title: Lea1-TAP (U2 snRNP) ChIP-CHIP

type: genomic

city: Waltham

first: Dan

last: Tardiff

address: 415 South Street

department: Biology

institute: Brandeis University

description: S. cerevisiae U2 ChIP-CHIP

hyb_protocol: Nimblegen. 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: Nimblegen. 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: Samples were scanned and with each channel [635(ch1) and 532(ch2)] normalized separately according to Nimblegen protocols.log(2) ratios were calculated from these normalized 635 and 532 signals, with Random control spots removed during processing.

molecule: genomic DNA

source_name: Immunoprecipitated genomic DNA from Lea1-TAP immunoprecipitation

label_protocol: (Pull-down)  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: Chromatin Immunoprecipitation (see Komarnitsky, Cho, and Buratowski, 2000)

tag: S. cerevisiae strain expressing C-terminal TAP tagged Lea1

source_name: Input genomic DNA from Lea1-TAP immunoprecipitation

label_protocol: (Input) 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: Patient 11 GF201 011

status: Public on Jan 20 2007

type: RNA

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe. Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience). The arrays were then washed twice with a solution containing 2 mM of MgCl2, 50 mM of Tris and 100 mM of NaCl, and with a solution containing 2 mM of MgCl2, 50 mM of Tris and 15 mM of NaCl. All procedures were carried out with the aid of custom-made AutoHybridizers (Fuji Photo Film, Tokyo, Japan).

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified with ArrayGauge software (Fuji Photo Film).

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  Averaged values of the first and the second hybridizations were used for further analyses.

molecule: total RNA

organism: Homo sapiens

source_name: primary lung cancer

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the GeneFilters (Invitrogen) with slight modification.

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. Careful attention was paid to the microdissection of only such tumor cell-rich areas, yielding an average of 75.4% tumor cell content (Figure 1i). RNAs were then isolated using RNAeasy (Quiagen, Valencia, CA, USA) according to the manufacturer's instruction, and their quality was checked with the RNA 6000 Nano Assay kit and the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

tag: Sample #

tag: Survival Period

tag: status after 5 years

value: Dead

tag: HIST

value: AD

tag: AGE

tag: SEX

value: Male

tag: pStage

value: IIB

tag: pT

tag: pN


title: Patient 12 GF201 012

value: Alive

value: Female

value: IA


title: Patient 14 GF201 014

value: IIIA


title: Patient 13 GF201 013

value: IIIB


title: U1C-TAP (U1 snRNP) ChIP-CHIP

status: Public on Jan 22 2007

state: MA

country: USA

description: S. cerevisiae U1 ChIP-CHIP

organism: Saccharomyces cerevisiae

source_name: Immunoprecipitated genomic DNA from U1C-TAP immunoprecipitation

tag: S. cerevisiae strain expressing C-terminal TAP tagged U1C

source_name: Input genomic DNA from U1C-TAP immunoprecipitation


title: Patient 10 GF201 010

value: LA

value: IIA


title: Patient 7 GF201 007


title: Patient 6 GF201 006


title: Patient 8 GF201 008


title: Patient 4 GF201 004

value: IB


title: Patient 9 GF201 009


title: Patient 3 GF201 003


title: Patient 5 GF201 005


title: Prp8-TAP (U5 snRNP) ChIP-CHIP

description: S. cerevisiae U5 ChIP-CHIP

source_name: Immunoprecipitated genomic DNA from Prp8-TAP immunoprecipitation

tag: S. cerevisiae strain expressing C-terminal TAP tagged Prp8

source_name: Input genomic DNA from Prp8-TAP immunoprecipitation


title: Patient 50 GF200 050

description: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the GeneFilters (Invitrogen) with slight modification.  The GeneFilters were prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe.  Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience).  The arrays were then washed twice with a solution containing 2 mM of MgCl2, 50 mM of Tris and 100 mM of NaCl, and with a solution containing 2 mM of MgCl2, 50 mM of Tris and 15 mM of NaCl.  All procedures were carried out with the aid of custom-made AutoHybridizers (Fuji Photo Film, Tokyo, Japan).  The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified with ArrayGauge software (Fuji Photo Film).  After each hybridization, the arrays were stripped by boiling them in 0.5% SDS solution for 60 min and scanned for residual hybridization before the next round of hybridization with a newly labeled probe of the same sample to acquire their expression profiles in duplicate.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF200 array.

value: SQ


title: Patient 48 GF200 048


title: Patient 49 GF200 049


title: Patient 1 GF201 001


title: Patient 47 GF200 047


title: Patient 46 GF200 046


title: Patient 42 GF200 042


title: Patient 41 GF200 041


title: Patient 44 GF200 044


title: Patient 43 GF200 043


title: Patient 40 GF200 040


title: Patient 45 GF200 045


title: Patient 2 GF201 002


title: Patient 36 GF200 036


title: Patient 35 GF200 035


title: Patient 38 GF200 038


title: Patient 37 GF200 037


title: Patient 33 GF200 033


title: Patient 39 GF200 039


title: Patient 34 GF200 034


title: Patient 30 GF200 030


title: Patient 31 GF200 031


title: Patient 32 GF200 032


title: Patient 28 GF200 028


title: Patient 26 GF200 026


title: Patient 24 GF200 024


title: Patient 25 GF200 025


title: Patient 21 GF200 021


title: Patient 29 GF200 029


title: Patient 22 GF200 022


title: Patient 23 GF200 023


title: Patient 20 GF200 020


title: Patient 19 GF200 019


title: Patient 27 GF200 027


title: Patient 18 GF200 018


title: Patient 17 GF200 017


title: Patient 16 GF200 016


title: Liver_BxD34

city: Sydney

first: Rohan

middle: Benjamin Hugh

last: Williams

state: NSW

address: High St, Randwick

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

hyb_protocol: Labeled cDNA was directly compared on a single glass slide two-color microarray containing the Compugen Mouse OligoLibrary representing 21,997 genes and Lucidea Universal ScoreCard (Clive and Vera Ramaciotti Center for Gene Function Analysis, UNSW, Sydney, Australia), in 100 ul of DIGEasy buffer (Roche, Basel, Switzerland) with 5 uL each yeast tRNA and calf thymus DNA as blockers (Invitrogen, Mt. Waverley, Vic, Australia). Utility controls from the Lucidea Scorecard were not used, and therefore served as additional negative controls. Hybridized microarrays were washed in 1xSSC, three times in 1xSSC, 0.1%SDS at 50 deg. C, and three times in 1xSSC, dried by centrifugation.

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments, Union City, CA, USA).

data_processing:
Image analysis was performed with the Spot image analysis software
version 2 (CSIRO, Australia, http://experimental.act.cmis.csiro.au/Spot/index.php). All further data processing and statistical analyses were performed using R version 2.0.0 (17). Gene expression data were morph background corrected and log2 transformed. Data for controls and the 232 replicated spots of the housekeeping gene Gapd (NM_008084) were removed prior to normalization to avoid bias. All 31 slides were normalized using print-tip loess (R/limma package) and then applied quantile normalization across arrays.

label: Alexa Fluor 647

organism: Mus musculus

source_name: whole liver, BxD/TyJ strain 34

label_protocol: Equal amounts of total RNA from three replicates of each strain were mixed to give a tissue pool representative of the genetic background. 20 ug of pooled RNA was reverse transcribed (SuperScript III Indirect cDNA Labeling System, Invitrogen, Mt. Waverley, Vic, Australia) and fluorescently labeled with Alexa Fluor 647.

tag: Strain

value: BxD/TyJ strain 34

tag: Gender

tag: Age

value: Eight weeks

tag: Tissue

value: Whole liver

label: Alexa Fluor 555

label_protocol:
20 ug of pooled RNA and 2 ug of Lucidea Universal Scorecard Spike-in (Amersham Biosciences, Castle Hill, NSW, Australia) were reverse transcribed using the
SuperScript III Indirect cDNA Labeling System (Invitrogen,
Mt. Waverley, Vic, Australia) and fluorescently labeled with Alexa
Fluor 555

extract_protocol:
Total RNA was extracted according to the manufacturer's instructions
with Trizol Reagent (Invitrogen, Mt.Waverley, Vic, Australia); purity and
integrity was assessed by OD_260/OD_280 readings greater than 2 and
intact rRNA bands analysis (Agilent Bioanalyzer, Agilent, Forest Hills, Vic,
Australia), respectively. Total RNA from whole liver of 9 individuals was pooled.


title: Patient 15 GF200 015


title: Patient 14 GF200 014


title: Patient 13 GF200 013


title: Ringer's vehicle control pool_n=4 vs. 08_GL3 control siRNA D

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: Two different siRNAs targeting peroxisome proliferator-activated receptor a (Ppara), and two control siRNAs targeting secreted alkaline phosphatase (SEAP) and GL3 were delivered to the mouse liver by hydrodynamic tail vein injection. Four animals per group were treated 48 hours before livers were collected. RNAs were extracted and profiled on a custom-designed mouse oligonucleotide microarray with approximately 25,000 genes. In total, the Ppara siRNA mouse expression profiles included eight profiles for the Ppara siRNAs targeted to two different fragments of the Ppara mRNA sequence, four profiles for the SEAP control siRNA, four profiles for the GL3 control siRNA, and eight profiles for a vehicle control (Ringer solution).

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using a pair of Fluor-Reversed samples normalised using the Rosetta Resolver Agilent Error Model

source_name: Liver

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: Mice were injected in the tail vein using the hydrodynamic technique. Briefly, siRNA (40 µg) was diluted in a volume of Ringer's solution (147 mM NaCl, 4 mM KCl and 1.13 mM CaCl2) equal to 10% of the animal's body weight. The entire volume was injected into the tail vein in 5–7 s using a 3 ml syringe fitted with a 27 gauge needle. See description for specific siRNA or vechicle delivered in the individual experiment

tag: Ringer's vehicle control pool_n=4

tag: 08_GL3 control siRNA D


title: Liver_BxD32

source_name: whole liver, BxD/TyJ strain 32

extract_protocol:
Total RNA was extracted according to the manufacturer's instructions
with Trizol Reagent (Invitrogen, Mt.Waverley, Vic, Australia); purity and
integrity was assessed by OD_260/OD_280 readings greater than 2 and
intact rRNA bands analysis (Agilent Bioanalyzer, Agilent, Forest Hills, Vic,
Australia), respectively.

value: BxD/TyJ strain 32


title: Patient 12 GF200 012

tag: Sample #


title: Liver_BxD36

source_name: whole liver, BxD/TyJ strain 36

value: BxD/TyJ strain 36


title: Liver_BxD39

source_name: whole liver, BxD/TyJ strain 39

value: BxD/TyJ strain 39


title: Ringer's vehicle control pool_n=4 vs. 07_GL3 control siRNA C

tag: 07_GL3 control siRNA C


title: Liver_BxD33

source_name: whole liver, BxD/TyJ strain 33

value: BxD/TyJ strain 33

value: Male


title: Liver_BxD38

source_name: whole liver, BxD/TyJ strain 38

value: BxD/TyJ strain 38


title: Ringer's vehicle control pool_n=4 vs. 06_GL3 control siRNA B

tag: 06_GL3 control siRNA B


title: Liver_BxD42

source_name: whole liver, BxD/TyJ strain 42

value: BxD/TyJ strain 42


title: Ringer's vehicle control pool_n=4 vs. 05_GL3 control siRNA A

tag: 05_GL3 control siRNA A


title: Ringer's vehicle control pool_n=4 vs. 16_SEAP-M control siRNA D

tag: 16_SEAP-M control siRNA D


title: Patient 10 GF200 010

tag: Survival Period

tag: status after 5 years

value: Alive

tag: HIST

tag: AGE

tag: SEX


title: Patient 11 GF200 011

value: Dead

value: AD

tag: pStage

value: IIB

tag: pT

tag: pN


title: Liver_BxD40

source_name: whole liver, BxD/TyJ strain 40

tag: Strain

value: BxD/TyJ strain 40

tag: Gender

tag: Age


title: Ringer's vehicle control pool_n=4 vs. 15_SEAP-M control siRNA C

tag: Ringer's vehicle control pool_n=4

tag: 15_SEAP-M control siRNA C


title: Patient 9 GF200 009

tag: Sample #

value: IIIA


title: Liver_BxD31

source_name: whole liver, BxD/TyJ strain 31

value: BxD/TyJ strain 31

tag: Tissue


title: Liver_BxD29

source_name: whole liver, BxD/TyJ strain 29

value: BxD/TyJ strain 29


title: Liver_BxD23

source_name: whole liver, BxD/TyJ strain 23

value: BxD/TyJ strain 23

value: Eight weeks


title: Liver_BxD28

source_name: whole liver, BxD/TyJ strain 28

value: BxD/TyJ strain 28

value: Whole liver


title: Liver_BxD21

source_name: whole liver, BxD/TyJ strain 21

value: BxD/TyJ strain 21


title: Patient 8 GF200 008

source_name: primary lung cancer

value: Female


title: Ringer's vehicle control pool_n=4 vs. 13_SEAP-M control siRNA A

tag: 13_SEAP-M control siRNA A


title: Patient 7 GF200 007

value: IIA


title: Liver_BxD22

source_name: whole liver, BxD/TyJ strain 22

value: BxD/TyJ strain 22

value: Male


title: Ringer's vehicle control pool_n=4 vs. 12_PPARa siRNA D

tag: 12_PPARa siRNA D


title: Liver_BxD27

source_name: whole liver, BxD/TyJ strain 27

value: BxD/TyJ strain 27


title: Liver_BxD24

source_name: whole liver, BxD/TyJ strain 24

value: BxD/TyJ strain 24


title: Patient 6 GF200 006

tag: Survival Period

value: Dead

value: AD


title: Ringer's vehicle control pool_n=4 vs. 14_SEAP-M control siRNA B

source_name: Liver

tag: 14_SEAP-M control siRNA B


title: Ringer's vehicle control pool_n=4 vs. 10_PPARa siRNA B

tag: 10_PPARa siRNA B


title: Ringer's vehicle control pool_n=4 vs. 11_PPARa siRNA C

tag: 11_PPARa siRNA C


title: Patient 4 GF200 004

tag: status after 5 years

tag: HIST

tag: AGE

tag: SEX

value: IB


title: Patient 5 GF200 005

value: Alive

tag: pStage

value: IA

tag: pT

tag: pN


title: Patient 3 GF200 003

value: LA


title: Liver_BxD18

source_name: whole liver, BxD/TyJ strain 18

tag: Strain

value: BxD/TyJ strain 18

tag: Gender

tag: Age


title: Liver_BxD14

source_name: whole liver, BxD/TyJ strain 14

value: BxD/TyJ strain 14

value: Eight weeks

tag: Tissue


title: Ringer's vehicle control pool_n=4 vs. 09_PPARa siRNA A

tag: Ringer's vehicle control pool_n=4

tag: 09_PPARa siRNA A


title: Patient 2 GF200 002

tag: Sample #

tag: Survival Period

value: SQ

value: IIIA


title: Myc ChIP-chip in HeLa cells replicate 3

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Arrays used for the ChIP are Nimblegen Hg17 arrays

hyb_protocol: Nimblegen proprietary protocol

scan_protocol: Nimblegen proprietary protocol

data_processing: Data was normalized by Nimblegen

source_name: Myc ChIP performed in HeLa cells

label_protocol: Nimblegen proprietary protocol

extract_protocol:
Cells were cross-linked by addition of formaldehyde (1 % final concentration) directly to tissue
culture plates for 7 min at room temperature. Cross-linking was terminated by adding glycine to
a final concentration of 125 mM. Cells were washed with cold phosphate-buffered saline (PBS)
containing PMSF, scraped off the plates, collected by centrifugation and washed again. After
centrifugation, the pellet was resuspended in SDS lysis buffer (1 % SDS, 10 mM EDTA, 50 mM
Tris-Cl pH 8.1, plus protease inhibitors) and incubated at room temperature for 20 min. Cells
were sonicated on ice and fragmented DNA was visualized on an agarose gel (average size 1
kb). The sample was centrifuged at 12000 rpm at 4 °C for 10 min and 10x ChIP dilution buffer
(0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, plus
protease inhibitors) was added to the collected supernatant. Sample was pre-cleared with
protein A-agarose beads (previously washed with 10x ChIP dilution buffer) at 4 °C for 1 hr. Pre-
cleared chromatin was incubated with the specific antibody at 4 °C
overnight. Pre-washed
protein A-agarose beads were added and protein-DNA complexes were recovered after a 2
hour incubation at 4 °C. Immunoprecipitated complexes were successively washed with Low-
salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5,
150 mM NaCl), High-salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50
mM HEPES pH 7.5, 500 mM NaCl), LiCl wash buffer (250 mM LiCl, 0.5 % NP-40, 0.5 %
Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM
EDTA). SDS elution buffer was added and incubated at 65 °C for 30 min to recover protein-DNA
complexes. Crosslinks were reversed by incubating at 65 °C overnight. The sample was treated
with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet
was resuspended in 25 µl of water.

tag: Myc ChIP enriched DNA derived from formaldehyde cross-linked HeLa cells using anti-myc antibody.

source_name: Mock IP performed in HeLa cells

extract_protocol: The protocol for Channel 1 was followed except that the antibody was left out.

tag: DNA derived from a mock IP performed in formaldehyde cross-linked HeLa cells.


title: Ringer's vehicle control pool_n=4 vs. 19_PPARa-M siRNA C

tag: 19_PPARa-M siRNA C


title: Liver_BxD13

source_name: whole liver, BxD/TyJ strain 13

value: BxD/TyJ strain 13

value: Whole liver


title: Ringer's vehicle control pool_n=4 vs. 20_PPARa-M siRNA D

tag: 20_PPARa-M siRNA D


title: Patient 1 GF200 001

source_name: primary lung

tag: status after 5 years

tag: HIST

tag: AGE

value: IIB


title: Myc ChIP-chip in HeLa cells replicate 2


title: Myc ChIP-chip in serum stimulated fibroblasts set 3

source_name: Myc ChIP performed in serum stimulated 2091 fibroblasts

tag: Myc ChIP enriched DNA derived from formaldehyde cross-linked serum stimulated 2091 fibroblasts using anti-myc antibody.

source_name: Mock IP performed in serum stimulated 2091 fibroblasts

tag: DNA derived from a mock IP performed in formaldehyde cross-linked serum stimulated fibroblasts.


title: Liver_BxD12

source_name: whole liver, BxD/TyJ strain 12

tag: Strain

value: BxD/TyJ strain 12

value: Male


title: Liver_BxD16

source_name: whole liver, BxD/TyJ strain 16

value: BxD/TyJ strain 16

tag: Gender


title: Ringer's vehicle control pool_n=4 vs. 18_PPARa-M siRNA B

tag: 18_PPARa-M siRNA B


title: Ringer's vehicle control pool_n=4 vs. 04_Ringer's vehicle control D

tag: 04_Ringer's vehicle control D


title: Myc ChIP-chip in HeLa cells replicate 1


title: Ringer's vehicle control pool_n=4 vs. 03_Ringer's vehicle control C

tag: Ringer's vehicle control pool_n=4

tag: 03_Ringer's vehicle control C


title: Myc ChIP-chip in serum stimulated fibroblasts set 1

tag: DNA derived from a mock IP performed in formaldehyde cross-linked DNA serum stimulated fibroblasts.


title: Ringer's vehicle control pool_n=4 vs. 17_PPARa-M siRNA A

tag: 17_PPARa-M siRNA A


title: Ringer's vehicle control pool_n=4 vs. 02_Ringer's vehicle control B

tag: 02_Ringer's vehicle control B


title: Myc ChIP-chip in serum stimulated fibroblasts set 2


title: Myc ChIP-chip in serum starved fibroblasts set 3

source_name: Myc ChIP performed in 2091 fibroblasts

tag: Myc ChIP enriched DNA derived from formaldehyde cross-linked serum starved 2091 fibroblasts using anti-myc antibody.

source_name: Mock IP performed in 2091 fibroblasts

tag: DNA derived from a mock IP performed in formaldehyde cross-linked serum starved fibroblasts.


title: Liver_BxD11

source_name: whole liver, BxD/TyJ strain 11

value: BxD/TyJ strain 11

tag: Age

tag: Tissue


title: Liver_BxD20

source_name: whole liver, BxD/TyJ strain 20

value: BxD/TyJ strain 20


title: Liver_BxD15

source_name: whole liver, BxD/TyJ strain 15

value: BxD/TyJ strain 15


title: Ringer's vehicle control pool_n=4 vs. 01_Ringer's vehicle control A

tag: 01_Ringer's vehicle control A


title: Liver_BxD8

source_name: whole liver, BxD/TyJ strain 8

value: BxD/TyJ strain 8


title: Htb1_K123R;htb2_delta0 vs. htb2_delta0 (array3)

status: Public on Jan 19 2007

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

country: Canada

institute: University of Western Ontario

description: Experiment was performed to analyze the effects of a histone H2 variant that cannot be ubiquitylated on gene expression.  This array is one of three replicates including one dye-swap.

hyb_protocol: Hybridization was performed at MOgene LC (St. Louis, MO).  Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment.  Wash conditions used were as outlined in the Agilent processing manual.

scan_protocol: Scanning was performed at MOgene LC (St. Louis, MO) using an Agilent scanner.

data_processing: Data processing was performed at MOgene LC (St. Louis, MO).  Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.

source_name: Cy3: CY1272 (Htb1_K123R; htb2_delta0) (Turner SD, et al. 2002. Mol Cell Biol 22:4011-4019)

label_protocol: Labeling was performed at MOgene LC (St. Louis, MO).  Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies).  1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.).  The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.).  All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.

extract_protocol: RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.

source_name: Cy5: By13026 (htb2_delta0)


title: Terephthalate 3rdTPAcy5Pycy3

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

institute: University of British Columbia

description: To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.

hyb_protocol: The microarray slides were pre-hybridized using 5x SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48oC and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). The hybridization was carried out at 42oC for 18 hours with mixing using 120 μL per slide of SlideHyb#1 hybridization solution (Ambion). The post hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2x SSC plus 0.1% SDS (medium stringency) at 42oC; 0.1x SSC plus 0.05% SDS (high stringency) at 25oC; and 0.1x SSC (low stringency) at 25oC.

scan_protocol: The slides scanned with a GenePix 4000B scanner (Axon Instruments). The spot intensities were quantified using Imagene 5.6 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using the LOWESS method. Average normalized expression ratios (treatment/control) were calculated for each gene and tested for significant variation between treatments (ANOVA p < 0.05).

organism: Rhodococcus jostii RHA1

source_name: experiment

label_protocol: Cy5 labeled cDNA were prepared by indirect labeling.

extract_protocol: Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).

tag: experiment

source_name: control

label_protocol: Cy3 labeled cDNA were prepared by indirect labeling.

tag: control


title: E2F4 chip-chip in serum starved 2091 fibroblasts replicate 3

description: Arrays used for the ChIP are Nimblegen hg17 ENCODE arrays

source_name: E2F4 ChIP performed in serum starved 2091 fibroblasts

extract_protocol: 2091 fibroblasts  were cross-linked by addition of formaldehyde (1 % final concentration) directly to tissue culture plates for 7 min at room temperature. Cross-linking was terminated by adding glycine to a final concentration of 125 mM. Cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. After centrifugation, the pellet was resuspended in SDS lysis buffer (1 % SDS, 10 mM EDTA, 50 mM Tris-Cl pH 8.1, plus protease inhibitors) and incubated at room temperature for 20 min. Cells were sonicated on ice and fragmented DNA was visualized on an agarose gel (average size 1 kb). The sample was centrifuged at 12000 rpm at 4 °C for 10 min and 10x ChIP dilution buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, plus protease inhibitors) was added to the collected supernatant. Sample was pre-cleared with protein A-agarose beads (previously washed with 10x ChIP dilution buffer) at 4 °C for 1 hr. Pre- cleared chromatin was incubated with an antibody against E2F4 (sc-1082x, Santa Cruz) at 4 °C overnight. Pre-washed protein A-agarose beads were added and protein-DNA complexes were recovered after a 2 hour incubation at 4 °C. Immunoprecipitated complexes were successively washed with Low- salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), High-salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), LiCl wash buffer (250 mM LiCl, 0.5 % NP-40, 0.5 % Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). SDS elution buffer was added and incubated at 65 °C for 30 min to recover protein-DNA complexes. Crosslinks were reversed by incubating at 65 °C overnight. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25 µl of water.

tag: E2F4 ChIP enriched DNA derived from formaldehyde cross-linked serum starved 2091 fibroblasts using anti-e2f4 antibody.

source_name: Mock IP performed in serum starved 2091 fibroblasts

extract_protocol: The protocol for Channel 1 was followed except that the anti-e2f4 antibody was left out.

tag: DNA derived from a mock IP performed in formaldehyde cross-linked serum starved 2091 fibroblasts.


title: Cholesterol 1stCholcy5Pycy3


title: Htb1_K123R;htb2_delta0 vs. htb2_delta0 (array1)

source_name: Cy5: BY13026 (htb2_delta0)


title: htb2_delta0 vs. Htb1_K123R;htb2_delta0 (array2)

source_name: Cy3: BY13026 (htb2_delta0)

source_name: Cy5: CY1272 (Htb1_K123R; htb2_delta0) (Turner SD, et al. 2002. Mol Cell Biol 22:4011-4019)


title: Cholesterol 2ndCholcy3Pycy5


title: Terephthalate 2ndTPAcy5Pycy3


title: Myc ChIP-chip in serum starved fibroblasts set 2


title: Cholesterol 3rdCholcy5Pycy3


title: Liver_BxD6

source_name: whole liver, BxD/TyJ strain 6

tag: Strain

value: BxD/TyJ strain 6

tag: Gender


title: E2F4 chip-chip in serum starved 2091 fibroblasts replicate 2

source_name: E2F4 ChIP performed on serum starved 2091 fibroblasts

extract_protocol: 2091 fibroblasts were cross-linked by addition of formaldehyde (1 % final concentration) directly to tissue culture plates for 7 min at room temperature. Cross-linking was terminated by adding glycine to a final concentration of 125 mM. Cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. After centrifugation, the pellet was resuspended in SDS lysis buffer (1 % SDS, 10 mM EDTA, 50 mM Tris-Cl pH 8.1, plus protease inhibitors) and incubated at room temperature for 20 min. Cells were sonicated on ice and fragmented DNA was visualized on an agarose gel (average size 1 kb). The sample was centrifuged at 12000 rpm at 4 °C for 10 min and 10x ChIP dilution buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, plus protease inhibitors) was added to the collected supernatant. Sample was pre-cleared with protein A-agarose beads (previously washed with 10x ChIP dilution buffer) at 4 °C for 1 hr. Pre- cleared chromatin was incubated with an antibody against E2F4 (sc-1082x, Santa Cruz) at 4 °C overnight. Pre-washed protein A-agarose beads were added and protein-DNA complexes were recovered after a 2 hour incubation at 4 °C. Immunoprecipitated complexes were successively washed with Low- salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), High-salt wash buffer (0.1 % Deoxycholate, 1 % Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), LiCl wash buffer (250 mM LiCl, 0.5 % NP-40, 0.5 % Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). SDS elution buffer was added and incubated at 65 °C for 30 min to recover protein-DNA complexes. Crosslinks were reversed by incubating at 65 °C overnight. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25 µl of water.


title: Myc ChIP-chip in serum starved fibroblasts set 1

source_name: Myc ChIP performed in 2091 fibroblasts


title: Phthalate 3rdPTHcy5Pycy3


title: fast(un-amplified RNA) compared to slow(amplified RNA)

status: Public on Jan 18 2007

city: Baltimore

first: Xiaodong

last: Mu

state: MD

address: 108 N. Greene street

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

description:
This is array 1 of a loop design (4 arrays in total).
Each gene has 6 replicates in one array.

hyb_protocol: Equal amounts (2 ug) of Cy3 and Cy5 labeled cRNA or CDNA probes were mixed, plus 10ug of mouse cot-1 DNA to block unspecific binding. Array hybridization was conducted with presence of 50% formamide (Invitrogene), 5 X SSC, and 0.1% SDS. The volumn of hybridization buffer was adjusted to 10ul. The custom spotted microarray slides was treated with prehybridization buffer (5X SSC, 0.1% SDS, and 1% BSA) at 42°C for 45 mins, and then washed with dH2O and 95% ethanol. The hybridization chamber (GeneMachines) carrying the microarry slides was put in the sealed wet box at 42°C for 14-16 hrs.

scan_protocol: Slides were scanned with a GSI Lumonics ScanArray 5000 chip scanner. with Cy3 being scanned at a wavelength of 532nm and Cy5 being scanned at a wavelength of 635nm. All scanning were conducted with same PMT gain and varying laser power. ImaGene5.5 (BioDiscovery) was used for image analysis.

data_processing:
TIFF files produced from the scanner were loaded to ImaGene5.5 (BioDiscovery) for image measurement and collecting the expression data. Data from ImaGene5.5 were converted to TAV file with TIGR-ExpressConverter. The integral signal intensities of the spots were used for data process.
TIGR Midas was used for checking the quality of the result and doing data normalization and filtering. “Total intensity normalization” method was selected partially because of similar number of fast and slow genes in our list of marker genes. “Slice analysis” function was used to classify and filter data to eliminate bad spots. The mean value of the 6 spots for one gene was gotten to do data interpretion.

source_name: fast skeletal muscle (FDB)-un-amplified RNA

label_protocol: cDNA-probe was produced from un-amplified mRNA, with a protocol from Brown’s lab and TIGR, with some modification. 10µg of total RNA from soleus was reverse transcribed with oligo(dT) priming and reverse transcriptase SuperScript II (Life Technologies), to get amino-ally-dUTP (Sigma) incorporated cDNA, and then coupled with Cy3 or Cy5 dye (AmershamPharmacia) to get dye-coupled cDNA-probe. All dye-coupling reactions were carried out in the presence of 16.67% of 1M sodium bicarbonate (Invitrogene/ Molecular probes) and 50% of DMSO (Sigma).

extract_protocol: The soleus or FDB muscle was isolated from 4-5 week old CD-1 mice. 1.0 ML of Trizol reagent (Invitrogen) was used to extract total RNA from each piece of muscle. And Ivitrogen protocol of Trizol reagent was followed.

tag: cDNA probes produced with total RNA isolated from slow skeletal muscle soleus

molecule: polyA RNA

source_name: slow skeletal muscle (soleus)-amplified RNA

tag: cRNA probes was produced with amplified RNA (Ambion amino ally MessageAMP II aRNA kit). Original RNA was isolated from over 100 cultured FDB fibers.


title: E2F4 chip-chip in serum starved 2091 fibroblasts replicate 1

source_name: Mock IP performed on formaldehyde cross-linked 2091 fibroblasts

tag: Mock IP derived DNA from formaldehyde cross-linked serum starved 2091 fibroblasts.


title: Liver_BxD1

source_name: whole liver, BxD/TyJ strain 1

value: BxD/TyJ strain 1


title: wt vs. ubp8_delta0 (array1)

description: Experiment was performed to analyze the effects of a histone H2 variant that cannot be ubiquitylated on gene expression.  This array is one of two dye-swapped replicates.

source_name: Cy5: BY10809 (ubp8_delta0)


title: ubp8_delta0 vs. wt (array2)

source_name: Cy3: BY10809 (ubp8_delta0)


title: Liver_BxD2

source_name: whole liver, BxD/TyJ strain 2

value: BxD/TyJ strain 2


title: slow(un-amplified RNA) compared to fast(amplified RNA)

source_name: slow skeletal muscle (soleus)-un-amplified RNA

source_name: fast skeletal muscle (FDB)-amplified RNA


title: Phthalate 2ndPTHcy5Pycy3

source_name: experiment

source_name: control


title: Phthalate 1stPTHcy5Pycy3


title: fast(amplified RNA) compared to fast(un-amplified RNA)


title: Htb1(K123R);htb2_delta0 vs. wt (array2)

source_name: Cy3: CY1272 (Htb1_K123R; htb2_delta0) (Turner SD, et al. 2002. Mol Cell Biol 22:4011-4019)


title: Htb1(K123R);htb2_delta0;ubp8_delta0 vs. wt (array2)


title: ES/Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 3)

description:
This is one array of a reference design (2 arrays in total).
Each gene has 6 replicates in one array.

hyb_protocol: Equal amounts (2 ug) of Cy3 and Cy5 labeled cRNA probes were mixed, plus 10ug of mouse cot-1 DNA to block unspecific binding. Array hybridization was conducted with presence of 50% formamide (Invitrogene), 5 X SSC, and 0.1% SDS. The volumn of hybridization buffer was adjusted to 10ul. The custom spotted microarray slides was treated with prehybridization buffer (5X SSC, 0.1% SDS, and 1% BSA) at 42°C for 45 mins, and then washed with dH2O and 95% ethanol. The hybridization chamber (GeneMachines) carrying the microarry slides was put in the sealed wet box at 42°C for 14-16 hrs.

source_name: day 3 of Kn62 treated FDB fibers subjected to slow-type electric-stimulation

label_protocol: mRNA amplification and probe-labeling were conducted with Amino Ally MessageAMP™ II aRNA kit (Ambion), to get Cy3-coupled or Cy5-coupled cRNA probes. Dye coupling reactions were carried out in the presence of 16.67% of 1M sodium bicarbonate (Invitrogene/ Molecular probes) and 50% of DMSO (Sigma).

growth_protocol: FDB fibers was cultured in MEM with 10% FBS and and 50ug/ml gentamicin sulfate. Cultures were maintained in an incubator at 5% CO2, 37°C. here, fibers were cultured for 3 days (day 3).

extract_protocol: 1.0 ML of Trizol reagent (Invitrogen) was used to extract total RNA from over 100 single FDB fibers. And Ivitrogen protocol of Trizol reagent was followed.

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN62, another specific CaMK pathway inhibitor (like KN93), and subjected to slow-fiber-type pattern of electrical stimulation.

source_name: reference sample

tag: Amplified RNA from a mix of equal amount original RNA from both fast and slow muscle.


title: ES/Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 2)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN62, another specific CaMK pathway inhibitor (like KN93), without slow-fiber-type pattern of electrical stimulation.


title: 3 days of unstimulated culture(denervation)(exp3)

description:
This is one array of a reference design (2 arrays in total).
Each gene has 6 replicates in one array.The mean value of the 6 spots for one gene was gotten do data interpretion.
TIFF files produced from the scanner were loaded to ImaGene5.5 (BioDiscovery) for image measurement and collecting the expression data. Data from ImaGene5.5 were converted to TAV file with TIGR-ExpressConverter. The integral signal intensities of the spots were used for data process.

data_processing:
TIFF files produced from the scanner were loaded to ImaGene5.5 (BioDiscovery) for image measurement and collecting the expression data. Data from ImaGene5.5 were converted to TAV file with TIGR-ExpressConverter. The integral signal intensities of the spots were used for data process.
TIGR Midas was used for checking the quality of the result and doing data normalization and filtering. “Total intensity normalization” method was selected partially because of similar number of fast and slow genes in our list of marker genes. “Slice analysis” function was used to classify and filter data to eliminate bad spots. The mean value of the 6 spots for one gene was gotten do data interpretion.

source_name: Day 3 of unstimulated culture of single FDB fibers

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes , without any treatment (electrical stimulation, chemical application et. al.).


title: 0 day of unstimulated culture(denervation)(exp3)

source_name: Day 0 of unstimulated culture of single FDB fibers

growth_protocol: FDB fibers was cultured in MEM with 10% FBS and and 50ug/ml gentamicin sulfate. Cultures were maintained in an incubator at 5% CO2, 37°C. here, fibers were cultured for 2 hrs (day 0).


title: wt vs. Htb1(K123R);htb2_delta0;ubp8_delta0 (array1)


title: Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 3)

source_name: day 3 of Kn62 treated FDB fibers


title: slow(amplfied) compared to slow(un-amplified RNA)


title: ES/Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 1)


title: Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 2)


title: Terephthalate 1stTPAcy5Pycy3


title: Liver_BxD19

source_name: whole liver, BxD/TyJ strain 19

value: BxD/TyJ strain 19


title: ES/Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 3)

source_name: day 3 of Kn92 treated FDB fibers subjected to slow-type electric-stimulation

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN92, the negative control of CaMK pathway inhibitor KN93, and subjected to slow-fiber-type pattern of electrical stimulation.


title: Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 3)

source_name: day 3 of Kn92 treated FDB fibers


title: Kn62 treated fibers to control (ES+Kn62 vs Kn62)(exp 1)


title: Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 2)/(Kn93 vs Kn92-unstimulated)(exp1)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN92, the negative control of CaMK pathway inhibitor KN93, without slow-fiber-type pattern of electrical stimulation.


title: ES/Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 1)


title: ES/Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 2)


title: Kn93 treated fibers to control (ES+Kn93 vs Kn93)(exp3)

source_name: day 3 of Kn93 treated FDB fibers

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN93, the specific CaMK pathway inhibitor, without slow-fiber-type pattern of electrical stimulation.


title: Liver_BxD9

source_name: whole liver, BxD/TyJ strain 9

value: BxD/TyJ strain 9

value: Eight weeks


title: ES/Kn93 treated fibers to control (ES+Kn93 vs Kn93)(exp 3)

source_name: day 3 of Kn93 treated FDB fibers subjected to slow-type electirc-stimulation

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN93, the specific CaMK pathway inhibitor, and subjected to slow-fiber-type pattern of electrical stimulation.


title: ES/Kn93 treated fibers to control (ES+Kn93 vs Kn93)(exp 2)


title: Kn93 treated fibers to control (ES+Kn93 vs Kn93)(exp2)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN93, the specific CaMK pathway inhibitor, without slow-fiber type pattern of electrical stimulation.


title: wt vs. Htb1(K123R);htb1_delta0 (array1)

source_name: Cy5: CY1272 (Htb1_K123R; htb2_delta0) (Turner SD, et al. 2002. Mol Cell Biol 22:4011-4019)


title: Kn93 treated fibers to control (ES+Kn93 vs  Kn93)(exp1)/Kn93 vs Kn92-unstimulated)(exp2)


title: ES/Kn93 treated fibers to control (ES+Kn93 vs Kn93)(exp1)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN93, the specific CaMK pathway inhibitor, and subjected to slow-fiber type pattern of electrical stimulation.


title: liver_BxD5

source_name: whole liver, BxD/TyJ strain 5

value: BxD/TyJ strain 5


title: ES/Kn92 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp3)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN92, the negative control of the specific CaMK pathway inhibitor KN93, and subjected to slow-fiber type pattern of electrical stimulation.


title: ES/Kn93 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp1)

source_name: day 3 of Kn93 treated FDB fibers subjected to slow-type electric-stimulation


title: Kn93 treated fibers to control (Kn93 vs Kn92-unstimulated)(exp3)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN93, the specific CaMK pathway inhibitor.


title: ES/Kn92 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp1)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN92, the negative control of CaMK pathway inhibitor KN93, and subjected to slow-fiber type pattern of electrical stimulation.


title: ES/Kn93 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp3)


title: Kn93 treated fibers to control (Kn93 vs Kn92-unstimulated)(exp1)


title: Kn92 treated fibers to control (Kn93 vs Kn92-unstimulated)(exp3)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and treated with KN92, the negative control of CaMK pathway inhibitor KN93.


title: ES/Kn93 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp2)


title: Kn92 treated fibers to control (Kn93 vs Kn92-unstimulated)(exp2)


title: Kn92 treated fibers to control (ES+Kn92 vs Kn92)(exp 1)


title: ES/Kn92 treated fibers to control (Kn93 vs Kn92-Electric-stimulated)(exp2)


title: control to fibers overexpression calcineurin(calcineurin pathway)(exp3)

description:
This is one array of a dye-swap design (2 arrays in total).
Each gene has 6 replicates in one array.The mean value of the 6 spots for one gene was gotten do data interpretion.

source_name: Day 3 of cultured single FDB fibers overexpressing NFAT-GFP

growth_protocol: FDB fibers was cultured in MEM with 10% FBS and and 50ug/ml gentamicin sulfate. Cultures were maintained in an incubator at 5% CO2, 37°C. here, fibers were cultured for 3 days after virus infection (day 3).

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and infected with adenovirus encoding NFAT-GFP only.

source_name: Day 3 of cultured single FDB fibers overexpressing constitutively active calcineurin plus NFAT-GFP

growth_protocol: same as channel 1


title: fibers overexpression calcineurin to control(calcineurin pathway)(exp2)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and infected with adenoviruses encoding constitutively active calcienrin plus NFAT-GFP.


title: fibers overexpression calcineurin to control(calcineurin pathway)(exp3)


title: control to fibers overexpression calcineurin(calcineurin pathway)(exp2)


title: control to 3 days of treated culture (electrical stimulation)(exp2)

source_name: Day 3 of un-stimulated culture of single FDB fibers(control)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and subjected to NO electrical stimulation.

source_name: Day 3 of electric-stimulated culture of single FDB fibers


title: 3 days of treated culture to control (electrical stimulation)(exp3)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and subjected to chronical slow-twitch-fiber pattern of electrical stimulation.


title: fibers overexpression calcineurin to control(calcineurin pathway)(exp1)


title: 3 days of treated culture to control (electrical stimulation)(exp2)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, and to chronical slow-twitch-fiber pattern of electrical stimulation.


title: control to fibers overexpression calcineurin(calcineurin pathway)(exp1)


title: control to 3 days of treated culture (electrical stimulation)(exp1)


title: control to 3 days of treated culture (electrical stimulation)(exp3)


title: 0 day of unstimulated culture(denervation)(exp2)

molecule: cytoplasmic RNA

source_name: reference sample


title: 3 days of treated culture  to control (electrical stimulation)(exp1)


title: 0 day of unstimulated culture(denervation)(exp1)

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes, without any treatment (electrical stimulation, chemical application et. al.).


title: slow compared to fast (amplified RNA)

description:
Each gene has 6 replicates in one array.The mean value of the 6 spots for one gene was gotten do data interpretion.
TIFF files produced from the scanner were loaded to ImaGene5.5 (BioDiscovery) for image measurement and collecting the expression data. Data from ImaGene5.5 were converted to TAV file with TIGR-ExpressConverter. The integral signal intensities of the spots were used for data process.

source_name: slow skeletal muscle (soleus)

tag: cRNA probes was produced with amplified RNA (Ambion amino ally MessageAMP II aRNA kit) from slow skeletal muscle soleus.

source_name: fast skeletal muscle (FDB)

tag: cRNA probes was produced with amplified RNA (Ambion amino ally MessageAMP II aRNA kit) from fast skeletal muscle FDB.


title: 3 days of unstimulated culture(denervation)(exp1)

source_name: Day 3 of unstimulated culture of single FDB fibers

treatment_protocol: whole FDB muscle was isolated from 4-5 week old CD-1 mice, and dissociated to get single FDB fibers. FDB fibers was cultured in 35mm plastic dishes , without any treatment (electrical stimulation, chemical application et. al.).


title: slow compared to fast(un-amplified RNA)

tag: cDNA probes produced with total RNA isolated from fast skeletal muscle FDB


title: fast compared to slow (amplified RNA)


title: Resveratrol+Beta-naphthoflavone (RB.B.2)Cy3 Vs Reference RNA Cy5

status: Public on Jan 17 2007

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

institute: Woods Hole Oceanographic Institution

description: Same reference RNA was used for hybridization of all the samples in the experiment.

hyb_protocol: Before hybridization, the Cy3 and Cy5 labeled samples were combined and dried in a speed vac. To the dried sample 26 l of hybridization buffer and 2 µl each of calf thymus DNA (10 mg/ml) and yeast tRNA (10 mg/ml) were added. The samples were denatured for 2 min at 95°C, snap cooled on ice for 1 min, and centrifuged for 1 min at maximum speed. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization was carried out overnight in a water bath at 37°C.

scan_protocol: Image analysis was carried out using Versarray chipreader software Version 3.1 (BioRad, Canada). For each microarray slide, two images were produced by illuminating the array at 635 nm (excitation of Cy5) and 532 nm (Cy3). For both illuminations, photomultiplier tube (gain and light amplification) settings were at 900 and laser power was set at 90%. All images were captured in a TIFF format.

data_processing: The data analysis followed microarray data analysis system (MIDAS) (Saeed et al.,2003). Poor or negative control spots were flagged as unreliable and were excluded from the analysis. For each spot, signal/noise (SN) threshold was calculated using the following formula: [I(A or B) + Bkg (A or B)]/ Bkg(A or B), where I(A) and I (B) denotes background corrected signal intensity for channel A and B;  Bkg(A) and Bkg(B) denotes background intensity for channel A and B respectively. The SN ratios for each channel was compared to the set threshold value of 2.0 and any spots which are less than or equal to 2.0 were marked as bad and excluded from downstream analysis. The data were then LOWESS normalized before calculating the gene expression ratios. The data for each treatment (fold change relative to the reference pool) was calculated as a ratio of normalized gene intensity for the sample to that of the reference on each slide.

organism: Oncorhynchus mykiss

label_protocol: Thirty micrograms of intact total RNA (either treatment sample or RP) were indirectly labeled with Cy3 following the TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) (Amersham Biosciences, Piscataway, NJ).

extract_protocol: Total RNA was extracted from the liver tissue using the RNAeasy extraction kit (Qiagen,ON). The quality of the total RNA obtained was checked by gel electrophoresis on a 1% agarose gel containing ethidium bromide and the concentration was determined spectrophotometrically at 260/280 nm using Cary 50 UV-Vis spectrophotometer (Varian Inc, ON).

treatment_protocol: Juvenile rainbow trout were exposed to both Resveratrol (20 mg/kg/day) and beta-naphthoflavone (10mg/kg/day) laced feed for 5 days before sampling brain tissue.

tag: Juvenile rainbow trout brain tissue exposed to resveratrol and beta-naphthoflavone.

source_name: Reference RNA

label_protocol: Thirty micrograms of intact total RNA (either treatment sample or RP) were indirectly labeled with Cy5 following the TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) (Amersham Biosciences, Piscataway, NJ).

treatment_protocol: Reference RNA was obtained by pooling equal concentrations of total RNA from all the treatments.

tag: Juvenile rainbow trout brain tissue


title: Reference RNA Cy3 Vs Resveratrol (R.B.4.) Cy5

source_name: Resveratrol (R.B.4)

treatment_protocol: Juvenile rainbow trout were exposed to Resveratrol (20 mg/kg/day) laced feed for 5 days before sampling brain tissue.

tag: Juvenile rainbow trout brain tissue exposed to Resveratrol


title: fast compared to slow(un-amplified RNA)


title: Reference RNA Cy3 Vs Resveratrol+Beta-naphthoflavone (RB.B.4)Cy5

description: Same reference RNA pool was used for the hybridizations done in this experiment.

label_protocol: Thirty micrograms of intact total RNA (either treatment sample or RP) were indirectly labeled with Cy5 and Cy3 following the TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) (Amersham Biosciences, Piscataway, NJ).

treatment_protocol: Reference RNA was obtained by pooling equal concentrations of RNA from all the treatments.

treatment_protocol: Juvenile rainbow trout were exposed to both Resveratrol (20 mg/kg/day) and Beta-naphthoflavone (10 mg/kg/day) for 5 days via feed before sampling.


title: Resveratrol (R.B.6.) Cy3 Vs Reference RNA Cy5

source_name: Resveratrol (R.B.6) Cy3

tag: Juvenile rainbow trout brain tissue exposed to resveratrol


title: Resveratrol+Beta-naphthoflavone (RB.B.3)Cy3 Vs Reference RNA Cy5


title: Resveratrol (R.B.3.) Cy3 Vs Reference Cy5

source_name: Resveratrol (R.B.3.)


title: Reference RNA Cy3 Vs Resveratrol+Beta-naphthoflavone (RB.B.3)Cy5


title: BNF (B.B.4.)Cy3 Vs Reference RNA Cy5

description: Same reference total RNA pool was used for all the 16 hybridizations done in the experiment.

hyb_protocol: Before hybridization, the Cy3 and Cy5 labeled samples were combined and dried in a speed vac. To the dried sample 26 ul of hybridization buffer and 2 µl each of calf thymus DNA (10 mg/ml) and yeast tRNA (10 mg/ml) were added. The samples were denatured for 2 min at 95°C, snap cooled on ice for 1 min, and centrifuged for 1 min at maximum speed. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization was carried out overnight in a water bath at 37°C.

source_name: Beta-naphthoflavone (B.B.4)

treatment_protocol: Rainbow trout were fed with beta-naphthoflavone (10 mg/kg body weight) for 5 days and brain tissues were sampled.

tag: Juvenile rainbow trout brain tissue exposed to beta-naphthoflavone

treatment_protocol: Reference RNA was pooled from all the treatment samples.


title: 3 days of unstimulated culture(denervation)(exp2)


title: Control (C.B.4.) Cy5 Vs Reference pool Cy3

description: Same reference RNA pool was used for all the 16 hybridizations done in this experiment.

source_name: Reference pool RNA

treatment_protocol: Brain samples were obtained from rainbow trout fed with either ethanol (vehicle) or treatment (beta-naphthoflavone, resveratrol)laced feed.

tag: Juvenile trout brain tissue

treatment_protocol: Brain samples were obtained from rainbow trout fed with ethanol (vehicle) laced feed.


title: Reference RNA.Cy3 Vs BNF (B.B.3.).Cy5

source_name: Beta-naphthoflavone (B.B.3.)

tag: Juvenile trout brain tissue exposed beta-naphthoflavone.


title: Control (C.B.3)Cy5 Vs Reference pool Cy3


title: BNF (B.B.2) Cy3 Vs Reference pool Cy5

source_name: Beta-naphthoflavone (B.B.2)


title: Reference RNA. Cy3 Vs BNF (B.B.6.).Cy5

source_name: Beta-naphthoflavone (B.B.6.)

tag: Trout brain tissue exposed to beta-naphthoflavone


title: Control (C.B.1.Cy3) Vs pooled Reference Cy5

source_name: Control trout total RNA

tag: Control Brain total RNA samples labelled with Cy3

source_name: Reference total RNA

tag: Reference RNA was obtained by pooling equal quantity of RNA from all the 16 samples used for microarray.


title: TIF1A

city: Nijmegen

first: S

last: Denissov

address: Geert Grooteplein 26

country: Netherlands

institute: NCMLS

description: ChIP

hyb_protocol: ChIP and input DNA was amplified by LM-PCR, labeled with Cy5 and Cy3 using random priming, purified and dissolved in hybridization buffer (33% formamide, 2.5X SSC, 6.6% dextran sulfate). Hybridization was performed overnight at 45oC. Slides were washed at RT for 20 min with 0.1X SSC

scan_protocol: Axon scanner

data_processing: GenePix

source_name: ChIP with chromatin from U2OS cells

label_protocol: random priming

growth_protocol: U2OS cells were growing in DMEM+10%FBS medium,37oC,5%CO2

extract_protocol: ChIP and LMPCR

treatment_protocol: cells were growing normally, without treatment

tag: LMPCR amplified

source_name: input chromatin from U2OS cells

extract_protocol: total DNA


title: AcK9H3

description: ChIP


title: TAFi110

description: ChIP


title: Control (C.B.2.)Cy3 Vs Reference pool Cy5


title: PAF53

description: ChIP


title: 3MeK4H3

description: ChIP


title: TBP

description: ChIP


title: UBF

description: ChIP


title: RPA116

description: ChIP


title: RNAPIII

description: ChIP


title: Bdp1

description: ChIP


title: SNAP19

description: ChIP


title: SNAP50

description: ChIP


title: SNAP45

description: ChIP


title: PCAF

description: ChIP


title: SNAP43

description: ChIP


title: TAF10

description: ChIP


title: CBP_p300

description: ChIP


title: TRRAP

description: ChIP


title: TAF12

description: ChIP


title: SNAP190

description: ChIP


title: TAF1

description: ChIP


title: TAF7

description: ChIP


title: TAF4

description: ChIP


title: Brf1

description: ChIP


title: NC2a

description: ChIP


title: RNAPIICTD

description: ChIP


title: Pancreatic T-eff_anti-ICOS-treated_rep3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA, unlogged

label: Biotin

source_name: pancreatic CD4+CD25- lymphocytes treated with anti-ICOS antibodies

label_protocol: Biotin

extract_protocol: FACS then trizol

tag: Strain

value: NOD

tag: Variant

value: BDC2.5 TCR Tg

tag: Age

value: 26 days

tag: Tissue

value: infiltrated pancreas


title: Pancreatic T-reg_control-treated IgG 2

source_name: pancreatic CD4+CD25+CD69- lymphocytes treated with IgG


title: Pancreatic T-eff_anti-ICOS-treated_rep1


title: Pancreatic T-reg_control-treated IgG 1

value: 4 weeks


title: Pancreatic T-eff_anti-ICOS-treated_rep2


title: TFIIEa

description: ChIP


title: cbc2 deletion 3

city: Fort Worth

first: Yiwei

last: Jiang

address: 3420 darcy Street

department: Cell biology and genetics

institute: University of North Texas Health Science Center

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is cbc2 deletion sample number 3.

hyb_protocol: according to Affymetrics protocol

scan_protocol: according to Affymetrics protocol

data_processing: according to Affymetrics protocol

label: according to Affymetrics protocol

label_protocol: according to Affymetrics protocol

growth_protocol: Cells were grown in SC medium at 30 degree to log phase (OD600=1.0)

extract_protocol: Total RNA was extracted using glass beads/phenol methods. Sample were examined by Northern Blot.

tag: cbc2 deletion strain with Ty1-URA3-33 reporter


title: TFIIB

description: ChIP


title: Pancreatic T-reg_anti-ICOS-treated_rep3

source_name: pancreatic CD4+CD25+ lymphocytes treated with anti-ICOS antibodies


title: cbc2 deletion 2

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is cbc2 deletion sample number 2.


title: Pancreatic T-reg_anti-ICOS-treated_rep1


title: Pancreatic T-reg_anti-ICOS-treated_rep2


title: cbc2 deletion 1

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is cbc2 deletion sample number 1.


title: Wild type 1

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is Wild type sample number 1.

growth_protocol: Cells were grown in SC medium at 30 degree to log phase (OD600=1.0).

tag: Wild type strain with Ty1-URA3-33 reporter


title: Normal prostate tissue adjacent to tumor from patient No.101 PN101U95B

status: Public on Jan 16 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

description: Gene expression data from normal prostate tissue adjacent to tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data 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 200.

label: biotin

source_name: PN101, normal prostate tissue adjacent to tumor from patient No.101

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 minutes of excision and stored in -80C until RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. For prostate tissues adjacent to tumor, samples free of cancer cells, high-grade prostatic neoplasia, or any obvious neoplastic alterations, containing at least 60% glandular cells were selected.

tag: Tissue:normal prostate tissue adjacent to tumor


title: Normal prostate tissue adjacent to tumor from patient No.100 PN100U95B

source_name: PN100, normal prostate tissue adjacent to tumor from patient No.100


title: Normal prostate tissue adjacent to tumor from patient No.107 PN107U95B

source_name: PN107, normal prostate tissue adjacent to tumor from patient No.107


title: Normal prostate tissue adjacent to tumor from patient No.88 PN88U95B

source_name: PN88, normal prostate tissue adjacent to tumor from patient No.88


title: Normal prostate tissue adjacent to tumor from patient No.105 PN105U95B

source_name: PN105, normal prostate tissue adjacent to tumor from patient No.105


title: Normal prostate tissue adjacent to tumor from patient No.92 PN92U95B

source_name: PN92, normal prostate tissue adjacent to tumor from patient No.92


title: Normal prostate tissue adjacent to tumor from patient No.90 PN90U95B

source_name: PN90, normal prostate tissue adjacent to tumor from patient No.90


title: Normal prostate tissue adjacent to tumor from patient No.95 PN95U95B

source_name: PN95, normal prostate tissue adjacent to tumor from patient No.95


title: Normal prostate tissue adjacent to tumor from patient No.94 PN94U95B

source_name: PN94, normal prostate tissue adjacent to tumor from patient No.94


title: Normal prostate tissue adjacent to tumor from patient No.87 PN87U95B

source_name: PN87, normal prostate tissue adjacent to tumor from patient No.87


title: Normal prostate tissue adjacent to tumor from patient No.91 PN91U95B

source_name: PN91, normal prostate tissue adjacent to tumor from patient No.91


title: Wild type 3

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is Wild type sample number 3.


title: Wild type 2

description: The experiment was designed to generate an expression profile for cbc2∆ cells. This is Wild type sample number 2.


title: Normal prostate tissue adjacent to tumor from patient No.107 PN107U95C

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95C array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: Normal prostate tissue adjacent to tumor from patient No.99 PN99U95B

source_name: PN99, normal prostate tissue adjacent to tumor from patient No.99


title: Normal prostate tissue adjacent to tumor from patient No.85 PN85U95B

source_name: PN85, normal prostate tissue adjacent to tumor from patient No.85


title: Normal prostate tissue adjacent to tumor from patient No.86 PN86U95B

source_name: PN86, normal prostate tissue adjacent to tumor from patient No.86


title: Normal prostate tissue adjacent to tumor from patient No.84 PN84U95B

source_name: PN84, normal prostate tissue adjacent to tumor from patient No.84


title: Normal prostate tissue adjacent to tumor from patient No.83 PN83U95B

source_name: PN83, normal prostate tissue adjacent to tumor from patient No.83


title: Normal prostate tissue adjacent to tumor from patient No.81 PN81U95B

source_name: PN81, normal prostate tissue adjacent to tumor from patient No.81


title: Normal prostate tissue adjacent to tumor from patient No.82 PN82U95B

source_name: PN82, normal prostate tissue adjacent to tumor from patient No.82


title: Normal prostate tissue adjacent to tumor from patient No.101 PN101U95C

source_name: PN101, normal prostate tissue adjacent to tumor from patient No.101


title: Normal prostate tissue adjacent to tumor from patient No.77 PN77U95B

source_name: PN77, normal prostate tissue adjacent to tumor from patient No.77


title: Normal prostate tissue adjacent to tumor from patient No.92 PN92U95C


title: Normal prostate tissue adjacent to tumor from patient No.90 PN90U95C


title: Normal prostate tissue adjacent to tumor from patient No.75 PN75U95B

source_name: PN75, normal prostate tissue adjacent to tumor from patient No.75


title: Normal prostate tissue adjacent to tumor from patient No.95 PN95U95C


title: Normal prostate tissue adjacent to tumor from patient No.79 PN79U95B

source_name: PN79, normal prostate tissue adjacent to tumor from patient No.79


title: Normal prostate tissue adjacent to tumor from patient No.87 PN87U95C


title: Normal prostate tissue adjacent to tumor from patient No.80 PN80U95B

source_name: PN80, normal prostate tissue adjacent to tumor from patient No.80


title: Normal prostate tissue adjacent to tumor from patient No.91 PN91U95C


title: Normal prostate tissue adjacent to tumor from patient No.88 PN88U95C

source_name: PN88, normal prostate tissue adjacent to tumor from patient No.88


title: Normal prostate tissue adjacent to tumor from patient No.99 PN99U95C


title: Normal prostate tissue adjacent to tumor from patient No.76 PN76U95B

source_name: PN76, normal prostate tissue adjacent to tumor from patient No.76


title: Normal prostate tissue adjacent to tumor from patient No.73 PN73U95B

source_name: PN73, normal prostate tissue adjacent to tumor from patient No.73


title: Normal prostate tissue adjacent to tumor from patient No.74 PN74U95B

source_name: PN74, normal prostate tissue adjacent to tumor from patient No.74


title: Normal prostate tissue adjacent to tumor from patient No.94 PN94U95C

source_name: PN94, normal prostate tissue adjacent to tumor from patient No.94


title: Normal prostate tissue adjacent to tumor from patient No.86 PN86U95C


title: Normal prostate tissue adjacent to tumor from patient No.72 PN72U95B

source_name: PN72, normal prostate tissue adjacent to tumor from patient No.72


title: Normal prostate tissue adjacent to tumor from patient No.71 PN71U95B

source_name: PN71, normal prostate tissue adjacent to tumor from patient No.71


title: Normal prostate tissue adjacent to tumor from patient No.85 PN85U95C

source_name: PN85, normal prostate tissue adjacent to tumor from patient No.85


title: Normal prostate tissue adjacent to tumor from patient No.83 PN83U95C


title: Normal prostate tissue adjacent to tumor from patient No.82 PN82U95C


title: Normal prostate tissue adjacent to tumor from patient No.68 PN68U95B

source_name: PN68, normal prostate tissue adjacent to tumor from patient No.68


title: Normal prostate tissue adjacent to tumor from patient No.69 PN69U95B

source_name: PN69, normal prostate tissue adjacent to tumor from patient No.69


title: Normal prostate tissue adjacent to tumor from patient No.66 PN66U95B

source_name: PN66, normal prostate tissue adjacent to tumor from patient No.66


title: Normal prostate tissue adjacent to tumor from patient No.80 PN80U95C


title: Normal prostate tissue adjacent to tumor from patient No.81 PN81U95C

source_name: PN81, normal prostate tissue adjacent to tumor from patient No.81


title: Normal prostate tissue adjacent to tumor from patient No.76 PN76U95C


title: Normal prostate tissue adjacent to tumor from patient No.70 PN70U95B

source_name: PN70, normal prostate tissue adjacent to tumor from patient No.70


title: Normal prostate tissue adjacent to tumor from patient No.63 PN63U95B

source_name: PN63, normal prostate tissue adjacent to tumor from patient No.63


title: Normal prostate tissue adjacent to tumor from patient No.74 PN74U95C


title: Normal prostate tissue adjacent to tumor from patient No.67 PN67U95B

source_name: PN67, normal prostate tissue adjacent to tumor from patient No.67


title: Normal prostate tissue adjacent to tumor from patient No.79 PN79U95C

source_name: PN79, normal prostate tissue adjacent to tumor from patient No.79


title: Normal prostate tissue adjacent to tumor from patient No.64 PN64U95B

source_name: PN64, normal prostate tissue adjacent to tumor from patient No.64


title: Normal prostate tissue adjacent to tumor from patient No.65 PN65U95B

source_name: PN65, normal prostate tissue adjacent to tumor from patient No.65


title: Reference RNA Cy3 Vs RVT (R.B.1.) Cy5

source_name: Reference RNA

tag: Juvenile rainbow trout brain tissue

source_name: Resveratrol (RVT; R.B.1.)


title: Normal prostate tissue adjacent to tumor from patient No.75 PN75U95C

source_name: PN75, normal prostate tissue adjacent to tumor from patient No.75


title: Normal prostate tissue adjacent to tumor from patient No.60 PN60U95B

source_name: PN60, normal prostate tissue adjacent to tumor from patient No.60


title: Normal prostate tissue adjacent to tumor from patient No.73 PN73U95C

source_name: PN73, normal prostate tissue adjacent to tumor from patient No.73


title: Normal prostate tissue adjacent to tumor from patient No.61 PN61U95B

source_name: PN61, normal prostate tissue adjacent to tumor from patient No.61


title: Normal prostate tissue adjacent to tumor from patient No.58 PN58U95B

source_name: PN58, normal prostate tissue adjacent to tumor from patient No.58


title: Normal prostate tissue adjacent to tumor from patient No.62 PN62U95B

source_name: PN62, normal prostate tissue adjacent to tumor from patient No.62


title: Normal prostate tissue adjacent to tumor from patient No.69 PN69U95C

source_name: PN69, normal prostate tissue adjacent to tumor from patient No.69


title: Normal prostate tissue adjacent to tumor from patient No.71 PN71U95C

source_name: PN71, normal prostate tissue adjacent to tumor from patient No.71


title: Normal prostate tissue adjacent to tumor from patient No.72 PN72U95C

source_name: PN72, normal prostate tissue adjacent to tumor from patient No.72


title: Normal prostate tissue adjacent to tumor from patient No.77 PN77U95C

source_name: PN77, normal prostate tissue adjacent to tumor from patient No.77


title: Normal prostate tissue adjacent to tumor from patient No.70 PN70U95C

source_name: PN70, normal prostate tissue adjacent to tumor from patient No.70


title: Normal prostate tissue adjacent to tumor from patient No.68 PN68U95C

source_name: PN68, normal prostate tissue adjacent to tumor from patient No.68


title: Normal prostate tissue adjacent to tumor from patient No.67 PN67U95C

source_name: PN67, normal prostate tissue adjacent to tumor from patient No.67


title: Normal prostate tissue adjacent to tumor from patient No.58 PN58U95C


title: Normal prostate tissue adjacent to tumor from patient No.45 PN45U95B

source_name: PN45, normal prostate tissue adjacent to tumor from patient No.45


title: Normal prostate tissue adjacent to tumor from patient No.55 PN55U95B

source_name: PN55, normal prostate tissue adjacent to tumor from patient No.55


title: Normal prostate tissue adjacent to tumor from patient No.56 PN56U95C

source_name: PN56, normal prostate tissue adjacent to tumor from patient No.56


title: Normal prostate tissue adjacent to tumor from patient No.51 PN51U95B

source_name: PN51, normal prostate tissue adjacent to tumor from patient No.51


title: Normal prostate tissue adjacent to tumor from patient No.54 PN54U95B

source_name: PN54, normal prostate tissue adjacent to tumor from patient No.54


title: Normal prostate tissue adjacent to tumor from patient No.55 PN55U95C


title: Normal prostate tissue adjacent to tumor from patient No.60 PN60U95C

source_name: PN60, normal prostate tissue adjacent to tumor from patient No.60


title: Normal prostate tissue adjacent to tumor from patient No.53 PN53U95B

source_name: PN53, normal prostate tissue adjacent to tumor from patient No.53


title: Normal prostate tissue adjacent to tumor from patient No.56 PN56U95B


title: Normal prostate tissue adjacent to tumor from patient No.44 PN44U95B

source_name: PN44, normal prostate tissue adjacent to tumor from patient No.44


title: Normal prostate tissue adjacent to tumor from patient No.42 PN42U95B

source_name: PN42, normal prostate tissue adjacent to tumor from patient No.42


title: Normal prostate tissue adjacent to tumor from patient No.39 PN39U95B

source_name: PN39, normal prostate tissue adjacent to tumor from patient No.39


title: Normal prostate tissue adjacent to tumor from patient No.54 PN54U95C


title: Normal prostate tissue adjacent to tumor from patient No.40 PN40U95B

source_name: PN40, normal prostate tissue adjacent to tumor from patient No.40


title: Normal prostate tissue adjacent to tumor from patient No.63 PN63U95C

source_name: PN63, normal prostate tissue adjacent to tumor from patient No.63


title: Normal prostate tissue adjacent to tumor from patient No.46 PN46U95B

source_name: PN46, normal prostate tissue adjacent to tumor from patient No.46


title: Normal prostate tissue adjacent to tumor from patient No.65 PN65U95C

source_name: PN65, normal prostate tissue adjacent to tumor from patient No.65


title: Normal prostate tissue adjacent to tumor from patient No.64 PN64U95C

source_name: PN64, normal prostate tissue adjacent to tumor from patient No.64


title: Normal prostate tissue adjacent to tumor from patient No.66 PN66U95C

source_name: PN66, normal prostate tissue adjacent to tumor from patient No.66


title: Normal prostate tissue adjacent to tumor from patient No.61 PN61U95C

source_name: PN61, normal prostate tissue adjacent to tumor from patient No.61


title: Normal prostate tissue adjacent to tumor from patient No.62 PN62U95C

source_name: PN62, normal prostate tissue adjacent to tumor from patient No.62


title: Normal prostate tissue adjacent to tumor from patient No.47 PN47U95B

source_name: PN47, normal prostate tissue adjacent to tumor from patient No.47


title: Normal prostate tissue adjacent to tumor from patient No.38 PN38U95B

source_name: PN38, normal prostate tissue adjacent to tumor from patient No.38


title: Normal prostate tissue adjacent to tumor from patient No.53 PN53U95C


title: Normal prostate tissue adjacent to tumor from patient No.41 PN41U95B

source_name: PN41, normal prostate tissue adjacent to tumor from patient No.41


title: Normal prostate tissue adjacent to tumor from patient No.43 PN43U95B

source_name: PN43, normal prostate tissue adjacent to tumor from patient No.43


title: Normal prostate tissue adjacent to tumor from patient No.51 PN51U95C

source_name: PN51, normal prostate tissue adjacent to tumor from patient No.51


title: Normal prostate tissue adjacent to tumor from patient No.35 PN35U95B

source_name: PN35, normal prostate tissue adjacent to tumor from patient No.35


title: Normal prostate tissue adjacent to tumor from patient No.46 PN46U95C


title: Normal prostate tissue adjacent to tumor from patient No.50 PN50U95C

source_name: PN50, normal prostate tissue adjacent to tumor from patient No.50


title: Normal prostate tissue adjacent to tumor from patient No.36 PN36U95B

source_name: PN36, normal prostate tissue adjacent to tumor from patient No.36


title: Normal prostate tissue adjacent to tumor from patient No.47 PN47U95C


title: Normal prostate tissue adjacent to tumor from patient No.48 PN48U95C

source_name: PN48, normal prostate tissue adjacent to tumor from patient No.48


title: Normal prostate tissue adjacent to tumor from patient No.48 PN48U95B


title: Normal prostate tissue adjacent to tumor from patient No.34 PN34U95B

source_name: PN34, normal prostate tissue adjacent to tumor from patient No.34


title: Normal prostate tissue adjacent to tumor from patient No.43 PN43U95C


title: Normal prostate tissue adjacent to tumor from patient No.45 PN45U95C

source_name: PN45, normal prostate tissue adjacent to tumor from patient No.45


title: Normal prostate tissue adjacent to tumor from patient No.44 PN44U95C

source_name: PN44, normal prostate tissue adjacent to tumor from patient No.44


title: Normal prostate tissue adjacent to tumor from patient No.42 PN42U95C

source_name: PN42, normal prostate tissue adjacent to tumor from patient No.42


title: Tumor samples from patient No.101 PT101U95B

description: Gene expression data from primary prostate cancer

source_name: PT101, tumor samples from patient No.101

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

value: primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: Normal prostate tissue adjacent to tumor from patient No.41 PN41U95C


title: Normal prostate tissue adjacent to tumor from patient No.50 PN50U95B


title: Tumor samples from patient No.97 PT97U95B

source_name: PT97, tumor samples from patient No.97


title: Tumor samples from patient No.99 PT99U95B

source_name: PT99, tumor samples from patient No.99


title: Tumor samples from patient No.100 PT100U95B

source_name: PT100, tumor samples from patient No.100


title: Normal prostate tissue adjacent to tumor from patient No.30 PN30U95B

source_name: PN30, normal prostate tissue adjacent to tumor from patient No.30


title: Normal prostate tissue adjacent to tumor from patient No.40 PN40U95C

source_name: PN40, normal prostate tissue adjacent to tumor from patient No.40


title: Tumor samples from patient No.96 PT96U95B

source_name: PT96, tumor samples from patient No.96


title: Normal prostate tissue adjacent to tumor from patient No.38 PN38U95C

source_name: PN38, normal prostate tissue adjacent to tumor from patient No.38


title: Tumor samples from patient No.107 PT107U95B

source_name: PT107, tumor samples from patient No.107


title: Tumor samples from patient No.105 PT105U95B

source_name: PT105, tumor samples from patient No.105


title: Normal prostate tissue adjacent to tumor from patient No.39 PN39U95C

source_name: PN39, normal prostate tissue adjacent to tumor from patient No.39


title: Normal prostate tissue adjacent to tumor from patient No.35 PN35U95C

source_name: PN35, normal prostate tissue adjacent to tumor from patient No.35


title: Normal prostate tissue adjacent to tumor from patient No.30 PN30U95C


title: Tumor samples from patient No.101 PT101U95C


title: Tumor samples from patient No.95 PT95U95B

source_name: PT95, tumor samples from patient No.95


title: Tumor samples from patient No.94 PT94U95B

source_name: PT94, tumor samples from patient No.94


title: Tumor samples from patient No.87 PT87U95B

source_name: PT87, tumor samples from patient No.87


title: Tumor samples from patient No.99 PT99U95C


title: Tumor samples from patient No.89 PT89U95B

source_name: PT89, tumor samples from patient No.89


title: Tumor samples from patient No.90 PT90U95B

source_name: PT90, tumor samples from patient No.90


title: Tumor samples from patient No.88 PT88U95B

source_name: PT88, tumor samples from patient No.88


title: Tumor samples from patient No.91 PT91U95B

source_name: PT91, tumor samples from patient No.91


title: Tumor samples from patient No.96 PT96U95C


title: Tumor samples from patient No.95 PT95U95C


title: Tumor samples from patient No.107 PT107U95C


title: Tumor samples from patient No.85 PT85U95B

source_name: PT85, tumor samples from patient No.85


title: Tumor samples from patient No.86 PT86U95B

source_name: PT86, tumor samples from patient No.86


title: Tumor samples from patient No.94 PT94U95C


title: Tumor samples from patient No.80 PT80U95B

source_name: PT80, tumor samples from patient No.80


title: Tumor samples from patient No.97 PT97U95C

source_name: PT97, tumor samples from patient No.97


title: Tumor samples from patient No.81 PT81U95B

source_name: PT81, tumor samples from patient No.81


title: Tumor samples from patient No.83 PT83U95B

source_name: PT83, tumor samples from patient No.83


title: Tumor samples from patient No.93 PT93U95C

source_name: PT93, tumor samples from patient No.93


title: Tumor samples from patient No.82 PT82U95B

source_name: PT82, tumor samples from patient No.82


title: Tumor samples from patient No.91 PT91U95C


title: Normal prostate tissue adjacent to tumor from patient No.34 PN34U95C

source_name: PN34, normal prostate tissue adjacent to tumor from patient No.34


title: Tumor samples from patient No.76 PT76U95B

source_name: PT76, tumor samples from patient No.76


title: Tumor samples from patient No.75 PT75U95B

source_name: PT75, tumor samples from patient No.75


title: Tumor samples from patient No.100 PT100U95C

source_name: PT100, tumor samples from patient No.100


title: Tumor samples from patient No.89 PT89U95C


title: Tumor samples from patient No.88 PT88U95C


title: Tumor samples from patient No.87 PT87U95C

source_name: PT87, tumor samples from patient No.87


title: Normal prostate tissue adjacent to tumor from patient No.100 PN100U95C

source_name: PN100, normal prostate tissue adjacent to tumor from patient No.100


title: Tumor samples from patient No.85 PT85U95C


title: Tumor samples from patient No.82 PT82U95C


title: Tumor samples from patient No.81 PT81U95C


title: Tumor samples from patient No.72 PT72U95B

source_name: PT72, tumor samples from patient No.72


title: Tumor samples from patient No.83 PT83U95C


title: Tumor samples from patient No.73 PT73U95B

source_name: PT73, tumor samples from patient No.73


title: Tumor samples from patient No.80 PT80U95C


title: Tumor samples from patient No.75 PT75U95C


title: Tumor samples from patient No.76 PT76U95C


title: Tumor samples from patient No.63 PT63U95B

source_name: PT63, tumor samples from patient No.63


title: Tumor samples from patient No.71 PT71U95B

source_name: PT71, tumor samples from patient No.71