title: S5_Muscle_Insulin_240min


title: S3_Muscle_Insulin_30min

status: Public on Sep 20 2007

type: RNA

city: San Antonio

first: Dawn

middle: K

last: Coletta

state: TX

address: 7703 Floyd Curl Drive

department: Medicine

country: USA

institute: UTHSCSA

description: Gene expression data from skeletal muscle following 30 minutes of a insulin infusion (80 mU clamp)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using protocol EukGE-ES2.

scan_protocol: The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray scanner G2500A; Agilent).

data_processing: The Affymetrix data acquisition programs in GCOS automatically generate a cell intensity file (CEL) from the stored images that contain a single intensity value for each probe cell on the array.  The CEL files were imported into the R software package (http://www.r-project.org) and the probe level data were converted to expression measures using the Affy package from Bioconductor. Expression values for each mRNA were obtained by GC-Robust Multi-Array Analysis (GCRMA).  CEL files were normalized together and the expression values obtained were submitted to analysis with linear models of microarray data (LIMMA) to identify genes that were significantly increased or decreased with a false discovery rate (FDR) of less than 5%, and a fold change of greater than 1.5.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Vastus Lateralis Muscle at 30 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).  A description of the protocol has been described previously (Richardson 2005)

extract_protocol: Muscle biopsies from each subject were homogenized in RNAStat solution (Tel-Test Inc., Friendswood, TX), using a Polytron homogenizer (Brinkmann Instruments Westbury, NY).  Total RNA was purified with RNeasy and DNase I treatment (Qiagen, Chatsworth, CA).

treatment_protocol: All subjects received a vastus lateralis muscle biopsy followed by a 180-min euglycemic, hyperinsulinemic (80 mU/m2.min) clamp, which was performed with infusion of 3-3H-glucose (prime=25 Ci, continuous infusion=0.25 Ci/min) to determine rates of glucose appearance and disposal, as previously described (DeFronzo, 1979). Biopsies of the vastus lateralis muscle were taken basally and at 30 and 240 minutes after the start of the insulin infusion, as previously described (Cusi 2000)

tag: Gender

value: Male

tag: Diabetes Status

value: Family History Negative

tag: Ethnicity

value: Mexican American


title: S3_Muscle_Baseline_0min

description: Gene expression data from skeletal muscle at baseline

source_name: Vastus Lateralis Muscle at 0 min


title: S5_Muscle_Insulin_30min

value: Female


title: B. pertussis Tohama I vs. PRCB2/H

type: genomic

city: Turku

first: Teemu

last: Kallonen

address: Kiinamyllynkatu 13

department: Derpartment of Infectious Disease Surveillance and Control

country: Finland

institute: National Institute for Health and Welfare

description: CGH

hyb_protocol: The labeled DNA was purified with the purification kit of the same manufacturer and then combined. The volume of labeled DNA was reduced below 15.7 µl in vacuum centrifuge, and 2.5 µl of yeast tRNA (10mg/ml, Invitrogen Life Technologies, Carlsbad, USA), 4.3 µl of 20 x SSC (1 x SSC was 8.8g/l NaCl and 4.4 g/ trisodiumcitrate) and 0.8 µl of 10% SDS were added. After denaturation at 100°C for 3 min, 1.7 µl of 10 x digoxigenin was added. The final volume for hybridization was adjusted with water to 25 µl. Before hybridization, slides were fixed by UV-cross linking with 90 mJ cm-2, washed for 1 min in 0.1% of SDS and 2 min in water to remove residual salt, and incubated at 50ºC for 30 min in BSA solution containing 1% of BSA fraction V, 2 x SSC and 0.1% of SDS to block nonspecific binding. The slides were further washed in 2 x SSC for 3 min and then in 0.2 x SSC for 3 min. Hybridization was conducted under 22 x 25mm LifterSlip ™ coverslip (Erie Scientific Company, Portsmouth, USA) in hybridization chamber at 65°C for 16 h. To control humidity inside the hybridization chamber, a strip of thin paper, humidified with approximately 100 µl of 3.4 x SSC, was placed under the slide. After hybridization slides were washed at 65°C for 10 min with 1 x SSC and 0.1% of SDS. The following washes were conducted at room temperature for 10 min with 0.5 x SSC and 0.01% SDS, and for 3 min and 1 min with 0.1 x SSC. Slides were dried in slide centrifuge.

scan_protocol: scanned with ScanArray ®5000 (PerkinElmer, Waltham, USA).

data_processing:
We concentrated on finding the "clear absent" genes in each studied strain, which were clearly separated from the "present" genes by their logratio; no normalization and no averaging were required. Specifically, using our own r-script, log-transformed CH2/CH1-ratio is calculated. For defining the lost genes, logratio is plotted against average of channel intensities (MA-plot) and a cutoff logratio is selected based on the MA-plot to separate absent genes from present genes. Fuller description provided in the related manuscript.
The VALUE column reports log2 (test/Tohama I) ratio data.

molecule: genomic DNA

organism: Bordetella pertussis

source_name: Tohama I

label_protocol: The 4 µg of digested DNA was labelled with the dye (Amershham Biosciences UK Limited, Buckinghamshire, England) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA). The labeled DNA was purified with the purification kit of the same manufacturer.

growth_protocol: Bacteria stored in -70°C were recultured on Charcoal agar (Oxoid Ltd, Basingstoke, England) with 10% defibrinated sheep blood. The plates were incubated at 35-36°C for 3 days. Bacteria were harvested and suspended in distilled water. Prior to DNA isolation, the concentration of bacterial suspension was adjusted to 2 x 109 cells/ml.

extract_protocol: B. pertussis DNA was isolated with GenElute™ Bacterial Genomic DNA Kit (Sigma-Aldrich Inc., St. Louis, USA) and then digested with Sma I (10 U/µg DNA, New England Biolabs, Ipswich, USA) according to the protocol of BioPrime®Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, USA).

tag: strain Tohama I; year of isolation

tag: strain PRCB2/H; year of isolation


title: S3_Muscle_Insulin_240min

description: Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp)

source_name: Vastus Lateralis Muscle at 240 min


title: S2_Muscle_Insulin_30min


title: GFP IP replicate 3

status: Public on Sep 21 2007

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

description: GFP IP of mixed staged AIN-2 promoter:GFP injection line

hyb_protocol: SOP H2.0: Hybridization Application  1.0 PURPOSE: To provide a standard operating procedure for hybridization of  fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass  slides.  2.0 SPECIAL NOTES:  3.0 AUTHORS: Mike Heinz  4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0  5.0 REQUIRED MATERIALS AND EQUIPMENT:  Labeled probe Hybridization chamber apparatus  Hybridization oven Heat block  4xSSC Air gun/ canister  Timers Microcentrifuge  Hybridization buffer (check vendor) Forceps  Microarray(s) Pipettes  Coverslips (Erie Scientific)  6.0 DEFINITIONS:  7.0 PROCEDURE:  7.1 Set up  7.1.1 Using an air gun canister, blow off all hybridization chamber parts  to ensure they are clean, especially the microarray and the  coverslip.  7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip  apparatus. Make sure that the coverslip is appropriately placed  over the entire arrayed area.  7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization  chamber.  7.1.4 If frozen, remove probes from the 20C freezer and thaw at room  temperature in the dark if frozen. Ensure that each probe has  enough volume for the hybridization (ie. For a 25x25mm  coverslip, 20ul is needed to cover the array surface). Each probe  should have at least +2ul of probe in the tube compared to that of  the volume to be applied to the array. If a probe does not contain  the appropriate volume, add hybridization buffer (use appropriate  vendor) to reach desired volume. Make sure to mix the solution if  adding hyb buffer.  7.1.5 By checking the paperwork/ jobticket, make sure that the  appropriate probes have been thawed and that the appropriate  arrays have been placed in the chambers.  7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for  appropriate denaturing temperatures and times).  7.1.7 Centrifuge the probes for 1 min. at max speed.  7.2 Application  7.2.1 Carefully pipette 20ul (or other amount) under the coverslip  covering the arrayed surface. Ensure that the array is completely  covered. If not completely covered, pipette additional probe under  the coverslip in increments of 2ul. Note any bubbles or  abnormalities.  7.2.2 Apply the coverglass and clamps. Using the torque wrench,  tighten the clamps. Make sure that the metal arms of the clamps  are not resting on the edge of the coverglass. Also, make certain  that the wrench is set at 46 lb/in.  7.2.3 Place the hybridization chambers in the hybrization box, then place  the hyb. box in the oven at 42C and hybridize overnight (minimum  of 12 hours). Make certain to place the chambers in the hyb. box  so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0. Note that this Sample represents the data from 1 channel of a 'technically' dual channel hybridization.

data_processing: Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp  transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm  strains. We then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile  of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP  replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was  utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p  value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used  the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in  AIN-1 or AIN-2 IP with p<0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal  (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on  each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP.

organism: Caenorhabditis elegans

label_protocol: The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

extract_protocol: RNAs were isolated from each immunocomplex after IP, or from total worm lysate, using the Trizol reagents (Invitrogen) according to vendor’s protocol.

tag: Immunoprecipitated RNA


title: Gr1-_2h LM infected_2_peritoneal lavage

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

hyb_protocol: Cy3 labeled cDNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min followed by a second wash with 0.06x SSPE containing 0.005% N-lauroylsarcosine for 1 min and a final wash step with acetonitrile for 30 sec. All washing steps were performed at room temperature.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files

molecule: polyA RNA

organism: Mus musculus

source_name: infected peritoneal cells, timepoint 2h

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Mice were intraperitonealy infected with 104 L. monocytogenes (EGDe strain) in exponential growth phase (bacteria were grown in BHI at 108/ml, and diluted 10.000x in PBS immediately before injection).

extract_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Cells were directly sorted in the SuperAmp Lysis Buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) using a FACS Aria cell-sorter (BD biosciences). Cell samples (1.103 cells per experimental point) were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions

tag: Six-weeks old (C57Bl6, Cx3cr1gfp/+) mice

tag: infected with 1x104 of L. monocytogenes (EGDe strain) in exponential growth phase

tag: Gr1- monocytes purified as NK1.1- CD3- B220- CD11b+ F4/80low Gr1-, gfphigh


title: Gr1-_2h LM infected_1_peritoneal lavage

description: Cells were directly sorted in the SuperAmp Lysis Buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) using a FACS Aria cell-sorter (BD biosciences).


title: B. pertussis Tohama I vs. KKK1277

description: CGH

tag: Strain KKK1277; year of isolation


title: S2_Muscle_Baseline_0min


title: B. pertussis Tohama I self vs. self

description: Quality control


title: Gr1-_uninf_3_blood

source_name: uninfected perioheral blood

tag: uninfected


title: B. pertussis Tohama I vs. PRCB406

description: CGH

tag: strain PRCB406; year of isolation


title: B. pertussis Tohama I vs. PRCB2

description: CGH

tag: strain PRCB2; year of isolation


title: Gr1-_uninf_1_blood


title: Gr1-_uninf_2_blood


title: B. pertussis PRCB406 vs. Tohama I

description: quality control, dye swap, CGH


title: S1_Muscle_Baseline_0min


title: Ac1-25 stimulated cells, biological rep3

status: Public on Sep 19 2007

city: Muenster

first: Carsten

last: Lange

state: NRW

address: Von-Esmarch-Str. 56

department: Medical Biochemistry

institute: ZMBE

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A arrays. 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 100.

label: biotin

source_name: human peripheral blood monocytes, 2h 50µM Annexin A1 peptide Ac1-25

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: extraction of total RNA was performed according to the manufacturer's instructions (Qiagen RNAeasy Kit).

tag: pooled buffy coats from four donors


title: Ac1-25 stimulated cells, biological rep1


title: S1_Muscle_Insulin_30min


title: unstimulated cells, biological rep3

source_name: human peripheral blood monocytes, 2h unstimulated


title: unstimulated cells, biological rep2


title: Ac1-25 stimulated cells, biological rep2


title: S1_Muscle_Insulin_240min


title: unstimulated cells, biological rep1


title: HUVEC sample of B7 rep2

city: Komaba

first: Shuichi

last: Tsutsumi

country: Japan

institute: The University of Tokyo

description: Gene expression data of HUVEC cells after TNF-alpha stimulation.

hyb_protocol: Following fragmentation, 5 microg of cDNA were hybridized for 16 hr at 45C on NimbleExpress Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix - GeneChipR Operating Software (GCOS) using Affymetrix default analysis settings.

source_name: Huvec cells treated by TNFalpha

label_protocol: Biotinylated single-strand DNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (GeneChipR Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005, Affymetrix).

growth_protocol: Before stimulation, HUVECs were serum-starved in EBM-2 (Clonetics) containing 0.5% FBS for 18 h.

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

treatment_protocol: HUVECs were treated with 10 ng/ml TNF (Peprotec) and samples collected every 7.5 min for 2 h

tag: HUVEC cell


title: HUVEC sample of B9 rep2


title: HUVEC sample of B8 rep2


title: HUVEC sample of B3 rep2


title: HUVEC sample of B15 rep2


title: HUVEC sample of B11 rep2


title: HUVEC sample of B9 rep1


title: HUVEC sample of B5 rep2


title: HUVEC sample of B13 rep2


title: HUVEC sample of B8 rep1


title: HUVEC sample of B7 rep1


title: HUVEC sample of B5 rep1


title: HUVEC sample of B2 rep2


title: HUVEC sample of B10 rep2


title: HUVEC sample of B12 rep2


title: HUVEC sample of B1 rep2


title: HUVEC sample of B6 rep1


title: HUVEC sample of B6 rep2


title: HUVEC sample of B16 rep2


title: HUVEC sample of B4 rep2


title: HUVEC sample of B1 rep1


title: HUVEC sample of B14 rep2


title: HUVEC sample of B4 rep1


title: HUVEC sample of B2 rep1


title: HUVEC sample of B3 rep1


title: HUVEC sample of B13 rep1


title: HUVEC sample of B14 rep1


title: HUVEC sample of B12 rep1


title: HUVEC sample of A3 biological rep2


title: HUVEC sample of A25 biological rep2


title: HUVEC sample of A9 biological rep2


title: HUVEC sample of A7 biological rep2


title: HUVEC sample of A8 biological rep2


title: HUVEC sample of A22 biological rep2


title: HUVEC sample of B10 rep1


title: HUVEC sample of A4 biological rep2


title: HUVEC sample of A17 biological rep2


title: HUVEC sample of B11 rep1


title: HUVEC sample of A2 biological rep2


title: HUVEC sample of A6 biological rep2


title: HUVEC sample of A5 biological rep2


title: HUVEC sample of A1 biological rep2


title: HUVEC sample of A19 biological rep2


title: HUVEC sample of A20 biological rep2


title: HUVEC sample of A21 biological rep2


title: HUVEC sample of A23 biological rep2


title: HUVEC sample of A24 biological rep2


title: HUVEC sample of A13 biological rep2


title: HUVEC sample of A18 biological rep2


title: HUVEC sample of A15 biological rep2


title: HUVEC sample of A16 biological rep2


title: HUVEC sample of A12 biological rep2


title: HUVEC sample of A11 biological rep2


title: SHED189

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

country: France

institute: Institut national de la santé et de la recherche médicale

description: Seventeen Caucasian morbidly obese women undergoing laparoscopic Roux-en-Y bypass were enrolled at Hôtel Dieu Hospital, Paris, France. To study the effects of weight loss on scWAT gene expression, we processed 10 high-quality RNAs from scWAT biopsies of the 17 collected before/after bypass by cDNA microarray technique.

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software.

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized using Stanford Microarray Database Online resources (http://genome-www5.stanford.edu/).The VALUE field represents the log(base2) of the print-tip loess normalized R/G ratio (mean).

source_name: T0 sWAT

label_protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit (Ambion, Austin, TX), and 3 µg aRNA was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit (Amersham Biosciences, Orsay, France) (available at http://cmgm.stanford.edu/pbrown/protocols/index).

extract_protocol: Total RNA from scWAT was prepared using the RNeasy RNA Mini Kit (Qiagen, Courtaboeuf, France).

tag: Subcutaneous WAT of obese subjects before bariatric surgery

source_name: T3M sWAT

tag: Subcutaneous WAT of obese subjects 3 months after bariatric surgery


title: HUVEC sample of A6 biological rep1


title: SHED190


title: HUVEC sample of A8 biological rep1


title: HUVEC sample of A7 biological rep1


title: HUVEC sample of A9 biological rep1


title: HUVEC sample of A4 biological rep1


title: SHED158


title: HUVEC sample of A24 biological rep1


title: SHED160


title: SHED159


title: SHED157


title: HUVEC sample of A18 biological rep1


title: HUVEC sample of A14 biological rep2


title: HUVEC sample of A21 biological rep1


title: HUVEC sample of A15 biological rep1


title: HUVEC sample of A17 biological rep1


title: HUVEC sample of A20 biological rep1


title: HUVEC sample of A1 biological rep1


title: HUVEC sample of A16 biological rep1


title: HUVEC sample of A5 biological rep1


title: HUVEC sample of A19 biological rep1


title: HUVEC sample of A22 biological rep1


title: HUVEC sample of A25 biological rep1


title: HUVEC sample of A3 biological rep1


title: HUVEC sample of A10 biological rep2


title: HUVEC sample of A2 biological rep1


title: HUVEC sample of A23 biological rep1


title: HUVEC sample of A14 biological rep1


title: Joint_DeclineControl_Replicate 2

status: Public on Sep 18 2007

city: Macclesfield

first: stephanie

middle: ann

last: roberts

state: Cheshire

address: Alderley Park

department: RIRA

country: United Kingdom

institute: astrazeneca

description: Genomic positive control spots were checked and negative controls were also checked. Positive control signals were weak. Signals were also weak for housekeeping controls. The data was not carried forward for statistical analysis

hyb_protocol: Hybridisation protocol 				1.Preheat R& D Systems hybridisation solution to 65oC 				2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 				3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 				4.Rinse arrays in 2 x SSPE for 5 mins 				5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 				6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 				7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 				8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 				9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 				10. repeat step 9 x 2 (3 washes in total) 				11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 				12. repeat step 11 once 				13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 				14. Remove the filters from the bottles and place between two sheets of Screen guard. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. 				Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

data_processing:
The data was exported from Arrayvision software in the form of a comma-delimited text file. The exported data contained raw signal data (MTM Dens-MDC/mm2) and a background signal calculation (taken from the regions surrounding the spots).

1. The background adjusted signal intensity value was calculated= Log (spot intensity/background). The data was logged so that it conformed to a normal distribution.
2. The average background adjusted signal intensity was calculated for duplicate spots by taking the mean of the log value computed in step 1 for both spots corresponding to the same gene.
3. The median background adjusted signal intensity value was calculated for the array.
4.Any duplicate spot background adjusted signal intensities that deviated significantly from the median were flagged as 'absent' . A spot is called absent if the log of the background adjusted signal is x2.5 the array median.
5.Global normalisation between arrays is computed. To compute the normalised signal value the array median signal is divided into each background adjusted duplicate average;
100 x (Background adjusted duplicate mean/ Background adjusted all duplicate spot median)

source_name: Paw Joint from Control mouse

label_protocol:
First Strand Probe Labelling
				1. In 1.5 ml screw cap tubes the following components were assembled;
				5ug Total RNA
				Mouse Cytokine specific primers
				DEPC H20 made up to 12ul
				2. Heat 70oC 10 mins
				3. Quench on ice for 2 mins
				4. Using Superscript II kit (Life Technologies, 18064-014) add:
				5x first strand buffer (5ul)
				DTT (0.1M)   (2.5ul)
				DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
				33P dATP (4ul)
				5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
				6. Incubate at 42oC for 120 mins
				7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
				8.Add 24ul TE and measure counts using a scintillation counter
				9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
				vortex column for 30 seconds
				open cap ¼ turn and snap off bottom
				place in a tube and spin @ 3K rpm for 1 min
				discard flow through and tube and place in a clean screw cap tube
				slowly add the sample at the top of the sephadex column
				spin at 3K rpm for 2 mins
				discard the column and measure the counts for the flow through
				10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40%
			 11. Heat at 100oC for 10 mins

extract_protocol: The joint samples were snap frozen in liquid nitrogen and homogenized in 1ml GT buffer, then sonicated for ~2 mins to disrupt the tissue. Aliquots of 500ml sonicated samples were added 50ml 3M NaOAc (pH4.0) and 500ml H2O-saturated phenol and 200ml chloroform. The top layer containing RNA was transferred to a new tube and added 500ml RNase-free isopropanol and store at -20°c for at least 20min. RNA was precipitated by centrifugation for 20min. The pellet was washed with 75% ethanol, air dry and dissolved in DEPC water. GT buffer: 4M Guanidine thiocyanate, 25mM Sodium citrate, 0.5% Sarkosyl, 0.1M b-mercaptoethanol.

treatment_protocol: Male DBA/1 mice (8-12 wks old) were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in microisolators in the Center of Comparative Medicine of Baylor College of Medicine. Animal experimentation was performed in accordance with protocols approved by Institutional Animal Care and Use Committee

tag: Strain

value: DBA/1 mice

tag: Gender

tag: Age

value: 22 weeks


title: SHED250


title: Joint_DeclineControl_Replicate 1

description: Genomic positive control spots were checked and negative controls were also checked. Positive control spot signals were weak. Weak signals were also obtained for housekeeping genes. This data was not carried forward for statistical analysis due to the weak signals


title: SHED248


title: Joint_EarlyControl_Replicate 3

description: Genomic positive control spots were checked and negative controls were also checked. These all behaved as expected.

value: 14 weeks


title: Joint_EarlyCIA_Replicate 1

source_name: Paw Joint from CIA mouse

treatment_protocol:
Male DBA/1 mice (8-12 wks old) were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in microisolators in the Center of Comparative Medicine of Baylor College of Medicine. Animal experimentation was performed in accordance with protocols approved by Institutional Animal Care and Use Committee
Induction of CIA was performed as previously described (Han S, Cao S, Bheekha-Escura R, Zheng B. Germinal center reaction in the joints of mice with collagen-induced arthritis: an animal model of lymphocyte activation and differentiation in arthritis joints.PG - 1438-43. Arthritis Rheum 2001;44(6):1438-43.). Briefly, mice were injected intradermally at the base of the tail with 200 mg bovine CII (Sigma, St. Louis, MO) dissolved in 0.05 M acetic acid and emulsified in equal volume of CFA. Three weeks after primary immunization, mice were given an i.p. booster injection of 100 mg aqueous CII mixed with 100 mg MPL/TDM (RIBI) adjuvant (Sigma). Mice were observed daily for the onset and severity of arthritis.


title: Joint_PeakCIA_Replicate 3

hyb_protocol: Hybridisation protocol 		1.Preheat R& D Systems hybridisation solution to 65oC 		2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 		3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 		4.Rinse arrays in 2 x SSPE for 5 mins 		5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 		6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 		7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 		8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 		9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 		10. repeat step 9 x 2 (3 washes in total) 		11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 		12. repeat step 11 once 		13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 		14. Remove the filters from the bottles and place between two sheets of Screen guard. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. 		Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

label_protocol:
First Strand Probe Labelling
		1. In 1.5 ml screw cap tubes the following components were assembled;
		5ug Total RNA
		Mouse Cytokine specific primers
		DEPC H20 made up to 12ul
		2. Heat 70oC 10 mins
		3. Quench on ice for 2 mins
		4. Using Superscript II kit (Life Technologies, 18064-014) add:
		5x first strand buffer (5ul)
		DTT (0.1M)   (2.5ul)
		DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
		ÃŽÂ±-33P dATP (4ul)
		5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
		6. Incubate at 42oC for 120 mins
		7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
		8.Add 24ul TE and measure counts using a scintillation counter
		9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
		vortex column for 30 seconds
		open cap Ã‚Â¼ turn and snap off bottom
		place in a tube and spin @ 3K rpm for 1 min
		discard flow through and tube and place in a clean screw cap tube
		slowly add the sample at the top of the sephadex column
		spin at 3K rpm for 2 mins
		discard the column and measure the counts for the flow through
		10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (70% incorporation with F039B)
	 11. Heat at 100oC for 10 mins

extract_protocol: The joint samples were snap frozen in liquid nitrogen and homogenized in 1ml GT buffer, then sonicated for ~2 mins to disrupt the tissue. Aliquots of 500ml sonicated samples were added 50ml 3M NaOAc (pH4.0) and 500ml H2O-saturated phenol and 200ml chloroform. The top layer containing RNA was transferred to a new tube and added 500ml RNase-free isopropanol and store at -20Â°c for at least 20min. RNA was precipitated by centrifugation for 20min. The pellet was washed with 75% ethanol, air dry and dissolved in DEPC water. GT buffer: 4M Guanidine thiocyanate, 25mM Sodium citrate, 0.5% Sarkosyl, 0.1M b-mercaptoethanol.

value: 18 weeks


title: Joint_PeakControl_Replicate 3

label_protocol:
First Strand Probe Labelling
		1. In 1.5 ml screw cap tubes the following components were assembled;
		5ug Total RNA
		Mouse Cytokine specific primers
		DEPC H20 made up to 12ul
		2. Heat 70oC 10 mins
		3. Quench on ice for 2 mins
		4. Using Superscript II kit (Life Technologies, 18064-014) add:
		5x first strand buffer (5ul)
		DTT (0.1M)   (2.5ul)
		DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
		ÃŽÂ±-33P dATP (4ul)
		5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
		6. Incubate at 42oC for 120 mins
		7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
		8.Add 24ul TE and measure counts using a scintillation counter
		9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
		vortex column for 30 seconds
		open cap Ã‚Â¼ turn and snap off bottom
		place in a tube and spin @ 3K rpm for 1 min
		discard flow through and tube and place in a clean screw cap tube
		slowly add the sample at the top of the sephadex column
		spin at 3K rpm for 2 mins
		discard the column and measure the counts for the flow through
		10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (
	 11. Heat at 100oC for 10 mins


title: Joint_EarlyControl_replicate 1


title: Joint_EarlyCIA_Replicate 3


title: Joint_ EarlyCIA_Replicate 2

hyb_protocol: Hybridisation protocol 			1.Preheat R& D Systems hybridisation solution to 65oC 			2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 			3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 			4.Rinse arrays in 2 x SSPE for 5 mins 			5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 			6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 			7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 			8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 			9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 			10. repeat step 9 x 2 (3 washes in total) 			11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 			12. repeat step 11 once 			13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 			14. Remove the filters from the bottles and place between two sheets of Screen guard. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. 			Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

label_protocol:
First Strand Probe Labelling
			1. In 1.5 ml screw cap tubes the following components were assembled;
			5ug Total RNA
			Mouse Cytokine specific primers
			DEPC H20 made up to 12ul
			2. Heat 70oC 10 mins
			3. Quench on ice for 2 mins
			4. Using Superscript II kit (Life Technologies, 18064-014) add:
			5x first strand buffer (5ul)
			DTT (0.1M)   (2.5ul)
			DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
			ÃƒÅ½Ã‚Â±-33P dATP (4ul)
			5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
			6. Incubate at 42oC for 120 mins
			7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
			8.Add 24ul TE and measure counts using a scintillation counter
			9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
			vortex column for 30 seconds
			open cap Ãƒâ€šÃ‚Â¼ turn and snap off bottom
			place in a tube and spin @ 3K rpm for 1 min
			discard flow through and tube and place in a clean screw cap tube
			slowly add the sample at the top of the sephadex column
			spin at 3K rpm for 2 mins
			discard the column and measure the counts for the flow through
			10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40%
		 11. Heat at 100oC for 10 mins

extract_protocol: The joint samples were snap frozen in liquid nitrogen and homogenized in 1ml GT buffer, then sonicated for ~2 mins to disrupt the tissue. Aliquots of 500ml sonicated samples were added 50ml 3M NaOAc (pH4.0) and 500ml H2O-saturated phenol and 200ml chloroform. The top layer containing RNA was transferred to a new tube and added 500ml RNase-free isopropanol and store at -20Ã‚Â°c for at least 20min. RNA was precipitated by centrifugation for 20min. The pellet was washed with 75% ethanol, air dry and dissolved in DEPC water. GT buffer: 4M Guanidine thiocyanate, 25mM Sodium citrate, 0.5% Sarkosyl, 0.1M b-mercaptoethanol.

treatment_protocol:
Male DBA/1 mice (8-12 wks old) were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in microisolators in the Center of Comparative Medicine of Baylor College of Medicine. Animal experimentation was performed in accordance with protocols approved by Institutional Animal Care and Use Committee
	Induction of CIA was performed as previously described (Han S, Cao S, Bheekha-Escura R, Zheng B. Germinal center reaction in the joints of mice with collagen-induced arthritis: an animal model of lymphocyte activation and differentiation in arthritis joints.PG - 1438-43. Arthritis Rheum 2001;44(6):1438-43.). Briefly, mice were injected intradermally at the base of the tail with 200 mg bovine CII (Sigma, St. Louis, MO) dissolved in 0.05 M acetic acid and emulsified in equal volume of CFA. Three weeks after primary immunization, mice were given an i.p. booster injection of 100 mg aqueous CII mixed with 100 mg MPL/TDM (RIBI) adjuvant (Sigma). Mice were observed daily for the onset and severity of arthritis.


title: SHED247


title: Joint_EarlyControl_Replicate 2

hyb_protocol: Hybridisation protocol 	1.Preheat R& D Systems hybridisation solution to 65oC 	2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 	3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 	4.Rinse arrays in 2 x SSPE for 5 mins 	5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 	6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 	7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 	8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 	9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 	10. repeat step 9 x 2 (3 washes in total) 	11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 	12. repeat step 11 once 	13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 	14. Remove the filters from the bottles and place between two sheets of Screen guard. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. 	Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

label_protocol:
First Strand Probe Labelling
	1. In 1.5 ml screw cap tubes the following components were assembled;
	5ug Total RNA
	Mouse Cytokine specific primers
	DEPC H20 made up to 12ul
	2. Heat 70oC 10 mins
	3. Quench on ice for 2 mins
	4. Using Superscript II kit (Life Technologies, 18064-014) add:
	5x first strand buffer (5ul)
	DTT (0.1M)   (2.5ul)
	DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
	Î±-33P dATP (4ul)
	5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
	6. Incubate at 42oC for 120 mins
	7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
	8.Add 24ul TE and measure counts using a scintillation counter
	9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
	vortex column for 30 seconds
	open cap Â¼ turn and snap off bottom
	place in a tube and spin @ 3K rpm for 1 min
	discard flow through and tube and place in a clean screw cap tube
	slowly add the sample at the top of the sephadex column
	spin at 3K rpm for 2 mins
	discard the column and measure the counts for the flow through
	10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40%
 11. Heat at 100oC for 10 mins


title: HUVEC sample of A11 biological rep1


title: Joint_PeakControl_Replicate 2

label_protocol:
First Strand Probe Labelling
	1. In 1.5 ml screw cap tubes the following components were assembled;
	5ug Total RNA
	Mouse Cytokine specific primers
	DEPC H20 made up to 12ul
	2. Heat 70oC 10 mins
	3. Quench on ice for 2 mins
	4. Using Superscript II kit (Life Technologies, 18064-014) add:
	5x first strand buffer (5ul)
	DTT (0.1M)   (2.5ul)
	DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
	Î±-33P dATP (4ul)
	5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
	6. Incubate at 42oC for 120 mins
	7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
	8.Add 24ul TE and measure counts using a scintillation counter
	9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
	vortex column for 30 seconds
	open cap Â¼ turn and snap off bottom
	place in a tube and spin @ 3K rpm for 1 min
	discard flow through and tube and place in a clean screw cap tube
	slowly add the sample at the top of the sephadex column
	spin at 3K rpm for 2 mins
	discard the column and measure the counts for the flow through
	10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (93% incorporation achieved for F031B) 11. Heat at 100oC for 10 mins


title: HUVEC sample of A10 biological rep1


title: Joint_DeclineControl_Replicate 3

description:
Genomic positive control spots were checked and negative controls were also checked. The signals were weak for the positive controls and housekeeping genes.
Due to the very weak signals from the declining control arrays they were not included in downstream data analysis

label_protocol:
First Strand Probe Labelling
	1. In 1.5 ml screw cap tubes the following components were assembled;
	5ug Total RNA
	Mouse Cytokine specific primers
	DEPC H20 made up to 12ul
	2. Heat 70oC 10 mins
	3. Quench on ice for 2 mins
	4. Using Superscript II kit (Life Technologies, 18064-014) add:
	5x first strand buffer (5ul)
	DTT (0.1M)   (2.5ul)
	DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
	33P dATP (4ul)
	5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
	6. Incubate at 42oC for 120 mins
	7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
	8.Add 24ul TE and measure counts using a scintillation counter
	9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
	vortex column for 30 seconds
	open cap ¼ turn and snap off bottom
	place in a tube and spin @ 3K rpm for 1 min
	discard flow through and tube and place in a clean screw cap tube
	slowly add the sample at the top of the sephadex column
	spin at 3K rpm for 2 mins
	discard the column and measure the counts for the flow through
	10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (It was difficult to detect incorporation) 11. Heat at 100oC for 10 mins


title: Joint_PeakCIA_Replicate 2

label_protocol:
First Strand Probe Labelling
	1. In 1.5 ml screw cap tubes the following components were assembled;
	5ug Total RNA
	Mouse Cytokine specific primers
	DEPC H20 made up to 12ul
	2. Heat 70oC 10 mins
	3. Quench on ice for 2 mins
	4. Using Superscript II kit (Life Technologies, 18064-014) add:
	5x first strand buffer (5ul)
	DTT (0.1M)   (2.5ul)
	DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
	Î±-33P dATP (4ul)
	5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
	6. Incubate at 42oC for 120 mins
	7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
	8.Add 24ul TE and measure counts using a scintillation counter
	9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
	vortex column for 30 seconds
	open cap Â¼ turn and snap off bottom
	place in a tube and spin @ 3K rpm for 1 min
	discard flow through and tube and place in a clean screw cap tube
	slowly add the sample at the top of the sephadex column
	spin at 3K rpm for 2 mins
	discard the column and measure the counts for the flow through
	10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (82% incorporation was achieved for F029B)
11. Heat at 100oC for 10 mins

treatment_protocol: Induction of CIA was performed as described (Han S, Cao S, Bheekha-Escura R, Zheng B. Germinal center reaction in the joints of mice with collagen-induced arthritis: an animal model of lymphocyte activation and differentiation in arthritis joints.PG - 1438-43. Arthritis Rheum 2001;44(6):1438-43.). Briefly, mice were injected intradermally at the base of the tail with 200 mg bovine CII (Sigma, St. Louis, MO) dissolved in 0.05 M acetic acid and emulsified in equal volume of CFA. Three weeks after primary immunization, mice were given an i.p. booster injection of 100 mg aqueous CII mixed with 100 mg MPL/TDM (RIBI) adjuvant (Sigma). Mice were observed daily for the onset and severity of arthritis. CIA usually begins to develop around 1 - 2 weeks after secondary immunization with CII, reaching to a peak at 3-4 weeks, then declining after weeks or months.


title: Joint_DeclineCIA_Replicate 2

label_protocol:
First Strand Probe Labelling
	1. In 1.5 ml screw cap tubes the following components were assembled;
	5ug Total RNA
	Mouse Cytokine specific primers
	DEPC H20 made up to 12ul
	2. Heat 70oC 10 mins
	3. Quench on ice for 2 mins
	4. Using Superscript II kit (Life Technologies, 18064-014) add:
	5x first strand buffer (5ul)
	DTT (0.1M)   (2.5ul)
	DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
	Î±-33P dATP (4ul)
	5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
	6. Incubate at 42oC for 120 mins
	7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
	8.Add 24ul TE and measure counts using a scintillation counter
	9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
	vortex column for 30 seconds
	open cap Â¼ turn and snap off bottom
	place in a tube and spin @ 3K rpm for 1 min
	discard flow through and tube and place in a clean screw cap tube
	slowly add the sample at the top of the sephadex column
	spin at 3K rpm for 2 mins
	discard the column and measure the counts for the flow through
	10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (79% incorporation was achieved for F030A)
11. Heat at 100oC for 10 mins


title: Joint_PeakControl_Replicate 1

hyb_protocol: Hybridisation protocol 1.Preheat R& D Systems hybridisation solution to 65oC 2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 4.Rinse arrays in 2 x SSPE for 5 mins 5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 10. repeat step 9 x 2 (3 washes in total) 11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 12. repeat step 11 once 13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 14. Remove the filters from the bottles and place between two sheets of ‘screen guard’. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

label_protocol:
First Strand Probe Labelling
1. In 1.5 ml screw cap tubes the following components were assembled;
5ug Total RNA
Mouse Cytokine specific primers
DEPC H20 made up to 12ul
2. Heat 70oC 10 mins
3. Quench on ice for 2 mins
4. Using Superscript II kit (Life Technologies, 18064-014) add:
5x first strand buffer (5ul)
DTT (0.1M)   (2.5ul)
DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
α-33P dATP (4ul)
5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
6. Incubate at 42oC for 120 mins
7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
8.Add 24ul TE and measure counts using a scintillation counter
9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
vortex column for 30 seconds
open cap ¼ turn and snap off bottom
place in a tube and spin @ 3K rpm for 1 min
discard flow through and tube and place in a clean screw cap tube
slowly add the sample at the top of the sephadex column
spin at 3K rpm for 2 mins
discard the column and measure the counts for the flow through
10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (69% incorporation was achieved for F029A)
11. Heat at 100oC for 10 mins

extract_protocol: The joint samples were snap frozen in liquid nitrogen and homogenized in 1ml GT buffer, then sonicated for ~2 mins to disrupt the tissue. Aliquots of 500ml sonicated samples were added 50ml 3M NaOAc (pH4.0) and 500ml H2O-saturated phenol and 200ml chloroform. The top layer containing RNA was transferred to a new tube and added 500ml RNase-free isopropanol and store at –20°c for at least 20min. RNA was precipitated by centrifugation for 20min. The pellet was washed with 75% ethanol, air dry and dissolved in DEPC water. GT buffer: 4M Guanidine thiocyanate, 25mM Sodium citrate, 0.5% Sarkosyl, 0.1M b-mercaptoethanol.


title: Joint_DeclineCIA_Replicate 1

label_protocol:
First Strand Probe Labelling
1. In 1.5 ml screw cap tubes the following components were assembled;
5ug Total RNA
Mouse Cytokine specific primers
DEPC H20 made up to 12ul
2. Heat 70oC 10 mins
3. Quench on ice for 2 mins
4. Using Superscript II kit (Life Technologies, 18064-014) add:
5x first strand buffer (5ul)
DTT (0.1M)   (2.5ul)
DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
α-33P dATP (4ul)
5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
6. Incubate at 42oC for 120 mins
7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
8.Add 24ul TE and measure counts using a scintillation counter
9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
vortex column for 30 seconds
open cap ¼ turn and snap off bottom
place in a tube and spin @ 3K rpm for 1 min
discard flow through and tube and place in a clean screw cap tube
slowly add the sample at the top of the sephadex column
spin at 3K rpm for 2 mins
discard the column and measure the counts for the flow through
10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (73% incorporation was achieved for F027B)
11. Heat at 100oC for 10 mins

treatment_protocol: Male DBA/1 mice (8-12 wks old) were purchased from The Jackson Laboratory (Bar Harbor, ME) and housed in microisolators in the Center of Comparative Medicine of Baylor College of Medicine. Animal experimentation was performed in accordance with protocols approved by Institutional Animal Care and Use CommitteeInduction of CIA was performed as described (Han S, Cao S, Bheekha-Escura R, Zheng B. Germinal center reaction in the joints of mice with collagen-induced arthritis: an animal model of lymphocyte activation and differentiation in arthritis joints.PG - 1438-43. Arthritis Rheum 2001;44(6):1438-43.). Briefly, mice were injected intradermally at the base of the tail with 200 mg bovine CII (Sigma, St. Louis, MO) dissolved in 0.05 M acetic acid and emulsified in equal volume of CFA. Three weeks after primary immunization, mice were given an i.p. booster injection of 100 mg aqueous CII mixed with 100 mg MPL/TDM (RIBI) adjuvant (Sigma). Mice were observed daily for the onset and severity of arthritis. CIA usually begins to develop around 1 - 2 weeks after secondary immunization with CII, reaching to a peak at 3-4 weeks, then declining after weeks or months.


title: Joint_PeakCIA_Replicate1

label_protocol:
First Strand Probe Labelling
1. In 1.5 ml screw cap tubes the following components were assembled;
5ug Total RNA
Mouse Cytokine specific primers
DEPC H20 made up to 12ul
2. Heat 70oC 10 mins
3. Quench on ice for 2 mins
4. Using Superscript II kit (Life Technologies, 18064-014) add:
5x first strand buffer (5ul)
DTT (0.1M)   (2.5ul)
DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
α-33P dATP (4ul)
5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
6. Incubate at 42oC for 120 mins
7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
8.Add 24ul TE and measure counts using a scintillation counter
9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
vortex column for 30 seconds
open cap ¼ turn and snap off bottom
place in a tube and spin @ 3K rpm for 1 min
discard flow through and tube and place in a clean screw cap tube
slowly add the sample at the top of the sephadex column
spin at 3K rpm for 2 mins
discard the column and measure the counts for the flow through
10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40% (84% incorporation was achieved for F027A)
11. Heat at 100oC for 10 mins

tag: Tissue

value: Paw Joint


title: WT.-.20|WT.50mM_3-AT.20

status: Public on Sep 17 2007

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

description: a complete description of the sample collection protocol and source strains can be found in PMID: PENDING EPUB DATE

hyb_protocol: Competitive hybridization at 65oC for 12h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 4.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: Genotype

value: WT

tag: Condition

tag: Time (min)

value: matched untreated for WT


title: RafERtx-3

city: LONDON

first: ALISON

middle: C

last: LLOYD

address: GOWER STREET

department: LMCB

institute: UNIVERSITY COLLEGE LONDON

description: control

hyb_protocol: affymetrix hybridization

scan_protocol: affymetrix scan

data_processing: Affymetrix CEL files were processed using RMA

label: affymetrix labelling

organism: Rattus norvegicus

source_name: primary Schwann cells from rat controls

label_protocol: affymetrix labelling

extract_protocol: QIagen RNeasy plus

value: sciatic nerve


title: RafERtx-2

description: control


title: RafERtx+1

description: 24 h tamoxifen treatment

source_name: primary Schwann cells from treated rats


title: WT.-.15|WT.50mM_3-AT.15


title: WT.-.4|WT.50mM_3-AT.4


title: RafERtx+2

description: 24 h tamoxifen treatment


title: WT.50mM_3-AT.4|Dgcn2.50mM_3-AT.4

value: matched WT for Dgcn2


title: WT.-.6|WT.50mM_3-AT.6


title: WT.-.2|WT.50mM_3-AT.2


title: WT.-.10|WT.50mM_3-AT.10


title: WT.50mM_3-AT.6|Dgcn2.50mM_3-AT.6


title: WT.50mM_3-AT.2|Dgcn2.50mM_3-AT.2


title: RafERtx+3

description: 24 h tamoxifen treatment


title: WT.50mM_3-AT.15|Dgcn2.50mM_3-AT.15


title: WT.50mM_3-AT.20|Dgcn2.50mM_3-AT.20


title: WT.50mM_3-AT.10|Dgcn2.50mM_3-AT.10


title: HUVEC sample of A13 biological rep1


title: RafERtx-1

description: control


title: HUVEC sample of A12 biological rep1


title: SHED249


title: Dgcn2.-.20|Dgcn2.50mM_3-AT.20

value: matched untreated for Dgcn2


title: Dgcn2.-.15|Dgcn2.50mM_3-AT.15


title: WT.50mM_3-AT.20|WT.-.20


title: Dgcn2.-.2|Dgcn2.50mM_3-AT.2


title: Dgcn2.-.4|Dgcn2.50mM_3-AT.4


title: Dgcn2.-.6|Dgcn2.50mM_3-AT.6


title: RW7000_vs_N2

city: Vancouver

first: Donald

last: Moerman

state: British Columbia

address: 301 - 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: The raw log2 intensity ratio were normalized with the LOESS regression.

source_name: C. elegans RW7000

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.

tag: Strain RW7000

tag: Hermaphrodites

tag: whole animals

source_name: C. elegans wild isolate N2

tag: Strain N2


title: Dgcn2.-.10|Dgcn2.50mM_3-AT.10


title: WT.50mM_3-AT.15|WT.-.15


title: WT.50mM_3-AT.10|WT.-.10


title: WT.50mM_3-AT.6|WT.-.6


title: WT.50mM_3-AT.4|WT.-.4


title: Dgcn2.50mM_3-AT.10|WT.50mM_3-AT.10


title: Dgcn2.50mM_3-AT.20|WT.50mM_3-AT.20


title: Dgcn2.50mM_3-AT.6|WT.50mM_3-AT.6


title: Dgcn2.50mM_3-AT.15|Dgcn2.-.15


title: Dgcn2.50mM_3-AT.20|Dgcn2.-.20


title: Dgcn2.50mM_3-AT.10|Dgcn2.-.10


title: Dgcn2.50mM_3-AT.6|Dgcn2.-.6


title: Dgcn2.50mM_3-AT.4|WT.50mM_3-AT.4


title: Dgcn2.50mM_3-AT.2|WT.50mM_3-AT.2


title: Dgcn2.50mM_3-AT.2|Dgcn2.-.2


title: Dgcn2.50mM_3-AT.4|Dgcn2.-.4


title: WT.-.30|WT.10%_EtOH.30


title: WT.-.20|WT.10%_EtOH.20


title: Dgcn2.50mM_3-AT.15|WT.50mM_3-AT.15


title: WT.-.25|WT.10%_EtOH.25


title: WT.-.15|WT.10%_EtOH.15


title: WT.50mM_3-AT.2|WT.-.2


title: WT.-.5|WT.10%_EtOH.5


title: WT.37C.20|prp8-1.37C[YPD].20


title: WT.MIN.-|Drai1.MIN.-

value: MIN

value: matched WT for Drai1


title: WT.MIN.-|Drrp6.MIN.-

value: matched WT for Drrp6


title: WT.37C.15|prp8-1.37C[YPD].15


title: WT.-.10|WT.10%_EtOH.10


title: WT.37C.10|prp8-1.37C[YPD].10


title: WT.37C.6|prp8-1.37C[YPD].6


title: WT.MIN.-|Dxrn1.MIN.-

value: matched WT for Dxrn1


title: WT.MIN.-|Dupf1.MIN.-

value: matched WT for Dupf1


title: WT.MIN.-|Drtt103.MIN.-

value: matched WT for Drtt103


title: WT.37C.2|prp8-1.37C[YPD].2


title: WT.37C.4|prp8-1.37C[YPD].4


title: Joint_DeclineCIA_Replicate 3

hyb_protocol: Hybridisation protocol 					1.Preheat R& D Systems hybridisation solution to 65oC 					2.Denature Salmon Testes DNA (Sigma D-7656) 100oC 5 mins, quench on ice 					3.Add the Salmon DNA to the hyb solution at 100ug/ml (dilute 1/105), keep at 65oC. 					4.Rinse arrays in 2 x SSPE for 5 mins 					5.Decant Rinse and add 5 ml of hyb solution, rotate 65oC for 1 hr minimum 					6. Replace the prehyb with 3 ml fresh hyb solution (with Salmon DNA) 					7. Pulse spin the probe to the bottom of the tube and then quickly pipette into the hyb buffer in the hyb tube. Do not allow the probe to directly touch the filters. Return tubes to 65oC as quickly as possible. 					8.Hybridise overnight (# 16 hrs) at 65oC gently rotating the tubes 					9. Wash Filters. 40ml wash solution 1 (0.5 x SSPE, 1% SDS) 3 mins, room temp 					10. repeat step 9 x 2 (3 washes in total) 					11. 40 ml prewarmed wash solution 1, 20 mins at 65oC 					12. repeat step 11 once 					13. 40 ml prewarmed wash solution 2 (0.1 SSPE, 1% SDS) 20 mins 65o C 					14. Remove the filters from the bottles and place between two sheets of Screen guard. Expose to phosphoimager screen

scan_protocol: After an appropriate exposure time (24hrs-7 days) the image was developed by scanning using the Storm Phosphoimager. 					Arrayvision software was used to view images and calculate spot signal intensities and background intensity levels (Imaging Research Inc). Background adjusted signals were exported into Excel (Microsoft, Redmond, WA) in comma-delimited format and normalisation of the data was performed.

label_protocol:
First Strand Probe Labelling
					1. In 1.5 ml screw cap tubes the following components were assembled;
					5ug Total RNA
					Mouse Cytokine specific primers
					DEPC H20 made up to 12ul
					2. Heat 70oC 10 mins
					3. Quench on ice for 2 mins
					4. Using Superscript II kit (Life Technologies, 18064-014) add:
					5x first strand buffer (5ul)
					DTT (0.1M)   (2.5ul)
					DNTP mix (20nM dC, G, TTP and 200uM dATP)   (0.5ul)
					33P dATP (4ul)
					5. Incubate at 42oC for 5 mins then add 1ul Superscript II (200u/ul)
					6. Incubate at 42oC for 120 mins
					7.Once 2 hour incubation of probe is complete add 1ul RNASEH (LifeTech, 18021-071) then incubate at 37oC for 20 mins.
					8.Add 24ul TE and measure counts using a scintillation counter
					9. Remove unincorporated nucleotides using ProbeQunat column (Amersham, 27-5335-01):
					vortex column for 30 seconds
					open cap Â¼ turn and snap off bottom
					place in a tube and spin @ 3K rpm for 1 min
					discard flow through and tube and place in a clean screw cap tube
					slowly add the sample at the top of the sephadex column
					spin at 3K rpm for 2 mins
					discard the column and measure the counts for the flow through
					10.Calculate the percentage incorporation of the probe and accept probes where the value is greater than 40%
				 11. Heat at 100oC for 10 mins

value: Male


title: WT.MIN.-|Dski2.MIN.-

value: matched WT for Dski2


title: WT.10%_EtOH.30|WT.-.30


title: WT.10%_EtOH.25|WT.-.25


title: WT.10%_EtOH.20|WT.-.20


title: WT.10%_EtOH.15|WT.-.15


title: WT.10%_EtOH.10|WT.-.10


title: Dupf1.MIN.-|WT.MIN.-


title: WT.10%_EtOH.5|WT.-.5


title: prp8-1.37C[YPD].20|WT.37C.20


title: Drrp6.MIN.-|WT.MIN.-


title: Dski2.MIN.-|WT.MIN.-


title: Drai1.MIN.-|WT.MIN.-


title: Drtt103.MIN.-|WT.MIN.-


title: prp8-1.37C[YPD].4|WT.37C.4


title: prp8-1.37C[YPD].6|WT.37C.6


title: MLP-29 KrasG12D Clone1 technical replicate b

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Oncogenic G12D mutation inserted by AAV-driven homologous recombination at the Kras gene in one allele.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: MLP-29, knock-in of G12D mutation in one Kras allele, Clone1

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: Liver progenitor cell line derived from E13 mouse embryo


title: MLP-29 Wild-type, technical replicate b

description: Control cells

source_name: MLP-29, control wild-type cells


title: MLP-29 Control NEO+ , technical replicate b

description: Neo resistance inserted by AAV-driven homologous recombination at the Kras gene in one allele, not affecting Kras sequence.

source_name: MLP-29, control clone with knock-in NEO+ (not affecting Kras sequence)


title: prp8-1.37C[YPD].15|WT.37C.15


title: prp8-1.37C[YPD].2|WT.37C.2


title: HDC-S_rep3

status: Public on Sep 15 2007

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: This array slide was evaluated as part of an experiment based on a two-color experimental design, comparing individual pooled tumor samples via the uniform reference sample.

hyb_protocol: 750 ng Cyanine 5-CTP-labeled cRNA per pooled tumor sample was mixed with an equal amount of Cyanine 3-CTP–labeled uniform reference cRNA, and hybridized to 44K Whole Mouse Genome Oligo Microarrays (Agilent) according to the manufacturer's protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=46782

scan_protocol: Array scanning, feature extraction and data normalization were done by Agilent’s DNA Microarray Scanner and Feature Extraction Software 8.5 (Agilent).

data_processing: Scanned data was transferred for statistical evaluation in the GeneSpring software package (Agilent) with default normalization scenario for Agilent two-color arrays. Identification of gene sets differentially expressed between HDC-A-, HDC-M- and HDC-S-transfected tumor groups was carried out by One-Way ANOVA with Benjamini-Hochberg multiple testing correction. Tukey’s All Pairwise Multiple Comparison was applied as post hoc test

source_name: B16-F10 HDC-S experimental tumors, pooled samples Nr.5-6

label_protocol: One ug of tumor-derived, pooled total RNA was spiked by an RNA Spike-In Kit (Agilent), reverse transcribed by a Low RNA Input Linear Amplification Kit (Agilent), and used for Cyanine 5-CTP-labeled (Perkin Elmer) cRNA synthesis in a linear amplification reaction. Successful labeling, cRNA yield and purity were controlled on an ND1000 (Nanodrop) spectrophotometer.

extract_protocol: Total RNA isolation was carried out from using RNeasy columns (Quiagen). RNA yield and purity were determined by an ND1000 spectrophotometer (Nanodrop). RNA integrity was checked by capillary electrophoresis using an RNA Series II 6000 Nano Kit (Agilent) and a 2100 Bioanalyzer (Agilent).

tag: The B16-F10 mouse melanoma cell line was stable transfected to express the full length mouse L-histidine decarboxylase (HDC) mRNA. This transgenic B16-F10 subclone, designated as B16-F10 HDC-S, displays enhanced HDC expression and histamine secretion.

tag: Experimental mouse melanoma tumors were induced by grafting 2x10E+5 B16-F10 HDC-S cells to 8-12 weeks old C57BL/6 female mice. At 15 days after grafting, mice were sacrificed, and tumors were excised.

tag: This channel sample consists of a pooled total RNA of two experimental tumors.

source_name: B16-F10 HDC-M cell line cultured in vitro, uniform reference sample

label_protocol: One ug of cell line-derived, pooled total RNA was spiked by an RNA Spike-In Kit (Agilent), reverse transcribed by a Low RNA Input Linear Amplification Kit (Agilent), and used for Cyanine 3-CTP-labeled (Perkin Elmer) cRNA synthesis in a linear amplification reaction. Successful labeling, cRNA yield and purity were controlled on an ND1000 (Nanodrop) spectrophotometer.

extract_protocol: Total RNA isolation was carried out from 1x10E+6 B16-F10 HDC-M cells using RNeasy columns (Quiagen). RNA yield and purity were determined by an ND1000 spectrophotometer (Nanodrop). RNA integrity was checked by capillary electrophoresis using an RNA Series II 6000 Nano Kit (Agilent) and a 2100 Bioanalyzer (Agilent).

tag: The mock-transfected subclone of the original B16-F10 mouse melanoma cell line is designated as B16-F10 HDC-M.


title: MLP-29 KrasG12D Clone1 technical replicate a


title: MLP-29 Control NEO+ , technical replicate a


title: prp8-1.37C[YPD].10|WT.37C.10


title: HDC-M_rep3

source_name: B16-F10 HDC-M experimental tumors, pooled samples Nr.5-6

tag: The B16-F10 mouse melanoma cell line was mock transfected. This transgenic B16-F10 subclone, designated as B16-F10 HDC-M, displays unmodified HDC expression and histamine secretion.

tag: Experimental mouse melanoma tumors were induced by grafting 2x10E+5 B16-F10 HDC-M cells to 8-12 weeks old C57BL/6 female mice. At 15 days after grafting, mice were sacrificed, and tumors were excised.


title: MLP-29 KrasG12D Clone2, technical replicate b

source_name: MLP-29, knock-in of G12D mutation in one Kras allele, Clone2


title: HDC-A_rep3

source_name: B16-F10 HDC-A experimental tumors, pooled samples Nr.5-6

tag: The B16-F10 mouse melanoma cell line was stable transfected to express an antisense RNA targeting the mouse L-histidine decarboxylase (HDC) mRNA. This transgenic B16-F10 subclone, designated as B16-F10 HDC-A, displays diminished HDC expression and histamine secretion.

tag: Experimental mouse melanoma tumors were induced by grafting 2x10E+5 B16-F10 HDC-A cells to 8-12 weeks old C57BL/6 female mice. At 15 days after grafting, mice were sacrificed, and tumors were excised.


title: MLP-29 Wild-type, technical replicate a

description: Control cells


title: MLP-29 KrasG12D Clone2, technical replicate a


title: HDC-S_rep2

source_name: B16-F10 HDC-S experimental tumors, pooled samples Nr.3-4


title: HDC-S_rep1

source_name: B16-F10 HDC-S experimental tumors, pooled samples Nr.1-2


title: HDC-M_rep1

source_name: B16-F10 HDC-M experimental tumors, pooled samples Nr.1-2


title: HDC-A_rep2

source_name: B16-F10 HDC-A experimental tumors, pooled samples Nr.3-4


title: HDC-A_rep1

source_name: B16-F10 HDC-A experimental tumors, pooled samples Nr.1-2


title: NB_E19 lung tissue

city: Toronto

first: Solmaz

last: Alizadeh-Azami

state: ON

address: 1 King's college circle

department: Pharmacology

institute: University of Toronto

description: Total RNA was extracted from E19 lung tissues using TRI reagent.The quality of all RNA samples checked with Agilent bioanalyzer. RNA was then reverse-transcribed into cDNA.cDNAs were later hybridized to the 22.4k cDNA chip (designed at UHN) and hybridized slides scanned with an Agilent(G2505B) GeneArray scanner.

hyb_protocol: cDNAs were then hybridized to 22.4k cDNA mouse array.

scan_protocol: Slides were scanned with G2505B (Agilent) Raw images analyzed and quantified by GenePix Pro 3.0.6.90 and raw data were normalized in genetraffic TM (Iobion informatics) and returned to us as gpr files.

data_processing:
Statistical analysis performed by LimmaGUI (linear models for microarrays Graphical User Interface)
Available on the web   http://bioinf.wehi.edu.au/limmaGUI/

source_name: NB_E19 wild type Bclaf1

label_protocol: cDNA generated from total RNA using superscript II reverse transcriptase (invitrogen). Transcribed cDNAs were labelled with fluorescent Cy5

extract_protocol: Total RNA was extracted from all tissues using TRI reagent according to the manufacturer protocol (Sigma).

tag: Gender:male & female

tag: Age:Embryonic day 19,Tissues:Fetal lung From Bclaf1 +/+

source_name: NB_E19 knock out Bclaf1

label_protocol: cDNA generated from total RNA using superscript II reverse transcriptase (invitrogen). Transcribed cDNAs were labelled with fluorescent Cy3

tag: Age:Embryonic day 19,Tissues:Fetal lung From Bclaf1 -/-


title: HDC-M_rep2

source_name: B16-F10 HDC-M experimental tumors, pooled samples Nr.3-4


title: AGILENT-SiIn-A

status: Public on Sep 14 2007

city: Manchester

first: Junfeng

last: Chen

address: Kilburn Building, Oxford Road

department: School of Computer Science

institute: University of Manchester

description: RNA extraction in Meyers Lab (http://mpss.udel.edu/). Agilent Experiment by Sean J Coughlan from Agilent (http://www.agilent.com/).

hyb_protocol: One ug of labeled cRNA (cy3 and cy5 labeled sample) was diluted to 175 µl and defragmented at 60°C for 30 min following the Agilent hybridization protocols (5184-3568; Agilent). Defragmented samples were diluted with concentrated hybridization buffer to 500 µl (30% formamide final concentration) as described in Hughes et al (2001) and hybridized for 20 h at 40°C using Agilent hybridization chambers.

scan_protocol: Arrays were washed and dried as described in Hughes et al (2001) and scanned on an Agilent G2565BA microarray scanner (Coughlan et al. 2004).

data_processing: The intensities of Cy3- and Cy5-labeled probes were normalized by comparing signal intensities of house keeping genes (positive controls) for both dyes and using the determined ratio as a correction factor for differences in labeling efficiencies(Agilent Feature Extraction v8.1 software). The genes that had valid signal in all six replicates were exported to Rosetta Resolver software, Seattle, Washington). The normalized values were used to calculate the ratio of channel intensities (Cy5/Cy3), which were then log10 transformed.

organism: Arabidopsis thaliana

source_name: Infloresence - mixed stage, immature buds, First Replica

label_protocol: Prior to hybridizations, the quality and quantity of the total RNA sample was confirmed by running  10ng samples on an Agilent bioanalyser (RNA chip), and by using a spectrophotometer. The oligoarray hybridization experiments included six technical replicates, of which three were dye-reversal. Five hundred ng of total RNA was used as template for cRNA production and Cyanine dyes was incorporated using the Agilent low RNA input linear amp kit (5198-3523; Agilent). Normal yields from 500 ng total RNA input using a 4 h in vitro transcription were 15 ug cRNA (15 pmole cyanine dye incorporated/ug cRNA).

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Immature inflorescence was harvested ~2 hours after dark. Tissue included inflorescence meristem and early stage floral buds (up to Stage 11/12). Total RNA was isolated using TRIzol reagent.

source_name: Silique - 24 to 48 hr post-fertilization, First Replica

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Siliques were harvested ~24-48 hours after fertilization, when petals have begun to detach (Stage 16-17). Tissue was harvested ~2 hours after dark. Length of siliques was 5-10 mm. Total RNA was isolated using TRIzol reagent.


title: AGILENT-RoLe-B

source_name: Leaves - 21 day, untreated, Second Replica

extract_protocol: Total RNA was isolated using TRIzol reagent

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark. Equal amounts of leaf tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.

source_name: Root - 21 day, untreated, Second Replica

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark, and roots were rinsed in water and frozen immediately. Equal amounts of root tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.


title: NB_E19 lung tissue2

hyb_protocol: cDNAs were hybridized to 22.4k cDNA mouse array.

data_processing:
Statistical analysis performed by LimmaGUI (linear models for microarrays Graphical User Interface)
Available on the web http://bioinf.wehi.edu.au/limmaGUI/

source_name: NB_E19 Bclaf1 wild type 2

label_protocol:
cDNA generated from total RNA using superscript II reverse ranscriptase (invitrogen).
Transcribed cDNAs were labelled with fluorescent Cy5

tag: Age:Embryonic day 19

tag: Tissues:Fetal lung From Bclaf1 +/+

source_name: NB_E19 Bclaf1 knock out 2

label_protocol:
cDNA generated from total RNA using superscript II reverse ranscriptase (invitrogen).
Transcribed cDNAs were labelled with fluorescent Cy3

tag: Tissues:Fetal lung From Bclaf1 -/-


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 22 of 38

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Chromatin immunoprecipitation was performed using monoclonal antibodiesd. DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides

hyb_protocol: NimbleGen human whole genome array

scan_protocol: GenePix 4000B

data_processing:
The raw data is provided directly from NimbleScan version 1.2
normalization done by QSPLINE

label: Samples were labeled by Cy3

source_name: Histone H3K27me3 associated genomic DNA in Human H1 ES cells

label_protocol: Immunoprecipitated total genomic DNA bound by Histone H3K27me3 was labeled Cy3

extract_protocol: Genomic DNA bound by Histone H3K27me3 extracted via immunoprecipitation

tag: Histone H3K27me3 associated genomic DNA were immunoprecipitated by H3K27me3 antibody from H1 human ES cells.

label: Samples were labeled by Cy5

label_protocol: Genomic DNA extracted via immunoprecipitation

extract_protocol: Genomic DNA was extracted via immunoprecipitation

tag: Total Genomic DNA from Human H1 ES cells used as input for the the immunoprecipitation


title: AGILENT-Ro-A

source_name: Root - 21 day, untreated, First Replica


title: AGILENT-SiIn-B

source_name: Infloresence - mixed stage, immature buds, Second Replica

source_name: Silique - 24 to 48 hr post-fertilization, Second Replica


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 29 of 38

source_name: Total Genomic DNA from Human H1 ES cells


title: AGILENT-RoLe-A

source_name: Leaves - 21 day, untreated, First Replica


title: AGILENT-In-B


title: AGILENT-Le-B


title: AGILENT-Ro-B


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 16 of 38

data_processing: normalization done by QSPLINE

source_name: Histone H3K4me3 associated genomic DNA in Human H1 ES cells

label_protocol: Immunoprecipitated total genomic DNA bound by Histone H3K4me3 was labeled Cy3

extract_protocol: Genomic DNA bound by Histone H3K4me3 extracted via immunoprecipitation

tag: Histone H3K4me3 associated genomic DNA were immunoprecipitated by H3K4me3 antibody from H1 human ES cells.


title: AGILENT-Le-A


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 14 of 38


title: AGILENT-In-A


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 29 of 38


title: AGILENT-Ca-A

source_name: Callus - actively growing, First Replica

tag: Callus was initiated from Col-0 seeds grown on media containing 1/2X MS salts, 3% sucrose in presence of 2,4D (0.5 mg/l), IAA (2 mg/l) and kinetin (0.1mg/l). Tissue was grown ~3 months in dark at 22C and transfered to fresh plates every ~10-14 days. Total RNA was isolated using TRIzol reagent.


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 22 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 16 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 35 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 37 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 5 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 7 of 38


title: Dxrn1.MIN.-|WT.MIN.-

tag: Genotype

tag: Condition

tag: Time (min)


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 5 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 7 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 14 of 38


title: AGILENT-Ca-B

source_name: Callus - actively growing, Second Replica


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 37 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 38 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 28 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 35 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 38 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 27 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 27 of 38


title: DAY 3 - Retionic acid gene expression time series in human embryonic stem cells

type: mixed

description: Total RNA from H1 ES cells or retinoic acid (RA) treated cells was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.

hyb_protocol: Hybridizations were performed in 3.6X SSC buffer with 35% formamide and 0.07% SDS at 42% C overnight.

scan_protocol: Arrays were washed, dried and scanned with the GenePix 4000B Scanner

data_processing: Gene Expression data was extracted using NimbleScan Software v2.1

source_name: Genomic DNA extracted from H1 Human Embryonic Stem Cells

label_protocol: Sonicated genomic DNA was primed with random octamers and labeled using Klenow in the present of 5-(3-aminoallyl)-dUTP

extract_protocol: Qiagen purification kit

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day3)

label_protocol: Total RNA was enriched for the polyA fraction using Oligotex mRNA Mini Kit (Qiagen). Enriched mRNA (250 ng) was primed using random hexamers and reversed transcribed using Superscript III (Invitrogen) in the presence of 5-(3-aminoallyl)-dUTP (Ambion).

extract_protocol: Qiagen in column kit


title: DAY 2 - Retionic acid gene expression time series in human embryonic stem cells

tag: Genomi DNA extracted from H1 Human Embryonic Stem Cells

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day 2)


title: DAY 1 - Retionic acid gene expression time series in human embryonic stem cells

tag: Genomic DNA extracted from H1 ES cells from passage

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day1)

tag: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day0).


title: DAY 1.5 - Retionic acid gene expression time series in human embryonic stem cells

tag: Genomic DNA extracted from H1 Human Embryonic Stem Cells

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day1.5)


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 25 of 38


title: DAY 4 - Retionic acid gene expression time series in human embryonic stem cells

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day 4)


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 26 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 26 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 12 of 38


title: DAY 5 - Retionic acid gene expression time series in human embryonic stem cells

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day 5)


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 28 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 24 of 38


title: DAY 0.5 - Retionic acid gene expression time series in human embryonic stem cells

tag: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day0.5).


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 25 of 38


title: DAY 0 - Retionic acid gene expression time series in human embryonic stem cells

source_name: Human Embryonic Stem cell H1/TeSR medium without retinoic acid treatment (day0)


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 12 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 24 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 10 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 11 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 10 of 38

source_name: Histone H3K27me3 associated genomic DNA in Human H1 ES cells


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 9 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 9 of 38


title: 12827361_w1118_2-4hr_unfertilized_eggs_vs_w1118_st_14

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

description: 12827361_w1118_2-4hr_unfertilized_eggs_vs_w1118_stage_14

scan_protocol: as previously described (Neal et al., 2003), using a PerkinElmer/GSI ScanArray 4000 scanner and the ScanArray software. The 16 bit TIFF image files were quantified using QuantArray Version 3 (PerkinElmer) using the adaptive quantification algorithm (www.flyarrays.com).

data_processing: Quantified data was analyzed using GeneTraffic Duo 3.2 (Iobion Informatics/Stratagene) after normalization to the known stable transcripts rpA1 and rp49. Values represent normalized log2 ratios.

organism: Drosophila melanogaster

source_name: w1118 2-4hr unfertilized eggs

label_protocol: Followed Canadian Drosophila Microarray Centre direct labelling protocol (www.flyarrays.com)

extract_protocol: Trizol procedure, added extra steps suggested by Canadian Drosophila Microarray Centre (RNA isolation file - www.flyarrays.com).

tag: 14 188 ugperml

source_name: w1118 stage 14


title: 12697225_w1118_2-4hr_unfertilized_eggs_vs_w1118_st_14

description: 12697225_w1118_2-4hr_unfertilized_eggs_vs_w1118_stage_14

tag: Extract W1118 Stage 14, 15


title: 12697311_w1118_2-4hr_unfertilized_eggs_vs_w1118_st_14

description: 12697311_w1118_2-4hr_unfertilized_eggs_vs_w1118_stage_14

tag: 18 105 ugperml

tag: 19 993ugperml


title: 12827359_w1118_0-2hr_unfertilized_eggs_vs_w1118_st_14

description: 12827359_w1118_0-2hr_unfertilized_eggs_vs_w1118_stage_14

source_name: w1118 0-2hr unfertilized eggs

tag: 12 377ugperml

tag: 14 117 ugperml


title: 12827382_w1118_0-2hr_unfertilized_eggs_vs_w1118_st_14

description: 12827382_w1118_0-2hr_unfertilized_eggs_vs_w1118_stage_14

tag: 4 458ugperml


title: 12827360_w1118_0-2hr_unfertilized_eggs_vs_w1118_st_14

description: 12827360_w1118_0-2hr_unfertilized_eggs_vs_w1118_stage_14

tag: 13 866ugperml

tag: 14 384ugperml


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 36 of 38

tag: Histone H3K27me3 associated genomic DNA were immunoprecipitated by H3K27me3 antibody from H1 human ES cells.

tag: Total Genomic DNA from Human H1 ES cells used as input for the the immunoprecipitation


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 32 of 38

source_name: Total Genomic DNA from Human H1 ES cells


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 34 of 38


title: 12663395_w1118_4-6hr_unfertilized_eggs_vs_w1118_st_14

description: 12663395_w1118_4-6hr_unfertilized_eggs_vs_w1118_stage_14

source_name: w1118 4-6hr unfertilized eggs

tag: 8120.6 ugperml


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 32 of 38

source_name: Histone H3K4me3 associated genomic DNA in Human H1 ES cells

tag: Histone H3K4me3 associated genomic DNA were immunoprecipitated by H3K4me3 antibody from H1 human ES cells.


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 34 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 20 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 36 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 20 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 33 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 30 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 31 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 31 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 23 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 19 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 18 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 11 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 33 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 21 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 21 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 23 of 38


title: 12663396_w1118_4-6hr_unfertilized_eggs_vs_w1118_st_14

description: 12663396_w1118_4-6hr_unfertilized_eggs_vs_w1118_stage_14

tag: 5117.8ug per ml


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 15 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 13 of 38


title: 12827385_w1118_4-6hr_unfertilized_eggs_vs_w1118_st_14

description: 12827385_w1118_4-6hr_unfertilized_eggs_vs_w1118_stage_14


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 30 of 38


title: 12697230_smg_0-2hr_vs_w1118_st_14_oocytes

description: 12697230_smg_0-2hr_vs_w1118_stage_14_oocytes

source_name: smg 0-2hr unfertlized eggs

label_protocol: Canadian Drosophila Microarray Centre labelling protocol (www.flyarrays.com)

extract_protocol: RNA TRIzol extraction procedure from the Canadian Drosophila Microarray Centre (www.flyarrays.com)

tag: collected unfertilized eggs from smg over deficiency mutants, mated virgin females with sterile males and collected unfertilized eggs at the three time points

tag: w1118 stage 14 oocytes were dissected on ice in 1XPBS, then frozen in dry ice and EtOH


title: 12706983_smg_0-2hr_vs_w1118_st_14_oocytes

description: 12706983_smg_0-2hr_vs_w1118_stage_14_oocytes


title: 12697314_smg_0-2hr_vs_w1118_st_14_oocytes

description: 12697314_smg_0-2hr_vs_w1118_stage_14_oocytes


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 18 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 19 of 38


title: 12706986_smg_2-4hr_vs_w1118_st_14_oocytes

description: 12706986_smg_2-4hr_vs_w1118_stage_14_oocytes

source_name: smg 2-4hr unfertlized eggs


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 15 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 4 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 17 of 38


title: 12697229_smg_4-6hr_unfertilized_eggs_vs_w1118_st_14_oocytes

description: 12697229_smg_4-6hr_unfertilized_eggs_vs_w1118_stage_14_oocytes

source_name: smg 4-6hr unfertilized eggs


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 13 of 38


title: 12827386_smg_4-6hr_unfertilized_eggs_vs_w1118_st_14_oocytes

description: 12827386_smg_4-6hr_unfertilized_eggs_vs_w1118_stage_14_oocytes


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 4 of 38

description: Chromatin immunoprecipitation was performed using monoclonal antibodiesd. DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides


title: 12697313_smg_4-6hr_unfertilized_eggs_vs_w1118_st_14_oocytes

description: 12697313_smg_4-6hr_unfertilized_eggs_vs_w1118_stage_14_oocytes


title: 12706985_smg_2-4hr_vs_w1118_st_14_oocytes

description: 12706985_smg_2-4hr_vs_w1118_stage_14_oocytes


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 3 of 38


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 17 of 38


title: PBMCs-Type 2 Diabetes-T2D_3_New

status: Public on Sep 12 2007

city: Dallas

first: Ellen

last: Grishman

address: 5323 Harry Hines Blvd

institute: UTSW Medical Center

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

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

source_name: PBMCs from Type 2 Diabetes patient and the timepoint at diagnosis.

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

extract_protocol: RNeasy Mini

tag: Age

value: 15 yrs, when sample taken.

tag: Gender

value: F

tag: Ethnicity

value: Not Hispanic or Latino

tag: Race

value: White

tag: Illness

value: Type 2 Diabetes

tag: Treatment

value: Insulin

tag: pH<7.30 at time of diagnosis

value: No


title: 12697312_smg_st_14_vs_w1118_st_14_oocytes

description: 12697312_smg_stage_14_vs_w1118_stage_14_oocytes

source_name: smg stage 14 oocytes

tag: dissected stage 14 oocytes out of smg over deficiency adult females in 1 X PBS, froze in dry ice and EtOH


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 8 of 38


title: 12697310_smg_st_14_vs_w1118_st_14_oocytes

description: 12697310_smg_stage_14_vs_w1118_stage_14_oocytes


title: 12697226_smg_2-4hr_vs_w1118_st_14_oocytes

description: 12697226_smg_2-4hr_vs_w1118_stage_14_oocytes


title: PBMCs-Type 1 Diabetes-IDDM59_T1D_1MO

source_name: PBMCs from Type 1 Diabetes patient and the timepoint 1 month after diagnosis.

value: 7 yrs, when sample taken.

value: Hispanic or Latino

value: (Race Not Reported)

value: Type 1 Diabetes

value: Yes


title: K27 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 6 of 38


title: PBMCs-Type 1 Diabetes-IDDM42_T1D_New

source_name: PBMCs from Type 1 Diabetes patient and the timepoint at diagnosis.

value: 10 yrs, when sample taken.

value: M


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 6 of 38


title: K4 Sample for Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27 8 of 38


title: PBMCs-Type 1 Diabetes-IDDM42_T1D_1MO

description: Type 1 Diabetes patient and the timepoint 1 month after diagnosis.


title: PBMCs-Type 1 Diabetes-IDDM46_T1D_1MO


title: 12697223_smg_st_14_vs_w1118_st_14_oocytes

description: 12697223_smg_stage_14_vs_w1118_stage_14_oocytes


title: PBMCs-Type 1 Diabetes-IDDM32_T1D_New

description: Type 1 Diabetes patient and the timepoint at diagnosis.

value: 14 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM7_T1D_New

value: 4 yrs, when sample taken.


title: PBMCs-Healthy-H171_Healthy

description: Healthy patient.

source_name: PBMCs from Healthy patient.

value: 13 yrs  when sample taken.

value: Black or African American

value: Healthy


title: PBMCs-Type 1 Diabetes-IDDM11_T1D_New

value: 13 yrs, when sample taken.

value: F

value: Not Hispanic or Latino