocytes

label_protocol: 1.6ug of α-33PdCTP label

extract_protocol: Total cellular RNA was extracted from individual enriched monocytes of 13 viremic HIV-1 and 12 control uninfected donors immediately following cell isolation using TRI reagent (Molecular Research Center, Inc., Cincinnati, OH).

tag: Viral Load RNA (copies/ml)

tag: Batch


title: Control 2 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
C02.B2


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 04 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 07 of 38


title: dES Nimblegen human expression array, set 01 of 1

type: mixed

description: Gene expression for dES cells.

source_name: total RNA from dES cells

label_protocol: Nimblegen

value: dES

source_name: total DNA from dES cells


title: Patient 13

description:
Total cellular RNA extracted from individual enriched monocytes
P13.MB0


title: ES Nimblegen human expression array, set 01 of 1

description: Gene expression for ES cells.

source_name: total RNA from ES cells

value: ES

source_name: total DNA from ES cells


title: Patient 4 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
P04.B2


title: Control 3 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
C03.B2


title: Control 4 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
C04.B2


title: Patient 10

description:
Total cellular RNA extracted from individual enriched monocytes
P10.MB0


title: Patient 12

description:
Total cellular RNA extracted from individual enriched monocytes
P12.MB0


title: Patient 8

description:
Total cellular RNA extracted from individual enriched monocytes
P08.MB0


title: Patient 11

description:
Total cellular RNA extracted from individual enriched monocytes
P11.MB0


title: Patient 9

description:
Total cellular RNA extracted from individual enriched monocytes
P09.MB0


title: Patient 4

description:
Total cellular RNA extracted from individual enriched monocytes
P04.MB0


title: Patient 3

description:
Total cellular RNA extracted from individual enriched monocytes
P03.MB0


title: Patient 2

description:
Total cellular RNA extracted from individual enriched monocytes
P02.MB0


title: Patient 3 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
P03.B2


title: Patient 2 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
P02.B2


title: Patient 1 follow-up

description:
Total cellular RNA extracted from individual enriched monocytes
P01.B2


title: Patient 7

description:
Total cellular RNA extracted from individual enriched monocytes
P07.MB0


title: Control 12

description:
Total cellular RNA extracted from individual enriched monocytes
C12.MB0


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 34 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3 antibody

label_protocol: Cy3 input Cy5 ChIP sample


title: Control 11

description:
Total cellular RNA extracted from individual enriched monocytes
C11.MB0


title: Patient 1

description:
Total cellular RNA extracted from individual enriched monocytes
P01.MB0


title: Patient 5

description:
Total cellular RNA extracted from individual enriched monocytes
P05.MB0


title: Control 9

description:
Total cellular RNA extracted from individual enriched monocytes
C09.MB0


title: Control 8

description:
Total cellular RNA extracted from individual enriched monocytes
C08.MB0


title: Patient 6

description:
Total cellular RNA extracted from individual enriched monocytes
P06.MB0


title: Control 10

description:
Total cellular RNA extracted from individual enriched monocytes
C10.MB0


title: Control 7

description:
Total cellular RNA extracted from individual enriched monocytes
C07.MB0


title: Control 5

description:
Total cellular RNA extracted from individual enriched monocytes
C05.MB0


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 34 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1 antibody


title: Control 4

description:
Total cellular RNA extracted from individual enriched monocytes
C04.MB0


title: Control 2

description:
Total cellular RNA extracted from individual enriched monocytes
C02.MB0


title: STAT1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 02 of 4

description: Chromatin immunoprecipitation was performed using antibodies against STAT1 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using STAT1 antibody

source_name: Input DNA from K562 cells


title: Control 3

description:
Total cellular RNA extracted from individual enriched monocytes
C03.MB0


title: Control 1

description:
Total cellular RNA extracted from individual enriched monocytes
C01.MB0


title: TIGR4 in Mn vs mntE1 in Mn replicate 3 - dye-swap

city: Memphis

first: Jason

middle: W

last: Rosch

state: TN

address: 262 Danny Thomas Place

department: Infectious Disease

institute: St Jude Children's Hospital

data_processing: To analyze the microarray data, a series of filtration algorithms were applied to eliminate spots with poor quality data. The following spots were excluded from further analysis: spots flagged (as bad, absent, or not found) by the image analysis software GenePix 6.0 (Axon Corp., Union City, CA), and spots having a signal-to-noise ratio < 1.5 or a background-corrected signal reading < 20 in both Cy3 and Cy5 channels. To correct the intensity bias, loess normalization was applied to each microarray. Out of those at least five replicate spots on each array, only genes whose corresponding spots pass the filtering criterion at least 50% of the times were reported in further analysis.

organism: Streptococcus pneumoniae TIGR4

source_name: mntE in Mn

label_protocol: The Institute for Genomic Research standard operating procedure, see GSE14324_M007.pdf in GSE14324

extract_protocol: Qiagen

tag: mntE in high Mn

source_name: T4 in Mn

extract_protocol: qiagen

tag: T4 grown in Mn


title: TIGR4 in Mn vs mntE1 in Mn replicate 2

hyb_protocol: The Institute for Genomic Research standard operating procedure

tag: T4 in Mn

tag: mntE grown in Mn


title: TIGR4 in ThyB vs. TIGR4 in Mn replicate 1

scan_protocol: The Institute for Genomic Research standard operating procedure

extract_protocol: Quiagen

tag: TIGR4 grown in ThyB

source_name: TIGR4 grown in Mn

tag: TIGR4 in 500 uM MnCl


title: TIGR4 in ThyB vs. TIGR4 in Mn replicate 3 - dye-swap


title: TIGR4 in Mn vs mntE1 in Mn replicate 1

tag: mntE mutant grown in Mn


title: Control 6

description:
Total cellular RNA extracted from individual enriched monocytes
C06.MB0


title: TIGR4 in ThyB vs. TIGR4 in Mn replicate 2

tag: TIGR4 grown in ThyB+Mn


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 33 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 33 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 17 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 32 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 16 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 31 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 31 of 38


title: experiment 3, oligo3b, 5000PM, no fragmentation

type: other

city: Mol

first: Jef

last: Hooyberghs

address: Boeretang 200

country: Belgium

institute: VITO nv

description: target3 = 5' CTTTGTCGAGCTGGTATTTGGAGAACACGT 3' & 20-mer poly A + Cy3  on 3'

hyb_protocol: Using standard Agilent products: target in  H2O to 19ul,  5ul 10x Blocking Agent,  (1ul 25x Fragmentation buffer for experiment1&2 OR 1ul H2O for experiment3&4), Incubate: 30' at 60ºC, 25ul 2x GE Hyb, buffer HI-RPM, Centrifuge: 1' @ 13000rpm, load 40ul, 40µl per array, Hybridize in agilent oven: 65°C; 17h; rotor setting 10

scan_protocol: Agilent scanner: Scan: High+Low + 80%, 5µm, Green

data_processing: Feature extration:GE1-v5_95_Feb07

molecule: other

organism: synthetic construct

source_name: synthetic oligo

label_protocol: 3' Cy3-labeled synthetic oligo

extract_protocol: N/A (synthetic oligo, Eurogentec)


title: experiment 3, oligo3b, 1000PM, no fragmentation


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 14 of 38


title: experiment 3, oligo3b, 50PM, no fragmentation


title: experiment 3, oligo3b, 10000PM, no fragmentation


title: experiment 3, oligo3a, 10000PM, no fragmentation


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 16 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 32 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 17 of 38


title: experiment 3, oligo3a, 1000PM, no fragmentation


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 14 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 15 of 38


title: experiment 3, oligo3a, 50PM, no fragmentation


title: experiment 3, oligo3a, 5000PM, no fragmentation


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 25 of 38


title: experiment 1, oligo1a, 7500PM, fragmentation performed

description: target1 = 5' GTTTTCGAAGATTGGGTGGCACTGTTGTAA 3' & 20-mer poly A + Cy3  on 3'


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 25 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 15 of 38


title: experiment 1, oligo1a, 5000PM, fragmentation performed


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 24 of 38


title: experiment 1, oligo1a, 10000PM, fragmentation performed


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 23 of 38


title: experiment 1, oligo1a, 1000PM, fragmentation performed


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 23 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 24 of 38


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 06 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: experiment 1, oligo1a, 2500PM, fragmentation performed


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 04 of 12


title: H3K27ac,120926 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 06 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120926 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120926 antibody


title: H3K27ac,120926 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 05 of 12


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 22 of 38


title: H3K4me3,120984 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 05 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120984 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120984 antibody


title: experiment 1, oligo1a, 100PM, fragmentation performed


title: experiment 1, oligo1a, 500PM, fragmentation performed


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 05 of 12


title: H3K4me3,120974 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 08 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120974 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120974 antibody


title: H3K27ac,120926 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 04 of 12


title: H3K4me3,120984 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 04 of 12


title: H3K4me3,120984 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 06 of 12


title: H3K27ac,120925 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 08 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120925 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120925 antibody


title: experiment 1, oligo1a, 50PM, fragmentation performed


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 09 of 38

source_name: Input DNA from HeLa cells


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 08 of 12


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 22 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 09 of 38


title: H3K27ac,120925 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 07 of 12


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 07 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 38 of 38

description: Chromatin immunoprecipitation was performed using antibodies against STAT1 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using STAT1 antibody


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 08 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 07 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 06 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 08 of 38


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 07 of 12


title: H3K4me3,120974 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 07 of 12


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 06 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 22 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 05 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 13 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 05 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 29 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 05 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 15 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 31 of 38


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 24 of 38


title: DNase_concentration_C.116875 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: DNase-chip was performed using HeLa cells and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116875


title: STAT1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 03 of 38


title: H3K4me3,120927 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 03 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120927 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120927 antibody


title: DNase_concentration_C.116936 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116936


title: STAT1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 01 of 4


title: DNase_concentration_B.116863 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116863


title: STAT1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 04 of 4

source_name: Chromatin immunoprecipitated DNA from K562 cells using STAT1 antibody


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 03 of 12

source_name: Input DNA from K562 cells


title: H3K27ac,120964 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 03 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120964 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120964 antibody


title: DNase_concentration_B.116861 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116861


title: H3K4me3,120916 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 12 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120916 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120916 antibody


title: H3K4me3,120966 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 12 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120966 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120966 antibody


title: DNase_concentration_B.116858 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116858


title: H3K4me3,120920 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 12 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120920 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120920 antibody


title: DNase_concentration_A.116907 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116907


title: p300,116781 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against p300,116781 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,116781 antibody


title: H3K27ac,120928 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 12 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120928 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120928 antibody


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 12 of 12

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: H3K4me3,120916 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 10 of 12


title: MED1,116879 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116879 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116879 antibody

source_name: Input DNA from HeLa cells


title: H3K4me3,120920 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 10 of 12


title: MED1,116880 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116880 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116880 antibody


title: DNase_concentration_A.116859 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116859


title: p300,117028 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against p300,117028 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,117028 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 38 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3 antibody


title: H3K27ac,126614 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,126614 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,126614 antibody


title: MED1,116881 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116881 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116881 antibody


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 37 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1 antibody


title: MED1,116874 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116874 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116874 antibody


title: H3K27ac,120928 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 10 of 12

source_name: Input DNA from K562 cells


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 10 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides


title: H3K27ac,117041 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,117041 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117041 antibody


title: H3K4me3,120966 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 10 of 12

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120966 antibody


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 38 of 38


title: Native (not activated) conventional CD4+T cells 1

city: los angeles

first: Brian

last: O'Connor

address: 2018 Griffith Park Blvd

institute: UCLA

description: Group 8

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was normalized using the justRMA algorithm from the Bioconductor group following the methods of the Celsius project.

label: Biotin

organism: Mus musculus

source_name: Peripheral CD4+Foxp3-EGFP- T cells

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

growth_protocol: Conventional CD4+Foxp3-EGFP- and natural CD4+Foxp3+EGFP+ regulatory T cells were isolated from secondary lymphoid tissues (spleens and lymph nodes) of bicistronic Foxp3/EGFP mice. Conventional CD4+Foxp3deltaEGFP- were isolated from Foxp3deltaEGFP mutant males, while CD4+Foxp3deltaEGFP+ regulatory T cell precursors were isolated from heterozygous Foxp3deltaEGFP females. The respective cell populations were isolated by cell sorting.

extract_protocol: Total RNA was isolated by Trizol extraction and was furher purified by Qiagen Rneasy spin columns following the manufacturer's specifications

treatment_protocol: Group 1: induced regulatory T cells, derived by treatment of CD4+Foxp3-EGFP– T cells of Foxp3EGFP bicistronic mice with anti-CD3+anti-CD28 monoclonal antibodies (mAbs) +TGF-beta for 3 days, then sorting for CD4+Foxp3+EGFP+ cells; Group 2: Failed induced regulatory T cells: CD4+Foxp3-EGFP– cells, derived from group 1 cultures that failed to express Foxp3EGFP following treatment with anti-CD3+anti-CD28 mAbs+TGF-beta; Group 3: induced CD4+Foxp3deltaEGFP+ cells, derived by treatment of CD4+Foxp3deltaEGFP– T cells of Foxp3deltaEGFP mutant mice with anti-CD3+anti-CD28 mAbs+TGF-beta for 3 days, then sorting for CD4+Foxp3deltaEGFP+ cells; Group 4: activated T cells, derived from conventional CD4+Foxp3-EGFP- T cells of Foxp3/EGFP bicistronic mice that were stimulated in vitro with anti-CD3+anti-CD28 mAbs but NO TGF-beta; Group 5: Activated natural regulatory T cells are CD4+Foxp3+EGFP+ T cells isolated from Foxp3/EGFP bicistronic mice and activated with anti-CD3+antiCD28 mAbs +TGF-beta to simulate treatment of groups  1-3; Group 6: native (not activated) CD4+Foxp3+EGFP+ natural regulatory T cells of Foxp3EGFP bicistronic mice; Group 7: Native (not activated) CD4+Foxp3deltaEGFP+ T cells isolated from heterozygos Foxp3deltaEGFP females; Group 8: Native (not activated) conventional CD4+T cells isolated from bicistonic Foxp3/EGFP mice; Group 9: IL-2-cultured induced regulatory T cells, derived by treatment of CD4+Foxp3-EGFP– T cells (from Foxp3EGFP bicistronic muce) with anti-CD3+anti-CD28 mAbs +TGF-beta for 3 days then sorting for CD4+Foxp3+EGFP+ cells and culturing those for one week with IL-2 at 100 units/ml; Group 10: IL-2-cultured induced CD4+Foxp3deltaEGFP+ cells, derived by treatment of CD4+Foxp3deltaEGFP– T cells (isolated from Foxp3deltaEGFP mice) with anti-CD3+anti-CD28 mAbs+TGF-beta for 3 days, then sorting for CD4+Foxp3deltaEGFP+ cells and culturing those for one week with IL-2 at 100 units/ml.

tag: Foxp3/EGFP bicistronic mice on BALB/c background


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 37 of 38


title: H3K27ac,117029 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,117029 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117029 antibody


title: H3K4me3,120927 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 01 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120927 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120927 antibody


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 01 of 12

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: H3K27ac,120964 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 01 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120964 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120964 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 35 of 38

source_name: Input DNA from HeLa cells


title: Native (not activated) natural regulatory T cells 4

description: Group 6

source_name: Peripheral CD4+Foxp3+EGFP+ T cells


title: Native (not activated) natural regulatory T cells 3

description: Group 6


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 29 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 30 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 36 of 38


title: H3K4me3,116780 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116780 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116780 antibody


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 29 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 35 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 36 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 30 of 38


title: DNase_concentration_A.116860 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: DNase-chip was performed using HeLa cells and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116860


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 27 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 26 of 38

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3 antibody


title: H3K4me1,116876 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116876 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116876 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 28 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 27 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 28 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 20 of 38


title: H3K4me1,116823 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116823 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116823 antibody


title: H3K4me1,116814 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116814 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116814 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 20 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 26 of 38

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1 antibody


title: Native (not activated) natural regulatory T cells 2

description: Group 6


title: DNase_concentration_C.116936 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116936


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 21 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 13 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 18 of 38


title: DNase_concentration_B.116861 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116861


title: DNase_concentration_B.116863 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116863


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 18 of 38


title: H3K4me3,116779 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116779 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116779 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 21 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 19 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 19 of 38


title: DNase_concentration_B.116858 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116858


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 13 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 11 of 38


title: DNase_concentration_C.116875 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116875


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 04 of 38


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 12 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 12 of 38


title: H3K4me3,116769 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 03 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116769 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116769 antibody


title: DNase_concentration_A.116907 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116907


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 10 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

source_name: Input DNA from HeLa cells


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 04 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 11 of 38


title: DNase_concentration_A.116860 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3


title: DNase_concentration_A.116859 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116859


title: MED1,116880 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116880 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116880 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 02 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 10 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 03 of 38


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 01 of 38


title: MED1,116881 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116881 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116881 antibody


title: H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 02 of 38

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 03 of 38

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3 antibody


title: p300,116781 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against p300,116781 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,116781 antibody


title: H3K4me3 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 01 of 38


title: H3K27ac,126614 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,126614 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,126614 antibody


title: H3K27ac,117029 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117029 antibody


title: STAT1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 03 of 4

description: Chromatin immunoprecipitation was performed using antibodies against STAT1 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using STAT1 antibody

source_name: Input DNA from K562 cells


title: H3K4me3,116780 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116780 antibody


title: MED1,116879 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116879 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116879 antibody


title: H3K4me3,116779 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116779 antibody


title: H3K4me3,120966 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 11 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120966 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120966 antibody


title: H3K4me3,116769 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3


title: experiment 4, oligo4b, 1000PM, no fragmentation

description: targte4 = 5' GCTTCTCCTTAATGTCACGCACGATTTCCC 3' & 20-mer poly A + Cy3  on 3'

source_name: synthetic oligo


title: H3K27ac,117041 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,117041 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117041 antibody


title: experiment 4, oligo4b, 500PM, no fragmentation


title: H3K4me1,116876 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116876 antibody


title: H3K4me3,120920 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 11 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120920 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120920 antibody


title: H3K4me3,120916 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 11 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120916 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120916 antibody


title: MED1,116874 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116874 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116874 antibody

source_name: Input DNA from HeLa cells


title: experiment 4, oligo4b, 100PM, no fragmentation


title: H3K4me1,116823 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116823 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116823 antibody


title: experiment 4, oligo4a, 1000PM, no fragmentation


title: experiment 4, oligo4b, 50PM, no fragmentation


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 09 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: experiment 2, oligo2b, 10000PM, fragmentation performed

description: target2 = 5' CAGGGCCTCGTTATCAATGGAGTAGGTTTC 3' & 20-mer poly A + Cy3  on 3'


title: H3K4me3,120974 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 09 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120974 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120974 antibody


title: experiment 4, oligo4a, 100PM, no fragmentation


title: experiment 4, oligo4a, 500PM, no fragmentation


title: experiment 4, oligo4a, 50PM, no fragmentation


title: experiment 2, oligo2b, 1000PM, fragmentation performed


title: experiment 2, oligo2b, 5000PM, fragmentation performed


title: DNase_concentration_B.116858 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: DNase-chip was performed using HeLa cells and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116858


title: DNase_concentration_C.116936 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116936


title: H3K4me1,116814 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116814 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116814 antibody


title: p300,117028 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 02 of 3

description: Chromatin immunoprecipitation was performed using antibodies against p300,117028 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,117028 antibody


title: experiment 2, oligo2b, 50PM, fragmentation performed


title: DNase_concentration_B.116863 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116863


title: DNase_concentration_B.116861 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_B.116861


title: DNase_concentration_C.116875 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_C.116875


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 11 of 12

source_name: Input DNA from K562 cells


title: experiment 2, oligo2a, 5000PM, fragmentation performed

source_name: synthetic oligo


title: DNase_concentration_A.116907 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116907


title: H3K27ac,120928 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 11 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120928 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120928 antibody


title: experiment 2, oligo2a, 50PM, fragmentation performed


title: experiment 2, oligo2a, 1000PM, fragmentation performed


title: H3K27ac,120925 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 09 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120925 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120925 antibody


title: H3K4me3,120927 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 02 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,120927 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3,120927 antibody


title: H3K27ac,120964 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 02 of 12

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,120964 and formaldehyde crosslinked chromatin from K562 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 12 sub-arrays on 4 physical arrays containing a total of 4 * 2.1 million 50 to 75-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27ac,120964 antibody


title: H3K4me1 K562 Nimblegen Economy HD2 Human tiling array of hg18 at 205bp resolution, set 02 of 12


title: Liver_WSB/EiJ_1067

status: Public on Feb 28 2009

city: Chapel Hill

first: Daniel

middle: M

last: Gatti

state: NC

address: 135 Dauer Dr.

department: Environmental Sciences & Engineering

institute: University of Noth Carolina

description: Analysis of mouse liver gene expression.

hyb_protocol: Labeled cRNA was processed and hybridized to Agilent Mouse Toxicology Arrays (catalog# 4121A, about 22,000 features) according the the manufacturer’s protocol. Following hybridization, arrays were washed using a custom protocol developed by Icoria, Inc. Briefly, array gaskets are removed under immersion in Wash Solution 1 (6X SSPE, 0.005% N-Lauroylsarcosine). Arrays were washed with Wash Solution 1 and incubated for one minute with gentle agitation on a magnetic stir plate. A second incubation was performed in Wash Solution 2 (0.06X SSPE, 0.005% N-Lauroylsarcosine).

scan_protocol: Agilent Scanner with Agilent Feature Extraction.

data_processing: Data was processed using the UNC Microarray data base at (http://genome.unc.edu). Loess normalization was performed.

source_name: Reference

label_protocol: In this study, all RNA samples were hybridized to arrays individually; none were pooled. RNA amplifications and labeling were performed using Low RNA Input Linear Amplification kits (Agilent Technologies). For hybridization, 750 ng of total RNA from each mouse liver was amplified and labeled with fluorescent dye (Cy5). In parallel, 750 ng of a common reference RNA (Icoria Inc., RTP, NC) was labeled with the fluorescent dye, Cy3, in order to standardize analysis of global gene expression between mouse strains.

extract_protocol: Reference RNA from Icoria.

tag: Icoria Reference RNA

tag: C57BL/6J male liver, kidney, lung, brain and spleen

source_name: liver, WSB/EiJ

extract_protocol: To eliminate variability in transcript expression that might arise between liver lobes, the left liver lobe was selected for the remainder of the data analysis and gene expression profiling. RNA was extracted from the 30 mg of tissue derived from the left lobe of sample livers using the Qiagen RNeasy kit (Qiagen, Valencia, CA). RNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and quality was verified using the Agilent Bio-Analyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Male mice (aged 7-9 weeks) were obtained from The Jackson Laboratory and housed in polycarbonate cages on Sani-Chips irradiated hardwood bedding (P.J. Murphy Forest Products Corp., Montville, NJ). Animals were fed NTP-2000 wafer feed (Zeigler Brothers, Inc., Gardners, PA) and water ad libitum, and maintained on a 12 h light-dark cycle. Mice utilized in this study comprise 36 inbred strains that are priority strains for the Mouse Phenome Project 13: 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BTBR T+ tf/J, BUB/BnJ, C3H/HeJ, C57BL/10J, C57BL/6J, C57BLKS/J, C57BR/CdJ, C57L/J, CAST/EiJ, CBA/J, CZECHII/EiJ, DBA/2J, FVB/NJ, JF1/Ms, KK/HlJ, LP/J, MA/MyJ, MSM/Ms, NOD/ShiLtJ (formerly NOD/LtJ), NON/LtJ, NZO/H1LtJ, NZW/LacJ, P/J, PERA/EiJ, PL/J, PWD/PhJ, RIIIS/J, SEA/GnJ, SJL/J, SM/J, SWR/J, and WSB/EiJ. F1 hybrid mice, B6C3F1/J, were also used for phenotypic measurements. Care of mice followed institutional guidelines under a protocol approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

tag: Strain

value: WSB/EiJ

tag: Gender

value: male


title: experiment 2, oligo2a, 10000PM, fragmentation performed


title: Liver_SWR/J_1018

source_name: liver, SWR/J

value: SWR/J


title: Liver_SM/J_1218

source_name: liver, SM/J

value: SM/J


title: Liver_SWR/J_1010


title: Liver_SM/J_1094


title: Liver_SJL/J_1055

source_name: liver, SJL/J

value: SJL/J


title: Liver_SEA/GnJ_1199

source_name: liver, SEA/GnJ

value: SEA/GnJ


title: Liver_WSB/EiJ_1120


title: Liver_RIIIS/J_1125

source_name: liver, RIIIS/J

value: RIIIS/J


title: Liver_SWR/J_1132


title: Liver_PWD/PhJ_1073

source_name: liver, PWD/PhJ

value: PWD/PhJ


title: Liver_PL/J_1007

source_name: liver, PL/J

value: PL/J


title: Liver_PL/J_1128


title: Liver_SEA/GnJ_1110


title: Liver_PERA/EiJ_1118

source_name: liver, PERA/EiJ

value: PERA/EiJ


title: Liver_P/J_1211

source_name: liver, P/J

value: P/J


title: DNase_concentration_A.116859 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116859

source_name: Input DNA from HeLa cells


title: Liver_PERA_1064

source_name: liver, PERA

value: PERA


title: Liver_RIIIS/J_1004


title: DNase_concentration_A.116860 HeLa Condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: DNase-chip using HeLa cells, DNase_concentration_A.116860


title: Liver_NZW/LacJ_1150

source_name: liver, NZW/LacJ

value: NZW/LacJ


title: Liver_NZW/LacJ_1028


title: Liver_PWD/PhJ_1192


title: Liver_PERA/EiJ_1116


title: Liver_NON/LtJ_1222

source_name: liver, NON/LtJ

value: NON/LtJ


title: Liver_NZO/H1LtJ_1079

source_name: Reference

source_name: liver, NZO/H1LtJ


title: Liver_NON/LtJ_1097


title: Liver_NOD/LtJ_1122

source_name: liver, NOD/LtJ

value: NOD/LtJ


title: Liver_MSM/Ms_1201

source_name: liver, MSM/Ms

value: MSM/Ms


title: Liver_NOD/LtJ_1001


title: MED1,116880 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116880 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116880 antibody

value: HeLa


title: Liver_MSM/Ms_1076


title: Liver_MA/MyJ_1085

source_name: liver, MA/MyJ

value: MA/MyJ


title: Liver_LP/J_1143

source_name: liver, LP/J

value: LP/J

value: male


title: Liver_MA/MyJ_1155


title: Liver_SJL/J_1206

source_name: liver, SJL/J


title: Liver_LP/J_1022


title: p300,117028 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,117028 antibody