title: 254706910071_b1 - T-24h_1 vs CMB+SiO2-24h_1

hyb_protocol: CMB+SiO2-24h_1 Cy5 / T-24h_1 Cy3 : 20pmol. (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: E11.5_placenta_mRNA_WT_rep3

status: Public on Feb 01 2017

type: RNA

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate3

hyb_protocol: For miRNA analysis, Cy3-labeled RNAs was hybridized with the miRNA Complete Labeling Reagent and Hyb Kit onto mouse miRNA Microarray rel.17.0 (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions. For mRNA analysis, 0.6ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized onto SurePrint G3 Mouse GE microarray 8x60K (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Scanning of microarray slides was performed with a DNA microarray scanner at 3 um resolution (Agilent Technologies).

data_processing: Scanned image files were processed to give signal intensities using Feature Extraction software (Agilent Technologies). All raw data were loaded into GeneSpring GX 12.5 software (Agilent Technologies) and normalized using default settings.

molecule: total RNA

organism: Mus musculus

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, wildtype, replicate3

label_protocol: For miRNA analysis, total RNA from placentas was labeled with the miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies). For mRNA analysis, total RNAs were labeled with a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: In vitro-fertilized embryos derived from wild-type and miRNA-deleted mice were cultured in KSOM medium at 37°C for 16 hours. Cultured embryos were transferred into pseudopregnant ICR females and E11.5 embryos were retrieved from the uterus.

extract_protocol: Placentas with deciduas removed were lysed and the total and miRNA isolated using a mirVana miRNA isolation kit (Themo Fisher Scientific).

tag: tissue

value: placenta

tag: embryonic day

tag: genotype

value: wildtype


title: 549628A06 - FEWWB1_1 vs FEWSB1_1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description:
harvest date:03-02-13
harvest date:03-02-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWSB1_1 Cy5 / FEWWB1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

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

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Lathyrus oleraceus

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: caulin leaf - Growth conditions (1-2-3-4):1. Media: perlite:sand (vol:vol 3:1) - hygrometry: 50% - Temperature: 15°C night; 18°C day -  Light: 16h photoper

treatment_protocol: Name:Water stressed - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 50percent .

value: mutant (CAMEOR)

value: leaf

treatment_protocol: Name:Well Watered - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 100percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.


title: E11.5_placenta_mRNA_WT_rep4

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate4

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, wildtype, replicate4


title: 254706910070_b3 - T-24h_2 vs CMB-SiO2-24h_2

description: Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication.

hyb_protocol: CMB-SiO2-24h_2 Cy5 / T-24h_2 Cy3 : 20pmol. (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,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

organism: Arabidopsis thaliana

growth_protocol: cell culture/primary cell - Media: Liquid growth medium (Axelos et al., 1992) Temperature: 24°C Light: 50 µE m–2 s–1

treatment_protocol: Name:CMB-SiO2 - compound based treatment - compound addition,nanoparticules (mg/l):quantity 100 time 24hour .  Cell cultures of Arabidopsis thaliana (ecotype Col-0) were maintained in 200 ml of culture medium (Axelos et al., 1992), under sterile conditions at 24 ° C under agitation (120 rpm). To study the impact of nanoparticles, this treatment was applied for 24h to A. thaliana cells 9 days after subculture: (iii) CS: CMB@SiO2 nanoparticles at 100 mg / L.

tag: ecotype

value: Columbia

tag: harvest date

tag: treatment

value: CS:CMB@SiO2 nanoparticles at 100 mg / L.

extract_protocol: T-24h_2:400mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: no treatment


title: E11.5_placenta_mRNA_WT_rep2

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate2

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, wildtype, replicate2


title: 549628A05 - FEWSB1_1 vs FEWWB1_1

hyb_protocol: FEWWB1_1 Cy5 / FEWSB1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_post_XD0087_rep1

city: London

first: Thalia

last: Eley

address: DeCrespigny Park, Denmark Hill

department: SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience

country: United Kingdom

institute: King's College London

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Stringent quality control processing of the data was conducted using standardised procedures from internal pipelines (available at https://github.com/snewhouse/BRC_MH_Bioinformatics). Expression data was background corrected using Module-based Background Correction for Beadarray (Ding et al., 2008). Probes were then filtered by selecting probes with expression levels >2SD greater than the mean intensity of the negative control (background) beads. Reported gender was compared to XIST gene expression (female specific) and Y chromosome gene expression (male specific). Each probe was then transformed and normalised using log2 transformation and Robust-Spline Normalisation (Schmid et al., 2010, Du et al., 2008). Sample relationships within the co-expression network were assessed and outliers were removed (Oldham et al., 2012).

label: biotin

organism: Homo sapiens

source_name: Human, Whole Blood, post-therapy

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina Sentrix Arrays.

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

tag: gender

value: FEMALE

value: Blood

tag: timepoint

value: post


title: 254706910078_b4 - 9_LT3 vs 11_OT3

description: Does light regulates germination via polysome association ?

hyb_protocol: 11_OT3 Cy5 / 9_LT3 Cy3 : 20pmol. (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.

growth_protocol: seed - Media:Petri dishes (coton+filter paper) imbibition 20h Temperature: 22°C Light: dark

treatment_protocol: Name:Darkness - environmental treatment - light,light:time 20hour . The seeds are placed on water for 20h at 22°C in darkness

tag: developmental stage (boyes et al. plant cell 2001)

value: Darkness

treatment_protocol: Name:Light - environmental treatment - light,light:time 20hour . The seeds are placed on water for 20h at 22°C in light

value: Light


title: Blood_pre_XD0087_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy

value: pre


title: 549628A02 - FEWWA3_3 vs FEWSB3_3

description:
harvest date:03-02-13
harvest date:27-01-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWSB3_3 Cy5 / FEWWA3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E11.5_placenta_mRNA_WT_rep1

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate1

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, wildtype, replicate1


title: 254706910078_b2 - 5_LT2 vs 7_OT2

hyb_protocol: 7_OT2 Cy5 / 5_LT2 Cy3 : 20pmol. (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: 254706910070_b4 - CMB-SiO2-24h_2 vs T-24h_2

hyb_protocol: T-24h_2 Cy5 / CMB-SiO2-24h_2 Cy3 : 20pmol. (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: 549628A03 - FEWSB4_4 vs FEWWA4_4

description:
harvest date:27-01-13
harvest date:03-02-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWWA4_4 Cy5 / FEWSB4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 254706910078_b3 - 11_OT3 vs 9_LT3

hyb_protocol: 9_LT3 Cy5 / 11_OT3 Cy3 : 20pmol. (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: 549628A04 - FEWWA4_4 vs FEWSB4_4

hyb_protocol: FEWSB4_4 Cy5 / FEWWA4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_fu_XD0081_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: 549628A01 - FEWSB3_3 vs FEWWA3_3

hyb_protocol: FEWWA3_3 Cy5 / FEWSB3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_post_XD0081_rep1

description: QC ok


title: 254706910070_b2 - CMB-SiO2-24h_1 vs T-24h_1

hyb_protocol: T-24h_1 Cy5 / CMB-SiO2-24h_1 Cy3 : 20pmol. (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.

extract_protocol: T-24h_1:400mg. (Qiagen_RNeasy.pdf)


title: 254706910078_b1 - 7_OT2 vs 5_LT2

hyb_protocol: 5_LT2 Cy5 / 7_OT2 Cy3 : 20pmol. (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: 254706910070_b1 - T-24h_1 vs CMB-SiO2-24h_1

hyb_protocol: CMB-SiO2-24h_1 Cy5 / T-24h_1 Cy3 : 20pmol. (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: Blood_pre_XD0081_rep1

description: QC ok


title: Blood_fu_XD0078_rep1

description: QC ok

value: MALE


title: Blood_post_XD0078_rep1

description: QC ok


title: Muscle_pHup_16

city: Nouzilly

first: Cécile

last: Berri

address: Centre INRA Val de Loire

institute: INRA

description: Chickens issued from the 6th generation of an experimental divergent selection on the Pectoralis major muscle ultimate pH (measured 24h postmortem)

hyb_protocol: Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent). A total of 31 samples were analysed, corresponding to 4 slides. 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/μg of cRNA) were fragmented at 60°C for 30 minutes following the manufacturer’s instructions. Subsequently,  Agilent Hybridization Buffer was added to the fragmentation mixture and hybridized to the arrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed according to the manufacturer’s recommendations.

scan_protocol: The slides were scanned on Agilent G2565CA Scanner System using one color scan setting for 8x60k array slide with a resolution of 3μm and a dynamic range of 20 bits.

data_processing: The .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE2_107_Sep09 protocol to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: Pectoralis major muscle, sampled 15 min postmortem

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared using 200ng of total RNA using the One-Color Low Imput Quick Amp Labeling kit (Agilent) following the recommended protocol. Specific activities and cRNA yields were determined using the NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: Chickens issued from the 6th generation of divergent selection on Pectoralis major ultimate pH were reared in standard conditions until 6 weeks of age at INRA UE1295 PEAT (Nouzilly, France)

extract_protocol: Total RNA was extracted from Pectoralis major muscle sampled at 15 min post-mortem using the Qiagen RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions.

tag: genetic line

value: pHu+

value: Male

tag: age

value: 6 weeks

value: Pectoralis major muscle

tag: nutritional status

value: unfed during 8h before slaughter


title: Blood_pre_XD0078_rep1

description: QC ok


title: Muscle_pHup_12


title: 254706910045_b3 - 3_OT1 vs 1_LT1

hyb_protocol: 1_LT1 Cy5 / 3_OT1 Cy3 : 20pmol. (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: 254706910045_b4 - 1_LT1 vs 3_OT1

hyb_protocol: 3_OT1 Cy5 / 1_LT1 Cy3 : 20pmol. (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: Blood_fu_XD0072_rep1

description: QC ok


title: Blood_fu_XD0087_rep1

description: QC ok


title: Muscle_pHup_15


title: Blood_post_XD0072_rep1

description: QC ok


title: 254706910045_b1 - 12_OP3 vs 10_LP3

hyb_protocol: 10_LP3 Cy5 / 12_OP3 Cy3 : 20pmol. (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: 254706910044_b4 - 6_LP2 vs 8_OP2

hyb_protocol: 8_OP2 Cy5 / 6_LP2 Cy3 : 20pmol. (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: Muscle_pHup_14


title: Muscle_pHup_10


title: 254706910045_b2 - 10_LP3 vs 12_OP3

hyb_protocol: 12_OP3 Cy5 / 10_LP3 Cy3 : 20pmol. (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: Muscle_pHup_11


title: Blood_pre_XD0072_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol


title: Muscle_pHup_13


title: 254706910044_b3 - 8_OP2 vs 6_LP2

hyb_protocol: 6_LP2 Cy5 / 8_OP2 Cy3 : 20pmol. (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: Muscle_pHup_08


title: Muscle_pHup_09


title: Blood_fu_XD0066_rep1

description: QC ok


title: 254706910044_b1 - 4_OP1 vs 2_LP1

hyb_protocol: 2_LP1 Cy5 / 4_OP1 Cy3 : 20pmol. (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: Muscle_pHup_07


title: 254706910044_b2 - 2_LP1 vs 4_OP1

hyb_protocol: 4_OP1 Cy5 / 2_LP1 Cy3 : 20pmol. (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: Muscle_pHup_06


title: Blood_post_XD0066_rep1

description: QC ok


title: Blood_pre_XD0066_rep1

description: QC ok


title: Blood_post_XD0062_rep1

description: QC ok


title: Muscle_pHup_04


title: Blood_fu_XD0062_rep1

description: QC ok


title: Muscle_pHup_05


title: 254706910038_b3 - R424_2 vs. R524_2

description: Observation of the effects of the product Tn on the expression of genes of Arabidopsis thaliana related to nutrition and development.

hyb_protocol: R524_2 Cy5 / R424_2 Cy3 : 20pmol. (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, Cy3:532nm,pmt voltage 650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%.

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

growth_protocol: caulin leaf - Media: treff M8 media. Hygrometry: 80% RH. Temperature: 18° C Day/20°C Night. Light: 16h photoperiod.

extract_protocol: R524_2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name: Elicitor treatment - compound based treatment - elicitor,elicitor. Elicitor treatment by spray.

value: leaf

value: 27.4 days

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:3.70

value: test

tag: time

extract_protocol: R424_2:100mg. (Qiagen_RNeasy.pdf)

value: reference


title: Muscle_pHup_03


title: Blood_pre_XD0062_rep1

description: QC ok

value: FEMALE

value: Blood


title: Muscle_pHup_01


title: 254706910038_b1 - R148_2 vs. R348_2

hyb_protocol: R348_2 Cy5 / R148_2 Cy3 : 20pmol. (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.

extract_protocol: R348_2:100mg. (Qiagen_RNeasy.pdf)

value: Columbia

extract_protocol: R148_2:100mg. (Qiagen_RNeasy.pdf)


title: Muscle_pHum_14

value: pHu-


title: 254706910038_b2 - R348_2 vs. R148_2

hyb_protocol: R148_2 Cy5 / R348_2 Cy3 : 20pmol. (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: Muscle_pHum_13


title: Blood_post_XD0052_rep1

description: QC ok

value: post


title: Muscle_pHum_15


title: Blood_pre_XD0052_rep1

description: QC ok

value: pre


title: Muscle_pHup_02


title: Blood_fu_XD0004_rep1

description: QC ok

value: follow-up


title: Muscle_pHum_12


title: 254706910038_b4 - R524_2 vs. R424_2

hyb_protocol: R424_2 Cy5 / R524_2 Cy3 : 20pmol. (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: Muscle_pHum_11


title: Blood_fu_XD0052_rep1

description: QC ok


title: 254706910047_b2 - M348_1 vs. M148_1

hyb_protocol: M148_1 Cy5 / M348_1 Cy3 : 20pmol. (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.

extract_protocol: M148_1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: M348_1:100mg. (Qiagen_RNeasy.pdf)


title: 254706910046_b3 - R148_2 vs. R248_2

hyb_protocol: R248_2 Cy5 / R148_2 Cy3 : 20pmol. (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.

extract_protocol: R248_2:100mg. (Qiagen_RNeasy.pdf)


title: 254706910047_b1 - M148_1 vs. M348_1

hyb_protocol: M348_1 Cy5 / M148_1 Cy3 : 20pmol. (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: 254706910048_b2 - M524_1 vs. M424_1

hyb_protocol: M424_1 Cy5 / M524_1 Cy3 : 20pmol. (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.

extract_protocol: M424_1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: M524_1:100mg. (Qiagen_RNeasy.pdf)


title: Blood_pre_XD0004_rep1

description: QC ok


title: Blood_post_XD0004_rep1

description: QC ok


title: 254706910046_b4 - R248_2 vs. R148_2

hyb_protocol: R148_2 Cy5 / R248_2 Cy3 : 20pmol. (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: Muscle_pHum_10

hyb_protocol: Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent). A total of 31 samples were analysed, corresponding to 4 slides. 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/μg of cRNA) were fragmented at 60°C for 30 minutes following the manufacturer’s instructions. Subsequently,  Agilent Hybridization Buffer was added to the fragmentation mixture and hybridized to the arrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed according to the manufacturer’s recommendations.


title: 254706910048_b1 - M424_1 vs. M524_1

hyb_protocol: M524_1 Cy5 / M424_1 Cy3 : 20pmol. (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: 254706910046_b2 - M248_1 vs. M148_1

hyb_protocol: M148_1 Cy5 / M248_1 Cy3 : 20pmol. (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.

extract_protocol: M248_1:100mg. (Qiagen_RNeasy.pdf)


title: 254706910046_b1 - M148_1 vs. M248_1

hyb_protocol: M248_1 Cy5 / M148_1 Cy3 : 20pmol. (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: Childhood melanocytic tumor #4

type: genomic

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Copy number alterations and allelic imblances

hyb_protocol: Arrays were hybridized for 16-18 hours, then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 Dx2, controlled by AMDS

data_processing: OncoScan SNP-array data were analyzed by the software couple of OncoScan Console (Affymetrix) and Nexus Express (BioDiscovery) using Affymetrix TuScan algorithm. All array data were also manually reviewed for subtle alterations not automatically called by the software.

molecule: genomic DNA

source_name: spitzoid melanoma of childhood

label_protocol: 80 ng FFPE-DNA was subjected to Annealing - Gap fill --- Linearization - 1st PCR - 2nd PCR – HaeIII digestion, and the fragments from HaeIII digestion were hybridized to arrays with biotinylated oligos which were targets for labeling. Labeling occurs during hybridization.

extract_protocol: DNA was extracted from FFPE tumor tissue using QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's instructions.

value: FFPE tumor tissue

value: NTRK3 intragenic copy number change


title: Muscle_pHum_09

value: Male

value: 6 weeks


title: Blood_pre_XB0109_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

value: MALE


title: Blood_fu_XB0107_rep1

description: QC ok


title: Blood_post_XB0109_rep1

description: QC ok


title: adhE*_Cellobiose_None_3

city: Oak Ridge

first: Jason

last: Whitham

address: 1 Bethel Valley Rd Bld 1505 Rm 366 MS 6038

institute: Oak Ridge National Labs

description: 27 mL Balch Tubes 10mL

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Microarrays were scanned with a SureScan High-Resolution DNA Microarray Scanner (5 μm) (Agilent), and the images were quantified using NimbleScan software (Roche NimbleGen, Madison, WI, USA). Raw data was log2 transformed and Loess normalized in JMP Genomics 5 (SAS Institute Inc., Cary, NC).

organism: Acetivibrio thermocellus DSM 1313

source_name: adhE* Cellobiose None 3

growth_protocol: Ruminiclostridium thermocellum DSM 1313 adhE*(EA) was grown at 55 deg C in 27 ml Balch Tubes (10ml culture volume) in modified CTFUD medium.

extract_protocol: Briefly, samples were centrifuged and total cellular RNA was extracted by the TRIzol reagent (Invitrogen, Carlsbad, CA) and bead beating. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: 0.3 g/L acetate was added to CTFUD medium as a treatment.

tag: strain

value: adhE*(EA)

tag: substrate

value: Cellobiose 5g/L

tag: harvest time (hrs post treatment)


title: Childhood melanocytic tumor #3

source_name: Spitz nevi in a 7-yr child

tag: tissue


title: adhE*_Cellobiose_None_2

description: 27 mL Balch Tubes 10mL

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

source_name: adhE* Cellobiose None 2


title: Muscle_pHum_07

value: Pectoralis major muscle

value: unfed during 8h before slaughter


title: Muscle_pHum_06


title: adhE*_Cellobiose_Acetate_3

description: 27 mL Balch Tubes 10mL

source_name: adhE* Cellobiose Acetate 3

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

value: Acetate 0.3g/L


title: Blood_post_XB0107_rep1

description: QC ok

value: FEMALE


title: adhE*_Cellobiose_Acetate_2

description: 27 mL Balch Tubes 10mL

source_name: adhE* Cellobiose Acetate 2


title: Blood_fu_XB0091_rep1

description: QC ok

value: Blood


title: Blood_pre_XB0107_rep1

description: QC ok


title: Blood_pre_XB0091_rep1

description: QC ok


title: Muscle_pHum_08


title: Blood_post_XB0091_rep1

description: QC ok


title: Muscle_pHum_05


title: adhE*_Cellobiose_None_1

description: 27 mL Balch Tubes 10mL

source_name: adhE* Cellobiose None 1


title: Blood_post_XB0077_rep1

description: QC ok


title: Blood_fu_XB0077_rep1

description: QC ok


title: Muscle_pHum_04


title: Muscle_pHum_02


title: Muscle_pHum_03


title: Blood_pre_XB0077_rep1

description: QC ok


title: adhE*_Cellobiose_Acetate_1

description: 27 mL Balch Tubes 10mL

source_name: adhE* Cellobiose Acetate 1


title: Nephron progenitors replicate #3

city: Pittsburgh

first: Jacqueline

last: Ho

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: Children's Hospital of Pittsburgh

hyb_protocol: Done by Exiqon

scan_protocol: Done by Exiqon

data_processing: The quantified signals were normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm, done by Exiqon

source_name: FACS isolated nephron progenitors at E14 replicate #3

label_protocol: miRCURY Hy3/Hy5 power labeling kit, done by Exiqon

extract_protocol: Total RNA was isolated using the Qiagen miRNeasy kit, as per manufacturer's directions

source_name: Embryonic day 14 kidney

value: Embryonic day 14 whole kidney


title: Childhood melanocytic tumor #2

source_name: Spitz nevi in a 15-yr child


title: Blood_fu_XB0070_rep1

description: QC ok


title: Blood_post_XB0070_rep1

description: QC ok


title: Ziram_rep_4_batch_1_arraySlide_16

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_2_1

hyb_protocol: Samples were hybridized to OakLabs ArrayXS Zebrafish microarrays using the Gene Experssion Hybridization Kit (Agilent)

scan_protocol: Slides were scanned after hybridization using the SureScan Microarray Scanner (Agilent)

data_processing: Scanned images were read and processed using Agilent Feature Extraction software (ver 11) and analzed using limma in R. Data were background corrected using the MLE method and then quantile normalized. Prior to linear modeling and differential expression calculation, control probes and any probe that was less than 10% brighter than the negative control probes on at least four of the arrays were excluded from the analysis. Data preprocessing also showed batch effects due to array slide. We corrected for thi batch effect using the ComBat algorithm prior to linear modeling. The following arrays were removed from analysis due to outlier detection: SG12414235_256950710038_S001_GE1_1105_Oct12_2_2.txt, SG12414235_256950710027_S001_GE1_1105_Oct12_1_4.txt, SG12414235_256950710030_S001_GE1_1105_Oct12_1_2.txt, SG12414235_256950710023_S001_GE1_1105_Oct12_2_4.txt, SG12414235_256950710029_S001_GE1_1105_Oct12_2_4.txt, SG12414235_256950710023_S001_GE1_1105_Oct12_2_2.txt, SG12414235_256950710025_S001_GE1_1105_Oct12_1_3.txt, SG12414235_256950710039_S001_GE1_1105_Oct12_2_3.txt, SG12414235_256950710029_S001_GE1_1105_Oct12_1_1.txt

organism: Danio rerio

source_name: Whole embryo_48 hpf_Ziram

label_protocol: 0.5 ug of Cy3-labeled cRNA was generated using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

extract_protocol: Total RNA was exctracted using the Quick-RNA MiniPrep kit (Zymo Research, Irvine, CA) according to manufacturer's protocols with the optional Dnase I digestion. Whole embryos were homogenized in 300 uL lysis buffer with 0.5 mm zirconium oxide beads using a bullet blender (Next Advance, Averill Park, NY) for 3 min at speed 8.

treatment_protocol: Dechorionated embryos were nominally exposed to statis aqueous concentrations of each chemical or vehicle control (maximum DMSO was 0.64% for all exposures) from 6-48 hpf. Embryos were maintained at 28 °C throughout exposure

value: whole embryo

value: Ziram


title: Ziram_rep_2_batch_1_arraySlide_6

description:
Gene expression after 48 hpf exposure
SG12414235_256950710029_S001_GE1_1105_Oct12_1_3


title: Muscle_pHum_01

value: pHu-


title: Vinclozolin_rep_3_batch_3_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_1_3

source_name: Whole embryo_48 hpf_Vinclozolin

value: Vinclozolin


title: Ziram_rep_3_batch_1_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_1_1


title: AL cells

city: Athens

first: Maria

middle: G

last: Roubelakis

address: Michalakopoulou 176

department: School of Medicine

country: Greece

institute: National and Kapodistrian University of Athens

description: Mesenchymal stem/stromal cells derived from amniotic fluid

hyb_protocol: Conducted by Exiqon. Hybridization Slide 1: AF3+AF9 / Adipo 1+Adipo 2, Hybridization Slide 2: Adipo 1+Adipo 2/ AF3+AF9.

scan_protocol: Conducted by Exiqon

data_processing:
Normalisation means background subtraction and normalisation with a global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
normalized log2 ratio (Hy5/Hy3) representing test/reference

source_name: Adipocyte like cells

label_protocol: The miRCURY™ Hy3™/Hy5™ labelling kit (Exiqon A/S, Vedbaek, Denmark) was used to label the samples

growth_protocol: AF-MSCs: Cells were cultured in DMEM-HG supplemented with 20% fetal bovine serum (FBS), 1% penicillin-streptomycin at 37ºC and 5% of CO2.  AL cells: AF-MSCs were differentiated into adipocyte-like cells (AL cells) using adipogenic medium [40% DMEM-HG, 50% F12, 10% rabbit serum, 10-2μΜ dexamethasone and 0.5 mg/ml insulin. for 21 days.

extract_protocol: Total RNA from 2 AF-MSCs and 2 AL cells samples, respectively were extracted using Trizol reagent according to the manufacturer’s protocol (Invitrogen Ltd., Paisley, Scotland) and further purified with Rneasy Qiamp column

tag: passage

source_name: AF-MSCs


title: AF-MSCs

description: Differentiated mesenchymal stem/stromal cells derived from amniotic fluid to Adipocyte-Like cells

source_name: Amniotic fluid MSCs

source_name: AL cells


title: Blood_pre_XB0070_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

value: pre


title: Ziram_rep_1_batch_1_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_2_1


title: Nephron progenitors replicate #2

source_name: FACS isolated nephron progenitors at E14 replicate #2


title: Nephron progenitors replicate #1

source_name: FACS isolated nephron progenitors at E14 replicate #1


title: Vinclozolin_rep_5_batch_3_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_2_1


title: Blood_post_XB0060_rep1

description: QC ok

source_name: Human, Whole Blood, post-therapy

value: post


title: Blood_fu_XB0063_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: Blood_post_XB0063_rep1

description: QC ok


title: Vinclozolin_rep_1_batch_3_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_2_1


title: Blood_fu_XB0060_rep1

description: QC ok


title: Blood_post_XB0062_rep1

description: QC ok


title: Blood_fu_XB0062_rep1

description: QC ok


title: Vinclozolin_rep_4_batch_3_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_1_4


title: Blood_fu_XB0066_rep1

description: QC ok


title: Tiratricol_rep_5_batch_1_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_2_2

source_name: Whole embryo_48 hpf_Tiratricol

value: Tiratricol


title: Tiratricol_rep_3_batch_1_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_2_3


title: Tiratricol_rep_1_batch_1_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_2_1


title: Raloxifene_hydrochloride_rep_4_batch_4_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_1_2


title: Raloxifene_hydrochloride_rep_1_batch_4_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_1_4


title: Tiratricol_rep_2_batch_1_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_2_3


title: Blood_pre_XB0060_rep1

description: QC ok

value: MALE


title: Blood_fu_XB0058_rep1

description: QC ok


title: Blood_post_XB0058_rep1

description: QC ok


title: Blood_fu_XB0051_rep1

description: QC ok


title: Propylparaben_rep_4_batch_3_arraySlide_14

description:
Gene expression after 48 hpf exposure
SG12414235_256950710037_S001_GE1_1105_Oct12_1_3

source_name: Whole embryo_48 hpf_Propylparaben

value: Propylparaben


title: Blood_post_XB0066_rep1

description: QC ok


title: Raloxifene_hydrochloride_rep_5_batch_4_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_2_4


title: Blood_pre_XB0048_rep1

description: QC ok


title: Propylparaben_rep_3_batch_3_arraySlide_13

description:
Gene expression after 48 hpf exposure
SG12414235_256950710036_S001_GE1_1105_Oct12_1_4


title: Blood_post_XB0051_rep1

description: QC ok


title: Blood_pre_XB0058_rep1

description: QC ok


title: Blood_post_XB0048_rep1

description: QC ok


title: Blood_pre_XB0051_rep1

description: QC ok


title: Blood_fu_XB0044_rep1

description: QC ok


title: Propylparaben_rep_1_batch_3_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_2_4


title: Propiconazole_rep_5_batch_1_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_2_3

source_name: Whole embryo_48 hpf_Propiconazole

value: Propiconazole


title: Blood_pre_XB0047_rep1

description: QC ok


title: Propylparaben_rep_5_batch_3_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_1_1


title: Perfluorooctanesulfoni_acid_rep_4_batch_2_arraySlide_14

description:
Gene expression after 48 hpf exposure
SG12414235_256950710037_S001_GE1_1105_Oct12_1_4


title: Perfluorooctanesulfoni_acid_rep_3_batch_2_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_2_3


title: Propiconazole_rep_1_batch_1_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_1_1


title: Blood_post_XB0047_rep1

description: QC ok


title: Blood_fu_XB0047_rep1

description: QC ok


title: Perfluorooctanesulfoni_acid_rep_1_batch_2_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_1_3


title: Pentachlorophenol_rep_1_batch_4_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_2_1

source_name: Whole embryo_48 hpf_Pentachlorophenol

value: Pentachlorophenol


title: Propiconazole_rep_3_batch_1_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_2_3


title: Blood_post_XB0044_rep1

description: QC ok


title: Perfluorooctanesulfoni_acid_rep_5_batch_2_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_2_2


title: Propiconazole_rep_4_batch_1_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_1_4


title: Blood_pre_XB0044_rep1

description: QC ok


title: Pentachlorophenol_rep_4_batch_4_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_1_1


title: Blood_fu_XB0038_rep1

description: QC ok


title: Blood_post_XB0038_rep1

description: QC ok


title: Patient 13 Gleason 3

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized using the Affymetrix hybridization kit according to manufacturer's protocol

scan_protocol: Samples were scanned using the Affymetrix GeneChip Scanner according to manufacturer's protocol

data_processing: Raw data were analyzed using the Affymetrix Expression Console

source_name: human radical prostatectomy specimen

label_protocol: Samples were labelled using the NuGEN Ovation, Exon and Biotinylation kits according to manufacturer's protocol

growth_protocol: not applicable

extract_protocol: Target regions were excised using an Arcturus Ti Laser Capture Microdissection microscope, and total RNA was extracted using the PaxGene RNA kit according to manufacturer's protocol

treatment_protocol: Samples were fixed in paxgene and processed to paraffin

tag: fixative

value: PaxGene

tag: gleason grade


title: Patient 11 Gleason 4


title: Kepone_rep_4_batch_1_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_2_4

source_name: Whole embryo_48 hpf_Kepone

value: Kepone


title: Patient 13 Gleason 4


title: Pentachlorophenol_rep_3_batch_4_arraySlide_6

description:
Gene expression after 48 hpf exposure
SG12414235_256950710029_S001_GE1_1105_Oct12_2_3


title: Blood_post_XB0036_rep1

description: QC ok


title: Patient 10 Gleason 3


title: Patient 10 Gleason 4


title: Patient 12 Gleason 4


title: Blood_fu_XB0036_rep1

description: QC ok


title: Blood_pre_XB0038_rep1

description: QC ok

value: FEMALE


title: Patient 11 Gleason 3


title: Blood_pre_XB0036_rep1

description: QC ok

value: Blood


title: Patient 9 Gleason 4


title: Pentachlorophenol_rep_2_batch_4_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_1_3


title: Kepone_rep_1_batch_1_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_2_3


title: Patient 12 Gleason 3


title: Haloperidol_rep_3_batch_1_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_2_3

source_name: Whole embryo_48 hpf_Haloperidol

value: Haloperidol


title: Haloperidol_rep_1_batch_1_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_1_3

value: whole embryo


title: Kepone_rep_3_batch_1_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_1_4


title: Blood_fu_XB0028_rep1

description: QC ok


title: Blood_post_XB0028_rep1

description: QC ok


title: Patient 8 Gleason 3


title: Patient 8 Gleason 4


title: Blood_pre_XB0062_rep1

description: QC ok


title: Patient 7 Gleason 4


title: Genistein_rep_3_batch_2_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_1_2

source_name: Whole embryo_48 hpf_Genistein

value: Genistein


title: Patient 6 Gleason 3


title: Haloperidol_rep_4_batch_1_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_1_3


title: Patient 6 Gleason 4


title: Patient 9 Gleason 3


title: Endrin_rep_1_batch_3_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_1_3

source_name: Whole embryo_48 hpf_Endrin

value: Endrin


title: Genistein_rep_4_batch_2_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_2_2


title: Patient 7 Gleason 3


title: Genistein_rep_2_batch_2_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_1_4


title: Patient 5 Gleason 3


title: Patient 4 Gleason 3


title: Blood_fu_XB0027_rep1

description: QC ok


title: Blood_post_XB0025_rep1

description: QC ok


title: DMSO_rep_3_batch_2_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_1_3

source_name: Whole embryo_48 hpf_DMSO

value: DMSO


title: Blood_pre_XB0028_rep1

description: QC ok

value: pre


title: Patient 4 Gleason 4


title: DMSO_rep_1_batch_4_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_1_4


title: Blood_pre_XB0025_rep1

description: QC ok


title: Blood_fu_XB0024_rep1

description: QC ok


title: Endrin_rep_3_batch_3_arraySlide_13

description:
Gene expression after 48 hpf exposure
SG12414235_256950710036_S001_GE1_1105_Oct12_2_4


title: Blood_fu_XB0025_rep1

description: QC ok


title: Patient 3 Gleason 4


title: Endrin_rep_4_batch_3_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_2_2


title: Blood_post_XB0027_rep1

description: QC ok

value: post


title: Blood_pre_XB0027_rep1

description: QC ok


title: Patient 3 Gleason 3


title: Patient 5 Gleason 4


title: Blood_post_XB0024_rep1

description: QC ok


title: Endrin_rep_2_batch_3_arraySlide_6

description:
Gene expression after 48 hpf exposure
SG12414235_256950710029_S001_GE1_1105_Oct12_1_2


title: Genistein_rep_1_batch_2_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_2_1


title: Blood_post_XB0017_rep1

description: QC ok


title: Blood_fu_XB0017_rep1

description: QC ok

value: follow-up


title: Blood_pre_XB0024_rep1

description: QC ok


title: Blood_fu_XB0012_rep1

description: QC ok


title: Blood_pre_XB0017_rep1

description: QC ok


title: Blood_fu_XB0014_rep1

description: QC ok


title: Blood_pre_XB0014_rep1

description: QC ok


title: DMSO_rep_4_batch_4_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_2_4


title: Patient 2 Gleason 3


title: Blood_post_XB0014_rep1

description: QC ok


title: DMSO_rep_2_batch_2_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_1_4


title: DMSO_rep_1_batch_3_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_1_3


title: DMSO_rep_2_batch_3_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_2_3


title: Patient 2 Gleason 4


title: DMSO_rep_3_batch_4_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_1_2


title: Patient 1 Gleason 4


title: Blood_pre_XB0012_rep1

description: QC ok


title: Blood_post_XB0012_rep1

description: QC ok


title: PXA_ID00858_1_AMBION; analysis of pleiomorphic xanthoastrocytoma surgical sample

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

institute: CU Anschutz Medical Campus

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values.

source_name: brain tumor (pleiomorphic xanthoastrocytoma)

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy or Allprep (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor

tag: disease state

value: pleiomorphic xanthoastrocytoma


title: DMSO_rep_2_batch_1_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_1_2

tag: treatment


title: DMSO_rep_1_batch_2_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_2_2


title: DMSO_rep_1_batch_1_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_1_2


title: DMSO_rep_5_batch_1_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_1_4


title: PXA_ID01080_1_AMBION; analysis of pleiomorphic xanthoastrocytoma surgical sample


title: DMSO_rep_3_batch_3_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_2_3


title: Blood_fu_XD0080_rep1

description: QC ok

tag: gender


title: Blood_post_XD0080_rep1

description: QC ok

tag: timepoint


title: PXA_ID01007_1_AMBION; analysis of pleiomorphic xanthoastrocytoma surgical sample


title: Blood_fu_XD0079_rep1

description: QC ok


title: Blood_pre_XD0079_rep1

description: QC ok


title: Blood_pre_XD0080_rep1

description: QC ok


title: PNET_ID00837_1_AMBION; reanalysis of GSM1661084

description: reanalysis of GSM1661084

source_name: brain tumor (primitive neuroectodermal tumor)

value: primitive neuroectodermal tumor


title: Blood_fu_XD0075_rep1

description: QC ok


title: Patient 1 Gleason 3


title: PXA_ID01120_1_AMBION; analysis of pleiomorphic xanthoastrocytoma surgical sample


title: PXA_ID00493_1; analysis of pleiomorphic xanthoastrocytoma surgical sample


title: PNET_ID00776_1; analysis of primitive neuroectodermal tumor surgical sample


title: PNET_ID00777_1; analysis of primitive neuroectodermal tumor surgical sample


title: Dimethipin_rep_4_batch_3_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_1_2

source_name: Whole embryo_48 hpf_Dimethipin

value: Dimethipin


title: PNET_ID00760_1; analysis of primitive neuroectodermal tumor surgical sample


title: Dimethipin_rep_2_batch_3_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_2_4


title: PNET_ID00599_1; analysis of primitive neuroectodermal tumor surgical sample


title: DMSO_rep_2_batch_4_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_1_3


title: Dimethipin_rep_1_batch_3_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_2_1


title: DMSO_rep_4_batch_3_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_1_2


title: PNET_ID00592_1_AMBION; reanalysis of GSM1661082

description: reanalysis of GSM1661082


title: Blood_pre_XD0075_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy


title: Blood_post_XD0075_rep1

description: QC ok


title: PNET_ID00640_1; reanalysis of GSM1661083

description: reanalysis of GSM1661083


title: Blood_fu_XD0074_rep1

description: QC ok

value: MALE


title: Diisobutyl_phthalate_rep_2_batch_4_arraySlide_14

description:
Gene expression after 48 hpf exposure
SG12414235_256950710037_S001_GE1_1105_Oct12_1_2


title: Blood_post_XD0074_rep1

description: QC ok


title: Blood_pre_XD0074_rep1

description: QC ok


title: Dimethipin_rep_3_batch_3_arraySlide_6

description:
Gene expression after 48 hpf exposure
SG12414235_256950710029_S001_GE1_1105_Oct12_2_1


title: PNET_ID00535_1; reanalysis of GSM1661081

description: reanalysis of GSM1661081


title: Diisobutyl_phthalate_rep_3_batch_4_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_2_2


title: Blood_post_XD0071_rep1

description: QC ok


title: PNET_ID00536_1; analysis of primitive neuroectodermal tumor surgical sample


title: CP-634384_rep_4_batch_2_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_1_4

source_name: Whole embryo_48 hpf_CP-634384


title: PNET_ID00383_1; analysis of primitive neuroectodermal tumor surgical sample


title: Blood_fu_XD0071_rep1

description: QC ok


title: Diisobutyl_phthalate_rep_4_batch_4_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_1_2


title: CP-634384_rep_1_batch_2_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_2_4


title: PNET_ID00224_1; analysis of primitive neuroectodermal tumor surgical sample


title: Diisobutyl_phthalate_rep_1_batch_4_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_1_1


title: Blood_fu_XD0067_rep1

description: QC ok


title: PA_ID00653_1; reanalysis of GSM2306203

description: reanalysis of GSM2306203

source_name: brain tumor (pilocytic astrocytoma)

value: pilocytic astrocytoma


title: PA_ID00631_1; reanalysis of GSM2306202

description: reanalysis of GSM2306202


title: Blood_post_XD0067_rep1

description: QC ok

source_name: Human, Whole Blood, post-therapy


title: Blood_pre_XD0071_rep1

description: QC ok


title: CP-634384_rep_3_batch_2_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_2_4


title: Blood_pre_XD0067_rep1

description: QC ok


title: PA_ID00519_1; reanalysis of GSM2306200

description: reanalysis of GSM2306200


title: Butylparaben_rep_4_batch_3_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_1_1

source_name: Whole embryo_48 hpf_Butylparaben

value: Butylparaben


title: Butylparaben_rep_1_batch_3_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_2_3


title: PA_ID00378_1; reanalysis of GSM2306198

description: reanalysis of GSM2306198


title: Blood_fu_XD0059_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: FEMALE


title: Butylparaben_rep_2_batch_3_arraySlide_13

description:
Gene expression after 48 hpf exposure
SG12414235_256950710036_S001_GE1_1105_Oct12_2_1


title: PA_ID00363_1; reanalysis of GSM2306197

description: reanalysis of GSM2306197


title: PA_ID00476_1; reanalysis of GSM2306199

description: reanalysis of GSM2306199


title: Blood_pre_XD0059_rep1

description: QC ok

value: Blood


title: PA_ID00257_1; reanalysis of GSM2306196

description: reanalysis of GSM2306196


title: Butylparaben_rep_3_batch_3_arraySlide_12

description:
Gene expression after 48 hpf exposure
SG12414235_256950710035_S001_GE1_1105_Oct12_1_1


title: Blood_post_XD0059_rep1

description: QC ok


title: NORMAL_ID99999_ChoroidPlexus; reanalysis of GSM1661065

description: reanalysis of GSM1661065

source_name: normal brain

value: brain

value: normal


title: Bisphenol_AF_rep_3_batch_3_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_2_4

source_name: Whole embryo_48 hpf_Bisphenol_AF

value: whole embryo


title: Blood_fu_XD0056_rep1

description: QC ok


title: PA_ID00160_1; reanalysis of GSM2306194

description: reanalysis of GSM2306194


title: PA_ID00563_1; reanalysis of GSM2306201

description: reanalysis of GSM2306201


title: PA_ID00249_1; reanalysis of GSM2306195

description: reanalysis of GSM2306195


title: Blood_fu_XD0054_rep1

description: QC ok


title: Blood_pre_XD0056_rep1

description: QC ok


title: Bisphenol_A_rep_1_batch_1_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_2_4

source_name: Whole embryo_48 hpf_Bisphenol_A


title: Bisphenol_AF_rep_2_batch_3_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_2_2


title: Blood_post_XD0056_rep1

description: QC ok


title: Blood_post_XD0054_rep1

description: QC ok


title: NORMAL_ID00953_ Pons_X; analysis of normal brain pons

description: analysis of normal brain pons


title: Bisphenol_A_rep_4_batch_1_arraySlide_14

description:
Gene expression after 48 hpf exposure
SG12414235_256950710037_S001_GE1_1105_Oct12_2_1


title: NORMAL_ID00996_Cerebellum_AMBION; reanalysis of GSM2306193

description: reanalysis of GSM2306193


title: Bisphenol_AF_rep_4_batch_3_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_2_4


title: Bisphenol_A_rep_5_batch_1_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_1_2


title: Bisphenol_AF_rep_1_batch_3_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_2_1


title: NORMAL_ID00897_Frontal_X_AMBION; analysis of normal brain frontal lobe

description: analysis of normal brain frontal lobe


title: Blood_pre_XD0054_rep1

description: QC ok


title: Bisphenol_A_rep_2_batch_1_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_1_1


title: Blood_fu_XD0048_rep1

description: QC ok


title: Abamectin_rep_1_batch_1_arraySlide_16

description:
Gene expression after 48 hpf exposure
SG12414235_256950710039_S001_GE1_1105_Oct12_1_2

source_name: Whole embryo_48 hpf_Abamectin

value: Abamectin


title: NORMAL_ID00897_Occipital_X_AMBION; reanalysis of GSM2306192

description: reanalysis of GSM2306192


title: NORMAL_ID00605_Temporal_AMBION; analysis of normal brain temporal lobe

description: analysis of normal brain temporal lobe


title: NORMAL_ID00897_Cerebellum_X_AMBION; reanalysis of GSM2306191

description: reanalysis of GSM2306191


title: Blood_pre_XD0048_rep1

description: QC ok


title: Blood_fu_XB0007_rep1

description: QC ok


title: Blood_fu_XD0044_rep1

description: QC ok


title: Blood_post_XD0048_rep1

description: QC ok


title: Blood_post_XD0044_rep1

description: QC ok


title: 5alpha_Dihydrotestosterone_rep_3_batch_4_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_1_3


title: Blood_fu_XD0037_rep1

description: QC ok


title: Abamectin_rep_2_batch_1_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_2_1


title: 5alpha_Dihydrotestosterone_rep_1_batch_4_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_2_3


title: Abamectin_rep_3_batch_1_arraySlide_8

description:
Gene expression after 48 hpf exposure
SG12414235_256950710031_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00605_Parietal_AMBION; reanalysis of GSM1661064

description: reanalysis of GSM1661064


title: NORMAL_ID00605_Occipital_AMBION; reanalysis of GSM1661063

description: reanalysis of GSM1661063


title: NORMAL_ID00605_Frontal_1; reanalysis of GSM2306190

description: reanalysis of GSM2306190


title: 5alpha_Dihydrotestosterone_rep_4_batch_4_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00605_ChoroidPlexus_1; reanalysis of GSM1661061

description: reanalysis of GSM1661061


title: 5alpha_Dihydrotestosterone_rep_2_batch_4_arraySlide_10

description:
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00605_Cerebellum_AMBION; reanalysis of GSM2306189

description: reanalysis of GSM2306189


title: NORMAL_ID00514_Temporal_AMBION; reanalysis of GSM2306188

description: reanalysis of GSM2306188


title: 353_Triiodothyronine_rep_4_batch_2_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_1_2


title: 353_Triiodothyronine_rep_3_batch_2_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00514_Thal; reanalysis of GSM1661059

description: reanalysis of GSM1661059


title: Blood_pre_XD0035_rep1

description: QC ok


title: Blood_fu_XD0035_rep1

description: QC ok


title: Blood_post_XD0035_rep1

description: QC ok


title: 3355-Tetraiodothyroacetic acid_rep_5_batch_1_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_2_4

source_name: Whole embryo_48 hpf_3355-Tetraiodothyroacetic acid

value: 3355-Tetraiodothyroacetic acid


title: Blood_pre_XD0037_rep1

description: QC ok

value: pre


title: NORMAL_ID00605_Pons_1; analysis of normal brain pons

description: analysis of normal brain pons


title: Blood_post_XD0037_rep1

description: QC ok

value: post


title: Blood_fu_XD0034_rep1

description: QC ok

value: follow-up


title: 3355-Tetraiodothyroacetic acid_rep_3_batch_1_arraySlide_15

description:
Gene expression after 48 hpf exposure
SG12414235_256950710038_S001_GE1_1105_Oct12_2_1


title: NORMAL_ID00514_Occipital_AMBION; reanalysis of GSM1661056

description: reanalysis of GSM1661056


title: Blood_fu_XD0033_rep1

description: QC ok


title: NORMAL_ID00514_Parietal_AMBION; reanalysis of GSM1661057

description: reanalysis of GSM1661057


title: Blood_pre_XD0034_rep1

description: QC ok


title: 3355-Tetraiodothyroacetic acid_rep_1_batch_1_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_1_3


title: NORMAL_ID00514_LumbarCord; analysis of normal brain lumbar cord

description: analysis of normal brain lumbar cord


title: 17B_estradiol_rep_4_batch_1_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_2_1

source_name: Whole embryo_48 hpf_17B_estradiol


title: 17B_estradiol_rep_2_batch_1_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_2_2


title: NORMAL_ID00514_Medulla_AMBION; reanalysis of GSM1661054

description: reanalysis of GSM1661054


title: 3355-Tetraiodothyroacetic acid_rep_2_batch_1_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00514_Frontal; reanalysis of GSM2306187

description: reanalysis of GSM2306187


title: Blood_post_XD0032_rep1

description: QC ok


title: 17B_estradiol_rep_3_batch_1_arraySlide_2

description:
Gene expression after 48 hpf exposure
SG12414235_256950710024_S001_GE1_1105_Oct12_2_2


title: Blood_fu_XD0032_rep1

description: QC ok


title: Blood_pre_XD0033_rep1

description: QC ok


title: 17alpha_Ethinylestradiol_rep_3_batch_2_arraySlide_6

description:
Gene expression after 48 hpf exposure
SG12414235_256950710029_S001_GE1_1105_Oct12_2_2


title: 17alpha_Ethinylestradiol_rep_4_batch_2_arraySlide_7

description:
Gene expression after 48 hpf exposure
SG12414235_256950710030_S001_GE1_1105_Oct12_2_3


title: Blood_pre_XD0032_rep1

description: QC ok


title: 17B_estradiol_rep_1_batch_1_arraySlide_3

description:
Gene expression after 48 hpf exposure
SG12414235_256950710025_S001_GE1_1105_Oct12_2_2


title: NORMAL_E00024_Hippocampus_1; analysis of normal brain hippocampus

description: analysis of normal brain hippocampus


title: Blood_fu_XD0029_rep1

description: QC ok


title: 17alpha_Ethinylestradiol_rep_1_batch_2_arraySlide_5

description:
Gene expression after 48 hpf exposure
SG12414235_256950710028_S001_GE1_1105_Oct12_1_4


title: 17alpha_Ethinylestradiol_rep_2_batch_2_arraySlide_13

description:
Gene expression after 48 hpf exposure
SG12414235_256950710036_S001_GE1_1105_Oct12_1_1


title: NORMAL_ID00514_Cerebellum; reanalysis of GSM2306186

description: reanalysis of GSM2306186


title: Blood_post_XD0034_rep1

description: QC ok


title: NORMAL_E00006_Hippocampus_1; analysis of normal brain hippocampus

description: analysis of normal brain hippocampus


title: NORMAL_E00005_Hippocampus_1; analysis of normal brain hippocampus

description: analysis of normal brain hippocampus


title: NORMAL_ID00514_ChoroidPlexus; reanalysis of GSM1661052

description: reanalysis of GSM1661052


title: Blood_post_XD0029_rep1

description: QC ok


title: Blood_pre_XD0029_rep1

description: QC ok


title: 17_Methyltestosterone_rep_3_batch_2_arraySlide_11

description:
Gene expression after 48 hpf exposure
SG12414235_256950710034_S001_GE1_1105_Oct12_1_2


title: MEN_ID01186_1_AMBION; analysis of meningioma surgical sample

description: analysis of meningioma surgical sample

source_name: brain tumor (meningioma)

value: brain tumor

value: meningioma


title: 17_Methyltestosterone_rep_2_batch_2_arraySlide_1

description:
Gene expression after 48 hpf exposure
SG12414235_256950710023_S001_GE1_1105_Oct12_1_4


title: 17_Methyltestosterone_rep_1_batch_2_arraySlide_4

description:
Gene expression after 48 hpf exposure
SG12414235_256950710027_S001_GE1_1105_Oct12_2_1


title: Blood_fu_XD0026_rep1

description: QC ok


title: Blood_post_XD0026_rep1

description: QC ok


title: Blood_pre_XD0026_rep1

description: QC ok


title: MEN_ID00634_1; reanalysis of GSM1661035

description: reanalysis of GSM1661035


title: NORMAL_ID00514_Midbrain_AMBION; reanalysis of GSM1661055

description: reanalysis of GSM1661055


title: 17_Methyltestosterone_rep_4_batch_2_arraySlide_9

description:
Gene expression after 48 hpf exposure
SG12414235_256950710032_S001_GE1_1105_Oct12_1_4


title: MEN_ID00711_1; reanalysis of GSM1661036

description: reanalysis of GSM1661036


title: MEDSHH_ID00719_1_AMBION; reanalysis of GSM2306181

description: reanalysis of GSM2306181

source_name: brain tumor (medulloblastoma group SHH)

value: medulloblastoma group SHH


title: Blood_pre_XD0021_rep1

description: QC ok


title: Glioblastoma_PBH

city: Hanover

last: Allaway

state: New Hampshire

address: Vail 501A, 72 College St

department: Department of Molecular and Systems Biology

institute: Geisel School of Medicine

description: Human glioblastoma samples were retained from pathological samples, flash frozen, stored, and obtained from the MMC BioBank, a core facility of Maine Medical Center Research Institute

hyb_protocol: Hybridization was performed using the WT Plus kit standard operating protocol for these arrays.

scan_protocol: Before scanning, washing and staining was performed with the WT Plus kit following the standard operating protocol for this array, on a GeneChip Fluidics 450. Scanning was performed on a GeneChip Scanner 3000.

data_processing:
Probe set intensites were summarized using robust multi-array analysis. Guided principle components analysis determeind wthat batch normalization was unnecessary. Probesets were collapsed into gene level measurements using the 'collapseRows()' function with the maxmean method from the R package WGCNA. R version: 3.2.3.
HTA-2.0.r1.Psrs.mps

label: Affymetrix Proprietary DNA Label linked to Biotin

source_name: flash-frozen globlastoma pathological sample

label_protocol: Samples were labeled with a WT Plus kit from Affymetrix, which was purchased with the arrays. PolyA controls were used.

extract_protocol: To isolate RNA, -80 C tumor fragments were placed in 5-10 volumes of RNAlater-ICE Frozen Tissue Transition Solution (Ambion) and placed at -20°C until RNA extraction with a mirVana miRNA isolation kit, without phenol, following the standard operating protocol (Thermo Scientific). RNA concentration and quality was determined using a Qubit Fluorometer (Thermo Scientific) and a Fragment Analyzer (Advanced Analytical Technologies).

value: glioblastoma tumor tissue

tag: tumor stage

value: WHO IV

value: F

tag: patient age


title: Glioblastoma_LNA

value: M


title: MEDSHH_ID00288_1; reanalysis of GSM2306180

description: reanalysis of GSM2306180


title: Glioblastoma_R7K


title: Glioblastoma_H5M


title: MEDSHH_ID00801_1_AMBION; reanalysis of GSM2306182

description: reanalysis of GSM2306182


title: Glioblastoma_3HQ


title: Glioblastoma_CB2


title: MEDSHH_ID00258_1; reanalysis of GSM2306179

description: reanalysis of GSM2306179


title: Blood_fu_XD0021_rep1

description: QC ok

value: FEMALE


title: Blood_post_XD0021_rep1

description: QC ok

value: Blood


title: NORMAL_E00003_Frontal_1; reanalysis of GSM2306185

description: reanalysis of GSM2306185

value: brain


title: Glioblastoma_VVN


title: Blood_post_XD0033_rep1

description: QC ok


title: Glioblastoma_YXL


title: Blood_fu_XD0020_rep1

description: QC ok


title: Blood_post_XD0020_rep1

description: QC ok


title: Blood_pre_XD0020_rep1

description: QC ok


title: MEDGP4_ID00437_1; reanalysis of GSM2306178

description: reanalysis of GSM2306178

source_name: brain tumor (medulloblastoma group 4)

value: medulloblastoma group 4


title: Glioblastoma_UNY


title: MEN_ID00762_1; reanalysis of GSM1661037

description: reanalysis of GSM1661037


title: MEDSHH_ID00831_1_AMBION; reanalysis of GSM2306183

description: reanalysis of GSM2306183


title: MEDGP4_ID00330_1; reanalysis of GSM2306177

description: reanalysis of GSM2306177


title: MEDGP3_ID00241_1; reanalysis of GSM2306170

description: reanalysis of GSM2306170

source_name: brain tumor (medulloblastoma group 3)

value: medulloblastoma group 3


title: MEDGP4_ID00254_1; reanalysis of GSM2306175

description: reanalysis of GSM2306175


title: MEDGP4_ID00186_1; reanalysis of GSM2306174

description: reanalysis of GSM2306174


title: Glioblastoma_TRM


title: MEDGP4_ID00262_1; reanalysis of GSM2306176

description: reanalysis of GSM2306176


title: MEDGP3_ID00277_1; reanalysis of GSM2306171

description: reanalysis of GSM2306171


title: Blood_fu_XD0011_rep1

description: QC ok

value: MALE


title: Glioblastoma_RIW


title: Blood_post_XD0011_rep1

description: QC ok


title: Blood_pre_XD0011_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy


title: Blood_fu_XD0010_rep1

description: QC ok


title: Blood_pre_XD0017_rep1

description: QC ok


title: Blood_post_XD0017_rep1

description: QC ok


title: Blood_fu_XD0017_rep1

description: QC ok


title: Blood_fu_XD0014_rep1

description: QC ok


title: Blood_pre_XD0014_rep1

description: QC ok