title: Treated Worm-18 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A2_SL3
PMT: 450


title: Patient1_control

status: Public on Oct 15 2009

type: RNA

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

country: USA

institute: University of Washington

description: Patient 1_control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human skin biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: skin


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after white RNAi (expression), replicate 1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: hybridization of biological replicates of white RNAi to control experimental variation

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel at 10 um resolution using a suitable scan area.

data_processing: Images of the expression arrays were analyzed using Agilent Feature Extraction Software version 9.5.1.1. Mean spot intensities without background subtraction were used to normalize with subarray loess and calculate weighted average ratios per reporter by a NKI platform adjusted Rosetta error model (Weng L. et al., Bioinformatics (2006)), tuned by self-self hybridizations. These mean, normalized data without spike-in control oligos are represented in the Supplementary data file 'Expression_norm.txt' together with associated A and p values. The matrix data table contains normalized  values before weighed averaging of duplicate REPORTER_IDs and replicate samples.

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, white RNAi

label_protocol: 1 µg of RNA was labeled with 0.3 µl of ULS-Cy5 or 1 µl of ULS-Cy3 label using the ULS labeling system from Kreatech. Details can be found at the website of the NKI Central Microarray Facility (http://cmfdb.nki.nl/process/protocolView).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Contaminating gDNA was degraded using DNaseI (1 unit/µg RNA), 15 min. at room temperature).

treatment_protocol: Cells were stored in Trizol at -80°C.

tag: cell line


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after white RNAi (expression), replicate 2


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3B RNAi (expression), replicate 1

description: change in expression after H3.3B RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, H3.3B RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul H3.3B dsRNA.


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3A+B RNAi (expression), replicate 2

description: change in expression after H3.3A+B RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, H3.3A+B RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 10 μg/ul H3.3A dsRNA and 10 μg/ul H3.3B dsRNA.


title: Control Worm-14 13 day (PMT 450)

status: Public on Oct 14 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A8_SL3
PMT: 450

hyb_protocol: 600 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array 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), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 350/450/510 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 016423_D_20070410.gal to obtain signal intensities.  Non-uniform spots and spots with a signal intensity outside the linear range were flagged.  Signal intensity was converted into relative RNA concentration based on the linear standard curve of spike-in RNAs.  The relative RNA concentration was normalized to the median value on each array.

organism: Eisenia fetida

source_name: whole organism

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Earthworms were kept in moistened sphagnum peat (pH 6.5–7.5, moisture content 50%) and fed ad libitum on a diet of with Magic Worm Food (Carolina Biological Supply).

extract_protocol: Total RNA was extracted from RNAlater-ICE fixed worms using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adults bearing clitelum and weighing 0.4~0.5 g were pulled out of the culture and allowed to depurate overnight prior to being exposed to CL-20 on filter paper (0.2 ug/cm2). Worms were snap-frozen upon experimental termination.

tag: protocol

value: 6 days treatment, 7 days recovery

tag: agent

value: control

value: whole organism


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3A+B RNAi (expression), replicate 1

description: change in expression after H3.3A+B RNAi


title: Treated Worm-10 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A3_SL1
PMT: 450


title: Treated Worm-15 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A6_SL2
PMT: 450


title: Treated Worm-11 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A1_SL1
PMT: 450


title: Control Worm-12 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A3_SL2
PMT: 450


title: Control Worm-18 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A6_SL3
PMT: 450


title: Horse #7 T0 vs T2 Rep2

city: Dublin

first: Beatrice

middle: Ann

last: McGivney

state: Dublin

address: Belfield

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: Unconditioned thoroughbred geldings were exercised to maximal heart rate or fatigue on an equine high-speed treadmill. Skeletal muscle biopsies were taken from the middle gluteal muscle before, immediately after and four hours after exercise.

hyb_protocol: Microarray hybridisations were performed on an automated HS400 hybridisation station (Tecan Ltd.) with the following protocol - Wash: 75°C, runs 1, wash 10 s, soak 20 s; probe injection: 85°C; denaturation: 95°C, 2 min; hybridisation: 42°C, agitation frequency medium, 4hrs; hybridisation: 35°C, agitation frequency medium, 4hrs; hybridisation: 30°C, agitation frequency medium, 4hrs; wash: 37°C, runs 2, wash 10 s, soak 20 s; wash: 25°C, runs 2, wash 15 s, soak 30 s; wash: 25°C, runs 2, wash 20 s, soak 40 s; slide drying: 25°C 2mins.

scan_protocol: Hybridised and dried slides were scanned with a GenePix 4000B scanner (Axon Instruments Inc.) using the GenePix 6.0 microarray image analysis package (Axon Instruments Inc.).

data_processing: Background correction (Limma “rma”) and print tip lowess normalization were performed. Log(base2) ratios were calculated for each spot on the microarray and duplicate spots were averaged.

label: Alexa Fluor 555

organism: Equus caballus

source_name: Equine skeletal muscle at T0

label_protocol: aRNA was reverse transcribed and directly labelled with Flour647 or Flour555 using the SuperScript™ Plus Direct cDNA Labeling System (BD Biosciences)

extract_protocol: Total RNA was amplified using a MessageAmpTM amplified RNA (aRNA) linear amplification kit (Ambion).

tag: exercise protocol

value: Skeletal muscle biopsy from gluteus medius of an unconditioned 4 year old Thoroughbred gelding pre exercise

value: gluteus medius

tag: age

value: 4 year old

tag: gender

value: gelding

label: Alexa Fluor 647

source_name: Equine skeletal muscle at T2

value: Skeletal muscle biopsy from gluteus medius of an unconditioned 4 year old Thoroughbred gelding 4 hours post exercise


title: Horse #7 T0 vs T2 Rep1


title: Control Worm-10 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A7_SL1
PMT: 450


title: Horse #8 T0 vs T2 Rep1


title: Treated Worm-9 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A1_SL3
PMT: 450

value: 6 days treatment


title: Horse #8 T0 vs T2 Rep2


title: Treated Worm-4 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A7_SL2
PMT: 450


title: Treated Worm-8 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A3_SL3
PMT: 450


title: Control Worm-13 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A1_SL2
PMT: 450


title: Horse #6 T0 vs T2 Rep2


title: Treated Worm-6 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A5_SL2
PMT: 450


title: Treated Worm-3 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A2_SL1
PMT: 450


title: Control Worm-11 13 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A5_SL1
PMT: 450


title: Horse #5 T0 vs T2 Rep2


title: Treated Worm-1 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A4_SL1
PMT: 450


title: Horse #5 T0 vs T2 Rep1


title: Control Worm-5 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A4_SL2
PMT: 450


title: Horse #4 T0 vs T2 Rep2


title: Horse #6 T0 vs T2 Rep1


title: Control Worm-8 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A7_SL3
PMT: 450


title: Control Worm-3 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A8_SL1
PMT: 450


title: Control Worm-4 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A6_SL1
PMT: 450


title: Control Worm-9 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A5_SL3
PMT: 450


title: Control Worm-6 6 day (PMT 450)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A2_SL2
PMT: 450


title: Horse #3 T0 vs T2 Rep1


title: Horse #2 T0 vs T2 Rep2


title: Horse #3 T0 vs T2 Rep2


title: Horse #2 T0 vs T2 Rep1


title: Horse #4 T0 vs T2 Rep1


title: Horse #1 T0 vs T2 Rep1


title: Horse #8 T0 vs T1 Rep2

source_name: Equine skeletal muscle at T1

value: Skeletal muscle biopsy from gluteus medius of an unconditioned 4 year old Thoroughbred gelding immediately (<8 minutes) post exercise


title: Treated Worm-18 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A2_SL3
PMT: 350


title: Treated Worm-10 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A3_SL1
PMT: 350


title: Horse #7 T0 vs T1 Rep2

description: Unconditioned thoroughbred geldings were exercised to maximal heart rate or fatigue on an equine high-speed treadmill. Skeletal muscle biopsies were taken from the middle gluteal muscle before, immediately after and four hours after exercise.


title: Treated Worm-15 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A6_SL2
PMT: 350


title: Treated Worm-11 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A1_SL1
PMT: 350


title: Horse #1 T0 vs T2 Rep2


title: Treated Worm-13 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A8_SL2
PMT: 350


title: Horse #8 T0 vs T1 Rep1


title: Horse #7 T0 vs T1 Rep1


title: Treated Worm-16 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A4_SL3
PMT: 350


title: prp43-Y402A (Cy5) vs. PRP43 (Cy3) at 37C for 30 min

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: A complete description of the protocols used can be found in the accompanying manuscript.

hyb_protocol: Competitive hybridization at 60C for 16 hours.

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 6.0.

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

organism: Saccharomyces cerevisiae

label_protocol: Aminoallyl dUTP incorporation in cDNA reaction, followed by coupling to NHS-ester

extract_protocol: phenol extraction

tag: genotype/variation

value: prp43 Y402A

tag: environmental factor

tag: time

value: 30 min


title: Control Worm-12 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A3_SL2
PMT: 350


title: Control Worm-14 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A8_SL3
PMT: 350


title: Control Worm-11 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A5_SL1
PMT: 350


title: Control Worm-18 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A6_SL3
PMT: 350


title: Horse #5 T0 vs T1 Rep2


title: Horse #6 T0 vs T1 Rep2


title: Control Worm-10 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A7_SL1
PMT: 350


title: Horse #6 T0 vs T1 Rep1


title: cwc23-deltaJ (Cy5) vs. CWC23 (Cy3) at 30C


title: Treated Worm-9 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A1_SL3
PMT: 350


title: CWC23 (Cy5) vs. cwc23-1-225 at 30C


title: PRP43 (Cy5) vs. prp43-Y402A (Cy3) at 37C for 30min


title: CWC23 (Cy5) vs. cwc23-deltaJ (Cy3) at 30C


title: Control Worm-13 13 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A1_SL2
PMT: 350


title: Treated Worm-4 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A7_SL2
PMT: 350


title: Horse #5 T0 vs T1 Rep1


title: Treated Worm-6 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A5_SL2
PMT: 350


title: E0xE150 Glucose 3000209198_L

status: Public on Oct 28 2009

city: São Paulo

first: André

last: Vieira

state: São Paulo

address: Av. Prof. Lineu Prestes 748

department: Bioquímica

country: Brazil

institute: Instituto de Química - USP

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization.

organism: Blastocladiella emersonii

label_protocol: 10ug of total RNA was reverse transcribed and labeled using “Superscript® Plus Indirect cDNA Labeling System” (Invitrogen®). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

extract_protocol: total RNA was extracted using Trizol regent (Invitrogen)

tag: growth protocol

value: Zero min sporulation cells in the presence of 1% glucose.

value: 150 min sporulation cells in the presence of 1% glucose.


title: Control Worm-5 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A4_SL2
PMT: 350


title: Horse #4 T0 vs T1 Rep2

description: Unconditioned thoroughbred geldings were exercised to maximal heart rate or fatigue on an equine high-speed treadmill. Skeletal muscle biopsies were taken from the middle gluteal muscle before, immediately after and four hours after exercise.


title: Treated Worm-1 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A4_SL1
PMT: 350


title: Horse #4 T0 vs T1 Rep1


title: CWC23 (Cy5) vs. cwc23-1-225 (Cy3) at 16C for 30 min


title: Control Worm-8 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A7_SL3
PMT: 350


title: Treated Worm-3 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A2_SL1
PMT: 350


title: Horse #3 T0 vs T1 Rep2


title: Control Worm-9 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A5_SL3
PMT: 350


title: cwc23-1-225 (Cy5) vs. CWC23 (Cy3) at 16C for 30 min

description: A complete description of the protocols used can be found in the accompanying manuscript.


title: Control Worm-6 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310002
Array#_SLide#: A2_SL2
PMT: 350


title: Horse #1 T0 vs T1 Rep2


title: Horse #3 T0 vs T1 Rep1


title: cwc23-1-225 (Cy5) vs. CWC23 (Cy3) at 30C


title: BRCA1 primary tumor_3

city: Madrid

first: Ricardo

last: Fernández-Ramires

state: Madrid

address: Melchor Fdez Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Center

description: Gene expression analysis of primary breast tumor that contains BRCA1 mutation

hyb_protocol: The microarrays were hybridized according to established methodology (Tracey, L., Villuendas, R., Ortiz, P., Dopazo, A., Spiteri, I., Lombardia, L., Rodriguez-Peralto, J. L., Fernandez-Herrera, J., Hernandez, A., Fraga, J., Dominguez, O., Herrero, J., Alonso, M. A., Dopazo, J. & Piris, M. A. (2002) Am J Pathol 161, 1825-37).

scan_protocol: Images were scanned using the Agilent scanner G2565BA.

data_processing: The data were normalized using default values of GEPAS 4.0 (within-array correction, print-tip lowess).

source_name: primary breast tumor, BRCA1 mutation

label_protocol: 5ug of tumoral-amplified RNA (MEGAscript) was labeled with Cy5 and the same amount of the reference RNA (Universal Reference RNA from Stratagene) was labeled with Cy3.

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

tag: RNA extracted from primary BRCA1-mutated tumors

source_name: Universal Human Reference RNA (Stratagene)

tag: Collection of RNA pooled from ten cell lines (adenocarcinoma, mammary gland hepatoblastoma, liver adenocarcinoma, cervix embryonal carcinoma, testis glioblastoma, brain melanoma liposarcoma histiocytic lymphoma; macrophase; histocyte lymphoblastic leukemia plasmacytoma; myeloma; B lymphocyte)

tag: Control


title: BRCA1 primary tumor_58


title: Horse #1 T0 vs T1 Rep1


title: Horse #2 T0 vs T1 Rep1


title: Horse #2 T0 vs T1 Rep2


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 5

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Replicate 5 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep5

hyb_protocol: 750ng of each cRNA were fragmented in the fragmentation buffer, in presence of blocking agent. Subsequently, samples were hybridized with hybridization buffer on microarrays slides  in a Surhyb gasket for 17h at 65°C.

scan_protocol: Slides were scanned on an Axon GenePix 4100A. Images were quantified using Axon GenePix Pro 6.1.0.2.

data_processing: Data were processed in the R statistical environement using the Limma package. Background correction was performed using the normexp method and normalization was performed using Loess.

source_name: Heteronemin & TNFalpha co-treated K562 cells

label_protocol: According to the manufacturer's instructions, reverse transcription were done with 700ng of RNA and labeling of the samples accured during transcription of cRNA.

growth_protocol: Cells were thawed 10 days before treatment and cultivated in RPMI-1640 complemented with 10%, 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions. RNA cleanup was realized with the RNeasy Mini Kit (Qiagen), quantity and quality of RNA were checked with a Nanodrop 1000 spectrophotometer and an Agilent bioanalyzer 4100,  respectively.

treatment_protocol: Cells were seeded the day before treatment in culture medium. At T0, cells were treated with 6μM of heteronemin or an equivalent volume of DMSO. At T+2h, cells were treated with 10ng/mL of TNFalpha, or equivalent volume of water. At T+6h cells were collected for RNA extraction and viability test.

value: DNSZ K562

tag: treatment

value: heteronemin & TNFalpha

source_name: TNFalpha-treated K562 cells

value: TNFalpha


title: BRCA1 primary tumor_33


title: BRCA1 primary tumor_36


title: BRCA1 primary tumor_28


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 3

description:
Replicate 3 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep3


title: Control Worm-4 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A6_SL1
PMT: 350


title: Control Worm-3 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310001
Array#_SLide#: A8_SL1
PMT: 350


title: BRCA1 primary tumor_62


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 6

description:
Replicate 6 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep6


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 4

description:
Replicate 4 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep4


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 2

description:
Replicate 2 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep2


title: BRCA1 primary tumor_1


title: 231-BR cells, vorinostat treated, 113

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description:
Human 231-BR cells injected into mouse, vorinostat treated.
113

hyb_protocol: Hybridization was done according to manufacturer recommendations.

scan_protocol: Scanning was done according to manufacturer recommendations.

data_processing: Data were processed using RMA.

source_name: 231-BR cells, vorinostat treated

label_protocol: Labeling was done according to manufacturer recommendations.

growth_protocol: All experiments were conducted under an approved animal use agreement with the National Cancer Institute. For efficacy studies, 5- to 7-week-old female BALB/c nude mice (Charles River Laboratories) were inoculated with 175,000 231-BR cells in 0.1 mL PBS in the left ventricle.

extract_protocol: Mice were euthanized under CO2 anesthesia 24 to 26 days post-injection and brains were excised. Mouse brains were bisected along the sagittal plane and the right hemisphere of the brain was fixed in 4% paraformaldehyde for 24 h at 4°C, transferred to 20% sucrose overnight at 4°C, and frozen in OCT. The left hemisphere was formalin-fixed and paraffin-embedded for immunohistochemistry. Ten serial sections (10 μm thick) every 300 μm through the right hemisphere were analyzed at a ×50 magnification on a Zeiss microscope, containing an ocular grid with squares of 0.8 mm2. Brain metastases from five vehicle-treated mice and six 150 mg/kg vorinostat-treated mice were procured by laser capture microdissection. RNA was extracted from the captured tumor cells from each brain and two rounds of linear amplification was done. The amplified RNA from each mouse was processed separately through microarray hybridization and analysis.

treatment_protocol: Three days after tumor cell inoculation, mice were randomized to treatment groups. One group began vorinostat treatment (150 mg/kg) on day 3 post-injection and a second group began vehicle treatment. Vorinostat was administered via intraperitoneal injection once daily, 7 days a week. The drug vehicle solution was 10% DMSO and 45% polyethylene glycol 400.

value: Vorinostat


title: Heteronemin-treated cells vs. untreated control cells, replicate 5

description:
Replicate 5 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep5

source_name: Heteronemin-treated K562 cells

value: heteronemin

source_name: Untreated K562 cells

value: untreated


title: Heteronemin-treated cells vs. untreated control cells, replicate 6

description:
Replicate 6 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep6


title: 231-BR cells, vorinostat treated, 102

description:
Human 231-BR cells injected into mouse, vorinostat treated.
102


title: BRCA1 primary tumor_17


title: Heteronemin & TNFalpha co-treated cells vs.TNFalpha-treated cells, replicate 1

description:
Replicate 1 of 6. Heteronemin & TNFalpha co-treated cells vs. TNFalpha-treated cells
H_T_vs_T-Rep1


title: Heteronemin-treated cells vs. untreated control cells, replicate 4

description:
Replicate 4 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep4


title: 231-BR cells, vorinostat treated, 97

description:
Human 231-BR cells injected into mouse, vorinostat treated.
97


title: BRCA1 primary tumor_15


title: Heteronemin-treated cells vs. untreated control cells, replicate 3

description:
Replicate 3 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep3


title: BRCA1 primary tumor_05T126


title: Heteronemin-treated cells vs. untreated control cells, replicate 2

description:
Replicate 2 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep2


title: 231-BR cells, vorinostat treated, 71

description:
Human 231-BR cells injected into mouse, vorinostat treated.
71


title: co-cultured OSCC cells rep 2

city: Gwangju

first: Da-Woon

last: jung

address: 1 Oryong-Dong

department: Life Science

institute: Gwangju Institute of Science and Technology

description: squamous cell carcinoma cell line derived from an OSCC patient

hyb_protocol: The labeled cDNA mixture was then concentrated using ethanol precipitation method. The concentrated Cy3 and Cy5 labeled cDNAs were resuspended in 30 mL of hybridization solution (GenoCheck, Korea). After two labeled cDNAs were mixed, placed on OpArray Human genome 35K (OPHSV4, Operon Biotechnologies, GmbH) and covered by a MAUI FL chamber (Biomicro systems, Inc. UT). The slides were hybridized for 12 h at 62 °C MAUI system (Biomicro systems, Inc. UT). The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: Hybridized slides were scanned with the Axon Instruments GenePix 4000B scanner. The scanned images were analyzed with the software program GenePix Pro 5.1 (Axon, CA) and GeneSpring GX 7.3.1 (Agilent Technologies, CA)

data_processing: Data were normalized by Global, lowess, print-tip and scaled normalization for data reliability. Data were clustered groups of genes that behave similarly across a time course experiments using GeneSpring GX 7.3.1(Agilent Technologies, CA).

source_name: OSCC cells co-cultured with CAF

label_protocol: Each total RNA sample (30 mg) was labeled with Cyanine (Cy3) or Cyanine (Cy5) conjugated dCTP (Amersharm, Piscataway, NJ) by a reverse transcription reaction using reverse transcriptase, SuperScrip ll (Invitrogen, Carlsbad, California).

growth_protocol: Cells were seeded in a 6-transwell plates containing collagen-coated, 1 mm pore transmembrane filters (Becton Dickinson, Franklin Lakes, NJ, USA).  Cells were incubated in serum-free media for 24 h at 37 °C

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

treatment_protocol: 1.7X105 OSCC cells (YD-10B) and 1.7X105 CAF were seeded in the upper chamber and lower chamber, respectively. Monoculture control samples were generated by culturing only CAF or OSCC cells on the same side of the filter as in the co-culture design.

tag: cell type

value: squamous cell carcinoma

source_name: mono-cultured OSCC cells


title: 231-BR cells, vorinostat treated, 87

description:
Human 231-BR cells injected into mouse, vorinostat treated.
87


title: 231-BR cells, vorinostat treated, 67

description:
Human 231-BR cells injected into mouse, vorinostat treated.
67


title: Heteronemin-treated cells vs. untreated control cells, replicate 1

description:
Replicate 1 of 6. Heteronemin-treated cells vs. untreated control-cells
H_vs_C-Rep1


title: BRCA1 primary tumor_04T91

description: Gene expression analysis of primary breast tumor that contains BRCA1 mutation


title: co-cultured OSCC cells rep 1


title: TNFalpha-treated cells vs. untreated control cells, replicate 4

description:
Replicate 4 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep4


title: BRCA1 primary tumor_02T144


title: TNFalpha-treated cells vs. untreated control cells, replicate 5

description:
Replicate 5 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep5


title: 231-BR cells, vehicle treated, 83

description:
Human 231-BR cells injected into mouse, vehicle treated.
83

source_name: 231-BR cells, vehicle treated

value: Vehicle


title: TNFalpha-treated cells vs. untreated control cells, replicate 6

description:
Replicate 6 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep6


title: 231-BR cells, vehicle treated, 105

description:
Human 231-BR cells injected into mouse, vehicle treated.
105


title: 231-BR cells, vehicle treated, 94

description:
Human 231-BR cells injected into mouse, vehicle treated.
94


title: co-cultured CAF rep 1

description: carcinoma-associated fibroblasts derived from the surgical specimen of an OSCC patient

source_name: CAF co-cultured with OSCC cells

value: carcinoma-associated fibroblasts

source_name: mono-cultured CAF


title: BRCA1 primary tumor_02T329I


title: TNFalpha-treated cells vs. untreated control cells, replicate 3

description:
Replicate 3 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep3


title: 6216

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: shoot apex _in vitro/LD/stage 1.02_rep d

hyb_protocol: A mixture of 10 pmol Cy5 incorporated dye and 14 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.1.1.1 (Agilent Technologies).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal) from Agilent Feature Extraction software v10.1.1.1 and compute log2-(Cy5/Cy3)-ratios. We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the features gIsPosAndSignif and  rIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-(Cy5/Cy3)-ratios are averaged.

organism: Arabidopsis thaliana

source_name: Ler control

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: RNeasyPlant mini kit

value: shoot apex

tag: genotype

value: Ler control

source_name: ang3 mutant

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

value: ang3 mutant


title: 231-BR cells, vehicle treated, 73

description:
Human 231-BR cells injected into mouse, vehicle treated.
73


title: BRCA1 primary tumor_02T329D


title: co-cultured CAF rep 2


title: TNFalpha-treated cells vs. untreated control cells, replicate 2

description:
Replicate 2 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep2


title: 6215

description: shoot apex _in vitro/LD/stage 1.02_rep c

tag: tissue


title: 6214

description: shoot apex _in vitro/LD/stage 1.02_rep b


title: Treated Worm-8 6 day (PMT 350)

description:
Gene expression profiling
barcode: 251642310003
Array#_SLide#: A3_SL3
PMT: 350

source_name: whole organism

value: 6 days treatment

value: whole organism


title: 24 hour Zf embyos_5azadC treated vs. control_Replicate 2

city: St. John's

first: Tamara

middle: Heather Lorraine

last: Smith

address: Memorial University of Newfoundland

department: Biochemistry

country: Canada

institute: Memorial University

description:
Biological replicates 2 of 3. 5azadC-treated vs. control zebrafish embryos collected at 24 hours.
300808

hyb_protocol: Agilent Hi-RPM Gene Expression Hybridization kit.  Arrays were hybridized at 20 rpm for 17 h at 60°C.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using GeneSpring 7.3.1.

data_processing: Linear Lowess Normalized.  Features with intensities at or below average background levels were filtered out of data set.

organism: Danio rerio

source_name: 24 hour zebrafish embryos treated with 5azadC

label_protocol: Standard labelling.

growth_protocol: Control embryos were raised in embryo medium for 24 hours.  Treated embryos were raised in 75uM 5-azadC embryo medium for 24 hours.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions with a final purification using the Rneasy clean-up kit following manufacturer's instructions.

value: pooled whole zebrafish embryos

tag: developmental stage

value: 24 hpf embryo

value: 5-aza-2'-deoxycytidine (5azadC)

source_name: 24 hour zebrafish embryos untreated


title: L428 a220T/a220IP

status: Public on Oct 13 2009

city: Groningen

first: Lu Ping

last: Tan

address: Hanzeplein 1

department: Department of Pathology

institute: University Medical Center Groningen

description: Dye swap replicate 2 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L428 cells transfected with anti-miR-220

hyb_protocol: Equal amounts of Cy3 or Cy5 labeled cRNA samples derived from the Ago2 immunoprecipitated fraction and from the total cell lysate fraction were mixed and hybridized in a dye swap design at 65°C overnight on Agilent 44k 60mer Human Whole Genome Oligo Microarray.

scan_protocol: On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).

data_processing: Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 9.1. Probes with no expression (ie. signal intensity similar to background) were filtered out in all tested RNA Samples.

source_name: RNA from total cell lysate fraction

label_protocol: First strand cDNA was synthesized from 200ng RNA, followed by cRNA amplification and labeling with Cy3 or Cy5 according to manufacturer's protocol (Agilent). Purification of Cy3 or Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.

growth_protocol: Both Hodgkin lymphoma cell lines, L428 and L1236 were cultured in RPMI 1640 supplemented with ultraglutamine, 100 U/mL penicillin/streptomycin, and 5% or 10% fetal bovine serum (Cambrex Biosciences, Walkersville, USA), respectively. Cells were diluted 1:2 on the day prior to transfection.

extract_protocol: RNA was isolated using Trizol and glycogen (Invitrogen) as a carrier in the ethanol precipitation step.

treatment_protocol: 5 million cells were transfected with 2.5nmole of specific anti-miRNA and Ago2 immnunoprecipitation was performed 16 hours post transfection.

value: Hodgkin lymphoma cell line

tag: cell line

value: L428 transfected with anti-miR-220

source_name: Ago2 coimmunoprecipitated RNA


title: L428 a17T/a17IP

description: Dye swap replicate 2 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L428 cells transfected with anti-miR-17/20/93/106

value: L428 transfected with anti-miR-17/20/93/106


title: 231-BR cells, vehicle treated, 66

description:
Human 231-BR cells injected into mouse, vehicle treated.
66


title: L428 a220IP/a220T

description: Dye swap replicate 1 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L428 cells transfected with anti-miR-220


title: HMVECs co-cultured with HT-29 cells and blood components rep2

city: Zürich

first: Lubor

last: Borsig

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zürich

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human microvascular endothelial cells (primary culture from Clonetics) + HT-29 cells + blood components

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

growth_protocol: HMVECs were grown to ~90% confluency according to Manufactures instroctions (Clonetics)

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

treatment_protocol: Tumor cells and/or blood components purified from healthy volunteers were added to HMVECs and co-cultured for 8 h. HMVECs were purified with the magnetic sorting to >95% purity.

value: endothelium

value: human microvascular endothelial cells (HMVECs)


title: TNFalpha-treated cells vs. untreated control cells, replicate 1

description:
Replicate 1 of 6. TNFalpha-treated cells vs. untreated control-cells
T_vs_C-Rep1

source_name: TNFalpha-treated K562 cells

value: DNSZ K562

value: TNFalpha

value: untreated


title: 24 hour Zf embyos_5azadC treated vs. control_Replicate 1

description:
Biological replicates 1 of 3. 5azadC-treated vs. control zebrafish embryos collected at 24 hours.
230808


title: L428 a17IP/a17T

description: Dye swap replicate 1 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L428 cells transfected with anti-miR-17/20/93/106


title: HMVECs co-cultured with LS180 cells and blood components rep3

source_name: Human microvascular endothelial cells (primary culture from Clonetics) + LS180 cells + blood components


title: HMVECs co-cultured with HT-29 cells and blood components rep1


title: L1236 a17IP/a17T

description: Dye swap replicate 1 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L1236 cells transfected with anti-miR-17/20/93/106

value: L1236 transfected with anti-miR-17/20/93/106


title: HMVECs co-cultured with blood components only rep2

source_name: Human microvascular endothelial cells (primary culture from Clonetics) + blood components


title: L1236 a17T/a17IP

description: Dye swap replicate 2 of 2. Ago2 immunoprecipitated fraction compared against total cell lysate fraction in L1236 cells transfected with anti-miR-17/20/93/106


title: HMVECs co-cultured with HT-29 cells rep2

source_name: Human microvascular endothelial cells (primary culture from Clonetics) + HT-29 cells


title: HMVECs co-cultured with HT-29 cells rep1


title: HMVECs co-cultured with blood components only rep1


title: HMVECs co-cultured with LS180 cells and blood components rep1


title: HMVECs co-cultured with blood components only rep3


title: HMVECs co-cultured with HT-29 cells rep3


title: U87MG cell line - rep3

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

description: U87MG cells are resistant to apoptosis induced by bortezomib and G5 but susceptible to necrosis induced by G5.

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned  with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with LIMMA. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. A threshold value of 2-fold change was applied.

source_name: Human glioblastoma cell line U87MG

label_protocol: A 6μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Human glioblastoma cell lines T98G and U87MG were grown in DMEM supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), glutamine (2mmol/L) and streptomycin (100 µg/ml) at 37°C in 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).


title: HMVECs co-cultured with LS180 cells and blood components rep2


title: HMVECs co-cultured with LS180 cells rep3

source_name: Human microvascular endothelial cells (primary culture from Clonetics) + LS180 cells


title: U87MG cell line - rep2


title: HMVECs co-cultured with LS180 cells rep2


title: 6213

description: shoot apex _in vitro/LD/stage 1.02_rep a

value: shoot apex


title: U87MG cell line - rep1


title: 24 hour Zf embyos_5azadC treated vs. control_Replicate 3

description:
Biological replicates 3 of 3. 5azadC-treated vs. control zebrafish embryos collected at 24 hours.
050908


title: HMVECs co-cultured with HT-29 cells and blood components rep3


title: HMVECs co-cultured with LS180 cells rep1


title: T98G cell line - rep3

description: T98G cells are susceptible to apoptosis induced by both inhibitors but show some resistance to G5-induced necrosis

source_name: Human glioblastoma cell line T98G


title: liver_PPARa_ko_fasted_repl_4

status: Public on Oct 12 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: no additional information

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor.

organism: Mus musculus

source_name: Liver from PPARalpha ko mouse fasted for 24h, biological replicate 4

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Livers were dissected from wildtype or PPARalpha knock-out mice that were either fed or fasted for 24h.

extract_protocol: Total RNA was prepared from mouse livers using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns.

treatment_protocol: Male mice were either fed or fasted for 24 hours. At the end of the experiment, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). Blood was collected by orbital puncture, after which the mice were sacrificed by cervical dislocation. Livers were dissected, snap frozen in liquid nitrogen and kept at -80ºC until further analysis. For RNA analyses, tissue from the same part of the liver lobe was used.

value: Male

value: liver

value: PPARα knockout mutant

tag: protocol

value: fasted


title: liver_PPARa_wt_fasted_repl_3

description: no additional information

source_name: Liver from PPARalpha wt mouse fasted for 24h, biological replicate 3

value: wt


title: quiescent HMVECs rep1

source_name: Human microvascular endothelial cells (primary culture from Clonetics)


title: T98G cell line - rep2


title: liver_PPARa_wt_fasted_repl_5

description: no additional information

source_name: Liver from PPARalpha wt mouse fasted for 24h, biological replicate 5


title: T98G cell line - rep1


title: liver_PPARa_ko_fasted_repl_5

description: no additional information

source_name: Liver from PPARalpha ko mouse fasted for 24h, biological replicate 5


title: liver_PPARa_ko_fasted_repl_1

description: no additional information

source_name: Liver from PPARalpha ko mouse fasted for 24h, biological replicate 1


title: liver_PPARa_wt_fed_repl_4

description: no additional information

source_name: Liver from PPARalpha wt fed mouse, biological replicate 4

value: fed


title: liver_PPARa_wt_fasted_repl_2

description: no additional information

source_name: Liver from PPARalpha wt mouse fasted for 24h, biological replicate 2


title: liver_PPARa_wt_fed_repl_3

description: no additional information

source_name: Liver from PPARalpha wt fed mouse, biological replicate 3


title: liver_PPARa_wt_fed_repl_2

description: no additional information

source_name: Liver from PPARalpha wt fed mouse, biological replicate 2


title: liver_PPARa_ko_fed_repl_3

description: no additional information

source_name: Liver from PPARalpha ko fed mouse, biological replicate 3


title: liver_PPARa_wt_fed_repl_1

description: no additional information

source_name: Liver from PPARalpha wt fed mouse, biological replicate 1


title: liver_PPARa_ko_fasted_repl_3

description: no additional information

source_name: Liver from PPARalpha ko mouse fasted for 24h, biological replicate 3


title: quiescent HMVECs rep3


title: liver_PPARa_ko_fed_repl_1

description: no additional information

source_name: Liver from PPARalpha ko fed mouse, biological replicate 1


title: quiescent HMVECs rep2


title: liver_PPARa_ko_fasted_repl_2

description: no additional information

source_name: Liver from PPARalpha ko mouse fasted for 24h, biological replicate 2


title: liver_PPARa_ko_fed_repl_2

description: no additional information

source_name: Liver from PPARalpha ko fed mouse, biological replicate 2


title: liver_PPARa_wt_fasted_repl_1

description: no additional information

source_name: Liver from PPARalpha wt mouse fasted for 24h, biological replicate 1


title: liver_PPARa_ko_fed_repl_4

description: no additional information

source_name: Liver from PPARalpha ko fed mouse, biological replicate 4


title: liver_PPARa_wt_fasted_repl_4

description: no additional information

source_name: Liver from PPARalpha wt mouse fasted for 24h, biological replicate 4


title: 2C_D4: wounded skin treated with control plasmid

city: Manchester

first: Kimberly

last: Mace

address: Michael Smith Building, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

country: United Kingdom

institute: University of Manchester

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68290.gif
Disease State: wound
Compound Based Treatment: control

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 75900; Parameter Laser Power = 3.55; Parameter Scan Time = 12:04:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.74; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 245952; Parameter Laser Power = 3.47; Parameter Scan Time = 12:04:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.74; Performer: John,,Rinn

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Mouse Universal Reference (Ambion AminoAlyl

label_protocol: not provided

extract_protocol: not provided

source_name: RNA isolated from wounded skin treated with control plasmid collected on day 4

tag: Simple annotation

value: Genome comparison, adult

tag: Image

tag: Disease State

value: wound

tag: Compound Based Treatment

value: control


title: Unwounded_1

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68283.gif
Disease State: no wound
Compound Based Treatment: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 75879; Parameter Laser Power = 3.55; Parameter Scan Time = 11:42:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 245931; Parameter Laser Power = 3.46; Parameter Scan Time = 11:42:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: John,,Rinn

tag: Stratagene Mouse Universal Reference (Ambion AminoAlyl

source_name: RNA isolated from unwounded skin

tag: RNA isolated from unwounded skin

value: no wound


title: Splenic Macrophage, Replicate 3

status: Public on Oct 10 2009

city: Bronx

first: Laureen

last: Ojalvo

address: Chanin 607, 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: At NimbleGen, quality and yield were verified prior to DNA end-labeling, hybridization and scanning.  Details on the protocols can be found on http://www.nimblegen.com/technology/index.html

hyb_protocol: Standard Nimblegen protocol (http://www.nimblegen.com/technology/index.html), performed at NimbleGen. Quality and yield were verified prior to hybridization.

scan_protocol: Standard Nimblegen protocol (http://www.nimblegen.com/technology/index.html), performed at NimbleGen. Quality and yield were verified prior to scanning.

data_processing: Raw data files for each sample were normalized, background-corrected and saved to logarithmic scale using a Robust Multi-Array Analysis28 (RMA) as implemented by NimbleScan software, version 2.2.33.  Normalized data was analyzed and presented using R project.  All samples fulfilled quality criteria as determined by generation of pair-wise scatter, MA and expression density plots.

source_name: splenic macrophages

label_protocol: Standard Nimblegen protocol (http://www.nimblegen.com/technology/index.html), performed at NimbleGen. Quality and yield were verified prior to DNA end-labeling.

extract_protocol:
Total RNA was extracted from FACS sorted TAMs and splenic macrophages using RNeasy Micro Kits (Qiagen, Valencia, CA, USA) according to the manufacturer’s instruction.  Amplification-grade DNase 1 treatment was performed on the RNA elution column to remove potential genomic DNA contamination.  Approximate yields were 150ng, quality was determined using a nano-biosizing assay (Agilent Bioanalyzer; Agilent Technologies, Palo Alto, CA, USA).
200ng of RNA from samples was re-suspended into 11 µl of RNase/DNase-free water, and a single round of linear amplification was performed by the in vitro transcription T7 promoter method as outlined by the manufacturer’s protocol (Ambion’s Message Amp T7 Kit; Ambion, Austin, TX). For microarray samples, a second round of linear amplification was performed with 200 ng of first round amplified material.  At all steps, yield and quality were established using spectrophotometry and an Agilent Bioanalyzer.
For samples to be used for microarray hybridization, Superscript III (Invitrogen) reverse transcriptase was used to prepare 5ug cDNA from amplified RNA.  Random primers (Invitrogen) were used to prime reaction.  Second-strand cDNA synthesis was performed using E. coli DNA Ligase (Invitrogen), E. coli DNA Polymerase 1 (Invitrogen) and T4 DNA Polymerase (Invitrogen).  RNase H (Invitrogen) treatment was additionally performed.  The reaction was stopped with 0.5M EDTA and then purified using a PCR purification kit (Qiagen) following manufacture’s protocol.  Samples were re-suspended to approximately 200ng/μl.

treatment_protocol: To avoid loss of surface markers, tumors and spleen were minced and filtered four times through graded nylon filters, centrifuged at 1200 RPM for five minutes and then re-suspended in erythrocyte lysis buffer (Beckman-Coulter, Marseille, France).  Cells were washed three times in nuclease-free PBS containing 2% bovine serum albumin (PBS+2%BSA).  Texas Red/EGFP double-positive cells were sorted on a DakoCytomation MoFlo High-Speed Cell Sorter (DakoCytomation, Inc, Fort Collins, Colorado, USA) at 23 p.s.i. into PBS+2%BSA.

tag: strain

value: FVB/N-Tg(MMTV-PyVmT)Mul x Tg(Csf1r-Gfp)Hume; PyMT Transgene negative; mixed background

value: spleen

value: macrophages

tag: sample type

value: littermate control, no tumor


title: TAM, Replicate 4

source_name: tumor-associated macrophages

value: FVB/N-Tg(MMTV-PyVmT)Mul x Tg(Csf1r-Gfp)Hume; mixed background

value: late-stage mouse mammary tumor


title: Unwounded_2

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68281.gif
Disease State: no wound
Compound Based Treatment: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 75894; Parameter Laser Power = 3.55; Parameter Scan Time = 11:57:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.67; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 245945; Parameter Laser Power = 3.46; Parameter Scan Time = 11:57:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.67; Performer: John,,Rinn


title: 1C_D4: wounded skin treated with control plasmid

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68285.gif
Disease State: wound
Compound Based Treatment: control

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 75908; Parameter Laser Power = 3.55; Parameter Scan Time = 12:11:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 245960; Parameter Laser Power = 3.44; Parameter Scan Time = 12:11:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: John,,Rinn

source_name: RNA isolated from wounded skin treated with control plasmid on day 4


title: TAM, Replicate 1


title: 3A3_D4: wounded skin treated with HOXA3 plasmid

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68289.gif
Disease State: wound
Compound Based Treatment: CMV-HOXA3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 75860; Parameter Laser Power = 3.55; Parameter Scan Time = 11:23:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 245912; Parameter Laser Power = 3.45; Parameter Scan Time = 11:23:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: John,,Rinn

source_name: RNA isolated from wounded skin treated with HOXA3 plasmid collected on day 4


title: 4A3_D4: wounded skin treated with HOXA3 plasmid

description:
Simple annotation: Genome comparison, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68291.gif
Disease State: wound
Compound Based Treatment: CMV-HOXA3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 3880; Software: type: feature extraction; Performer: John,,Rinn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 75886; Parameter Laser Power = 3.55; Parameter Scan Time = 11:49:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: John,,Rinn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 245938; Parameter Laser Power = 3.46; Parameter Scan Time = 11:49:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: John,,Rinn

tag: RNA isolated from wounded skin treated with HOXA3 plasmid collected on day 4


title: Splenic Macrophage, Replicate 1


title: TAM, Replicate 3


title: Splenic Macrophage, Replicate 2


title: Splenic Macrophage, Replicate 4


title: TAM, Replicate 2


title: mES DEHP-0.001mM

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

description: Expose 0.001mM bis(2-ethylhexyl)phthalate for 48hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with the QIAGEN RLT buffer, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Chemicals were treated into the culture media at the iniciated stage after removing LIF.

tag: genetic background

value: embryonic stem cell


title: mES Thalidomide-0.01mM

description: Expose 0.01mM thalidomide for 48hours


title: mES Permethrin-100nM

description: Expose 100nM permethrin for 48hours


title: mES Methoprene-0.1mM

description: Expose 0.1mM methoprene acid for 48hours


title: mES Cyclopamine-100nM

description: Expose 100nM cyclopamine for 48hours


title: Picea_D2_C1_needle

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

institute: University of British Columbia

description: Picea_D2_C1_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 11, 07).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon tests DNA (Invitrogen). The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird .  Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D2_C1_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea mariana

source_name: D2: Second biological replicate of black spruce

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol:  40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy5/Alexa Fluor 647 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

extract_protocol:
Total RNA extraction used the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified using spectrophotometry and quality checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) in respect to the distinct peaks of electropherogram and gel profile.

treatment_protocol: Needles pooled from various shoots of the individual tree were flash-frozen on the field by liquid nitrogen on Apr. 24, 07, and kept in -80 ºC freezer until extraction.

tag: species

value: black spruce

value: Fresh current-year needles were sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC, Canada (collection established 1977).

organism: Picea abies

source_name: C1: First biological replicate of Norway spruce

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol:  40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy3/Alexa Fluor 546 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

value: Norway spruce


title: Picea_D3_G2_needle

description: Picea_D3_G2_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 16, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D3_G2_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: D3: Third biological replicate of black spruce

organism: Picea glauca

source_name: G2: Second biological replicate of white spruce

value: white spruce


title: mES Cyclopamine-0.01mM

description: Expose 0.01mM cyclopamine for 48hours

tag: cell type


title: mES Permethrin-0.01mM

description: Expose 0.01mM permethrin for 48hours


title: Picea_F1_E3_needle

description: Picea_F1_E3_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 16, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F1_E3_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea jezoensis

source_name: F1: First biological replicate of jezo spruce

value: jezo spruce

organism: Picea omorika

source_name: E3: Third biological replicate of Serbian spruce

value: Serbian spruce


title: Picea_C1_G3_needle

description: Picea_C1_G3_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 18, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C1_G3_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: G3: Third biological replicate of white spruce


title: mES Methoprene-0.001mM

description: Expose 0.001mM methoprene acid for 48hours


title: mES 4OHPCB-10nM

description: Expose 10nM 4(OH)-2'3,3',4',5'-penta-chlorobiphenyl for 48hours


title: Picea_G2_F1_needle

description: Picea_G2_F1_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 11, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G2_F1_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: mES Thalidomide-100nM

description: Expose 100nM thalidomide for 48hours


title: Picea_E2_D1_needle

description: Picea_E2_D1_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 11, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E2_D1_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: E2: Second biological replicate of Serbian spruce

source_name: D1: First biological replicate of black spruce


title: mES DEX-10nM

description: Expose 10nM dexamethasone for 48hours


title: mES 4OHPCB-1nM

description: Expose 1nM 4(OH)-2'3,3',4',5'-penta-chlorobiphenyl for 48hours


title: mES DEHP-0.1mM

description: Expose 0.1mM bis(2-ethylhexyl)phthalate for 48hours


title: mES TCDD-1nM

description: Expose 1nM 2,3,7,8-tetrachlorodibenzo-p-dioxin for 48hours


title: Picea_F3_D2_needle

description: Picea_F3_D2_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 14, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F3_D2_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: F3: Third biological replicate of jezo spruce


title: Picea_C3_F2_needle

description: Picea_C3_F2_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 16, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C3_F2_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: C3: Third biological replicate of Norway spruce

source_name: F2: Second biological replicate of jezo spruce


title: Picea_D1_C3_needle

description: Picea_D1_C3_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 21, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_D1_C3_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: mES T3-10nM

description: Expose 10nM triiodothyronine for 48hours


title: mES DEX-1nM

description: Expose 1nM dexamethasone for 48hours


title: Picea_F2_E1_needle

description: Picea_F2_E1_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 11, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_F2_E1_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: E1: First biological replicate of Serbian spruce


title: mES TCDD-10nM

description: Expose 10nM 2,3,7,8-tetrachlorodibenzo-p-dioxin for 48hours


title: Picea_G3_E2_needle

description: Picea_G3_E2_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 14, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G3_E2_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: Picea_G1_F3_needle

description: Picea_G1_F3_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 18, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G1_F3_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

source_name: G1: First biological replicate of white spruce


title: mES T3-1nM

description: Expose 1nM triiodothyronine for 48hours


title: mES BPA-1pM

description: Expose 1pM bisphenol A for 48hours


title: Picea_E1_D3_needle

description: Picea_E1_D3_needle is a required hybridization of a series of 15 cross-species microarray hybridizations from the needle sources of tissue in accordance with a modified loop design (hybridization date: Aug. 16, 07).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_E1_D3_needle hybridization together with 14 other microarray hybridizations of the needle tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).


title: mES DHT-10nM

description: Expose 10nM dehydrotestosterone for 48hours


title: Picea_G1_F3_bark_phloem

description: Picea_G1_F3_bark_phloem is a required hybridization of a series of 15 cross-species microarray hybridizations from the bark/phloem sources of tissue in accordance with a modified loop design (hybridization date: Aug. 21, 07).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon testes DNA (Invitrogen). The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird.  Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_G1_F3_bark_phloem hybridization together with 14 other microarray hybridizations of the bark/phloem tissue sources were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species, an adjustment for dye bias and array effect indicating which Cy5/Cy3 pair on each array. For each gene-by-treatment (biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

extract_protocol:
Total RNA extraction used the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Specimen (bark/phloem sources of tissue) pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: Bark and the attached phloem were separated from the inner layers of the shoots, sampled from mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC, Canada (collection established 1977).

treatment_protocol: Bark/phloem sources of tissue pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.