title: Naïve_Mono_2h_6

source_name: Uninfected, monolayer A549s, 2 hour post infection

value: Uninfected

value: 2 hour


title: Year1 day4 0.05% sewage rep3

status: Public on Dec 01 2012

type: RNA

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

country: Canada

institute: Simon Fraser University

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

scan_protocol: Slides were scanned at 10 um resolution on a PerkinElmer ScanArray Express or PerkinElmer ProScanArray.

data_processing: Image TIFF files from the scanned microarrays were imported into ImaGene software version 6.1 (BioDiscovery Inc.).  ImaGene output files were imported into GeneSpring software version 7.3.1 (Agilent Technologies Inc.) for statistical analysis.  Each timepoint for each experiment was treated as a unique block and analyzed independently of other timepoints.  The data were normalized to the 50th percentile of the median values for all genes across the microarrays within each timepoint.  Statistical analysis of this normalized data was performed using one-way ANOVA, and then Welch t-tests (variances not assumed equal) were performed to compare the gene expressions in a sewage treatment versus the control with significant differences noted when p < 0.05.  NOTE: Extracted GeneSpring v7 files into GeneSpring v11 in 2012 to obtain data for each slide (in contrast, for thesis and manuscript data analysis, data was exported from GS by treatment).

molecule: total RNA

organism: Oncorhynchus tshawytscha

source_name: liver, 0.05% sewage, Yr1d4

label_protocol: 25 ug of liver total RNA was labelled with Cy5-dUTP using Superscript Direct cDNA Labeling System kits (Invitrogen), as per the manufacturer's instructions.  Cy3-labelled UDR cDNA sample was made from 600 ng of UDR stock material using 1 nmol of Cy3-dCTP dye (Amersham) and Ready-To-Go beads (Amersham) as per the manufacturer’s protocol, except a 2 h incubation at 37 degree Celcius was used to maximize yield.

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

treatment_protocol: Two experiments were conducted in the month of June but exactly one year apart (called Yr 1 and Yr 2), using untreated sewage from the Capital Regional District in Victoria, British Columbia, Canada.  Juvenile chinook salmon were exposed to seawater negative control, or sewage concentrations made in seawater of 0.05%, 0.1%, 0.7%, 2% and 5/10% for 8 days (with sampling events at days 1, 4 and 8), and then a portion of fish were transferred to clean seawater to recover for 8 days and sampled at the day 16 timepoint.

tag: treatment

value: 0.05% sewage

tag: time

value: year 1 day 4

tag: tissue

value: liver

tag: developmental stage

value: juvenile

organism: Oncorhynchus mykiss

source_name: liver, mixture of Universal DNA Reference (UDR) material

tag: sample type


title: 14162915 - nlp7-1 T10 BR1 vs col T10 BR1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Short term nitrate induction kinetics in wildtype, nlp7-1, nlp7-3 and nlp6nlp7

hyb_protocol: col T10 BR1 Cy5 / nlp7-1 T10 BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: col T10 BR1

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

growth_protocol: whole plant - Media: modified Hoagland  hygrometry: 80  Temperature: 22  Light: 100

extract_protocol: col T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 10min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 10min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.

tag: ecotype

value: Columbia

tag: age

value: (Boyes et al. Plant Cell 2001):boyes:1.02

tag: genotype/variation

value: col

source_name: nlp7-1 T10 BR1

extract_protocol: nlp7-1 T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 10min - mut - time course study - gene disruption,nitrate:quantity 3mM time 10min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: 14162914 - col T10 BR1 vs nlp7-1 T10 BR1

hyb_protocol: nlp7-1 T10 BR1 Cy5 / col T10 BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Naïve_Mono_2h_4

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours

scan_protocol: scanned using the Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and data was extracted using GenePix® pro 6.1

data_processing: 75th percentile normalisation using GeneSpring GX v 11.5.1

organism: Homo sapiens

label_protocol: RNA was labelled with Cy3 using the Quick Amp Labelling kit (Agilent) as per the manufacturer’s instructions.

growth_protocol: Grown in RWVs in Dulbeccos modified eagle's media with 10% foetal calf serum and 4mM l-glutamine

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: Cells infected with F. tularensis SchuS4 for 3 hours MOI 100. RNA extracted from RWVs or Monolayers at 2, 6 and 22 hours postin infection and placed into Qiagen RLT (lysis buffer) containing B-mercaptoethanol

tag: gender

value: Male

tag: cell line

value: A549 epithelial cells

tag: culture condition

value: monolayer

tag: infection


title: B. canis from infected cells (5h), rep1 (set 2)

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

country: USA

institute: University of Wisconsin-Madison

description: This sample is of B. canis from RAW cells infected 5h. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled samples (1.5 µg) were hybridized at 42ºC to Brucella ovis custom designed array (Nimblegen), using a 1X mixing chamber (Nimblegen) and Maui hybridization system (BioMicro).  After 18-20 h, chambers were removed and slides were washed according to the manufacturer’s protocol.

scan_protocol: Slides were scanned at 5µm at a wavelength of 532 using a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).

data_processing: Fluorescent intensity levels were determined using Nimblescan (Nimblegen) software.  The acquired images were normalized using quantile normalization and gene expression signals were generated using the Robust Multichip Average (RMA) algorithm.

organism: Brucella canis

source_name: B. canis ATCC#23365

label_protocol: Samples were labeled and hybridized utilizing a Nimblegen protocol.

growth_protocol:
B. canis was grown to log phase on a shaker platform at 37ºC in Brucella broth (Difco) for 1-2 days.  Optical density (absorbance at 600nm) was determined and an appropriate aliquot was added to Brucella broth to achieve log phase within 24 h. All work performed with Brucella spp. was conducted in a BSL3 environment.
The mouse macrophage cell line, RAW 264.7 (ATCC TIB71), was maintained at 37ºC with 5% CO2 in supplemented RPMI 1640 (10% bovine growth serum and 0.2mM L-glutamine).  One day prior to infection, 1-2 x 107 RAW 264.7 cells were plated in T75 flasks.  On the day of infection, RAW cells in a sample flask were counted, and the optical density of the bacteria was determined.  Bacteria were added to the RAW cells to achieve an MOI of 100.  All work performed with Brucella spp. was conducted in a BSL3 environment.

extract_protocol:
For RNA isolation from broth cultures, 4 ml of Protect (Qiagen) was added to 2 ml of log phase bacteria.  Cultures were incubated for 5 min at room temperature and then centrifuged at 1100 x g for 10 min.  Supernatant was decanted and the pellet resuspended in 200 µl of lysis buffer (TE containing 66 µg/ml Proteinase K (Epicentre) and 0.193 KU/ml ReadyLyse (Epicentre).  Cells were incubated at room temperature for 10 min with vortexing every 2 min.  RLT buffer (700 µl) with β-mercaptoethanol (Qiagen) was added and samples were transferred to 2 ml tubes containing 30-50 mg acid washed glass beads (1.0 mm).  Bacteria were mechanically disrupted in a BeadBeater (Biospec Products, Inc) twice for 50s at 4800 rpm.  Tubes were quick-spun to pellet beads and supernatant transferred to new tubes.  RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.  On-column DNase treatment was included in the isolation protocol.  Yield and quality were determined using a spectrophotometer (Nanodrop Technologies) and Agilent bioanalyzer (Agilent).
For RNA isolation from infected cells, RAW264.7 cells were infected at an MOI of 100 for 24 h.  Flasks were washed twice with supplemented RPMI 1640 to remove extracellular bacteria and 2 ml of Protect diluted 2:1 in PBS was added.  Cells were transferred to centrifuge tubes, pelleted, and resuspended in 200 µl of lysis buffer.  Cell lysis and mechanical disruption were performed as described above.  RNA was isolated using RNeasy Mini Kit (Qiagen) with DNase treatment.  Yield and quality were determined using a Nanodrop spectrophotometer and Agilent bioanalyzer, respectively. Bacterial RNA was enriched from RAW infected cells using MICROBEnrich kit (Ambion).  Oligo Magbeads were washed with nuclease-free water and equilibrated in binding buffer.  RNA was resuspended in binding buffer, mixed with capture oligo, incubated at 70ºC for 10 min and annealed at 37ºC for 1 h.  The RNA/capture oligo mix was added to the magbeads and incubated at 37ºC for 15 min.  The oligo Magbeads were removed, and the supernatant was collected.  Bacterial enriched RNA was assessed for yield and quality using a Nanodrop spectrophotometer and Agilent bioanalyzer.

tag: strain

tag: host

value: 5 h


title: miRNA profiling in CEM-SS cells

city: Hangzhou

first: Jin

last: Yang

address: Qingchun Road 79

country: China

institute: Zhejiang University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: CEM-SS

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: CEM-SS cells were cultured in DMEM medium with 10% FBS and 1x Antibiotic-Antimycotic (GIBCO).

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen).

treatment_protocol: The low-passage (3rd)CEM-SS cells (1×10^7) were used to isolate total RNA .

tag: cell type

value: lymphocyte

value: CEM-SS

value: uninfected


title: miRNA profiling in HIV-1 infected cells

growth_protocol: H9/IIIB cells were cultured in DMEM medium with 10% FBS and 1x Antibiotic-Antimycotic (GIBCO).

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen)

treatment_protocol: The low-passage (3rd)H9/IIIB cells (1×10^7) were used to isolate total RNA .

value: HIV-1 LAI persistent infection


title: Sulfate-repetition2

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

description: mM/µM

hyb_protocol: hybridizations were performed for 17h at 65°C in dedicated micro-chambers with 100pmol of the different labelled samples.hybridization buffer was from Agilent (ref 5188-5242)

scan_protocol: Agilent G2565 Scanner in extended dynamic range with a resolution of 5nm per pixel

data_processing:
intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differential analysis was performed with the varmixt package of R.
genes with both a P-value < 0,05 and a ratio higher than 2 were considered as diffrentially expressed

organism: Yarrowia lipolytica

source_name: growth on 10mM sulfate

label_protocol: RNA was labeled using the Superscript indirect cDNA labeling system kit (Invitrogen) with anchored oligo(dT)20 primer according to manufacturer's instructions

growth_protocol: Y. lipolytica cells were grown in exponential growth  for ten generations thanks to transfer on fresh medium. The growth medium is a chemically defined medium according to Mansour et al. Appl. Env. Microbiol. (2008) 74:6505-6512.

extract_protocol: Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)

tag: growth condition

value: 10mM sulfate

source_name: growth on10µM sulfate

value: 10µM sulfate


title: Sulfate-repetition3

description: mM/µM


title: Naïve_Mono_2h_3

value: Uninfected

value: 2 hour


title: Sulfate-repetition1

description: mM/µM


title: Sulfate-repetition2-dye swap

description: µM/mM


title: B. canis, broth culture, rep1

description: This sample is of B.canis from broth culture. It is the first of two biological replicates used in this experiment, each from separate cultures.

value: control


title: Naïve_Mono_2h_2


title: Sulfate-repetition3-dye swap

description: µM/mM


title: B. canis, broth culture, rep2

description: This sample is of B.canis from broth culture. It is the second of two  biological replicates used in this experiment, each from separate cultures.


title: Sulfate-repetition1-dye swap

description: µM/mM


title: Cystine-repetition3-dye swap

description: µM/mM

source_name: growth on 1mM cystine

value: 1mM cystine

source_name: growth on 1µM cystine

value: 1µM cystine


title: B. canis from infected cells (5h), rep2

description: This sample is of B.canis from RAW cells infected for 5h. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: B. canis from infected cells (24h), rep1

description: This sample is of B.canis from RAW cells infected for 24h. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: Naïve_Mono_2h_1


title: B. canis from infected cells (24h), rep2

description: This sample is of B.canis from RAW cells infected for 24h. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: miRNA profiling in HIV-1 latently infected cells

source_name: CEM-Bru

value: Bru latently infected


title: Cystine-repetition3

description: mM/µM


title: B. canis from infected cells (5h), rep1


title: Cystine-repetition2

description: mM/µM


title: B. melitensis from infected cells (24h), rep1

description: This sample is of B. melitensis 16M from RAW cells infected for 24h. It is the first of two  biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled samples (1.5 µg) were hybridized at 42ºC to B. melitensis (Nimblegen A4357-001-01) or custom designed arrays (Nimblegen), using a 1X mixing chamber (Nimblegen) and Maui hybridization system (BioMicro).  After 18-20 h, chambers were removed and slides were washed according to the manufacturer’s protocol.

organism: Brucella melitensis bv. 1 str. 16M

source_name: B. melitensis ATCC#23456

growth_protocol:
B. melitensis was grown to log phase on a shaker platform at 37ºC in Brucella broth (Difco) for 1-2 days.  Optical density (absorbance at 600nm) was determined and an appropriate aliquot was added to Brucella broth to achieve log phase within 24 h. All work performed with Brucella spp. was conducted in a BSL3 environment.
The mouse macrophage cell line, RAW 264.7 (ATCC TIB71), was maintained at 37ºC with 5% CO2 in supplemented RPMI 1640 (10% bovine growth serum and 0.2mM L-glutamine).  One day prior to infection, 1-2 x 107 RAW 264.7 cells were plated in T75 flasks.  On the day of infection, RAW cells in a sample flask were counted, and the optical density of the bacteria was determined.  Bacteria were added to the RAW cells to achieve an MOI of 100.  All work performed with Brucella spp. was conducted in a BSL3 environment.


title: B. melitensis from infected cells (24h), rep2

description: This sample is of B. melitensis 16M from RAW cells infected for 24h. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: Cystine-repetition1-dye swap

description: µM/mM


title: B. melitensis, broth culture rep2

description: This sample is of B. melitensis 16M from broth culture. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: Cystine-repetition1

description: mM/µM


title: TLE04

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Biological replicate4

hyb_protocol: Fragmented Cy3-labeled cRNA (800ng) of the control sample were mixed with equal amounts of Cy5-labeled cRNA of the intractable medial temporal lobe epilepsy (spiking) sample, and the mixtures were hybridized onto 44K whole human genome DNA microarrays (Agilent Technologies) for 17 hrs at 65°C with constant rotation (10 rpm)

scan_protocol: The arrays were washed with gene expression wash buffers kit (Agilent Technologies) and scanned with Agilent DNA microarray scanner (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for feature extraction.

source_name: Adjacent non-spiking tissue

label_protocol: Low RNA input linear amplification kit from Agilent was used and labeling was done based on manufacturer's instructions. cRNA from normal tissues were labeled with Cy3 and cRNA from tumor tissues were labeled with Cy5

extract_protocol: Total RNA isolation using RNeasy minikit following manufacturer's instructions

value: adjacent to the medial temporal lobe epilepsy tissue (non-spiking)

source_name: Intractible medial temporal lobe epilepsy (spiking) tissue


title: TLE09

description: Biological replicate9

value: medial temporal lobe epilepsy (spiking) tissue


title: Cystine-repetition2-dye swap

description: µM/mM


title: TLE10

description: Biological replicate10


title: B. melitensis, broth culture rep1

description: This sample is of B. melitensis 16M from broth culture. It is the first of two  biological replicates used in this experiment, each from separate cultures.


title: TLE07

description: Biological replicate7


title: TLE05

description: Biological replicate5


title: Methionine-repetition2

description: mM/µM

source_name: growth on 10mM methionine

value: 10mM methionine

source_name: growth on 10µM methionine

value: 10µM methionine


title: TLE06

description: Biological replicate6


title: Methionine-repetition2-dye swap

description: µM/mM


title: TLE08

description: Biological replicate8


title: TLE02

description: Biological replicate2


title: TLE03

description: Biological replicate3


title: Mid-exponential ∆lpsB, biological rep 3

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from mid-exponential ATCC 17978 cells containing ∆lpsB mutation

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on an A. baumannii Affymetrix GeneChip (PMDacba1a520551F).  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: Biotin

organism: Acinetobacter baumannii

source_name: Mid-exponential ∆lpsB

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix).

growth_protocol: Cells were grown to mid-exponential phase in Luria Bertani medium at 37C with aeration (180 rotations per minute).

extract_protocol: Total bacterial RNA was isolated using mechanical disruption using lysing matrix B tubes (MP Biomedicals) in a FP120 shaker and Qiagen RNeasy mini columns, following the manufacturer's recommendations for prokaryotic RNA purification.

treatment_protocol: Once reaching mid-exponential phase (3.5 hr incubation of a 1:100 diluted overnight starter culture) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases.

tag: strain background

value: ∆lpsB (deletion of lpsB)

value: Whole cell

tag: growth phase

value: Mid-exponential


title: Mid-exponential ∆lpsB, biological rep 2


title: 099 Migratory vs. non-migratory (MM/MNM)

city: New Orleans

first: Reza

last: Izadpanah

state: Louisiana

address: 1430 Tulane Avenue

department: Medicien

institute: Tulane University

hyb_protocol: Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification was done using ImaGene software version 8.0.1 (BioDiscovery, Los Angeles, MA). Normalization was performed using the calibration oligos

source_name: 098 Control-Migratory (099 M5)

label_protocol: 2 µg of the respective total RNAs were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA mix was hybridized in a dual colour approach to microarrays.

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

tag: msc type

value: 099 Control-Migratory (099 M5)

source_name: Human breast adipose tissue derived MSCs (B-ASCs)

value: 099 non-migratory (MNM)


title: 098 Control-Migratory (098 M5/NM5)

source_name: 098 Control-Migratory (098 M5)

value: 098 Control-Migratory (098 M5)

value: 098 Control-non-migratory (098 NM5)


title: 098 Migratory vs. non-migratory (MM/MNM)

source_name: 098 Migratory (MM)

value: 098 Migratory (MM)

value: 098 non-migratory (MNM)


title: Methionine-repetition1

description: mM/µM


title: B. canis from infected cells (5h), rep2 (set 2)

source_name: B. canis ATCC#23365

tag: time

value: 5 h


title: Whole blood 173

type: genomic

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

institute: Mount Sinai Hospital

description: sample id: 683

hyb_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips

data_processing: Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips

label: Biotin-NTP

molecule: genomic DNA

source_name: Whole blood

extract_protocol: Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)

value: F

tag: tissue

value: Whole blood


title: 098 Control-Par

source_name: Control-Par MSCs

value: Control-parental MSCs

value: 101 Control-parental MSCs


title: Whole blood 172

description: sample id: 488

scan_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips

value: M


title: Mid-exponential ∆lpsB, biological rep 1


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P2-2

city: Barcelona

first: Clara

last: Alsinet

state: Catalonia

address: Rosselló 153

country: Spain

institute: IDIBAPS - Hospital Clínic

hyb_protocol: After purification, 1.65 μg of cRNA was fragmented and hybridized to the array for 17 hr. at 65°C.

scan_protocol: Hibridized slides were washed and scanned with Agilent G2565BA Microarray Scanner. Images were analyzed with Feature Extraction 9.5  from Agilent Technologies.

data_processing:
Array quality in mice studies was assessed with the arrayQualityMetrics package of Bioconductor (http://www.bioconductor.org). Data were normalized and logged-2 transformed using the RMA algorithm. Raw data were filtered according to variability using the PreprocessDataset module as implemented in Gene Pattern.
R-based GenePattern modules and custom-generated R code  (version 2.13.1, http://www.r-project.org/) were used for RMA preprocessing and data analysis

organism: Mus musculus

source_name: Liver

label_protocol: Approximately 700 ng of total RNA was amplified and labeled with Cy3 using the Low RNA Input Linear Amp Kit PLUS, One-Color  from Agilent Technologies.

growth_protocol: Mice were maintained in a pathogen-free environment. All studies were performed in accordance with policies for the humane use of animals established by the University of Pennsylvania and the NIH.

extract_protocol: RNA was extracted from both monogenic and bigenic liver tissues at days 0 and 2 using Qiagen RNeasy Mini kit and eluted in water.

treatment_protocol: Mice harboring the AFP-promoter driving the expression of Cre were crossed to animals with the Rosa26-lsl-NICD allele. Litters were genotyped and sacrificed for RNA extraction on day of birth (day 0) and 2 days after (day 2).

value: Postnatal Day 2

value: liver

tag: genotype

tag: genetic background

value: hybrid 129 x C57BL/6


title: Mid-exponential lpsB:Tn5, biological rep 1

description: Gene expression data from mid-exponential ATCC 17978 cells containing lpsB:Tn5 mutation

source_name: Mid-exponential lpsB:Tn5

value: lpsB:Tn5 (ATCC 17978 derivative harboring a transposon within lpsB)

value: Whole cell


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P2-3

tag: age


title: Mid-exponential 17978, biological rep 3

description: Gene expression data from mid-exponential phase wildtype ATCC 17978 cells

source_name: Mid-exponential 17978

tag: genotype/variation

value: Wild type

value: Mid-exponential


title: Methionine-repetition1-dye swap

description: µM/mM

value: 10mM methionine

value: 10µM methionine


title: Naïve_Mono_2h_5

source_name: Uninfected, monolayer A549s, 2 hour post infection

tag: gender

value: Male

value: A549 epithelial cells

value: monolayer

value: Uninfected

value: 2 hour


title: Mid-exponential lpsB:Tn5, biological rep 2


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P0-2

value: Postnatal Day 0


title: High3

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Labelled RNA was hybridised for 16 hours at 65 °C to miRCURY LNA™ microRNA microarrays 5th generation (Exiqon, Denmark) which contain 1,891 capture probes in quadruplicate.

scan_protocol: After washing and drying, the microarrays were scanned in a DNA Microarray Scanner (Agilent) and the resulting images were quantified using Imagene v. 8.0 (BioDiscovery, CA).

data_processing:
Only pig probes are relevant to this study.
The hybridizations are setup as dual channel, but we completely disregard the reference channel in the analysis. Reference: pool of RNA from the six samples.
Inter-slide normalisation was performed using a non-linear quantile-based normalisation algorithm in Rosetta Resolver (Rosetta Biosoftware). Following normalisation, data was Log2 transformed. Two filtering steps were conducted. First, a variance filter was applied to remove all signals with variance below 0.02, and then, filtering for an absolute Log2Difference > 0.2 (corresponding to a 15 % difference in signal) between low and high prolificacy groups was applied. Overall, 84 probe signals were left for further analysis (ie, were used in paper). Student’s t-test was applied to test for differentially expressed miRNAs between low and high prolificacy groups. Heat maps and two-way hierarchical clustering were based on Pearson correlation coefficients and performed in Qlucore Omics Explorer v.2.2 (Qlucore, Lund, Sweden). The 84 probes with more variable expression between the two groups were manually checked in miRBase v.18 and then annotated to the pig genome (Sus scrofa, Ensembl release 64 - September 2011)

organism: Sus scrofa

source_name: uterus, S.C. 787

label_protocol: One microgram of total RNA from each sample was labelled using the miRCURY™ Power Labelling Kit (Exiqon, Denmark) following manufacturer’s specifications

extract_protocol: Total RNA was extracted using the TRIzol® reagent (Invitrogen) following the manufacturer’s instructions. RNA quality was evaluated with the RNA 6000 Nano Kits on an Agilent 2100 Bioanalyzer (Agilent, Germany) and the RNA quantity was assessed using Nanodrop 1000 Spectrophotometer (Thermo Scientific, USA).

tag: proliferation

value: High


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P2-1


title: Mid-exponential 17978, biological rep 1


title: Mid-exponential 17978, biological rep 2


title: TLE01

description: Biological replicate1

source_name: Adjacent non-spiking tissue

value: adjacent to the medial temporal lobe epilepsy tissue (non-spiking)

value: medial temporal lobe epilepsy (spiking) tissue


title: Whole blood 171

description: sample id: 318

label_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips

value: F

value: Whole blood


title: Whole blood 170

description: sample id: 293


title: High2

source_name: uterus, S.C. 389


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P0-3

value: liver

value: hybrid 129 x C57BL/6


title: Low3

source_name: uterus, S.C. 486

value: Low


title: High1

source_name: uterus, S.C. 373


title: Low2

source_name: uterus, S.C. 360


title: B. canis, broth culture, rep1 (set 2)

value: control


title: DAPT rep3

city: Madrid

first: Antonio

last: Maraver

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas

description: human lung cancer cell line mutated in KRAS

hyb_protocol: Standard

scan_protocol: Standard

data_processing: Background correction was carried out using normexp, data was normalized using quantiles between-arrays normalization. Data processing was carried out using Bioconductor´s limma package.

source_name: DAPT rep3

label_protocol: Standard

growth_protocol: 10% FCS in  DMEM

extract_protocol: RNA was extracted with Trizol and then purified with Rneasy Micro kit

treatment_protocol: Cells were treated with the gamma-secretase inhibitor DAPT

tag: cell line

value: NSCLC H358

tag: treatment

value: DAPT


title: Low1

source_name: uterus, S.C. 350


title: Double transgenic AFP-Cre/Rosa26-lsl-NICD mutant P0-1


title: Mono transgenic Rosa26-lsl-NICD control P2-3

description: Mono transgenic Rosa26-lsl-NICD

value: Postnatal Day 2

value: Mono transgenic Rosa26-lsl-NICD


title: Mono transgenic Rosa26-lsl-NICD control P2-1

description: Mono transgenic Rosa26-lsl-NICD


title: Mono transgenic Rosa26-lsl-NICD control P2-2

description: Mono transgenic Rosa26-lsl-NICD


title: Mono transgenic Rosa26-lsl-NICD control P0-1

description: Mono transgenic Rosa26-lsl-NICD


title: DAPT rep1

source_name: DAPT rep1

value: human lung cancer cell line mutated in KRAS


title: DAPT rep2

source_name: DAPT rep2


title: Mono transgenic Rosa26-lsl-NICD control P0-2

description: Mono transgenic Rosa26-lsl-NICD


title: vehicle rep1

source_name: vehicle rep1

value: vehicle


title: vehicle rep2

source_name: vehicle rep2


title: vehicle rep3

source_name: vehicle rep3


title: Sample#G63Tumor DNA _NSP

status: Public on Nov 30 2012

city: Salamanca

first: MariaDolores

last: Tabernero

address: Paseo San Vicente 58-182

institute: Hospital Universitario de Salamanca y Centro del Cáncer

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array images were acquired using GeneChip® Operating Software (GCOS) and Affymetrix GeneChip®Command Console Software (AGCC). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotyping Console version  4.1.1.834 (chp files). Genomic analysis was performed by using the DNA chip Analyze (dChip) and CNAG 3.3.0.1 software.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: GBM tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from GBM  tissues and  from peripheral blood at diagnosis using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer  and agarose gel electrophoresis.

value: Glioblastoma tissue

value: Female

tag: grade

value: IV

tag: karnofsky index(%)

tag: tumor localization

value: Insular

tag: number of relapses

tag: survival after surgery


title: Sample#G64Blood DNA_NSP

description: Hybridized to 250K_Nsp

source_name: Peripheral blood

value: Pheripheral blood

value: Male

value: not applicable


title: Sample#G54Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G45Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: Temporal


title: Sample#G62Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: Occipital


title: Sample#G50Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G55Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G55Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: Frontal


title: Sample#G52Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G53Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G54Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: Parietal


title: Sample#G44Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G52Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G46Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G43Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G64Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G63Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G57Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G44Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G62Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G53Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G50Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G56Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G51Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G57Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G45Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G46Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G56Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G43Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G51Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G42Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G37Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G37Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G42Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G39Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G41Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G35Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G34Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G30Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G41Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G25Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G40Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G17Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G29Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G40Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G29Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G34Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G25Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G23Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G17Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G39Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G15Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G31Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G23Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G30Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G35Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G14Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G15Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G31Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G14Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G12Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G10Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G10Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G13Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#45 Tumor DNA _NSP

description: Hybridized to 250K_Nsp

data_processing:
The array images were acquired using Affymetrix GeneChip®  Operating Software (GCOS) and Command Console Software (AGCC). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotyping Console version  4.1.1.834. Genomic analysis was performed by using the DNA chip Analyze (dChip) and CNAG 3.3.0.1 softwares.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Meningioma tumor

extract_protocol: Genomic DNA was extracted from meningiomas  tissues and  from peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer  and agarose gel electrophoresis.

tag: tumor

value: Meningioma tumor

tag: who grade

value: I


title: Sample#G13Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G6Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G6Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#50 Blood DNA_NSP

description: Hybridized to 250K_Nsp

value: Not applicable


title: Sample#49 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#50 Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: II


title: Sample#47 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#48 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G12Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#42 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#42 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#43 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#46 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#44 Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: III


title: Sample#43 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#44 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G8Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#46 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#49 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#47 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#48 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G8Tumor DNA _NSP

description: Hybridized to 250K_Nsp

value: Deep


title: Sample#45 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#41 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#41 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#40 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#39 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#39 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#37 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#40 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#36 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#38 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#35 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#38 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#32 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#35 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#37 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#28 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#32 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#31 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#34 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#34 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#33 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#33 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#28 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#30 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#29 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#29 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#31 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#30 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#36 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#26 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#27 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#25 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#24 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#26 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#23 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#27 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#25 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#24 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#21 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#22 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#22 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#17 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#17 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#19 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#18 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#18 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#20 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#19 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#16 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#20 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#12 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#23 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#13 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#14 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#15 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#14 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#13 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#16 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#15 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#10 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#11 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#12 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#9 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#21 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#11 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#9 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#10 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#7 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#6 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#3 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#4 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G63Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Glioblastoma tissue


title: Sample#5 Blood DNA_NSP

description: Hybridized to 250K_Nsp

value: Female


title: Sample#G62Tumor DNA _STY

description: Hybridized to 250K_Sty

value: IV


title: Sample#5 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#7 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#1 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#6 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#8 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G57Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G64Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#2 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G56Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G64Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G55Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G54Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#1 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G56Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G62Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G55Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#8 Tumor DNA _NSP

description: Hybridized to 250K_Nsp


title: Sample#G54Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#4 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#3 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G53Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G52Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G53Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G52Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G46Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G40Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G50Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G46Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G45Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G44Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G44Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G51Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G43Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G42Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G43Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G63Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G42Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G51Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G50Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#2 Blood DNA_NSP

description: Hybridized to 250K_Nsp


title: Sample#G39Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_4_BB1_15

city: Durham

first: Daniel

last: Runcie

state: NC

department: Biology Department

institute: Duke University

description: Used

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina DASL scanning protocol

data_processing:
Raw, pre-BeadStudio files were processed using tools in the beadarray package in R. Details are in the accompanying manuscript. Briefly, probe measurements from the Cy3 channel were averaged, and then log-transformed. Each probe was first corrected for background effects by regression against data from negative control probes. Then all samples were normalized to the average expression of probes targeting the gene RBM8A.
Normalized intensities for each probe included in the final analysis. Several probes were excluded because they appeared to target other transcripts.

organism: Strongylocentrotus purpuratus

source_name: gastrula 15 degrees

label_protocol: Standard Illumina DASL label protocol

growth_protocol: Sea urchins spawned, fertilized, washed and cultured in artificial sea water (CoralLife) until the mid-gastrula stage

extract_protocol: Embryos were concentrated and disrupted in Qiagen RLT buffer with 1% BME, and then extracted with the RNeasy kit. All RNA concentrations were above 10ng/ul. RNA concentrations above 200 ng/ul were diluted to this value.

treatment_protocol: Cultures were grown in a growth chamber at 12C, 15C or 18C

tag: deveopmental stage

value: gastrula stage embryo

tag: female

tag: male

tag: replicate

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

value: H

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G45Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade

tag: karnofsky index(%)

tag: tumor localization


title: Sample#G39Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: number of relapses

tag: survival after surgery


title: gastrula 15 degreesBlock_4_CC2_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: Sample#G37Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Male


title: gastrula 15 degreesBlock_4_BC2_15

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: Sample#G41Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G40Blood DNA_STY

description: Hybridized to 250K_Sty

value: Pheripheral blood

value: not applicable


title: Sample#G35Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_4_CA2_18

description: Used

source_name: gastrula 18 degrees

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 15 degreesBlock_4_AB1_15

description: Used


title: gastrula 18 degreesBlock_4_DD1_18

description: Used


title: gastrula 15 degreesBlock_4_CB1_15

description: Used


title: Sample#G34Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 15 degreesBlock_4_CD1_15

description: Used


title: Sample#G57Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 15 degreesBlock_4_CC1_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: gastrula 18 degreesBlock_4_BA1_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

value: G


title: Sample#G41Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_4_BA1_15

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 15 degreesBlock_4_AA1_15

description: Used


title: gastrula 15 degreesBlock_4_BC1_15

description: Used


title: gastrula 15 degreesBlock_4_DD1_15

description: Used


title: Sample#G31Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade

value: Frontal


title: Sample#G31Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 15 degreesBlock_4_BB2_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: Sample#G34Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Temporal


title: Sample#G37Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_4_DB1_15

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: gastrula 15 degreesBlock_4_DB2_15

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G35Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 15 degreesBlock_4_CB2_15

description: Used


title: gastrula 15 degreesBlock_4_CA1_15

description: Used


title: gastrula 15 degreesBlock_4_BD2_15

description: Used


title: gastrula 15 degreesBlock_4_AD1_15

description: Used


title: gastrula 15 degreesBlock_4_AB2_15

description: Used


title: gastrula 15 degreesBlock_4_DD2_15

description: Used


title: gastrula 15 degreesBlock_4_BA2_15

description: Used

value: F


title: Sample#G25Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 15 degreesBlock_4_BD1_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: gastrula 15 degreesBlock_4_DA1_15

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: Sample#G30Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_4_AC1_15

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G29Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade

value: Parietal


title: gastrula 15 degreesBlock_4_AA2_15

description: Used


title: gastrula 15 degreesBlock_4_DC2_15

description: Used


title: gastrula 15 degreesBlock_4_AC2_15

description: Used


title: Sample#G23Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 15 degreesBlock_4_DC1_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: gastrula 15 degreesBlock_4_AD2_15

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: gastrula 18 degreesBlock_4_AC1_18

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G30Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 18 degreesBlock_4_BC2_18

description: Used


title: gastrula 15 degreesBlock_4_CA2_15

description: Used


title: gastrula 18 degreesBlock_4_AA1_18

description: Used

value: E


title: Sample#G17Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_4_BD2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: Sample#G29Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G17Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#G13Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G15Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G25Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_4_AB1_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: Sample#G13Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_4_DA2_18

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G14Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: Sample#G10Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_4_BA2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: gastrula 18 degreesBlock_4_DC1_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: gastrula 18 degreesBlock_4_CA1_18

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_4_DB1_18

description: Used


title: gastrula 18 degreesBlock_4_AC2_18

description: Used


title: Sample#G23Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 15 degreesBlock_4_DA2_15

description: Used

value: D


title: gastrula 18 degreesBlock_4_CC2_18

description: Used


title: gastrula 18 degreesBlock_4_BB2_18

description: Used


title: gastrula 18 degreesBlock_4_DA1_18

description: Used


title: gastrula 18 degreesBlock_4_AA2_18

description: Used


title: Sample#G12Blood DNA_STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_4_DB2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: Sample#G10Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_4_AB2_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: gastrula 18 degreesBlock_4_CB1_18

description: Used

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_4_DC2_18

description: Used


title: Sample#G15Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 18 degreesBlock_4_BD1_18

description: Used


title: Sample#G12Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_4_AD1_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: Sample#G8Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#50 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tumor

value: Meningioma tumor

tag: who grade

value: II


title: Sample#50 Blood DNA_STY

description: Hybridized to 250K_Sty

value: Not applicable


title: Sample#G6Blood DNA_STY

description: Hybridized to 250K_Sty

value: Female


title: gastrula 18 degreesBlock_4_BC1_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column


title: Sample#G14Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tissue

tag: age

tag: gender

tag: grade


title: gastrula 18 degreesBlock_4_DD2_18

description: Used

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_4_CD1_18

description: Used

tag: deveopmental stage

tag: female


title: gastrula 18 degreesBlock_4_BB1_18

description: Used

tag: male

tag: replicate

value: C


title: Sample#48 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tumor

tag: who grade


title: gastrula 18 degreesBlock_4_CD2_18

description: Used

value: gastrula stage embryo

tag: block

tag: temperature ©


title: gastrula 18 degreesBlock_4_AD2_18

description: Used

tag: sampling,time

tag: dasl,plate


title: Sample#G6Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Glioblastoma tissue

value: IV

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_4_CB2_18

description: Used

tag: dasl,plate,row

tag: dasl,plate,column


title: Sample#49 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: age

tag: gender

value: Male

value: I


title: gastrula 12 degreesBlock_4_AA1_12

description: Used

source_name: gastrula 12 degrees

tag: deveopmental stage

tag: female

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 12 degreesBlock_4_AA2_12

description: Used

tag: male

tag: replicate


title: gastrula 12 degreesBlock_4_DC1_12

description: Used

tag: block

tag: temperature ©


title: gastrula 12 degreesBlock_4_CB1_12

description: Used

tag: sampling,time

tag: dasl,plate


title: Sample#47 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

value: Pheripheral blood

tag: who grade


title: Sample#G8Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tissue

tag: grade

value: not applicable

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: Sample#49 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: age

tag: gender


title: gastrula 12 degreesBlock_4_BC2_12

description: Used

tag: deveopmental stage

tag: female

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_4_CC1_18

description: Used

tag: male

tag: replicate

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: gastrula 12 degreesBlock_4_DD2_12

description: Used


title: gastrula 12 degreesBlock_4_AC1_12

description: Used


title: Sample#48 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: who grade


title: gastrula 12 degreesBlock_4_CC2_12

description: Used


title: Sample#47 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_CA1_12

description: Used

value: B


title: Sample#42 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#46 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_AD1_12

description: Used


title: gastrula 12 degreesBlock_4_DB1_12

description: Used


title: Sample#42 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#43 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#44 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: III


title: Sample#43 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_AB2_12

description: Used


title: Sample#40 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#44 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#46 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#45 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#45 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_BD1_12

description: Used


title: gastrula 12 degreesBlock_4_BA2_12

description: Used


title: gastrula 12 degreesBlock_4_CB2_12

description: Used


title: gastrula 12 degreesBlock_4_CD1_12

description: Used


title: Sample#39 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#39 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#41 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_BB2_12

description: Used


title: Sample#38 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_DB2_12

description: Used


title: gastrula 12 degreesBlock_4_AD2_12

description: Used


title: gastrula 12 degreesBlock_4_DA1_12

description: Used

value: A


title: Sample#37 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#37 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_AB1_12

description: Used


title: Sample#36 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_CA2_12

description: Used


title: gastrula 12 degreesBlock_4_BD2_12

description: Used


title: Sample#38 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#40 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#36 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_CC1_12

description: Used


title: gastrula 12 degreesBlock_4_AC2_12

description: Used


title: Sample#35 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_DC2_12

description: Used


title: gastrula 12 degreesBlock_4_DA2_12

description: Used


title: gastrula 12 degreesBlock_4_CD2_12

description: Used


title: gastrula 12 degreesBlock_4_DD1_12

description: Used


title: Sample#34 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_BC1_12

description: Used


title: Sample#41 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#31 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_BA1_12

description: Used


title: gastrula 15 degreesBlock_3_BC2_15

description: Used

value: H


title: gastrula 15 degreesBlock_3_AB1_15

description: Used


title: gastrula 18 degreesBlock_3_AD2_18

description: Used


title: Sample#30 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 12 degreesBlock_4_BB1_12

description: Used


title: Sample#35 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#31 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#32 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_BB1_15

description: Used


title: Sample#32 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#29 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_AD2_15

description: Used


title: gastrula 15 degreesBlock_3_CC2_15

description: Used


title: Sample#28 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#28 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_DA2_15

description: Used


title: Sample#26 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#25 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#30 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_CA2_15

description: Used


title: Sample#24 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_DC2_15

description: Used


title: Sample#33 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_AC2_15

description: Used


title: Sample#27 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#29 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_3_BB1_18

description: Used

value: G


title: Sample#25 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_AA2_15

description: Used


title: gastrula 15 degreesBlock_3_DC1_15

description: Used


title: Sample#24 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_AC1_15

description: Used


title: gastrula 15 degreesBlock_3_CD1_15

description: Used


title: gastrula 15 degreesBlock_3_BD1_15

description: Used


title: 80112_megagametophyte#44_532

city: Quebec

first: Jukka-Pekka

last: Verta

state: QC

address: 1030 Avenue de la Medecine, Pavillon Charles-Eugene-Marchand, bureau 2225

department: Department of Wood and Forest Sciences

institute: Centre for Forest Research

description: FLAG column defines whether spot had normal (1) or abnormal (0) morphology.

hyb_protocol: Each microarray was hybridized with two random samples labelled with different dyes. The samples to be hybridized to a microarray were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed with the PowerScanner (Tecan) microarray scanner at 5 micron resolution and image analysis was carried out using ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA).

data_processing: The data analyses were carried out on data (trimmed spot intensity means) from the two channels separately. An RGList object was built for each replicate sample set (i.e. analysis channel) with Limma (G. K. Smyth, Bioinformatics and Computational Biology Solutions using R and Bioconductor, Springer [New York] [2005]) in the R statistical environment (R. Ihaka & R. Gentleman, J Comp Graph Stat 5, 299 [1996]). These single color microarray fluorescence data were then background-corrected and normalized using the normexp and quantile -methods.

molecule: polyA RNA

organism: Picea glauca

source_name: Megagametophyte

label_protocol: The mRNA (9 ng) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 and 647 dyes (Invitrogen, Carlsbad, CA, USA), one for each replicated sample set, and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: The seed materials were obtained from Canadian Forest Service (CFS) seed bank in Quebec City, Canada (Dr J. Beaulieu). These seed lots were from a single tree and each seed lot was collected in a single year. The mother trees used in this study (77111 and 80112) correspond to trees studied by Pelgas et al. (BMC Genomics 12, 145 [2011]). Before stratification, the seeds were surface sterilized with 70% EtOH (1 min) and 3% Na-hypochlorite (10 min), rinsing the seeds three times with sterilized water between and after treatments. The seeds were stratified by immersing them in cold (4° Celsius) sterile water for 24 hours, followed by storage in 4° Celsius for 28 days. The germination process was then started by incubating the stratified seeds in 26° Celsius in the dark for four hours.

extract_protocol: The megagametophytes were dissected from the rest of the seeds under a dissecting microscope, separated in two halves of equal size, flash frozen on liquid nitrogen and store at -80 Celsius until used for RNA extraction. Megametophyte tissues were ground using a pestle in liquid nitrogen and mRNA was isolated using the Dynabeads mRNA Mikro kit (Dynal/Invitrogen, Oslo, Norway) following manufacturers instructions.The mRNA quality and concentration were determined with mRNA Pico assays (Agilent Technologies Inc., Santa Clara, CA, USA) on Agilent BioAnalyzer.

tag: tissue

value: Megagametophyte

tag: tree number


title: gastrula 15 degreesBlock_3_DA1_15

description: Used


title: 80112_megagametophyte#37_532


title: Sample#23 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Meningioma tumor

tag: age

tag: gender


title: Sample#22 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#78_532


title: Sample#27 Blood DNA_STY

description: Hybridized to 250K_Sty

value: Not applicable


title: gastrula 15 degreesBlock_3_BA2_15

description: Used

tag: deveopmental stage

tag: female


title: Sample#23 Blood DNA_STY

description: Hybridized to 250K_Sty

value: Female


title: 80112_megagametophyte#59_532


title: Sample#26 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#20 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#19 Blood DNA_STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#57_532


title: gastrula 15 degreesBlock_3_CB2_15

description: Used

tag: dasl,plate,row

tag: dasl,plate,column


title: gastrula 15 degreesBlock_3_DB1_15

description: Used

tag: culture,stage,mean

tag: culture,stage,sd


title: 80112_megagametophyte#71_532


title: Sample#20 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#33 Blood DNA_STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#79_532


title: gastrula 15 degreesBlock_3_BD2_15

description: Used

tag: male

tag: replicate


title: Sample#19 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_AB2_15

description: Used

tag: block

tag: temperature ©


title: Sample#34 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#22 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#17 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: II


title: Sample#18 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#64_532


title: gastrula 15 degreesBlock_3_DB2_15

description: Used

value: gastrula stage embryo

tag: sampling,time

tag: dasl,plate

value: F


title: 80112_megagametophyte#67_532


title: 80112_megagametophyte#51_532


title: Sample#18 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: who grade


title: Sample#21 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_DD2_15

description: Used


title: gastrula 15 degreesBlock_3_BB2_15

description: Used


title: 80112_megagametophyte#58_532

tag: tissue

tag: tree number


title: Sample#17 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: age

tag: gender


title: Sample#15 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#21 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#15 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#16 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#14 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_DD1_15

description: Used

tag: deveopmental stage

tag: female


title: 80112_megagametophyte#53_532


title: 80112_megagametophyte#74_532


title: gastrula 15 degreesBlock_3_AD1_15

description: Used

tag: dasl,plate,row

tag: dasl,plate,column


title: gastrula 15 degreesBlock_3_BA1_15

description: Used

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 15 degreesBlock_3_CA1_15

description: Used

tag: male

tag: replicate


title: Sample#13 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_CD2_15

description: Used

tag: block

tag: temperature ©


title: 80112_megagametophyte#65_532


title: Sample#13 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: Sample#12 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#80_532


title: gastrula 15 degreesBlock_3_AA1_15

description: Used

tag: sampling,time

tag: dasl,plate


title: Sample#G97Blood DNA SNP_6.0

description: Hybridize to Genome-Wide Human SNP 6.0 Array

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: 80112_megagametophyte#48_532

tag: tissue

tag: tree number


title: Sample#11 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tumor

tag: age

tag: gender

tag: who grade


title: Sample#14 Blood DNA_STY

description: Hybridized to 250K_Sty


title: gastrula 15 degreesBlock_3_CC1_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#12 Blood DNA_STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#39_532


title: Sample#G97Tumor DNA SNP_6.0

value: Glioblastoma tissue

tag: grade

value: IV

tag: karnofsky index(%)

value: Temporal


title: gastrula 15 degreesBlock_3_BC1_15

description: Used

tag: replicate

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate


title: 80112_megagametophyte#73_532

tag: tissue

tag: tree number


title: Sample#16 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

value: Pheripheral blood

tag: age

tag: gender

tag: who grade


title: gastrula 15 degreesBlock_3_CB1_15

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: dasl,plate,row


title: Sample#10 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#9 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: I


title: 80112_megagametophyte#71_635


title: 80112_megagametophyte#51_635


title: Sample#11 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G93Tumor DNA SNP_6.0

value: Male

tag: grade

tag: tumor localization

value: Occipital

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_3_DA2_18

description: Used

tag: replicate

tag: block

tag: temperature ©

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G94Blood DNA SNP_6.0

tag: tissue

tag: age

value: not applicable

tag: karnofsky index(%)


title: Sample#G94Tumor DNA SNP_6.0

tag: gender


title: 80112_megagametophyte#58_635

tag: tree number


title: 80112_megagametophyte#37_635


title: gastrula 18 degreesBlock_3_DD1_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: sampling,time

tag: dasl,plate

value: E


title: Sample#10 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tumor

tag: who grade


title: Sample#9 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G92RTumor DNA SNP_6.0

value: Relapsed Glioblastoma Tissue

tag: grade

tag: tumor localization

value: Parietal

tag: number of relapses

tag: survival after surgery


title: Sample#G93Blood DNA SNP_6.0


title: gastrula 18 degreesBlock_3_DC1_18

description: Used

tag: replicate

tag: block

tag: temperature ©

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_3_AB1_18

description: Used

tag: deveopmental stage

tag: female


title: Sample#8 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Meningioma tumor

tag: age

tag: gender


title: Sample#8 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

value: Not applicable


title: gastrula 18 degreesBlock_3_BA2_18

description: Used

tag: male

tag: sampling,time

tag: dasl,plate


title: Sample#6 Tumor DNA _STY

description: Hybridized to 250K_Sty

value: Female

tag: who grade


title: 80112_megagametophyte#64_635

tag: tissue

value: Megagametophyte

tag: tree number


title: Sample#7 Blood DNA_STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#44_635


title: 80112_megagametophyte#59_635


title: gastrula 18 degreesBlock_3_AC1_18

description: Used

value: gastrula stage embryo

tag: replicate

tag: block


title: Sample#G92RBlood DNA SNP_6.0

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: Sample#7 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_3_BC2_18

description: Used

tag: deveopmental stage

tag: female

tag: temperature ©

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G91Tumor DNA SNP_6.0

tag: age

tag: gender


title: gastrula 18 degreesBlock_3_DB1_18

description: Used

tag: male

tag: sampling,time

tag: dasl,plate


title: Sample#G91Blood DNA SNP_6.0

tag: tissue

tag: grade


title: Sample#G92Tumor DNA SNP_6.0

tag: karnofsky index(%)

tag: tumor localization


title: 80112_megagametophyte#79_635

tag: tree number


title: Sample#G92Blood DNA SNP_6.0

tag: number of relapses

tag: survival after surgery


title: 80112_megagametophyte#48_635


title: gastrula 18 degreesBlock_3_BD2_18

description: Used

tag: deveopmental stage

tag: female

tag: replicate

tag: block

tag: temperature ©


title: Sample#6 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: age

tag: who grade


title: gastrula 18 degreesBlock_3_BA1_18

description: Used

tag: male

tag: sampling,time

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: 80112_megagametophyte#57_635

tag: tissue

tag: tree number


title: gastrula 18 degreesBlock_3_CA1_18

description: Used

tag: dasl,plate


title: Sample#G90Tumor DNA SNP_6.0

tag: gender

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: Sample#5 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: age


title: Sample#4 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: who grade


title: Sample#G89Tumor DNA SNP_6.0


title: 80112_megagametophyte#73_635


title: 80112_megagametophyte#80_635


title: Sample#4 Blood DNA_STY

description: Hybridized to 250K_Sty


title: Sample#G90Blood DNA SNP_6.0


title: 80112_megagametophyte#53_635


title: Sample#2 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: gastrula 18 degreesBlock_3_CC2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: block

tag: temperature ©

tag: sampling,time


title: Sample#3 Tumor DNA _STY

description: Hybridized to 250K_Sty


title: 80112_megagametophyte#78_635

tag: tissue

tag: tree number


title: gastrula 18 degreesBlock_3_DA1_18

description: Used

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#3 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: gender


title: 80112_megagametophyte#39_635


title: Sample#G89Blood DNA SNP_6.0

tag: age

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: gastrula 18 degreesBlock_3_CB2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: block

tag: temperature ©

value: D


title: Sample#5 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: who grade


title: Sample#G88Tumor DNA SNP_6.0

tag: tissue

value: Glioblastoma tissue


title: 80112_megagametophyte#67_635

tag: tree number


title: 80112_megagametophyte#74_635


title: gastrula 18 degreesBlock_3_AA2_18

description: Used

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Sample#G87Tumor DNA SNP_6.0

tag: age

tag: gender

tag: grade

value: IV

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses


title: Sample#2 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor


title: 80112_megagametophyte#65_635


title: gastrula 18 degreesBlock_3_DB2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: block

tag: temperature ©


title: gastrula 18 degreesBlock_3_BB2_18

description: Used

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row


title: 77111_megagametophyte#58_532

tag: tissue

tag: tree number


title: 77111_megagametophyte#69_532


title: gastrula 18 degreesBlock_3_CB1_18

description: Used

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 18 degreesBlock_3_AC2_18

description: Used


title: 77111_megagametophyte#65_532


title: gastrula 18 degreesBlock_3_BD1_18

description: Used


title: Sample#G88Blood DNA SNP_6.0

tag: age

tag: gender

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: survival after surgery


title: Sample#1 Tumor DNA _STY

description: Hybridized to 250K_Sty

tag: tumor

tag: who grade


title: gastrula 18 degreesBlock_3_DC2_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: block

tag: temperature ©


title: Patient_32

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

country: Germany

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

description: Gene expression in peripheral blood, conservation of RNA with PAXGENE system

hyb_protocol: Hybridization was performed with 1.65 µg of labeled cDNA per array at a temperature of 65°C overnight.

scan_protocol: An Agilent G2565CA DNA microarray scanner was used to scan the arrays at a resolution of 5 µm. The Feature Extraction Software 9.5.3.1 was then used to process and analyze array images. The software returns a series of spot quality measures to evaluate the quality and reliability of spot intensity estimates.

data_processing: The raw data were analyzed using GeneSpring GX 10.0 (normalization: shift to 75.0 percentile, baseline transformation: median of all samples). The normalized data were filtered to exclude probes flagged absent in all samples. The remaining probes were tested for statistical significance of expression using a two sample t-test (unpaired) with an asymptotic p-value computation and a p-value cut-off of 0.05. Multiple testing correction was performed by controlling the false discovery rate (FDR) according to Benjamini-Hochberg with a FDR cut-off of 0.05. The cut off for the fold change (FC) was FC=2 (1 log2) up- or down-regulation.

source_name: Peripheral Blood, Patient 32

label_protocol: Sample labeling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Briefly, for the hybridization of the microarrays, 0.5 µg of total RNA was reverse transcribed into cDNA and labeled with Cy3 using the one-color Quick Amp Labeling Kit (Agilent).

extract_protocol: At the time of sampling, blood was collected for routine clinical laboratory values as well as in PAXGENE tubes (Preanalytix) for RNA preservation. RNA was isolated by the use of the Quiagen RNeasy mini kit as directed by the manufacturer including DNase treatment. Before gene expression analysis, RNA concentration was determined using a UV-Vis spectrophotometer NanoDrop® ND-1000 (NanoDrop Technologies, Wilmington, USA). RNA integrity and quality was then estimated on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and RNA integrity number (RIN) index was calculated for each sample using the Agilent 2100 Expert software. RIN provides a numerical assessment of the integrity of RNA that facilitates the standardization of the quality interpretation; for microarray processing, only RNAs with RIN number >8.0 were further processed to reduce experimental biases due to poor RNA quality.

tag: tissue

value: whole blood

tag: group

value: Progression


title: Patient_31

source_name: Peripheral Blood, Patient 31

value: Stable


title: 77111_megagametophyte#39_532

tag: tree number


title: Sample#G83Blood DNA SNP_6.0

value: Pheripheral blood

tag: age

value: Male

tag: number of relapses


title: gastrula 18 degreesBlock_3_AB2_18

description: Used

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean

tag: culture,stage,sd


title: Patient_30

source_name: Peripheral Blood, Patient 30


title: Sample#1 Blood DNA_STY

description: Hybridized to 250K_Sty

tag: tumor

tag: gender

tag: who grade


title: gastrula 18 degreesBlock_3_AD1_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate


title: 77111_megagametophyte#72_532

tag: tissue


title: Sample#G82Tumor DNA SNP_6.0

tag: grade

tag: karnofsky index(%)

tag: tumor localization

value: Frontal

tag: survival after surgery


title: 77111_megagametophyte#51_532

tag: tree number


title: Sample#G87Blood DNA SNP_6.0

tag: age

value: not applicable

tag: number of relapses


title: gastrula 18 degreesBlock_3_CC1_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column

tag: culture,stage,mean


title: Patient_28

source_name: Peripheral Blood, Patient 28

tag: group


title: Sample#G83Tumor DNA SNP_6.0

tag: gender

value: Temporal


title: Sample#G81Tumor DNA SNP_6.0

tag: tissue


title: 77111_megagametophyte#68_532


title: Patient_27

source_name: Peripheral Blood, Patient 27


title: gastrula 18 degreesBlock_3_CD1_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: culture,stage,sd


title: gastrula 18 degreesBlock_3_DD2_18

description: Used


title: 77111_megagametophyte#57_532

tag: tree number


title: gastrula 18 degreesBlock_3_AA1_18

description: Used

value: C


title: Patient_29

source_name: Peripheral Blood, Patient 29


title: Patient_26

source_name: Peripheral Blood, Patient 26


title: Sample#G82Blood DNA SNP_6.0

tag: age

tag: grade

tag: karnofsky index(%)

tag: tumor localization

tag: number of relapses

tag: survival after surgery


title: 77111_megagametophyte#53_532


title: Sample#G81Blood DNA SNP_6.0


title: 77111_megagametophyte#42_532


title: Sample#G80RTumor DNA SNP_6.0

value: Relapsed Glioblastoma tissue


title: gastrula 18 degreesBlock_3_CD2_18

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column


title: 77111_megagametophyte#55_532

tag: tissue


title: Patient_25

source_name: Peripheral Blood, Patient 25

tag: group


title: 77111_megagametophyte#46_532


title: Patient_22

source_name: Peripheral Blood, Patient 22


title: gastrula 18 degreesBlock_3_BC1_18

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: culture,stage,mean


title: gastrula 18 degreesBlock_3_CA2_18

description: Used

tag: culture,stage,sd


title: Patient_23

source_name: Peripheral Blood, Patient 23


title: Sample#G80RBlood DNA SNP_6.0

tag: age

tag: gender

tag: grade

tag: karnofsky index(%)

tag: tumor localization


title: Sample#G80Tumor DNA SNP_6.0

source_name: GBM tumor

tag: number of relapses

tag: survival after surgery


title: 77111_megagametophyte#56_532

tag: tree number


title: Patient_24

source_name: Peripheral Blood, Patient 24


title: gastrula 12 degreesBlock_3_AA2_12

description: Used

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row

tag: dasl,plate,column


title: Patient_21

source_name: Peripheral Blood, Patient 21

tag: tissue

tag: group


title: gastrula 12 degreesBlock_3_DC1_12

description: Used

tag: deveopmental stage

tag: female

tag: male

tag: replicate

tag: culture,stage,mean

tag: culture,stage,sd


title: gastrula 12 degreesBlock_3_AA1_12

description: Used


title: 77111_megagametophyte#41_532


title: Patient_20

source_name: Peripheral Blood, Patient 20


title: 77111_megagametophyte#47_532


title: Sample#G73Tumor DNA SNP_6.0

tag: age

tag: gender

tag: grade

tag: karnofsky index(%)

tag: tumor localization

value: Parietal

tag: number of relapses


title: Patient_19

source_name: Peripheral Blood, Patient 19


title: Patient_18

source_name: Peripheral Blood, Patient 18


title: Sample#G73Blood DNA SNP_6.0

source_name: Peripheral blood

value: Female

tag: survival after surgery


title: gastrula 12 degreesBlock_3_CB1_12

description: Used

source_name: gastrula 12 degrees

tag: block

tag: temperature ©

tag: sampling,time

tag: dasl,plate

tag: dasl,plate,row


title: Sample#G72Tumor DNA SNP_6.0

tag: tissue


title: Sample#G79Tumor DNA SNP_6.0

value: Occipital