title: Synchronized cells, 130 min, biological replicate F | array yoG_18B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.


title: 48hpi_rep4

status: Public on Oct 04 2008

type: RNA

city: Brisbane

first: Elizabeth

middle: A

last: Williams

state: QLD

address: St Lucia campus

department: School of Integrative Biology

country: Australia

institute: University of Queensland

description: loop design

hyb_protocol: 4X SSC, 40% deionized formamide (Astral Scientific) and 0.1% SDS were added to the probe mix to create the hybridisation buffer. Following incubation at 95ºC for 5 min and 45ºC for 90 min, the labelled probe mix was loaded onto the microarray chip, and placed in a hybridisation chamber (Corning) with 10 μl H2O at each end in a 45 ºC oven for 16 h (as per Woods et al. 2004).

scan_protocol: Following hybridisation, chips were washed once in a 0.2X SSC, 0.05% SDS solution and twice in 0.2X SSC solution, then dried by low speed centrifugation. Washed slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices). Spot intensities from raw scan data were quantified using GenePix Pro 6.0 software (Molecular Devices). Spots were flagged as present or absent based on circularity and diameter (circularity </= 70 and diameter < 100 = absent) or sum of means (Cy5 intensity/Cy3 intensity < 200 = absent).

data_processing: Quantified data was transferred as a one-colour analysis into Genespring version 7.0 (Silicon Genetics). Raw data was normalised per chip to the 50th percentile and per gene to the median, and measurements < 0.01 were set to 0.01. Median polishing was performed per chip and per gene.

molecule: total RNA

organism: Haliotis asinina

source_name: pooled whole postlarvae

label_protocol: 2.5 μg total RNA was used to prepare labelled cDNA for each developmental stage. cDNA was transcribed with an oligo(dT)15 primer using a dNTP mix with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma) and Superscript III Reverse Transcriptase (Invitrogen) according to manufacturers’ instructions. Aminoallyl-labelled cDNA (aa-cDNA) was purified, dried and redissolved in 100 mM sodium carbonate pH 9. Cy3 and Cy5 reactive dyes (Amersham) were added to their respective aa-cDNA samples and the coupling reaction allowed to proceed. After 1 h, 4.5 μl 4 M hydroxylamine was added to remove unincorporated dyes. Cy3- and Cy5-labeled cDNA were combined and purified with a PCR cleanup kit (Qiagen). To prevent non-specific binding, 10 μg human Cot1 DNA (Invitrogen) and 0.125 A260 units poly dA (Roche) were added to the purified probe mix. This solution was dehydrated in a speed-vac to a volume of 8 μl.

growth_protocol: Spawning of adult Haliotis asinina and larval culture were carried out at Heron Island Research Station on the Great Barrier Reef, Australia (23°27’S; 151°55’E) as previously described (Counihan et al. 2001; Jackson et al. 2005). Larval cultures were derived from gametic contributions from at least 3 females and 3 males, and were treated for 2 hours daily with 20 μg/L rifampicin to protect against bacterial invasion. Larvae were allowed to develop to 96 hours post fertilisation (hpf), at which time a subset were introduced into 0.5 L plastic chambers containing ~11.5 cm2 surface area of the encrusting coralline algae, Mastophora pacifica, previously shown to be an effective inducer of Haliotis asinina metamorphosis (Jackson et al. 2005). After 2 h, chambers were supplied with a gentle flow of seawater, such that any larvae not in constant contact with the coralline algae were washed out of the chamber. At 8 h after their introduction, the algal shards were removed from chambers and all attached larvae were washed into fresh 0.5 L plastic chambers using a jet of 0.22 μM filtered seawater (FSW). Once again, chambers were supplied with a gentle flow of seawater so that only larvae exhibiting constant crawling behaviour were maintained. Washed larvae were allowed to develop for a further 48 h, at which point the experiment ended. Throughout the induction experiment, postlarvae were treated with rifampicin as described above. A subset of larvae were maintained in the original culture chambers to act as an non-induced control.

extract_protocol: Abalone larvae were collected for RNA extraction at 66, 78, 90, 108, 120 and 144 hpf. Competent larvae were induced by exposure to coralline algae at 96 hpf (see above) and postlarval samples were collected at 12, 24 and 48 hpi. This meant that postlarvae 12, 24 and 48 hpi were actually the same age as larvae 108, 120 and 144 hpf. Total RNA was extracted using TRIreagent (Sigma) as described by the manufacturer. Quantity and quality of RNA was assessed using UV spectrophotometry (Nanodrop ND-1000) and agarose gel electrophoresis.

tag: SOURCE POP

value: Heron Island

tag: CHIP #

tag: HYB DATE


title: Expt IV, asf1D, 90 min turnover | array na_30_153

type: genomic

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Medical School

description: Strain PKY4214 was cultured in YPA raffinose medium supplemented with 300 ug/ml hygromycin and treated for 3 hrs with alpha factor (5 ?g/ml) to induce G1 arrest. Expression of the plasmid-borne FLAG-tagged H3 was induced for 90 min by the addition of 0.2% galactose.  Cells were then crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3, respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

hyb_protocol: Amplified ChIP and ChIP input were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 (Cy5/Cy3) ratios were calculated to produce the values given in the data table. The Cy5/Cy3 ratio represents the fold enrichment of the IP relative to the input, except in dye-flip samples, where it is the Cy3/Cy5 ratio.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: asf1D, Gal 90', input

label_protocol: The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled DNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

tag: Strain

source_name: asf1D, Gal 90', anti-FLAG IP

extract_protocol: Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.


title: 144hpf_rep2

description: loop design

source_name: pooled whole larvae


title: 144hpf_rep3

description: loop design


title: K56Ac cell cycle, 30 min, array replicate 3 | array na_22_15

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K56Ac (unsynchronized)

source_name: 30 min


title: 48hpi_rep3

description: loop design


title: 48hpi_rep2

description: loop design


title: 144hpf_rep1

description: loop design


title: Synchronized cells, 0 min, biological replicate F | array yoG_13T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were immediately harvested, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression (Cy5/Cy3) ratios were calculated to produce the values given in the data table.  The Cy5/Cy3 ratio represents the fold change in expression level for the indicated time point relative to unsynchronized cells growing in mid-log phase.

source_name: Mid-log mRNA (unsynchronized)

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

source_name: 0 min

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: 24hpi_rep4

description: loop design


title: K56Ac cell cycle, 50 min, array replicate 3 | array na_22_18

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 50 min


title: K56Ac cell cycle, 40 min, array replicate 3 | array na_22_17

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 40 min


title: 24hpi_rep2

description: loop design


title: K56Ac cell cycle, 110 min, array replicate 3 | array na_22_14

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 110 min


title: 24hpi_rep3

description: loop design


title: 120hpf_rep4

description: loop design


title: K56Ac cell cycle, 150 min, array replicate 3 | array na_22_16

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 150 min


title: Synchronized cells, 50 min, biological replicate F | array yoG_63B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.


title: 12hpi_rep4

description: loop design


title: 120hpf_rep2

description: loop design


title: 120hpf_rep3

description: loop design


title: 12hpi_rep1

description: loop design


title: 12hpi_rep2

description: loop design


title: 108hpf_rep3

description: loop design


title: 108hpf_rep4

description: loop design


title: 90hpf_rep4

description: loop design


title: 12hpi_rep3

description: loop design


title: 90hpf_rep3

description: loop design


title: 90hpf_rep2

description: loop design


title: 120hpf_rep1

description: loop design


title: 66hpf_rep4

description: loop design


title: 78hpf_rep2

description: loop design


title: 108hpf_rep2

description: loop design


title: 108hpf_rep1

description: loop design


title: 78hpf_rep3

description: loop design


title: 78hpf_rep4

description: loop design


title: 66hpf_rep2

description: loop design


title: 66hpf_rep3

description: loop design


title: 90hpf_rep1

description: loop design


title: 78hpf_rep1

description: loop design


title: 66hpf_rep1

description: loop design


title: Control patient 7 - hybridization 2

status: Public on Oct 03 2008

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: control patient 7 - hybridyzation 2

hyb_protocol: Hybridization of the [α 33P]-labelled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

organism: Homo sapiens

source_name: Control

label_protocol: Within each RNA preparation prepared as above the target poly(A) mRNAs were labelled as follows : 10μg total RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg 5'(dT23)VN3' oligonucleotide were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labelled cDNAs were immediately used for hybridization.

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.

tag: 29 years old man


title: Control patient 7 - hybridization 3

description: control patient 7 - hybridyzation 3


title: Control patient 7 - hybridization 1

description: control patient 7 - hybridyzation 1


title: Control patient 6 - hybridization 3

description: control patient 6 - hybridyzation 3

tag: 27 years old man


title: Control patient 6 - hybridization 2

description: control patient 6 - hybridyzation 2


title: Zilberman Methylation IP/total DNA WT6-III (WT sample 3)

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: Antibody-based methylation mapping of the Arabidopsis genome. Genomic DNA was extracted from wild type, met1-6 or pie1-5 lines in the Columbia background. The values are log2 signal ratios of immunoprecipitated DNA /input DNA.

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

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

data_processing: Log base 2 ratios were bi-weight mean centered by NimbleGen

organism: Arabidopsis thaliana

source_name: Sonciated total genomic DNA

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). 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: Methods are described in publication Zilberman, et al. Nature Genetics 2007 (GSE5974).

tag: Ecotype

value: Columbia, Age:12 days, Tissue:whole seedlings

source_name: Immunoprecipitated methylated genomic DNA

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). 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.


title: Control patient 6 - hybridization 1

description: control patient 6 - hybridyzation 1


title: Zilberman met1-6 RNA/WT RNA 102388 (met1-6/WT 1)

description: Transcriptional profiling of the Arabidopsis genome. Total RNA was extracted from wild type or met1-6 lines in the Colombia background. The values are log2 signals of met1-6 total RNA / wild type total RNA.

source_name: Wild type total RNA

value: Columbia, Age:25 days, Tissue:whole plants without roots

source_name: met1-6 total RNA


title: BT6

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

label: C-Bio and A-DNP

source_name: Breast carcinoma

label_protocol: Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: Gender

value: Female


title: Zilberman Methylation IP/total DNA PIE6-III (WT sample 2)

source_name: Sonicated total genomic DNA


title: Zilberman Methylations IP/total DNA WT6 (WT sample 1)

value: Columbia, Age:12 days, Tissue:whole seelings


title: Zilberman H2A.Z IP/total DNA 1825302 (Ab-1 met1-6)

description: Affinity-based mapping of histone H2A.Z in the Arabidopsis genome. H2A.Z-containing nucleosomes were extracted from wild type or met1-6 lines in the Colombia background. The values are log2 signal ratios of H2A.Z-associated DNA/input DNA.

source_name: DNA isolated from immunoprecipitated histone H2A.Z

extract_protocol: Methods are described in publication Zilberman, et al. Nature 2008.

value: Columbia, Age:28 days, Tissue:cultured roots

source_name: DNA isolated from nuclei treated with micrococcal nuclease


title: Zilberman Methylation IP/total DNA PIE6-II (pie1-5 sample 2)


title: Control patient 5 - hybridization 2

description: control patient 5 - hybridyzation 2

tag: age unknown, man


title: Zilberman Methylation IP/total DNA 103548 (met1-6 aerial)


title: Control patient 5 - hybridization 1

description: control patient 5 - hybridyzation 1


title: Zilberman met1-6 RNA/WT RNA 110048 (met1-6/WT 2)


title: BT4


title: Control patient 5 - hybridization 3

description: control patient 5 - hybridyzation 3


title: Zilberman Methylation IP/total DNA 1862602 (WT root-2)


title: Zilberman Methylation IP/total DNA PIE6-in (pie1-5 sample 1)


title: BT5


title: Zilberman Methylation IP/total DNA 1864302 (met1-6 root-2)


title: BT2


title: Zilberman H2A.Z IP/total DNA 1824902 (Ab-1 WT)


title: Zilberman H2A.Z IP/total DNA 1825002 (Ab-2 met1-6)


title: Control patient 4 - hybridization 2

description: control patient 4 - hybridyzation 2

tag: 33 years old woman


title: Control patient 4 - hybridization 3

description: control patient 4 - hybridyzation 3


title: Control patient 4 - hybridization 1

description: control patient 4 - hybridyzation 1


title: Control patient 3 - hybridization 3

description: control patient 3 - hybridyzation 3

tag: 25 years old man


title: Zilberman Methylation IP/total DNA 1882402 (met1-6 root-1)


title: Zilberman H2A.Z IP/total DNA 1364902 (BLRP-3)

source_name: DNA isolated from affinity purified histone H2A.Z


title: Zilberman Methylation IP/total DNA WT6-II (pie1-5 sample 3)


title: Zilberman H2A.Z IP/total DNA 1823502 (Ab-2 WT)


title: Control patient 3 - hybridization 1

description: control patient 3 - hybridyzation 1


title: Control patient 2 - hybridization 3

description: control patient 2 - hybridyzation 3

tag: 26 years old man


title: Zilberman H2A.Z IP/total DNA 1365602 (BLRP-4)


title: Control patient 3 - hybridization 2

description: control patient 3 - hybridyzation 2


title: Zilberman H2A.Z IP/total DNA 90984 (BLRP-1)


title: Zilberman H2A.Z IP/total DNA 1364702 (BLRP-2)


title: Control patient 1 - hybridization 3

description: control patient 1 - hybridyzation 3

tag: 22 years old woman


title: BT3


title: Control patient 2 - hybridization 1

description: control patient 2 - hybridyzation 1


title: Control patient 1 - hybridization 2

description: control patient 1 - hybridyzation 2


title: Zilberman Methylation IP/total DNA 1881802 (WT root-1)


title: Control patient 1 - hybridization 1

description: control patient 1 - hybridyzation 1


title: Long-standing RA patient 4 - hybridization 2

description: long-standing RA patient 4 - hybridyzation 2

source_name: Rheumatoid Arthritis patient

tag: 64 years old woman


title: Long-standing RA patient 4 - hybridization 3

description: long-standing RA patient 4 - hybridyzation 3


title: BT1


title: Long-standing RA patient 2 - hybridization 3

description: long-standing RA patient 2 - hybridyzation 3

tag: 45 years old woman


title: Long-standing RA patient 2 - hybridization 2

description: long-standing RA patient 2 - hybridyzation 2


title: Long-standing RA patient 1 - hybridization 3

description: long-standing RA patient 1 - hybridyzation 3

tag: 42 years old woman


title: Long-standing RA patient 2 - hybridization 1

description: long-standing RA patient 2 - hybridyzation 1


title: Early RA patient 4 - hybridization 3

description: early RA patient 4 - hybridyzation 3

tag: 40 years old man


title: Long-standing RA patient 1 - hybridization 2

description: long-standing RA patient 1 - hybridyzation 2


title: Long-standing RA patient 3 - hybridization 3

description: long-standing RA patient 3 - hybridyzation 3


title: Long-standing RA patient 1 - hybridization 1

description: long-standing RA patient 1 - hybridyzation 1


title: Early RA patient 4 - hybridization 1

description: early RA patient 4 - hybridyzation 1


title: Early RA patient 3 - hybridization 3

description: early RA patient 3 - hybridyzation 3


title: Long-standing RA patient 3 - hybridization 1

description: long-standing RA patient 3 - hybridyzation 1


title: Control patient 2 - hybridization 2

description: control patient 2 - hybridyzation 2


title: Early RA patient 2 - hybridization 1

description: early RA patient 2 - hybridyzation 1

tag: 26 years old woman


title: Early RA patient 2 - hybridization 2

description: early RA patient 2 - hybridyzation 2


title: Early RA patient 1 - hybridization 3

description: early RA patient 1 - hybridyzation 3

tag: 32 years old woman


title: Early RA patient 3 - hybridization 1

description: early RA patient 3 - hybridyzation 1


title: Long-standing RA patient 3 - hybridization 2

description: long-standing RA patient 3 - hybridyzation 2


title: Early RA patient 2 - hybridization 3

description: early RA patient 2 - hybridyzation 3


title: Early RA patient 3 - hybridization 2

description: early RA patient 3 - hybridyzation 2


title: Early RA patient 1 - hybridization 1

description: early RA patient 1 - hybridyzation 1


title: Early RA patient 4 - hybridization 2

description: early RA patient 4 - hybridyzation 2


title: Early RA patient 1 - hybridization 2

description: early RA patient 1 - hybridyzation 2


title: TEL-AML1-SNP-#8

status: Public on Oct 02 2008

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

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

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: B-progenitor ALL with ETV6-RUNX1 fusion


title: TEL-AML1-SNP-#34


title: Long-standing RA patient 4 - hybridization 1

description: long-standing RA patient 4 - hybridyzation 1


title: TEL-AML1-SNP-#44


title: TEL-AML1-SNP-#9


title: TEL-AML1-SNP-#37


title: TEL-AML1-SNP-#6


title: TEL-AML1-SNP-#4


title: TEL-AML1-SNP-#3


title: TEL-AML1-SNP-#29


title: TEL-AML1-SNP-#32


title: TEL-AML1-SNP-#7


title: TEL-AML1-SNP-#5


title: TEL-AML1-SNP-#33


title: TEL-AML1-SNP-#28


title: TEL-AML1-SNP-#25


title: TEL-AML1-SNP-#31


title: TEL-AML1-SNP-#21


title: TEL-AML1-SNP-#22


title: TEL-AML1-SNP-#20


title: TEL-AML1-SNP-#36


title: TEL-AML1-SNP-#2


title: TEL-AML1-SNP-#26


title: TEL-AML1-SNP-#18


title: TEL-AML1-SNP-#15


title: TEL-AML1-SNP-#24


title: TEL-AML1-SNP-#19


title: TEL-AML1-SNP-#14


title: TEL-AML1-SNP-#1


title: TEL-AML1-SNP-#13


title: TEL-AML1-SNP-#16


title: TEL-AML1-SNP-#12


title: TEL-AML1-SNP-#11


title: BCR-ABL-SNP-#8

tag: B-progenitor ALL with BCR-ABL1 fusion


title: TEL-AML1-SNP-#17


title: TEL-AML1-SNP-#10


title: BCR-ABL-SNP-#9


title: BCR-ABL-SNP-#5


title: BCR-ABL-SNP-#6


title: BCR-ABL-SNP-#18


title: BCR-ABL-SNP-#20


title: BCR-ABL-SNP-#19


title: BCR-ABL-SNP-#17


title: BCR-ABL-SNP-#15


title: BCR-ABL-SNP-#3


title: BCR-ABL-SNP-#4


title: BCR-ABL-SNP-#14


title: BCR-ABL-SNP-#10


title: BCR-ABL-SNP-#13


title: Pseudodip-SNP-#9

tag: B-progenitor ALL with normal chromosome number but structural rearrangements


title: Pseudodip-SNP-#6


title: BCR-ABL-SNP-#11


title: Pseudodip-SNP-#5


title: BCR-ABL-SNP-#2


title: BCR-ABL-SNP-#1


title: Pseudodip-SNP-#23


title: Pseudodip-SNP-#7


title: Pseudodip-SNP-#21


title: Pseudodip-SNP-#22


title: Pseudodip-SNP-#3


title: Pseudodip-SNP-#2


title: BCR-ABL-SNP-#12


title: Pseudodip-SNP-#16


title: Pseudodip-SNP-#4


title: Pseudodip-SNP-#24


title: Pseudodip-SNP-#11


title: Pseudodip-SNP-#1


title: Other-SNP-#8

tag: Miscellaneous B-progenitor ALL


title: Other-SNP-#7


title: Other-SNP-#38


title: Other-SNP-#9


title: Other-SNP-#4


title: Other-SNP-#3


title: Other-SNP-#37


title: Pseudodip-SNP-#12


title: Other-SNP-#6


title: Pseudodip-SNP-#10


title: Other-SNP-#20


title: Other-SNP-#26


title: Other-SNP-#42


title: Other-SNP-#5


title: Other-SNP-#22


title: Other-SNP-#24


title: Other-SNP-#25


title: Other-SNP-#19


title: Other-SNP-#23


title: Other-SNP-#2


title: Other-SNP-#17


title: Other-SNP-#15


title: Other-SNP-#18


title: Other-SNP-#12


title: Other-SNP-#21


title: Other-SNP-#14


title: Hyperdip47-50-SNP-#7

tag: B-progenitor ALL with high hyperdiploidy (47-50 chromosomes)


title: Other-SNP-#1


title: Hyperdip47-50-SNP-#9


title: Hyperdip47-50-SNP-#3


title: Hyperdip47-50-SNP-#8


title: Hyperdip47-50-SNP-#5


title: Hyperdip47-50-SNP-#15


title: Hyperdip47-50-SNP-#6


title: Hyperdip47-50-SNP-#24


title: Hyperdip47-50-SNP-#4


title: Hyperdip47-50-SNP-#10


title: Hyperdip47-50-SNP-#12


title: Hyperdip47-50-SNP-#13


title: Hyperdip47-50-SNP-#1


title: Hyperdip47-50-SNP-#14


title: MLL-SNP-#9

tag: B-progenitor ALL with MLL rearrangement


title: Hyperdip47-50-SNP-#11


title: MLL-SNP-#5


title: MLL-SNP-#8


title: Anaplastic carcinom_RUT30

city: Skövde

first: Sandra

last: Karlsson

address: Högskolevägen 1

department: School of Life Sciences

institute: University of Skövde

description: no additional information

hyb_protocol: Prior to hybridizations, the slides were subjected to pre-soaking, dehydration and pre-hybridization according to the manufacturer's protocol (pronto! PLUS direct labeling v1.2, Corning). Pooled samples were co-hybridized to cDNA microarrays in Corning hybridization chambers in Pronto Hybridization buffer (Corning Life Sciences). Hybridization was performed at 42°C for 16-20 h in a volume of 40 Âµl after which the slides were washed and dried prior to scanning in an Agilent Microarray scanner (Agilent technologies, USA).

scan_protocol: The slides were scanned using the agilent DNA microarray scanner

data_processing: Quality control of the GenePix Extraction results was performed using methods available from Bioconductor packages (marray, limma, arrayQuality) in the statistical software package R. Intensities of negative and positive controls were inspected, as well as spatial effects, M/A plots and signal-to-noise distributions. No unexpected results were found, thus indicating an overall high quality of hybridizations and scanning. Subsequent to image acquisition and analysis and data extraction using GenePix pro 6.0, the microarray data were up-loaded into the BioArray Software Environment (BASE) (Saal et al. 2002) for analysis. The data were cleaned to eliminate bad quality spots and subsequently print-tip lowess- and scale normalized. The replicates were merged during the normalization procedures. Spots that were present on less than 30 arrays (of the total 45) were rejected. The data was also subjected to variation filtering, i.e. all position-reporter pairs with standard deviation (SD) smaller than 0.8 were rejected. After cleaning, filtering and normalization procedures, 4336 probes/reporters out of 6000 remained.

organism: Rattus norvegicus

source_name: Cross: (BDIIxBN)F2

label_protocol: cDNA was synthesized by use of chipshot reverse transcriptase (pronto! PLUS direct labeling kit v1.2, Corning) and labeled with the green fluorescent dye, Cy3 (Amersham, USA) from 5 µg total RNA from each of the cell lines of the different cell types or with the red fluorescent dye, Cy5 from 5 µg rat reference RNA. Universal rat reference RNA (Stratagene) was used as a common RNA reference. Labeled cDNA was purified and subsequently quantified using the NanoDrop instrument. The Cy3 (60-80umol) and Cy5 (45-60umol) labeled cDNA, were pooled and dried using a DNA120 speedvac system (Thermo Electron Corporation, USA)

growth_protocol: Primary cell cultures established from the endometrial tumors and other uterine tumors were maintained in culture containing Dulbecco's modified Eagle medium, supplemented with 100 IU/100 µg/ml penicillin/streptomycin, L-glutamine, MEM amino acids, MEM Non Essential Amino acids, MEM Vitamins solution and 10% heat-inactivated fetal bovine serum, for 3-5 passages in order to obtain required amount of cells for RNA extraction. The NME cell lines were cultured under the same conditions but in medium containing 20% serum. The cells were grown at 37°C in an atmosphere of 95% humidity and 5% CO2 and harvested by trypzination at a confluence of 80-90% (approx 1x106 cells).

extract_protocol: Total RNA were automatically extracted from the harvested cells of the different cell lines with a KingFisher mL Instrument (Thermo Electron Corporation, USA) according to the manufacturer's protocol (MagAttract Tissue Mini M48 Kit, Qiagen). RNA was quantified using a NanoDrop (NanoDrop technologies, USA). RNA quality was assessed using a 2100 Bioanalyser instrument (Agilent technologies, USA).

tag: Malignant

tag: strains

value: BD11, BN

tag: Intercross

tag: Age

value: 689 days

tag: Tissue

value: Uterus

tag: Tissue culture

source_name: Universal rat reference RNA

tag: Stratagene, #740200


title: MLL-SNP-#7


title: MLL-SNP-#6


title: Hyperdip47-50-SNP-#2


title: Hyperdip>50-SNP-#40

tag: B-progenitor ALL with high hyperdiploidy (>50 chromosomes)


title: Endometrial adenocarcioma_RUT12

description: no additional information

value: 677 days

value: Endometrium


title: Endometrial adenocarcioma_RUT13

description: no additional information

source_name: Cross: (BDIIxSPRD-Cu3)F2

value: BD11, SPRD-Cu3

value: 666 days


title: MLL-SNP-#4


title: Endometrial adenocarcioma_RUT2

description: no additional information

value: 565 days


title: Endometrial adenocarcioma_RUT7

description: no additional information

value: 662 days


title: Endometrial squamous cell cancer_RUT5

description: no additional information

value: 518 days


title: MLL-SNP-#23


title: MLL-SNP-#18


title: MLL-SNP-#2


title: MLL-SNP-#11


title: MLL-SNP-#17


title: Endometrial adenocarcioma_NUT128

description: no additional information

source_name: Cross: (BDIIxBN)xBDII

tag: Non-malignant

tag: Backcross

value: 748 days


title: Non-malignant endometrium_NUT123

description: no additional information

value: 742 days


title: MLL-SNP-#1


title: MLL-SNP-#10


title: Endometrial adenocarcioma_NUT127

description: no additional information


title: Non-malignant endometrium_NUT122

description: no additional information


title: Hypodip-SNP-#9

tag: B-progenitor ALL with hypodiploidy


title: Non-malignant endometrium_NUT129

description: no additional information


title: Hypodip-SNP-#4


title: Hypodip-SNP-#5


title: Cervical cell squamous cell polyps_NUT114

description: no additional information

value: 737 days

value: Cervix


title: Non-malignant endometrium_NUT110

description: no additional information

value: 732 days


title: Non-malignant endometrium_NUT118

description: no additional information

value: 738 days


title: Endometrial adenocarcioma_NUT100

description: no additional information


title: Hypodip-SNP-#3


title: Hypodip-SNP-#6


title: Endometrial adenocarcioma_NUT98

description: no additional information


title: Hypodip-SNP-#1


title: Endometrial adenocarcioma_NUT99

description: no additional information


title: Endometrial adenocarcioma_NUT84

description: no additional information

source_name: Cross: (BDIIxSPRD-Cu3)xBDII

value: 735 days


title: Hypodip-SNP-#26


title: Hyperdip>50-SNP-#8


title: Endometrial adenocarcioma_NUT82

description: no additional information

value: BD11, BN


title: Non-malignant endometrium_NUT89

description: no additional information


title: Endometrial adenocarcioma_NUT97

description: no additional information


title: Non-malignant endometrium_NUT91

description: no additional information


title: Hyperdip>50-SNP-#5


title: Hyperdip>50-SNP-#7


title: Hyperdip>50-SNP-#6


title: Non-malignant endometrium_NUT75

description: no additional information

value: 704 days


title: Endometrial adenocarcioma_NUT81

description: no additional information


title: Non-malignant endometrium_NUT56

description: no additional information

value: 771 days


title: Hyperdip>50-SNP-#9


title: Non-malignant endometrium_NUT58

description: no additional information


title: Malignant uterus tumor_NUT61

description: no additional information

value: uterus


title: Hyperdip>50-SNP-#3


title: Hyperdip>50-SNP-#24


title: Hyperdip>50-SNP-#30


title: Hyperdip>50-SNP-#4


title: Endometrial adenocarcioma_NUT52

description: no additional information

value: 673 days

value: Endometrium


title: Endometrial adenocarcioma_NUT51

description: no additional information

value: 709 days


title: Hyperdip>50-SNP-#29


title: Hyperdip>50-SNP-#23


title: Hyperdip>50-SNP-#22


title: Hyperdip>50-SNP-#21


title: Hyperdip>50-SNP-#16


title: Hyperdip>50-SNP-#27


title: Endometrial adenocarcioma_NUT47

description: no additional information

value: BD11, SPRD-Cu3

value: 710 days


title: Non-malignant endometrium_NUT48

description: no additional information


title: Hyperdip>50-SNP-#15


title: Endometrial adenocarcioma_NUT50

description: no additional information

value: 674 days


title: Endometrial adenocarcioma_NUT42

description: no additional information

value: 740 days


title: Hyperdip>50-SNP-#2


title: Endometrial adenocarcioma_NUT43

description: no additional information

value: 670 days


title: Endometrial adenocarcioma_NUT46

description: no additional information

value: 666 days


title: Hyperdip>50-SNP-#13


title: Hyperdip>50-SNP-#12


title: Endometrial papillary adenoma_NUT15

description: no additional information

value: 652 days


title: Hyperdip>50-SNP-#19


title: Hyperdip>50-SNP-#18


title: Hyperdip>50-SNP-#14


title: Hyperdip>50-SNP-#17


title: Endometrial adenocarcioma_NUT31

description: no additional information

value: 640 days


title: Non-malignant endometrium_NUT18

description: no additional information

value: 644 days


title: Endometrial adenocarcioma_NUT41

description: no additional information

value: 686 days


title: Malignant uterus tumor_NUT37

description: no additional information

value: BD11, BN

value: 657 days

value: Uterus


title: Endometrial adenocarcioma_NUT12

description: no additional information

value: 691 days


title: Endometrial adenocarcioma_NUT39

description: no additional information

value: 714 days


title: Hyperdip>50-SNP-#11


title: Endometrial adenocarcioma_NUT7

description: no additional information

value: 591 days

value: Endometrium


title: E2A-PBX1-SNP-#9

tag: B-progenitor ALL with TCF3-PBX1 fusion


title: Hyperdip>50-SNP-#10


title: E2A-PBX1-SNP-#3


title: E2A-PBX1-SNP-#17


title: E2A-PBX1-SNP-#7


title: E2A-PBX1-SNP-#5


title: Endometrial adenocarcioma_NUT6

description: no additional information

value: 471 days


title: E2A-PBX1-SNP-#2


title: E2A-PBX1-SNP-#4


title: E2A-PBX1-SNP-#6


title: E2A-PBX1-SNP-#14


title: E2A-PBX1-SNP-#16


title: E2A-PBX1-SNP-#15


title: E2A-PBX1-SNP-#10


title: intestine Q direct 24h

city: Barcelona

first: Joan

middle: C

last: Balasch

address: UAB Bellaterra faculty of Biosciences

department: Dpt. Cell Biology, Physiology and Immunology

country: Spain

institute: Universitat Autonoma Barcelona

description: To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes.

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, immunodiet and control diet cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. All samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning was performed with Axon scanner 4000B and images were processed with GenePix Pro 6.0.The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: After subtraction of mean background, locally weighted non-linear regression (Lowess) normalization was performed separately for each slide.

organism: Oncorhynchus mykiss

source_name: Diet Q (Immunostimulant) intestine LPS

label_protocol: cDNA Cy5 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: TriReagent manufacturer's protocol. RNA was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions.The RNA was stored at -80 ºC in ethanol 70% until use.

tag: RNA from intestine of fish fed with diet Q immunostimulant, LPS injected

source_name: Diet Q (Immunostimulant) intestine PBS

label_protocol: cDNA Cy3 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

tag: RNA from intestine of fish fed with diet Q immunostimulant, PBS injected


title: E2A-PBX1-SNP-#13


title: intestine Q reverse 24h


title: Malignant uterus tumor_NUT1

description: no additional information

value: BD11, SPRD-Cu3

value: 454 days

value: Cervix


title: E2A-PBX1-SNP-#12


title: E2A-PBX1-SNP-#11


title: pUC-18_EBER2_1

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

description: pUC-18-EBER2 transfected HEK293 cells

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturer’s protocol (P/N 4339627).

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.

label: DIG-UTP

source_name: HEK293 cell line

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 μg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol(P/N 4365710).

extract_protocol: RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer

tag: pUC-18-EBER2 transfected HEK293 cells


title: F1 hybrid Testis, biological rep 1

status: Public on Sep 03 2008

city: Hamilton

first: Frederic

last: Chain

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description: 1 of 3 biological replicates of gene expression data from sexually mature testis.

hyb_protocol: Hybridization to Affymetrix Xenopus laevis Genome expression array followed the manufacturer's (Affymetrix) protocol.

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

data_processing:
Data were RMA normalized using RMA Express and a probemask (based on perfect match probes for X.laevis and X.borealis).
Normalization of 3 biological replicates were performed with 3 biological replicates of X.laevis testis and 3 biological replicates of X.borealis testis.

label: biotin

organism: Xenopus laevis x Xenopus borealis

source_name: F1 Hybrid (X.laevis female x X.borealis male), sexually mature testis

label_protocol: Two micrograms of total RNA was used to prepare biotin labeled cRNA probes following the manufacturer’s (Affymetrix) protocol.

extract_protocol: Total RNA was isolated using TRIzol® Reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol and purified with RNeasy Mini Kit (Qiagen).

treatment_protocol: Animal was immersed in MS222 and gonad was immediately extracted

tag: Mother

value: X.laevis (laboratory stock); Father:X.borealis (Kenya) Age:450 days


title: pUC-18_EBER2_3

description: pUC-18-EBER2 transfected HEK293 cells


title: pUC-18_EBER2_2

description: pUC-18-EBER2 transfected HEK293 cells


title: pUC-18_EBER2-L2_2

description: pUC-18-EBER2-L2 transfected HEK293 cells


title: gills Q reverse 24h

source_name: Diet Q (Immunostimulant) gills PBS

tag: RNA from gills of fish fed with diet Q Immunostimulant, PBS injected

source_name: Diet Q (Immunostimulant) gills LPS

tag: RNA from gills of fish fed with diet Q Immunostimulant, LPS injected


title: intestine D direct 24h

source_name: Diet D (control) intestine LPS

tag: RNA from intestine of fish fed with diet D control, LPS injected

source_name: Diet D (control) intestine PBS

tag: RNA from intestine of fish fed with diet D control, PBS injected


title: intestine D reverse 24h


title: PABP1.Cy5.Msi1.Cy3.2

status: Public on Jul 19 2008

city: San Antonio

first: Luiz

last: Penalva

state: TX

address: 8403 Floyd Curl Drive

department: GCCRI

institute: UTHSCSA

description: PABP1-Cy5, Msi1-Cy3 Replicate 2

hyb_protocol: Samples were hybridized using Agilent's Gene Expression Hybridization Kit.

scan_protocol: Scanned with Agilent G2565 BA Scanner, 10 µm resolution.

data_processing: TIFF images were quantified using Agilent Feature Extraction Software 8.5.

source_name: HEK293T Cells

label_protocol: cRNA synthesis was carried out using Agilent's Low RNA Linear Amplification Kit Plus, two-color.

growth_protocol: Grown at 37°C in 5% CO2.

extract_protocol: Phenol/chloroform extraction and isopropanol precipitation.

treatment_protocol: HEK293T cells were transfected with BAP (Biotin Acceptor Peptide) tagged with Msi1. After 48 hours cells were lysed and complexes were immunoprecipitated with streptavidin beads. After proteinase K treatment RNA was purified by phenol/chloroform extraction and isopropanol precipitation.

tag: Treatment

value: Transient transfection with BAP tagged with Msi1

tag: Time

value: 48 hours

treatment_protocol: HEK293T cells were transfected with BAP (Biotin Acceptor Peptide) tagged with PABP1. After 48 hours cells were lysed and complexes were immunoprecipitated with streptavidin beads. After proteinase K treatment RNA was purified by phenol/chloroform extraction and isopropanol precipitation.

value: Transient transfection with BAP tagged with PABP1


title: Msi1.Cy5.PABP1.Cy3.2

description: Msi1-Cy5, PABP1-Cy3 Replicate 2


title: pUC-18_2

description: pUC-18 transfected HEK293 cells

tag: pUC-18 transfected HEK293 cells


title: gills Q direct 24h


title: gills D reverse 24h

source_name: Diet D (control) gills PBS

tag: RNA from gills of fish fed with diet D control, PBS injected

source_name: Diet D (control) gills LPS

tag: RNA from gills of fish fed with diet D control, LPS injected


title: F1 hybrid Testis, biological rep 3

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

value: X.laevis (laboratory stock); Father:X.borealis (Kenya)

tag: Age

value: 450 days


title: pUC-18_1

description: pUC-18 transfected HEK293 cells


title: pUC-18_EBER2-L2_5

tag: pUC-18-EBER2-L2 transfected HEK293 cells


title: gills D direct 24h


title: Msi1.Cy5.GFP.Cy3.2

description: Msi1-Cy5, GFP-Cy3 Replicate 2

treatment_protocol: HEK293T cells were transfected with BAP (Biotin Acceptor Peptide) tagged with GFP. After 48 hours cells were lysed and complexes were immunoprecipitated with streptavidin beads. After proteinase K treatment RNA was purified by phenol/chloroform extraction and isopropanol precipitation.

value: Transient transfection with BAP tagged with GFP


title: pUC-18_3

description: pUC-18 transfected HEK293 cells


title: E2A-PBX1-SNP-#1


title: Msi1.Cy5.PABP1.Cy3.1

description: Msi1-Cy5, PABP1-Cy3 Replicate 1


title: pUC-18_EBER2-L2_4


title: pUC-18_EBER2-L2_3


title: GFP.Cy5.Msi1.Cy3.2

description: GFP-Cy5, Msi1-Cy3 Replicate 2


title: PABP1.Cy5.Msi1.Cy3.1

description: PABP1-Cy5, Msi1-Cy3 Replicate 1


title: F1 hybrid Testis, biological rep 2


title: pUC-18_EBER2-L2_1


title: GFP.Cy5.Msi1.Cy3.1

description: GFP-Cy5, Msi1-Cy3 Replicate 1


title: Msi1.Cy5.GFP.Cy3.1

description: Msi1-Cy5, GFP-Cy3 Replicate 1


title: Cu_treatment_130µM_3

status: Public on Apr 30 2008

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

description: Oryza sativa leaf treated with 130 µM Cu for 1 day, replicate 3

hyb_protocol: One microgram of Cy3-labeled cRNA was mixed with the same amount of Cy5-labeled cRNA and used for subsequent hybridization.  Hybridization was carried out for 17 h with rotation at 60˚C.

scan_protocol: Slides were scanned using a GenePix 4000A scanner (Axon Instruments Inc., Foster City, CA, USA) with 550 V and 680 V of PMT voltage for Cy3 and Cy5 detection, respectively.

data_processing: DATA were quantified by Microarray Suite 2.0 (IPLab Spectrum Software, Scanalytics, Fairfax, VA, USA)

organism: Oryza sativa

label_protocol: Cy3- and Cy5-labeled cRNA was prepared from 400 ng of total RNA from rice leaves, using a Low RNA Input Linear Amplification Kit (Agilent Technologies, Inc., Palo Alto, CA, USA) and Cy3- and Cy5-CTP (Perkin Elmer).  Labeled cRNA was purified with RNeasy mini spin columns (Qiagen).

extract_protocol: Total RNA was extracted from three different leaf samples per treatment using an RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks.  Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week.  Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with hydroponic solutions containing 130 µM CuCl2.

tag: Oryza sativa L. cv. Nipponbare leaf treated with 130 µM Cu for 1 day

source_name: Oryza sativa leaf treated with 0.3 µM Cu (control) for 1 day

treatment_protocol: Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks.  Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week.  Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with normal hydroponic solutions containing 0.3 µM CuCl2 as the control.

tag: Oryza sativa L. cv. Nipponbare leaf treated with 0.3 µM Cu (control) for 1 day


title: Zinc limited Aerobic chemostat culture -1

status: Public on Oct 16 2007

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
LH17
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

scan_protocol: Affymetrix Scanner 3000

data_processing: GCOS

label: SAPE

source_name: Chemostat culture

label_protocol:
EukGE-ws2v4
Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x

growth_protocol:
C)hemostat cultivation
Steady-state chemostat cultures of S. cerevisiae CEN.PK113-7D strain were performed in a 2-liter fermenter (Applikon) with a working volume of 1 liter (van den Berg et al 1996) . These cultures were fed with synthetic medium (see below) which limited growth by carbon, nitrogen or zinc with all other growth requirements in excess and at constant residual concentration (Boer et al 2003). The dilution rate was set at 0.1 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The stirrer speed was set at 800 rpm. Anaerobic conditions were maintained by sparging the medium reservoir (0.05 liter.min-1) and the fermenter with pure nitrogen gas (0.5 liter.min-1). Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures (Visser et al 1990). The off-gas was cooled by a condenser connected to a cryostat set at 2 °C. Oxygen and carbon dioxide were measured off-line with an NGA 2000 Rosemont gas analyzer. Cultures were assumed to be in steady-state when, after 4 to 5 volume changes, culture dry-weight, glucose concentration, carbon-dioxide production rate and oxygen consumption rate varied by less than 2 % during one volume change (Ferea et al, 1999; Jansen etal 2004). Steady-state samples were taken after 10 generations at the latest to avoid strain adaptation due to long-term cultivation. Each cultivation condition was performed in triplicate.
Growth media
The synthetic media composition was based on that described by Verduyn (1992). In all chemostats except for those limited by carbon, residual glucose concentration was targeted to 17 g.liter-1 in order to sustain glucose repression at the same level. The media composition for aerobic cultivations was the following: for zinc-limited cultivation, 5.0 g.liter-1 (NH4)2SO4, 3.0 g.liter-1 KH2PO4, 0.5 g.liter-1 MgSO4•7H2O, 66 g.liter-1 glucose and 0.014 mg.liter-1 ZnSO4•7H2O.
	van den Berg, M. A., P. de Jong-Gubbels, C. J. Kortland, J. P. van Dijken, J. T. Pronk, and H. Y. Steensma. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J. Biol. Chem. 271:28953-28959.
van Dijken, J. P., J. Bauer, L. Brambilla, P. Duboc, J. M. Francois, C. Gancedo, M. L. Giuseppin, J. J. Heijnen, M. Hoare, H. C. Lange, E. A. Madden, P. Niederberger, J. Nielsen, J. L. Parrou, T. Petit, D. Porro, M. Reuss, R. N. van, M. Rizzi, H. Y. Steensma, C. T. Verrips, J. Vindelov, and J. T. Pronk. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb. Technol. 26:706-714.
Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1990. Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J. Gen. Microbiol. 136:405-412.
Verduyn, C., E. Postma, W. A. Scheffers, and J. P. van Dijken. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8:501-517.
Visser, W., W. A. Scheffers, Batenburg-van der Vegte WH, and J. P. van Dijken. 1990. Oxygen requirements of yeasts. Appl. Environ. Microbiol. 56:3785-3792.
Boer, V. M., J. H. de Winde, J. T. Pronk, and M. D. Piper. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278:3265-3274.
	Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U. S. A 96:9721-9726.
	Jansen, M. L., P. Daran-Lapujade, J. H. de Winde, M. D. Piper, and J. T. Pronk. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl. Environ. Microbiol. 70:1956-1963.

treatment_protocol: Liquid nitrogen

tag: The haploid prototrophic S. cerevisiae strain CEN.PK 113-7D (MATa) was obtained from Dr. P. Kötter, Frankfurt, Germany. Zinc-depleted cells were obtained by four serial transfers of yeast cells in shake flasks containing synthetic medium91 from which zinc was omitted, and subsequently mixed with glycerol (final concentration 20%), aliquoted and stored at -80 °C.


title: Zinc-limited aerobic chemostat culture-2

description:
LH18
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

hyb_protocol: Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates. Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x

tag: The haploid prototrophic S. cerevisiae strain CEN.PK 113-7D (MATa) was obtained from Dr. P. Kötter, Frankfurt, Germany. Zinc-depleted cells were obtained by four serial transfers of yeast cells in shake flasks containing synthetic medium from which zinc was omitted, and subsequently mixed with glycerol (final concentration 20%), aliquoted and stored at -80 °C.


title: Cu_treatment_45µM_3

description: Oryza sativa leaf treated with 45 µM Cu for 1 day, replicate 3

treatment_protocol: Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks.  Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week.  Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with hydroponic solutions containing 45 µM CuCl2.

tag: Oryza sativa L. cv. Nipponbare leaf treated with 45 µM Cu for 1 day


title: C-lim aerobic chemostat with phenylalanine as N-source 2

status: Public on Nov 15 2007

hyb_protocol: [Fluidics] Protocol	EukGE-WS2v4

scan_protocol: [Scanner] Pixel Size	3 Filter	570 Number of Scans	2 Scanner Type	HP

data_processing: MAS 5.1

molecule: polyA RNA

source_name: chemostat culture with phenylalanine as N-source

label_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).

growth_protocol:
The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1,2) was grown at 30°C in 1.0-liter working volume chemostats (3). Cultures were fed with a synthetic medium (4) that supported glucose-limited growth. The glucose concentration in the reservoir medium was 7.5 g·l-1. The nitrogen source was used, at the following concentration: L-phenylalanine, 5.0 g·l-1. When an amino acid served as nitrogen source, the synthetic medium was supplemented with 6.6 g·l-l K2SO4. The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples for arrays were taken after 10 to 14 volume changes to minimize the impact of evolutionary adaptation that occurs after long term cultivation (5,6). Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.
(1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10): 706-714.
(2) Daran-Lapujade P et al. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res 4: 285-296.
(3) van den Berg et al. 1996. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J Biol Chem 271: 28953-28959.
(4) Verduyn et al. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-17.
(5) Ferea et al. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721-9726.
(6) Jansen et al. 2004. Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity. Appl Environ Microbiol 70: 1956-1963.

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D (MATa) (1)


title: Cu_treatment_45µM_2

description: Oryza sativa leaf treated with 45 µM Cu for 1 day, replicate 2


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 10

status: Public on Jul 01 2007

city: Berlin

first: Roland

last: Distl

address: Am Augustenburger Platz 1

department: Institute of Neuropathology

country: Germany

institute: Charité Universitätsmedizin Berlin

description: Replicate 1 of 3 (same genotype, same age). All replicates were individual animals.

hyb_protocol: according to Affymetrix

scan_protocol: according to Affymetrix

data_processing: Arrays were scanned twice with GeneChip Scanner 3000 (Affymetrix) and analysed with GeneChip Operating Software 1.3 (Affymetrix). Average hybridisation intensity  was set to 500 per gene.

organism: Mus musculus

source_name: BALB/c Npc1-/- and Npc1+/+ cerebellum

label_protocol: according to Affymetrix

growth_protocol:
Housing conditions: 12 hours light/dark cycle
Standard chow diet

extract_protocol: The tissue was minced in liquid nitrogen using pestle and mortar. Then, the TRIZOL (Life technologies, Karlsruhe, Germany) was used followed by the RNeasy Mini Kit procedure (Qiagen) including DNAse treatment. Quality and quantity of the extract was checked with RNA 6000 Pico LabChip (Agilent).

treatment_protocol:
Npc1 genotype was determined by PCR
Sacrified by cervical extension without anaesthetics at P21
Cerebellum was removed and tissue stored in RNAlater RNA stabilization reagent (Qiagen, Hilden, Germany) at –80 centigrade

tag: Strain

value: BALB/c Npc1

tag: Tissue

value: cerebellum

tag: Time point

tag: Genotype

tag: Gender

value: male


title: Cu_treatment_10µM_3

description: Oryza sativa leaf treated with 10 µM Cu for 1 day, replicate 3

treatment_protocol: Rice plants (Oryza sativa L. cv. Nipponbare) were grown hydroponically (Kamachi et al. (1991) Plant Physiol. 96, 411-417.) in an environment-controlled greenhouse with a photoperiod of 12 h light (25 to 28˚C) for 6 to 7 weeks.  Three rice plants were grown in each 500-ml plastic pot containing a nutrient solution which was renewed once a week.  Rice plants whose 8th leaf was fully expanded were used for experimental treatments. Rice plants which had been grown as described above were treated with hydroponic solutions containing 10 µM CuCl2.

tag: Oryza sativa L. cv. Nipponbare leaf treated with 10 µM Cu for 1 day


title: Cu_treatment_45µM_1

description: Oryza sativa leaf treated with 45 µM Cu for 1 day, replicate 1


title: Zinc-limited Aerobic chemostat culture -3

description:
LH19
Establishment of Zn-free culture vessels
Glassware and fermenters employed in this study were all acid-washed and deionised according to the following procedure: overnight soak in 2 % nitric acid, two washes with deionised water, one wash with 0.1 M EDTA and four washes with deionised water. The glassware was dried prior to use. This procedure was fundamental to avoid any contamination of zinc from all glassware including the fermenter

extract_protocol:
Microarray analysis. Sampling of cells from chemostats and total RNA extraction was performed as previously described in Abbott et al. (2007). Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 g of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies). Results for each growth condition were derived from three independent culture replicates.
Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ. (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. doi:10.1111/j.1567-1364.2007.00242.x


title: Cu_treatment_10µM_1

description: Oryza sativa leaf treated with 10 µM Cu for 1 day, replicate 1

data_processing: DATA were quantified by Microarray Suite 2.0 (IPLab Spectrum Software, Scanalytics, Fairfax, VA, USA).


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 5

description: Replicate 2 of 3 (same genotype, same age). All replicates were individual animals.

value: female


title: Cu_treatment_130µM_1

description: Oryza sativa leaf treated with 130 µM Cu for 1 day, replicate 1


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 8


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 12

description: Replicate 3 of 3 (same genotype, same age). All replicates were individual animals.


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 7


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 9


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 2

description: Replicate No 2 of 3 (same genotype, same age), all replicates were individual animals.


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 3

description: Replicate No 3 of 3 (same genotype, same age), all replicates were individual animals.


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 4


title: C-lim aerobic chemostat with phenylalanine as N-source 3

extract_protocol: Sampling of cells from chemostats, probe preparation and hybridization to Affymetrix GeneChip® Microarrays was performed as described by Piper et al (Piper et al., 2002).

tag: (1) van Dijken et al. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26(9,10)


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 11


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 6


title: Cu_treatment_10µM_2

description: Oryza sativa leaf treated with 10 µM Cu for 1 day, replicate 2


title: Differential gene expression in BALB/c Npc1-/- and Npc1+/+ cerebellum - animal No 1

treatment_protocol:
Npc1 genotype was determined by PCR
Housing conditions: 12 hours light/dark cycle
Standard chow diet
Sacrified by cervical extension without anaesthetics at P21
Cerebellum was removed and tissue stored in RNAlater RNA stabilization reagent (Qiagen, Hilden, Germany) at –80 centigrade


title: Cu_treatment_130µM_2

description: Oryza sativa leaf treated with 130 µM Cu for 1 day, replicate 2


title: 2900_d_1

status: Public on Apr 30 2007

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

institute: National institute of radiological sciences

description: during treatment, radiotherapy alone

data_processing: global median normalization

source_name: biopsy

tag: female, cervical cancer


title: 2900_d_2

description: during treatment, radiotherapy alone


title: 2518_p_2

description: prior to treatment, radiotherapy alone


title: 2900_p_2

description: prior to treatment, radiotherapy alone


title: 2315_d_1

description: during treatment, radiotherapy alone


title: 2518_d_2

description: during treatment, radiotherapy alone


title: 2788_p_1

description: prior to treatment, radiotherapy alone


title: 2900_p_1

description: prior to treatment, radiotherapy alone


title: 2788_d_1

description: during treatment, radiotherapy alone


title: 2518_d_1

description: during treatment, radiotherapy alone


title: 1690_d_2

description: during treatment, radiotherapy alone


title: 2315_p_2

description: prior to treatment, radiotherapy alone


title: 1590_d_2

description: during treatment, radiotherapy alone


title: 2315_p_1

description: prior to treatment, radiotherapy alone


title: 1590_d_1

description: during treatment, radiotherapy alone


title: 1690_p_2

description: prior to treatment, radiotherapy alone


title: 1690_p_1

description: prior to treatment, radiotherapy alone


title: 1688_d_1

description: during treatment, radiotherapy alone


title: 1688_p_2

description: prior to treatment, radiotherapy alone


title: 1688_p_1

description: prior to treatment, radiotherapy alone


title: 1690_d_1

description: during treatment, radiotherapy alone


title: 2315_d_2

description: during treatment, radiotherapy alone


title: 1688_d_2

description: during treatment, radiotherapy alone


title: 2788_p_2

description: prior to treatment, radiotherapy alone


title: 1590_p_2

description: prior to treatment, radiotherapy alone


title: 2791_p_2

description: prior to treatment, chemoradiotherapy


title: 2774_d_2

description: during treatment, chemoradiotherapy


title: 2791_d_2

description: during treatment, chemoradiotherapy


title: 2791_d_1

description: during treatment, chemoradiotherapy


title: 1590_p_1

description: prior to treatment, radiotherapy alone


title: 2774_d_1

description: during treatment, chemoradiotherapy


title: 2774_p_2

description: prior to treatment, chemoradiotherapy


title: 2512_d_1

description: during treatment, chemoradiotherapy


title: 2512_d_2

description: during treatment, chemoradiotherapy


title: 2320_d_1

description: during treatment, chemoradiotherapy


title: 2512_p_2

description: prior to treatment, chemoradiotherapy


title: 2320_p_2

description: prior to treatment, chemoradiotherapy


title: 2320_d_2

description: during treatment, chemoradiotherapy


title: 2509_p_1

description: prior to treatment, chemoradiotherapy


title: 2788_d_2

description: during treatment, radiotherapy alone


title: 1677_d_2

description: during treatment, chemoradiotherapy


title: 2509_d_2

description: during treatment, chemoradiotherapy


title: 2509_p_2

description: prior to treatment, chemoradiotherapy


title: 2512_p_1

description: prior to treatment, chemoradiotherapy


title: 1676_d_2

description: during treatment, chemoradiotherapy


title: 2320_p_1

description: prior to treatment, chemoradiotherapy


title: 2518_p_1

description: prior to treatment, radiotherapy alone


title: 1677_p_2

description: prior to treatment, chemoradiotherapy


title: 2774_p_1

description: prior to treatment, chemoradiotherapy


title: 2509_d_1

description: during treatment, chemoradiotherapy


title: 1677_p_1

description: prior to treatment, chemoradiotherapy


title: 1676_p_1

description: prior to treatment, chemoradiotherapy


title: 1676_p_2

description: prior to treatment, chemoradiotherapy


title: 1583_d_2

description: during treatment, chemoradiotherapy


title: 2791_p_1

description: prior to treatment, chemoradiotherapy


title: 1677_d_1

description: during treatment, chemoradiotherapy


title: 1990_d_2

description: during treatment, radiotherapy alone


title: 1993_p_1

description: prior to treatment, radiotherapy alone


title: 1583_p_1

description: prior to treatment, chemoradiotherapy


title: 1583_p_2

description: prior to treatment, chemoradiotherapy


title: 1243_d_2

description: during treatment, radiotherapy alone


title: 1990_d_1

description: during treatment, radiotherapy alone


title: 1993_d_2

description: during treatment, radiotherapy alone


title: 1250_p_2

description: prior to treatment, chemoradiotherapy


title: 1353_d_2

description: during treatment, chemoradiotherapy


title: 1687_d_2

description: during treatment, chemoradiotherapy


title: 1353_d_1

description: during treatment, chemoradiotherapy


title: 1993_d_1

description: during treatment, radiotherapy alone


title: 1993_p_2

description: prior to treatment, radiotherapy alone


title: 1353_p_1

description: prior to treatment, chemoradiotherapy


title: 1243_p_2

description: prior to treatment, radiotherapy alone


title: 1676_d_1

description: during treatment, chemoradiotherapy


title: 1583_d_1

description: during treatment, chemoradiotherapy


title: 1353_p_2

description: prior to treatment, chemoradiotherapy


title: 1844_p_1

description: prior to treatment, radiotherapy alone


title: 1844_d_2

description: during treatment, radiotherapy alone


title: 1250_d_2

description: during treatment, chemoradiotherapy


title: 275_d_2

description: during treatment, radiotherapy alone


title: 1584_d_2

description: during treatment, radiotherapy alone


title: 1356_d_2

description: during treatment, chemoradiotherapy


title: 1587_d_2

description: during treatment, chemoradiotherapy


title: 783_d_2

description: during treatment, chemoradiotherapy


title: 1246_p_2

description: prior to treatment, chemoradiotherapy


title: 1599_d_2

description: during treatment, radiotherapy alone


title: 1581_d_2

description: during treatment, chemoradiotherapy


title: 1356_p_1

description: prior to treatment, chemoradiotherapy


title: 1246_d_2

description: during treatment, chemoradiotherapy


title: 1356_d_1

description: during treatment, chemoradiotherapy


title: 1243_d_1

description: during treatment, radiotherapy alone


title: 445_d_2

description: during treatment, radiotherapy alone


title: 380_d_1

description: during treatment, radiotherapy alone


title: 783_d_1

description: during treatment, chemoradiotherapy


title: 1246_p_1

description: prior to treatment, chemoradiotherapy


title: 1250_d_1

description: during treatment, chemoradiotherapy


title: 1581_d_1

description: during treatment, chemoradiotherapy


title: 1250_p_1

description: prior to treatment, chemoradiotherapy


title: 1599_d_1

description: during treatment, radiotherapy alone


title: 1584_d_1

description: during treatment, radiotherapy alone


title: 380_p_2

description: prior to treatment, radiotherapy alone


title: 1599_p_2

description: prior to treatment, radiotherapy alone


title: 275_d_1

description: during treatment, radiotherapy alone


title: 1584_p_2

description: prior to treatment, radiotherapy alone


title: 1252_d_2

description: during treatment, chemoradiotherapy


title: 1844_p_2

description: prior to treatment, radiotherapy alone


title: 1243_p_1

description: prior to treatment, radiotherapy alone


title: 1252_p_2

description: prior to treatment, chemoradiotherapy


title: 1844_d_1

description: during treatment, radiotherapy alone


title: 1246_d_1

description: during treatment, chemoradiotherapy


title: 1252_d_1

description: during treatment, chemoradiotherapy


title: 445_d_1

description: during treatment, radiotherapy alone


title: 1687_p_1

description: prior to treatment, chemoradiotherapy


title: 1587_d_1

description: during treatment, chemoradiotherapy


title: 1842_d_1

description: during treatment, radiotherapy alone


title: 1356_p_2

description: prior to treatment, chemoradiotherapy


title: 380_d_2

description: during treatment, radiotherapy alone


title: 1687_p_2

description: prior to treatment, chemoradiotherapy


title: 783_p_2

description: prior to treatment, chemoradiotherapy


title: 1584_p_1

description: prior to treatment, radiotherapy alone


title: 1990_p_1

description: prior to treatment, radiotherapy alone


title: 1587_p_2

description: prior to treatment, chemoradiotherapy


title: 1599_p_1

description: prior to treatment, radiotherapy alone


title: 1587_p_1

description: prior to treatment, chemoradiotherapy


title: 1252_p_1

description: prior to treatment, chemoradiotherapy


title: 445_p_1

description: prior to treatment, radiotherapy alone


title: 1842_d_2

description: during treatment, radiotherapy alone


title: 2314_d_1

description: during treatment, radiotherapy alone


title: 275_p_2

description: prior to treatment, radiotherapy alone


title: 1687_d_1

description: during treatment, chemoradiotherapy


title: 1581_p_2

description: prior to treatment, chemoradiotherapy


title: 1581_p_1

description: prior to treatment, chemoradiotherapy


title: 1990_p_2

description: prior to treatment, radiotherapy alone


title: 380_p_1

description: prior to treatment, radiotherapy alone


title: 2314_p_1

description: prior to treatment, radiotherapy alone


title: 2030_d_2

description: during treatment, chemoradiotherapy


title: 445_p_2

description: prior to treatment, radiotherapy alone


title: 2314_p_2

description: prior to treatment, radiotherapy alone


title: 2037_d_2

description: during treatment, chemoradiotherapy


title: 2037_d_1

description: during treatment, chemoradiotherapy


title: 1989_d_2

description: during treatment, radiotherapy alone


title: 1842_p_2

description: prior to treatment, radiotherapy alone


title: 1989_d_1

description: during treatment, radiotherapy alone


title: 2037_p_2

description: prior to treatment, chemoradiotherapy


title: 2037_p_1

description: prior to treatment, chemoradiotherapy


title: 1988_d_2

description: during treatment, radiotherapy alone


title: 1988_d_1

description: during treatment, radiotherapy alone


title: 2030_p_2

description: prior to treatment, chemoradiotherapy


title: 1989_p_1

description: prior to treatment, radiotherapy alone


title: E. histolytica strain HM1 replicate 1

status: Public on Mar 01 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Trophozoites after long term axenic growth. Isolated mid-log phase.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: Trophozoites grown in TYI

label_protocol: Affymetrix single amplification

tag: Media

value: TYI

tag: Long term axenic growth


title: Dicer T00312751_15773_6

status: Public on Mar 24 2007

city: Houston

first: Ankang

last: Li

address: 2121 West Holcombe

department: CMDD

institute: IBT

description: control group

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: GeneSpring analysis

source_name: embryonic heart control group

label_protocol: CodeLink Expression Assay protocol

extract_protocol: For RNA isolation, embryonic heart was dissected out and lysed using QiaShredder. RNA was isolated using RNeasy micro columns following the manufacturer's instructions, and including an on-column DNase digestion step.

tag: embryonic day 11.5 heart


title: 1989_p_2

description: prior to treatment, radiotherapy alone


title: E. histolytica strain HM1 replicate 2