title: 56272_BXC CHR4 H3_1/Input_1

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: This study analyzed the BXC region of 3R and chr 4. Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen . 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 . 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 (56272_635/56272_532) ratios were bi-weight mean centered

source_name: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells

label_protocol: Sample labeling protocol provided and performed by NimbleGen . Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: (Pull-down) Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.

source_name: Input DNA

label_protocol: Sample labeling protocol provided and performed by NimbleGen . Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: (Input) Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.

tag: Input DNA


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 9 ENC1587

status: Public on Mar 01 2007

type: genomic

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

country: USA

institute: Ludwig Institute for Cancer Research

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

data_processing: raw data

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: NimbleGen

source_name: Input DNA from HeLa cells

tag: Input DNA from HeLa cells


title: HSC3 cell line

type: RNA

city: Chiba

first: Satoya

last: Shimizu

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba university

description: HSC3 cell line

hyb_protocol: Hybridized for 20 h at 50 C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitach Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).

data_processing: This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. Data from each microarray were normalized by LOWESS normalization.

molecule: total RNA

source_name: Human Universal Reference Total RNA

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™  aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

extract_protocol: purchased total RNA

tag: Human Universal Reference Total RNA (Clontech, Mountain View, CA)

source_name: HSC3 cell line

growth_protocol: HSC3 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

extract_protocol: TriZol procedure

tag: HSC3 cell line is derived from oral squamous cell carcinoma.


title: 58788_BXC CHR4 H33FL_1/INPUT_2

data_processing: Log base 2 (58788_635/58788_532) ratios were bi-weight mean centered

organism: Drosophila melanogaster

source_name: Chromatin affinity-purified DNA with tagged histone H3.3 region from Drosophila S2 cells

extract_protocol: (Pull-down) Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3 or Cy5 and hybridization to oligonucleotide arrays.

extract_protocol: (Input) Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3 or Cy5 and hybridization to oligonucleotide arrays.


title: H3K4me1 IMR90 RenLab ENCODE PCR tiling array replicate 1 ENC1631

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me1 antibody

source_name: Input DNA from IMR90 cells

tag: Input DNA from IMR90 cells


title: TAFII p250 (6B3) Tonsil RenLab ENCODE PCR tiling array replicate 3 ENC1580

source_name: Chromatin immunoprecipitated DNA from Tonsil cells using TAFII p250 (6B3) antibody

source_name: Input DNA from Tonsil cells

tag: Input DNA from Tonsil cells


title: D562 cell line

description: D562 cell line

source_name: D562 cell line

growth_protocol: D562 cell line was maintained in RPMI1640.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: Detroit562 (D562) cell line is derived from pharyngeal squamous cell carcinoma.


title: H4K20me1 HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1576

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me1 antibody


title: H4K20me2 HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1577

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me2 antibody


title: FaDu cell line

description: FaDu cell line

source_name: FaDu cell line

growth_protocol: FaDu cell line was maintained in RPMI1640.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: FaDu cell line is derived from pharyngeal squamous cell carcinoma.


title: 78832_BXC Nucleosomal/Genomic

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.c om/products/chip/index.html). Axon Scanner (model 4000B). Turn on the power of t he scanner. The switch is on the back right hand side. Launch GenePix Software 1 0 minutes before scanning to allow lasers to warm. Open the scanner door and ope n the side carriage. Place chip in carriage so that array is face down and barco de 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 th e 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. Op en 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 Gai n to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0microme ter. 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 vi ew 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 Tool s on the left side of the screen, click the Scan Area icon. Click and drag to de fine a box that bounds the visibile array area. The box dimensions should be str etched 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, ad just the PMT setting as appropriate. The features should be mostly yellow. If yo ur 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 t he 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 che ck global intensity of the features. On the top left side of the screen make sur e you have the 532 and 635 wavelength boxes checked so both wavelength histogram s are displayed. Make sure the Log Axis box is checked. You want the red and gre en curves to be as close as possible to one another. If the red curve is above t he 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 t he two curves on top of each other is more important than hitting the 1% saturat ion mark.  The histogram only graphs the area of the image that is viewable in t he screen on the image tab. If the histogram is no longer changing then either t he chip is done scanning or the area that you can see on the image screen has be en 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 6 35nm images as separate single image tif files.

source_name: genomic DNA

extract_protocol: Genomic DNA was purified from nuclei and fragmented by MNase digestion to an average size of 500-1000 bp.

tag: genomic DNA

source_name: nucleosomal DNA

extract_protocol: Nuclei were prepared from Drosophila S2 cells as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Nucleosomal DNA was purified for microarray analysis using a standard protocol (RNase and ProteinaseK treatment, Phenol/Chloroform and Chloroform extraction followed by ethanol precipitation) and provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.

tag: nucleosomal DNA


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 16 ENC1566

tag: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody


title: HSC2 cell line

description: HSC2 cell line

source_name: HSC2 cell line

growth_protocol: HSC2 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: HSC2 cell line is derived from oral squamous cell carcinoma.


title: Sa3 cell line

description: Sa3 cell line

source_name: Sa3 cell line

growth_protocol: Sa3 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: Sa3 cell line is derived from oral squamous cell carcinoma.


title: H1 cell line

description: H1 cell line

source_name: H1 cell line

growth_protocol: H1 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: H1 cell line is derived from oral squamous cell carcinoma.


title: HO1N1 cell line

description: H1 cell line

source_name: HO1N1 cell line

growth_protocol: HO1N1 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: HO1N1 cell line is derived from oral squamous cell carcinoma.


title: Ca9-22 cell line

description: Ca9-22 cell line

source_name: Human Universal Reference Total RNA

source_name: Ca9-22 cell line

growth_protocol: Ca9-22 cell line was maintained in DMEM/F12.  It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.

tag: Ca9-22 cell line is derived from oral squamous cell carcinoma.


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 8 ENC1562

source_name: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody

source_name: Input DNA from HeLa cells


title: TAFII p250 (6B3) Tonsil RenLab ENCODE PCR tiling array replicate 2 ENC1561

tag: Chromatin immunoprecipitated DNA from Tonsil cells using TAFII p250 (6B3) antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 7 ENC1557


title: TAFII p250 (6B3) Tonsil RenLab ENCODE PCR tiling array replicate 1 ENC1545


title: HepG2_Phenol rep3

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

institute: Hokkaido University

description: Gene expression data from Phenol treated Hep G2 cells

hyb_protocol: Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).

label: biotin

source_name: Hep G2 treated with Phenol

label_protocol: Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter.  cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).

growth_protocol: Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.

extract_protocol: The cells were were washed with phosphate buffered saline (PBS) and  lysed directly on culture dishes.  Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 mM Phenol for 6h at 37 °C.

tag: Cell bank no

tag: Cell name

value: Hep G2

tag: Sex

value: male

tag: Age of sampling

value: 15 years

tag: Tissue derived

value: liver

tag: Case history

value: hepatocyte carcinoma

tag: Life span

value: infinite

tag: Classification

value: Transformed


title: HepG2_Phenol rep2


title: HepG2_DMN rep3

description: Gene expression data from DMN treated Hep G2 cells

source_name: Hep G2 treated with N-Nitrosodimethylamine

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 5.4 mM N-Nitrosodimethylamine for 48h at 37 °C.


title: HepG2_Phenol rep1


title: 87139_BXC Nucleosomal/Genomic

description: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

tag: genomic DNA


title: HepG2_DMN rep2


title: HepG2_DMNQ rep2

description: Gene expression data from DMNQ treated Hep G2 cells

source_name: Hep G2 treated with 2,3-Dimethoxy-1,4-naphthoquinone

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM  2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.


title: HepG2_DMN rep1


title: HepG2_DMNQ rep3

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1377

tag: Input DNA from HeLa cells


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 6 ENC1504

tag: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody


title: H4K20me3 HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1444

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me3 antibody


title: H3K27Ac HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1427

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27Ac antibody


title: HepG2_DMNQ rep1


title: H2A.Z HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1217

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H2A.Z antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1378


title: H4K20me1 HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1442

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me1 antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 5 ENC1417


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 4 ENC1379


title: 82589_BXC Nucleosomal/Genomic

description: This study analyzed the BXC region of 3R and the distal region of 2L. Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

source_name: genomic DNA

tag: nucleosomal DNA


title: H2A.Z HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1429

tag: Chromatin immunoprecipitated DNA from HeLa cells using H2A.Z antibody


title: p300(C-20) IMR90 RenLab ENCODE PCR tiling array replicate 3 slide ENC1681p300

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using p300(C-20) antibody

source_name: Input DNA from IMR90 cells

tag: Input DNA from IMR90 cells


title: H3K18Ac HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1350

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K18Ac antibody


title: H4K20me2 HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1443

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me2 antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1345


title: H3K4me1 IMR90 RenLab ENCODE PCR tiling array replicate 3 slide ENC1681H3K4me1

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me1 antibody


title: HepG2_Cr rep3

description: Gene expression data from Cr treated Hep G2 cells

scan_protocol: Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).

source_name: Hep G2 treated with Potassium dichromate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Potassium dichromate for 6h at  37 °C.


title: HepG2_Hg rep2

description: Gene expression data from Hg treated Hep G2 cells

source_name: Hep G2 treated with Mercury (II) chloride

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Mercury (II) chloride for 6h at  37 °C.


title: HepG2_Sb rep3

description: Gene expression data from Sb treated Hep G2 cells

source_name: Hep G2 treated with Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 200 uM Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate for 6h at  37 °C.


title: HepG2_Cr rep1


title: HepG2_Sb rep2


title: HepG2_Hg rep3


title: HepG2_Ni rep3

description: Gene expression data from Ni treated Hep G2 cells

source_name: Hep G2 treated with Nickel (II) chloride hexahydrate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6.5 mM Nickel (II) chloride hexahydrate for 6h at  37 °C.


title: HepG2_Sb rep1


title: HepG2_Ni rep2

hyb_protocol: Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten †g of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).


title: HepG2_Hg rep1


title: HepG2_Ni rep1


title: HepG2_Cd rep2

description: Gene expression data from Cd treated Hep G2 cells

source_name: Hep G2 treated with Cadmium chloride 2.5-hydrate

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM Cadmium chloride 2.5-hydrate for 6h at  37 °C.


title: 58588_BXC H3_1/Input_1

data_processing: Log base 2 (58588_635/58588_532) ratios were bi-weight mean centered

source_name: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells

source_name: Input DNA

tag: Input DNA


title: HepG2_As rep2

description: Gene expression data from As treated Hep G2 cells

source_name: Hep G2 treated with Arsenic (III) oxide

treatment_protocol: Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Arsenic (III) oxide for 6h at  37 °C


title: HepG2_As rep3


title: 58888_BXC H33FL_1/INPUT_2

data_processing: Log base 2 (58888_635/58888_532) ratios were bi-weight mean centered

source_name: Chromatin affinity-purified DNA with tagged histone H3.3 region from Drosophila S2 cells

label_protocol: (Pull-down) Sample labeling protocol provided and performed by NimbleGen . Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.


title: HepG2_Cd rep1


title: HepG2_Cd rep3


title: HepG2_control rep2

description: Gene expression data from untreated Hep G2 cells

source_name: human hepatoma cell line, Hep G2


title: HepG2_control rep3

hyb_protocol: Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 ¡C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 ¡C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

growth_protocol: Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 ¡C and 5% CO2.


title: HepG2_As rep1


title: HepG2_control rep1


title: 2 hrs Pre-clamp sample 6

city: Malmö

first: Hemang

last: Parikh

address: Building 91, Plan 12, CRC, Entrance 72, Malmö University Hospital

department: Department of Clinical Sciences-Diabetes and Endocrinology

country: Sweden

institute: Lund University

description: Skeletal muscle biopsy was obtained before a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data was normalized via means scaling

source_name: Skeletal muscle biopsy

label_protocol: standard Affymetrix procedures

extract_protocol: Muscle biopsy was extracted by guadinium thiocyanate method

tag: Muscle biopsy was obtained from the vastus lateralis muscle


title: 2 hrs Pre-clamp sample 3


title: 2 hrs Post-clamp sample 4

description: Skeletal muscle biopsy was obtained after a two-hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp


title: 2 hrs Post-clamp sample 6


title: no3AT2_GluSS_3

city: Haifa

first: Shay

last: Stern

address: Haifa

department: Chemical Engineering, Physics

country: Israel

institute: Technion- Israel Institute of Technology

hyb_protocol: refer to www.microarray.ca

scan_protocol: genepix scanner

data_processing: spots filter: R2>0.6, FG-BG>300, size>55 Dia>50, num of replicates>1, slide normalization: ratio based normalization

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: no3AT2 chemostat, Glucose steady-state 3

label_protocol: refer to www.microarray.ca

extract_protocol: Hot phenol extraction

source_name: reference sample, Galactose +Glucose pool


title: HeLa cells control 3 (Luciferase siRNA transfection)

city: Heidelberg

first: Marcelo

last: Viegas

address: IM NEUENHEIMER FELD 156

country: Germany

institute: EMBL-MMPU

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the third control (luciferase siRNA transfection).

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Oligonucleotide arrays were scanned using a confocal laser scanner (GeneArrayTM, Hewlett Packard, Palo Alto, CA).

data_processing: We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each of the 22,283 probe sets on the U133A oligonucleotide arrays.

molecule: cytoplasmic RNA

source_name: HeLa cells, 72 hs after transfection

label_protocol: Standard Affymetrix protocol

extract_protocol: protocol used in (Gehring et al., Mol.Cell, 2003); PMID: 12718880

tag: HeLa cells

tag: (cervical cancer cells)


title: 2 hrs Pre-clamp sample 5


title: no3AT2_GluSS_2

source_name: no3AT2 chemostat, Glucose steady-state 2

source_name: reference sample. Galactose+Glucose pool


title: no3AT2_Glu_328h

source_name: no3AT2 chemostat, Glucose, time=328h

tag: no3AT2 chemostat, Glucose, time=328h

source_name: reference sample, Galactose+Glucose pool


title: HeLa cells control 2 (Luciferase siRNA transfection)

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the second control (luciferase siRNA transfection).


title: 2 hrs Pre-clamp sample 2


title: 2 hrs Pre-clamp sample 1


title: HeLa cells transfected with UPF1 siRNA 2 (experiment)

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the second experiment (UPF1 siRNA transfection).


title: 2 hrs Post-clamp sample 2


title: 2 hrs Post-clamp sample 5


title: 2 hrs Post-clamp sample 3


title: HeLa cells transfected with UPF1 siRNA 1 (experiment)

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the first experiment (UPF1 siRNA transfection).


title: HeLa cells transfected with UPF1 siRNA 3 (experiment)

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the third experiment (UPF1 siRNA transfection).


title: no3AT2_GluSS_1

source_name: no3AT2 chemostat, Glucose steady-state 1

tag: reference sample, Galactose+Glucose pool


title: no3AT2_GalSS

source_name: no3AT2 chemostat, Galactose steady-state

source_name: Reference sample, Glucose+Galactose pool


title: 40mM_Glu_850h

description: non

data_processing: spots filter: R2>0.6, FG-BG>300, size>55 Dia, num of replicates>1, slide normalization: ratio based normalization

source_name: 40mM 3AT chemostat, Glucose, time=850h

tag: 40mM 3AT chemostat, Glucose, time=850h

tag: Reference sample, Glucose+Galactose pool


title: no3AT2_Glu_315h

source_name: no3AT2 chemostat, Glucose, time=315h

tag: no3AT2 chemostat, Glucose, time=315h


title: 40mM_Glu_574h

description: non

source_name: 40mM 3AT chemostat, Glucose, time=574h

tag: 40mM 3AT chemostat, Glucose, time=574h


title: 40mM_Glu_937h

description: non

source_name: 40mM 3AT chemostat, Glucose setady-state, time=937h


title: 40mM_Gal_477h

description: non

source_name: 40mM 3AT chemostat, Galactose steady-state, time=477h


title: 40mM_Gal_522h

description: non

source_name: 40mM 3AT chemostat, Galactose steady-state, time=522h


title: no3AT_Glu_526h

description: non

source_name: no3AT chemostat, Glucose steady-state, time=526h


title: 40mM_Glu_552h

description: non

source_name: 40mM 3AT chemostat, Glucose, time=552h

tag: 40mM 3AT chemostat, Glucose, time=552h


title: 2 hrs Post-clamp sample 1

source_name: Skeletal muscle biopsy


title: no3AT_Glu_507h

description: non

source_name: no3AT chemostat, Glucose steady-state, time=507h


title: no3AT_Gal_316h

description: non

source_name: no3AT chemostat, Galactose steady-state, time=316h


title: no3AT_Glu_385h

description: non

source_name: no3AT chemostat, Glucose, time=385h

tag: no3AT chemostat, Glucose, time=385h


title: 40mM_Glu_592h

description: non

source_name: 40mM 3AT chemostat, Glucose, time=592h

tag: 40mM 3AT chemostat, Glucose, time=592h


title: 40mM_Glu_878h

description: non

source_name: 40mM 3AT chemostat, Glucose, time=878h

tag: 40mM 3AT chemostat, Glucose, time=878h


title: 2 hrs Pre-clamp sample 4


title: no3AT_Gal_305h

description: non

data_processing: spots filter: R2>0.6, FG-BG>300, size>55Dia ,num of replicates>1, slide normalization: ratio based normalization

source_name: no3AT chemostat, Galactose steady state, time=305h


title: no3AT_Glu_353h

description: non

source_name: no3AT chemostat, Glucose, time=353h

tag: no3AT chemostat, Glucose, time=353h


title: no3AT_Glu_344h

description: non

source_name: no3AT chemostat, Glucose, time=344h

tag: no3AT chemostat, Glucose, time=344h

source_name: Reference sample, Glucose+Galactose pool


title: no3AT_Glu_478h

description: non

source_name: no3AT chemostat, Glucose, time=478h

tag: no3AT chemostat, Glucose, time=478h


title: AML genome hybridization-ID73-L

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

description: Leukemic fractions of ID73 AML patient have been hybridized.

hyb_protocol: 100 ug of genomic DNA were hybridized for 16 hr at 48C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The mean value for all probe sets was set to be 500.

label_protocol: Biotinylated genomic DNA were prepared according to the Affymetrix GeneChip Mapping 100K Assay protocol from 100 ug genomic DNA (GeneChip Mapping 100K Assay Manual, 2004, Affymetrix).

extract_protocol: Genomic DNA was extracted by QIAamp DNA Mini Kit (Qiagen, Inc).

tag: Leukemic fractions of ID73 AML patient


title: A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep3

city: Boston

first: Kimberly

last: Stegmaier

state: MA

address: 44 Binney Street

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston, Harvard Medical School

description: Gene expression data from A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50).

hyb_protocol: 3.5 ug of cRNA was hybridized to Affymetrix 96-well Gene Chip HT human array with standard hybridization, blocking, washing, and staining per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

scan_protocol: Scanned per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings.  The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.

source_name: A673 cell line, a human EWS/FLI translocated Ewing sarcoma cell line.

label_protocol: Two micrograms of RNA was used for target preparation as per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

growth_protocol: The Ewing sarcoma cell line A673 was grown in Dulbecco's Modified Eagle Media (DMEM) (Cellgro) with 10% Fetal calf serum (FCS) (Sigma Aldrich) and 2 mM sodium pyruvate (Cellgro) at 37C with 5% CO2.

extract_protocol: RNA was extracted with Trizol per the manufacturer's protocol (Invitrogen) and prepared for hybridization to Affymetrix high-throughput arrays.


title: AML genome hybridization-ID73-C

description: Control fractions of ID73 AML patient have been hybridized.

tag: Control fractions of ID73 AML patient


title: A673 treated with Puromycin for 5 days with concentration of 0.18 uM (2 x EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.18 uM (2 x EC50).


title: A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50).


title: AML genome hybridization-ID72-L

description: Leukemic fractions of ID72 AML patient have been hybridized.

tag: Leukemic fractions of ID72 AML patient


title: A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep2

tag: A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50).


title: A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep1


title: HepG2_Cr rep2

description: Gene expression data from Cr treated Hep G2 cells

source_name: Hep G2 treated with Potassium dichromate

tag: Cell bank no

tag: Cell name

tag: Sex

tag: Age of sampling

tag: Tissue derived

tag: Case history

tag: Life span

tag: Classification


title: A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep2

tag: A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50).


title: AML genome hybridization-ID72-C

description: Control fractions of ID72 AML patient have been hybridized.

tag: Control fractions of ID72 AML patient


title: A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep1


title: AML genome hybridization-ID70-L

description: Leukemic fractions of ID70 AML patient have been hybridized.

tag: Leukemic fractions of ID70 AML patient


title: A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep2

description: Gene expression data from A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.09 uM (EC50).


title: A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep3

tag: A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.09 uM (EC50).


title: AML genome hybridization-ID70-C

description: Control fractions of ID70 AML patient have been hybridized.

tag: Control fractions of ID70 AML patient


title: AML genome hybridization-ID60-L

description: Leukemic fractions of ID60 AML patient have been hybridized.

tag: Leukemic fractions of ID60 AML patient


title: A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep2

description: Gene expression data from A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.09 uM (EC50).


title: A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep3

tag: A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.09 uM (EC50).


title: A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50).


title: AML genome hybridization-ID61-C

description: Control fractions of ID61 AML patient have been hybridized.

tag: Control fractions of ID61 AML patient


title: A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep1


title: A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep1


title: AML genome hybridization-ID60-C

description: Control fractions of ID60 AML patient have been hybridized.

tag: Control fractions of ID60 AML patient


title: AML genome hybridization-ID71-L

description: Leukemic fractions of ID71 AML patient have been hybridized.

tag: Leukemic fractions of ID71 AML patient


title: AML genome hybridization-ID61-L

description: Leukemic fractions of ID61 AML patient have been hybridized.

tag: Leukemic fractions of ID61 AML patient


title: AML genome hybridization-ID71-C

description: Control fractions of ID71 AML patient have been hybridized.

tag: Control fractions of ID71 AML patient


title: AML genome hybridization-ID59-C

description: Control fractions of ID59 AML patient have been hybridized.

tag: Control fractions of ID59 AML patient


title: AML genome hybridization-ID59-L

description: Leukemic fractions of ID59 AML patient have been hybridized.

tag: Leukemic fractions of ID59 AML patient


title: A673 treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50), biological rep1

tag: A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep2

tag: A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50).


title: A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50).


title: A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep1


title: A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep1

tag: A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep1

tag: A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50).


title: A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50).


title: A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep1

tag: A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50).


title: A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep2

tag: A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50).


title: A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep2


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep1

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50).


title: A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep1


title: A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep2

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50).


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep1

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50).


title: A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep1

tag: A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50).


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep2

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50).


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep3

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50).


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep2


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep3


title: A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep2


title: A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep3


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep2

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50).


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep3

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50).


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep1


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep3

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50).


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep1

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50).


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep1

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50).


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep2

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50).


title: A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep2


title: A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep3


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep1

description: Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50).


title: A673 treated with DMSO vehicle control for 24 hours, biological rep6

description: Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 24 hours.


title: A673 treated with DMSO vehicle control for 24 hours, biological rep5

tag: A673 cell line that has been treated with DMSO vehicle control for 24 hours.


title: A673 treated with DMSO vehicle control for 3 days, biological rep4

description: Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 3 days.


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep2

tag: A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50).


title: A673 treated with DMSO vehicle control for 5 days, biological rep6

description: Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 5 days.


title: A673 treated with DMSO vehicle control for 3 days, biological rep6

tag: A673 cell line that has been treated with DMSO vehicle control for 3 days.


title: A673 treated with DMSO vehicle control for 5 days, biological rep2

tag: A673 cell line that has been treated with DMSO vehicle control for 5 days.


title: A673 treated with DMSO vehicle control for 5 days, biological rep1


title: A673 treated with DMSO vehicle control for 5 days, biological rep5


title: A673 treated with DMSO vehicle control for 24 hours, biological rep2


title: A673 treated with DMSO vehicle control for 24 hours, biological rep4


title: A673 treated with DMSO vehicle control for 5 days, biological rep4


title: A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep3


title: A673 treated with DMSO vehicle control for 5 days, biological rep3


title: A673 treated with DMSO vehicle control for 3 days, biological rep1


title: A673 treated with DMSO vehicle control for 3 days, biological rep2


title: A673 treated with DMSO vehicle control for 3 days, biological rep5


title: A673 treated with DMSO vehicle control for 24 hours, biological rep3


title: A673 treated with DMSO vehicle control for 24 hours, biological rep1


title: AML genome hybridization ID49-L

description: Leukemic fractions of ID49 AML patient have been hybridized.

tag: Leukemic fractions of ID49 AML patient


title: AML genome hybridization ID48-C

description: Control fractions of ID48 AML patient have been hybridized.

tag: Control fractions of ID48 AML patient


title: AML genome hybridization ID43-C

description: Control fractions of ID43 AML patient have been hybridized.

tag: Control fractions of ID43 AML patient


title: AML genome hybridization ID44-L

description: Leukemic fractions of ID44 AML patient have been hybridized.

tag: Leukemic fractions of ID44 AML patient


title: AML genome hybridization ID36-C

description: Control fractions of ID36 AML patient have been hybridized.

tag: Control fractions of ID36 AML patient


title: AML genome hybridization ID29-L

description: Leukemic fractions of ID29 AML patient have been hybridized.

tag: Leukemic fractions of ID29 AML patient


title: AML genome hybridization ID49-C

description: Control fractions of ID49 AML patient have been hybridized.

tag: Control fractions of ID49 AML patient


title: AML genome hybridization ID47-C

description: Control fractions of ID47 AML patient have been hybridized.

tag: Control fractions of ID47 AML patient


title: AML genome hybridization ID28-C

description: Control fractions of ID28 AML patient have been hybridized.

tag: Control fractions of ID28 AML patient


title: AML genome hybridization ID44-C

description: Control fractions of ID44 AML patient have been hybridized.

tag: Control fractions of ID44 AML patient


title: AML genome hybridization ID32-C

description: Control fractions of ID32 AML patient have been hybridized.

tag: Control fractions of ID32 AML patient


title: AML genome hybridization ID13-L

description: Leukemic fractions of ID13 AML patient have been hybridized.

tag: Leukemic fractions of ID13 AML patient


title: AML genome hybridization ID29-C

description: Control fractions of ID29 AML patient have been hybridized.

tag: Control fractions of ID29 AML patient


title: AML genome hybridization ID48-L

description: Leukemic fractions of ID48 AML patient have been hybridized.

tag: Leukemic fractions of ID48 AML patient


title: AML genome hybridization ID47-L

description: Leukemic fractions of ID47 AML patient have been hybridized.

tag: Leukemic fractions of ID47 AML


title: AML genome hybridization ID10-C

description: Control fractions of ID10 AML patient have been hybridized.

tag: Control fractions of ID10 AML patient


title: AML genome hybridization ID10-L

description: Leukemic fractions of ID10 AML patient have been hybridized.

tag: Leukemic fractions of ID10 AML patient


title: AML genome hybridization ID43-L

description: Leukemic fractions of ID43 AML patient have been hybridized.

tag: Leukemic fractions of ID43 AML patient


title: AML genome hybridization ID09-L

description: Leukemic fractions of ID09 AML patient have been hybridized.

tag: Leukemic fractions of ID09 AML patient


title: AML genome hybridization ID09-C

description: Control fractions of ID09 AML patient have been hybridized.

tag: Control fractions of ID09 AML patient


title: AML genome hybridization ID13-C

description: Control fractions of ID13 AML patient have been hybridized.

tag: Control fractions of ID13 AML patient


title: AML genome hybridization ID28-L

description: Leukemic fractions of ID28 AML patient have been hybridized.

tag: Leukemic fractions of ID28 AML patient


title: AML genome hybridization ID36-L

description: Leukemic fractions of ID36 AML patient have been hybridized.

tag: Leukemic fractions of ID36 AML patient


title: AML genome hybridization ID32-L

description: Leukemic fractions of ID32 AML patient have been hybridized

tag: Leukemic fractions of ID32 AML patient


title: AML genome hybridization ID06-L

description: Leukemic fractions of ID06 AML patient have been hybridized.

tag: Leukemic fractions of ID06 AML patient


title: AML genome hybridization ID07-C

description: Control fractions of ID07 AML patient have been hybridized.

tag: Control fractions of ID07 AML patient


title: AML genome hybridization ID07-L

description: Leukemic fractions of ID07 AML patient have been hybridized.

tag: Leukemic fractions of ID07 AML patient


title: Expression data of  Colorectal Cancer 62

status: Public on Feb 28 2007

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

description: Sporadic Ca

data_processing: Affymetrix Microarray Suite version 5.0

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated nonneoplastic rectal mucosa were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: Tissue

value: Colorecal Cancer


title: AML genome hybridization ID06-C

description: Control fractions of ID06 AML patient have been hybridized

tag: Control fractions of ID06 AML patient


title: Expression data of  Colorectal Cancer 63

description: Sporadic Ca


title: AML genome hybridization ID05-C

description: Control fractions of ID05 AML patient have been hybridized.

tag: Control fractions of ID05 AML patient


title: Expression data of  Colorectal Cancer 68

description: Sporadic Ca


title: AML genome hybridization ID04-L

description: Leukemic fractions of ID04 AML patient have been hybridized.

tag: Leukemic fractions of ID04 AML patient


title: AML genome hybridization ID05-L

description: Leukemic fractions of ID05 AML patient have been hybridized.

tag: Leukemic fractions of ID05 AML patient


title: Expression data of  Colorectal Cancer 66

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 65

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 59

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 60

description: Sporadic Ca


title: AML genome hybridization ID04-C

description: Control fractions of ID04 AML patient have been hybridized.

tag: Control fractions of ID04 AML patient


title: Mouse ileum with L.monocytogenes(delta-inlA)_A_5545

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

hyb_protocol: Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

scan_protocol: Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx

data_processing: MAS5; scaling = 500

organism: Mus musculus

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-inlA)_A_5545

label_protocol: In vitro transcription (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) was performed on cRNA derived from 40ug total RNA followed by standard fragmentation.  For detailed protocol see http://pathimm.wustl.edu/~mgacore/protocols.htm

extract_protocol: RNA was purified from ileum of each mouse [Midi RNeasy kit (Qiagen) with on-column DNase digestion]. Equivalent amounts of RNA from mice in each treatment group (n=4/experiment) were pooled and two biotinylated cRNA targets (40 ug/replicate) were independently prepared from each sample.

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlA)_A_5545


title: Mouse ileum with L.innocua_A_5547

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua_A_5547

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua_A_5547


title: Mouse ileum with L.monocytogenes(delta-inlA)_B_5546

source_name: Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.monocytogenes(delta-inlA)_B_5546

tag: 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J  transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.monocytogenes(delta-inlA)_B_5546


title: Expression data of  Colorectal Cancer 64

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 57

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 61

description: Sporadic Ca


title: control sample, replicate 4

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Control samples: Biological replicate 4 of 4. Technical repeat 1 and 2.

hyb_protocol: The cDNA was applied to the pre-blocked surface (0.1M Tris, 50mM ethanolamine, pH 9.0 at 50ºC for 30 minutes, rinsed 2x with deionized water, then 4 x SSC, 0.1% SDS (pre-warmed to 50ºC) for 30 minutes, thereafter rinsed with deionized water and dried) of the array slide and allowed to hybridize to the oligonucleotides. The hybridization reaction was performed in 25 % formamide, 5×SSC, and 0.1 % SDS at 42°C for 18 h. in an airtight box, with a 6cm diameter petri containing 5mls of water in the base. After hybridization, the arrays were washed ( two washes in 2 x SSC, 0.1% SDS at 42ºC for 5 minutes, one wash in 0.2 x SSC at room temperature for 1 minute and one wash in 0.1 x SSC at room temperature for 1 minute) and dried.

scan_protocol: Slides were scanned using a ScanArray HTII scanner (Perkin Elmer).

data_processing: Normalized data corrected for background intensity using local background correction (“divide by percentile and use all genes”), flagged spots removed, values below 20.0 set to 20.0, base-2.0-Log-Minus-0.0: take difference and combine replicates “combined by mean, use all points"

organism: Caenorhabditis elegans

source_name: C.elegans control exposure replicate 4, technical repeat 1 and 2

label_protocol: To produce fluorescently labeled cDNA, a two-step labeling of the RNA was performed using the Amino Allyl cDNA Labeling Kit (Ambion) and monoreactive succinimide ester (NHS) derivatives of Cy5 (Amersham Biosciences). Reverse Transcription: 20 µg total RNA was reverse transcribed using an anchored oligo d(T) primer, aa-dUTP/dNTP mix and reverse transcriptase at 42C for 90 minutes. The sample was precipitated using sodium acetate / ethanol and resuspend into 10 µl sodium bicarbonate (0.1 M). NHS Cy Dye was added to the cDNA, incubated in dark at room temperature for one hour and quenched using hydroxylamine. following a precipitation, the Cy labelled cDNA were purified via GFX DNA purification columns (Amersham Biosciences). All experimental procedures followed the instructions of the suppliers and essentially as described in the CodeLink activated slide processing protocol.

growth_protocol: A synchronous culture was generated by rinsing freshly hatched nematodes from NGM plates and subsequently filtered through a 10 µm membrane filter (SM 16510/11, Sartorius, Germany), which retains all but first-stage juveniles. Animals were grown at at 20 ºC.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

tag: Age

value: young adult (48 h post staged L1)

value: whole animal

tag: Strain

value: N2 (Bristol)

source_name: C.elegans universal reference for control

treatment_protocol: Maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. The sample is an equi-molar fractional representation of all samples/replications generated equating to 50 % of animals exposed to control conditions and 50 % to PCB52 (5 mg/L).


title: Expression data of  Colorectal Cancer 58

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 67

description: Sporadic Ca


title: PCB52 exposed sample, replicate 3

description: PCB52 exposed samples: Biological replicate 3 of 4. Technical repeat 1 and 2.

source_name: C.elegans PCB52 exposure replicate 3, technical repeat 1 and 2

growth_protocol: A synchronous culture was generated by rinsing freshly hatched nematodes from NGM plates and subsequently filtered through a 10 µm membrane filter (SM 16510/11, Sartorius, Germany), which retains all but first-stage juveniles. Animals were grown at at 20 ºC in the presence of 5 mg/L PCB52.

treatment_protocol: Maintained at 20 ºC on standard nematode growth media (NGM) plates. using Escherichia coli OP50 as food source. NGM and OP50 were supplemented with 5 mg/L PCB52.

tag: The sample is an equi-molar fractional representation of all samples/replications generated equating to 50 % of animals exposed to control conditions and 50 % to PCB52 (5 mg/L)


title: PCB52 exposed sample, replicate 4

description: PCB52 exposed samples: Biological replicate 4 of 4. Technical repeat 1 and 2.

source_name: C.elegans PCB52 exposure replicate 4, technical repeat 1 and 2

growth_protocol: A synchronous culture was generated by rinsing freshly hatched nematodes from NGM plates and subsequently filtered through a 10 µm membrane filter (SM 16510/11, Sartorius, Germany), which retains all but first-stage juveniles.


title: PCB52 exposed sample, replicate 1

description: PCB52 exposed samples: Biological replicate 1 of 4. Technical repeat 1 and 2.

source_name: C.elegans PCB52 exposure replicate 1, technical repeat 1 and 2


title: A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep2

description: Gene expression data from A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50).


title: Histidine perturbation in a histidine-limited chemostat (8.52 hours)

city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

institute: Weizmann Institute of Science

hyb_protocol: cDNA samples were labeled with Cy3 and Cy5 and combined with blockers: 5?g Herring sperm (Promega), 5?g tRNA (Gibco) and 17.5?g Poly A (Poly A oligos were synthesized with mixed length of 40, 50 and 60 Adenine residues). The labeled cDNAs were concentrated to 40?l using Microcon (Millipore) and 40?l of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs were pre-hybridized by incubating at 42C for 45 minutes in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS. The slides were washed in sterile water and dried by centrifugation (3 minutes, 2000 rpm). The labeled samples were boiled for 5 minutes, centrifuged for 1 minute, hybridized on the slide and placed in a hybridization chamber (Corning) for overnight incubation at 42C. The slides were then washed for 5 minutes at 42C with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by three additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet DNA microarray scannerand image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was removed by subtracting the mean array intensity and the ratios of the two dyes were log2-transformed. The two spots corresponding to each gene were then averaged, and genes with low intesity were excluded by manual inspection).

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (8.52 hours)

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse TranscriptaseRNase H Minus (Promega) and labeled by the indirect amino-allyl method.

growth_protocol: Cells were grown in a histidine-limited chemostat (2 mg/l) and reached steady state. Histidine was then inoculated into the chemostat to reach a final concentration of 4 mg/l.

extract_protocol: Cells were collected, pelleted and immediately frozen.Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

value: WT BY4741, haploid

source_name: Batch culture cells grown in a histidine-limited medium to late log phase

growth_protocol: Overnight cells (SD) were washed, transferred to histidine-limited medium (2 mg/l) and grown to late log phase


title: Histidine perturbation in a histidine-limited chemostat (15.08 hours)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (15.08 hours)


title: Histidine perturbation in a histidine-limited chemostat (22.12 hours)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (22.12 hours)


title: Histidine perturbation in a histidine-limited chemostat (11.1 hours)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (11.1 hours)


title: Expression data of  Colorectal Cancer 54

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 51

description: Sporadic Ca


title: control sample, replicate 2

description: Control samples: Biological replicate 2 of 4. Technical repeat 1 and 2.

source_name: C.elegans control exposure replicate 2, technical repeat 1 and 2

treatment_protocol: Maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source.


title: Expression data of  Colorectal Cancer 56

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 53

description: Sporadic Ca


title: Histidine perturbation in a histidine-limited chemostat (5.08 hours)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (5.08 hours)


title: Expression data of  Colorectal Cancer 55

description: Sporadic Ca


title: control sample, replicate 1

description: Control samples: Biological replicate 1 of 4. Technical repeat 1 and 2.

hyb_protocol: The cDNA was applied to the pre-blocked surface  (0.1M Tris, 50mM ethanolamine, pH 9.0 at 50ºC for 30 minutes, rinsed 2x with deionized water, then 4 x SSC, 0.1% SDS (pre-warmed to 50ºC) for 30 minutes, thereafter rinsed with deionized water and dried) of the array slide and allowed to hybridize to the oligonucleotides. The hybridization reaction was performed in 25 % formamide, 5×SSC, and 0.1 % SDS at 42°C for 18 h. in an airtight box, with a 6cm diameter petri containing 5mls of water in the base. After hybridization, the arrays were washed ( two washes in 2 x SSC, 0.1% SDS at 42ºC for 5 minutes, one wash in 0.2 x SSC at room temperature for 1 minute and one wash in 0.1 x SSC at room temperature for 1 minute) and  dried.

source_name: C.elegans control exposure replicate 1, technical repeat 1 and 2


title: Histidine perturbation in a histidine-limited chemostat (-1.52h hours)

source_name: Cells grown in a histidine-limited chemostat 1.52 hours before the histidine perturbation


title: Clotrimazole perturbation in a histidine-limited chemostat (30.8 hours)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (30.8 hours)

growth_protocol: Cells were grown in a histidine-limited chemostat (2 mg/l) and reached steady state. Clotrimazole (10 microM) was dissolved in DMSO and then inoculated into the chemostat


title: Histidine perturbation in a histidine-limited chemostat (1.07 hour)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (1.07 hour)


title: Histidine perturbation in a histidine-limited chemostat (0.17 hours)

source_name: Cells upon histidine perturbation in a histidine-limited chemostat (0.17 hours)


title: Expression data of  Colorectal Cancer 50

description: Sporadic Ca


title: PCB52 exposed sample, replicate 2

description: PCB52 exposed samples: Biological replicate 2 of 4. Technical repeat 1 and 2.

source_name: C.elegans PCB52 exposure replicate 2, technical repeat 1 and 2


title: Expression data of  Colorectal Cancer 47

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 49

description: Sporadic Ca


title: Clotrimazole perturbation in a histidine-limited chemostat (26.45 hours)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (26.45 hours)


title: Expression data of  Colorectal Cancer 52

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 48

description: Sporadic Ca


title: Clotrimazole perturbation in a histidine-limited chemostat (14.18 hours)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (14.18 hours)


title: Clotrimazole perturbation in a histidine-limited chemostat (5.03 hours)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (5.03 hours)


title: Expression data of  Colorectal Cancer 46

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 45

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 44

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 41

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 43

description: Sporadic Ca


title: Clotrimazole perturbation in a histidine-limited chemostat (0.25 hour)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (0.25 hour)


title: Clotrimazole perturbation in a histidine-limited chemostat (9.78 hours)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (9.78 hours)


title: Clotrimazole perturbation in a histidine-limited chemostat (1.2 hour)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (1.2 hour)

source_name: Batch culture cells grown in a histidine-limited medium to late log phase


title: Clotrimazole perturbation in a histidine-limited chemostat (2.87 hour)

source_name: Cells upon clotrimazole perturbation in a histidine-limited chemostat (2.87 hour)


title: Clotrimazole perturbation in a histidine-limited chemostat (-0.48 hours)

source_name: Cells grown in a histidine-limited chemostat 0.48 hours before the NaCl perturbation


title: Expression data of  Colorectal Cancer 42

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 37

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 39

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 40

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 34

description: UC-associated Ca


title: Expression data of  Colorectal Cancer 36

description: Sporadic Ca


scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience)and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed.Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as missing values (along with other genes which were flagged by the image analysis software or removed by manual inspection).

source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (5.28 hours)

growth_protocol: Cells were grown in a histidine-limited chemostat (0.02%) and reached steady state. NaCl (0.31M) was then inoculated into the chemostat

growth_protocol: Overnight cells (SD) were washed, transferred to histidine-limited medium (0.02%) and grown to late log phase


title: Expression data of  Colorectal Cancer 38

description: Sporadic Ca


source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (7.37 hours)


source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (17.15 hours)


title: Clotrimazole perturbation in a histidine-limited chemostat (-1.58 hours)

source_name: Cells grown in a histidine-limited chemostat 1.58 hours before the NaCl perturbation


source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (2.9 hours)


source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (1.82 hours)


title: Expression data of  Colorectal Cancer 33

description: UC-associated Ca


title: NaCl perturbation in a histidine-limited chemostat (-2.03 hours)

source_name: Cells grown in a histidine-limited chemostat 2.03 hours before the NaCl perturbation


source_name: Cells upon NaCl perturbation in a histidine-limited chemostat (0.23 hours)


title: NaCl perturbation in a histidine-limited chemostat (-5.13 hours)

source_name: Cells grown in a histidine-limited chemostat 5.13 hours before the NaCl perturbation


title: Heat shock perturbation in a histidine-limited chemostat (23.62 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (23.62 hours)

growth_protocol: Cells were grown in a histidine-limited chemostat (2 mg/l) and reached steady state at 30 degrees (C). The cells were then subjected to heat shock of 37 degrees for 5 hours

growth_protocol: Overnight cells (SD) were washed, transferred to histidine-limited medium (2 mg/l) and grown to late log phase at 30 degrees (C)


title: control sample, replicate 3

description: Control samples: Biological replicate 3 of 4. Technical repeat 1 and 2.

source_name: C.elegans control exposure replicate 3, technical repeat 1 and 2

source_name: C.elegans universal reference for control


title: Heat shock perturbation in a histidine-limited chemostat (9.2 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (9.2 hours)


title: Heat shock perturbation in a histidine-limited chemostat (15.77 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (15.77 hours)


title: Heat shock perturbation in a histidine-limited chemostat (5.38 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (5.38 hours)

source_name: Batch culture cells grown in a histidine-limited medium to late log phase


title: Heat shock perturbation in a histidine-limited chemostat (2.47 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (2.47 hours)


title: Expression data of  Colorectal Cancer 31

description: UC-associated Ca


title: Expression data of  Colorectal Cancer 35

description: UC-associated Ca


title: Expression data of  Colorectal Cancer 28

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 30

description: UC-associated Ca


title: Heat shock perturbation in a histidine-limited chemostat (-0.28 hours)

source_name: Cells grown in a glucose-limited chemostat 0.28 hours before the heat shock perturbation


title: Heat shock perturbation in a histidine-limited chemostat (0.25 hour)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (0.25 hour)


title: Expression data of  Colorectal Cancer 27

description: Sporadic Ca


title: Heat shock perturbation in a histidine-limited chemostat (0.75 hours)

source_name: Cells upon heat shock perturbation in a histidine-limited chemostat (0.75 hours)


title: Expression data of  Colorectal Cancer 24

description: Sporadic Ca


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (28.62 hours)

growth_protocol: Cells were grown in a histidine-limited chemostat (2 mg/l) and reached steady state. DTT (6mM) was then inoculated into the chemostat


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (19.32 hours)


title: Expression data of  Colorectal Cancer 25

description: Sporadic Ca


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (10.72 hours)


title: Heat shock perturbation in a histidine-limited chemostat (-1.07 hours)

source_name: Cells grown in a glucose-limited chemostat 1.07 hours before the heat shock perturbation


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (6.55 hours)


title: Expression data of  Colorectal Cancer 21

description: Sporadic Ca


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (1 hour)


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (0.25 hours)


title: Expression data of  Colorectal Cancer 19

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 18

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 22

description: Sporadic Ca


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (9.8 hours)

growth_protocol: Cells were grown in a glucose-limited chemostat (0.02%) and reached steady state. Glucose was then inoculated into the chemostat to reach a final concentration of 0.04%.

source_name: Batch culture cells grown in a glucose-limited medium to late log phase

growth_protocol: Overnight cells (SD) were washed, transferred to Glucose-limited medium (0.02%) and grown to late log phase


title: Expression data of  Colorectal Cancer 32

description: UC-associated Ca


title: Expression data of  Colorectal Cancer 29

description: Sporadic Ca


source_name: Cells upon DTT perturbation in a histidine-limited chemostat (3.1 hours)


title: Expression data of  Colorectal Cancer 23

description: Sporadic Ca


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (8.08 hours)


title: Expression data of  Colorectal Cancer 20

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 26

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 15

description: Sporadic Ca


title: Expression data of  Colorectal Cancer 16

description: Sporadic Ca


source_name: Cells upon Glucose perturbation in a glucose-limited chemostat (1.58 hours)