title: Pellet_4_(C3H2A_vs_VPN_277877-2)

status: Public on Apr 01 2009

description: DNA from 600mM NaCl-extracted pellet, H2AV DNAs Input Pellet vs H2AV DNAs Nuc Pellet

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperature to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bottom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microliter Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the NimbleGen arrays. They are required for proper extraction of array data from the scanned image. Mix the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disassembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put the array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sample may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If there are, very gently massage any bubbles to either of the ends, away from the center of the array. Avoid applying too much pressure since this will force liquid out of the ports. Place the loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Close the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm that the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solutions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One dish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works well. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften the adhesive on the hybridization chamber; this will help prevent braking the array. Place the remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I: 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C. Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not let the surface of the slide dry out at any point during washing. While the chip is submerged, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfer the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agitation. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wash over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation. Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dark desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Axon Scanner (model 4000B). Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Open the scanner door and open the side carriage. Place chip in carriage so that array is face down and barcode end is closest to you. Move the black lever on the left side of the carriage left until the array is lying flat in the carriage. Release the lever so that the arry is pushed over gently to the right side of the carriage and held firmly. Close the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simultaneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the full arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array image and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side of the screen, click the Scan Area icon. Click and drag to define a box that bounds the visibile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan image. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole image and adjust the brightness and contrast of the displayed image to eliminate visible saturation. Based on the appearance of the array features, adjust the PMT setting as appropriate. The features should be mostly yellow. If your features are mostly green, either decrease the 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 532 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check global intensity of the features. On the top left side of the screen make sure you have the 532 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure the Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the green PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity level (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark.  The histogram only graphs the area of the image that is viewable in the screen on the image tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are properly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the 532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered

source_name: Drosophila S2 cells H2Av DNA extract pellet

label_protocol:
Strand-displacement labeling for NimbleGen arrays  Steve Henikoff 5/2008. This is a modification of the NimbleGen protocol for ChIP-chip labeling (http://www.nimblegen.com/). It yields adequate amounts of end-labeled material without PCR amplification starting with ? 0.2 ug fragmented DNA.  1) In a 0.5ml PCR tube, mix up to 20uL ds DNA with 20uL either Cy3- or Cy5-labeled 9mers in random primer buffer (Cy3 and Cy5 9mer Wobble from TriLink are mixed according to the NimbleGen protocol, aliquoted and stored frozen). Use 0.2-3ug DNA, the more the better, and add water to 20uL. Protect the dye-labeled material from direct light, especially Cy5, throughout the procedure.  2) Heat 98oC 10 min. Quick chill in ice-water (this is important).  3) While the samples are denaturing, make a master mix with Klenow exo- (NEB 50,000u/ml) and dNTPs. For example, for 10 samples mix 42uL water, 10.5uL Klenow, 52.5uL 10mM dNTPs (aliquoted and stored frozen). While samples are still in the ice-water bath and chilled, add 10uL master mix to each tube with 10 or more strokes of the Pipetteman tip.  4) Following a brief spin, transfer tubes to a 37oC cycler. Incubate overnight (16 hr).
5) Prepare 1.5ml tubes with NaCl+EDTA (equivalent of 5uL 0.5M EDTA, 5.7uL 5M NaCl, which can be added together). Remove the tubes from the cycler and transfer contents from the cycler to these 1.5 ml tubes. Add 60uL 2-propanol (the volume is important). Let sit in dark 10' at room temperature.  6) Spin 13.2krpm 10 room temperature. Carefully decant the supernatant from the deeply colored pellet with a P200. Add 500uL ice-cold 80% ethanol and spin briefly in the cold. Carefully pour or pull off the ethanol - large pellets tend to dislodge. Quick spin and pull off the excess ethanol. Let air dry (~10min room temperature).  7) Add 20uL water to dissolve. Note that the deepness of the red (Cy3) or blue (Cy5) is a good measure of the yield. For samples in which there was little starting material, and/or the DNA was small, there will not be enough for an array, and the color will be faint. For samples with deep color, add an additional 30uL water. Measure OD260 and calculate yield. Store at 4oC for brief periods or at -20oC longer term in dark.
8) For sample with less than 30ug/array, do another round of labeling, using 20uL of the labeled DNA from the first round prep. The second round is much more efficient than the first round and consistently yields ? 60ug.  9) Check sizes on a 1.5% gel without ethidium. Cy3 fluoresces well enough to see 1 ug, but Cy5 is much fainter and might not be visible. DNA should be about the same average size as the starting material. Follow with ethidium staining: DNA typically smears up towards the top of the gel, but this material is evidently low in molar amount of label and does not appear to cause a problem.  10) For each 2.1M array, mix 30ug Cy3-labeled DNA with 30ug Cy5-labeled DNA and speed-vac dry on low or medium. If Cy3 is input DNA then Cy5 is pull-down DNA and vice versa.  11) Reduce volume by speedvac on low to 12.3 ML, or lyophilize samples for hybridization to NimbleGen arrays using standard NimbleGen hybridization protocol.

extract_protocol:
Nuclei were prepared as previously described (McKittrick et al. 2004) and chromatin was extracted by modification of our previous procedure (Mito et al. 2005). Briefly, cells were suspended in TM2 (10mM Tris pH7.4, 2mM MgCl2, 0.5mM pmsf) with gentle vortexing to a concentration of 1-2x108/ml, held 1' in ice-water, and 10% NP-40 was added with gentle vortexing to 1.5%. After 2-5min on ice, crude nuclei were pelleted at 800 rpm in a Sorvall SS-34 rotor at 4oC, the supernatant was carefully removed, and the pellet was transferred with cold TM2 to a 2ml microfuge tube. Nuclei were spun in an Eppendorf microcentrifuge at 1000 rpm and the pellet was resuspended in TM2 to an estimated concentration of 0.5-1x109/ml for MNase digestion. CaCl2 was added to 1mM, the tubes were warmed to 37oC for 1', then digested by addition of MNase (Sigma 1.6U/ml) for 10'. Tubes were transferred to ice and reactions were stopped by addition of 0.2M EGTA (Na+) to 2mM. Nuclei were pelleted 10' at 2000 rpm 4oC, washed in TM2 and resuspended in 0.7ml cold 80mM or 150mM buffer: 140mM (or 70mM) NaCl, 10mM Tris 7.4, 2mM MgCl2, 2mM EGTA, 0.1% Triton X-100, 0.5mM pmsf pH7.5. After 1-2 hr rotation on a nutator at 4oC, nuclei were pelleted 10' at 2000rpm, and the pellet was gently resuspended in 0.7ml cold 600mM NaCl, 10mM Tris 7.4, 2mM MgCl2, 2mM EGTA, 0.1% Triton X-100, 0.5mM pmsf pH7.5. Supernatants from each extraction were clarified by spinning 2' at 13,200 rpm and held on ice to be used for pulldowns with aliquots taken for DNA and protein analyses (80mM, 150mM and 80-150mM extractions). The 600mM resuspended pellet was rotated overnight at 4oC, pelleted 10' at 2000rpm, and the supernatant was clarified and held on ice (80-600mM and 150-600mM extractions).
For some experiments, MNase treatment was stopped by addition of EDTA (Na+ at pH 8) to 10mM, and after pelleting and saving the supernatant, nuclei were suspended in 0.6ml 10mM Tris 0.25mM EDTA pH7.4. The suspension was passed five times through a 26-gauge needle and combined with the supernatant (EDTA-needle extraction) (Jin and Felsenfeld 2007). For experiments described in Fig. 3D, DNAs extracted from samples prepared in this way were electrophoresed and the mononucleosome band was excised, and the DNA was extracted using the Qiagen Qiaquick kit.
Affinity purification was performed by addition of streptavidin-Sepharose and rotating for 2hrs at 4¡C as described (Mito et al. 2005), except that the same buffer (without Triton) was used for washing the resin, which was brought up in 0.2ml 150mM buffer (without Triton) and (usually) frozen at -20oC prior to extraction. Aliquots of MNase-digested nuclei and clarified soluble nucleosomes were also frozen prior to extraction.
DNA was purified from chromatin fractions and pulldown samples as described (Mito et al. 2005). Briefly, samples were RNAse-treated, deproteinized with SDS and proteinase K, extracted using a mixture of phenol/chloroform/isoamyl alcohol (25:24:1) followed by chloroform extraction, and DNA was precipitated with 2 vol ethanol.
References: Jin, C. and Felsenfeld, G. 2007. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21: 1519-1529.  McKittrick, E., Gafken, P.R., Ahmad, K., and Henikoff, S. 2004. Histone H3.3 is enriched in covalent modifications associated with active  chromatin. Proc Natl Acad Sci USA 101: 1525Ð1530.  Mito, Y., Henikoff, J., and Henikoff, S. 2005. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37: 1090-1097.

value: S2 cells

source_name: Drosophila S2 cells DNA nuc

extract_protocol: See Sample_extract_protocol_ch1.


title: H3.3_150-600_(33-6_185167-1)

status: Public on Dec 12 2008

type: genomic

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Biotin-H3.3 pulldown of 150-600mM NaCl-extracted fraction (Cy3/Cy5)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila S2 cells, H3.3 DNA Pull-down

tag: cell type

source_name: Drosophila S2 cells, H3.3 DNA Input


title: H3.3_80_(33_80_271147)

description: Biotin-H3.3 pulldown of 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: H2Av_bulk_(C3H2A_vs_VPDINP_276912-2)

description: Biotin-H2Av pulldown of EDTA-needle-extracted chromatin, H2Av pull-down vs H2Av input

data_processing: Log base 2 (Cy5/Cy3) ratios were bi-weight mean centered

source_name: Drosophila S2 cells H2Av pull-down

source_name: Drosophila S2 cells H2Av input


title: H2Av_bulk_(C2.2AVIPD_237448)

status: Public on Apr 13 2009

description: Biotin-H2Av pulldown of EDTA-needle-extracted chromatin

source_name: Drosophila S2 cells, H2Av DNA pull-down

tag: Drosophila S2 cells

source_name: Drosophila S2 cells, H2Av DNA input


title: 80_fraction_10_(C4_vs_80N_138967-5)

description: 80mM NaCl-extracted chromatin, DNAs Input vs DNAs Nuc

source_name: Drosophila S2 cells DNA input 80mM fraction

extract_protocol:
For some experiments, MNase treatment was stopped by addition of EDTA (Na+ at pH 8) to 10mM, and after pelleting and saving the supernatant, nuclei were suspended in 0.6ml 10mM Tris 0.25mM EDTA pH7.4. The suspension was passed five times through a 26-gauge needle and combined with the supernatant (EDTA-needle extraction) (Jin and Felsenfeld 2007). For experiments described in Fig. 3D, DNAs extracted from samples prepared in this way were electrophoresed and the mononucleosome band was excised, and the DNA was extracted using the Qiagen Qiaquick kit.
Affinity purification was performed by addition of streptavidin-Sepharose and rotating for 2hrs at 4¡C as described (Mito et al. 2005), except that the same buffer (without Triton) was used for washing the resin, which was brought up in 0.2ml 150mM buffer (without Triton) and (usually) frozen at -20oC prior to extraction. Aliquots of MNase-digested nuclei and clarified soluble nucleosomes were also frozen prior to extraction.
DNA was purified from chromatin fractions and pulldown samples as described (Mito et al. 2005). Briefly, samples were RNAse-treated, deproteinized with SDS and proteinase K, extracted using a mixture of phenol/chloroform/isoamyl alcohol (25:24:1) followed by chloroform extraction, and DNA was precipitated with 2 vol ethanol.
References: Jin, C. and Felsenfeld, G. 2007. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21: 1519-1529.  McKittrick, E., Gafken, P.R., Ahmad, K., and Henikoff, S. 2004. Histone H3.3 is enriched in covalent modifications associated with active  chromatin. Proc Natl Acad Sci USA 101: 1525Ð1530.  Mito, Y., Henikoff, J., and Henikoff, S. 2005. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37: 1090-1097.

extract_protocol: Nuclei were prepared as previously described (McKittrick et al. 2004) and chromatin was extracted by modification of our previous procedure (Mito et al. 2005). Briefly, cells were suspended in TM2 (10mM Tris pH7.4, 2mM MgCl2, 0.5mM pmsf) with gentle vortexing to a concentration of 1-2x108/ml, held 1' in ice-water, and 10% NP-40 was added with gentle vortexing to 1.5%. After 2-5min on ice, crude nuclei were pelleted at 800 rpm in a Sorvall SS-34 rotor at 4oC, the supernatant was carefully removed, and the pellet was transferred with cold TM2 to a 2ml microfuge tube. Nuclei were spun in an Eppendorf microcentrifuge at 1000 rpm and the pellet was resuspended in TM2 to an estimated concentration of 0.5-1x109/ml for MNase digestion. CaCl2 was added to 1mM, the tubes were warmed to 37oC for 1', then digested by addition of MNase (Sigma 1.6U/ml) for 10'. Tubes were transferred to ice and reactions were stopped by addition of 0.2M EGTA (Na+) to 2mM. Nuclei were pelleted 10' at 2000 rpm 4oC, washed in TM2 and resuspended in 0.7ml cold 80mM or 150mM buffer: 140mM (or 70mM) NaCl, 10mM Tris 7.4, 2mM MgCl2, 2mM EGTA, 0.1% Triton X-100, 0.5mM pmsf pH7.5. After 1-2 hr rotation on a nutator at 4oC, nuclei were pelleted 10' at 2000rpm, and the pellet was gently resuspended in 0.7ml cold 600mM NaCl, 10mM Tris 7.4, 2mM MgCl2, 2mM EGTA, 0.1% Triton X-100, 0.5mM pmsf pH7.5. Supernatants from each extraction were clarified by spinning 2' at 13,200 rpm and held on ice to be used for pulldowns with aliquots taken for DNA and protein analyses (80mM, 150mM and 80-150mM extractions). The 600mM resuspended pellet was rotated overnight at 4oC, pelleted 10' at 2000rpm, and the supernatant was clarified and held on ice (80-600mM and 150-600mM extractions).


title: 150-600_fraction_(5-S2_600_271135)

description: Chromatin from 600mM NaCl extraction of 150mM NaCl extracted pellet, DNAs Input vs DNAs Nuc

source_name: Drosophila S2 cells, DNA input, 150-600mM fraction

source_name: Drosophila S2 cells, DNA Nuc


title: H2A_bulk_(C3H2A_vs_PDINP_277408-2)

description: Biotin-H2A pulldown of EDTA-needle-extracted chromatin

source_name: Drosophila S2 cells H2A pull-down

source_name: Drosophila S2 cells H2A input


title: H3.3deltaN_80_(dN_80_271145)

description: Biotin-H3.3_N-terminal-deleted pulldown of 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: H2A_bulk_(C2.2AIPD_237467)

source_name: Drosophila S2 cells, H2A DNA pull-down

source_name: Drosophila S2 cells, H2A DNA input


title: Pellet_3_(516pell_271522)

description: DNA from 600mM NaCl-extracted pellet (Cy5/Cy3)

source_name: Drosophila S2 cells, H2AV DNA Nuc Pellet

source_name: Drosophila S2 cells, H2AV DNA Input Pellet


title: 80-150_fraction_3_(5-S2_150_271134)

description: Chromatin from 150mM NaCl extraction of 80mM NaCl extracted pellet, DNAs Input vs DNAs Nuc

source_name: Drosophila S2 cells, DNA input, 80-150mM fraction


title: H3.3_80-600_(3.3_600bd_271145)

description: Biotin-H3.3 pulldown of 80-600mM NaCl-extracted chromatin, H33 DNAs Input vs H33 DNAs Pull-down

source_name: Drosophila S2 cells, H3.3 DNA pull-down

source_name: Drosophila S2 cells, H3.3 DNA input


title: 80-150_fraction_2_(2-AvN150_271532)

description: Chromatin from 150mM NaCl extraction of 80mM NaCl extracted pellet (Cy5/Cy3)

source_name: Drosophila S2 cells, H2AV DNA Nuc

source_name: Drosophila S2 cells, H2AV DNA Input


title: Pellet_1_(507pell_271517)


title: 80_fraction_9_(5-S2_80_270387)

source_name: Drosophila S2 cells DNA input

source_name: Drosophila S2 cells DNA nuc, 80mM fraction


title: 80_fraction_8_(2-AvN80_271522)

description: 80mM NaCl-extracted chromatin (Cy5/Cy3)


title: Pellet_2_(508pell_271518)


title: H3.3_bulk_(2-33E_269900)

description: Biotin-H3.3 pulldown of EDTA-needle-extracted chromatin (Cy3/Cy5)

source_name: Drosophila S2 cells, H3.3 DNA Pull-down

source_name: Drosophila S2 cells, H3.3 DNA Input


title: Fusion: No, Deletion: No (prostate_44453)

status: Public on May 28 2008

type: RNA

city: New York

first: Mark

middle: A.

last: Rubin

state: NY

address: 1300 York Avenue Room C 410-A

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical Center

description: no additional

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene.

label: Cy3 and Cy5

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer

extract_protocol: Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).

tag: FUSION

value: NO

tag: DELETION


title: 80_fraction_4_(033N_237468)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)

source_name: Drosophila S2 cells, H3.3 DNA Nuc


title: Fusion: Yes, Deletion: Yes (prostate_44354)

description: no additional

scan_protocol: Refer to the Illumina DASL Assay System Manual

value: YES


title: 80-600_fraction_1_(8D3N6_138961)

description: Chromatin from 600mM NaCl extraction of 80mM NaCl extracted pellet ((Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_44271)

description: no additional

label_protocol: Refer to the Illumina DASL Assay System Manual


title: 80_fraction_5_(8D3N8_185156)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_44263)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_44180)

description: no additional


title: 80_fraction_7_(1-AvN0.8_271522)

description: 80mM NaCl-extracted chromatin (Cy5/Cy3)


title: 80_fraction_6_(833N8_138377)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_44131)

description: no additional


title: Fusion: Yes, Deletion: No (prostate_44149)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_44115)

description: no additional

tag: DELETION:


title: H2A_bulk_(4AED_237369)

description: Biotin-H2A pulldown of EDTA-needle-extracted chromatin (Cy3/Cy5)

source_name: Drosophila S2 cells, H2A DNA Pull-down

source_name: Drosophila S2 cells, H2A DNA Input


title: 80-150_fraction_1_(1-AvN1.5_271532)

description: Chromatin from 150mM NaCl extraction of 80mM NaCl extracted pellet (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_44099)

description: no additional


title: H2Av_bulk_(4VED_237467)

description: Biotin-H2A pulldown of EDTA-needle-extracted chromatin  (Cy3/Cy5)

source_name: Drosophila S2 cells, H2AV DNA Pull-down


title: 80-600_fraction_2_(833N6_138960)

description: Chromatin from 600mM NaCl extraction of 80mM NaCl extracted pellet (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_44081)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_44214)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_43604)

description: no additional


title: Fusion: No, Deletion: No (prostate_43620)

description: no additional


title: 80_fraction_2_(4NA80_237370)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)

source_name: Drosophila S2 cells, H2A DNA Nuc


title: Fusion: No, Deletion: No (prostate_43893)

description: no additional


title: Fusion: Yes, Deletion: No (prostate_43877)

description: no additional


title: Fusion: No, Deletion: No (prostate_43455)

description: no additional


title: Fusion: Yes, Deletion: No (prostate_43554)

description: no additional


title: 80_fraction_3_(0AVN_2347448)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: Fusion: No, Deletion: unknown (prostate_43141)

description: no additional


title: Fusion: No, Deletion: No (prostate_43208)

description: no additional


title: cDNA_(TR-33Con_237369)

type: mixed

description: Oligo(dT)-primed cDNA from total RNA/genomic DNA, Genomic vs H33 Total RNA (Cy3/Cy5)

data_processing:
Log base 2 (Cy3/Cy5) ratios were bi-weight mean centered.

The supplementary file 'GSM333845_gene_expr.txt' contains per-gene processed expression data.

source_name: Drosophila S2 cells, Total RNA

extract_protocol: Total RNA was extracted from S2 cells using the Trizol (Invitrogen) method following the manufacturer's instructions. Genomic DNA was isolated from nuclei that were prepared as described (McKittrick et al. 101:1525, 2004). Samples were RNAse-treated, deproteinized with SDS and proteinase K, extracted using a mixture of phenol/chloroform/isoamyl alcohol (25:24:1) followed by chloroform extraction, and DNA was precipitated with 2 vol ethanol.

source_name: Drosophila S2 cells, Genomic DNA


title: 80_fraction_1_(4NV80_237371)

description: 80mM NaCl-extracted chromatin (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_43083)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_43109)

description: no additional


title: 150-600_fraction_(1-AvN0.6_269899)

description: Chromatin from 600mM NaCl extraction of 80mM NaCl extracted pellet, H2AV DNA Input vs H2AV DNA Nuc

source_name: Drosophila S2 cells, H2Av DNA nuc, 150-600mM fraction

source_name: Drosophila S2 cells, H2Av DNA input


title: Fusion: No, Deletion: No (prostate_42770)

description: no additional


title: Fusion: No, Deletion: No (prostate_43067)

description: no additional


title: Fusion: No, Deletion: No (prostate_42978)

description: no additional


title: Fusion: No, Deletion: No (prostate_42895)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_42952)

description: no additional


title: Fusion: No, Deletion: No (prostate_42846)

description: no additional


title: Nucl_dens_2_(9NG_185156-3)

description: Mnase-treated nuclear/genomic DNA (Cy5/Cy3)

source_name: Drosophila S2 cells, H2AV Genomic DNA


title: Fusion: Yes, Deletion: unknown (prostate_42523)

description: no additional


title: 150-600_fraction_3_(116N_237448-1)

description: Chromatin from 600mM NaCl extraction of 150mM NaCl extracted pellet (Cy3/Cy5)

source_name: Drosophila S2 cells, H2AV DNA Nuc


title: 150-600_fraction_2_(96N_138961-3)

source_name: Drosophila S2 cells, H2AV DNA Input


title: Fusion: No, Deletion: No (prostate_42515)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_41970)

description: no additional


title: 150_fraction_2_(9LN_138960-3)

description: 150mM NaCl-extracted chromatin (Cy3/Cy5)


title: Fusion: No, Deletion: unknown (prostate_43315)

description: no additional


title: Fusion: No, Deletion: No (prostate_41459)

description: no additional


title: Fusion: No, Deletion: No (prostate_42556)

description: no additional


title: Mononucleosomes_1_(AvM_238066)

description: Gel-extracted mononucleosomes (Cy3/Cy5)


title: Fusion: No, Deletion: No (prostate_43026)

description: no additional


title: Fusion: No, Deletion: No (prostate_41657)

description: no additional


title: Nucl_dens_3_(11NG_237467-1)


title: Fusion: No, Deletion: No (prostate_40956)

description: no additional


title: Fusion: No, Deletion: No (prostate_33555)

description: no additional


title: Fusion: No, Deletion: No (prostate_41277)

description: no additional


title: Fusion: No, Deletion: No (prostate_40766)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_33571)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_40535)

description: no additional


title: Fusion: No, Deletion: No (prostate_40394)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_41111)

description: no additional


title: Nucl_dens_1_(NG_185167-3)

description: Mnase-treated nuclear/genomic DNA (Cy3/Cy5)


title: 150-600_fraction_1_(Av-N_185168-1)

description: Chromatin from 600mM NaCl extraction of 150mM NaCl extracted pellet  (Cy5/Cy3)


title: Fusion: No, Deletion: No (prostate_33530)

description: no additional


title: Fusion: No, Deletion: No (prostate_33027)

description: no additional


title: Mononucleosomes_2_(33M_236126)

description: Gel-extracted mononucleosomes (Cy3/Cy5)


title: Fusion: Yes, Deletion: No (prostate_32979)

description: no additional


title: Fusion: No, Deletion: No (prostate_31930)

description: no additional


title: Fusion: No, Deletion: No (prostate_32599)

description: no additional


title: Fusion: No, Deletion: No (prostate_32706)

description: no additional


title: Fusion: No, Deletion: No (prostate_32490)

description: no additional


title: Fusion: No, Deletion: No (prostate_30734)

description: no additional


title: Fusion: No, Deletion: No (prostate_32284)

description: no additional


title: Fusion: No, Deletion: No (prostate_31765)

description: no additional


title: Fusion: No, Deletion: No (prostate_30577)

description: no additional


title: 150_fraction_1_(VN_185168-3)


title: Fusion: No, Deletion: No (prostate_31526)

description: no additional


title: H3.3_150_(3L_185168-2)

description: Biotin-H3.3 150mM NaCl-extracted chromatin (Cy3/Cy5)

source_name: Drosophila S2 cells, H3.3 DNA Pull-down, 150mM fraction


title: H3_150-600_(H36_185170-3)

description: Biotin-H3 chromatin from 600mM NaCl extraction of 150mM NaCl extracted pellet (Cy3/Cy5)

source_name: Drosophila S2 cells, H3 DNA Pull-down, 150-600mM salt fraction

source_name: Drosophila S2 cells, H3 DNA Input


title: Fusion: No, Deletion: unknown (prostate_30502)

description: no additional


title: Fusion: No, Deletion: No (prostate_21493)

description: no additional


title: Fusion: No, Deletion: No (prostate_21519)

description: no additional


title: Fusion: No, Deletion: No (prostate_21790)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_31468)

description: no additional


title: Fusion: No, Deletion: No (prostate_21402)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_21451)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_30254)

description: no additional


title: Fusion: No, Deletion: No (prostate_30403)

description: no additional


title: 150_fraction_3_(11LN_237468-1)


title: Fusion: No, Deletion: No (prostate_21246)

description: no additional


title: Fusion: No, Deletion: No (prostate_20834)

description: no additional


title: Fusion: No, Deletion: No (prostate_13227)

description: no additional


title: Fusion: No, Deletion: No (prostate_21220)

description: no additional


title: Fusion: No, Deletion: No (prostate_12971)

description: no additional


title: Fusion: No, Deletion: No (prostate_20099)

description: no additional


title: Fusion: No, Deletion: No (prostate_13011)

description: no additional


title: Fusion: No, Deletion: No (prostate_13482)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_12831)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_12179)

description: no additional


title: Fusion: No, Deletion: No (prostate_21238)

description: no additional


title: Fusion: No, Deletion: No (prostate_12161)

description: no additional


title: Fusion: No, Deletion: No (prostate_11627)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_11460)

description: no additional


title: Fusion: No, Deletion: No (prostate_10884)

description: no additional


title: Fusion: No, Deletion: No (prostate_10348)

description: no additional


title: Fusion: No, Deletion: No (prostate_11981)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_11189)

description: no additional


title: Fusion: No, Deletion: No (prostate_10389)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_2022)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_83)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_1941)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_810)

description: no additional


title: Fusion: unknown, Deletion: unknown (prostate_430)

description: no additional

tag: FUSION:


title: Fusion: unknown, Deletion: unknown (prostate_1164)

description: no additional


title: Fusion: Yes, Deletion: No (prostate_41616)

description: no additional information


title: Fusion: No, Deletion: No (prostate_1552)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_679)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_42754)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_42366)

description: no additional information


title: Fusion: No, Deletion: No (prostate_41541)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_41756)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_760)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_41517)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_42440)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_41558)

description: no additional information


title: Fusion: No, Deletion: No (prostate_2253)

description: no additional


title: Fusion: Yes, Deletion: No (prostate_41236)

description: no additional information


title: Fusion: Yes, Deletion: No (prostate_42325)

description: no additional


title: Fusion: Yes, Deletion: Yes (prostate_10207)

description: no additional


title: Fusion: No, Deletion: unknown (prostate_41053)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_41699)

description: no additional information


title: Fusion: No, Deletion: No (prostate_40782)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_40188)

description: no additional information


title: Fusion: No, Deletion: No (prostate_40774)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_33464)

description: no additional information


title: Fusion: No, Deletion: No (prostate_33134)

description: no additional information


title: Fusion: No, Deletion: No (prostate_40048)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_33357)

description: no additional information


title: Fusion: No, Deletion: No (prostate_41038)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_33175)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_32763)

description: no additional information


title: Fusion: Yes, Deletion: No (prostate_32664)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32771)

description: no additional information


title: Fusion: No, Deletion: No (prostate_33142)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32292)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32888)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_40246)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_32250)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32425)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_32383)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32987)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_32276)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_32235)

description: no additional information


title: Fusion: No, Deletion: No (prostate_31872)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32029)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32060)

description: no additional information


title: Fusion: No, Deletion: No (prostate_31955)

description: no additional information


title: Fusion: No, Deletion: No (prostate_31757)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30726)

description: no additional information


title: Fusion: No, Deletion: No (prostate_31948)

description: no additional information


title: Fusion: Yes, Deletion: unknown (prostate_31799)

description: no additional information


title: Fusion: No, Deletion: No (prostate_32227)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_30544)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30452)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30247)

description: no additional information


title: Fusion: Yes, Deletion: unknown (prostate_30510)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30213)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_30205)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30171)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21774)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_30411)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21436)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21543)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30049)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30130)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21899)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_20271)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21162)

description: no additional information


title: Fusion: Yes, Deletion: No (prostate_20891)

description: no additional information


title: Fusion: No, Deletion: No (prostate_30098)

description: no additional information


title: Fusion: No, Deletion: No (prostate_20180)

description: no additional information


title: Fusion: Yes, Deletion: No (prostate_20206)

description: no additional information


title: Fusion: No, Deletion: No (prostate_20107)

description: no additional information


title: Fusion: No, Deletion: No (prostate_20057)

description: no additional information


title: Fusion: No, Deletion: No (prostate_13334)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_13532)

description: no additional information


title: Fusion: No, Deletion: No (prostate_13193)

description: no additional information


title: Fusion: No, Deletion: No (prostate_13466)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_12898)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_12146)

description: no additional information


title: Fusion: No, Deletion: No (prostate_20248)

description: no additional information


title: Fusion: No, Deletion: No (prostate_12872)

description: no additional information


title: Fusion: Yes, Deletion: unknown (prostate_11999)

description: no additional information


title: Fusion: No, Deletion: No (prostate_12823)

description: no additional information


title: Fusion: No, Deletion: No (prostate_12229)

description: no additional information


title: Fusion: No, Deletion: No (prostate_21808)

description: no additional information


title: Fusion: No, Deletion: No (prostate_11510)

description: no additional information


title: Fusion: No, Deletion: No (prostate_11346)

description: no additional information


title: Fusion: Yes, Deletion: Yes (prostate_10041)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10512)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10447)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10124)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_10132)

description: no additional information


title: Fusion: No, Deletion: No (prostate_1909)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_1453)

description: no additional information


title: Fusion: No, Deletion: No (prostate_1834)

description: no additional information


title: Fusion: No, Deletion: No (prostate_1982)

description: no additional information


title: Fusion: No, Deletion: No (prostate_12278)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10231)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10520)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_11809)

description: no additional information


title: Fusion: No, Deletion: No (prostate_11304)

description: no additional information


title: Fusion: Yes, Deletion: No (prostate_1073)

description: no additional information


title: Fusion: No, Deletion: No (prostate_10488)

description: no additional information


title: Fusion: unknown, Deletion: unknown (prostate_380)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_356)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_2329)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_281)

description: no additional information


title: Fusion: unknown, Deletion: unknown (prostate_1354)

description: no additional information


title: Fusion: No, Deletion: No (prostate_1099)

description: no additional information


title: Fusion: No, Deletion: unknown (prostate_1412)

description: no additional information


title: m_tudCy_head_GL- / m_tudCy_head_GL+

status: Public on May 01 2008

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Expression is assayed in vairous adult tissues with germline ablated directly or genetically.  Additional descriptive information is available at Parisi et.al (2004) Genome Biol. 2004;5(6):R40. PMID: 15186491

hyb_protocol: Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41).

scan_protocol: Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA). Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA).

data_processing: Normalization by within-slide print tip loess, along with subsequent analyses, were performed using the bioconductor package LIMMA 2.12.0 (Smyth et.al, 2004).

label_protocol: Probes were labeled with Cy3 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations (determined by absorbance at 260 nm) ranging from 1 to 5000 ng/ml. A Millennium RNA size ladder (Ambion, Austin, TX) was used to generate standard curves and unknown samples were diluted as necessary. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 200 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using a custom labeling kit (Incyte Genomics). Each reaction contained 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer.

growth_protocol: Flies were grown at 22C on standard cornmeal medium (Tucson, AZ) for 3 to 5 days post eclosion and mated.  Adult flies were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

extract_protocol: Adult flies collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

tag: Genotype = tud[1] bw[1] sp[1]/CyO DTS (mat

value: tud[1] bw[1] sp[1]); Sex = M; Stage = Adult; Tissue = Head

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = M; Stage = Adult; Tissue = Head


title: m_pi2_carc / m_tud_carc_GL+

growth_protocol: Flies were grown at 29C on standard cornmeal medium (Tucson, AZ) until the first instar stage, and then transferred to 22C until 3 to 5 days post eclosion and mated.  Adult flies were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

tag: Genotype = y[1] w[67c]/+ (pat

value: pi[[2]]); Sex = M; Stage = Adult; Tissue = Carcass

tag: Genotype = tud[1] bw[1] sp[1] (mat

value: tud[1] bw[1] sp[1]/CyO); Sex = M; Stage = Adult; Tissue = Carcass


title: f_tud_carc_GL- / f_tud_carc_GL+

value: tud[1] bw[1] sp[1]); Sex = F; Stage = Adult; Tissue = Carcass

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = F; Stage = Adult; Tissue = Carcass


title: m_tud_carc_GL+ / m_tud_carc_GL-

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = M; Stage = Adult; Tissue = Carcass

value: tud[1] bw[1] sp[1]); Sex = M; Stage = Adult; Tissue = Carcass


title: m_gs_carc_GL- / m_gs_carc_GL+

growth_protocol: Flies were grown at 25C for 3 to 5 days post eclosion and mated.  Adult flies were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

tag: Genotype = gs(1)N441 (mat

value: gs(1)N441); Sex = M; Stage = Adult; Tissue = Carcass

value: gs(1)N441/FM7c); Sex = M; Stage = Adult; Tissue = Carcass


title: f_tud_GL- / f_tud_GL+

value: tud[1] bw[1] sp[1]); Sex = F; Stage = Adult; Tissue = Whole Fly

value: tud[1] bw[1] sp[1]/CyO); Sex = F; Stage = Adult; Tissue = Whole Fly


title: f_tud_GL- / f_tud_GL+ (replicate 2)

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = F; Stage = Adult; Tissue = Whole Fly


title: m_tud_GL- / m_tud_GL+

value: tud[1] bw[1] sp[1]); Sex = M; Stage = Adult; Tissue = Whole Fly

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = M; Stage = Adult; Tissue = Whole Fly


title: m_tudCy_head_GL+ / m_tudCy_head_GL-


title: f_gs_carc_GL- / f_gs_carc_GL+

value: gs(1)N441); Sex = F; Stage = Adult; Tissue = Carcass

value: gs(1)N441/FM7c); Sex = F; Stage = Adult; Tissue = Carcass


title: f_tudCy_carc_GL+ / f_pi2_carc

value: pi[[2]]); Sex = F; Stage = Adult; Tissue = Carcass


title: f_tud_carc_GL+ / f_tud_carc_GL-


title: f_tud_GL+ / f_tud_GL-


title: m_gs_carc_GL+ / m_gs_carc_GL-


title: m_tud_head_GL- / m_tud_head_GL- (0139)

value: tud[1] bw[1] sp[1]); Sex = M; Stage = Adult; Tissue = Head


title: m_tud_carc_GL+ / m_pi2_carc

value: pi[[2]]); Sex = M; Stage = Adult; Tissue = Carcass


title: m_tud_head_GL+ / m_tud_head_GL- (0138)

value: tud[1] bw[1] sp[1]/CyO DTS); Sex = M; Stage = Adult; Tissue = Head


title: f_pi2_carc / f_tudCy_carc_GL+


title: f_gs_carc_GL+ / f_gs_carc_GL-


title: KOD1 - WT , sample 1

status: Public on Apr 19 2008

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

description: KOD1 - WT , sample 1

hyb_protocol: Pairs of Cy3- and Cy5-labeled probes were pooled and hybridized to the P. yoelii microarrays for 14 to 16 h at 60°C in a 60-µl mixture.

scan_protocol: slides were scanned using a GenePix 4000A microarray laser scanner (Axon Instruments Inc., Union City, CA), and the fluorescence intensity of each DNA feature was determined at 532 nm (Cy3) and at 635 nm (Cy5).

data_processing: The data was normalized to the global intensity of the microarray.

organism: Plasmodium yoelii

source_name: Plasmodium yoelii YM - HMGB2 KO strain clone D1

label_protocol: To prepare each probe, 10 µg of P. yoelii RNA was reverse transcribed into cDNA in the presence of aminoallyl-dUTP (FairPlay microarray labeling kit; Stratagene, La Jolla, CA). The cDNA was then fluorescently labeled by reaction with monofunctional, normal N-hydroxysuccinimide-activated Cy3 or Cy5 dye (Amersham Biosciences Inc., Piscataway, NJ). The Cy dye-labeled cDNA was purified, and the yield and specific activity of each probe were determined by absorption spectroscopy. Pairs of Cy3- and Cy5-labeled probes were pooled.

growth_protocol: Two mice per group were infected with one million purified schizonts from the WT and two clones (B3 and D1) of the pyhmgb2 KO lines. Parasitemia reached 10 to 20 % and equivalent gametocytemia.

extract_protocol: total RNA was extracted from the WT and the B3 and D1 clones of the KO parasite lines using the Trizol method on saponin lysed of parasites.

tag: cDNA.

source_name: Plasmodium yoelii YM - WT strain


title: KOB3 - WT , sample 3

description: KOB3 - WT , sample 3

source_name: Plasmodium yoelii YM - HMGB2 KO strain clone B3

extract_protocol: Two mice per group were infected with one million purified schizonts from the WT and two clones (B3 and D1) of the pyhmgb2 KO lines. Parasitemia reached 10 to 20 % and equivalent gametocytemia.


title: m_carc / m_carc

growth_protocol: Flies were grown at 25C on standard cornmeal medium (Tucson, AZ) for 3 to 5 days post eclosion and mated.  Adult flies were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

tag: Genotype = y[1] w[67c]; Sex = M; Stage = Adult; Tissue = Carcass


title: m_tud_carc_GL- / m_tud_carc_GL+


title: m_tud_GL+ / m_tud_GL-

growth_protocol: Flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion and mated.  Adult flies were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

value: tud[1] bw[1] sp[1]/CyO); Sex = M; Stage = Adult; Tissue = Whole Fly


title: KOB3 - WT , sample 4

description: KOB3 - WT , sample 4


title: cntrl2 2-16 hours / cntrl1 2-16 hours - 92

status: Public on Jan 28 2008

description: Menin overexpression mutants were generated using transgenic lines bearing the full-length Mnn1 cDNA (Guru et al., 2001) under the control of the yeast GAL4 UAS promoter (Brand and Perrimon, 1993).  The constructs were introduced into flies by P-element mediated transgenesis (Rubin and Spradling, 1982).  Mutants are described in Cerrato et al., Dev Biol. 2006 Oct 1;298(1):59-70.  Control samples are flies that have the same driver, but do not have the without the Mnn1 overexpressing P-element construct.

data_processing: Normalization by within-slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA 2.12.0 (Smyth et.al, 2004).

source_name: cntrl2 2-16 hours

growth_protocol: Flies were grown at 25°C on PB medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion and mated.  Embryos were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

extract_protocol: Embryos collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

tag: control sample, 2-16 hour old embryos

source_name: cntrl1 2-16 hours


title: cntrl2 2-16 hours / mnn++ 2-16 hours - 91

source_name: mnn++ 2-16 hours

tag: mnn overexpression, 2-16 hours old embryos


title: cntrl2 4-6 hours / mnn++ 4-6 hours - 89

source_name: cntrl2 4-6 hours

tag: control sample, 4-6 hour old embryos

source_name: mnn++ 4-6 hours

tag: mnn overexpression, 4-6 hours old embryos


title: KOD1 - WT , sample 2

description: KOD1 - WT , sample 2


title: mnn-affy-10: mnn- Y79_X46 male

description: Sample is from flies homozygous for protein-null Mnn1 alleles and is described in detail in Cerrato et al., Dev Biol. 2006 Oct 1;298(1):59-70.

hyb_protocol: Hybridization was performed by the NIDDK core facility and is described at http://genomics.niddk.nih.gov/

scan_protocol: Scanning was performed by the NIDDK core facility and is described at http://genomics.niddk.nih.gov/

data_processing: CEL files were processed using the Bioconductor Affy package, version 2.12.0 (Bolstad et al., 2003; Irizarry et al., 2003).  The Robust Multichip Average (RMA) function was used to normalize intensities and extract expression value. Specifically, RMA implements a probe specific correction of the PM probes using a model based on observed intensity (the sum of signal and noise), followed by normalization of corrected PM probes using quantile normalization, and finally, calculation of expression measure using a median polish.

label: Biotin

source_name: mnn- Y79_X46 male

label_protocol: Labelling was performed by the NIDDK core facility and is described at http://genomics.niddk.nih.gov/

growth_protocol: Flies were grown at 25°C on PB medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion.  Adults were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).

extract_protocol: Adults were collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).


title: mnn-affy-11: mnn- Y79_Y79 male

source_name: mnn- Y79_Y79 male


title: mnn-affy-9: mnn- X46_Y79 male

source_name: mnn- X46_Y79 male


title: mnn-affy-8: mnn- Y79_X46 female

source_name: mnn- Y79_X46 female


title: cntrl1 2-16 hours / mnn++ 2-16 hours - 87

tag: 2-15 hours post mnn overexpression


title: cntrl1 2-16 hours / cntrl2 2-16 hours - 86


title: cntrl2 2-4 hours / mnn++ 2-4 hours - 90

source_name: cntrl2 2-4 hours

tag: control sample, 2-4 hour old embryos

source_name: mnn++ 2-4 hours

tag: mnn overexpression, control sample, 2-4 hour old embryos


title: mnn-affy-7: mnn- X46_Y79 female

source_name: mnn- X46_Y79 female


title: mnn-affy-4: heterozygote - X113_Y79 female

source_name: heterozygote - X113_Y79 female


title: mnn-affy-5: heterozygote - X84_X46 female

source_name: heterozygote - X84_X46 female


title: mnn-affy-6: control - X113_X84 male

source_name: control - X113_X84 male


title: cntrl1 2-4 hours / mnn++ 2-4 hours - 85

source_name: cntrl1 2-4 hours

tag: mnn overexpression, 2-4 hours old embryos


title: cntrl2 6-8 hours / mnn++ 6-8 hours - 88

source_name: cntrl2 6-8 hours

tag: control sample, 6-8 hour old embryos

source_name: mnn++ 6-8 hours

tag: mnn overexpression in 6-8 hours old embryo


title: mnn-affy-2: wt male

source_name: wt male

tag: y[1]w[67c] adult males


title: mnn-affy-1: wt female

source_name: wt female

tag: y[1]w[67c] adult females


title: mnn++ 2-16 hours / cntrl2 2-16 hours - 80

source_name: mnn++ 2-16 hours

source_name: cntrl2 2-16 hours


title: mnn++ 2-16 hours / cntrl1 2-16 hours - 81

source_name: cntrl1 2-16 hours


title: mnn++ 2-4 hour / cntrl1 2-4 hours - 78

source_name: mnn++ 2-4 hour


title: cntrl1 6-8 hours / mnn++ 6-8 hours - 83

source_name: cntrl1 6-8 hours


title: cntrl1 4-6 hours / mnn++ 4-6 hours - 84

source_name: cntrl1 4-6 hours

source_name: mnn++ 4-6 hours


title: mnn++ 4-6 hours / cntrl2 4-6 hours - 77

source_name: cntrl2 4-6 hours


title: mnn++ 2-4 hour / cntrl2 2-4 hours - 79

source_name: cntrl2 2-4 hours


title: mnn++ 4-6 hours / cntrl1 4-6 hours - 76


title: mnn++ 6-8 hours / cntrl2 6-8 hours - 75

tag: mnn overexpression, 6-8 hours old embryos


title: Single cell profile of retinal progenitor cell F8

status: Public on Dec 31 2007

city: Boston

first: jeffrey

last: trimarchi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle. The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.

label: biotin

organism: Mus musculus

source_name: E12.5 single retinal progenitor cell F8

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: Single retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: cell type

value: retinal progenitor

tag: background strain

tag: developmental stage

value: embryonic day 12.5 (E12.5)


title: mnn++ 6-8 hours / cntrl1 6-8 hours - 74


title: mnn-affy-3: control - X113_X84 female

source_name: control - X113_X84 female


title: Dvir_male_rep2

status: Public on Nov 08 2007

description: Biological replicate 2 of 5.

hyb_protocol: CPK6 50mer fiducial oligo control and hybridization buffer were added, and samples were applied to microarrays enclosed in custome-made chambers at 42C for 16-20 hours. Slides were then washed according to the protocol described by Nimblegen (Madison, WI) and dried by centrifugation.

scan_protocol: Scanned on an Axon GenePix 4000B scanner. Data were extracted from the scanned images using the NimbleScan 2.1 program (NimbleGen Systems, Inc.).

data_processing: VSN normalized.

label: Cy3 or Cy5

molecule: polyA RNA

organism: Drosophila virilis

source_name: Drosophila virilis adult male

label_protocol: 600ng adult fly poly(A)+ RNA was labeled with Cy3 or Cy5 random nonamer primer oligonucleotides (TriLink Biotechnologies, San Diego, CA) by reversed transcription in the presence of SuperScript II Reverse Transcriptase (Invitrogen). The labeled sample was purified with Chroma Spin column TE-10 (Clontech, Mountain View, CA).

extract_protocol: Total RNA was extracted using Trizol procedure, followed by mRNA isolation using an Oligotex mRNA Kit (Qiagen, Valencia, CA).

tag: 5-7 day aged adult flies


title: Dvir_male_rep3

description: Biological replicate 3 of 5.


title: Dvir_male_rep5

description: Biological replicate 5 of 5.


title: Dsim011_female_rep2

description: Biological replicate 2 of 3.

organism: Drosophila simulans

source_name: Drosophila simulans w[501] adult female


title: Dmel_female_rep2

description: Biological replicate 2 of 4.

source_name: Drosophila melanogaster adult female


title: Dsim011_female_rep1

description: Biological replicate 1 of 3.


title: Dsim_female_rep5

description: Biological replicate 5 of 5.

source_name: Drosophila simulans adult female


title: Dvir_female_rep4

description: Biological replicate 4 of 4.

source_name: Drosophila virilis adult female


title: Dsim_female_rep1

description: Biological replicate 1 of 5.


title: Dmel_male_rep1

description: Biological replicate 1 of 4.

source_name: Drosophila melanogaster adult male


title: Dsim011_male_rep2

description: Biological replicate 2 of 2.

source_name: Drosophila simulans w[501] adult male


title: Dmel_female_rep3

description: Biological replicate 3 of 4.


title: Dmel_male_rep4

description: Biological replicate 4 of 4.


title: Dsim_male_rep4

description: Biological replicate 4 of 4.

source_name: Drosophila simulans adult male


title: Dmel_female_rep1

description: Biological replicate 1 of 4.


title: Dmel_male_rep3

description: Biological replicate 3 of 4.


title: Dsim_female_rep4

description: Biological replicate 4 of 5.


title: Dvir_female_rep3

description: Biological replicate 3 of 4.


title: Dsim011_female_rep3

description: Biological replicate 3 of 3.


title: Dvir_male_rep1

description: Biological replicate 1 of 5.


title: Dvir_female_rep2

description: Biological replicate 2 of 4.


title: Dsim_female_rep2

description: Biological replicate 2 of 5.


title: Dyak_male_rep7

description: Biological replicate 7 of 7.

organism: Drosophila yakuba

source_name: Drosophila yakuba adult male


title: Dmel_female_rep4

description: Biological replicate 4 of 4.


title: Dvir_male_rep4

description: Biological replicate 4 of 5.


title: Dsim_male_rep3

description: Biological replicate 3 of 4.


title: Dmel_male_rep2

description: Biological replicate 2 of 4.


title: Dsim_female_rep3

description: Biological replicate 3 of 5.


title: Dsim011_male_rep1

description: Biological replicate 1 of 2.


title: Dyak_male_rep6

description: Biological replicate 6 of 7.


title: Dana_male_rep2

description: Biological replicate 2 of 5.

organism: Drosophila ananassae

source_name: Drosophila ananassae adult male


title: Dyak_male_rep5

description: Biological replicate 5 of 7.


title: Dyak_male_rep4

description: Biological replicate 4 of 7.


title: Dana_male_rep4

description: Biological replicate 4 of 5.


title: Dana_female_rep6

description: Biological replicate 6 of 6.

source_name: Drosophila ananassae adult female


title: Dpse_male_rep4

description: Biological replicate 4 of 5.

organism: Drosophila pseudoobscura

source_name: Drosophila pseudoobscura adult male


title: Dmoj_male_rep3

description: Biological replicate 3 of 4.

organism: Drosophila mojavensis

source_name: Drosophila mojavensis adult male


title: Dyak_male_rep3

description: Biological replicate 3 of 7.


title: Dmoj_female_rep4

description: Biological replicate 4 of 5.

source_name: Drosophila mojavensis adult female


title: Dvir_female_rep1

description: Biological replicate 1 of 4.


title: Dpse_male_rep3

description: Biological replicate 3 of 5.


title: Dpse_female_rep4

description: Biological replicate 4 of 4.

source_name: Drosophila pseudoobscura adult female


title: Dana_male_rep3

description: Biological replicate 3 of 5.


title: Dyak_female_rep5

description: Biological replicate 5 of 5.

source_name: Drosophila yakuba adult female


title: Dsim_male_rep1

description: Biological replicate 1 of 4.


title: Dyak_male_rep2

description: Biological replicate 2 of 7.


title: Dsim_male_rep2

description: Biological replicate 2 of 4.


title: Dyak_male_rep1

description: Biological replicate 1 of 7.


title: Dana_male_rep5

description: Biological replicate 5 of 5.


title: Dmoj_male_rep4

description: Biological replicate 4 of 4.


title: Dmoj_male_rep2

description: Biological replicate 2 of 4.


title: Dana_male_rep1

description: Biological replicate 1 of 5.


title: Dana_female_rep4

description: Biological replicate 4 of 6.


title: Dpse_male_rep5

description: Biological replicate 5 of 5.


title: Dana_female_rep5

description: Biological replicate 5 of 6.


title: Dmoj_male_rep1

description: Biological replicate 1 of 4.


title: Dyak_female_rep4

description: Biological replicate 4 of 5.


title: Dpse_male_rep2

description: Biological replicate 2 of 5.


title: Dpse_male_rep1

description: Biological replicate 1 of 5.


title: Dmoj_female_rep5

description: Biological replicate 5 of 5.


title: Dmoj_female_rep3

description: Biological replicate 3 of 5.


title: Dyak_female_rep2

description: Biological replicate 2 of 5.


title: RH strain, 1meH3K4, replicate 2

status: Public on May 21 2007

description: Toxoplasma gondii RH strain

hyb_protocol: Hybe overnight at 42°C Washes: Submerge entire 12well in a 1L 42°C Wash 1 bath. Pump through ports heated wash 1, disassemble. Move to 50mL tube of Wash 1 + 1 nM Cy3-CPK6 fiducial oligo + 200nM Cy5-CPK6 fiducial oligo and incubate for 2 min. Move to Wash 2 and incubate for 1 min. Move to Wash 3 for 15 sec

scan_protocol: Two-Color Scanning © Copyright NimbleGen Systems, Inc. | 2005 All Rights Reserved Step 1. Array Scanning Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Select the following settings for scanning: · Wavelength (532=Cy3, 635=Cy5) · Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750 · Power % = 100% · Pixel Size=5 m · Lines to average = 1 · Focus position = 0mm · Under Image on the left side of the screen select Ratio to view both channels simultaneously.

data_processing: After background correction, log base 2  ratios of immunoprecipitated DNA signal over input DNA signal is given in this table.  Data not normalized.

organism: Toxoplasma gondii RH

source_name: Toxoplasma gondii RH strain

label_protocol:
1 ug experimental + 1 ug total dried down then add (bring back up in) 1.9 ul H2O
ADD
3.5ul 2x Hybridization Buffer
1.4ul Hybridization component A
0.1 ul 50nM Cy3-CPK6 50mer oligo
0.1ul 150nM Cy5-CPK6 50mer oligo
1.9ul DNA (from above)
7ul
Heat 95°C 5 min, then 45°C 5 min.
Load 6.15ul with pipette.

growth_protocol: Toxoplasma gondii RH strain was maintained in confluent monolayers of human foreskin fibroblasts (HFF). Parasites were harvested 24 hours after invasion of HFF cells and purified.

extract_protocol: Chromatin from intracellular parasites grown in HFF for 24 hours was cross-linked 10 minutes with 1% formaldehyde at room temperature and purified after a sonication step yielding fragments of 500-1000 bp.  Immunoprecipitations were performed with the appropriate rabbit serum.  Crosslinking was reversed and the DNA precipitated over-night. DNA was further subjected to a treatment with proteinase K for 2 hours and then purified using the Qiagen PCR purification kit. Amplification of immunoprecipitated DNA and 100 ng input DNA was performed using the Ligation mediated-PCR technique.

tag: immunoprecipitated DNA with the 1meH3K4 antibody.

extract_protocol: Chromatin from intracellular parasites grown in HFF for 24 hours was cross-linked 10 minutes with 1% formaldehyde at room temperature and purified after a sonication step yielding fragments of 500-1000 bp.Crosslinking was reversed and the DNA precipitated over-night. DNA was further subjected to a treatment with proteinase K for 2 hours and then purified using the Qiagen PCR purification kit. Amplification of immunoprecipitated DNA and 100 ng input DNA was performed using the Ligation mediated-PCR technique.

tag: input


title: RH strain, acH3K9, replicate 2

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the acH3K9 antibody.


title: RH strain, 2meH3R17, replicate 1

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the 2meH3R17 antibody.


title: RH strain, PKA2, replicate 1

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the PKA2 antibody.


title: RH strain, PKA2, replicate 2

description: Toxoplasma gondii RH strain


title: RH strain, acH3K9, replicate 1

description: Toxoplasma gondii RH strain


title: RH strain, 2meH3K4, replicate 2

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the 2meH3K4 antibody.


title: RH strain, acH4 RH, replicate 1

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the acH4 RH antibody.


title: RH strain, cDNA, replicate 1

description: Human HFF cells

hyb_protocol: 1 ug experimental + 1 ug total dried down then add (bring back up in) 1.9 ul H2O ADD 3.5ul 2x Hybridization Buffer 1.4ul Hybridization component A 0.1 ul 50nM Cy3-CPK6 50mer oligo 0.1ul 150nM Cy5-CPK6 50mer oligo 1.9ul DNA (from above) 7ul Heat 95°C 5 min, then 45°C 5 min. Load 6.15ul with pipette. Hybe overnight at 42°C Washes: Submerge entire 12well in a 1L 42°C Wash 1 bath. Pump through ports heated wash 1, disassemble. Move to 50mL tube of Wash 1 + 1 nM Cy3-CPK6 fiducial oligo + 200nM Cy5-CPK6 fiducial oligo and incubate for 2 min. Move to Wash 2 and incubate for 1 min. Move to Wash 3 for 15 sec

scan_protocol: Two-Color Scanning © Copyright NimbleGen Systems, Inc. | 2005 All Rights Reserved Step 1. Array Scanning  Turn on the power of the scanner. The switch is on the back right hand side.  Launch GenePix Software 10 minutes before scanning to allow lasers to warm. ! Select the following settings for scanning: · Wavelength (532=Cy3, 635=Cy5) · Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750 · Power % = 100% · Pixel Size=5 m · Lines to average = 1 · Focus position = 0mm · Under Image on the left side of the screen select Ratio to view both channels simultaneously.

data_processing: After background correction, log base 2 ratios of CH1 over CH2 signal is given in this table.  Data normalized using random probes on the microarray.  The figures in the accompanying paper come from these data tables without any other normalization.

label_protocol: Ten micrograms of total RNA was retrotranscribed using the BD Sprint Powerscript kit with random hexamers as primers. The cDNA was further subjected to a double strand reaction using E. coli polymerase I. The double stranded cDNA (dscDNA) was labeled using random hexamer coupled to a fluorochrome using Nimblegen protocols.

extract_protocol: RNA was purified using Trizol and its integrity was verified on the Agilent Bioanalyzer.

tag: dscDNA.

source_name: HFF cells (control)


title: Dyak_female_rep3

description: Biological replicate 3 of 5.


title: RH strain, 2meH3R17, replicate 2

description: Toxoplasma gondii RH strain


title: RH strain, 3meH3K4 RH, replicate 1

description: Toxoplasma gondii RH strain

tag: immunoprecipitated DNA with the 3meH3K4 RH antibody.


title: Dana_female_rep3

description: Biological replicate 3 of 6.


title: Dmoj_female_rep1

description: Biological replicate 1 of 5.


title: RH strain, 2meH3K4, replicate 1

description: Toxoplasma gondii RH strain


title: RH strain, 1meH3K4, replicate 1

description: Toxoplasma gondii RH strain


title: RH strain, cDNA, replicate 3

description: Human HFF cells

data_processing: After background correction, log base 2 ratios of CH1 over CH2 signal is given in this table. Data normalized using random probes on the microarray.  The figures in the accompanying paper come from these data tables without any other normalization.

label_protocol: . Ten micrograms of total RNA was retrotranscribed using the BD Sprint Powerscript kit with random hexamers as primers. The cDNA was further subjected to a double strand reaction using E. coli polymerase I. The double stranded cDNA (dscDNA) was labeled using random hexamer coupled to a fluorochrome using Nimblegen protocols.


title: Dpse_female_rep1

description: Biological replicate 1 of 4.


title: RH strain, acH4 RH, replicate 2

description: Toxoplasma gondii RH strain


title: RH strain, cDNA, replicate 2

description: Human HFF cells

extract_protocol: RNA was purified using Trizol and its integrity was verified on the Agilent Bioanalyzer


title: Dana_female_rep1

description: Biological replicate 1 of 6.


title: Dmoj_female_rep2

description: Biological replicate 2 of 5.


title: Dpse_female_rep3

description: Biological replicate 3 of 4.


title: RV64.09_CHF_day25_Slide40

status: Public on Feb 01 2006

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: day 25 post 80mg monocrotaline/kg bw injection

data_processing: standardized ratio between standardized sample intrensity vs. Reference pool intensity

organism: Rattus norvegicus

extract_protocol: Polytron - TriZol

tag: Strain

value: Wistar, Sex:male

source_name: Reference pool

tag: pooled total RNA from interventricular septum tissue


title: RV64.02_CONTROL_day25_Slide41

description: day 25 post saline injection/control


title: RV64.04_CONTROL_day25_Slide50

description: day 25 post saline injection/control


title: RV64.06_HYP_day25_Slide48

description: day 25 post 30mg monocrotaline/kg bw injection


title: RV64.03_CONTROL_day25_Slide51

description: day 25 post saline injection/control


title: RV64.05_HYP_day25_Slide49


title: RV64.10_CHF_day25_Slide47


title: RV64.08_HYP_day25_Slide42


title: RV63.10_CHF_day19_Slide44

description: day 19 post 80mg monocrotaline/kg bw injection


title: RV63.06_HYP_day19_Slide36

description: day 19 post 30mg monocrotaline/kg bw injection


title: RV63.04_CONTROL_day19_Slide35

description: day 19 post saline injection/control


title: RV64.11_CHF_day25_Slide46


title: RV63.08_HYP_day19_Slide39


title: RV63.07_HYP_day19_Slide37


title: RV63.03_CONTROL_day19_Slide34

description: day 19 post saline injection/control


title: RV63.09_CHF_day19_Slide45


title: Dyak_female_rep1

description: Biological replicate 1 of 5.


title: Dpse_female_rep2

description: Biological replicate 2 of 4.


title: RV63.01_CONTROL_day19_Slide33

description: day 19 post saline injection/control


title: RV63.12_CHF_day19_Slide43


title: Dana_female_rep2

description: Biological replicate 2 of 6.


title: RH strain, 3meH3K4 RH, replicate 2

description: Toxoplasma gondii RH strain


title: RV83.09_CHF_day10_Slide76

description: day 10 post 80mg monocrotaline/kg bw injection


title: RV83.10_CHF_day10_Slide60


title: RV83.06_HYP_day10_Slide55

description: day 10 post 30mg monocrotaline/kg bw injection


title: RV82.09_CHF_day10_Slide58


title: RV82.03_CONTROL_day10_Slide54

description: day 10 post saline injection/control


title: RV83.02_CONTROL_day10_Slide52

description: day 10 post saline injection/control


title: RV83.05_HYP_day10_Slide57


title: RV82.01_CONTROL_day10_Slide53

description: day 10 post saline injection/control


title: (XX;AA) Sxl ovarian tumors / (X;AA) testis - 227

status: Public on Dec 15 2005

description: Whole adult Drosophila melanogaster y  Sxl[fs3]/y cm Sxl[7BO] and y[1] w[67c] male flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris�HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 �g Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).

source_name: (XX;AA) Sxl ovarian tumor

source_name: (XX;AA) y[1] w[67c] testis


title: (XX;AA) Sxl ovarian tumors / (XX;AA) ovary - 226

description: Whole adult Drosophila melanogaster y  Sxl[fs3]/y cm Sxl[7BO] and y[1] w[67c] female  flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).

source_name: (XX;AA) y[1] w[67c] ovary


title: (XX;AA) otu ovarian tumor / (XX;AA) Sxl ovarian tumors - 211

description: Whole adult Drosophila melanogaster ct otu[1] v[24]/y w otu[17] and y Sxl[fs3]/y cm Sxl[7BO] flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).

source_name: (XX;AA) otu ovarian tumor


title: (XX;AA) Sxl ovarian tumors / (XX;AA) otu ovarian tumor - 215

description: Whole adult Drosophila melanogaster y Sxl[fs3]/y cm Sxl[7BO] and ct otu[1] v[24]/y w otu[17] flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).


title: (XX;AA) Sxl ovarian tumors / (XX;AA) ovary - 218

description: Whole adult Drosophila melanogaster y Sxl[fs3]/y cm Sxl[7BO] and y[1] w[67c] female  flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).


title: (X;AA) hs-tra ovarian tumors / (XX;AA) testis - 233

description: Whole adult Drosophila melanogaster w/BsY; P{w+ hs-tra[83]}/+ and y[1] w[67c] male flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors and wild type testis were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).

source_name: (X;AA) hs-tra ovarian tumor


title: Df(2L)JH/+ ovaries / Dp(2;2)Cam3/+ ovaries - 300

description: Whole adult Drosophila melanogaster Df(2L)JH/+ and Dp(2;2)Cam3/+ female flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovaries were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using riboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations  determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase  (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41).

data_processing: Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004).

source_name: Df(2L)JH/+ ovaries

tag: Df(2L)JH/+ ovaries

source_name: Dp(2;2)Cam3/+ ovaries

tag: Dp(2;2)Cam3/+ ovaries


title: (XX;AA) otu ovarian tumors / (XX;AA) Sxl ovarian tumor - 216