title: H202 24 hrs WT - mAdbID:49191

status: Public on Dec 01 2005

city: Bethesda

first: Ana

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: mAdb experiment ID: 49191

hyb_protocol: protocol_name: Oligo Microarray Hybridization other: The probes were finally concentrated to a volume of 14 µl and mixed with 1 µl COT-1 DNA (8-10 µg/µl) (Invitrogen), 1 µl yeast tRNA (4 µg/µl) (Sigma), and 1 µl poly-dA DNA (8-10 µg/µl) (Amersham). Before hybridization, the probes were denatured for 2 minutes at 100?C and cooled to room temperature. We used 70-mer oligo glass slides featuring 22,149 spots, corresponding to approximately 9,800 unique Unigene Clusters (Qiagen Human Version 2.0 set), which were printed by the National Cancer Institute Microarray Facility, Advanced Technology Center, Gaithersburg, MD. Arrays were pre-hybridized for 60 minutes at 42°C using a pre-hybridization buffer consisting of 5X SSC (sodium chloride-sodium citrate), 1% bovine serum albumin, and 0.1% SDS (sodium dodecyl sulfate). They were then washed in dH2O, immersed in isopropanol for 2 minutes, and air-dried. Denatured probes were mixed at a 1:1 ratio with hybridization buffer consisting of 50% formamide (Ambion), 1X SSC, and 0.1% SDS, and hybridized onto the microarrays at 42°C for 14–16 hours in a water bath. After hybridization, the slides were washed for 1 minute in 1X SSC with 0.1% SDS, for 1 minute in 1X SSC, and twice for 1 minute in 0.2X SSC. The arrays were finally scanned at a 10µm resolution with a GenePix 4000A scanner (Axon Instruments, Foster City, CA) with variable voltages to achieve saturated signal intensities for about 1% of the total spot number.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Untreated WT

label_protocol:
protocol_name: Cy3 Label Protocol
label_method: indirect labeling
other: For the preparation of fluorescence-labeled cDNA targets, 20 µg total RNA for each channel (Cy3 and Cy5) were reverse-transcribed using Superscript II enzyme reaction kit (Invitrogen, Carlsbad, CA). Briefly, total RNA was mixed with 4 µg of oligo dT (20-mer) primer for a total volume of 25 µl, denatured at 70°C, and cooled to room temperature. Then, a mix containing 2.5 µl of 20 mM dNTP pool [10 mM of dATP, dGTP, dCTP, and 4 mM of dTTP (Amersham), and 6 mM of aminoallyl-dUTP (Sigma-Aldrich, St. Louis, MO)], 10 µl of 5X first strand buffer (Invitrogen), 5 µl of 0.1M dithiothreitol (Invitrogen), 1.0 µl of Superase Inhibitor (Ambion, Austin, TX), 3.2 µl of dH2O, and 3.3 µl of Superscript II reverse transcriptase were added and incubated for 60 minutes at 42°C, followed by a 5-minute incubation at 75°C. Remaining RNA was degraded by adding 2 µl of RNAse H (2 U/µl) (Invitrogen), followed by incubation at 37°C for 20 minutes. To remove traces of protein, 10 µl of Quick Clean Enzyme Removal Resin (Clontech, Palo Alto, CA) were added to the cDNA, mixed by 1-minute vortex, and centrifuged at 14,000 rpm for 1 minute. The resulting supernatant was filtered through a 0.65 µm Ultra-free MC filter (Millipore, Bedford, MA) to remove any resin residues. The cDNA probes were precipitated by adding 5.5 µl of 3M sodium acetate (pH = 5.2) and 137.5 µl of cold 190-proof ethanol, and incubated for 60 minutes at -20°C, followed by centrifugation for 15 minutes at 14,000 rpm and 4°C. The cDNA precipitate was washed twice with 70% ethanol, air-dried, and dissolved with 17 µl of 0.1M sodium bicarbonate. For the dye-coupling reaction, the monoreactive Cy3 (for control probes) and Cy5 dyes (for treated probes) (Amersham) were dissolved with 2 µl of dH2O, mixed with the corresponding cDNA probe and incubated for 60 minutes in the dark. The labeled cDNA samples were again precipitated by adding 2.5 µl of 3 M sodium acetate (pH = 5.2) and 50 µl of cold 190-proof ethanol, followed by an incubation for 90 minutes, and a centrifugation for 10 minutes at 14,000 rpm and 4°C. The supernatant was discarded, probes were washed twice with 70% ethanol, and air-dried. To remove unincorporated dye residues, probes were cleaned-up using the Nucleospin Extraction Kit (Clontech) following the manufacturer’s recommendations. To further clean-up the probes, the eluate from the previous step was washed twice with TE buffer (tris ethylenediaminetetraacetic acid) (pH = 7.4) using a Microcon YM-30 column (Millipore).

growth_protocol:
protocol_name: Cell culture
media: McCoy's 5A medium containing 10% FBS, 4 mM glutamine, 10 u/ml penicillin, 10 ug/ml streptomycin

extract_protocol:
protocol_name: RNA extraction with TRIZOL
extraction_method: TRIZOL
other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturer’s instructions. RNA integrity was assessed by the presence of 28S and 18S bands in denaturing agarose gel eletrophoresis and spectrophotometry with A260/A280 ratios > 2.0 after dilution in TE-buffer.

value: colon cancer

source_name: H2O2 24 Hrs WT

label_protocol:
protocol_name: Cy5 Label Protocol
label_method: indirect labeling
other: For the preparation of fluorescence-labeled cDNA targets, 20 µg total RNA for each channel (Cy3 and Cy5) were reverse-transcribed using Superscript II enzyme reaction kit (Invitrogen, Carlsbad, CA). Briefly, total RNA was mixed with 4 µg of oligo dT (20-mer) primer for a total volume of 25 µl, denatured at 70°C, and cooled to room temperature. Then, a mix containing 2.5 µl of 20 mM dNTP pool [10 mM of dATP, dGTP, dCTP, and 4 mM of dTTP (Amersham), and 6 mM of aminoallyl-dUTP (Sigma-Aldrich, St. Louis, MO)], 10 µl of 5X first strand buffer (Invitrogen), 5 µl of 0.1M dithiothreitol (Invitrogen), 1.0 µl of Superase Inhibitor (Ambion, Austin, TX), 3.2 µl of dH2O, and 3.3 µl of Superscript II reverse transcriptase were added and incubated for 60 minutes at 42°C, followed by a 5-minute incubation at 75°C. Remaining RNA was degraded by adding 2 µl of RNAse H (2 U/µl) (Invitrogen), followed by incubation at 37°C for 20 minutes. To remove traces of protein, 10 µl of Quick Clean Enzyme Removal Resin (Clontech, Palo Alto, CA) were added to the cDNA, mixed by 1-minute vortex, and centrifuged at 14,000 rpm for 1 minute. The resulting supernatant was filtered through a 0.65 µm Ultra-free MC filter (Millipore, Bedford, MA) to remove any resin residues. The cDNA probes were precipitated by adding 5.5 µl of 3M sodium acetate (pH = 5.2) and 137.5 µl of cold 190-proof ethanol, and incubated for 60 minutes at -20°C, followed by centrifugation for 15 minutes at 14,000 rpm and 4°C. The cDNA precipitate was washed twice with 70% ethanol, air-dried, and dissolved with 17 µl of 0.1M sodium bicarbonate. For the dye-coupling reaction, the monoreactive Cy3 (for control probes) and Cy5 dyes (for treated probes) (Amersham) were dissolved with 2 µl of dH2O, mixed with the corresponding cDNA probe and incubated for 60 minutes in the dark. The labeled cDNA samples were again precipitated by adding 2.5 µl of 3 M sodium acetate (pH = 5.2) and 50 µl of cold 190-proof ethanol, followed by an incubation for 90 minutes, and a centrifugation for 10 minutes at 14,000 rpm and 4°C. The supernatant was discarded, probes were washed twice with 70% ethanol, and air-dried. To remove unincorporated dye residues, probes were cleaned-up using the Nucleospin Extraction Kit (Clontech) following the manufacturer’s recommendations. To further clean-up the probes, the eluate from the previous step was washed twice with TE buffer (tris ethylenediaminetetraacetic acid) (pH = 7.4) using a Microcon YM-30 column (Millipore).

treatment_protocol:
treatment_type: compound
compound: hydrogen peroxide
treatment_dose: 0.1 mM
treatment_time: 24 hrs


title: H202 24 hrs KO - mAdbID:49195

type: RNA

state: MD

country: USA

description: mAdb experiment ID: 49195

molecule: total RNA

organism: Homo sapiens

source_name: Untreated KO

value: gene knock out

source_name: H2O2 24 hrs KO


title: NO 24 hrs KO - mAdbID:49189

description: mAdb experiment ID: 49189

source_name: NO 24 hrs KO

treatment_protocol:
treatment_type: compound
compound: Sper/NO
treatment_dose: 1 mM
treatment_time: 24 hrs


title: NO 1 hrs KO - mAdbID:49178

description: mAdb experiment ID: 49178

source_name: NO 1 hrs KO

treatment_protocol:
treatment_type: compound
compound: Sper/NO
treatment_dose: 1 mM
treatment_time: 1 hrs


title: Hypoxia 24 hrs KO - mAdbID:49129

description: mAdb experiment ID: 49129

source_name: Hypoxia 24 hrs KO

treatment_protocol:
treatment_type: stress
treatment_stress: hypoxia/hyperbolic chamber
treatment_time: 24 hrs


title: Hypoxia 12 hrs KO - mAdbID:49128

description: mAdb experiment ID: 49128

source_name: Hypoxia 12 hrs KO

treatment_protocol:
treatment_type: stress
treatment_stress: hypoxia/hyperbolic chamber
treatment_time: 12 hrs


title: Hypoxia 1 hrs WT - mAdbID:49126

description: mAdb experiment ID: 49126

source_name: Hypoxia 1 Hrs WT

treatment_protocol:
treatment_type: stress
treatment_stress: hypoxia/hyperbolic chamber
treatment_time: 1 hrs


title: Hypoxia 1 hrs KO - mAdbID:49127

description: mAdb experiment ID: 49127

source_name: Hypoxia 1 hrs KO


title: HU 12 hrs WT - mAdbID:49125

description: mAdb experiment ID: 49125

source_name: HU 12 Hrs WT

treatment_protocol:
treatment_type: compound
compound: hydroxy urea
treatment_dose: 1.5 mM
treatment_time: 12 hrs


title: H202 1 hrs WT - mAdbID:49123

description: mAdb experiment ID: 49123

source_name: H2O2 1 Hrs WT

treatment_protocol:
treatment_type: compound
compound: hydrogen peroxide
treatment_dose: 0.1 mM
treatment_time: 1 hrs


title: NO 8 hrs WT - mAdbID:49122

description: mAdb experiment ID: 49122

source_name: NO 8 Hrs WT

treatment_protocol:
treatment_type: compound
compound: Sper/NO
treatment_dose: 1 mM
treatment_time: 8 hrs


title: Hypoxia 24 hrs WT - mAdbID:48988

description: mAdb experiment ID: 48988

source_name: Hypoxia 24 Hrs WT


title: MDS24

status: Public on Jul 01 2006

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

description: Gene expression data from CD34+ cells isolated from bone marrow

hyb_protocol: Following fragmentation. 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: Affymetrix CEL files were used for Robust MultiChip Analysis (RMA)

label: biotin

source_name: CD34+ cells isolated from the bone marrow of an MDS patient

label_protocol: Biotinylated cRNA were prepared according to the Two-cycle Affymetrix protocol from 50 nanograms total RNA

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

tag: Subtype

tag: Karyotype

value: other


title: H202 24 hrs WT - mAdbID:48985

description: mAdb experiment ID: 48985


title: HU 1 hrs WT - mAdbID:48987

description: mAdb experiment ID: 48987

source_name: HU 1 Hrs WT

treatment_protocol:
treatment_type: compound
compound: hydroxy urea
treatment_dose: 1.5 mM
treatment_time: 1 hrs


title: H202 24 hrs KO - mAdbID:48986

description: mAdb experiment ID: 48986


title: MDS35

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

value: RARS

value: normal


title: NO 24 hrs KO - mAdbID:48984

description: mAdb experiment ID: 48984


title: NO 24 hrs KO - mAdbID:48737

description: mAdb experiment ID: 48737


title: NO 8 hrs KO - mAdbID:48736

description: mAdb experiment ID: 48736

source_name: NO 8 hrs KO


title: H202 24 hrs WT - mAdbID:48664

description: mAdb experiment ID: 48664

source_name: Untreated WT


title: NO 1 hrs KO - mAdbID:48982

description: mAdb experiment ID: 48982


title: NO 24 hrs WT - mAdbID:49177

description: mAdb experiment ID: 49177

source_name: NO 24 Hrs WT


title: NO 8 hrs WT - mAdbID:48662

description: mAdb experiment ID: 48662


title: NO 8 hrs WT - mAdbID:48661

description: mAdb experiment ID: 48661


title: HU 1 hrs WT - mAdbID:48658

description: mAdb experiment ID: 48658


title: Hypoxia 24 hrs KO - mAdbID:48660

description: mAdb experiment ID: 48660

source_name: Untreated KO


title: NO 24 hrs WT - mAdbID:48654

description: mAdb experiment ID: 48654


title: NO 1 hrs WT - mAdbID:48653

description: mAdb experiment ID: 48653

source_name: NO 1 Hrs WT


title: HU 12 hrs KO - mAdbID:48485

description: mAdb experiment ID: 48485

source_name: HU 12 hrs KO


title: Hypoxia 24 hrs KO - mAdbID:48479

description: mAdb experiment ID: 48479


title: Hypoxia 1 hrs KO - mAdbID:48468

description: mAdb experiment ID: 48468


title: H202 24 hrs KO - mAdbID:48738

description: mAdb experiment ID: 48738

source_name: H2O2 24 hrs KO


title: Hypoxia 12 hrs WT - mAdbID:48461

description: mAdb experiment ID: 48461

source_name: Hypoxia 12 Hrs WT


title: Hypoxia 12 hrs KO - mAdbID:48473

description: mAdb experiment ID: 48473

source_name: Hypoxia 12 hrs KO


title: Hypoxia 1 hrs WT - mAdbID:48460

description: mAdb experiment ID: 48460

source_name: Hypoxia 1 Hrs WT


title: HU 12 hrs KO - mAdbID:48457

description: mAdb experiment ID: 48457


title: HU 24 hrs KO - mAdbID:48459

description: mAdb experiment ID: 48459

source_name: HU 24 hrs KO

treatment_protocol:
treatment_type: compound
compound: hydroxy urea
treatment_dose: 1.5 mM
treatment_time: 24 hrs


title: Hypoxia 24 hrs WT - mAdbID:48451

description: mAdb experiment ID: 48451


title: Hypoxia 24 hrs WT - mAdbID:48456

description: mAdb experiment ID: 48456


title: Hypoxia 1 hrs KO - mAdbID:48453

description: mAdb experiment ID: 48453

source_name: Hypoxia 1 hrs KO


title: HU 24 hrs KO - mAdbID:48043

description: mAdb experiment ID: 48043


title: N10

source_name: CD34+ cells isolated from the bone marrow of a normal control


title: Hypoxia 12 hrs WT - mAdbID:48449

description: mAdb experiment ID: 48449


title: Hypoxia 24 hrs WT - mAdbID:48045

description: mAdb experiment ID: 48045


title: Hypoxia 1 hrs WT - mAdbID:48448

description: mAdb experiment ID: 48448


title: NO 8 hrs KO - mAdbID:48663

description: mAdb experiment ID: 48663


title: HU 12 hrs KO - mAdbID:48042

description: mAdb experiment ID: 48042


title: H202 24 hrs WT - mAdbID:48656

description: mAdb experiment ID: 48656

source_name: H2O2 24 Hrs WT


title: HU 24 hrs WT - mAdbID:48040

description: mAdb experiment ID: 48040

source_name: HU 24 Hrs WT


title: HU 12 hrs WT - mAdbID:48039

description: mAdb experiment ID: 48039

source_name: HU 12 Hrs WT


title: HU 1 hrs WT - mAdbID:48038

description: mAdb experiment ID: 48038

source_name: HU 1 Hrs WT


title: HU 24 hrs WT - mAdbID:47991

description: mAdb experiment ID: 47991


title: H202 4 hrs KO - mAdbID:47988

description: mAdb experiment ID: 47988

source_name: H2O2 4 hrs KO

treatment_protocol:
treatment_type: compound
compound: hydrogen peroxide
treatment_dose: 0.1 mM
treatment_time: 4 hrs


title: Hypoxia 12 hrs KO - mAdbID:48454

description: mAdb experiment ID: 48454


title: H202 4 hrs KO - mAdbID:47910

description: mAdb experiment ID: 47910


title: NO 1 hrs WT - mAdbID:47984

description: mAdb experiment ID: 47984

source_name: Untreated WT


title: NO 1 hrs KO - mAdbID:47986

description: mAdb experiment ID: 47986

source_name: NO 1 hrs KO


title: HU 12 hrs WT - mAdbID:47990

description: mAdb experiment ID: 47990


title: H202 24 hrs KO - mAdbID:47911

description: mAdb experiment ID: 47911

source_name: Untreated KO


title: NO 1 hrs KO - mAdbID:47908

description: mAdb experiment ID: 47908


title: NO 24 hrs WT - mAdbID:47985

description: mAdb experiment ID: 47985

source_name: NO 24 Hrs WT


title: HU 1 hrs KO - mAdbID:48041

description: mAdb experiment ID: 48041

source_name: HU 1 hrs KO


title: NO 1 hrs WT - mAdbID:47904

description: mAdb experiment ID: 47904

source_name: NO 1 Hrs WT


title: HU 1 hrs KO - mAdbID:48484

description: mAdb experiment ID: 48484


title: H202 1 hrs KO - mAdbID:47841

description: mAdb experiment ID: 47841

source_name: H2O2 1 hrs KO


title: H202 4 hrs WT - mAdbID:47839

description: mAdb experiment ID: 47839

source_name: H2O2 4 Hrs WT


title: H202 1 hrs WT - mAdbID:47838

description: mAdb experiment ID: 47838

source_name: H2O2 1 Hrs WT


title: H202 4 hrs WT - mAdbID:47712

description: mAdb experiment ID: 47712


title: H202 4 hrs KO - mAdbID:43657

description: mAdb experiment ID: 43657


title: H202 24 hrs KO - mAdbID:43769

description: mAdb experiment ID: 43769

source_name: H2O2 24 hrs KO


title: HU 1 hrs WT - mAdbID:43770

description: mAdb experiment ID: 43770


title: HU 24 hrs KO - mAdbID:43773

description: mAdb experiment ID: 43773

source_name: HU 24 hrs KO


title: H202 1 hrs KO - mAdbID:43656

description: mAdb experiment ID: 43656


title: H202 4 hrs WT - mAdbID:43654

description: mAdb experiment ID: 43654


title: H202 24 hrs WT - mAdbID:43655

description: mAdb experiment ID: 43655


title: Mouse_V275_villi

status: Public on Nov 29 2005

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Villi were isolated from the small intestine of a 12 week old mouse.

data_processing: RMA processing using quantile normalization

label: Phycoerythrin

organism: Mus musculus

source_name: Small intestinal villi

extract_protocol: Qiagen RNeasy total RNA extraction system with on column DNAse I digestion

tag: Strain

value: C57BL/6, Age:12 weeks, tissue:small intestinal villi


title: Mouse_V41_villi


title: Mouse_K41_crypt

description: Crypts were isolated from the small intestine of a 12 week old mouse.

source_name: Small intestinal crypts

value: C57BL/6, Age:12 weeks, tissue:small intestinal crypts


title: Mouse_V12_villi


title: Mouse_K21_crypt


title: HU 24 hrs WT - mAdbID:43771

description: mAdb experiment ID: 43771

source_name: HU 24 Hrs WT


title: H202 4 hrs KO - mAdbID:47713

description: mAdb experiment ID: 47713


title: Mouse_K12_crypt


title: Mouse_E12_Endoderm

description: Endoderm form E12 mouse embryos was dissected out from collagenase digested fetal intestine. Material from 35 fetuses were pooled.

source_name: Endoderm

tag: Endoderm form E12 mouse embryos were dissected out from collagenase digested fetal intestine. Material from 35 fetuses were pooled.


title: Mouse_E12_mesenchyme

description: Mesenchyme form E12 mouse embryos were dissected out from collagenase digested fetal intestine. Material from 35 fetuses were pooled.

source_name: mesenchyme

tag: Strain:C57BL/6, Tissue:E12 mesenchyme


title: slide74

status: Public on Nov 10 2005

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description: Yersina pestis 48h

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence. Laser power was kept constant and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan was done for each slide with the PMT such that <1% of the elements are saturated in order to characterize spots which were saturated at the higher PMT setting. This is refered to here as the low PMT scan.  Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer).

data_processing: What is submitted is the raw output of Scanarray. VALUE = log2 (test/ref)

organism: Yersinia pestis

source_name: Yersina pestis, pulmonary

label_protocol: Total RNA (500 ng) was amplified using the MessageAmp II Bacteria amplified antisense RNA (aRNA) kit (Ambion) according to the manufacturer’s instructions. aRNA (5 ug) was labeled using Micromax ASAP (PerkinElmer) according to the manufacturer’s instructions. The labeled aRNA was resuspended in a formamide based hybridization buffer (MWG “Coverslips Hybridization buffer”), hybridized to the microarrays at 42ºC overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each.

extract_protocol: Total RNA was extracted bacteria using the RiboPure-Bacteria kit (Ambion).

tag: 10 mice each were independently infected with Yersina pestis strain CO92. After 48 hours, mice were sacrificed, their tracheas cannulated and lungs lavaged with 3 x 1 ml PBS. After each wash, lavage fluid was immediately mixed with an excess of RNAlater stabilization solution (Ambion) to inhibit additional transcription and prevent RNA degradation. The lavage fluid/RNAlater mixture was centrifuged for 15 minutes at 27,000 x g to pellet the host and bacterial cells, and the supernatant was discarded. The pelleted cells were resuspended in a host cell lysis buffer (0.2% saponin in 50% PBS/50% RNAlater) and mixed at room temperature for 10 minutes. The mixture was centrifuged again for 2 minutes and washed once with lysis buffer.

source_name: Yersina pestis, cultured

growth_protocol: Yersina pestis was grown in BHI broth at 26ºC for 6-8 hours in a roller drum before being diluted to an O.D.620 of 0.05-0.1 in 10 ml BHI broth with 2.5 mM CaCl2 in a 125-ml Erlenmeyer flask. Bacteria were incubated at 37ºC in a water bath shaker set at 250 revolutions per minute for 16-18 hours.

tag: Yersina pestis strain CO92 grown in BHI broth


title: slide72

description: Yersina pestis 48h


title: slide70

description: Yersina pestis 48h


title: H202 1 hrs WT - mAdbID:43653

description: mAdb experiment ID: 43653

source_name: Untreated WT


title: NO 1 hrs KO - mAdbID:43649

description: mAdb experiment ID: 43649

source_name: Untreated KO

source_name: NO 1 hrs KO


title: slide72 (low PMT)

description: Yersina pestis 48h


title: slide68

description: Yersina pestis 48h


title: slide70 (low PMT)

description: Yersina pestis 48h


title: slide69 (low PMT)

description: Yersina pestis 48h


title: slide67 (low PMT)

description: Yersina pestis 48h


title: slide73 (low PMT)

description: Yersina pestis 48h


title: slide73

description: Yersina pestis 48h


title: slide74 (low PMT)

description: Yersina pestis 48h


title: slide71

description: Yersina pestis 48h


title: slide67

description: Yersina pestis 48h


title: slide66 (low PMT)

description: Yersina pestis 48h


title: slide66

description: Yersina pestis 48h


title: slide62 (low PMT)

description: Yersina pestis 48h


title: slide59

description: Yersina pestis 48h


title: slide69

description: Yersina pestis 48h


title: slide64 (low PMT)

description: Yersina pestis 48h


title: slide64

description: Yersina pestis 48h


title: slide68 (low PMT)

description: Yersina pestis 48h


title: slide71 (low PMT)

description: Yersina pestis 48h


title: slide63 (low PMT)

description: Yersina pestis 48h


title: slide59 (low PMT)

description: Yersina pestis 48h


title: Hypoxia 24 hrs WT - mAdbID:43500

description: mAdb experiment ID: 43500

source_name: Hypoxia 24 Hrs WT


title: slide65 (low PMT)

description: Yersina pestis 48h


title: slide63

description: Yersina pestis 48h


title: rep A Pathogen Saprotroph (12384346)

status: Public on Dec 21 2004

city: Raleigh

first: Debbie

middle: Ross

last: Craig

state: NC

address: 840 Main Campus Drive

department: Forestry

institute: North Carolina State University

description: rep A Pathogen Saprotroph (12384346)

organism: Pinus sylvestris

source_name: rep A Saprotroph (Cy5)

source_name: rep A Pathogen (Cy3)


title: slide62

description: Yersina pestis 48h


title: slide58 (low PMT)

description: Yersina pestis 48h


title: slide65

description: Yersina pestis 48h


title: rep A Control Saprotroph (12380189)

description: rep A Control Saprotroph (12380189)

source_name: rep A Control (Cy3)


title: slide58

description: Yersina pestis 48h


title: rep C Mycorrhiza Saprotroph (12380362)

description: rep C Mycorrhiza Saprotroph (12380362)

source_name: rep C Mycorrhiza (Cy5)

source_name: rep C Saprotroph (Cy3)


title: rep A Control Mycorrhiza (12380187)

description: rep A Control Mycorrhiza (12380187)

source_name: rep A Control (Cy5)

source_name: rep A Mycorrhiza (Cy3)


title: rep A Pathogen Mycorrhiza (12384347)

description: rep A Pathogen Mycorrhiza (12384347)

source_name: rep A Mycorrhiza (Cy5)


title: rep A Control Saprotroph (12380361)

description: rep A Control Saprotroph (12380361)

source_name: rep A Saprotroph (Cy3)


title: rep C Pathogen Saprotroph (12379943)

description: rep C Pathogen Saprotroph (12379943)

source_name: rep C Pathogen (Cy5)


title: rep C Control Saprotroph (12380340)

description: rep C Control Saprotroph (12380340)

source_name: rep C Saprotroph (Cy5)

source_name: rep C Control (Cy3)


title: slide60

description: Yersina pestis 48h

source_name: Yersina pestis, cultured

source_name: Yersina pestis, pulmonary


title: rep C Control Saprotroph (12379944)

description: rep C Control Saprotroph (12379944)

source_name: rep C Control (Cy5)


title: rep A Pathogen Mycorrhiza (12380339)

description: rep A Pathogen Mycorrhiza (12380339)

source_name: rep A Pathogen (Cy5)


title: rep A Control Mycorrhiza (12384344)

description: rep A Control Mycorrhiza (12384344)


title: slide60 (low PMT)

description: Yersina pestis 48h


title: rep C Control Mycorrhiza (12383854)

description: rep C Control Mycorrhiza (12383854)

source_name: rep C Mycorrhiza (Cy3)


title: rep B Pathogen Saprotroph (12380052)

description: rep B Pathogen Saprotroph (12380052)

source_name: rep B Pathogen (Cy5)

source_name: rep B Saprotroph (Cy3)


title: rep C Control Mycorrhiza (12380337)

description: rep C Control Mycorrhiza (12380337)


title: rep B Pathogen Saprotroph (12380359)

description: rep B Pathogen Saprotroph (12380359)

source_name: rep B Saprotroph (Cy5)

source_name: rep B Pathogen (Cy3)


title: rep B Control Saprotroph (12384451)

description: rep B Control Saprotroph (12384451)

source_name: rep B Control (Cy5)


title: rep B Pathogen Mycorrhiza (12383915)

description: rep B Pathogen Mycorrhiza (12383915)

source_name: rep B Mycorrhiza (Cy5)


title: rep A Pathogen Control (12384350)

description: rep A Pathogen Control (12384349)

source_name: rep A Control (Cy5)

source_name: rep A Pathogen (Cy3)


title: rep B Control Saprotroph (12383919)

description: rep B Control Saprotroph (12383919)

source_name: rep B Control (Cy3)


title: rep B Control Mycorrhiza (12383852)

description: rep B Control Mycorrhiza (12383852)

source_name: rep B Mycorrhiza (Cy3)


title: rep C Pathogen Mycorrhiza (12383917)

description: rep C Pathogen Mycorrhiza (12383917)

source_name: rep C Pathogen (Cy5)


title: rep B Control Mycorrhiza (12383853)

description: rep B Control Mycorrhiza (12383853)


title: rep C Pathogen Mycorrhiza (12384444)

description: rep C Pathogen Mycorrhiza (12384444)

source_name: rep C Mycorrhiza (Cy5)

source_name: rep C Pathogen (Cy3)


title: rep A Mycorrhiza Saprotroph (12380186)

description: rep A Mycorrhiza Saprotroph (12380186)

source_name: rep A Mycorrhiza (Cy5)

source_name: rep A Saprotroph (Cy3)


title: rep C Pathogen Saprotroph (12379941)

description: rep C Pathogen Saprotroph (12379941)

source_name: rep C Saprotroph (Cy5)


title: rep A Pathogen Control (12384349)

description: rep A Pathogen Control (12384349)

source_name: rep A Pathogen (Cy5)

source_name: rep A Control (Cy3)


title: rep A Mycorrhiza Saprotroph (12380188)

description: rep A Mycorrhiza Saprotroph (12380188)

source_name: rep A Saprotroph (Cy5)

source_name: rep A Mycorrhiza (Cy3)


title: rep A Pathogen Saprotroph (12380185)

description: rep A Pathogen Saprotroph (12380185)


title: rep C Pathogen Control (12379942)

description: rep C Pathogen Control (12379942)

source_name: rep C Control (Cy5)


title: rep B Mycorrhiza Saprotroph (12383916)

description: rep B Mycorrhiza Saprotroph (12383916)

source_name: rep B Saprotroph (Cy5)


title: rep B Mycorrhiza Saprotroph (12384450)

description: rep B Mycorrhiza Saprotroph (12384450)

source_name: rep B Mycorrhiza (Cy5)

source_name: rep B Saprotroph (Cy3)


title: rep B Pathogen Mycorrhiza (12380051)

description: rep B Pathogen Mycorrhiza (12380051)

source_name: rep B Pathogen (Cy5)


title: rep B Pathogen Control (12383918)

description: rep B Pathogen Control (12383918)

source_name: rep B Control (Cy5)

source_name: rep B Pathogen (Cy3)


title: rep B Pathogen Control (12384449)

description: rep B Pathogen Control (12384449)

source_name: rep B Control (Cy3)


title: rep C Pathogen Control (12380338)

description: rep C Pathogen Control (12380338)

source_name: rep C Pathogen (Cy5)

source_name: rep C Control (Cy3)


title: HU 1 hrs KO - mAdbID:43772

description: mAdb experiment ID: 43772

source_name: Untreated KO

source_name: HU 1 hrs KO


title: rep C Mycorrhiza Saprotroph (12380363)

description: rep C Mycorrhiza Saprotroph (12380363)

source_name: rep C Saprotroph (Cy5)

source_name: rep C Mycorrhiza (Cy3)


title: Embryonic Drosophila cells, Kc167 cells, Lam Ecdysone DamID, array 3428

status: Public on Aug 29 2006

type: genomic

city: Amsterdam

first: Maarten

last: Fornerod

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, (partly) redundant or ambiguous proves, hybridization data of 7,542 probes was used for analyses. Signals were not background-subtracted, normalized between arrays using the ÒvsnÓ procedure of the limma package (Smyth, G.K., Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 1, 2004). Various contrasts of the Lam ecdysone microarray experiment can be extracted using the multifactorial capabilities of the limma package

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lam, grown in the presence of Ecdysone

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco), at 23¡C. Full length Lam was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 1 micromolar Ecdysone for 24h proir to lysis.

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Dam-Lam plus Ecdysone

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, grown in the presence of Ecdysone

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23¡C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000). Cells were grown in the presence of 1 micromolar Ecdysone for 24h proir to lysis.

tag: Dam plus Ecdysone


title: Patient DT Acute RNA_rep1 (DT494 Acute)

status: Public on Aug 23 2006

city: Pittsburgh

first: Mandal.

middle: K.

last: Singh

state: PA

address: 3460 Fifth Ave

department: Transplant

institute: Childrens Hospital of Pittsburgh

description: Bitynylated cRNA is probe is prepared and hybridization is carried out following the Codelink protocols and reagents

hyb_protocol: Standard CodeLink procedures

scan_protocol: Standard CodeLink procedures

data_processing: Normalized intensities analysed by by SAM using two fold cutoff.

label: Biotin

source_name: Patient DT Acute RNA_rep1

label_protocol: The Codelink Reagents for IVT kit is used to label 2 µg of total RNA to produce UTP-biotinylated cRNA targets.

extract_protocol: PBMC total RNA is prepared by RNAeasy protocol. RNA quality checked on bioanalyzer.

tag: PBMC


title: 53_5dPA_MK02X012

status: Public on Aug 11 2006

city: Indianapolis

first: Matthew

last: Grow

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

description: Gene expression data from Hindlimbs at either st53 were amputated unilaterally or bilaterally at the mid-zeugopodia level. Five days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation.  Total RNA was isolated using RNaqueous micro kit (Ambion, inc.).

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.

organism: Xenopus laevis

source_name: amputation blastema-proximal (1mm) tissue from Xenopus laevis hindlimbs

tag: Stage 53 Xenopus leavis hindlimbs, 5 days post-amputation