title: M982Catlin-THB_7h_r2

status: Public on Jul 31 2013

type: RNA

city: Marcy l'Etoile

first: Bachra

last: Rokbi

address: 1541 Av M Mérieux

country: France

institute: sanofi pasteur

description:
Analysis used bacteria cultured in different media at different times.
M982 bacteria cultured in THB medium versus Catlin medium during 7h.

hyb_protocol: The Cy3- and Cy5-specific cDNAs were combined and purified using the QIAquick PCR purification kit (QIAGEN) according to the manufacturer specifications. The labeled cDNAs were concentrated using Microcon YM-30 filter units (Millipore) and then vacuum concentrated. The samples were heated to 95°C for 2 min and briefly cooled before addition of 1 volume of Microarray hybridization buffer (Amersham) and 2 volumes of deionized formamide (Sigma Aldrich). The labeled cDNA samples were hybridized to the array at 42°C for 16h.

scan_protocol: Slides were scanned with a GenePix Personal 4100A scanner (Axon Instruments). The signal intensities were measured with the GenePix PRO v6.1 software.

data_processing: Data analysis were carried out with Rosetta Resolver software v4 (Rosetta biosoftware). Data normalization and transformation was performed with the Axon/GenePix error model when loading data into Rosetta Resolver. All experiments were performed in dye swap.

molecule: total RNA

organism: Neisseria meningitidis

source_name: M982 bacteria cultured in Catlin medium during 7h

label_protocol: For each set of conditions, 20 µg of RNA were labeled differentially with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences) in a first-strand Reverse Transcription reaction using Superscript II RNase H RT (Invitrogen).

growth_protocol: Strains MC58 and M982 were grown on BHI (brain-heart infusion [Difco]) agar or GC (gonococcal culture [Difco]) agar supplemented with 1% Vitox (Oxoid), at 37°C with 10% CO2 overnight. Bacteria were harvested, resuspended in D-PBS (Dulbecco’s phosphate-buffered saline [Gibco]) and then used to inoculate 50 ml of liquid growth medium in baffled shake flasks at initial OD600 of 0.25. Bacteria previously grown on plates of BHI agar or GC agar were inoculated, respectively, in THB (Todd Hewitt Broth [Difco]) or in the modified Catlin medium MC.2. Cultures were incubated at 37°C in a shaking incubator for 1h or 7h.

extract_protocol: RNA was isolated using RNAwiz (Ambion) according to the manufacturer specifications with slight modifications.

treatment_protocol: Cultures were harvested by centrifugation for 20 min (3000 g, 4°C), and pellets were stored at -80°C.

tag: strain

tag: serotype

value: B

tag: medium

value: Catlin

tag: time

value: 7 hours

source_name: M982 bacteria cultured in THB medium during 7h

value: THB


title: M982Catlin-THB_7h_r3


title: M982Catlin-THB_7h_r1


title: MC58THB_r1

description:
Analysis used bacteria cultured in different media at different times.
MC58 bacteria cultured in THB medium during 1h versus 7h.

organism: Neisseria meningitidis MC58

value: 1 hour

source_name: MC58 bacteria cultured in THB medium during 7h


title: MC58THB_r2

source_name: MC58 bacteria cultured in THB medium during 1h


title: MC58THB_r3


title: M982THB_r1

description:
Analysis used bacteria cultured in different media at different times.
M982 bacteria cultured in THB medium during 1h versus 7h.


title: M982THB_r3

source_name: M982 bacteria cultured in THB medium during 1h


title: M982THB_r2


title: WT low Pi Cy3 mak-2 low Pi Cy5_3

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

description: dye swap

hyb_protocol: The pre-hybridization, hybridization and the slides washing were performed using Pronto!™ hybridization kit (Corning Life Sciences).

scan_protocol: Scanning of the hybridized slides was performed using a Genepix 4000B scanner (Axon Instruments).

data_processing: Data normalization was performed using regression technique LOWESS resulting in the log2 ratios (M values) and the average log2 intensities (A value) of Cy3 and Cy5 signals for each array.

organism: Neurospora crassa

source_name: WT low Pi

label_protocol: cDNA synthesis and labeling were performed using the ChipShot Indirect Labeling and Clean-Up System (Promega). The Cy3 and Cy5 cyanine dyes (GE Healthcare) were incorporated into the cDNAs by adding Cy3 or Cy5 monofunctional N-hydroxysuccinimide ester dye to the cDNA solution for 1 h at 22 °C. The cDNA was subsequently cleaned with a ChipShot membrane column and dried under vacuum.

growth_protocol: Fries liquid Medium, pH 5.4 at 30 ºC for 5 hours

extract_protocol: Total RNA was extracted from about 100 mg mycelia with the illustra RNAspin mini isolation kit (GE Healthcare), treated with RNAse-free DNAse I (Invitrogen), and purified with the RNAeasy kit (Qiagen).

treatment_protocol: Growth in low Pi or high Pi medium, respectively, 10 μM or 15 mM Pi, final concentration

tag: treatment

value: high Pi

source_name: mak-2 low Pi

value: low Pi

value: delta mak-2 (FGSC #11482)


title: WT low Pi Cy3 mak-2 low Pi Cy5_4

description: dye swap


title: Retina_Si 100_7days_rep2

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: retina, PBS, 7 days

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: We intravitreally injected PBS or nanoparticles (gold and silicate nanoparticles with the diameter of 20 and 100 nm) into the right eyes of 5-week-old male C57BL/6 mice. One week later, the mice were sacrificed and the eyes were enucleated.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.

tag: gender

value: male

tag: tissue

value: retina

tag: developmental stage

value: adult

value: PBS

source_name: retina, Si100, 7 days

value: 100 nM Si

tag: age


title: mak-2 low Pi Cy3 WT low Pi Cy5_2

description: dye swap


title: WT low Pi Cy3 mak-2 low Pi Cy5_1

description: dye swap


title: Retina_Au 20_7days_rep3

source_name: retina, Au20, 7 days

value: 20 nM Au


title: tanmei mutant, non-embryogenic tissues, 10d

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description: non-embryogenic

data_processing: Data analysis was performed using SDS 2.2.1 software (Applied Biosystems). All amplification curves were analysed with a normalized reporter (Rn: the ratio of the fluorescence emission intensity of SYBR Green to the fluorescence signal of the passive reference dye) threshold of 0.3 to obtain the CT (threshold cycle) values. Four replicates of the reference control gene, UBQ, were measured in each PCR run, and their median CT was used for relative expression analyses. The analysis was performed in two ways: (1) to identify differentially expressed TFs that are specific for the different time points in Col-0, and (2) to identify TFs differentially expressed between Col-0 and tan1-2 independent of the time points. The fold change was calculated using (2)–ΔΔCT, where ΔΔCT represents ΔCT reference condition - ΔCT compared condition.

label: SYBR Green

organism: Arabidopsis thaliana

source_name: SE-impaired tanmei (tan1-2) mutant

growth_protocol: Plants were grown in Jiffy-7 peat pots of 42 mm diameter (Jiffy) in a ‘walk-in’ type phytotron, under controlled conditions: 22°C, 16h/8h (light/dark), 100 µE/m2s light intensity.

treatment_protocol: Explants, i.e., immature zygotic embryos (IZEs) at the late cotyledonary stage of development, were excised from siliques 10 - 12 days after pollination. Siliques were surface-sterilized with sodium hypochlorite (20% commercial bleach) and washed thoroughly with sterile water. Then IZEs were isolated and placed on E5 solid medium containing B5 salts and vitamins and supplemented with 5 µM 2,4-D, 20 g l-1 sucrose and 3.5 g l-1 Phytagel (Sigma). At selected time points of the culture (0, 5 and 10 d), explants of Col-0 and tan1-2 were sampled for transcriptome analysis.

tag: tissue/developmental stage

value: the advanced phase of embryogenesis related to somatic embryo formation

value: 10 days


title: WT low Pi Cy3 mak-2 low Pi Cy5_2

description: dye swap


title: Retina_Si 20_7days_rep3

source_name: retina, Si20, 7 days

value: 20 nM Si


title: Retina_Au 100_7days_rep3

source_name: retina, Au100, 7 days

value: 100 nM Au


title: Retina_Si 100_7days_rep3


title: Retina_Si 20_7days_rep2


title: mak-2 low Pi Cy3 WT low Pi Cy5_3

description: dye swap


title: mak-2 low Pi Cy3 WT low Pi Cy5_1

description: dye swap


title: Retina_Au 100_7days_rep2


title: Retina_Si 100_7days_rep1


title: WT high Pi Cy3 WT low Pi Cy5_3

description: dye swap

source_name: WT high Pi


title: Retina_Au 20_7days_rep2


title: WT low Pi Cy3 WT high Pi Cy5_2

description: dye swap


title: WT low Pi Cy3 WT high Pi Cy5_4

description: dye swap


title: WT high Pi Cy3 WT low Pi Cy5_4

description: dye swap


title: Retina_Au 20_7days_rep1


title: Retina_Au 100_7days_rep1


title: tanmei mutant, non-embryogenic tissues, 5d

description: non-embryogenic

value: explant tissue subjected to SE induction

value: 5 days


title: WT low Pi Cy3 WT high Pi Cy5_3

description: dye swap


title: mak-2 low Pi Cy3 WT low Pi Cy5_4

description: dye swap


title: WT high Pi Cy3 WT low Pi Cy5_2

description: dye swap


title: WT low Pi Cy3 WT high Pi Cy5_1

description: dye swap


title: WT high Pi Cy3 WT low Pi Cy5_1

description: dye swap


title: Retina_Si 20_7days_rep1


title: Columbia-0, advanced embryogenic cultures /advanced SE stage

description: highly embryogenic

source_name: Wild-type Col-0 ecotype


title: tanmei mutant, non-embryogenic tissues, 0d

description: non-embryogenic

value: freshly isolated explants competent to undergo embryogenic transition

value: 0 day


title: Columbia-0, early embryogenic cultures /early SE stage

description: highly embryogenic


title: Columbia-0 explants

description: highly embryogenic


title: ppabi1b w/o ABA rep3

city: Setagaya-ku

first: Kenji

last: KOMATSU

state: Tokyo

address: 1-1-1 Sakuragaoka

department: Department of Bioproduction Technology

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression without ABA condition in ppabi1b protonemata

hyb_protocol: Hybridization were performed by Agilent one-color method according to Agilent manufactures’ instruction

scan_protocol: Scanning were performed by Agilent one-color method according to Agilent manufactures’ instruction

data_processing: Spot signal values were calculated by Feature Extraction ver.9.1software supplied by Agilent

organism: Physcomitrium patens

source_name: ppabi1b protonemata, w/o ABA, replicate 3

label_protocol: Labeling were performed by Agilent one-color method according to Agilent manufactures’ instruction

growth_protocol: P. patens subspecies patens (Gransden) was the wildtype strain. Protonemal tissue was grown at 25 ºC under continuous light (50 - 80 µmol photons m-2 s-1) on 0.8% (w/v) agar plates of modified BCDAT medium [1.84 mM KH2PO4 (pH 6.5), 10 mM KNO3, 1 mM MgSO4, 1 mM CaCl2, 45 µM FeSO4, 10 µM H3BO3, 2 µM MnCl2, 0.22 µM CuSO4, 0.23 µM CoCl2, 0.19 µM ZnSO4, 0.1 µM Na2MoO4, 5 mM ammonium tartrate]

extract_protocol: Total RNAs were extracted from ABA-treated or non-treated one-week-old protonemal tissues using RNeasy plant mini Kit (QIAGEN)

treatment_protocol: Wildtype and PpABI1 disruptants one-week-old protonemata were transferred to 1 μM or 10 μM ABA contain BCDAT media. The protonemal tissue were  incubated for 1, 3, 6 and 12 hours at 25 ºC under continuous light.

value: protonemata

tag: genotype


title: wild-type 1hr 10 μM ABA

description: Gene expression after 1 hours in 10uM ABA treated wildtype protonemata

source_name: wildtype protonemata, 1 h 10 μM ABA

value: 10 μM ABA

value: wild type


title: wild-type 3hr 1 μM ABA rep1

description: Gene expression after 3 hours in 1uM ABA treated wildtype protonemata

source_name: wildtype protonemata, 3 h 1 μM ABA, replicate 1

value: 1 μM ABA


title: ppabi1a/b 3hr 10 μM ABA

description: Gene expression after 3 hours in 10uM ABA treated ppabi1a/b protonemata

source_name: ppabi1a/b protonemata,  3 h 10 μM ABA


title: wild-type w/o ABA-2 rep2

description: Gene expression without ABA condition in wildtype protonemata

source_name: wildtype protonemata, w/o ABA, replicate 2


title: ppabi1a/b w/o ABA rep1

description: Gene expression without ABA condition in ppabi1a/b protonemata

source_name: ppabi1a/b protonemata, w/o ABA, replicate 1


title: ppabi1a/b w/o ABA rep3

source_name: ppabi1a/b protonemata, w/o ABA, replicate 3


title: ppabi1a w/o ABA rep3

description: Gene expression without ABA condition in ppabi1a protonemata

source_name: ppabi1a protonemata, w/o ABA, replicate 3


title: wild-type 3hr 10 μM ABA

description: Gene expression after 3 hours in 10uM ABA treated wildtype protonemata

source_name: wildtype protonemata, 3 h 10 μM ABA


title: ppabi1a w/o ABA rep1

source_name: ppabi1a protonemata, w/o ABA, replicate 1


title: ppabi1b w/o ABA rep2

source_name: ppabi1b protonemata, w/o ABA, replicate 2


title: ppabi1a/b 6hr 10 μM ABA

description: Gene expression after 6 hours in 10uM ABA treated ppabi1a/b protonemata

source_name: ppabi1a/b protonemata,  6 h 10 μM ABA


title: ppabi1a/b w/o ABA rep2

source_name: ppabi1a/b protonemata, w/o ABA, replicate 2


title: wild-type 12hr 10 μM ABA

description: Gene expression after 12 hours in 10uM ABA treated wildtype protonemata

source_name: wildtype protonemata, 12 h 10 μM ABA


title: wild-type 3hr 1 μM ABA rep3

source_name: wildtype protonemata, 3 h 1 μM ABA, replicate 3


title: ppabi1a/b 1hr 10 μM ABA

description: Gene expression after 1 hours in 10uM ABA treated ppabi1a/b protonemata

source_name: ppabi1a/b protonemata,  1 h 10 μM ABA


title: ppabi1b w/o ABA rep1

source_name: ppabi1b protonemata, w/o ABA, replicate 1


title: wild-type 6hr 10 μM ABA

description: Gene expression after 6 hours in 10uM ABA treated wildtype protonemata

source_name: wildtype protonemata, 6 h 10 μM ABA


title: Salvia miltiorrhiza, replicates 1 & 2

type: genomic

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

description: This Sample represents 2 biological replicates.

hyb_protocol: The SDA slides were pre-hybridized for 45 min at 42°C in a pre-warmed solution containing 5X standard saline citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 1% bovine serum albumin (BSA) and 25% formamide. The slides were rinsed twice with sterile MilliQ water and immediately dried with an air gun. The biotin-labelled targets (30 ng) were added to 17.5 μL of fresh 2X Hybridization buffer (250 μL of formamide, 250 μL of 10X SSC, 10 μL of 10% SDS), 0.5 µl of 1 mg/ml Human Cot1 DNA (Invitrogen); 0.5 µl of 5 mg/ml PolyA (Sigma-Aldrich) and 0.5 µl of 10 mg/ml salmon sperm DNA (Sigma-Aldrich). The mixture (made up to 35 µl with sterile water) was denatured at 100°C for 2 min and immediately applied onto the array under a 22 × 22-mm lifter slip (Grale Scientific, Victoria, Australia). The slides were then placed in waterproof, humidified hybridization chambers (Corning Incorporated Life Sciences) and incubated overnight in a 42°C water bath. After hybridization, the coverslips were removed and the slides were washed twice in 1 x SSC, 0.1% SDS at 40°C for 8 min, once in 0.1 x SSC, 0.1% SDS at 40°C for 8 min and once in 0.1 x SSC at room temperature for 5 min. Subsequently the slides were transferred to 500 mL of 6X SSPE-T buffer (0.9 M NaCl, 0.06 M NaH2PO4.H2O, 0.006 M EDTA, 0.005% Triton X-100, pH 7.4) without allowing them to dry. The biotinylated DNA targets bound on the array were then labelled with fluorescent FluoroLink™ streptavidin-labelled Cy3 dye (Amersham Pharmacia, UK) using a biotin-streptavidin system. Briefly, 200 μL of a Detection solution (0.5 µL of 0.8 µg/µL streptavidin-labelled Cy3, 0.8 µl of 25 µg/µL BSA, made to 200 µL with 6X SSPE-T) was applied directly onto the array surface and a 25x60-mm lifter slip was placed over it to evenly distribute the solution on the array. The slides were placed in hybridization chambers, wrapped in aluminum foil and incubated at 37 °C for 40 min in the dark. Finally, the slides were washed thrice in 6X SSPE-T for 5 min and rinsed with deionized water before being dried with an air gun. All hybridizations were performed with four technical replicates (subarrays) and two biological replicates, for a total of eight data points per array feature.

scan_protocol: Slides were scanned with a ScanArray Gx (PerkinElmer Life and Analytical Sciences, Downers Grove, IL) microarray scanner in conjunction with the supplied software. The slides were scanned with a resolution of 10 µm at 532 nm (Cy3, green laser) and at 50% photomultiplicator (PMT) gain whilst keeping background noise low. The scanned array was quantified using PerkinElmer ScanArray Express software v 2.0. The program individually quantified the signal intensity at each probe and normalized the data using the adaptive circle and LOWESS functions.

data_processing: Probes which did not hybridize were automatically flagged by the scanning software and labelled as 'bad'. Manual flagging was used to remove spots displaying inconsistent hybridization such as 'donut' spots. 'Good' probes were accepted as having a mean 'signal-to-noise ratio' (SNR) value of greater than 7 in more than half of the technical replications. Data analysis included: Calulation of the mean signal-to-noise ratio for each feature between the four technical replicates. Normalization across the slides using the mean signal-to-noise ratio for all 285 spots in all hybridizations performed. Average of the biological replicates after normalization to produce a single value per feature.

label: Biotin

molecule: genomic DNA

organism: Salvia miltiorrhiza

source_name: Salvia miltiorrhiza leaves

label_protocol: The preparation of targets in all cases involved the double digestion of gDNA with AluI and HaeIII, and purification using the Qiaquick® PCR Purification Kit (Qiagen Inc.). Approximately 150 ng of purified digested DNA was labeled with Biotin-11-dUTP using the Biotin DecaLabelTM DNA Labeling Kit (Fermentas, ON, Canada). The reaction was incubated during 20 h and no further purification was performed.

growth_protocol: Fresh or preserved leaf samples were obtained.

extract_protocol: Total DNA was extracted from leaves using a modification of the standard CTAB procedure.Approximately 0.5 g of leaves was ground with liquid nitrogen to a fine powder. The powder was dissolved in 5 ml of CTAB Buffer (3% CTAB, 100 mM Tris-HCL pH 8.0, 20 mM EDTA pH 8.0, 1.4 M NaCl), 1 ml of 10% PVP and 1.2 ml of 10% CTAB. Subsequently, the mixture was incubated at 60 °C for 1 h and centrifuged at 13,000 rpm for 10 min. The supernatant obtained was further purified with a double chloroform extraction followed by precipitation with 7.5 M ammonium acetate and 100% ethanol. The precipitated DNA was resuspended in sterile water and subsequent cleanup was performed by using the DNeasy® column of the DNeasy® Plant Mini Kit (Qiagen) following the protocol in the user manual.

value: leaves

tag: family

value: Lamiaceae

tag: order

value: Lamiales


title: Salvia sinica, replicates 1 & 2

organism: Salvia sinica

source_name: Salvia sinica leaves


title: ppabi1a/b 12hr 10 μM ABA

description: Gene expression after 12 hours in 10uM ABA treated ppabi1a/b protonemata

source_name: ppabi1a/b protonemata,  12 h 10 μM ABA


title: Salvia lanceolata, replicates 1 & 2

organism: Salvia lanceolata

source_name: Salvia lanceolata leaves


title: Salvia przewalskii, replicates 1 & 2

organism: Salvia przewalskii

source_name: Salvia przewalskii leaves


title: wild-type w/o ABA-2 rep3

source_name: wildtype protonemata, w/o ABA, replicate 3


title: ppabi1a w/o ABA rep2

source_name: ppabi1a protonemata, w/o ABA, replicate 2


title: wild-type w/o ABA-2 rep1

source_name: wildtype protonemata, w/o ABA, replicate 1


title: wild-type w/o ABA rep2

source_name: wildtype protonemata, w/o ABA, replicate 2


title: wild-type 3hr 1 μM ABA rep2

source_name: wildtype protonemata, 3 h 1 μM ABA, replicate 2

value: 1μM ABA


title: wild-type w/o ABA rep1


title: wild-type w/o ABA rep3


title: Salvia mexicana, replicates 1 & 2

organism: Salvia mexicana

source_name: Salvia mexicana leaves


title: Salvia runcinata, replicates 1 & 2

organism: Salvia runcinata

source_name: Salvia runcinata leaves


title: Salvia elegans, replicates 1 & 2

organism: Salvia elegans

source_name: Salvia elegans leaves


title: Salvia lyrata, replicates 1 & 2

organism: Salvia lyrata

source_name: Salvia lyrata leaves


title: Salvia sclarea, replicates 1 & 2

organism: Salvia sclarea

source_name: Salvia sclarea leaves


title: Salvia fruticosa, replicates 1 & 2

organism: Salvia fruticosa

source_name: Salvia fruticosa leaves


title: Salvia officinalis var. purple, replicates 1 & 2

organism: Salvia officinalis

source_name: Salvia officinalis var. purple leaves

tag: variety

value: purple


title: Salvia lavandulifolia, replicates 1 & 2

organism: Salvia officinalis subsp. lavandulifolia

source_name: Salvia lavandulifolia leaves


title: Salvia officinalis var. grey, replicates 1 & 2

source_name: Salvia officinalis var. grey leaves

value: grey


title: Salvia officinalis, replicates 1 & 2

source_name: Salvia officinalis leaves


title: Salvia microphylla, replicates 1 & 2

organism: Salvia microphylla

source_name: Salvia microphylla leaves


title: Oryzias_melastigma_Larvae_7days_High_20_rep1

city: xiamen city

first: geng

last: hong

address: School of Life Sciences, Xiamen University,

department: Biology

country: China

institute: School of life sciences

description: medaka larvae,7days,High_20,replicate 1

hyb_protocol: After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryzias melastigma

source_name: medaka larvae,7days,High_20nM HBCD

label_protocol: Each Slide was hybridized with Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven

growth_protocol: Fish was maintained in the laboratory in aerated 30‰ filtered seawater.Medaka was The brood stock was kept under a 14: 10 h light: dark photo-period and the dissolved oxygen level at 5-7mg/L，temperatures of 28±2℃.

extract_protocol: At the end of the treatment period,30 larvae/sample were pooled, homogenized in RNA iso Plus(Takara Biotechnology Co., Ltd) and stored in -80 until RNA extraction.Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

treatment_protocol: medaka larvae(within 24 hours post-hatch) were exposed to 0(control),0.2nM,2nM and 20nM of HBCD(dimethyl sulfoxide with a final concentration of 1:30000 v/v water )for 7 days.In all experiments,90% of the contaminated water was changed every day for the duration of the expose period.Each HBCD treatment had three replicates with 100 larvae for each Petri dish

value: medaka larvae

value: 7 days


title: Oryzias_melastigma_Larvae_7days_Low_0.2_rep3

description: medaka larvae,7days,Low_0.2,replicate 3

source_name: medaka larvae,7days,Low_0.2nM HBCD


title: Oryzias_melastigma_Larvae_7days_Low_0.2_rep2

description: medaka larvae,7days,Low_0.2,replicate 2


title: Oryzias_melastigma_Larvae_7days_Medium_2_rep1

description: medaka larvae,7days,Medium_2,replicate 1

source_name: medaka larvae,7days,Medium_2nM HBCD


title: Peripheral blood mononuclear cells of 150-Cy3 pre-treatment dasatinib responder patient

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

description:
Raw data file:
251559510047_2007-07-20_562_558_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: 825ng of each Cy3 and Cy5 labeled cRNA was hybridized using Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T2.150Cy3_pre

organism: Homo sapiens

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-3

label_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis protocol: Starting with 200 ng of total RNA, we performed cDNA synthesis and generated fluorescent labeled cRNA targets using Agilent Low RNA Input Fluorescent Linear Amplification Kit and oligo-dT-T7 promoter primer. Each patient sample was separately labeled with Cy3 and Cy5 to perform a dye swap technical replicate.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen), treated with RNase-free DNase I and purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.

tag: dasatinib treatment

value: Pre-treatment

tag: drug response

value: responder

tag: cell type

value: peripheral blood mononuclear cells

value: male

tag: age (yrs) at dasatinib start

tag: treatments prior to dasatinib

value: HU, IFN, araC, ASCT, IM

tag: mutations detected in the bcr/abl kinase domain before dasatinib treatment

value: not detected

tag: ph+ metaphases before dasatinib treatment (%)

tag: additional cytogenetic abnormalities after dasatinib treatment

value: does not apply


title: Peripheral blood mononuclear cells of 234-Cy5 post-treatment dasatinib responder patient

description:
Raw data file:
251559510047_2007-07-20_562_558_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.234Cy5_post

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-5

value: Post-treatment

tag: gender

value: female

value: HU, IFN, araC, IM


title: Oryzias_melastigma_Larvae_7days_Control_0_rep3

description: medaka larvae,7days,Control_0,replicate 3

source_name: medaka larvae,7days,Control_0

tag: tissue


title: Oryzias_melastigma_Larvae_7days_Medium_2_rep3

description: medaka larvae,7days,Medium_2,replicate 3


title: S.cerevisiae genes: rck1 vs. RCK1 over-expressed cells

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

institute: Korea university

description: rck1 vs RCK1 OE

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

organism: Saccharomyces cerevisiae

source_name: rck1 mutant_vector control

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).

growth_protocol: Yeast cell was grown on SD-leu medium. Yeast cell was grown on SD-leu medium. Yeast cell was grown overnight at 30°C. The culture was refreshed to 0.2 O.D and grown at 30°C for 2h 30min. Cell wall stress was applied by addition of zymolyase to a final concentration of 5 unit/ml. Cells were collected at 2 hours of growth.

extract_protocol: Total RNA was isolated using TRIzol reagent (Life Technologies). RNA concentrations were determined by measuring absorbance at 260nm.

treatment_protocol: RCK1 was subcloned into yeast multicopy vector ( pRS425 )

tag: strain

value: rck1 mutant

tag: transformed with

value: empty vector; pRS425

source_name: RCK1 over-expressed strain

value: pRS425-RCK1 (RCK1 over-expression)


title: Oryzias_melastigma_Larvae_7days_Control_0_rep2

description: medaka larvae,7days,Control_0,replicate 2

tag: age


title: ox-clpX LL16 IPTG-

city: Hirakata, Osaka

first: Keiko

last: Imai

address: 2-5-1 shinmachi

institute: Kansai medical university

description: Gene expression data from Synechococcus elongatus PCC 7942. ox-clpx cells collected at hour 16 under LL  without IPTG.

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 to detect each fluorescent spot (30 match+mismatch primers per each gene) and determine the raw signal using Affymetrix default settings. These values were divided by the corresponding signals of the genomic DNA sample (GSM356504). The GCOS values before dividing by the genomic DNA signal are supplied as Sample data tables.

label: biotin

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: ox-clpx cells,  LL 16, without IPTG

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30˚C under the light (40.5 micromol/m^2/sec)

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80˚C until use

tag: treatment

value: untreated

tag: genotype

value: IPTG-inducible clpX overexpressor strain containing a Ptrc::clpX construct with a kanamycin-resistance gene at the neutral site II (NSII)


title: Peripheral blood mononuclear cells of 152-Cy3 pre-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.152Cy3_pre


title: Oryzias_melastigma_Larvae_7days_High_20_rep3

description: medaka larvae,7days,High_20,replicate 3

value: medaka larvae


title: ox-clpX LL20 IPTG+ 4h

description: Gene expression data from Synechococcus elongatus PCC 7942. ox-clpx cells collected at hour 20 under LL  with 100µM IPTG (hour 4 after IPTG-induction).

source_name: ox-clpx cells, LL 20,  with 100µM IPTG (hour 4 after IPTG-induction)

value: IPTG


title: Peripheral blood mononuclear cells of 150-Cy5 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510047_2007-07-20_562_558_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T2.150Cy5_pre

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-5

value: Pre-treatment


title: WT LL20 IPTG+ 4h

description: Gene expression data from Synechococcus elongatus PCC 7942. Synechococcus wild type cells collected at hour 20 under LL  with 100µM IPTG for 4hours (control).

source_name: Synechococcus wild type cells, LL 20,  with 100µM IPTG for 4hours (control)

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: Peripheral blood mononuclear cells of 240-Cy5 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T2.240Cy5_post

value: responder

value: peripheral blood mononuclear cells


title: Oryzias_melastigma_Larvae_7days_Control_0_rep1

description: medaka larvae,7days,Control_0,replicate 1

value: 7 days


title: WT LL16 IPTG-

description: Gene expression data from Synechococcus elongatus PCC 7942. Synechococcus wild type cells collected at hour 16 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture (control).

source_name: Synechococcus wild type cells, LL16, without IPTG  (control)


title: Oryzias_melastigma_Larvae_7days_High_20_rep2

description: medaka larvae,7days,High_20,replicate 2


title: Oryzias_melastigma_Larvae_7days_Low_0.2_rep1

description: medaka larvae,7days,Low_0.2,replicate 1


title: Peripheral blood mononuclear cells of 148-Cy5 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510046_2007-07-20_570_566_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.148Cy5_pre

value: non-responder

value: not detected


title: Peripheral blood mononuclear cells of 195-Cy3 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.195Cy3_post

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-3

value: Post-treatment


title: Peripheral blood mononuclear cells of 240-Cy3 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T2.240Cy3_post

value: male

value: HU, IFN, araC, ASCT, IM


title: Peripheral blood mononuclear cells of 195-Cy5 post-treatment dasatinib responder patient

description:
Raw data file:
251559510046_2007-07-20_570_566_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.195Cy5_post

value: female

value: HU, IFN, araC, IM


title: Peripheral blood mononuclear cells of 221-Cy3 post-treatment dasatinib responder patient

description:
Raw data file:
251559510046_2007-07-20_570_566_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.221Cy3_post

value: HU, IFN, IM


title: Peripheral blood mononuclear cells of 136-Cy5 pre-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.136Cy5_pre

value: does not apply


title: Oryzias_melastigma_Larvae_7days_Medium_2_rep2

description: medaka larvae,7days,Medium_2,replicate 2


title: Peripheral blood mononuclear cells of 148-Cy3 pre-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.148Cy3_pre


title: Peripheral blood mononuclear cells of 221-Cy5 post-treatment dasatinib responder patient

description:
Raw data file:
251559510046_2007-07-20_570_566_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.221Cy5_post


title: Liver Tissue_400mg.kg.day_DIA_rat4

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

institute: Bayer Cropscience

description: Gene expression in liver of control rat treated 7 days with 400 mg/kg/day Diazepam.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µL of 2x GEx Hybridization Buffer HI-RPM was then added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile and 30 seconds with Stabilization and Drying Solution, and then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100% (high) and 10% (low)).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.
Ratio (treated/control) calculations and extraction of differentially expressed genes (probes) were then performed using GeneSpring software version 10.0 (Agilent Technologies). For normalization per array, the 75th percentile of the signal values taken from each microarray was used as the normalizing reference. Per gene normalization was based on calculating fold expression levels relative to the median of the control animals.

organism: Rattus norvegicus

source_name: Liver tissue, 400 mg/kg/day DIA

label_protocol: Labeled cRNA targets were prepared using a Low RNA Input Linear Amplification Kit according to the One-Color Microarray-Based Gene Expression Analysis protocol provided by the manufacturer (Agilent Technologies). The resulting labeled cRNAs were purified using an RNeasy Mini Kit to remove unlabeled products and quantified by absorbance at 260nm. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from liver samples using RNeasy Mini kits (Qiagen, CA) in accordance with the manufacturer's instructions.

treatment_protocol: CAR and PXR inducers were administered to rats at a daily dose for 7 consecutive days. At necropsy, liver were excised from each rat and flash-frozen in liquid nitrogen prior to storing at -80°C until transcriptomic analyses.

value: 8 weeks

value: liver

value: diazepam

tag: dosage

value: 400 mg/kg/day


title: Peripheral blood mononuclear cells of 155-Cy5 pre-treatment adasatinib responder patient

description:
Raw data file:
251559510053_2007-08-07_576_570_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T4.155Cy5_pre

value: Pre-treatment


title: Peripheral blood mononuclear cells of 235-Cy3 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T4.235Cy3_post


title: Peripheral blood mononuclear cells of 136-Cy3 pre-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
R.y.T3.136Cy3_pre

value: responder


title: Peripheral blood mononuclear cells of 155-Cy3 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510053_2007-08-07_576_570_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T4.155Cy3_pre

value: peripheral blood mononuclear cells


title: Peripheral blood mononuclear cells of 131-Cy5 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510052_2007-08-07_650_559_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.131Cy5_pre


title: Peripheral blood mononuclear cells of 235-Cy5 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T4.235Cy5_post


title: Liver Tissue_400mg.kg.day_DIA_rat1


title: Liver Tissue_400mg.kg.day_DIA_rat3


title: Liver Tissue_50mg.kg.day_DES_rat3

description: Gene expression in liver of control rat treated 7 days with 50 mg/kg/day Diethylstilbestrol.

source_name: Liver tissue, 50 mg/kg/day DES

value: diethylstilbestrol

value: 50 mg/kg/day


title: Peripheral blood mononuclear cells of 205-Cy5 post-treatment dasatinib responder patient

description:
Raw data file:
251559510052_2007-08-07_650_559_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.205Cy5_post

value: non-responder

value: not detected


title: Liver Tissue_50mg.kg.day_DES_rat4

value: male


title: Liver Tissue_50mg.kg.day_DES_rat1


title: Peripheral blood mononuclear cells of 131-Cy3 pre-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.131Cy3_pre


title: Peripheral blood mononuclear cells of 205-Cy3 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.205Cy3_post

value: Post-treatment


title: Liver Tissue_125mg.kg.day_PCN_rat4

description: Gene expression in liver of control rat treated 7 days with 125 mg/kg/day Pregnenolone 16α-carbonitrile.

source_name: Liver tissue, 125 mg/kg/day PCN

value: pregnenolone 16α-carbonitrile

value: 125 mg/kg/day


title: Liver Tissue_125mg.kg.day_PCN_rat2


title: Peripheral blood mononuclear cells of 128-Cy5 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510052_2007-08-07_650_559_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.128Cy5_pre

value: HU, IFN, IM


title: Liver Tissue_125mg.kg.day_PCN_rat3


title: Liver Tissue_50mg.kg.day_CLO_rat4

description: Gene expression in liver of control rat treated 7 days with 50 mg/kg/day Clotrimazole.

source_name: Liver tissue, 50 mg/kg/day CLO

value: clotrimazole


title: Liver Tissue_125mg.kg.day_PCN_rat1

value: 8 weeks


title: Liver Tissue_50mg.kg.day_CLO_rat3

value: liver


title: Liver Tissue_50mg.kg.day_CLO_rat2


title: Peripheral blood mononuclear cells of 239-Cy3 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.239Cy3_post

value: not available


title: Peripheral blood mononuclear cells of 128-Cy3 pre-treatment dasatinib responder patient

description:
Raw data file:
251559510052_2007-08-07_650_559_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.128Cy3_pre

value: does not apply


title: Peripheral blood mononuclear cells of 239-Cy5 post-treatment dasatinib responder patient

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.239Cy5_post


title: Liver Tissue_50mg.kg.day_CLO_rat1


title: Rheumatoid arthritis FLS_patient S4_NK: Interleukin-1beta pre-stimulated

city: graz

first: margherita

last: breisach

address: Auenbruggerplatz 5

country: Austria

institute: Medical university of graz

description: Array 3

hyb_protocol: GeneChip HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing: Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Software, v.6.4): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); paired t-test

source_name: fibroblast-like synoviocytes (FLS) from patient S4

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay; Kits : WT cDNA Synthesis and Amplification Kit 30 rxn, (Cat No. 900673); WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Fresh synovial membrane tissue was dissected into 1 mm slices, and with 0.2% collagenase B in DMEM-HG growth medium containing 10% FCS and antibiotics digested. After overnight incubation at 37C, the cell suspension was filtered with a nylon membrane and plated in T75 culture flasks. Cells were cultured in growth medium at 37C in a humidified atmosphere with 5% CO2 for expansion.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) according to manufacturer

treatment_protocol: Immediately after growing pre-stimulation with 10 ng/ml IL-1β for 1 h. Subsequently  RA-FLS were incubated in medium containing 100µM resveratrol.

value: Rheumatoid arthritis (RA) synovial membrane

value: In virto cultured fibroblast-like synoviocytes (FLS)


title: Liver Tissue_0mg.kg.day_ctlPXR_rat2

description: Gene expression in liver of control rat PXR treated 7 days with vehicle.

source_name: Liver tissue, 0 mg/kg/day, control PXR

value: vehicle

value: 0 mg/kg/day


title: Liver Tissue_0mg.kg.day_ctlPXR_rat3


title: Rheumatoid arthritis FLS_patient S2_Interleukin-1beta pre-stimulated and resveratrol treated

description: Array 2

source_name: fibroblast-like synoviocytes (FLS) from patient S2


title: Rheumatoid arthritis FLS_patient S4_Interleukin-1beta pre-stimulated and resveratrol treated

description: Array 4


title: Liver Tissue_225mg.kg.day_PHE_rat4

description: Gene expression in liver of control rat treated 7 days with 225 mg/kg/day Phenytoin.

source_name: Liver tissue, 225 mg/kg/day PHE

value: phenytoin

value: 225 mg/kg/day


title: Liver Tissue_15mg.kg.day_DIC_rat4

description: Gene expression in liver of control rat treated 7 days with 15 mg/kg/day Diclofenac.

source_name: Liver tissue, 15 mg/kg/day DIC

value: diclofenac

value: 15 mg/kg/day


title: Rheumatoid arthritis FLS_patient S2_NK: Interleukin-1beta pre-stimulated

description: Array 1


title: Liver Tissue_15mg.kg.day_DIC_rat5

value: male


title: Liver Tissue_15mg.kg.day_DIC_rat2


title: Liver Tissue_225mg.kg.day_PHE_rat2


title: Rheumatoid arthritis FLS_patient S41_NK: Interleukin-1beta pre-stimulated

description: Array 5

source_name: fibroblast-like synoviocytes (FLS) from patient S41


title: Liver Tissue_0mg.kg.day_ctlPXR_rat4


title: Rheumatoid arthritis FLS_patient S41_Interleukin-1beta pre-stimulated and resveratrol treated

description: Array 6


title: Liver Tissue_100mg.kg.day_DDE_rat4

description: Gene expression in liver of control rat treated 7 days with 100 mg/kg/day 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene.

source_name: Liver tissue, 100 mg/kg/day DDE

value: 100 mg/kg/day


title: Liver Tissue_0mg.kg.day_ctlPXR_rat1


title: Liver Tissue_225mg.kg.day_PHE_rat3


title: MB231RN-LM-miR-18a_CoCl2_1

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

description:
replicate 1
7018861076_G

hyb_protocol: Biotinylated cRNA were hybridized to the Illumina array per manufacturer's instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina Genome Studio software was used for data processing: background subtraction and Quantile normalization

source_name: CoCL2 200uM, 4h

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: cells were maintained in gelatin-coated flasks in DMEM/F12 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS, 30% human foreskin fibroblast conditioned medium, 100 units/ml penicillin, 100 µg/ml streptomycin, 10 mg/ml fungin (InvivoGen, San Diego, CA) and 400 ug/ml G418.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: cells were untreated or treated with CoCL2 (200uM, 4h)

value: breast cancer cell line

tag: cell line

value: MB231RN-LM, derived from MDA-MB-231

tag: genotype/variation

value: transfected with has-miR-18a


title: Liver Tissue_15mg.kg.day_DIC_rat3

value: 8 weeks


title: MB231RN-LM-miR-18a_2

description:
replicate 2
7018861076_F

source_name: untrated


title: MB231RN-LM-miR-18a_CoCl2_2

description:
replicate 2
7018861076_H


title: Liver Tissue_100mg.kg.day_DDE_rat5

value: liver


title: MB231RN-LM-GFP_CoCl2_2

description:
replicate 2
7018861076_D

value: transfected with GFP (control)


title: MB231RN-LM-miR-18a_1

description:
replicate 1
7018861076_E


title: Liver Tissue_100mg.kg.day_DDE_rat3


title: Liver Tissue_225mg.kg.day_PHE_rat1


title: MB231RN-LM-GFP_CoCl2_1

description:
replicate 1
7018861076_C


title: MB231RN-LM-GFP_2

description:
replicate 2
7018861076_B


title: Liver Tissue_100mg.kg.day_DDE_rat1


title: MB231RN-LM-GFP_1

description:
replicate 1
7018861076_A


title: Liver Tissue_75mg.kg.day_PB_rat3

description: Gene expression in liver of control rat treated 7 days with 75 mg/kg/day Phenobarbital.

source_name: Liver tissue, 75 mg/kg/day PB

value: phenobarbital

value: 75 mg/kg/day


title: Liver Tissue_75mg.kg.day_PB_rat5


title: PDK1 replicate 3

city: Singapore

first: Peiyong

last: Guan

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: replicate 3

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Illumina GenomeStudio 2010, quantile normalization

source_name: Human Embryonic Kidney Cells (HEK-TERV)

label_protocol: standard Illumina protocol

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen).

treatment_protocol: HEK-PMN, PDK1, MYC and E545K are stable cell lines we constructed as following: human full length of PDK1, MYC and constitutively mutant PIK3CA-E545K were cloned into retroviral vector pMN-IRES-GFP. The genes are stably ectopic expressed in human embryonic kidney epithelial cells HEK-TERV.

value: HEK-TERV


title: MYC replicate 2

description: replicate 2

value: MYC


title: PDK1 replicate 1

description: replicate 1


title: E545K replicate 2

description: replicate 2


title: MYC replicate 3

description: replicate 3


title: E545K replicate 1

description: replicate 1


title: Liver Tissue_0mg.kg.day_ctlCAR_rat4

description: Gene expression in liver of control rat CAR treated 7 days with vehicle.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.
Ratio (treated/control) calculations and extraction of differentially expressed genes (probes) were then performed using GeneSpring software version 10.0 (Agilent Technologies). For normalization per array, the 75th percentile of the signal values taken from each microarray was used as the normalizing reference. Per gene normalization was based on calculating fold expression levels relative to the median of the control animals.

source_name: Liver tissue, 0 mg/kg/day, control CAR

value: vehicle

value: 0 mg/kg/day


title: PMN replicate 2

description: replicate 2

value: PMN


title: Liver Tissue_0mg.kg.day_ctlCAR_rat3


title: Liver Tissue_75mg.kg.day_PB_rat4


title: Liver Tissue_75mg.kg.day_PB_rat1


title: Liver Tissue_0mg.kg.day_ctlCAR_rat1


title: MM_163: CD138_selected_plasma_cells_presentation

city: London

first: Gareth

last: Morgan

address: 15 Cotswold Road

department: Division of Molecular Pathology

country: United Kingdom

institute: The Institute of Cancer Research

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

hyb_protocol: The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0 following Affymetrix recommended protocol.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G scanner.

data_processing: The data were extracted using Affymetrix miRNA QC tool software using default analysis settings for normalization and summarization methods.

source_name: pre-treatment bone marrow

label_protocol: small RNA was processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in Trizol, RNA was isolated using Trizol and the Invitrogen Micro-to-Midi total RNA purification kit and then enriched with small RNA

value: myeloma cells

tag: extraction

value: Trizol

tag: storage


title: PMN replicate 3

description: replicate 3


title: E545K replicate 3

description: replicate 3


title: MM_162: CD138_selected_plasma_cells_presentation


title: MM_161: CD138_selected_plasma_cells_presentation


title: Liver Tissue_0mg.kg.day_ctlCAR_rat5

value: male


title: MYC replicate 1

description: replicate 1


title: Br-P25-rep4

city: Oldenburg

first: Hans Gerd

last: Nothwang

state: Lower Saxony

address: Carl von Ossietzky Str. 9-11

department: Neurogenetics

institute: University of Oldenburg

hyb_protocol: 825ng of Cy3-labelled and 825ng of Cy5-labelled cRNA were mixed and fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 11 µl 10x Agilent blocking agent. 55 µl GEx hybridization buffer HI-RMP was added to the fragmentation mixture and 100 µl were hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F, 4x44k format) for 17 hours at 65°C (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) followed by 1 min with 37°C prewarmed GE Wash Buffer 2 (Agilent).

scan_protocol: Immediately after the washing steps, the microarrays were scanned with an The Agilent DNA microarray Scanner (48-slide scanning system). The settings were: scan area 61x21.6 mm, Scan resolution 5µm, Dye channel Red & Green, PMT for both channels XDR Hi 100% and XDR Lo 10%.

data_processing: Raw data analysis was performed with Agilent Feature Extraction Software (v8.1) and data normalization and statistics by in-house software packages and algorithms of the Fraunhofer ITWM, Kaiserslautern. This implied a Lowess transformation with smoothing parameter of 0.2 to reduce intensity dependent errors. To identify differentially expressed genes, the non-parametric Fisher-Pitman-Test was used.

source_name: whole brain-tissue-P25-replicate4

label_protocol: The synthesis of the cRNA samples (Cy3 or Cy5) was performed according to the manufacturers protocol with the Agilent Low RNA Input Linear Amplification Kit. 1,000 ng total RNA were used as starting material. The cRNA samples were purified by RNAeasy columns (QIAGEN). The incorporation rate was measured with a Nanodrop ND-1000 UV-Vis Spectrophotometer (specific activity > 9.0 pmol Cy3 or Cy5/µg cRNA).

growth_protocol: rats were deeply anestesized with 7% chloralhydrate (1ml/100g bodyweight), Tissue preparation was carried out in chilled buffer solution (~4 °C) containing (mM): 25 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 1 MgCl2, 2 CaCl2, 260 D-glucose, 2 sodium pyruvate, 3 myo-inositol and 1 kynurenic acid. The solution was gassed 30 min with 95% O2 and 5% CO2 to adjust the pH to 7.4. The brainstem was dissected and coronal slices (300-µm thickness) containing the SOC were cut with a vibratome. The SOC was dissected and collected. Whole brain and SOC tissue was stored in RNAlater (Ambion) at -80°C.

extract_protocol: Total RNA used for hybridization experiments was isolated from one entire brain, or from the SOCs of single animals at P16 and P25; the SOCs from 4 animals were pooled at P0 and from 2 animals at P4. Total RNA extraction from SOC tissue was performed with the RNeasy Lipid Tissue Kit (Qiagen), from the whole brain with the RNeasy Midi Kit (Qiagen), both according to the manufacturers instructions.

value: whole brain


title: PDK1 replicate 2

description: replicate 2


title: Br-P25-rep6

source_name: whole brain-tissue-P25-replicate6


title: Br-P25-rep5

source_name: whole brain-tissue-P25-replicate5


title: Br-P25-rep2

source_name: whole brain-tissue-P25-replicate2


title: Br-P4-rep5

source_name: whole brain-tissue-P4-replicate5


title: PMN replicate 1

description: replicate 1


title: Br-P25-rep3

source_name: whole brain-tissue-P25-replicate3


title: Br-P25-rep1

source_name: whole brain-tissue-P25-replicate1


title: MM_157: CD138_selected_plasma_cells_presentation


title: MM_154: CD138_selected_plasma_cells_presentation


title: MM_159: CD138_selected_plasma_cells_presentation


title: MM_155: CD138_selected_plasma_cells_presentation


title: MM_156: CD138_selected_plasma_cells_presentation


title: MM_158: CD138_selected_plasma_cells_presentation


title: Br-P4-rep3

source_name: whole brain-tissue-P4-replicate3


title: MM_160: CD138_selected_plasma_cells_presentation


title: Br-P4-rep2

source_name: whole brain-tissue-P4-replicate2


title: MM_150: CD138_selected_plasma_cells_presentation


title: MM_153: CD138_selected_plasma_cells_presentation


title: Br-P4-rep6

source_name: whole brain-tissue-P4-replicate6


title: MM_152: CD138_selected_plasma_cells_presentation


title: MM_149: CD138_selected_plasma_cells_presentation


title: MM_146: CD138_selected_plasma_cells_presentation


title: Br-P4-rep4

source_name: whole brain-tissue-P4-replicate4


title: SOC-P25-rep9

description: 2 hybridizations

value: SOC


title: MM_151: CD138_selected_plasma_cells_presentation


title: MM_148: CD138_selected_plasma_cells_presentation


title: MM_145: CD138_selected_plasma_cells_presentation

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, RNA extracted and small RNA enriched using Qiagen AllPrep DNA/RNA mini kit

value: AllPrep

value: RLT


title: MM_147: CD138_selected_plasma_cells_presentation


title: SOC-P25-rep8

description: 3 hybridizations


title: SOC-P25-rep6


title: SOC-P25-rep7

description: 2 hybridizations


title: MM_143: CD138_selected_plasma_cells_presentation


title: SOC-P25-rep3

description: 2 hybridizations


title: Br-P4-rep1

source_name: whole brain-tissue-P4-replicate1


title: SOC-P25-rep4

description: technical dye swap


title: SOC-P25-rep5


title: SOC-P25-rep2

description: 2 hybridizations


title: MM_144: CD138_selected_plasma_cells_presentation


title: MM_141: CD138_selected_plasma_cells_presentation


title: MM_139: CD138_selected_plasma_cells_presentation


title: SOC-P25-rep1


title: MM_140: CD138_selected_plasma_cells_presentation


title: MM_142: CD138_selected_plasma_cells_presentation


title: MM_138: CD138_selected_plasma_cells_presentation


title: SOC-P16-rep9


title: SOC-P16-rep5


title: MM_135: CD138_selected_plasma_cells_presentation


title: MM_137: CD138_selected_plasma_cells_presentation


title: SOC-P16-rep3

description: 2 hybridizations


title: SOC-P16-rep8

description: 2 hybridizations


title: SOC-P16-rep7


title: MM_136: CD138_selected_plasma_cells_presentation


title: SOC-P4-rep5


title: SOC-P16-rep6

description: technical dye swap


title: SOC-P16-rep2


title: MM_133: CD138_selected_plasma_cells_presentation


title: SOC-P16-rep1

description: technical dye swap


title: SOC-P4-rep6

description: 2 hybridizations


title: SOC-P16-rep4


title: MM_132: CD138_selected_plasma_cells_presentation


title: MM_134: CD138_selected_plasma_cells_presentation

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, RNA extracted using Qiagen RNA/DNA kit and small RNA enriched

value: RNA/DNA kit


title: MM_131: CD138_selected_plasma_cells_presentation


title: MM_130: CD138_selected_plasma_cells_presentation


title: MM_128: CD138_selected_plasma_cells_presentation


title: MM_129: CD138_selected_plasma_cells_presentation


title: MM_125: CD138_selected_plasma_cells_presentation


title: MM_127: CD138_selected_plasma_cells_presentation


title: MM_126: CD138_selected_plasma_cells_presentation


title: SOC-P4-rep2


title: SOC-P4-rep4

description: 3 hybridizations


title: SOC-P0-rep5


title: SOC-P4-rep3


title: SOC-P4-rep1

description: 2 hybridizations


title: MM_121: CD138_selected_plasma_cells_presentation


title: SOC-P0-rep6


title: MM_124: CD138_selected_plasma_cells_presentation


title: SOC-P0-rep3


title: MM_123: CD138_selected_plasma_cells_presentation


title: SOC-P0-rep1


title: SOC-P0-rep4


title: Testis, Control, Rep3

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Fundulus heteroclitus

source_name: Testis, Control

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Microarray analysis was performed with four biological replicates (4 control and 4 treatment).  Individuals from the high concentration, 50 ug/L DHT, were used for the microarray analysis.

treatment_protocol: DHT waterborne exposure at 5 and 50 ug/L for 21 days

value: adult

tag: Sex

value: testis


title: Peripheral blood mononuclear cells of 150-Cy5 pre-treatment and 240-Cy3 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):75.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_2.txt

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_150.240_Cy5.txt

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-5

tag: dasatinib treatment

value: pre-treatment

tag: drug response

value: responder

tag: cell type

value: peripheral blood mononuclear cells

value: M

tag: age (yrs) at dasatinib start

tag: treatments prior to dasatinib

value: HU, IFN, araC, ASCT, IM

value: Not detected

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-3

value: post-treatment

tag: mutations detected in the bcr/abl kinase domain after dasatinib treatment

tag: ph+ metaphases after dasatinib treatment (%)

value: Not detected.


title: Testis, Control, Rep4

tag: tissue


title: Peripheral blood mononuclear cells of 152-Cy3 pre-treatment and 234-Cy5 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 30; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013127_2007-07-12_509-524_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_152.234_Cy3.txt

source_name: Total RNA from peripheral blood mononuclear cells of pre-treatment labeled with Cyanine-3

tag: gender

value: F

value: HU, IFN, araC, IM

tag: mutations detected in the bcr/abl kinase domain before dasatinib treatment

tag: ph+ metaphases before dasatinib treatment (%)

source_name: Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-5

tag: additional cytogenetic abnormalities after dasatinib treatment


title: Peripheral blood mononuclear cells of 150-Cy3 pre-treatment and 240-Cy5 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):75.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 25; Treatments prior to dasatinib: HU, IFN, araC, ASCT, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_150.240_Cy3.txt


title: Peripheral blood mononuclear cells of 152-Cy5 pre-treatment and 234-Cy3 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 34; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 30; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013127_2007-07-12_546-541_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_152.234_Cy5.txt


title: SOC-P0-rep2

tag: age


title: Testis, DHT50, Rep4

source_name: Testis, 5α-dihydrotestosterone (DHT)

value: male


title: MM_120: CD138_selected_plasma_cells_presentation

source_name: pre-treatment bone marrow

value: myeloma cells

value: Trizol


title: Peripheral blood mononuclear cells of 136-Cy5 pre-treatment and 221-Cy3 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: 8+.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_2.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_136.221_Cy5.txt

value: HU, IFN, IM


title: Testis, Control, Rep2


title: Peripheral blood mononuclear cells of 136-Cy3 pre-treatment and 221-Cy5 post-treatment dasatinib responder patient

description:
ch1: pre-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 39; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%): 0; Additional cytogenetic abnormalities after dasatinib treatment: 8+.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_R_136.221_Cy3.txt


title: MM_119: CD138_selected_plasma_cells_presentation

value: AllPrep

value: RLT


title: Peripheral blood mononuclear cells of 148-Cy5 pre-treatment and 195-Cy3 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain in before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):90; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_148.195_Cy5.txt

value: non-responder

tag: mutations detected in the bcr/abl kinase domain in before dasatinib treatment


title: MM_118: CD138_selected_plasma_cells_presentation

tag: extraction


title: Peripheral blood mononuclear cells of 155-Cy3 pre-treatment and 235-Cy5 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485012777_2007-08-07_505_495_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_155.235_Cy3.txt

value: pre-treatment


title: Peripheral blood mononuclear cells of 155-Cy5 pre-treatment and 235-Cy3 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 59; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485012777_2007-08-07_505_495_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_155.235_Cy5.txt


title: Testis, DHT50, Rep2

value: adult

value: testis


title: Testis, DHT50, Rep3


title: Peripheral blood mononuclear cells of 131-Cy5 pre-treatment and 205-Cy3 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: F317L; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: F317L; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_4.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_131.205_Cy5.txt

value: peripheral blood mononuclear cells

value: M


title: Testis, Control, Rep1


title: MM_115: CD138_selected_plasma_cells_presentation

tag: storage


title: Peripheral blood mononuclear cells of 148-Cy3 pre-treatment and 195-Cy5 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC; IM; Mutations detected in the BCR/ABL kinase domain in before dasatinib treatment: Not detected; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: F; Age (yrs) at dasatinib start: 63; Treatments prior to dasatinib: HU, IFN, araC, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not detected; Ph+ metaphases after dasatinib treatment (%):90; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013126_2007-07-12_497-513_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_148.195_Cy3.txt

value: Not detected


title: Peripheral blood mononuclear cells of 128-Cy3 pre-treatment and 239-Cy5 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: G250E; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 65; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: Not available; Ph+ metaphases after dasatinib treatment (%):95; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_1.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_128.239_Cy3.txt

value: post-treatment

value: Not available


title: Peripheral blood mononuclear cells of 131-Cy3 pre-treatment and 205-Cy5 post-treatment dasatinib non-responder patient

description:
ch1: pre-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain before dasatinib treatment: F317L; Ph+ metaphases before dasatinib treatment (%):100.
ch2: post-treatment sample; non-responder patient; cell type: peripheral blood mononuclear cells; Gender: M; Age (yrs) at dasatinib start: 66; Treatments prior to dasatinib: HU, IFN, IM; Mutations detected in the BCR/ABL kinase domain after dasatinib treatment: F317L; Ph+ metaphases after dasatinib treatment (%):100; Additional cytogenetic abnormalities after dasatinib treatment: Not detected.

Raw data file:
251485013131_2007-08-07_512_508_GE2-v5_95_Feb07_1_3.txt

data_processing:
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 75% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
Pre_NR_131.205_Cy3.txt

value: Not detected.