title: B_melitensis_16M_broth_rep2

description: cDNA levels normalized to gDNA levels


title: F2.D06.v1.12947599

status: Public on May 01 2008

type: RNA

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

description:
Multiple stress for 6 days
Replicates; Biological (2/4) - Technical (2/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

hyb_protocol: Hybridization, blocking and washing was performed following the procedure provided at TIGR, PFGRC; http://pfgrc.jcvi.org/index.php/microarray/protocols.html

scan_protocol: QuantArray (ver. 3.0, Perkin Elmer) was used for 16-bit TIFF image quantification and intial visualization.

data_processing: scal-MAD and ratio-intensity quantile normalization using R (ver. 2.1.1) package (http://www.bioconductor.org) & S-plus ArrayAnalyzer (ver.2.0). Regardless of dyes used in dye-swap cases, signals from reference sample were always denoted as Green during normaliztion. Signals from scratched or bad spots (ie. Intensity - Background <0) were tagged and removed before normalization.

molecule: total RNA

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis H37Rv grown without multiple stress in normal Dubos medium (pH7.0) with glycerol until OD600=0.2.

label_protocol: Labeled cDNA was prepared as follows: 10 μg of total RNA and 2 μg of random oligonucleotide hexamers (Invitrogen, CA) were incubated 15 min at 65 °C, cooled on ice, combined with Stratascript RTase buffer, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.02 mM dUTP, 1.5 nmol aminoallyl-dUTP (Amersham, NJ), and 2 μl Stratascript RTase II (Invitrogen, CA) in a total volume of 30 μl. This mixture was incubated 10 min at room temperature, and 42 °C overnight. Synthesized cDNA was purified by QIAquick PCR purification kit (Qiagen, CA) according to the manufacturer’s recommendation. The aminoallyl-dUTP-conjugated cDNA probes was spin-dried (SpeedVac, Savant), resuspended in 50 mM sodium carbonate buffer (pH 9.3) and cyanine monofunctional dyes (Amersham) for 1 h at room temperature followed by quenching with 4 M hydoxylamine. Cyanine-labeled probes were purified again by QIAquick PCR purification kit (Qiagen).

growth_protocol: Wild-type M. tuberculosis H37RV was grown in the complete normal Dubos medium supplemented with 1.5% glycerol at pH7.0. The cells were incubated in vented cap bottles aerobically at 37C until OD600 reached to 0.2. To synchronize growth before inoculation, cells were diluted in the same medium and grown again until OD600 value of 0.2 before harvest (i.e. seed culture for microarray control sets).

extract_protocol: Cells were harvested and quickly frozen in a dry ice-ethanol both. Total RNA was isolated using glass beads (Bio101, Lysing Matrix B), a TRIzol (InVitrogen) extraction and purified by Rneasy (Qiagen) kit according to the manufacturers' recommendations.

treatment_protocol: Once the seed culture reached the above OD600 (OD600=0.2), part of the cell culture was harvested, and frozen in liquid nitrogen before storing at -80C. The total RNA isolated from each harvest cells served as control in the microarray hybridization.

tag: Reference cells diluted in multiple stress medium at day 0.

source_name: M. tuberculosis H37Rv grown under multiple stress for 6 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

growth_protocol: The seed culture for microarray control sets was collected by centrifugation, and resuspended with 150 mL standard multiple stress medium to recover the original OD600 (OD600=0.2) in a 1 liter glass bottle with a 24/40 standard joint neck. The standard multiple stress medium was prepared by mixing 1X Dubos Broth base and 10% (v/v) albumin supplement at pH5.0, finally comprising 0.75% Dextrose, 0.5% BSA, and 0.85% NaCl in acidic condition. No glycerol was added in the multiple stress medium except 0.02% (v/v) Tween 80. The head air space in each bottle was replaced every other day for 5 minutes with gas mixture (5% O2, 10% CO2 and 85 % N2) passing through a 0.2 um filter attached to a 18-G needle. The bottles were sealed with a rubber septum flip top cap, and molten paraffin wax on the outside of the cap to ensure air-tight. Sealed culture bottles were rolled in a roller incubator at 37C.

treatment_protocol: Cells were harvested after 0, 1, 2, 3, 6, and 12 days incubation under the given multiple stresses. After centrifugation, cells were snap-frozen in liquid nitrogen.

tag: Multiple stressed for 6 days


title: B_melitensis_16M_broth_rep1

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

country: USA

institute: University of Wisconsin - Madison

description: cDNA levels normalized to gDNA levels

hyb_protocol: Cy3-labeled cDNA was mixed with 0.75 g cy5-labeled gDNA, and hybridization buffer (Pronto Plus Kit, Promega) was added to a final volume of 35 l.  The entire sample was loaded onto the printed array and covered with a HybriSlip coverslip (Molecular Probes).  Arrays were placed in specialized hybridization chambers (Telechem Inc., Sunnyvale, CA), and incubated at 42°C overnight.  Slides were washed using the Pronto Plus Hybridization System (Promega) and dried by centrifugation at 1000 rpm for 5 min.

scan_protocol: Slides were scanned using the GenePix4000B scanner (Axon Instruments) with independent excitation of the fluorophores Cy3 and Cy5.  Background intensities for each spot were calculated using GenPixPro 3.0 software (Axon Instruments) via the segmentation method.  The signal intensity for each spot was calculated as the difference between the average signal intensity and the average local background intensity.

data_processing: Data was normalized to gDNA levels by calculating the ratios of cDNA to gDNA for each spot.  Data was then log2 transformed, and the signal ratio for each spot was divided by the mean signal ratio of the entire array to validate comparisons between different arrays.  Data normalization and statistical analysis were performed using TIGR MeV

organism: Brucella melitensis

source_name: Brucella melitensis, log phase, in broth

label_protocol: cDNA was synthesized from 7 ug of total RNA in the presence of CyDye-3-dCTP (Amersham Biosciences).  The labeled cDNA was purified using the ChipShot cDNA System (Promega).  For each sample, RNA was extracted from two independently grown cultures and cDNA was generated three times for each RNA sample.

growth_protocol: TSB

extract_protocol: Bacteria were grown in TSB until mid/late-log phase.  Before RNA isolation, phenol-ethanol (1:19) was added, cells were pelleted by centrifugation and stored at -80°C.  Total RNA was extracted from cell pellets using the MasterPure RNA Purification Kit (Epicentre), and DNA was removed using TURBO DNA-free (Ambion).

tag: Brucella melitensis, strain 16M, log phase growth in broth


title: Lateral root, 12 hours after salt treatment

city: Hachioji

first: Yuichi

last: Tada

state: Tokyo

address: 1404-1 Katakura

country: Japan

institute: Tokyo University of Technology

description: Lateral root from Bruguiera gymnorhiza treated with 500 mM NaCl for hours.

hyb_protocol: Following fragmentation, 12 microg of cRNA were hybridized to the CustomArray 12K (CombiMatrix Corporation, WA, USA). The microarray contained 11,997 oligoprobes (35-40 mers oligonuleotide)  from B. gymnorhiza.

scan_protocol: GeneChips were scanned using the ScanArray 4000XL (Perkin Elmer, MA, USA)

data_processing: Spot signal intensities were qualified with MicroArray Imager software (CombiMatrix, WA, USA) and analyzed using ArrayAssist software (STRATAGENE, CA, USA). Local background substitution, Lowess normalization and pair wise t-test were applied to identify differentially expressed genes.

organism: Bruguiera gymnorhiza

source_name: Lateral root from Bruguiera gymnorhiza under salt stress

label_protocol: aRNA was labelled with Cy5 using the Kreatech ULS labelling system (Kreatech Biotechnology, Amsterdam, Netherlands).

extract_protocol:
Plants were pulled from pots, the roots were washed briefly in water, wiped with paper, separated from the rest of the plant.
RNA extraction was parformed as previously described (Miyama and Hanagata 2007). Total RNA was then cleaned up using an RNeasy Plant RNA purification Kit (QIAGEN, Tokyo, Japan). aRNA was amplified from 1 µg of total RNA using Ambion MessageAmpII kit (Ambion, TX, USA)

tag: Lateral root

tag: Age

value: 4 months

tag: Period of salt treatment

value: 12 hours

tag: NaCl concentration applied


title: F1.D12.v1.12946944

description:
Multiple stress for 12 days
Replicates; Biological (1/2) - Technical (1/7), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 12 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 12 days


title: Lateral root, 12 hours after salt treatment b


title: F1.D06.v1.12958475

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (8/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F2.D06.v1.12947597

description:
Multiple stress for 6 days
Replicates; Biological (2/4) - Technical (1/4), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D06.v1.12958470

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (6/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D06.v1.12958467

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (3/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 6 hours after salt treatment a

hyb_protocol: Following fragmentation, 12 microg of cRNA were hybridized to the CustomArray 12K (CombiMatrix Corporation, WA, USA). The microarray contained 11,997 oligoprobes (35–40 mers oligonuleotide)  from B. gymnorhiza.

value: 6 hours


title: F1.D06.v1.12958469

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (5/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D06.v1.12958468

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (4/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D06.v1.12958474

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (7/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 1 hour after salt treatment c

value: 1 hour c

value: 500　mM


title: lateral root, 0 hour after salt treatment c

value: 0 hour


title: F1.D06.v1.12948084

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (1/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F1.D06.v1.12958455

description:
Multiple stress for 6 days
Replicates; Biological (1/4) - Technical (2/8), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: F4.D03.v1.12959290

description:
Multiple stress for 3 days
Replicates; Biological (2/5) - Technical (2/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).

source_name: M. tuberculosis H37Rv grown under multiple stress for 3 days in Dubos medium (pH5.0) without glycerol starting from OD600=0.2.

tag: Multiple stressed for 3 days


title: F2.D03.v1.12947606

description:
Multiple stress for 3 days
Replicates; Biological (1/5) - Technical (2/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 3 hours after salt treatment

value: 3 hours


title: F2.D03.v1.12947614

description:
Multiple stress for 3 days
Replicates; Biological (1/5) - Technical (3/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 1 hour after salt treatment

value: 1 hour


title: Lateral root, 3 hours after salt treatment a


title: F4.D03.v1.12959288

description:
Multiple stress for 3 days
Replicates; Biological (2/5) - Technical (1/2), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: Lateral root, 6 hours after salt treatment b


title: Lateral root, 1 hour after salt treatment b


title: lateral root, 0 hour after salt treatment b

tag: (lateral root, main root, leaf)

value: 0 hour b


title: F2.D03.v1.12947604

description:
Multiple stress for 3 days
Replicates; Biological (1/5) - Technical (1/3), Grown in rolling bottle, Replacing head space every other day with gas mixture (O2:CO2:N2 = 5:10:85).


title: H2-2003-2179 D18-2-2

status: Public on Apr 30 2008

city: Castanet-Tolosan Cedex

first: Agnes

last: Bonnet

address: Chemin de Borde-Rouge  BP 52627

country: France

institute: INRA

description: granulosa RNA

data_processing: VALUE: LOG10(QIM_CONST) and mean normalization

organism: Sus scrofa

source_name: 3 mm

tag: MF

tag: SF MF LF animals

value: MF 6

tag: annotation SF/MF/LF

value: MF

tag: annotation animal

tag: annotation animal SF MF LF

value: 6 MF


title: H2-2003-2180 D20-2-1

description: granulosa RNA

source_name: 2 mm

tag: SF

value: SF 6

value: SF

value: 6 SF


title: H2-2003-2178 D17-2-2

description: granulosa RNA

source_name: 1  to  2 mm


title: H2-2003-2180 D20-2-2

description: granulosa RNA


title: H2-2003-2179 D18-2-1

description: granulosa RNA


title: H2-2003-2170 D12-2-2

description: granulosa RNA

source_name: Ovaire 17 : 07/04/2003,96h after Régumate treatment; 10 follicules; diameter 5 to 6.5 mm (quality of smear 1)

tag: LF

value: LF 17

value: LF

value: 17 LF


title: H2-2003-2166 D11-2-2

description: granulosa RNA

source_name: Ovaire 14 : 10/02/2000,96h after Régumate treatment; 5 follicules; diameter 5 to 6.5 mm (quality of smear 1)

value: LF 14

value: 14 LF


title: H2-2003-2178 D17-2-1

description: granulosa RNA


title: H2-2003-2170 D12-2-1

description: granulosa RNA


title: H2-2003-2172 D13-2-2

description: granulosa RNA


title: H2-2003-2166 D11-2-1

description: granulosa RNA


title: H2-2003-1980 D08-2-2

description: granulosa RNA

source_name: > 5 mm

value: LF 8

value: 8 LF


title: H2-2003-2163 D09-2-2

description: granulosa RNA

source_name: Ovaires 12 : 10/09/99,24h after Régumate treatment; 8 follicules; diameter 3 to 3.5 mm (quality of smear 1)

value: MF 12

value: 12 MF


title: H2-2003-2172 D13-2-1

description: granulosa RNA


title: H2-2003-2163 D09-2-1

description: granulosa RNA


title: H2-2003-1973 D03-2-2

description: granulosa RNA

value: SF 7

value: 7 SF


title: H2-2003-1976 D05-2-2

description: granulosa RNA

source_name: 3  to  4 mm

value: MF 7

value: 7 MF


title: H2-2003-1979 D07-2-1

description: granulosa RNA


title: H2-2003-1979 D07-2-2

description: granulosa RNA


title: H1-2003-2172 D06-1-1

description: granulosa RNA


title: H2-2003-1973 D03-2-1

description: granulosa RNA


title: H2-2003-1980 D08-2-1

description: granulosa RNA


title: H1-2003-2170 D05-1-2

description: granulosa RNA


title: H2-2003-1976_2 D06-2-1

description: granulosa RNA

value: MF


title: H1-2003-2172 D06-1-2

description: granulosa RNA


title: H1-2003-2163 D02-1-1

description: granulosa RNA


title: H1-2003-1974 D12-1-2

description:
desc
granulosa RNA

source_name: 3 to 4 mm


title: H1-2003-1980 D15-1-1

description: granulosa RNA


title: H1-2003-2170 D05-1-1

description: granulosa RNA


title: H1-2003-1980 D15-1-2

description: granulosa RNA


title: H2-2003-1976_2 D06-2-2

description: granulosa RNA


title: H1-2003-2165 D03-01-1

description: granulosa RNA

source_name: Ovaire 9D : 09/07/99,24h after Régumate treatment; 24 follicules; diameter 2 mm (follicules de quality of smear 1, 1+)

value: SF 9

value: 9 SF


title: H1-2003-2165 D03-1-2

description: granulosa RNA

value: SF


title: H1-2003-1971 D10-1-1

description: granulosa RNA


title: H1-2003-1971 D10-1-2

description:
RNA granulosa
granulosa RNA


title: AB_Ho2003-1 dev1-1-2

type: other

description: T7 oligo

data_processing: without

molecule: other

source_name: T7 primer

tag: T7 primer


title: AB_Ho2003_2 dev20-1-2

description: T7 oligo


title: H1-2003-1979 D14-1-2

description: granulosa RNA


title: Lateral root, 0 hour after salt treatment

value: 4 months

value: 0 hour

value: 500　mM


title: H1-2003-2163 D02-1-2

description: granulosa RNA


title: H1-2003-2166 D04-1-2

description: granulosa RNA

value: LF 14

value: LF


title: AB_Ho2003-1dev1-1-1

description: T7 oligo


title: H2-2003-1976 D05-2-1

description: granulosa RNA


title: H1-2003-1979 D14-1-1

description: granulosa RNA

value: LF 8


title: AB_Ho2003_2 dev20-1-1

description: T7 oligo


title: H1-2003-1976 D13-1-1

description: granulosa RNA


title: H1-2003-2166 D04-1-1

description: granulosa RNA

value: 14 LF


title: sample 44a _ SNP _ CALL-preB without t(9;22)

status: Public on Apr 25 2008

type: genomic

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description:
NK_ALL_1875_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were analyzed using R software [www.r-project.org] with BioConductor package [www.bioconductor.org]

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: White blood human cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: Leukemia samples

tag: Bone Marrow sample


title: sample 46a _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1896_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 54a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1925_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 46b _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1896_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 51b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1911_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 55a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1926_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 39a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1844_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 67a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1965_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 51a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1911_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 34a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1831_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 44b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1875_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 61a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1945_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 32a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1829_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 68b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1978_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 29b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1816_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 43a _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_2012_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 54b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1925_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 29a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1816_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 33a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1828_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 35a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1833_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 40a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1850_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 16b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1782_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 28a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_2013_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 23b _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1794_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 23b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1802_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 23a _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1794_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 62a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1946_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 17a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1781_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 23a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1802_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 21a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_2014_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 16a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1782_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 17c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1781_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 28b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_2013_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 13a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1765_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 9b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1746_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 43b _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_2012_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 21b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_2014_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 68a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1978_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 61b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1945_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 55b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1926_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 30a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1244_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 10a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1755_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 27a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1092_Hind
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 27b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1092_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 73 _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_2011_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 67b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1965_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 54d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1925_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 62b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1946_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 30b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1244_REM_Hind
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 54c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1925_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 46c _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1896_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 46d _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1896_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 44c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1875_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 34b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1831_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 40b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1850_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 51c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1911_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 51d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1911_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 29d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1816_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 32b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1829_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 35b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1833_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 44d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1875_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 33b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1828_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 17d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1781_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 23c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1802_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 13b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1765_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 23d _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1794_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 10b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1755_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: Treated MCF-7 - repeat 1 - mAdbID:87255

status: Public on Apr 15 2008

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description: mAdb experiment ID: 87255

hyb_protocol: Sample Hybridization Protocol Other: The arrays were prehybridized with buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 1 h. Slides were washed in deionized water followed by 2-propanol. Cy5- and Cy3-labeled cDNA samples were mixed with 1 µl of COT1-DNA (10 µg/µl; Invitrogen, Carlsbad, CA), polyadenylate (8–10 µg/µl; Amersham Pharmacia Biotech, Piscataway, NJ), and yeast tRNA (4 µg/µl; Ambion, Austin, TX) for hybridization. The mixed samples were denatured and after the addition of 20 µl of 2x hybridization buffer (50% formamide, 10x SSC, 0.2% SDS) the entire sample was loaded onto the slides for overnight hybridization at 42°C. After hybridization, the hybridized slides were then washed in 2x SSC, 0.1%, 1x SSC, 0.1% SDS, and 0.2x SSC, for 4 min each, followed by a 1-min wash in 0.05x SSC. Slides were then placed in 2-propanol followed by spin drying.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [65293] PMTVolts: 610;; 620 ScanPower: 100;; 100 LaserPower: 1.9;; 1.74 Temperature: 34.67

data_processing:
Data Processing Protocol
Calculation Method: Preliminary filtering of raw data was performed using mAdb tools with the following setting: All flagged spots were treated as missing values and the data was subjected to spot quality filter with signal to background ratios >2, a minimum background corrected signal of 250 counts, and 60% of pixels in the spots with an intensity greater than a SD plus background. Further data analysis was carried out using R software package (R Development Core Team, 2005) ( http://www.R-project.org. ) and custom written scripts. Genes with missing values in greater than 70% of arrays were removed from the analysis and the rest of the missing values were imputed using K-means nearest neighbor method. Lowess normalization (Yang, Y.H. et al., Nucleic Acids Res., 2002) was performed on log2 transformed data. The normalized signal intensity was divided by the control channel intensity and the resulting log ratios from duplicate hybridizations were averaged. After the above processing, 6227 probes remained for further analysis. To show replicate sample similarity, and cell grouping based on gene expression patterns, hierarchical clustering was performed using average linkage and Pearson correlation metric.

source_name: Universal Human Reference RNA

label_protocol:
Cy5 Sample Labeling Protocol
Other: Three µg of universal reference RNA were labeledand Cy5 by using Stratagene Fairplay-3 microarray labeling kit (Cedar Creek TX).

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: Other

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

molecule: polyA RNA

source_name: Treated MCF-7

label_protocol:
Cy3 Sample Labeling Protocol
Other: Three µg of cell line polysome RNA were labeled with Cy3 by using Stratagene Fairplay-3 microarray labeling kit (Cedar Creek TX).

extract_protocol:
Polysomal Extraction Protocol
Other: Polysomes were isolated using sucrose-gradient fractionation basically as described by Galban et al. Cells were grown to 80% confluence in 150-mm2 tissue culture dishes and incubated in 100 µg of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [10 mmol/L Tris-HCl (pH 8), 140 mmol/L NaCl, 1.5 mmol/L MgCl2, 0.5% NP40, 10 mmol/L DTT, 100 µg/mL cycloheximide, 500 µg/mL heparin, 1 mmol/L phenylmethanesulfonyl fluoride, and 500 units/mL RNasin (Promega, Madison, WI)]. After 10 minutes on ice, lysates were centrifuged (10,000 x g for 10 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 x g for 3 hours at 4°C and 1-mL fractions collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIZOL and used for Northern analysis, or fractions 5 to 11 (corresponding to polysome-bound RNA) were pooled.

treatment_protocol:
Treatment type: stress
Stress: radiation
Treatment dose: 2 Gy
Treatment time: 6 hours
In-vivo treatment: Cells were irradiated using a Pantak (Solon, OH) X-ray source at a dose rate of 1.55 Gy/minute.

tag: Tissue

value: breast

tag: Cell line

tag: Cell type

value: Adenocarcinoma- mammary gland; breast

tag: Disease state

value: Breast cancer


title: sample 30c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1244_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: Untreated MCF-7 - repeat 1 - mAdbID:87252

description: mAdb experiment ID: 87252

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 610;; 510 ScanPower: 100;; 100 LaserPower: 3.9;; 3.29 Temperature: 29.87

source_name: Untreated MCF-7


title: Treated Hop62 - repeat 2 - mAdbID:86926

description: mAdb experiment ID: 86926

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [65293] PMTVolts: 565;; 635 ScanPower: 100;; 100 LaserPower: 1.86;; 1.76 Temperature: 33.51

source_name: Treated Hop62

value: lung

value: Adenocarcinoma-ud; Non-Small Cell Lung

value: Non-Small Cell Lung cancer


title: Untreated MCF-7 - repeat 2 - mAdbID:87253

description: mAdb experiment ID: 87253

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 605;; 510 ScanPower: 100;; 100 LaserPower: 3.91;; 3.29 Temperature: 28.92


title: sample 16d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1782_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 16c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1782_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: Treated MCF-7 - repeat 2 - mAdbID:87256

description: mAdb experiment ID: 87256

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [65293] PMTVolts: 615;; 620 ScanPower: 100;; 100 LaserPower: 1.87;; 1.76 Temperature: 33.76


title: sample 9a _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1746_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: Untreated Hop62 - repeat 1 - mAdbID:86922

description: mAdb experiment ID: 86922

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 550;; 500 ScanPower: 100;; 100 LaserPower: 3.92;; 3.31 Temperature: 30.05

source_name: Untreated Hop62


title: sample 27d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1092_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: Untreated Hop62 - repeat 2 - mAdbID:86923

description: mAdb experiment ID: 86923

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 530;; 500 ScanPower: 100;; 100 LaserPower: 3.99;; 3.26 Temperature: 28.55


title: sample 30d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1244_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: sample 27c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1092_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: sample 23d _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1802_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: Untreated A549 - repeat 1 - mAdbID:86916

description: mAdb experiment ID: 86916

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 545;; 500 ScanPower: 100;; 100 LaserPower: 3.86;; 3.31 Temperature: 28.13

source_name: Untreated A549

value: Adenocarcinoma-p/md;Non-Small Cell Lung


title: Treated Hop62 - repeat 1 - mAdbID:86925

description: mAdb experiment ID: 86925

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [65293] PMTVolts: 565;; 630 ScanPower: 100;; 100 LaserPower: 1.92;; 1.75 Temperature: 34.83


title: Treated A549 - repeat 2 - mAdbID:86920

description: mAdb experiment ID: 86920

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 545;; 500 ScanPower: 100;; 100 LaserPower: 3.77;; 3.29 Temperature: 29.29

source_name: Treated A549


title: Treated A549 - repeat 1 - mAdbID:86919

description: mAdb experiment ID: 86919

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 565;; 500 ScanPower: 100;; 100 LaserPower: 3.97;; 3.3 Temperature: 28.65


title: Untreated T47D - repeat 1 - mAdbID:83116

description: mAdb experiment ID: 83116

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.74;; 3.3 Temperature: 28.71

source_name: Untreated T47D

value: infiltrating ductal carcinoma


title: Untreated T47D - repeat 2 - mAdbID:83117

description: mAdb experiment ID: 83117

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.56;; 3.3 Temperature: 29.13


title: Treated T47D - repeat 1 - mAdbID:83136

description: mAdb experiment ID: 83136

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.06;; 1.63 Temperature: 33.98

source_name: Treated T47D


title: sample 17b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1781_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: Untreated A549 - repeat 2 - mAdbID:86917

description: mAdb experiment ID: 86917

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [100404] PMTVolts: 550;; 500 ScanPower: 100;; 100 LaserPower: 3.93;; 3.32 Temperature: 28.43


title: Untreated BxPC3 - repeat 1 - mAdbID:83060

description: mAdb experiment ID: 83060

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.63;; 3.3 Temperature: 29.81

source_name: Untreated BxPC3

value: pancreas

value: Adenocarcinoma

value: Pancreatic cancer


title: Treated BJ1 - repeat 2 - mAdbID:80629

description: mAdb experiment ID: 80629

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.14;; 1.61 Temperature: 41.41

source_name: Treated BJ1

value: foreskin

value: Fibroblast


title: Untreated BJ1 - repeat 1 - mAdbID:80626

description: mAdb experiment ID: 80626

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.49;; 3.29 Temperature: 30.78

source_name: Untreated BJ1


title: Untreated BxPC3 - repeat 2 - mAdbID:83061

description: mAdb experiment ID: 83061

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.69;; 3.3 Temperature: 30.11


title: Treated BxPC3 - repeat 2 - mAdbID:83059

description: mAdb experiment ID: 83059

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.15;; 1.57 Temperature: 36.74

source_name: Treated BxPC3


title: sample 23c _ SNP _ CALL-preB without t(9;22) and TEL deleted

description:
NK_ALL_1794_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.


title: sample 39b _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1844_Xba
SNP arrays data from pediatric acute leukemia samples at diagnosis


title: Treated BxPC3 - repeat 1 - mAdbID:83062

description: mAdb experiment ID: 83062

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.12;; 1.58 Temperature: 35.59


title: Treated MRC5 - repeat 1 - mAdbID:80013

description: mAdb experiment ID: 80013

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.99;; 1.68 Temperature: 35.99

source_name: Treated MRC5


title: Untreated BJ1 - repeat 2 - mAdbID:80627

description: mAdb experiment ID: 80627

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.6;; 3.3 Temperature: 31.27


title: Treated T47D - repeat 2 - mAdbID:83114

description: mAdb experiment ID: 83114

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.12;; 1.62 Temperature: 35.17


title: sample 29c _ SNP _ CALL-preB without t(9;22)

description:
NK_ALL_1816_REM_Xba
SNP arrays data from pediatric acute leukemia samples at remission


title: Treated MRC9 - repeat 2 - mAdbID:80127

description: mAdb experiment ID: 80127

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.08;; 1.63 Temperature: 38.61

source_name: Treated MRC9


title: Treated MRC5 - repeat 2 - mAdbID:80014

description: mAdb experiment ID: 80014

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.06;; 1.65 Temperature: 37.27


title: Untreated MRC5 - repeat 2 - mAdbID:80012

description: mAdb experiment ID: 80012

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.61;; 3.3 Temperature: 31.27

source_name: Untreated MRC5


title: Treated BJ1 - repeat 1 - mAdbID:80628

description: mAdb experiment ID: 80628

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.14;; 1.61 Temperature: 41.21


title: Untreated MRC5 - repeat 1 - mAdbID:80010

description: mAdb experiment ID: 80010

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.66;; 3.28 Temperature: 30.39


title: Untreated MRC9 - repeat 1 - mAdbID:80123

description: mAdb experiment ID: 80123

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.55;; 3.27 Temperature: 32

source_name: Untreated MRC9


title: Treated MEC - repeat 2 - mAdbID:79756

description: mAdb experiment ID: 79756

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.95;; 1.71 Temperature: 35.67

source_name: Universal Human Reference RNA

source_name: Treated MEC

value: MEC

value: Mammary epithelial


title: Untreated MEC - repeat 1 - mAdbID:79751

description: mAdb experiment ID: 79751

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.64;; 3.33 Temperature: 29.93

source_name: Untreated MEC


title: Treated MEC - repeat 1 - mAdbID:79754

description: mAdb experiment ID: 79754

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.91;; 1.74 Temperature: 34.95


title: Treated MRC9 - repeat 1 - mAdbID:80124

description: mAdb experiment ID: 80124

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 2.06;; 1.65 Temperature: 37.45


title: Untreated MEC - repeat 2 - mAdbID:79753

description: mAdb experiment ID: 79753

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.68;; 3.27 Temperature: 30.36


title: Untreated MRC9 - repeat 2 - mAdbID:80126

description: mAdb experiment ID: 80126

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.54;; 3.28 Temperature: 32.16


title: Treated MDA-MB-231 - repeat 2 - mAdbID:77844

description: mAdb experiment ID: 77844

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.8;; 3.31 Temperature: 27

source_name: Treated MDA-MB-231

value: Adenocarcinoma-mammary gland; breast; epithelial


title: Untreated MDA-MB-231 - repeat 1 - mAdbID:77841

description: mAdb experiment ID: 77841

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.77;; 3.31 Temperature: 28.1

source_name: Untreated MDA-MB-231

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: Treated U251 - repeat 2 - mAdbID:77556

description: mAdb experiment ID: 77556

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.9;; 3.29 Temperature: 27.3

source_name: Treated U251

value: brain

value: Glioblastoma,ud; brain/CNS

value: Brain cancer


title: Treated PANC1 - repeat 1 - mAdbID:77291

description: mAdb experiment ID: 77291

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.81;; 1.73 Temperature: 29.31

source_name: Treated PANC1

value: Epithelioid carcinoma


title: Untreated MDA-MB-231 - repeat 2 - mAdbID:77842

description: mAdb experiment ID: 77842

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.73;; 3.29 Temperature: 28.74

value: breast

value: Breast cancer


title: Untreated PANC1 - repeat 2 - mAdbID:77290

description: mAdb experiment ID: 77290

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.88;; 3.3 Temperature: 27.33

source_name: Untreated PANC1


title: Treated PANC1 - repeat 2 - mAdbID:77292

description: mAdb experiment ID: 77292

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.82;; 1.74 Temperature: 29.84


title: Untreated PANC1 - repeat 1 - mAdbID:77289

description: mAdb experiment ID: 77289

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.91;; 3.31 Temperature: 25.93


title: Treated SF295 - repeat 1 - mAdbID:77094

description: mAdb experiment ID: 77094

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.76;; 3.3 Temperature: 26.88

source_name: Treated SF295

value: Glioblastoma, ud; brain/CNS


title: Treated Aspc1 - repeat 2 - mAdbID:77136

description: mAdb experiment ID: 77136

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.82;; 3.31 Temperature: 26.36

source_name: Treated Aspc1

value: Pancreatic carcinoma


title: Treated Aspc1 - repeat 1 - mAdbID:77135

description: mAdb experiment ID: 77135

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.94;; 3.29 Temperature: 24.53

value: pancreas


title: Untreated Aspc1 - repeat 1 - mAdbID:77137

description: mAdb experiment ID: 77137

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.81;; 1.73 Temperature: 29.29

source_name: Untreated Aspc1


title: Untreated SF295 - repeat 2 - mAdbID:77093

description: mAdb experiment ID: 77093

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.81;; 1.74 Temperature: 30.24

source_name: Untreated SF295


title: Untreated U251 - repeat 2 - mAdbID:77393

description: mAdb experiment ID: 77393

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.89;; 3.31 Temperature: 25.81

source_name: Untreated U251


title: Untreated MiaPaCa - repeat 2 - mAdbID:76928

description: mAdb experiment ID: 76928

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.74;; 3.31 Temperature: 27.79

source_name: Untreated MiaPaCa

value: MiaPaCa


title: Treated MiaPaCa - repeat 1 - mAdbID:76925

description: mAdb experiment ID: 76925

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.8;; 1.76 Temperature: 30.24

source_name: Treated MiaPaCa

value: Pancreatic cancer


title: Untreated MiaPaCa - repeat 1 - mAdbID:76924

description: mAdb experiment ID: 76924

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.74;; 3.31 Temperature: 26.85


title: Treated SF295 - repeat 2 - mAdbID:77092

description: mAdb experiment ID: 77092

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.92;; 3.29 Temperature: 25.78


title: Untreated SF539 - repeat 2 - mAdbID:76599

description: mAdb experiment ID: 76599

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.73;; 3.31 Temperature: 28.01

source_name: Untreated SF539

value: Glial cell neoplasm; brain/CNS


title: Untreated Aspc1 - repeat 2 - mAdbID:77138

description: mAdb experiment ID: 77138

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.83;; 1.73 Temperature: 30.42


title: Treated SF126 - repeat 1 - mAdbID:76734

description: mAdb experiment ID: 76734

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.86;; 1.69 Temperature: 33.96

source_name: Treated SF126

value: Glioblastoma; brain/CNS


title: Treated MiaPaCa - repeat 2 - mAdbID:76929

description: mAdb experiment ID: 76929

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.82;; 1.75 Temperature: 31.14

source_name: Universal Human Reference RNA


title: Untreated SF295 - repeat 1 - mAdbID:77091

description: mAdb experiment ID: 77091

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.8;; 1.75 Temperature: 29.75


title: Treated MDA-MB-231 - repeat 1 - mAdbID:77843

description: mAdb experiment ID: 77843

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.76;; 3.31 Temperature: 26.6


title: Treated SF539 - repeat 2 - mAdbID:76600

description: mAdb experiment ID: 76600

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.89;; 1.67 Temperature: 31.3

source_name: Treated SF539


title: Untreated U87 - repeat 2 - mAdbID:71823

description: mAdb experiment ID: 71823

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.77;; 1.74 Temperature: 33.04

source_name: Untreated U87

value: Glioblastoma; astrocytoma; brain/CNS


title: Treated SF539 - repeat 1 - mAdbID:76598

description: mAdb experiment ID: 76598

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.83;; 1.69 Temperature: 29.45


title: DC cholera toxin 24h  1

status: Public on Apr 14 2008

city: Pittsburgh

first: Prabir

last: Ray

state: PA

address: 3459 Fifth Avenue

department: Medicine/Pulmonary

institute: University of Pittsburgh

hyb_protocol: The labeled cRNA was then fragmented at 94 C for 20 min and hybridized to CodeLink UniSet Mouse I Bioarrays (GE Healthcare) for 21 hrs at 37 C.  Each cRNA sample was hybridized to one bioarray.  After hybridization, the bioarrays were washed in 0.75x TNT buffer and stained with Alexa Fluor 647-Streptavidin (Invitrogen, Carlsbad, CA) and then washed again in 1x TNT and 0.05% Tween 20.  The bioarrays were dried in an Eppendorf Centrifuge 5810 R (Westbury, NY)

scan_protocol: The hybridized bioarrays were scanned using the GenePix 4000B Array Scanner (Axon Instruments, Union City, CA) at a 10 um resolution, which resulted in TIFF images for each bioarray.  The TIFF files were then processed as a “batch” using CodeLink Expression Analysis v4.0 software, which performs spot calculations and background subtraction, resulting in “Raw Intensities” for each gene.

data_processing: Spot data was analyzed using CodeLink System Software version 2.3.2 which calculated raw intensities, and also median normalized each array.  The median normalized intensities for each gene were then globally normalized using a geometric method across all arrays by the analysis package ScoreGenes.

organism: Mus musculus

source_name: bone marrow dendritic cells

label_protocol: Total RNA quality was assessed prior to cRNA target preparation and labeling.  The total RNA concentration and purity were determined by using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).  The quality was determined by denaturing gel electrophoresis.  cRNA was synthesized from the total RNA samples by using the CodeLink Expression Assay Reagent Kit (GE Healthcare).  mRNA was first primed with a T7 RNA polymerase promoter 5’ to a d(T)24 sequence, and then first strand cDNA was reverse transcribed at 42 C for 2 hrs.  Next, second strand cDNA was synthesized at 16 C for 2 hrs, followed by cDNA column purification.  The cDNA then served as a template for the in vitro transcription (IVT) of cRNA and labeling with Biotin-11-UTP (PerkinElmer life sciences, Boston, MA), which took place at 37 C for 14 hrs.

growth_protocol: For DC cultures, the femur and tibia of mice were removed and the bone marrow flushed using a 27 gauge needle. The cells were washed and cultured with 10 ng/ml recombinant murine GM-CSF (Peprotech). On the third day, the cells were refed with fresh medium and cytokine. On day 6, the loosely adherent cells were harvested. Prior to harvest, the flask was gently shaken at 7 hertz per second for 5 min on a MicroMix shaker (DPC instruments). The cells were then subjected to purification using magnetically labeled anti-mouse CD11c+ beads (Miltenyi Biotech). The labeled cells were passed through the magnetic column twice and CD11c expression was >98%. The contaminating population of CD3+ and CD19+ was negligible. These cells were considered immature DCs as ascertained by low expression of CD40, CD86, and MHC class II.

extract_protocol: The DCs  were lysed in Trizol Reagent (Invitrogen, Carlsbad, California) for RNA isolationTotal RNA was isolated by the addition of Chloroform (Sigma, St. Louis, MO) following the manufacturer’s recommendations.  The total RNA was then column purified by using the RNeasy Mini Kit from Qiagen (Valencia, CA), following the company’s protocol.  After column purification, any possible DNA contamination was removed by using DNA-free DNase Treatment and Removal Reagents from Ambion (Austin, Texas).  The RNA was then stored at -80 C.

treatment_protocol: The DCs were left with or without CT(1 mg/ml).

tag: STRAIN

value: BALBc/ByJ

tag: AGE

tag: SEX

value: male

tag: Treatment

value: CT

tag: Timepoint


title: Treated U87 - repeat 2 - mAdbID:71821

description: mAdb experiment ID: 71821

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.63;; 3.3 Temperature: 27.27

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: Treated U87

value: brain


title: DC cholera toxin 24h  2


title: DC cholera toxin 24h  3


title: DC con 24h  3

value: control


title: Untreated SF539 - repeat 1 - mAdbID:76597

description: mAdb experiment ID: 76597

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.76;; 3.29 Temperature: 26.45

value: Brain cancer


title: Untreated SF126 - repeat 1 - mAdbID:76733

description: mAdb experiment ID: 76733

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.68;; 3.31 Temperature: 29.17

source_name: Untreated SF126


title: DC con 24h  2


title: Untreated U87 - repeat 1 - mAdbID:71822

description: mAdb experiment ID: 71822

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.78;; 1.74 Temperature: 32.16


title: 13555909 - A_Col_1 vs B_without_phenotype_1

status: Public on Apr 12 2008

city: Evry Cedex

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

description: Identification of potential targets of the non-protein codding RNA npc48.

hyb_protocol: B_without_phenotype_1 Cy5 / A_Col_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 800V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - medium : MS/2 1% SUCROSE temperature : 21°C light : 16h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia) yes - harvest date:01-06-06

tag: Arabidopsis thaliana (columbia)  - harvest date:01-06-06


title: Untreated U251 - repeat 1 - mAdbID:77392

description: mAdb experiment ID: 77392

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.93;; 3.31 Temperature: 25.41

value: Glioblastoma,ud; brain/CNS


title: 13555931 - C_with_phenotype_1 vs A_Col_1

hyb_protocol: A_Col_1 Cy5 / C_with_phenotype_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: DC con 24h  1


title: 13561537 - A_Col_1 vs C_with_phenotype_1

hyb_protocol: C_with_phenotype_1 Cy5 / A_Col_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13555914 - B_without_phenotype_1 vs A_Col_1

hyb_protocol: A_Col_1 Cy5 / B_without_phenotype_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561533 - A_Col_2 vs B_without_phenotype_2

hyb_protocol: B_without_phenotype_2 Cy5 / A_Col_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia) yes - harvest date:01-05-06

tag: Arabidopsis thaliana (columbia)  - harvest date:01-05-06


title: 13555927 - A_Col_2 vs C_with_phenotype_2

hyb_protocol: C_with_phenotype_2 Cy5 / A_Col_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13555934 - B_without_phenotype_2 vs A_Col_2

hyb_protocol: A_Col_2 Cy5 / B_without_phenotype_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3hour-B

status: Public on Apr 03 2008

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description: Herpes simplex virus infected mouse embryo fibroblasts. Wild type (KOS) virus is co-hybridized with vhs null virus (NHB). Each time-point is hybridized in quadruplicate.

hyb_protocol: Each sample pair was suspended in SDS-based hybridization buffer (Genisphere) and Array 50dT blocker (Genisphere). Two hybridizations were carried out   in a sequential manner. The primary hybridization was performed under a supported glass coverslip (Erie Scientific, Portsmouth, NH) at 62ºC for 16-20 hrs. Prior to the secondary hybridization, slides were washed as described in the manufacturer’s protocol. Secondary hybridization was carried out using the 3DNA Array 350 kit (Genisphere) according to the manufacturer’s protocol, washed and t 1 reated with Dyesaver (Genisphere) before scanning.

scan_protocol: Slides were scanned immediately following hybridization on a ScanArray Express HT scanner (PerkinElmer, Waltham, MA). Laser power was kept constant, and photomultiplier tube values were set for optimal intensity with minimal background.

data_processing: Gridding and analysis of images were performed with Scanarray software express v3.0 (PerkinElmer). The resulting median pixel values were imported into Genespring v7.3 software (Agilent), and local background intensities were subtracted from individual spot intensities. To account for dye swap, the ‘signal’ channel and ‘control’ channel measurements were reversed in such samples so that signal derived from Dvhs-infected MEF RNA occupied the ‘signal’ channel and KOS-infected MEF RNA the ‘control’ channel. The mean signal and control intensities of the on-slide duplicate spots were calculated, and the control values were normalized with GeneSpring’s “Normalize to Positive Control Genes” function using 4 SpotReport® Oligo Array Validation System spike-in controls. If the control channel was lower than 10 relative fluorescence units (rfu), then 10 was used instead. Signal-to-normalized controlled ratios were calculated and the cross-chip averages were derived from the antilog of the mean of the natural log ratios across all biologic replicates. Oligonucleotide elements that received a detectable call (intensity >200 rfu or local signal-to-background >2 in at least one channel) by Scanarray software in either the Cy3 or Cy5 in at least 2 of 4 samples of at least 1 time-point were identified, and all others were excluded from the analysis. Genes were not filtered based on significance in order to be able to visualize global trends. Differences in dye incorporation and quantum yield were normalized by  addition of A. thaliana mRNA spikes into the reverse 1 transcription reaction in equal molar amounts along with the experimental mRNA. Data represent two independent biological experiments with dye swaps such that two technical experiments were performed for each independent biological sample.

source_name: vsf- HSV infected 3hour-B

label_protocol: First strand cDNA was generated by random and oligo dT primed reverse transcription (Superscript II, Invitrogen, Carlsbad, CA) utilizing the 3DNA Array 900MPX kit (Genisphere, Hatfield, PA), according to the manufacturer’s protocol. The cDNAs were quantitated via spectrophotometry to confirm recovery. Samples were paired and balanced by mass.

growth_protocol: Viral stocks were grown and titered on Vero cells. Mouse embryo fibroblast (MEF) cultures were generated from 129 Sv/Ev mice at embryonic day 15, and passaged once before being plated for infection. MEFs were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, 0.1 mM sodium pyruvate, 250 U/mL penicillin, 250 μg/mL streptomycin, and 250 ng/mL amphotericin B.

extract_protocol: RNA was purified and DNase-treated with the RNeasy Mini Kit (Qiagen, Valencia, CA). Total RNA quality was determined by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) according to manufacturer’s recommendations.

treatment_protocol: Cultures of 2.5x106 5 MEF cells in 100mm dishes were infected at an MOI of 5 with KOS or Dvhs1 for 30 min followed by removal of inoculum and addition of complete medium.

tag: MEF from 129 Sv/Ev mice at embryonic day 27

tag: vsf-null HSV infected MEF cells

source_name: wt HSV infected 3hour-B

tag: wild type HSV infected MEF cells


title: 6hour-B

source_name: vsf- HSV infected 6hour-B

tag: MEF from 129 Sv/Ev mice at embryonic day 29

source_name: wt HSV infected 6hour-B


title: 6hour-B ds

source_name: vsf- HSV infected 6hour-B dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 30

source_name: wt HSV infected 6hour-B dye-swap


title: 12hour-B

source_name: vsf- HSV infected 12hour-B

tag: MEF from 129 Sv/Ev mice at embryonic day 33

source_name: wt HSV infected 12hour-B


title: 9hour-B

source_name: vsf- HSV infected 9hour-B

tag: MEF from 129 Sv/Ev mice at embryonic day 31

source_name: wt HSV infected 9hour-B


title: 9hour-B ds

source_name: vsf- HSV infected 9hour-B dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 32

source_name: wt HSV infected 9hour-B dye-swap


title: 13555928 - C_with_phenotype_2 vs A_Col_2

hyb_protocol: A_Col_2 Cy5 / C_with_phenotype_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 12hour-B ds

source_name: vsf- HSV infected 12hour-B dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 34

source_name: wt HSV infected 12hour-B dye-swap


title: 3hour-B ds

source_name: vsf- HSV infected 3hour-B dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 28

source_name: wt HSV infected 3hour-B dye-swap


title: 1hour-B

source_name: vsf- HSV infected 1hour-B

tag: MEF from 129 Sv/Ev mice at embryonic day 25

source_name: wt HSV infected 1hour-B


title: 12hour-A ds

source_name: vsf- HSV infected 12hour-A dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 24

source_name: wt HSV infected 12hour-A dye-swap


title: 1hour-B ds

source_name: vsf- HSV infected 1hour-B dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 26

source_name: wt HSV infected 1hour-B dye-swap


title: MDR1_mice_curcumin_rep4

status: Public on Apr 10 2008

city: Palmerston North

first: Katia

last: Nones

address: Private Bag 11-600

country: New Zealand

institute: Crop & Food Research

description: MDR1_mice_curcumin_rep4 (Slide 251269421382 High Scan)

hyb_protocol: Labeled cRNAs were hybridised using an In Situ Hybridization Plus Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s protocols, using 750 ng of experimental and reference cRNA onto 44k mouse oligonucleotide arrays (Agilent Technologies, Santa Clara, CA, USA). After hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with photomultiplier tube (PMT) voltage of 580 V. Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

data_processing:
Microarray data were analysed using the Limma package in Bioconductor. Image analyses of the extracted foreground and background fluorescence intensity measurements were evaluated to select the best background correction for the experiment, but no background correction was necessary due to homogeneous hybridisation. Data were normalised using a local linear regression analysis (LOESS). Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed before normalization. Boxplots, density plots and spatial images of the raw and normalized data were examined in order to check the quality of the microarray data, and that no unusual results for any slide were observed. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.
The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0*05) were considered to be differentially expressed between the groups fed the diets.

source_name: Swiss Mouse fed curcumin (AIN-76A + 0.2% curcumin) diet (Colon Tissue)

label_protocol: cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Reverse transcription used 500 ng of total RNA and oligo-dT primers. cRNA was synthesised and labeled with either cyanine3 (samples) or cyanine5 (reference) dye (Perkin-Elmer/NEN Life Science, Boston, MA, USA) and the dye incorporation evaluated using a Nanodrop ND-1000 spectrophotometer. Samples ranged from 10 to 22 pmol of dye/µg of RNA.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

tag: Strain:Swiss Mouse

tag: Gender

tag: Age

value: 7 weeks

tag: Tissue

value: colon tissue

source_name: MDR1A-/- Mouse fed curcumin (AIN-76A + 0.2% curcumin) diet (Colon Tissue)

tag: Strain:mdr1a-/- mouse


title: 12hour-A

source_name: vsf- HSV infected 12hour-A

tag: MEF from 129 Sv/Ev mice at embryonic day 23

tag: vsf-null HSV infected MEF cells

source_name: wt HSV infected 12hour-A


title: 9hour-A

source_name: vsf- HSV infected 9hour-A

tag: MEF from 129 Sv/Ev mice at embryonic day 21

source_name: wt HSV infected 9hour-A

tag: wild type HSV infected MEF cells


title: MDR1_mice_curcumin_rep1

description: MDR1_mice_curcumin_rep1 (Slide 251269421250 High scan)

tag: Strain:mdr1a-/- mice


title: 6hour-A ds

source_name: vsf- HSV infected 6hour-A dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 20

source_name: wt HSV infected 6hour-A dye-swap


title: Treated U251 - repeat 1 - mAdbID:77540

description: mAdb experiment ID: 77540

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.79;; 3.31 Temperature: 26.48

source_name: Universal Human Reference RNA

tag: Other

source_name: Treated U251

tag: Cell line

tag: Cell type

tag: Disease state


title: MDR1_mice_curcumin_rep3

description: MDR1_mice_curcumin_rep3 (Slide 251269421361 high scan)


title: 3hour-A

source_name: vsf- HSV infected 3hour-A

tag: MEF from 129 Sv/Ev mice at embryonic day 17

source_name: wt HSV infected 3hour-A


title: 3hour-A ds

source_name: vsf- HSV infected 3hour-A dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 18

source_name: wt HSV infected 3hour-A dye-swap


title: 1hour-A ds

source_name: vsf- HSV infected 1hour-A dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 16

source_name: wt HSV infected 1hour-A dye-swap


title: 6hour-A

source_name: vsf- HSV infected 6hour-A

tag: MEF from 129 Sv/Ev mice at embryonic day 19

source_name: wt HSV infected 6hour-A


title: 1hour-A

source_name: vsf- HSV infected 1hour-A

tag: MEF from 129 Sv/Ev mice at embryonic day 15

source_name: wt HSV infected 1hour-A


title: 9hour-A ds

source_name: vsf- HSV infected 9hour-A dye-swap

tag: MEF from 129 Sv/Ev mice at embryonic day 22

source_name: wt HSV infected 9hour-A dye-swap


title: AML3_HELP_Replicate2

status: Public on Apr 01 2008

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

description: All samples for microarray hybridization were processed at the Roche NimbleGen Service Laboratory.

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: scanned using a GenePix 4000B scanner (Axon Instruments) (See Selzer RR, et al. Genes Chromosomes Cancer 44: 305-319.)

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities.  Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data.

label_protocol: Random 9-mers pre-labeled with Cy5

extract_protocol: Representation of the genome generated by digestion with HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: Female

tag: Acute Myeloid Leukemia with t(10;11)(q22;q23)

tag: Undifferentiated AML, CD65 negative

tag: negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD

label_protocol: Random 9-mers pre-labeled with Cy3

extract_protocol: Representation of the genome generated by digestion with MspI and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)


title: AML3_HELP_Replicate1


title: AML2_HELP_Replicate3

tag: Acute Myeloid Leukemia with CD11b Positive, co-expression of CD7; negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD


title: AML2_HELP_Replicate2


title: ALL2_HELP_Replicate1

hyb_protocol: See Roche NimbleGen website  and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

tag: Acute Lymphoblastic Leukemia with t(9;22)(q34;q11.2), add(16)(q21), -20, +mar

tag: Early Pre-B ALL with co-expression of CD33 and CD13

tag: BCR-ABL p190 (e1a2)


title: MPI_Chen_HeLa_Solexa_2007

status: Public on Apr 07 2008

type: MPSS

city: Berlin

first: wei

last: chen

address: Ihestrasse 73

country: Germany

institute: MPI molecular genetics

description: small RNAs

data_processing: output from Bustard application (part of Solexa/Illumina package)

source_name: HeLa cells

extract_protocol: total RNA, ~20-30nt RNAs isolated using Novex 15% TBE-Urea gel (invitrogen)

tag: ATCC-CCL-2 HeLa cell line, not synchronized, 20 deg C


title: AML1_HELP_Replicate3

tag: Male

tag: Acute Myeloid Leukemia with 46,XY, t(5;21;8)(q15;q22;q22)

tag: Undifferentiated AML CD65 negative, CD19 positive, CD11a negative

tag: AML1/ETO positive


title: AML2_HELP_Replicate1


title: AML1_HELP_Replicate2


title: MDR1_mice_curcumin_rep2

description: MDR1_mice_curcumin_rep2 (Plate 251269421254 high scan)

source_name: Swiss Mouse fed curcumin (AIN-76A + 0.2% curcumin) diet (Colon Tissue)

tag: Strain:Swiss Mouse

tag: Gender

tag: Age

tag: Tissue

source_name: MDR1A-/- Mouse fed curcumin (AIN-76A + 0.2% curcumin) diet (Colon Tissue)

tag: Strain:mdr1a-/- mouse


title: AML1_HELP_Replicate1


title: ALL1_HELP_Replicate3

tag: Female

tag: Acute Lymphoblastic Leukemia with t(9;22)(q34;q11)


title: ALL1_HELP_Replicate2


title: AML3_HELP_Replicate3

tag: Acute Myeloid Leukemia with t(10;11)(q22;q23)

tag: Undifferentiated AML, CD65 negative

tag: negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD


title: ALL2_HELP_Replicate2

tag: Acute Lymphoblastic Leukemia with t(9;22)(q34;q11.2), add(16)(q21), -20, +mar

tag: Early Pre-B ALL with co-expression of CD33 and CD13


title: AML2_GE_Replicate1

hyb_protocol: See Roche NimbleGen website for details and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

scan_protocol: See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (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: Raw data (.pair files) from the scanner were processed with Roche NimbleGen's version of the RMA algorithm (without background correction) in NimbleScan 2.3 software.

label_protocol: Random 9mers pre-labeled with Cy3

extract_protocol: Qiagen RNeasy Plus mini

tag: Acute Myeloid Leukemia. CD11b Positive, co-expression of CD7; negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD


title: ALL2_GE_Replicate2

label_protocol: Random 9mers pre-labeled with Cy5

tag: BCR-ABL p190 (e1a2)


title: AML1_GE_Replicate2

tag: Male

tag: Acute Myeloid Leukemia with 46,XY, t(5;21;8)(q15;q22;q22)


title: ALL1_GE_Replicate2


title: ALL1_HELP_Replicate1


title: AML2_GE_Replicate2


title: AML1_GE_Replicate1

tag: Undifferentiated AML CD65 negative, CD19 positive, CD11a negative

tag: AML1/ETO positive


title: AML3_GE_Replicate2


title: AML3_GE_Replicate1


title: ALL2_GE_Replicate1


title: MPI_Chen_domestic_dog_Solexa_2007

description: small RNAs

organism: Canis lupus familiaris

source_name: domestic dog

tag: lymphocytes collected from the blood of a male dog (race "Griechischer Laufhund") by centrifugation


title: Lym647 - mAdbID:22713

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

description: Tumor biopsies from 71 untreated patients with mantle cell lymphoma

hyb_protocol: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual: http://nciarray.nci.nih.gov/reference/nciarrayspacket01-04A.pdf)

scan_protocol: standard

data_processing: Values are log2 of 50th Percentile normalized Mean (CY5 int)-Median(CY5 bkg)/Mean (CY3 int)-Median(CY3 bkg). Axon GenePix Pro program was used for Feature extraction.

source_name: lymph node

label_protocol: standard

extract_protocol: 2 ug poly-A RNA extracted with Invitrogen fast track

tag: Overall survival (years)

source_name: reference

tag: cell lines reference


title: Lym650 - mAdbID:22821


title: Lym653 - mAdbID:22823


title: Lym652 - mAdbID:22824


title: unwounded versus wounded drosophila embryos B

city: Bristol

first: Mark

middle: Owen

last: Winfield

address: Woodland Road

department: Biological Sciences

country: United Kingdom

institute: Bristol University

hyb_protocol: ARRAY PREHYBRIDIZATION WITH MILK Updated 09.29.2003 *In 500mL graduated cylinder, measure the following: 370mL Nano-H2O 125mL 20X SSC 5mL 10% SDS *Weigh out 15grams of powdered non-fat milk and place in beaker (at least 500mL beaker). *Pour prehybridization solution from beaker into slide dish. Cover with plastic wrap and place in 42C water bath. Water level should be the same level as solution in dish…no higher. *Allow solution to heat for about 45 minutes. *Place rack of slides to be prehybridized into preheated solution. Dip up and down a few times to get slides wet. Cover the dish with a metal lid or plastic wrap and let sit (still in the 42C bath) for approximately 1 hour. *Remove slides from prehybridization solution and immediately place in a dish of Nano-H2O. Dip up and down 15-20 times vigorously. *Transfer rack of slides to a dish of 100% Isopropanol. Dip up and down 15-20 times vigorously. *Immediately transfer to centrifuge and spin dry at 500xg for 5 minutes. HYBRIDIZATION AND WASH PROTOCOL Updated 09.10.2003 Array (Slide) Examination *Prescan Array slide with Axon scanner at low resolution. *Prehybridize Arrays in 3% Milk solution for 1 hour. (See MILK PREHYBRIDIZATION PROTOCOL). Sample Preparation *Allow Labeled RNA sample(s) to thaw. *Add 0.6ul 10% SDS (Do not ice after adding SDS). *Heat @ 99.9°C for 2 min. on heatblock. *Centrifuge @ 14,000 RPM for 3 min. *Cool to RT. Hybridization Setup *Place array slide in Hybridization chamber. *Add 10ul 3X SSC to slide (well away from spotted array). *Add probe sample onto array area. (Do NOT touch surface with pipette) *Apply coverslip PROMPTLY over array. (Position carefully and Avoid bubbles) *Seal hybridization chamber. *Incubate @ 63°C ~ 16 hrs. by submerging in water bath immediately. Post-Hybridization Washes Wash 1A (with SDS): 1X SSC/ 0.03% SDS *Remove array slide from Hybridization chamber. *Place slide in Slide rack submerged in wash. (If coverslip begins to come off, allow it to fall free in wash to avoid scratching array) *Soak in solution for 2 min. *Dip slide rack until coverslip(s) falls free. Wash 1B (NO SDS): 1X SSC *Dip slide (rack) 15 times to remove excess SDS. Wash 2: 0.2X SSC *Soak and Shake @ 60RPM protected from light for 20 min. Wash 3: 0.05X SSC *Soak and Shake @ 60RPM protected from light for 10 min. Note: Immediate transfer of slide(s) through wash steps will avoid drying effects. Drying *Centrifuge slide(s) @ 1000RPM for 5 min. COVERSLIP CLEANING Updated 10.14.2003 *The following protocol is for cleaning glass coverslips. *The recipes are for two slide staining dishes with volumes of ~500ml. *Do not use powdered gloves *To avoid dust, keep glass slides covered or submerged at all times *Prepare wash solution: 70g NaOH pellets 420 ml 95% EtOH 280 ml nanopure H20 *Mix solution until NaOH is completely dissolved (add EtOH last). *Rinse two glass staining dishes thoroughly with DI water. Add racks to staining dish and pour wash solution over coverslips. Cover dishes with dish cover or plastic cling wrap. *Shake glass coverslips in wash solution for 2 hours using an orbital shaker (~80 rev/min). *Rinse slides with copious amounts of DI H20 (4 washes/dish) then perform final wash with Nanopure H20. *Immediately spin down racks with slides in table-top centrifuge w/ 96-well plate carriers at 600 rpm for 5 min. *Place racks in 50°C vacuum oven for 2 min. under 20 In. Hg vacuum. *Store in clean, well-labeled boxes to prevent exposure to dust.

scan_protocol: Contact FHCRC microarray facilities for details

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Drosophila melanogaster

source_name: unwounded drosophila embryos

label_protocol: Amino-allyl reverse transcription labeling protocol

extract_protocol: Trizol followed by RNeasy cleanup

tag: unwounded wild-type drosophila embryos

source_name: wounded drosophila embryos

tag: wounded wild-type drosophila embryos


title: unwounded versus wounded drosophila embryos A


title: Lym610 - mAdbID:22478


title: Lym613 - mAdbID:22486


title: Lym608 - mAdbID:22463


title: ALL1_GE_Replicate1

tag: Female

tag: Acute Lymphoblastic Leukemia with t(9;22)(q34;q11)


title: Lym614 - mAdbID:22482


title: Lym625 - mAdbID:22516


title: Lym658 - mAdbID:22840


title: Lym607 - mAdbID:22458


title: unwounded versus wounded drosophila embryos C


title: Lym666 - mAdbID:25516


title: Lym618 - mAdbID:22484


title: Lym655 - mAdbID:22838


title: Lym659 - mAdbID:22843


title: Lym602 - mAdbID:22453


title: Lym604 - mAdbID:22462


title: Lym605 - mAdbID:22461


title: Treated U87 - repeat 1 - mAdbID:71820

description: mAdb experiment ID: 71820

hyb_protocol: Sample Hybridization Protocol Other: The arrays were prehybridized with buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 1 h. Slides were washed in deionized water followed by 2-propanol. Cy5- and Cy3-labeled cDNA samples were mixed with 1 µl of COT1-DNA (10 µg/µl; Invitrogen, Carlsbad, CA), polyadenylate (8–10 µg/µl; Amersham Pharmacia Biotech, Piscataway, NJ), and yeast tRNA (4 µg/µl; Ambion, Austin, TX) for hybridization. The mixed samples were denatured and after the addition of 20 µl of 2x hybridization buffer (50% formamide, 10x SSC, 0.2% SDS) the entire sample was loaded onto the slides for overnight hybridization at 42°C. After hybridization, the hybridized slides were then washed in 2x SSC, 0.1%, 1x SSC, 0.1% SDS, and 0.2x SSC, for 4 min each, followed by a 1-min wash in 0.05x SSC. Slides were then placed in 2-propanol followed by spin drying.

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [100404] ScanPower: 100;; 100 LaserPower: 3.58;; 3.3 Temperature: 26.45

source_name: Universal Human Reference RNA

tag: Other

source_name: Treated U87

tag: Tissue

tag: Cell line

tag: Cell type

tag: Disease state


title: Hemocyte deficient embryos wound vs non-wound

source_name: laser wounded serpent mutant drosophila embryo

tag: laser wounded serpent mutant embryo

source_name: unwounded serpent mutant drosophila embryo

tag: unwounded serpent mutant embryo


title: Hemocyte plus vs Hemocyte minus embryos B

source_name: hemocyte plus drosophila embryos

source_name: hemocyte minus drosophila embryos

tag: unwounded serpent mutant drosophila embryos


title: Lym601 - mAdbID:22459


title: Treated SF126 - repeat 2 - mAdbID:76736

description: mAdb experiment ID: 76736

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000A [65293] ScanPower: 100;; 100 LaserPower: 1.97;; 1.64 Temperature: 35.09

source_name: Treated SF126


title: Lym600 - mAdbID:22460


title: Lym594 - mAdbID:22434


title: Hemocyte plus vs Hemocyte minus embryos A

source_name: unwounded hemocyte minus drosophila embryos

source_name: unwounded hemocyte plus drosophila embryos


title: Lym599 - mAdbID:22443


title: Lym593 - mAdbID:22438


title: Lym592 - mAdbID:22433


title: Lym590 - mAdbID:22391


title: Lym561 - mAdbID:22369


title: Lym562 - mAdbID:22374


title: Lym564 - mAdbID:22368


title: Lym581 - mAdbID:22440


title: Lym587 - mAdbID:22390


title: Lym586 - mAdbID:22383


title: Lym565 - mAdbID:22375


title: Lym558 - mAdbID:22366


title: Lym560 - mAdbID:22367


title: Lym568 - mAdbID:22384