title: 532720A12 - OXIoe_flg_bio3 vs. OXIoe_mock_bio3

hyb_protocol: OXIoe_mock_bio3 Cy5 / OXIoe_flg_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: OXIoe

value: seedling

value: 2 weeks

value: boyes:1.14 (Boyes et al. Plant Cell 2001)

tag: treatment

value: mock


title: HT1080_ETP_0.3_r2

status: Public on Dec 01 2014

type: RNA

city: Research Triangle Park

first: Rebecca

middle: A

last: Clewell

state: NC

address: 6 Davis Drive

department: Institute for Chemical Safety Sciences

country: USA

institute: The Hamner Institutes for Health Sciences

description: Sample 18

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).  Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide.  The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip™

growth_protocol: HT1080 cells were grown under the conditions recommended by ATCC:  Eagle’s Minimum Essential media (EMEM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 mg/L streptomycin and 100 U/mL of penicillin G at 37 °C in a humidified atmosphere of 95% air and 5% CO2

extract_protocol: total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA).  A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA (Qiagen)

treatment_protocol: Cells were plated in complete media containing 10% heat-inactivated FBS and allowed to attach overnight. Stock solutions of chemicals were prepared in DMSO at 1,000-fold higher concentrations than the final target doses.  Stock solutions were aliquoted and stored at -20C for up to 1 week. Dosing solutions were prepared immediately prior to treatment of the cells by diluting stock solutions 1:200 in complete media.  24 hrs after seeding the cells, the media in each well was supplemented with the dosing solutions (1:5 v/v), for a final chemical dilution of 1:1000 (0.1% vehicle). Cells were maintained in original complete media throughout the course of the experiment.  Immediately following treatment, media was removed and the cells were washed with PBS and prepared for subsequent analyses

tag: cell line

tag: cell type

value: human fibrosarcoma cells

tag: treated with

value: etoposide (ETP) for 24hrs


title: 93_DNA_methylation

type: genomic

city: New York

first: Marsha

last: Reyngold

state: NY

address: 1275 York Ave

department: Radiation Oncology

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: strandard Illumina protocol

scan_protocol: arrays were imagined using BeadArray Reader using strandard recommended Illumina scanner settings

data_processing:
data were analyzed using Partek software (version 6.5)
Processed data are presented as Average Beta. Raw data (unmethylated_and_methylated_signals.txt) are available on the series level where the Unmethylated (Signal_A) and methylated (Signal_B) signal intensities are provided.

molecule: genomic DNA

source_name: breast tumor tissue_AW_primary tumor

label_protocol: biotin

extract_protocol: Genomic DNA was extracted from snap-frozen tissue sections using DNeasy Tissue kit (Qiagen)

tag: tissue

value: breast tumor

tag: unique patient id

value: AW

tag: sample type

value: primary tumor


title: 532934A02 - oxi_mock_bio1 vs. col_mock_bio1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Analysis of flg22-induced transcriptional changes in oxi1, OXI1oe, pti1-4, CA-MPK4 and ice1 mutant lines

hyb_protocol: col_mock_bio1 Cy5 / oxi_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: 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: Arabidopsis thaliana

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: rosette - 0,5x MS (sigma6899), 0.5g/L MES, pH media:5.7, 0.5g/l Agar Type E  hygrometry: 45%  temperature: 22°C  light: 6h - 22h

treatment_protocol: Name:30 min H2O - compound based treatment - control,h2o:time 30min .

tag: genotype

value: col

tag: ecotype

value: Columbia

tag: age

tag: developmental stage

value: oxi


title: 532720A11 - OXIoe_mock_bio3 vs. OXIoe_flg_bio3

hyb_protocol: OXIoe_flg_bio3 Cy5 / OXIoe_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:30 min 1µM flg22 - compound based treatment - biotic stress,flg22:quantity 1uM time 30min .


title: 532934A01 - col_mock_bio1 vs. oxi_mock_bio1

hyb_protocol: oxi_mock_bio1 Cy5 / col_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 532720A10 - OXIoe_flg_bio2 vs. OXIoe_mock_bio2

hyb_protocol: OXIoe_mock_bio2 Cy5 / OXIoe_flg_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HT1080_ETP_0.003_r2

description: Sample 16


title: first visit [GG1_000069]

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression module)

data_processing: The raw log2 transformed probes were normalized by ANOVA fitting technical effects of date of hybridization and RIN score. The reason why there are so many missing probes in the normalized dataset is because they are below the expression threshold and so not included in the normalization process.

source_name: whole peripheral blood

label_protocol: Illumina BeadArray protocol

extract_protocol: Total RNA was extracted from whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.

tag: Sex

value: M

tag: body mass index

tag: ethnicity

value: AFR

tag: gad7 score

tag: anxiety case/control

value: control

tag: hybridization batch

value: Z

tag: rin


title: 532935A03 - oxi_mock_bio3 vs. oxi_flg_bio3

hyb_protocol: oxi_flg_bio3 Cy5 / oxi_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: oxi_flg_bio3:100mg. (Qiagen_RNeasy.pdf)

tag: treatment


title: 91_DNA_methylation

source_name: breast tumor tissue_AV_primary tumor

value: AV


title: first visit [GG1_000068]

value: F

value: CAU


title: HT1080_ETP_0.3_r1

description: Sample 15

tag: cell line

tag: cell type


title: HT1080_ETP_0.03_r1

description: Sample 14

tag: treated with


title: 532720A08 - OXIoe_flg_bio1 vs. OXIoe_mock_bio1

hyb_protocol: OXIoe_mock_bio1 Cy5 / OXIoe_flg_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: OXIoe

tag: tissue

value: seedling

value: 2 weeks

value: boyes:1.14 (Boyes et al. Plant Cell 2001)


title: HT1080_ETP_0.003_r1

description: Sample 13

value: human fibrosarcoma cells

value: etoposide (ETP) for 24hrs


title: 532720A09 - OXIoe_mock_bio2 vs. OXIoe_flg_bio2

hyb_protocol: OXIoe_flg_bio2 Cy5 / OXIoe_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mock


title: 90_DNA_methylation

source_name: breast tumor tissue_AU_lymph node metastasis

value: breast tumor

tag: unique patient id

value: AU

tag: sample type

value: lymph node metastasis


title: 88_DNA_methylation

source_name: breast tumor tissue_AT_lymph node metastasis

value: AT


title: first visit [GG1_000065]

value: AFR


title: first visit [GG1_000066]

value: case


title: first visit [GG1_000067]

value: M

value: Z


title: first visit [GG1_000064]

value: control


title: 532720A07 - OXIoe_mock_bio1 vs. OXIoe_flg_bio1

hyb_protocol: OXIoe_flg_bio1 Cy5 / OXIoe_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

tag: ecotype

value: Columbia


title: first visit [GG1_000063]

tag: age

value: F

value: CAU


title: 532720A05 - col_mock_bio3 vs. OXIoe_mock_bio3

hyb_protocol: OXIoe_mock_bio3 Cy5 / col_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: OXIoe

value: seedling

value: 2 weeks

tag: developmental stage

value: col


title: HT1080_ETP_0.01_r6

description: Sample 11

value: human fibrosarcoma cells

value: etoposide (ETP) for 24hrs


title: HT1080_ETP_0.1_r6

description: Sample 12


title: 86_DNA_methylation

source_name: breast tumor tissue_AS_lymph node metastasis

value: breast tumor

value: AS


title: 84_DNA_methylation

source_name: breast tumor tissue_AR_lymph node metastasis

value: AR

value: lymph node metastasis


title: 532720A04 - OXIoe_mock_bio2 vs. col_mock_bio2

hyb_protocol: col_mock_bio2 Cy5 / OXIoe_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: boyes:1.14 (Boyes et al. Plant Cell 2001)

value: mock


title: first visit [GG1_000062]

tag: Sex

value: M

tag: body mass index

value: AFR

value: Z


title: 89_DNA_methylation

source_name: breast tumor tissue_AU_primary tumor

value: AU

value: primary tumor


title: 532720A06 - OXIoe_mock_bio3 vs. col_mock_bio3

hyb_protocol: col_mock_bio3 Cy5 / OXIoe_mock_bio3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: OXIoe


title: first visit [GG1_000061]

value: F

tag: ethnicity

value: CAU

tag: gad7 score

value: control


title: 87b_DNA_methylation

source_name: breast tumor tissue_AT_primary tumor

value: AT


title: HT1080_ETP_0.01_r6-nf

description: Sample 10

value: human fibrosarcoma cells

value: etoposide (ETP) for 24hrs


title: 532720A03 - col_mock_bio2 vs. OXIoe_mock_bio2

hyb_protocol: OXIoe_mock_bio2 Cy5 / col_mock_bio2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: seedling

value: 2 weeks

value: col


title: first visit [GG1_000060]

tag: anxiety case/control

tag: hybridization batch


title: 83_DNA_methylation

source_name: breast tumor tissue_AR_primary tumor

value: breast tumor

value: AR


title: HT1080_ETP_0.01_r5

description: Sample 8


title: 85_DNA_methylation

source_name: breast tumor tissue_AS_primary tumor

value: AS


title: first visit [GG1_000059]

value: M

value: Z

tag: rin


title: 82_DNA_methylation

source_name: breast tumor tissue_AQ_lymph node metastasis

value: AQ

value: lymph node metastasis


title: first visit [GG1_000058]


title: first visit [GG1_000057]

value: AFR


title: 81_DNA_methylation

source_name: breast tumor tissue_AQ_primary tumor

value: primary tumor


title: first visit [GG1_000056]

value: F

value: case


title: HT1080_ETP_0.01_r4

description: Sample 6

tag: cell line


title: first visit [GG1_000055]

value: CAU


title: 532720A01 - col_mock_bio1 vs. OXIoe_mock_bio1

hyb_protocol: OXIoe_mock_bio1 Cy5 / col_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: OXIoe

value: Columbia

value: boyes:1.14 (Boyes et al. Plant Cell 2001)

tag: treatment

value: mock


title: HT1080_ETP_0.1_r3

description: Sample 5

tag: cell type

value: human fibrosarcoma cells

tag: treated with

value: etoposide (ETP) for 24hrs


title: HT1080_ETP_0.01_r1

description: Sample 1


title: HT1080_ETP_0.1_r2

description: Sample 3


title: 80_DNA_methylation

source_name: breast tumor tissue_AP_lymph node metastasis

tag: tissue

value: breast tumor

tag: unique patient id

value: AP


title: HT1080_ETP_0.1_r1

description: Sample 2


title: 78_DNA_methylation

source_name: breast tumor tissue_AN_lymph node metastasis

value: AN

tag: sample type


title: first visit [GG1_000054]

value: ASN

value: Z


title: Green quantum dots replicate 3

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

description:
Biological replicate 3 of 3
Qds_green_rep3

hyb_protocol: Hybridization buffer (6X SSC buffer; 0.2 % SDS; 5 % Denhardt's solution; Salmon sperm DNA 13 µg/ml; 25 % deionized formamide; 23 µl of tagged cDNA) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an ScanArray Gx scanner (PerkinElmer)

data_processing: LOESS normalized, Normexp background subtracted data obtained from log2 of processed Red signal/processed Green signal; Bioconductor package (v.2.14)

label: Alexa Fluor 647

organism: Escherichia coli K-12

source_name: green quantum dot exposed cultures

label_protocol: 20 µg of total RNA were primed with 2 µl of 3 µg/µl Random primer at 80°C for 5 min, then reversed transcribed at 42°C for 2.5 h in the presence of 200 U SuperScript II Reverse transcriptase (Invitrogen), and 10 mM each dATP, dCTP, dGTP, with 4 mM dTTP, 1 mM Alexa fluor 555 aha dUTP (or 1mM Alexa fluor 647 aha dUTP)

growth_protocol: An overnight E. coli culture was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cultures were exposed to green CdTe Quantum Dots 50 µg/ml or red CdTe Quantum Dots during 15 min.

tag: strain

tag: exposed to

value: green CdTe quantum dots 50 µg/ml for 15 min

label: Alexa Fluor 555

source_name: untreated cultures

value: none (control)


title: HT1080_ETP_0.1_r5

description: Sample 9

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).


title: 532720A02 - OXIoe_mock_bio1 vs. col_mock_bio1

hyb_protocol: col_mock_bio1 Cy5 / OXIoe_mock_bio1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

value: col

tag: ecotype

value: seedling

tag: age

value: 2 weeks

tag: developmental stage


title: HT1080_ETP_0.01_r3

description: Sample 4


title: 79_DNA_methylation

hyb_protocol: strandard Illumina protocol

source_name: breast tumor tissue_AP_primary tumor

value: primary tumor


title: 77_DNA_methylation

source_name: breast tumor tissue_AN_primary tumor


title: first visit [GG1_000053]

source_name: whole peripheral blood

tag: Sex

value: M

tag: body mass index

tag: ethnicity

value: CAU

tag: gad7 score

value: control


title: HT1080_ETP_0.1_r4

description: Sample 7

tag: cell line


title: first visit [GG1_000052]

value: F

tag: anxiety case/control

tag: hybridization batch

tag: rin


title: 71_DNA_methylation

source_name: breast tumor tissue_AK_primary tumor

tag: tissue

value: AK


title: Green quantum dots replicate 1

description:
Biological replicate 1 of 3
Qds_green_rep1


title: 72_DNA_methylation

source_name: breast tumor tissue_AK_lymph node metastasis

tag: unique patient id

value: lymph node metastasis


title: first visit [GG1_000051]

value: case


title: Red quantum dots replicate 1

description:
Biological replicate 1 of 3
Qds_red_rep1

source_name: red quantum dot exposed cultures

value: red CdTe quantum dots 50 µg/ml for 15 min


title: Red quantum dots replicate 3

description:
Biological replicate 3 of 3
Qds_red_rep3


title: first visit [GG1_000048]


title: first visit [GG1_000046]


title: first visit [GG1_000049]


title: Red quantum dots replicate 2

description:
Biological replicate 2 of 3
Qds_red_rep2


title: 70_DNA_methylation

source_name: breast tumor tissue_AJ_lymph node metastasis

value: breast tumor

value: AJ

tag: sample type


title: 68_DNA_methylation

source_name: breast tumor tissue_AI_lymph node metastasis

value: AI


title: first visit [GG1_000045]

value: AFR

value: Z


title: first visit [GG1_000050]


title: 69_DNA_methylation

source_name: breast tumor tissue_AJ_primary tumor


title: 66_DNA_methylation

source_name: breast tumor tissue_AH_lymph node metastasis

value: AH


title: 67b_DNA_methylation

source_name: breast tumor tissue_AI_primary tumor


title: first visit [GG1_000044]

value: ASN


title: first visit [GG1_000043]


title: Green quantum dots replicate 2

description:
Biological replicate 2 of 3
Qds_green_rep2

tag: strain

value: green CdTe quantum dots 50 µg/ml for 15 min

value: none (control)


title: first visit [GG1_000042]

value: M


title: first visit [GG1_000041]


title: first visit [GG1_000040]


title: mES Ptn Delta Rep4

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Gene expression following Ptn(TALE)Delta transfection

hyb_protocol: 600ngs of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 il of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Mouse GE 8x60K microarray (Agilent; G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 2x1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 2x1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned on a Nimblegen scanner at 2um resolution to generate single channel TIFF images.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain non-background subtracted and spatially detrended Processed Signal intensities.

molecule: polyA RNA

organism: Mus musculus

source_name: mES, Ptn Delta transfected, Replicate 4

label_protocol: 1mg of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent – 5188-5282) and the mixture labelled with cyanine 3 (Cy3) using the Amino Allyl MessageAmp™ II with Cy™3 kit (Ambion; AM1795) according to manufacturer’s instructions.

growth_protocol: E14 ES cells were grown in GMEM supplemented with 15% fetal bovine serum (FBS), 1,000 units/ml LIF, nonessential amino acids, sodium pyruvate, 2-β-mercaptoethanol, L-glutamine, and Penicillin/Streptomycin.

extract_protocol: RNA was prepared using RNeasy mini kit (Qiagen) according to manufacturer’s protocol, including a DNaseI (Qiagen) treatment for 15mn at room temperature

treatment_protocol: ESCs were transfected with plasmids using Lipofectamine® 2000 Reagent (Invitrogen cat. N°11668) following the manufacturer recommendations. Briefly, 1x106 ESCs were transfected in a 6-well plate with 3µg of plasmid and 7µl of lipofectamin. Medium was changed 5h after transfection. Transfected cells were sorted based on eGFP expression by FACS 24h after transfection, re-seeded for another 24h before harvesting for experiment

tag: cell type

value: mouse ES cells

tag: genotype/variation

value: Ptn(TALE)Delta transfection


title: first visit [GG1_000038]

value: CAU


title: mES Ptn Delta Rep3

source_name: mES, Ptn Delta transfected, Replicate 3


title: first visit [GG1_000039]


title: 57_DNA_methylation

source_name: breast tumor tissue_AD_primary tumor

value: AD

value: primary tumor


title: mES Ptn Delta Rep2

source_name: mES, Ptn Delta transfected, Replicate 2


title: 61_DNA_methylation

source_name: breast tumor tissue_AF_primary tumor

value: AF


title: 64_DNA_methylation

source_name: breast tumor tissue_AG_lymph node metastasis

value: AG

value: lymph node metastasis


title: 56_DNA_methylation

source_name: breast tumor tissue_AC_lymph node metastasis

value: breast tumor

value: AC


title: 65_DNA_methylation

source_name: breast tumor tissue_AH_primary tumor


title: mES Ptn Delta Rep1

source_name: mES, Ptn Delta transfected, Replicate 1


title: 58_DNA_methylation

source_name: breast tumor tissue_AD_lymph node metastasis


title: mES Ptn DEL Rep4

description: Gene expression following Ptn(TALE)DEL transfection

source_name: mES, Ptn DEL transfected, Replicate 4

value: Ptn(TALE)DEL transfection


title: first visit [GG1_000037]

source_name: whole peripheral blood

value: F

value: AFR

value: case

value: Z


title: mES Ptn DEL Rep3

source_name: mES, Ptn DEL transfected, Replicate 3


title: mES Ptn DEL Rep1

source_name: mES, Ptn DEL transfected, Replicate 1


title: first visit [GG1_000036]

value: control


title: first visit [GG1_000035]

value: M


title: mES Ptn VP64 Rep4

description: Gene expression following Ptn(TALE)VP64 transfection

source_name: mES, Ptn VP64 transfected, Replicate 4

value: mouse ES cells

value: Ptn(TALE)VP64 transfection


title: first visit [GG1_000034]

value: CAU


title: mES Ptn DEL Rep2

source_name: mES, Ptn DEL transfected, Replicate 2


title: mES Ptn VP64 Rep2

source_name: mES, Ptn VP64 transfected, Replicate 2


title: first visit [GG1_000033]


title: mES Ptn VP64 Rep3

source_name: mES, Ptn VP64 transfected, Replicate 3


title: first visit [GG1_000032]


title: 63_DNA_methylation

source_name: breast tumor tissue_AG_primary tumor


title: 55_DNA_methylation

source_name: breast tumor tissue_AC_primary tumor


title: mES EGFP Rep4

description: Gene expression following EGFP transfection

source_name: mES, EGFP transfected, Replicate 4

value: EGFP transfection


title: 49_DNA_methylation

source_name: breast tumor tissue_Z_primary tumor

value: primary tumor


title: 51_DNA_methylation

source_name: breast tumor tissue_AA_primary tumor

value: AA


title: first visit [GG1_000030]


title: mES Ptn VP64 Rep1

source_name: mES, Ptn VP64 transfected, Replicate 1


title: first visit [GG1_000031]


title: 52_DNA_methylation

source_name: breast tumor tissue_AA_lymph node metastasis


title: 46_DNA_methylation

source_name: breast tumor tissue_X_lymph node metastasis

value: X


title: mES EGFP Rep2

source_name: mES, EGFP transfected, Replicate 2


title: first visit [GG1_000029]


title: 48_DNA_methylation

source_name: breast tumor tissue_Y_lymph node metastasis

value: Y

value: lymph node metastasis


title: first visit [GG1_000028]

source_name: whole peripheral blood


title: KO2_2

city: Cologne

first: Snehlata

last: Kumari

address: Kerpener Strasse 62

country: Germany

institute: University of Cologne

description: RelAE-MUT mice

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K, AMADID 028005) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Ear tissue

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted using Tri-Reagent (Sigma-Aldrich) following manufacturer's instructions.

treatment_protocol: Mouse ear was treated with 2,4- Dinitro fluorobenzene and left for 48 h, prior to sample collection

value: K14Cre RelAfl/fl


title: mES EGFP Rep3

source_name: mES, EGFP transfected, Replicate 3


title: KO1_2

description: RelAE-MUT mice


title: first visit [GG1_000026]


title: 50_DNA_methylation

source_name: breast tumor tissue_Z_lymph node metastasis

value: breast tumor


title: first visit [GG1_000025]


title: WT1_2

description: Wild Type mice

value: RelAfl/fl


title: 44_DNA_methylation

source_name: breast tumor tissue_W_lymph node metastasis

value: W


title: first visit [GG1_000023]

value: F

value: AFR

value: case


title: 43_DNA_methylation

source_name: breast tumor tissue_W_primary tumor


title: first visit [GG1_000021]

value: M

value: Z


title: 42_DNA_methylation

source_name: breast tumor tissue_V_lymph node metastasis

value: V


title: 47_DNA_methylation

source_name: breast tumor tissue_Y_primary tumor


title: 40_DNA_methylation

source_name: breast tumor tissue_U_lymph node metastasis

value: U


title: first visit [GG1_000022]

value: CAU


title: 39_DNA_methylation

source_name: breast tumor tissue_U_primary tumor

value: primary tumor


title: NAC_virgin_biological rep6

city: Madison

first: Stephen

middle: Coull

last: Gammie

state: WI

address: 430 Lincoln Drive

department: Zoology

institute: University of Wisconsin

hyb_protocol: Samples were hybridized to arrays at 45 degrees C for 16 hours following procedures outlined in the GeneChip WT Terminal Labeling and Hybridization Use Manual , Rev. 4.

scan_protocol: Arrays were scanned on the Affymetrix GC3000 G7 scanner, and data were extracted and processed using Affymetrix Command Console v3.1.1.1229.

data_processing: Raw array data were normalized and summarized at the probeset level using Affymetrix Power Tools v1.12.0 with default settings for PLIER with GC-bin background correction. Summarized data were analyzed using limma for BioConductor v3.6.9

source_name: virgin adult female_nucleus accumbens

label_protocol: 200ng of each total RNA sample were labeled with an Ambion GeneChip WT Expression Kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.

growth_protocol: The strain of mice used was outbred hsd:ICR mice purchased from Harlan labs (Madison, WI). Maternal were housed with a breeder male for two weeks while virgin mice were co-housed with two other female mice for the same time period. After the mating period, all females from both groups were individually housed through parturition until tissue collection (postpartum day 7). Each virgin control sample was collected on the same day as a postpartum day 7 maternal sample.

extract_protocol: Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA), which uses a guanidinium thiocyanate-phenol-chloroform extraction followed by a spin column cleanup and purification. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was assessed using an RNA Pico Chip on an Agilent BioAnalyzer 2100.

treatment_protocol: Tissue was collected on postpartum day 7 or age-matched for virgin controls.  On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11. Tissue was collected on postpartum day 7.  On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11. Tissue was collected on postpartum day 7.

value: outbred hsd:ICR

value: adult

tag: sample group

value: age-matched virgin mouse

value: microdissected nucleus accumbens


title: NAC_virgin_biological rep4

tag: age


title: first visit [GG1_000018]

hyb_protocol: Illumina's BeadArray protocol


title: 41_DNA_methylation

source_name: breast tumor tissue_V_primary tumor


title: NAC_virgin_biological rep5


title: NAC_virgin_biological rep2


title: NAC_virgin_biological rep3


title: 62_DNA_methylation

source_name: breast tumor tissue_AF_lymph node metastasis

value: AF

value: lymph node metastasis


title: first visit [GG1_000016]

value: control


title: first visit [GG1_000015]


title: 38_DNA_methylation

source_name: breast tumor tissue_T_lymph node metastasis

value: breast tumor

value: T


title: 45_DNA_methylation

source_name: breast tumor tissue_X_primary tumor

value: X


title: first visit [GG1_000014]

value: F


title: 36_DNA_methylation

source_name: breast tumor tissue_S_lymph node metastasis

value: S


title: first visit [GG1_000013]

value: Z


title: first visit [GG1_000012]

value: AFR


title: NAC_maternal_biological rep6

source_name: maternal adult female_nucleus accumbens

value: lactating maternal (postpartum) mouse


title: first visit [GG1_000011]

source_name: whole peripheral blood

value: CAU


title: 37_DNA_methylation

source_name: breast tumor tissue_T_primary tumor

value: primary tumor


title: NAC_virgin_biological rep1

value: outbred hsd:ICR


title: 34_DNA_methylation

source_name: breast tumor tissue_R_lymph node metastasis

value: R


title: 35_DNA_methylation

source_name: breast tumor tissue_S_primary tumor


title: NAC_maternal_biological rep4

value: adult


title: NAC_maternal_biological rep5

value: microdissected nucleus accumbens


title: WT2_2

description: Wild Type mice

source_name: Ear tissue

value: RelAfl/fl


title: 32_DNA_methylation

source_name: breast tumor tissue_Q_lymph node metastasis

value: Q

value: lymph node metastasis


title: NAC_maternal_biological rep2


title: 33b_DNA_methylation

source_name: breast tumor tissue_R_primary tumor

value: breast tumor


title: MMIS_MOCK2

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in limma 3.14.1 for R

source_name: GC sensitive MM1S cell line (CRL-2974) purchased from ATCC

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: GC sensitive MM1S (CRL-2974) and GC resistant MM1R cell lines (CRL-2975)  were purchased from ATCC®.  Cells were cultivated in RPMI-1640 Medium supplied with 10% Fetal Bovine Serum (E.U Approved; South American Origin) and 0.5% Penicillin/Streptomycin Solution (Invitrogen). The cell lines were additionally supplemented with 1% MEM Non-Essential Amino Acids and 1% Sodium Pyruvate (Invitrogen). Each cell line was maintained at 37°C in the atmosphere of 5% CO2 and 95% air, 95-98% humidity, until confluence. Cell viability was assessed by using colorimetric assay with 3-(4, 5-dimethylthiozol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) (Sigma Aldrich, St. Louis, MO, United States of America).

extract_protocol: Total RNA was extracted using the RNAqueousTM Micro Kit (Life Technologies, USA) for nucleic acid extraction from small cell populations. All cell populations of interest were lysed directly on the membranes without prior enzymatic detachment.

treatment_protocol: MM1S and MM1R cells were either induced with dexamethasone or transfected with 150nM/L synthetic mir-150-5p for 72hrs

tag: treatment

value: mock treated


title: NAC_maternal_biological rep3


title: 31_DNA_methylation

source_name: breast tumor tissue_Q_primary tumor


title: NAC_maternal_biological rep1


title: MMIS_MOCK1

description: replicate 1


title: MMIS_MOCK3

description: replicate 3


title: 30_DNA_methylation

source_name: breast tumor tissue_P_lymph node metastasis

value: P


title: DBA-Male Macrophages

city: Chapel Hill

first: Yukako

last: Kayashima

address: 701 Brinkhous-Bullitt Building

institute: University of North Carolina at Chapel Hill

description: Gene expression data of peritoneal macrophages pooled from three mice.

hyb_protocol: Affymetrix arrays (Affymetrix, Santa Clara, CA) were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 640 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader. GeneChip Command Console Software (AGCC) was used for washing, staining and scanning control of the instrumentation.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control.

source_name: Peritoneal macrophages isolated from DBA/2J male mice

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. Briefly, the WT Expression Kit (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip Terminal Labeling Kit.  Fragmented and labeled cDNA was then added to a hybridization cocktail (25 µg/µl fragmented cDNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 7 % DMSO, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20).

growth_protocol: Wild type 129S6/SvEvTac and DBA2/J mice mice were fed with a regular chow.

extract_protocol: Total RNA was extracted by RNeasy kit (Qiagen) according to the manufacturer's instructions.  Equal amounts of RNA from three mice in each group were pooled.

treatment_protocol: Three mice per group (males and females of each strain) were treated with 1 ml 4 % thioglycolate medium by intra-peritoneal injection and sacrificed 4 days after injection followed by intra-peritoneal lavage with 10 ml PBS. Macrophages were plated at in 100 mm plates and cultured overnight in DMEM supplemented with 10% FBS.

tag: gender

value: male

value: peritoneal macrophage


title: MMIS_MIMIC1

description: replicate 1

value: synthetic mir-150-5p transfection


title: 28_DNA_methylation

source_name: breast tumor tissue_O_lymph node metastasis

value: O


title: MMIS_MIMIC3

description: replicate 3


title: MMIS_MIMIC2

description: replicate 2


title: 27_DNA_methylation

source_name: breast tumor tissue_O_primary tumor


title: 129-Male Macrophages

source_name: Peritoneal macrophages isolated from 129S6/SvEv male mice


title: DBA-Female Macrophages

source_name: Peritoneal macrophages isolated from DBA/2J female mice

value: female


title: 29_DNA_methylation

source_name: breast tumor tissue_P_primary tumor


title: 25_DNA_methylation

source_name: breast tumor tissue_N_primary tumor

value: N


title: 129-Female Macrophages

source_name: Peritoneal macrophages isolated from 129S6/SvEv female mice


title: MMIR_MOCK1

description: replicate 1

source_name: GC resistant MM1R cell line (CRL-2975) purchased from ATCC


title: 20_DNA_methylation

source_name: breast tumor tissue_K_lymph node metastasis

value: K


title: 26_DNA_methylation

source_name: breast tumor tissue_N_lymph node metastasis


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_45

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description: Gene expression data from PBMCs isolated from whole blood.

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays (Freeman et al. in BMC Biol 2012, 10:90). Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 was performed according to Affymetrix protocols.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor. Then, normalized probeset data were transformed by RMA algorithm.

organism: Sus scrofa

source_name: PBMC, LR, day 140

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer's protocol. After DNaseI treatment, the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Vaccination, 1 ml (30 IU) of tetanus toxoid (Equilis Tetanus-Vaccine).

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: low-reactive

tag: Sex

value: tetanus vaccination

tag: sampling time point

value: day 140

tag: pig identifier


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_47

source_name: PBMC, HR, day 140

value: high-reactive


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_48


title: MMIR_MOCK2

description: replicate 2

tag: cell line


title: 21_DNA_methylation

source_name: breast tumor tissue_L_primary tumor

value: L

value: primary tumor


title: MMIR_MOCK3

description: replicate 3

value: mock treated


title: 19_DNA_methylation

source_name: breast tumor tissue_K_primary tumor

value: breast tumor


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_46

value: male


title: 22_DNA_methylation

source_name: breast tumor tissue_L_lymph node metastasis

value: lymph node metastasis


title: MM1S_DEX2_1µM

description: replicate 2

source_name: GC sensitive MM1S cell line (CRL-2974) purchased from ATCC

value: dexamethasone


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_44


title: MMIR_MIMIC2

description: replicate 2

value: synthetic mir-150-5p transfection


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_43

value: female


title: MMIR_MIMIC3

description: replicate 3


title: MMIR_MIMIC1

description: replicate 1


title: 15_DNA_methylation

source_name: breast tumor tissue_H_primary tumor

value: H


title: MM1S_DEX1_1µM

description: replicate 1


title: MM1S_UNTR3

description: replicate 3

value: untreated


title: 17_DNA_methylation

source_name: breast tumor tissue_J_primary tumor

value: J


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_42

value: German Landrace

value: peripheral blood mononuclear cells


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_41

value: low-reactive

value: tetanus vaccination


title: MM1S_UNTR2

description: replicate 2


title: 13_DNA_methylation

source_name: breast tumor tissue_G_primary tumor

value: G


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_39

value: high-reactive

value: day 140


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_38


title: MM1S_DEX3_1µM

description: replicate 3


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_40


title: 18_DNA_methylation

source_name: breast tumor tissue_J_lymph node metastasis


title: 16_DNA_methylation

source_name: breast tumor tissue_H_lymph node metastasis


title: 14_DNA_methylation

source_name: breast tumor tissue_G_lymph node metastasis


title: B cell-primed CD8+ T cells (Round3)

city: Durham

first: Regina

last: Lin

address: 207 Research Drive, #305

department: Immunology

institute: Duke University

description: Control

data_processing:
miRNA Ct values from B cell-primed and DC-primed CD8+ T cells were first evaluated by two-way ANOVA to determine variations generated by independent rounds of experiments. Ct values of each miRNA species in a sample was normalized by the geometric mean of all Ct values of that sample. dCt values were analyzed by two-tailed paired t-test to determine statistical significance.
Fold Change worksheet reports test/control (i.e., DC-primed CD8+ T cells/B cell-primed CD8+ T cells) ratios.

label: SYBR Green

source_name: CD8+ pMel-1 transgenic T cells

label_protocol:
Polyadenylated tails were added to the 3’-end of all RNA molecules using the Poly(A) Polymerase Tailing Kit (Epicentre).
After annealing oligo-dT primers, cDNA was synthesized using the qScript Flex cDNA synthesis kit (Quanta Biosciences) as per the manufacturer’s instructions for gene specific priming, with one modification:
a universal tag that would extend from the 3’-end of cDNA molecules was added during reverse transcription. With the addition of this universal tag, individual miRNAs were detected with miRNA-specific forward primers and a reverse universal primer mix.

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% FBS, 100 U/ml penicillin, 100 U/ml streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids and 50 μM 2-Mercaptoethanol (henceforth referred to as complete RPMI) in a humidified 37°C incubator with 7% CO2.

extract_protocol: Total RNA was extracted with the mirVana miRNA Isolation Kit (Ambion) followed by DNase I treatment.

treatment_protocol: CD8+ pMel-1 T cells were activated with either hgp100(25-33)-loaded splenic B cells or LPS-matured bone marrow-derived dendritic cells in vitro for 3 days.

value: CD8+ pMel-1 transgenic T cells

value: B cell-primed

tag: culture

value: Primed in vitro for 3 days


title: DC-primed CD8+ T cells (Round3)

description: Test

value: DC-primed


title: B cell-primed CD8+ T cells (Round2)

description: Control


title: 11_DNA_methylation

source_name: breast tumor tissue_F_primary tumor

tag: tissue

value: breast tumor

value: F

value: primary tumor


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_37

value: male


title: MM1S_UNTR1

description: replicate 1

value: untreated


title: DC-primed CD8+ T cells (Round2)

description: Test


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_36


title: MM1R_UNTR3

description: replicate 2

source_name: GC resistant MM1R cell line (CRL-2975) purchased from ATCC


title: MM1R_UNTR2

description: replicate 1


title: 12_DNA_methylation

source_name: breast tumor tissue_F_lymph node metastasis

tag: unique patient id

value: lymph node metastasis


title: MM1R_DEX3_1µM

description: replicate 3

value: dexamethasone


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_34

value: German Landrace

value: peripheral blood mononuclear cells

value: female


title: DC-primed CD8+ T cells (Round1)

description: Test


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_35

value: tetanus vaccination


title: MM1R_UNTR1

description: replicate 3


title: 4_DNA_methylation

source_name: breast tumor tissue_B_lymph node metastasis

value: B

tag: sample type


title: 2_DNA_methylation

source_name: breast tumor tissue_A_lymph node metastasis

value: A


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_31

source_name: PBMC, LR, day 140

value: low-reactive

value: day 140


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_33


title: MM1R_DEX1_1µM

description: replicate 1


title: Cd_4 - AaF49

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

institute: université de Bordeaux UMR ePOC

description: Cd [4µg/L]_water

hyb_protocol: For cDNA hybridization, microarray was pre-hybridized in 5X SSC buffer; 0.1% SDS; 0.1 g.L-1 BSA during 45 min at 55°C. Microarray was washed twice 5 min in 0.1X SSC at RT followed by 30s in purified water under continuous agitation. Microarray was then centrifuged 2 min for drying.   800ng of cDNA sample was pooled with 800ng of cDNA reference and hybridized on microarray in 2X hybridization buffer (8X SSC; 0.4% SDS; 0.1g.L-1 calf thymus DNA) and incubated at 55°C in Agilent chamber overnight. Hybridized microarray was washed at 55°C in 2X SSC; 0.1% SDS buffer, washed, twice 5 min in 2X SSC; 0.1% SDS buffer under agitation at RT; twice 5 min in 0.1X SSC; 0.1% SDS buffer and finally 4 times in 0.1X SSC buffer and dried by centrifugation (2 min).

scan_protocol: Microarray data were generated by the Innoscan 710 microarray scanner using Mapix software.

data_processing:
The filtering of raw data was done for both green and red channels. The median foreground (F635median and F532median) and median background (B635median and B532median) was chosen for the data normalization. If the ratio Fmedian/Bmedian was lower than 1.5, data were removed from the analysis. For each channel, the background was removed of the foreground data and the mean of triplicates (three spots for each gene) was then calculated and both green and red channels were used for data normalization. Normalization and statistical analysis was done by using the BRB-arrayTools version 4.4.0 software package (http://linus.nci.nih.gov/BRB-ArrayTools.html). Each array was median normalized over entire arrays and genes were excluded if 50% of values were missing in the complete set of arrays.
Data were normalized by median-centering log(red/green)-ratios in each array, based on the average of the red and green log-intensities.

organism: Anguilla anguilla

source_name: Fish from laboratory cadmium experiment

label_protocol: For the first step of reverse-transcription procedure, 10µg of RNA was mixed with 3µg of random primer and 2µg of oligodT. Water was added for 20µl qs. Mix was incubated 5 min at 70°C followed by10 min at 18°C and finally stored at 4°C. 20µl of the RT mix (GoScript™ 5X Reaction Buffer: 8µl; DTT [0.1M]: 4µl; MgCl2 [25mM]: 4.8µl; 50X aa-dNTP mix (25mM each): 1µl; dUTP: 1µl; GoScript™ RT: 2µl) was added to the RNA mix. The mix was incubated during 12h at 42°C followed by 5 min at 18 °C and stored at 4°C. RNAs were then hydrolyzed with 4µl of EDTA [0.2M] pH 8 and 6µl of NaOH [1M] during 10 min at 70°C.  To re-adjust the pH, 6µl of HCL [1M] was then added. cDNA purification was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol. cDNA was eluted in 60µl of sodium bicarbonate [0.1M] pH 9 and placed at -20°C before labeling.   In order to normalize microarray data, we used a common reference design. This was composed by a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012). This reference was combined in equal amounts with each sample before to be hybridized on the microarray slide. . Reference and sample cDNAs were labeled with CyDye™ Post-Labelling Reactive Dye Pack (Amersham). Each cDNA sample and reference was mix with 1 vial of CyDye (Cy3 for sample and Cy5 for reference) and incubated at RT in the dark during 90 min. Reaction was stopped by adding 15µl of hydroxylamine hydrochloride [4M] and incubated during 15 min in the dark. Purification of labeled cDNA was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol and eluted in 60µl of water. Amount of labeled cDNA  as well as the frequency of incorporation (FOI) were determined spectrophotometrically (Epoch, Biotek).

extract_protocol: RNA extraction was carried out by means of the SV total RNA islotaion Kit, promega). Sampleswere placed in 450 µl of RNA lysis (Promega) buffer in sterile microtube and were homogenized by means of two metal beads and tissue homogenizer (Retsch). After 2 min of centrifugation at 10,000 rpm, 400 µl of the lysate was recovered.  One volume of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 was then added. The homogenate was vortexed 10s and centrifuged 10 min at RT. The upper phase was recovered. One volume of 75% EtOH was adeed. After homogenization by vortexing, the mix was transferred to a spin column and the standard manufacturer’s procedures were followed (including DNAseI treatment).. Quality and integrity of the total RNA were controlled by electrophoresis on a 1% agarose gel.

tag: source location

value: laboratory

tag: agent

value: Cd

tag: dose

value: Liver

source_name: reference RNA

tag: reference composition

value: liver


title: MM1R_DEX2_1µM

description: replicate 2


title: Cd_4 - AaF48

description: Cd [4µg/L]_water

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)


title: ACL-MSC_ACL reconstruction_rep 4

city: Seoul

first: Dae-Hee

last: Lee

address: 126-1, Anam-dong 5-ga, Seongbuk-gu

department: Department of Orthopaedic Surgery

country: South Korea

institute: Korea University College of Medicine

description:
replicate 4
ACL 4

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0) software. Array probes with detection p-value ≥ 0.05 (similar to signal to noise) in over 50% samples were filtered out. Selected gene signal value was transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using Fold change. Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). All data analysis and visualization of differentially expressed genes was conducted using R 2.15.1 (www.r-project.org).

source_name: Human ACL-MSC, ACL reconstruction

label_protocol: Biotinylated cRNA samples were prepared from 550 ng of total RNA using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) according to the manufacturer’s instructions.

growth_protocol: After isolation, 1 × 105 cells were plated in a 100-mm diameter culture dish in 10 mL of complete Poietics Mesenchymal Stem Cell Growth Medium (MSCGM) (Lonza Walkersville, Inc., Walkersville, MD, USA) and incubated in a humidified 5% CO2 incubator at 37°C. The attached cells were harvested with 1 mM ethylenediaminetetraacetic acid (EDTA) in PBS after 14 days (P1). Then, 1 × 105 P1 cells were plated in a 100-mm diameter culture dish in 10 mL of MSCGM and incubated in a humidified 5% CO2 incubator at 37°C for 7 days (P2).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA) and purified using RNeasy columns (Qiagen, Valencia, USA) in accordance with the manufacturers’ protocol. Then, RNA samples were treated with DNase 1 and subjected to additional clean-up procedures. RNA samples were quantified, aliquoted and stored at -80°C until use. Quality control was performed using denaturing gel electrophoresis, OD 260/280 ratio, and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: Male

tag: age

value: ACL


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_32

tag: cell type

tag: treatment


title: 3_DNA_methylation

source_name: breast tumor tissue_B_primary tumor

value: breast tumor

value: primary tumor


title: Cd_4 - AaF47

description: Cd [4µg/L]_water


title: Cd_4 - AaF50

description: Cd [4µg/L]_water


title: 10_DNA_methylation

source_name: breast tumor tissue_E_lymph node metastasis

value: E

value: lymph node metastasis


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_30

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

value: female


title: ACL-MSC_ACL reconstruction_rep 3

description:
replicate 3
ACL 3

tag: gender


title: B cell-primed CD8+ T cells (Round1)

description: Control

value: CD8+ pMel-1 transgenic T cells

value: B cell-primed

value: Primed in vitro for 3 days


title: Control - AaF9

description: Control

value: laboratory

value: Control


title: Control - AaF10

description: Control

value: Liver


title: 1_DNA_methylation

source_name: breast tumor tissue_A_primary tumor

value: A


title: ACL-MSC_ACL reconstruction_rep 2

description:
replicate 2
ACL 2


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_29

source_name: PBMC, HR, day 140

tag: temperament group

value: high-reactive

tag: Sex

value: tetanus vaccination

value: day 140


title: ACL-MSC_TKA_rep 1

description:
replicate 1
TKA 1

source_name: Human ACL-MSC, TKA

value: Female

value: ACL


title: ACL-MSC_TKA_rep 2

description:
replicate 2
TKA 2


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_25

value: male

tag: sampling time point

tag: pig identifier


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_26


title: 9_DNA_methylation

source_name: breast tumor tissue_E_primary tumor

value: breast tumor

value: E

value: primary tumor


title: Control - AaF8

description: Control

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: Cd_4 - AaF45

description: Cd [4µg/L]_water

value: Cd


title: Control - AaF7

description: Control


title: Control - AaF6

description: Control


title: Cd_4 - Aa50

description: Cd [4µg/L]_water

value: Caudal fin


title: subject 224, group C, stimulation U, time 0 days 8659387204_J

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

department: Jenner Institute

institute: University of Oxford

hyb_protocol: Illumina HT-12 v4 kit according to manufacturer's instructions

scan_protocol: Illumina iScan machine scanned to produce summary idat files. Idat files read by genome studio with no correction or background subtraction

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value >0.05 in all samples) and normalising with neqc using the control probes.

source_name: PBMC

label_protocol: Ambion Illumina Totalprep  and Illumina chip kits according to manufacturer's instructions

extract_protocol: Qiagen RNeasy kit according to instructions including DNase I digest

treatment_protocol: PBMC extracted in and cryopreserved. PBMC thawed and rested overnight with benzonase then counted on a casy counter and 1-2 million cells stimulated with R10 media alone (U) or with 1-4 million cfu of SSI BCG (B) for 12 hours. PBMC pelleted and frozen in 350uL Qiagen RLT buffer containing beta-mercaptoethanol.

value: PBMC

tag: time (days)

tag: stimulation

value: U

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_27

value: German Landrace

value: peripheral blood mononuclear cells


title: Cd_4 - Aa49

description: Cd [4µg/L]_water

tag: source location

value: laboratory

tag: agent

tag: tissue


title: subject 235, group C, stimulation U, time 0 days 8659387204_K


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_24

value: low-reactive

value: female

value: tetanus vaccination

value: day 140


title: Cd_4 - Aa48

description: Cd [4µg/L]_water

tag: dose

tag: reference composition


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_28

tag: cell type

value: male

tag: treatment


title: subject 234, group C, stimulation U, time 0 days 8659387204_I


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_23

tag: breed

value: high-reactive


title: Cd_4 - Aa47

description: Cd [4µg/L]_water


title: subject 228, group C, stimulation U, time 0 days 8659387204_H


title: Cd_4 - Aa45

description: Cd [4µg/L]_water


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_21

tag: temperament group


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_22

tag: Sex


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_19

tag: sampling time point


title: PCB_300 - Aa35

description: PCB [300ng/g PS]_diet

source_name: Fish from laboratory PCBs experiment

value: PCB

value: [300ng/g PS]_diet


title: subject 227, group C, stimulation U, time 7 days 8659387204_G


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_18

tag: pig identifier


title: subject 228, group C, stimulation B, time 7 days 8659387204_E

tag: time (days)

value: B


title: subject 225, group C, stimulation B, time 2 days 8659387204_D

tag: stimulation


title: subject 222, group C, stimulation B, time 2 days 8659387204_C

tag: group


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_20


title: subject 224, group C, stimulation B, time 14 days 8659387204_B

tag: volunteer


title: subject 202, group C, stimulation B, time 7 days 8659387204_F

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_17


title: subject 223, group C, stimulation B, time 2 days 8659387204_A


title: PCB_300 - Aa33

description: PCB [300ng/g PS]_diet

tag: source location

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_16


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_14


title: ACL-MSC_ACL reconstruction_rep 1

description:
replicate 1
ACL 1

tag: gender

value: Male

tag: age

value: ACL


title: PCB_300 - Aa32

description: PCB [300ng/g PS]_diet

tag: agent

tag: dose

tag: tissue

value: Caudal fin


title: PCB_300 - Aa31

description: PCB [300ng/g PS]_diet

tag: reference composition


title: PCB_50 - Aa29

description: PCB [50ng/g PS]_diet

value: [50ng/g PS]_diet


title: PCB_300 - Aa34

description: PCB [300ng/g PS]_diet


title: subject 235, group C, stimulation U, time 14 days 8659387173_K

tag: cell type

value: PBMC

value: U

value: C


title: PCB_50 - Aa28

description: PCB [50ng/g PS]_diet

value: laboratory


title: subject 225, group C, stimulation U, time 14 days 8659387173_L


title: PCB_50 - Aa26

description: PCB [50ng/g PS]_diet


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_12

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

tag: treatment

value: tetanus vaccination


title: subject 203, group C, stimulation U, time 14 days 8659387173_J


title: PCB_50 - Aa27

description: PCB [50ng/g PS]_diet


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_10

value: low-reactive

tag: Sex

value: male

tag: sampling time point

value: day 140

tag: pig identifier


title: subject 204, group C, stimulation U, time 7 days 8659387173_H

tag: time (days)

tag: stimulation

tag: group


title: PCB_50 - Aa25

description: PCB [50ng/g PS]_diet

tag: source location

value: PCB


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_15


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_13

value: high-reactive


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_08


title: subject 203, group C, stimulation U, time 7 days 8659387173_G

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_11


title: Control - Aa10

description: Control

source_name: Fish from laboratory contamination experiment

tag: agent

value: Control

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: Control - Aa8

description: Control

tag: dose

value: Caudal fin


title: Control - Aa9

description: Control

tag: tissue


title: subject 227, group C, stimulation B, time 2 days 8659387173_D

value: B


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_06

value: female


title: subject 227, group C, stimulation B, time 0 days 8659387173_E

value: PBMC


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_09


title: Control - Aa7

description: Control

tag: reference composition


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_07

tag: cell type


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_04

tag: breed


title: Control - Aa6

description: Control


title: subject 228, group C, stimulation B, time 14 days 8659387173_F

value: C


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_05

tag: temperament group


title: Garonne - A365

description: Garonne

source_name: Fish from Garrone natural site

value: Garrone natural site


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_03

value: German Landrace

tag: treatment


title: subject 222, group C, stimulation B, time 14 days 8659387173_B


title: Garonne - A362

description: Garonne


title: Garonne - A360

description: Garonne


title: subject 225, group C, stimulation B, time 7 days 8659387173_A


title: Garonne - A359

description: Garonne


title: subject 223, group C, stimulation U, time 7 days 8659387160_L

value: U


title: subject 204, group C, stimulation U, time 0 days 8659387160_K


title: PBMC response to tetanus toxoid, LR, day 140, Phenomics_02

value: peripheral blood mononuclear cells

tag: Sex

value: tetanus vaccination


title: PBMC response to tetanus toxoid, HR, day 140, Phenomics_01

tag: sampling time point


title: Garonne - A353

description: Garonne


title: subject 223, group C, stimulation U, time 14 days 8659387160_J


title: Gironde - A315

description: Gironde

source_name: Fish from Gironde natural site

value: Gironde natural site


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_47

source_name: PBMC, HR, day 28

value: male

value: day 28

tag: pig identifier


title: Gironde - A306

description: Gironde


title: subject 203, group C, stimulation U, time 2 days 8659387160_H

tag: time (days)


title: neural crest transition at T=7, rep 3

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: SAMPLE 17

hyb_protocol: Following fragmentation,  4.4μg fragmented cDNA were hybridized for 16 h at 45ºC and 65 rpm on an Affymetrix HG-U133_plus_2 microarray followed by washing, staining, and scanning on a GeneChip Fluidics 450 station (Affymetrix)

scan_protocol: Affymetrix HG-U133_plus_2 microarrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Affymetrix probe intensities were subjected to robust multi-array analysis (RMA), background correction with quantile normalization, and a median polish probeset summarization as implemented in the Partek Genomics Suite 6.6 software (Partek).

source_name: neural crest transition (from SCC058)

label_protocol: 10ng of total RNA was reverse transcribed using the NuGen Ovation Pico WTA Systems V2, followed by fragmentation, and 3’-biotin-labeling with the NuGen Encore Biotin module (NuGEN Technologies).

growth_protocol: SCC058 foreskin fibroblasts (Millipore) were cultured for 2 days at 37°C, 5% CO2 in low serum FibroGro (Millipore) containing 1mM Valproic acid (VPA, Sigma) and 6ug/ml polybrene. Thereafter, fibroblast were cultivated for 4 days in suspension in NSC medium containing 2μM multikinase inhibitor CB (Roche). Then, cells were cultivated for another 3 days in suspension in NSC medium supplemented with 2μM multikinase inhibitor CB and an inhibitor mix consisting of 500ng/ml Noggin (Peprotech), 10μM SB431542 (Tocris), and 1μM CP21 (Roche). Thereafter, cells were plated on polyornithine-laminin coated dishes. After 24hours medium was replaced with neural differentiation medium supplemented with the inhibitor mix consisting of 500ng/ml Noggin (Peprotech), 10μM SB431542 (Tocris), and 1μM CP21 (Roche). Cells were cultivated for 7 days in  neural differentiation medium supplemented with the inhibitor mix consisting of 500ng/ml Noggin (Peprotech), 10μM SB431542(Tocris), and 1μM CP21 (Roche). Then, cells were cultivated for >20 days in neural differentiation medium. Human primary Schwann cells (Sciencell) were cultured on poly-L-lysine coated dishes in Schwann cell medium (Sciencell) according to the manufacturer’s instructions.

extract_protocol: for total RNA extraction, cells were homogenized in tubes prefilled with 1.4 mm ceramic beads and QIAzol lysis reagent using a FastPrep-24 instrument (MP Biomedicals) and the Qiagen miRNeasy Mini Kit with DNase treatment (Qiagen).

treatment_protocol: no treatment prior RNA extraction

tag: cell type origin

value: foreskin fibroblasts

value: neural crest transition

tag: time in culture

value: 7 days


title: subject 202, group C, stimulation U, time 2 days 8659387160_I

tag: stimulation

tag: group


title: subject 217, group C, stimulation B, time 0 days 8659387173_C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_48

value: high-reactive


title: Gironde - A305

description: Gironde

tag: source location

value: Caudal fin

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: subject 222, group C, stimulation B, time 0 days 8659387160_E

value: PBMC

value: B


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_46

source_name: PBMC, LR, day 28

value: low-reactive


title: subject 222, group C, stimulation U, time 7 days 8659387160_G

value: C


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_44

value: German Landrace

value: female


title: Gironde - A302

description: Gironde

tag: tissue


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_42

value: peripheral blood mononuclear cells

value: tetanus vaccination


title: neural crest transition at T=7, rep 2

description: SAMPLE 16


title: subject 217, group C, stimulation B, time 2 days 8659387160_C


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_43


title: Schwann cells, rep 3

description: SAMPLE 14

source_name: primary Schwann cells

value: primary Schwann cells


title: subject 235, group C, stimulation B, time 2 days 8659387160_D


title: Schwann cells, rep 2

description: SAMPLE 13


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_41

value: day 28


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_45

value: male


title: Certes - A210

description: Certes

source_name: Fish from Certes natural site

value: Certes natural site

source_name: reference RNA

tag: reference composition


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_39

tag: cell type


title: subject 224, group C, stimulation B, time 7 days 8659387160_B


title: subject 227, group C, stimulation B, time 14 days 8659387160_A


title: Schwann cells, rep 1

description: SAMPLE 11


title: Certes - A207

description: Certes


title: induced Schwann cells at T=39, rep 3

description: SAMPLE 12

source_name: induced Schwann cells (from SCC058)

value: foreskin fibroblasts

value: induced Schwann cells

value: 39 days


title: neural crest transition at T=7, rep 1

description: SAMPLE 15

value: neural crest transition

value: 7 days


title: Certes - A205

description: Certes

value: Caudal fin

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: subject 204, group C, stimulation U, time 14 days 8659387159_L

value: PBMC

value: U

value: C


title: subject 224, group C, stimulation U, time 2 days 8659387159_K


title: Certes - A201

description: Certes


title: induced Schwann cells at T=39, rep 2

description: SAMPLE 10


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_40

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

value: high-reactive


title: late neural crest at T=18, rep 2

description: SAMPLE 8

source_name: late neural crest (from SCC058)

value: late neural crest

value: 18 days


title: Certes - A203

description: Certes

value: Certes natural site


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_38

tag: temperament group

value: female

value: tetanus vaccination

value: day 28


title: induced Schwann cells at T=39, rep 1

description: SAMPLE 9

value: foreskin fibroblasts

value: induced Schwann cells

value: 39 days


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_36

value: low-reactive

value: male

tag: treatment


title: subject 228, group C, stimulation U, time 2 days 8659387159_H

value: PBMC


title: late neural crest at T=18, rep 1

description: SAMPLE 7


title: subject 235, group C, stimulation U, time 7 days 8659387159_J

value: U


title: early neural crest at T=11, rep 3

description: SAMPLE 6

source_name: early neural crest (from SCC058)

value: early neural crest

value: 11 days


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_37

value: German Landrace

value: peripheral blood mononuclear cells

tag: Sex


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_35

value: high-reactive

tag: sampling time point


title: ArthrospiraPCC8005_irradiated5000Gy-2

city: Mol

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

description: Arthrospira sp. PCC8005 irradiated with 5000Gy

hyb_protocol: Hybridization mixture with 2µg Cy3-labeled cDNA was subsequently prepared. Samples were hybridized to Arthrospira_ HX12 array (Nimblegen) for 18 hours at 42 ºC.

scan_protocol: The arrays were washed and scanned in a Roche-Nimblegen MS 200 scanner. Raw data files (Pair and XYS files) were obtained from images using DEVA software (Roche-Nimblegen).

data_processing: Raw data were pre-processed using the “Oligo” package (version 1.24) in BioConductor (version 2.12 / R version 3.0.1) as follows: i) background correction based on the Robust Multichip Aver-age (RMA) convolution model (Irizarry et al., 2003), ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), and iii) summarization of multiple probe intensities for each probe set to one expression value per gene using the median polish approach (Irizarry et al., 2003). To test for differential expression between the different irradiated conditions and the reference conditions (no irradiation) the Bayesian adjusted t-statistics was used as implemented in the “LIMMA” package (version 2.18.0)(Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini & Hochberg, 1995). Transcripts were considered significantly differentially expressed when the corresponding adjusted p-value was lower than 0.05 and their absolute FC was equal or larger than 2 for upregulated genes, and equal or miner than 0.5 for the down regulated ones. Gene annotation was curated manually.

organism: Limnospira indica PCC 8005

label_protocol: RNA extracts and the new designed Arthrospira HX12 arrays (Nimblegen) microarray chips were provided to IRBB in Barcelona. cDNA library preparation and amplification were performed from 25 ng total RNA using the Complete Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich), according to the instructions of the manufacturer, with 17 cycles of amplification, resulting in microgram quantities of cDNA. Labelling and hybridization of the cDNA onto the microarray, were performed according to Roche-Nimblegen expression guide v5p1. For each sample, 1µg cDNA was labelled by Cy3 nonamers primers and Klenow polymerization.

growth_protocol: The strain of Arthrospira sp. PCC 8005 was obtained from Pasteur Culture Collection. Three in-dependent cultures (n=3) were used for irradiation. They were grown separately on a rotatory shaker in an incubator at 30°C (Binder KBW 400), in 500 ml Zarrouk medium (Zarrouk) to mid-exponential corresponding to an OD750 ~1. Cultures were illuminated with a photon flux density of ~ 42 µE m -2 s-1 provided by three Osram daylight tubes. The cultures were then divided at 50 ml/flask into thirty vented cell culture flasks (CELLSTAR® Filter Cap Cell Culture Flasks) which were also divided into two parts as controls and samples for irradiation

extract_protocol: Due to the high exopolysaccharide and secondary metabolites content of Arthrospira, that inter-fers with the yield and quality of extracted RNA, the RNA extraction procedure had to be opti-mized. In total, 30 ml of irradiated and control Arthrospira cultures were centrifuged 20 min at 10000 g. Cell pellets were frozen immediately at -80°C, until analysis (ca. 5 days). The breakage of the cells was done by applying a heat shock procedure. Cells resuspended in Trizol (Invitro-gen), were incubated at 95°C for 5 min and then submerged immediately on ice for additional 5 min. Next, the released RNA was separated from the cell debris by centrifugation (Eppendorf) at (10000 g, 10 min) at 4°C. RNA purification was performed using the Direct-zol RNA miniprep 2050 from (Zymosearch) following the manufacturer's instructions. RNA samples (150 µg) were then treated 30 min at 37°C using DNAse (TURBO DNA-free™, Ambion) following the manu-facturer's instructions. The RNA was concentrated using RNA Clean & Concentrator™-25 (Zy-mosearch). RNA quatity and purity was assessed by spectrophotometric analysis using NanoDrop ND-1000 Spectrophotometer (Thermo scientific). The quality and integrity of RNA was assessed using the Bioanalyzer 2100 (Agilent) according to manufacturer's instructions.  It is worthwhile to mention, that the Bioanalyser RNA profiles for Arthrospira are however different from standard profiles obtained for most other bacteria, as the rRNA profile for Arthrospira  contains 3 fragments (3 peaks) instead of 2, representing 16S and 23S rRNA, as has also been reported with Nostoc punctiforme (Pinto et al., 2009).

treatment_protocol: The irradiation was performed using RITA facility at the Belgian Reactor N°2 (BR2) (Supple-mentary Figure 1). The irradiation was done in dark, inside a closed canister, surrounded by four sources of 60Co gamma rays (Energy of 1.33 Mev and 1.17 Mev). Different doses of gamma rays were given at a constant dose rate of 527 Gy/h. “Scheme 1 supplementary file” illustrate the dif-ferent tested doses and the occurred irradiation time. The temperature inside the irradiation canis-ter was automatically monitored and ranged between 26-27°C. The time required for irradiation was dose-dependent and so respective controls were kept at the same conditions as irradiated samples. All analyses were performed immediately (i.e. within 1 hour) after irradiation.


title: subject 217, group C, stimulation U, time 14 days 8659387159_G

value: C


title: ArthrospiraPCC8005_irradiated5000Gy-1

source_name: Arthrospira sp. PCC8005 irradiated with 5000Gy


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_33

tag: pig identifier


title: fibroblast at T=0, rep 3

description: SAMPLE 3

source_name: SCC058 foreskin fibroblasts

value: SCC058 foreskin fibroblasts

value: 0 days


title: early neural crest at T=11, rep 2

description: SAMPLE 5


title: early neural crest at T=11, rep 1

description: SAMPLE 4


title: subject 234, group C, stimulation B, time 14 days 8659387159_F

tag: time (days)

value: B


title: subject 202, group C, stimulation B, time 14 days 8659387159_E


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_34

value: female

value: tetanus vaccination

value: day 28


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_32


title: fibroblast at T=0, rep 2

description: SAMPLE 2

tag: cell type origin

value: foreskin fibroblasts


title: ArthrospiraPCC8005_irradiated5000Gy-3


title: ArthrospiraPCC8005_control5000Gy-3

description: Arthrospira sp. PCC8005 control condition non-irradiated for 5000Gy

value: 0 Gy


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_31

value: low-reactive


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_30


title: subject 225, group C, stimulation B, time 0 days 8659387159_C

value: PBMC


title: subject 223, group C, stimulation B, time 0 days 8659387159_D


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_29


title: fibroblast at T=0, rep 1

description: SAMPLE 1

tag: time in culture


title: ArthrospiraPCC8005_irradiated3200Gy-2

description: Arthrospira sp. PCC8005 irradiated with 3200Gy


title: ArthrospiraPCC8005_irradiated3200Gy-3

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy


title: subject 202, group C, stimulation B, time 0 days 8659387159_B

source_name: PBMC

tag: stimulation


title: HRG 08h00m Rep2

city: Yokohama

first: Mariko

last: Okada-Hatakeyama

state: KANAGAWA

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0008h00m00s.r02

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: 6KR HRG 08h00m Rep2

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion

tag: age

value: 69 years adult

tag: gender

tag: ethnicity

value: Caucasian

tag: agent

value: HRG

tag: time


title: subject 235, group C, stimulation B, time 0 days 8670586019_K

tag: cell type

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_28

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

tag: Sex

value: male

tag: treatment

tag: sampling time point

tag: pig identifier


title: Gironde - A310

description: Gironde

tag: source location

value: Gironde natural site

tag: tissue

value: Caudal fin

tag: reference composition

value: a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012)

value: liver


title: ArthrospiraPCC8005_control5000Gy-2

source_name: Arthrospira sp. PCC8005 control condition non-irradiated for 5000Gy

value: 0 Gy


title: HRG 08h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0008h00m00s.r01

source_name: 6KR HRG 08h00m Rep1

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: disease

tag: derived from metastatic site

tag: age

tag: gender

value: female


title: subject 224, group C, stimulation B, time 0 days 8670586019_J

tag: cell type

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_27

tag: breed

tag: temperament group

value: high-reactive

value: tetanus vaccination

value: day 28


title: subject 217, group C, stimulation B, time 7 days 8659387159_A

tag: volunteer

tag: bcg quantity (pcr)


title: subject 234, group C, stimulation B, time 0 days 8670586019_I


title: ArthrospiraPCC8005_control3200Gy-3

description: Arthrospira sp. PCC8005 control condition non-irradiated for 3200Gy

tag: treatment


title: ArthrospiraPCC8005_irradiated3200Gy-1


title: HRG 06h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0006h00m00s.r01

source_name: 6KR HRG 06h00m Rep1

value: mammary gland; breast

value: epithelial

value: adenocarcinoma

value: pleural effusion

value: 69 years adult

tag: ethnicity

value: Caucasian

tag: agent

value: HRG

tag: time


title: HRG 04h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0004h00m00s.r02

source_name: 6KR HRG 04h00m Rep2

tag: cell line

tag: tissue


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_25

source_name: PBMC, HR, day 28

value: German Landrace

value: peripheral blood mononuclear cells

tag: Sex

value: male

tag: sampling time point

tag: pig identifier