title: Imprinting_G2R_MGC_VZ_1

description: Chip ID: Imprinting_G2R_MGC_VZ_1

source_name: MIRA-chip in G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero

source_name: Input DNA of G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero


title: Human_fibroblast_P10

status: Public on Feb 17 2015

type: RNA

city: Brescia

first: Nadia

last: Cattane

state: BS

address: Viale Europa 11

department: Department of Translational and Molecular Medicine

country: Italy

institute: University of Brescia

description: Cell line was cultured until the 5th passage

hyb_protocol: Following fragmentation, 5.5 µg of ssDNA were hybridized for 20 hours at 48°C on Human Gene 1.1 ST Array Strip. Array Strips were washed and stained using the GeneAtlas instrument.

scan_protocol: Array Strips were scanned using the GeneAtlas instrument.

data_processing: Data processing was performed using R/Bioconductor. Oligo package was used to read CEL files and compute the log intensities of gene expression by exploiting Robust Multi-array Average (RMA) algorithm. Linear models fitting (LmFit) and Empirical Bayes method (eBayes) from the BioConductor limma package were used to test the differences in mRNA levels.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: patient 10

label_protocol: ssDNA was labelled with biotin according to the standard Affymetrix protocol (GeneAtlasTM WT Expression Kit User Manual)

growth_protocol: Skin biopsies (3 mm2) were collected under local anaesthesia from the scapular region using aseptic conditions and immediately immersed in a saline solution (PBS). All primary cultures were grown in Eagle’s minimum essential medium supplemented with 10% of foetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 μg/ml), non-essential amino acids (1% v/v) and glutamine (1% v/v) under optimal conditions (37° C, 5% CO2).

extract_protocol: RNA from fibroblasts was extracted using the NucleoSpin kit (MACHEREY-NAGEL, Düren , Germany) according to the manufacturer’s instructions.

tag: disease state

value: schizophrenia

tag: tissue

value: skin

tag: cell type

value: fibroblast

tag: gender

value: Male

tag: age


title: Human_fibroblast_P6

source_name: patient 6


title: Human_fibroblast_P4

source_name: patient 4


title: Imprinting_G1R_MGC_DEHP_1

status: Public on Feb 18 2015

type: genomic

city: Grand Rapids

first: Piroska

middle: E

last: Szabo

state: MI

address: 333 Bostwick Ave. NE

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

description: Chip ID: Imprinting_G1R_MGC_DEHP_1

hyb_protocol: According to NimbleGen Kit.

scan_protocol: Following NimbleScan's default using Agilent Scanner.

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Mus musculus

source_name: MIRA-chip in G1R prospermatogonia treated with DEHP in utero

label_protocol: According to standard NimbleGen Protocol.

extract_protocol: For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify MIRA-enriched DNA.

tag: epigenetic feature

value: DNA methylation

tag: mouse cross to generate experimental fetus

value: mouse fetal prospermatogonia

tag: generation of germ cell

tag: treatment in utero of g0 mother

value: DEHP

source_name: Input DNA of G1R prospermatogonia treated with DEHP in utero


title: untreated SK-Mel-147 2

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

country: Germany

institute: INP Greifswald

description: gene expression of untreated control

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides(Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocolGE1_1105 and Grid: 06247_D_F_20131210) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SK-Mel-147 untreated control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop and Bioanalyzer (Agilent, USA).

growth_protocol: SK-Mel-147 were cultured in Dulbecco`s Modified Eagle Medium (DMEM; Lonza, Switzerland) supplemented with 10 % fetal calf serum (FCS; Sigma, USA), 2 mM L-glutamine, 0.1 mg∙L-1 streptomycin and 100 U∙mL-1 penicillin (Lonza, Switzerland).

extract_protocol: After incubating the cells in plasma-treated medium for 2 h, cells were harvested and RNA isolated according to the manufacturer’s instruction (Bio&SELL, Germany). Then, RNA was reversely transcribed using Transcriptor First Strand Synthesis Kit the cDNA synthesis (Roche, Germany). cDNA was conjugated with a fluorescence dye and applied onto whole genome chips (OaksLab, Germnany)

treatment_protocol: For plasma treatment, cells were sub-cultivated and 1×106 cells mL-1 were seeded in a 60 mm-dish 24 h before plasma treatment. Plasma treatment was conducted with the atmospheric pressure argon plasma jet kinpen 09 (neoplas GmbH, Greifswald, Germany) as previously described [29]. A gas flow rate of 3 standard liters per minute was utilized. An indirect treatment regime was chosen to avoid mechanical stress to the cells due to the gas flow. Therefore, 5 mL of DMEM was treated for the indicated time lengths (ranging from 0 s to 180 s) in a meandering pattern. Afterwards, the cells were immediately exposed to the treated medium.

tag: treatment

value: control

tag: cell line


title: Imprinting_G1R_MGC_DEHP_3

description: Chip ID: Imprinting_G1R_MGC_DEHP_3


title: Imprinting_G1R_MGC_VZ_3

description: Chip ID: Imprinting_G1R_MGC_VZ_3

source_name: MIRA-chip in G1R prospermatogonia treated with VZ in utero

value: VZ

source_name: Input DNA of G1R prospermatogonia treated with VZ in utero


title: Human_fibroblast_P1

source_name: patient 1


title: Human_fibroblast_P2

source_name: patient 2


title: Imprinting_G1R_MGC_VZ_1

description: Chip ID: Imprinting_G1R_MGC_VZ_1


title: Imprinting_G1R_MGC_DEHP_2

description: Chip ID: Imprinting_G1R_MGC_DEHP_2


title: Imprinting_G1R_MGC_VZ_2

description: Chip ID: Imprinting_G1R_MGC_VZ_2


title: Human_fibroblast_C15

source_name: control 15

value: Female


title: Imprinting_G1R_MGC_BPA_3

description: Chip ID: Imprinting_G1R_MGC_BPA_3

source_name: MIRA-chip in G1R prospermatogonia treated with BPA in utero

value: BPA

source_name: Input DNA of G1R prospermatogonia treated with BPA in utero


title: Human_fibroblast_C20

source_name: control 20


title: Human_fibroblast_C14

source_name: control 14


title: Human_fibroblast_C18

source_name: control 18


title: Human_fibroblast_C13

source_name: control 13


title: Human_fibroblast_C9

source_name: control 9


title: Human_fibroblast_C16

source_name: control 16


title: Human_fibroblast_C19

source_name: control 19


title: Human_fibroblast_P5

source_name: patient 5


title: Human_fibroblast_C11

source_name: control 11


title: Human_fibroblast_P9

source_name: patient 9


title: Human_fibroblast_C8

source_name: control 8


title: Human_fibroblast_C10

source_name: control 10


title: Human_fibroblast_C17

source_name: control 17


title: Human_fibroblast_C6

source_name: control 6


title: Human_fibroblast_C7

source_name: control 7


title: Imprinting_G1R_MGC_OIL_2

description: Chip ID: Imprinting_G1R_MGC_OIL_2

source_name: MIRA-chip in G1R prospermatogonia treated with OIL in utero

value: oil control

source_name: Input DNA of G1R prospermatogonia treated with OIL in utero


title: Human_fibroblast_C4

source_name: control 4


title: Human_fibroblast_P7

source_name: patient 7


title: Human_fibroblast_C5

source_name: control 5


title: Human_fibroblast_C3

source_name: control 3


title: Human_fibroblast_C1

source_name: control 1


title: Human_fibroblast_C2

source_name: control 2


title: Imprinting_G1R_MGC_OIL_1

description: Chip ID: Imprinting_G1R_MGC_OIL_1


title: HuMonocytes_Medium_1hr_LPS_2hr_rep3

city: London

first: Ana

last: Cehovin

state: United Kingdom

address: Exhibition Road

department: Centre for Molecular Microbiology and Infection

country: United Kingdom

institute: Imperial College London

description: Study on inhibitory activity of M. tuberculosis Cpn60.1 on activated human monocytes

hyb_protocol: Biotinylated cDNA was addded to the hybridization cocktail, and incubated on Human GeneChip ST Array for 17 hours, at 60rpm at 46°C. Staining and washing was done on Fluidics station 450.

scan_protocol: Human GeneChip arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: The arrays were normalized with Robust Multi-Chip Average algorithm (RMA) using the Affymetrix Expression Console 1.1. Probe sets with signals below the 85% percentile across all arrays or without gene annotation were removed from the data set leaving 17,649 probe sets for further analysis. The statistical analysis of samples (comparing triplicate biological replicates of treated to untreated cells) was performed using a moderated t-test in Limma using a p-value ≤ 0.05 adjusted for multiple testing, and a minimum fold change of 1.5.

source_name: Human monocytes, pre-incubated in medium for 1 hr, stimulated with 1ng/ml LPS for 2 hrs

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol described in GeneChip® Whole Transcript (WT) Sense Target   Labeling Assay Manual v.4

growth_protocol: Human monocytes were purified from peripheral blood by negative selection and maintained in RPMI medium containing 2% autologous plasma before stimuation.

extract_protocol: Total RNA was isolated from three healthy donors using the RNEasy Kit according to the manufacturer’s instructions (Qiagen)

treatment_protocol: To study the pro-inflammatory activities of Cpn60.1, human monocytes were purified from three healthy donors and incubated with 10 μg/ml M. tuberculosis Cpn60.1 (or 100 ng/ml LPS as a positive control or medium only as a negative control). To study the inhibitory effectds of Cpn60.1 on human monocytes, the cells were pre-exposed to 10μg/ml or 0.1ng/ml of Cpn60.1, washed and incubated with 1ng/ml LPS for further 2 hours. For positive control, the cells were pre-exposed to medium before washing and LPS stimulation while for the negative control, the cells were pre-exposed to medium, washed and again exposed to medium alone.

value: Human peripheral blood-derived monocytes

tag: agent


title: HuMonocytes_Cpn60.1 0.1_1hr_LPS_2hr_rep2

source_name: Human monocytes, pre-incubated with 0.1ng/ml Cpn60.1 for 1 hr, stimulated with 1ng/ml LPS for 2 hrs


title: HuMonocytes_Cpn60.1 10_1hr_LPS_2hr_rep2

source_name: Human monocytes, pre-incubated with 10μg/ml Cpn60.1 for 1 hr, stimulated with 1ng/ml LPS for 2 hrs


title: HuMonocytes_Cpn60.1 0.1_1hr_LPS_2hr_rep1

value: pre-incubated with 0.1ng/ml Cpn60.1 for 1 hr, stimulated with 1ng/ml LPS for 2 hrs


title: HuMonocytes_Medium_1hr_LPS_2hr_rep1

value: pre-incubated in medium for 1 hr, stimulated with 1ng/ml LPS for 2 hrs


title: HuMonocytes_Cpn60.1 0.1_1hr_LPS_2hr_rep3


title: HuMonocytes_Medium_1hr_LPS_2hr_rep2


title: Imprinting_G1R_MGC_BPA_1

description: Chip ID: Imprinting_G1R_MGC_BPA_1

source_name: MIRA-chip in G1R prospermatogonia treated with BPA in utero

source_name: Input DNA of G1R prospermatogonia treated with BPA in utero


title: HuMonocytes_Cpn60.1_2hr_rep3

description: Study of pro-inflammatory activity of M. tuberculosis Cpn60.1 on human monocytes

source_name: Human monocytes, incubated with 10μg/ml Cpn60.1 for 2 hrs


title: HuMonocytes_Medium_2hr_rep3

source_name: Human monocytes, incubated in medium alone for 2 hrs

value: incubated in medium alone for 2 hrs


title: HuMonocytes_Cpn60.1_2hr_rep1

value: incubated with 10μg/ml Cpn60.1 for 2 hrs


title: HuMonocytes_Cpn60.1 10_1hr_LPS_2hr_rep3

value: pre-incubated with 10μg/ml Cpn60.1 for 1 hr, stimulated with 1ng/ml LPS for 2 hrs


title: HuMonocytes_Cpn60.1_2hr_rep2


title: HuMonocytes_Medium_1hr_Medium_2hr_rep1

source_name: Human monocytes, pre-incubated in medium for 1 hr, incubated in medium for 2 hrs


title: Human_fibroblast_P3

source_name: patient 3

value: schizophrenia

value: skin


title: HuMonocytes_Medium_2hr_rep2


title: HuMonocytes_Cpn60.1 10_1hr_LPS_2hr_rep1


title: HuMonocytes_LPS_2hr_rep3

source_name: Human monocytes, incubated with 100ng/ml LPS for 2 hrs

value: incubated with 100ng/ml LPS for 2 hrs


title: HuMonocytes_Medium_1hr_Medium_2hr_rep3

value: pre-incubated in medium for 1 hr, incubated in medium for 2 hrs


title: HuMonocytes_Medium_1hr_Medium_2hr_rep2


title: HuMonocytes_LPS_2hr_rep2


title: HuMonocytes_LPS_2hr_rep1


title: HuMonocytes_Medium_2hr_rep1


title: Imprinting_G1R_MGC_BPA_2

description: Chip ID: Imprinting_G1R_MGC_BPA_2

value: DNA methylation

value: mouse fetal prospermatogonia


title: Human_fibroblast_C12

source_name: control 12

value: control

value: fibroblast


title: OLS ID: 9753 - Assay ID: 9172 [HK layout]

type: protein

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the higher-quality scan was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: The 8-mer Z-scores were calculated as the average of normalized intensities of probes (i.e. probe Z-scores) that contained the 8-mer.

molecule: protein

organism: synthetic construct

source_name: Egr1 variant_Ciona intestinalis

label_protocol: Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

tag: region


title: OLS ID: 9599 - Assay ID: 9171 [ME layout]

source_name: Egr1 variant_Homo sapiens


title: OLS ID: 9308 - Assay ID: 9207 [HK layout]


title: OLS ID: 9599 - Assay ID: 9187 [HK layout]


title: OLS ID: 7460 - Assay ID: 9280 [HK layout]

source_name: Egr1 variant_Mus musculus


title: OLS ID: 7754 - Assay ID: 10306 [ME layout]


title: OLS ID: 692 - Assay ID: 10300 [HK layout]

source_name: Egr1 variant_Ashbya gossypii


title: Imprinting_G1R_MGC_OIL_3

description: Chip ID: Imprinting_G1R_MGC_OIL_3

source_name: MIRA-chip in G1R prospermatogonia treated with OIL in utero

source_name: Input DNA of G1R prospermatogonia treated with OIL in utero


title: OLS ID: 6120 - Assay ID: 9240 [HK layout]


title: OLS ID: 6120 - Assay ID: 9224 [ME layout]


title: OLS ID: 9753 - Assay ID: 9156 [ME layout]


title: OLS ID: 7460 - Assay ID: 9264 [ME layout]


title: OLS ID: 7754 - Assay ID: 10370 [HK layout]


title: OLS ID: 6212 - Assay ID: 9167 [ME layout]


title: OLS ID: 7212 - Assay ID: 9223 [ME layout]


title: OLS ID: 7212 - Assay ID: 9239 [HK layout]


title: OLS ID: 6114 - Assay ID: 9259 [ME layout]


title: OLS ID: 5992 - Assay ID: 9248 [HK layout]

source_name: Egr1 variant_Drosophila pseudoobscura


title: OLS ID: 9308 - Assay ID: 9191 [ME layout]


title: OLS ID: 7675 - Assay ID: 10285 [ME layout]


title: OLS ID: 6114 - Assay ID: 9275 [HK layout]


title: OLS ID: 692 - Assay ID: 10284 [ME layout]


title: OLS ID: 7675 - Assay ID: 10536 [HK layout]


title: OLS ID: 6212 - Assay ID: 9183 [HK layout]


title: OLS ID: 6002 - Assay ID: 9086 [HK layout]


title: OLS ID: 6002 - Assay ID: 9070 [ME layout]


title: OLS ID: 5967 - Assay ID: 9209 [HK layout]


title: OLS ID: 5992 - Assay ID: 9232 [ME layout]


title: OLS ID: 46986 - Assay ID: 10282 [ME layout]

source_name: Egr1 variant_Zebrafish


title: OLS ID: 5926 - Assay ID: 9369 [HK layout]

source_name: Egr1 variant_Aedes aegypti


title: OLS ID: 5926 - Assay ID: 9353 [ME layout]


title: OLS ID: 4626 - Assay ID: 9378 [HK layout]

source_name: Egr1 variant_Macaca fascicularis


title: OLS ID: 45658 - Assay ID: 9144 [HK layout]


title: OLS ID: 45719 - Assay ID: 9175 [HK layout]


title: OLS ID: 46758 - Assay ID: 9368 [HK layout]


title: OLS ID: 5322 - Assay ID: 9267 [ME layout]


title: OLS ID: 5967 - Assay ID: 9193 [ME layout]


title: OLS ID: 44516 - Assay ID: 9225 [ME layout]

source_name: Egr1 variant_Sea squirt


title: OLS ID: 46986 - Assay ID: 10298 [HK layout]


title: OLS ID: 46164 - Assay ID: 9115 [HK layout]


title: OLS ID: 44831 - Assay ID: 9344 [HK layout]


title: OLS ID: 46164 - Assay ID: 9099 [ME layout]


title: OLS ID: 45658 - Assay ID: 9128 [ME layout]


title: OLS ID: 46758 - Assay ID: 9352 [ME layout]


title: OLS ID: 45173 - Assay ID: 9094 [ME layout]


title: OLS ID: 44223 - Assay ID: 9119 [HK layout]


title: OLS ID: 5322 - Assay ID: 9283 [HK layout]


title: OLS ID: 44516 - Assay ID: 9241 [HK layout]


title: OLS ID: 43867 - Assay ID: 9334 [HK layout]


title: OLS ID: 4626 - Assay ID: 9362 [ME layout]


title: OLS ID: 44223 - Assay ID: 9103 [ME layout]


title: OLS ID: 45719 - Assay ID: 9159 [ME layout]


title: OLS ID: 44831 - Assay ID: 9328 [ME layout]


title: OLS ID: 45173 - Assay ID: 9110 [HK layout]


title: OLS ID: 43744 - Assay ID: 9413 [HK layout]


title: OLS ID: 43502 - Assay ID: 10375 [HK layout]


title: OLS ID: 43502 - Assay ID: 10311 [ME layout]


title: OLS ID: 43353 - Assay ID: 9210 [HK layout]


title: OLS ID: 4251 - Assay ID: 10347 [ME layout]


title: OLS ID: 43867 - Assay ID: 9318 [ME layout]


title: OLS ID: 4251 - Assay ID: 10363 [HK layout]


title: OLS ID: 42469 - Assay ID: 10346 [ME layout]

source_name: Egr1 variant_Sloth


title: OLS ID: 42425 - Assay ID: 9148 [HK layout]


title: OLS ID: 43353 - Assay ID: 9194 [ME layout]


title: OLS ID: 43744 - Assay ID: 9131 [ME layout]


title: OLS ID: 42425 - Assay ID: 9132 [ME layout]


title: OLS ID: 41340 - Assay ID: 10374 [HK layout]

source_name: Egr1 variant_Guinea pig


title: OLS ID: 42469 - Assay ID: 10362 [HK layout]


title: OLS ID: 40844 - Assay ID: 9060 [ME layout]

source_name: Egr1 variant_Dog


title: OLS ID: 40570 - Assay ID: 9203 [ME layout]


title: OLS ID: 39611 - Assay ID: 9080 [HK layout]

source_name: Egr1 variant_Cow


title: OLS ID: 4108 - Assay ID: 9273 [HK layout]


title: OLS ID: 4108 - Assay ID: 9257 [ME layout]


title: OLS ID: 41340 - Assay ID: 10310 [ME layout]


title: OLS ID: 39611 - Assay ID: 9064 [ME layout]


title: OLS ID: 39058 - Assay ID: 9278 [HK layout]


title: OLS ID: 3912 - Assay ID: 9281 [HK layout]


title: OLS ID: 40570 - Assay ID: 9219 [HK layout]


title: OLS ID: 40940 - Assay ID: 9293 [ME layout]


title: OLS ID: 39218 - Assay ID: 10517 [ME layout]


title: OLS ID: 42271 - Assay ID: 9078 [HK layout]


title: OLS ID: 42271 - Assay ID: 9062 [ME layout]


title: OLS ID: 39596 - Assay ID: 10532 [HK layout]


title: OLS ID: 39596 - Assay ID: 10516 [ME layout]


title: OLS ID: 40844 - Assay ID: 9076 [HK layout]


title: OLS ID: 38776 - Assay ID: 9091 [HK layout]


title: OLS ID: 38776 - Assay ID: 9075 [ME layout]


title: OLS ID: 40940 - Assay ID: 9309 [HK layout]


title: OLS ID: 39058 - Assay ID: 9262 [ME layout]


title: OLS ID: 38884 - Assay ID: 10367 [HK layout]


title: OLS ID: 39218 - Assay ID: 10533 [HK layout]


title: OLS ID: 38732 - Assay ID: 9121 [HK layout]


title: OLS ID: 38884 - Assay ID: 10351 [ME layout]


title: OLS ID: 3912 - Assay ID: 9265 [ME layout]


title: OLS ID: 38732 - Assay ID: 9105 [ME layout]


title: OLS ID: 37961 - Assay ID: 9406 [HK layout]


title: OLS ID: 37961 - Assay ID: 9390 [ME layout]


title: OLS ID: 37799 - Assay ID: 9081 [HK layout]


title: OLS ID: 37855 - Assay ID: 9215 [HK layout]


title: OLS ID: 37919 - Assay ID: 9271 [HK layout]


title: OLS ID: 37919 - Assay ID: 9255 [ME layout]


title: OLS ID: 37169 - Assay ID: 10275 [ME layout]


title: OLS ID: 37146 - Assay ID: 9320 [ME layout]


title: OLS ID: 3475 - Assay ID: 10378 [HK layout]


title: OLS ID: 37542 - Assay ID: 9130 [ME layout]


title: OLS ID: 3489 - Assay ID: 9237 [HK layout]


title: OLS ID: 35742 - Assay ID: 10295 [HK layout]

source_name: Egr1 variant_Anole lizard


title: OLS ID: 34341 - Assay ID: 9244 [HK layout]


title: OLS ID: 3475 - Assay ID: 10314 [ME layout]


title: OLS ID: 37799 - Assay ID: 9065 [ME layout]


title: OLS ID: 37169 - Assay ID: 10291 [HK layout]


title: OLS ID: 35742 - Assay ID: 10279 [ME layout]


title: OLS ID: 36768 - Assay ID: 9243 [HK layout]

source_name: Egr1 variant_Anopheles mosquito


title: OLS ID: 34341 - Assay ID: 9228 [ME layout]


title: OLS ID: 37542 - Assay ID: 9146 [HK layout]


title: OLS ID: 34199 - Assay ID: 9297 [ME layout]


title: OLS ID: 37855 - Assay ID: 9199 [ME layout]


title: OLS ID: 3489 - Assay ID: 9221 [ME layout]


title: OLS ID: 33254 - Assay ID: 10274 [ME layout]


title: OLS ID: 32985 - Assay ID: 10272 [ME layout]


title: OLS ID: 34199 - Assay ID: 9313 [HK layout]


title: OLS ID: 37146 - Assay ID: 9336 [HK layout]


title: OLS ID: 32786 - Assay ID: 9104 [ME layout]


title: OLS ID: 32985 - Assay ID: 10288 [HK layout]


title: OLS ID: 36768 - Assay ID: 9227 [ME layout]


title: OLS ID: 32786 - Assay ID: 9120 [HK layout]


title: OLS ID: 33254 - Assay ID: 10290 [HK layout]


title: OLS ID: 3264 - Assay ID: 9272 [HK layout]


title: OLS ID: 31376 - Assay ID: 9079 [HK layout]


title: OLS ID: 32622 - Assay ID: 10302 [HK layout]


title: OLS ID: 29907 - Assay ID: 9145 [HK layout]


title: OLS ID: 29907 - Assay ID: 9129 [ME layout]


title: OLS ID: 32622 - Assay ID: 10286 [ME layout]


title: OLS ID: 31820 - Assay ID: 10471 [HK layout]


title: OLS ID: 31820 - Assay ID: 10455 [ME layout]


title: OLS ID: 31376 - Assay ID: 9063 [ME layout]


title: OLS ID: 31276 - Assay ID: 9111 [HK layout]


title: OLS ID: 30111 - Assay ID: 9202 [ME layout]


title: OLS ID: 30467 - Assay ID: 9186 [HK layout]


title: OLS ID: 31276 - Assay ID: 9095 [ME layout]


title: OLS ID: 30467 - Assay ID: 9170 [ME layout]


title: OLS ID: 30111 - Assay ID: 9218 [HK layout]


title: OLS ID: 3264 - Assay ID: 9256 [ME layout]


title: OLS ID: 29680 - Assay ID: 9163 [ME layout]


title: OLS ID: 27479 - Assay ID: 9184 [HK layout]


title: OLS ID: 28598 - Assay ID: 9269 [HK layout]


title: OLS ID: 28598 - Assay ID: 9253 [ME layout]


title: OLS ID: 28130 - Assay ID: 10293 [HK layout]


title: OLS ID: 2820 - Assay ID: 9331 [ME layout]


title: OLS ID: 2820 - Assay ID: 9347 [HK layout]


title: OLS ID: 27985 - Assay ID: 9263 [ME layout]


title: OLS ID: 27985 - Assay ID: 9279 [HK layout]


title: OLS ID: 27384 - Assay ID: 9254 [ME layout]


title: OLS ID: 27479 - Assay ID: 9168 [ME layout]


title: OLS ID: 28130 - Assay ID: 10277 [ME layout]


title: OLS ID: 29680 - Assay ID: 9179 [HK layout]


title: OLS ID: 26892 - Assay ID: 9077 [HK layout]


title: OLS ID: 26686 - Assay ID: 9343 [HK layout]


title: OLS ID: 26528 - Assay ID: 9066 [ME layout]


title: OLS ID: 26686 - Assay ID: 9327 [ME layout]


title: OLS ID: 26528 - Assay ID: 9082 [HK layout]


title: OLS ID: 25707 - Assay ID: 9178 [HK layout]


title: OLS ID: 27384 - Assay ID: 9270 [HK layout]


title: OLS ID: 26093 - Assay ID: 9340 [HK layout]


title: OLS ID: 26093 - Assay ID: 9324 [ME layout]


title: OLS ID: 25474 - Assay ID: 9246 [HK layout]


title: OLS ID: 26550 - Assay ID: 9160 [ME layout]


title: OLS ID: 25474 - Assay ID: 9230 [ME layout]


title: OLS ID: 26892 - Assay ID: 9061 [ME layout]


title: OLS ID: 26471 - Assay ID: 10361 [HK layout]


title: OLS ID: 26550 - Assay ID: 9176 [HK layout]


title: OLS ID: 25707 - Assay ID: 9162 [ME layout]


title: OLS ID: 25245 - Assay ID: 9349 [ME layout]


title: OLS ID: 26471 - Assay ID: 10345 [ME layout]


title: OLS ID: 24033 - Assay ID: 9363 [ME layout]

source_name: Egr1 variant_Caenorhabditis briggsae


title: OLS ID: 23735 - Assay ID: 9092 [ME layout]


title: Stable transfectant A20 IgE+ clone 41.2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Stable transfectant A20 IgE+ clone 41.2

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing

source_name: Lymphocyte

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% of fetal bovin serum and 50µM beta-mercaptoethanol at 500 000 cells/mL

extract_protocol: Cells were harvested and resuspended in one ml of Tri-reagent® (Ambion, Austin, TX), RNA was extracted using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion). Samples were stored at -80ºC until used. RNA quality and quantity were verified with RNA 6000 Nanokit (Agilent technologies) and 1 µg were used for cDNA synthesis and microarray hybridization on Agilent chips mmu 8x60k 41442.

value: B lymphoma cell line A20

tag: transfection

value: Stable transfectant IgE+ clone 41


title: OLS ID: 24152 - Assay ID: 9358 [ME layout]

source_name: Egr1 variant_Ciona intestinalis


title: OLS ID: 25025 - Assay ID: 9339 [HK layout]


title: Stable transfectant A20 IgE+ clone 41.1

description: Stable transfectant A20 IgE+ clone 41.1


title: OLS ID: 24152 - Assay ID: 9374 [HK layout]


title: OLS ID: 24970 - Assay ID: 9182 [HK layout]


title: OLS ID: 24970 - Assay ID: 9166 [ME layout]


title: OLS ID: 23735 - Assay ID: 9108 [HK layout]

source_name: Egr1 variant_Mus musculus


title: OLS ID: 23734 - Assay ID: 9274 [HK layout]

source_name: Egr1 variant_Equus caballus


title: OLS ID: 25025 - Assay ID: 9323 [ME layout]


title: OLS ID: 23322 - Assay ID: 9116 [HK layout]

source_name: Egr1 variant_Chaetomium globosum


title: OLS ID: 24033 - Assay ID: 9379 [HK layout]


title: OLS ID: 25245 - Assay ID: 9365 [HK layout]


title: OLS ID: 23321 - Assay ID: 9117 [HK layout]

source_name: Egr1 variant_Gibberella zeae


title: OLS ID: 23322 - Assay ID: 9100 [ME layout]


title: OLS ID: 22787 - Assay ID: 9153 [HK layout]

source_name: Egr1 variant_Saccharomyces cerevisiae


title: Stable transfectant A20 IgE+ clone 18.2

description: Stable transfectant A20 IgE+ clone 18.2

value: Stable transfectant IgE+ clone 18


title: Stable transfectant A20 IgE+ clone 18.1

description: Stable transfectant A20 IgE+ clone 18.1


title: OLS ID: 23321 - Assay ID: 9101 [ME layout]


title: OLS ID: 23312 - Assay ID: 9138 [ME layout]


title: Stable transfectant A20 IgM+.1

description: Stable transfectant A20 IgM+.1

value: Stable transfectant IgM+


title: Stable transfectant A20 IgM+.2

description: Stable transfectant A20 IgM+.2


title: Untransfected A20.2

description: Untransfected A20.2

value: Untransfected


title: OLS ID: 23734 - Assay ID: 9258 [ME layout]


title: OLS ID: 22787 - Assay ID: 9137 [ME layout]


title: OLS ID: 21597 - Assay ID: 9181 [HK layout]

source_name: Egr1 variant_Anopheles gambiae


title: Untransfected A20.1

description: Untransfected A20.1


title: UCP1 Transgene sk.muscle, LFD, replicate 7

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool  (pool of equimolar amounts of all samples of SUPERSERIES) according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with Ozone-barrier slides.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: UCP1 Transgene, Low Fat Diet

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).

extract_protocol: Total RNA was isolated from gastrocnemius skeletal muscle tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: Animals were fed a purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes & Nutrition 2012) for 12 weeks.

tag: background strain

value: male

tag: developmental stage

value: adult

value: gastrocnemius skeletal muscle

tag: genotype/variation

value: UCP1 transgene

source_name: reference pool

tag: sample type

value: reference pool


title: OLS ID: 20426 - Assay ID: 9151 [HK layout]

source_name: Egr1 variant_Tetraodon nigroviridis


title: OLS ID: 19114 - Assay ID: 9345 [HK layout]


title: OLS ID: 21597 - Assay ID: 9165 [ME layout]


title: OLS ID: 20426 - Assay ID: 9135 [ME layout]


title: UCP1 Transgene sk.muscle, LFD, replicate 5

tag: tissue


title: OLS ID: 20496 - Assay ID: 10476 [HK layout]

source_name: Egr1 variant_Aedes aegypti


title: UCP1 Transgene sk.muscle, LFD, replicate 4


title: OLS ID: 19114 - Assay ID: 9329 [ME layout]


title: OLS ID: 19279 - Assay ID: 9157 [ME layout]


title: OLS ID: 17492 - Assay ID: 9088 [HK layout]

source_name: Egr1 variant_Drosophila melanogaster


title: OLS ID: 20496 - Assay ID: 10460 [ME layout]


title: UCP1 Transgene sk.muscle, LFD, replicate 1


title: control WT, LFD, replicate 6

source_name: WT, Low Fat Diet

value: wild-type


title: OLS ID: 17821 - Assay ID: 10528 [HK layout]

source_name: Egr1 variant_Oryza sativa


title: OLS ID: 17821 - Assay ID: 10512 [ME layout]


title: UCP1 Transgene sk.muscle, LFD, replicate 3


title: OLS ID: 17480 - Assay ID: 9071 [ME layout]


title: OLS ID: 17480 - Assay ID: 9087 [HK layout]


title: OLS ID: 19279 - Assay ID: 9173 [HK layout]


title: OLS ID: 17492 - Assay ID: 9072 [ME layout]


title: UCP1 Transgene sk.muscle, LFD, replicate 2


title: OLS ID: 17269 - Assay ID: 9377 [HK layout]

source_name: Egr1 variant_Neurospora crassa


title: OLS ID: 17269 - Assay ID: 9361 [ME layout]


title: OLS ID: 17172 - Assay ID: 9142 [HK layout]


title: OLS ID: 17239 - Assay ID: 9335 [HK layout]

source_name: Egr1 variant_Cryptococcus neoformans


title: control WT, LFD, replicate 3


title: OLS ID: 17239 - Assay ID: 9319 [ME layout]


title: control WT, LFD, replicate 5


title: OLS ID: 17171 - Assay ID: 9316 [ME layout]


title: control WT, LFD, replicate 2


title: control WT, LFD, replicate 4


title: OLS ID: 16727 - Assay ID: 9305 [HK layout]


title: OLS ID: 17172 - Assay ID: 9126 [ME layout]


title: OLS ID: 16521 - Assay ID: 9222 [ME layout]

source_name: Egr1 variant_Phaeosphaeria nodorum


title: OLS ID: 23312 - Assay ID: 9154 [HK layout]


title: OLS ID: 16400 - Assay ID: 9109 [HK layout]


title: OLS ID: 16355 - Assay ID: 9107 [ME layout]

source_name: Egr1 variant_Sus scrofa


title: OLS ID: 16521 - Assay ID: 9238 [HK layout]


title: OLS ID: 16467 - Assay ID: 9214 [HK layout]

source_name: Egr1 variant_Brachydanio rerio


title: OLS ID: 16727 - Assay ID: 9289 [ME layout]


title: OLS ID: 16320 - Assay ID: 9370 [HK layout]

source_name: Egr1 variant_Mus musculus


title: OLS ID: 17171 - Assay ID: 9332 [HK layout]


title: OLS ID: 16467 - Assay ID: 9198 [ME layout]


title: OLS ID: 16285 - Assay ID: 9204 [HK layout]


title: OLS ID: 16285 - Assay ID: 9188 [ME layout]


title: OLS ID: 16320 - Assay ID: 9354 [ME layout]


title: OLS ID: 16400 - Assay ID: 9093 [ME layout]


title: OLS ID: 16355 - Assay ID: 9123 [HK layout]


title: OLS ID: 16252 - Assay ID: 9290 [ME layout]


title: OLS ID: 16252 - Assay ID: 9306 [HK layout]


title: OLS ID: 15873 - Assay ID: 9247 [HK layout]

source_name: Egr1 variant_Homo sapiens


title: OLS ID: 15886 - Assay ID: 9364 [HK layout]


title: OLS ID: 15886 - Assay ID: 9348 [ME layout]


title: control WT, LFD, replicate 1


title: OLS ID: 15873 - Assay ID: 9231 [ME layout]


title: OLS ID: 15707 - Assay ID: 9212 [HK layout]


title: OLS ID: 15673 - Assay ID: 9245 [HK layout]

source_name: Egr1 variant_Primates


title: OLS ID: 15660 - Assay ID: 10365 [HK layout]

source_name: Egr1 variant_Ciona intestinalis


title: OLS ID: 15707 - Assay ID: 9196 [ME layout]


title: OLS ID: 15685 - Assay ID: 9341 [HK layout]


title: OLS ID: 15673 - Assay ID: 9229 [ME layout]


title: OLS ID: 15605 - Assay ID: 9150 [HK layout]


title: OLS ID: 15445 - Assay ID: 9211 [HK layout]


title: OLS ID: 15660 - Assay ID: 10349 [ME layout]


title: OLS ID: 15000 - Assay ID: 10307 [ME layout]

source_name: Egr1 variant_Anopheles gambiae


title: OLS ID: 15531 - Assay ID: 9355 [ME layout]


title: OLS ID: 15445 - Assay ID: 9195 [ME layout]


title: OLS ID: 15685 - Assay ID: 9325 [ME layout]


title: OLS ID: 1483 - Assay ID: 9312 [HK layout]


title: OLS ID: 15438 - Assay ID: 9141 [HK layout]

source_name: Egr1 variant_Cnidaria


title: OLS ID: 14627 - Assay ID: 9326 [ME layout]


title: OLS ID: 14526 - Assay ID: 9346 [HK layout]


title: OLS ID: 15000 - Assay ID: 10371 [HK layout]


title: UCP1 Transgene sk.muscle, LFD, replicate 6

source_name: UCP1 Transgene, Low Fat Diet

source_name: reference pool


title: OLS ID: 14627 - Assay ID: 9342 [HK layout]


title: OLS ID: 14526 - Assay ID: 9330 [ME layout]

source_name: Egr1 variant_Tetraodon nigroviridis


title: OLS ID: 15605 - Assay ID: 9134 [ME layout]


title: OLS ID: 15531 - Assay ID: 9371 [HK layout]

source_name: Egr1 variant_Drosophila melanogaster


title: OLS ID: 15438 - Assay ID: 9125 [ME layout]


title: OLS ID: 13741 - Assay ID: 9220 [ME layout]


title: OLS ID: 13741 - Assay ID: 9236 [HK layout]


title: OLS ID: 13699 - Assay ID: 9152 [HK layout]


title: OLS ID: 13699 - Assay ID: 9136 [ME layout]


title: OLS ID: 13400 - Assay ID: 9200 [ME layout]


title: OLS ID: 13399 - Assay ID: 9338 [HK layout]


title: OLS ID: 13124 - Assay ID: 9206 [HK layout]

source_name: Egr1 variant_Dugesia japonica


title: OLS ID: 12682 - Assay ID: 9405 [HK layout]


title: OLS ID: 13399 - Assay ID: 9322 [ME layout]


title: OLS ID: 13379 - Assay ID: 10502 [HK layout]


title: OLS ID: 1483 - Assay ID: 9296 [ME layout]


title: OLS ID: 13124 - Assay ID: 9190 [ME layout]


title: OLS ID: 13379 - Assay ID: 10486 [ME layout]


title: OLS ID: 12109 - Assay ID: 9337 [HK layout]

source_name: Egr1 variant_Aspergillus oryzae


title: OLS ID: 12402 - Assay ID: 9201 [ME layout]


title: OLS ID: 12402 - Assay ID: 9217 [HK layout]


title: OLS ID: 12681 - Assay ID: 9124 [ME layout]


title: OLS ID: 11124 - Assay ID: 9261 [ME layout]

source_name: Egr1 variant_Xenopus laevis


title: OLS ID: 10732 - Assay ID: 9213 [HK layout]


title: OLS ID: 11124 - Assay ID: 9277 [HK layout]


title: OLS ID: 10732 - Assay ID: 9197 [ME layout]


title: OLS ID: 12681 - Assay ID: 9140 [HK layout]


title: OLS ID: 11781 - Assay ID: 10273 [ME layout]


title: OLS ID: 12109 - Assay ID: 9321 [ME layout]


title: OLS ID: 11781 - Assay ID: 10289 [HK layout]


title: OLS ID: 10605 - Assay ID: 9177 [HK layout]

source_name: Egr1 variant_Aedes aegypti


title: OLS ID: 13400 - Assay ID: 9216 [HK layout]


title: Sort-purified Flvcr-/- DP thymocytes replicate#3

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr-/-mice and FACS sorted
KO3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi

source_name: thymus

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

extract_protocol: After FACS-sorting , DP thymocytes were washed twice with cold PBS and cell pellets were frozen and stored at -80C until all samples were collected. RNA was isolated using Qiagen RNeasy Plus Mini Kit per the manufacturer’s instructions and the yield was determined on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). Samples that had an appropriate yield (typically 100ng total RNA) were subsequently analyzed for RNA integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: cell type

value: Flvcr-/-

value: CD4+CD8+ DP thymocyte

tag: strain

value: C57BL/6 background


title: OLS ID: 10510 - Assay ID: 10278 [ME layout]


title: Sort-purified Flvcr-/- DP thymocytes replicate#2

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr-/-mice and FACS sorted
KO2


title: Sort-purified Flvcr+/+ DP thymocytes replicate#1

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr+/+ mice and FACS sorted
WT1

value: Flvcr+/+


title: OLS ID: 10605 - Assay ID: 9161 [ME layout]


title: OLS ID: 10510 - Assay ID: 10294 [HK layout]


title: Sort-purified Flvcr+/+ DP thymocytes replicate#2

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr+/+ mice and FACS sorted
WT2


title: Sort-purified Flvcr-/- DP thymocytes replicate#1

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr-/-mice and FACS sorted
KO1


title: OLS ID: 12682 - Assay ID: 9389 [ME layout]


title: Sort-purified Flvcr+/+ DP thymocytes replicate#3

description:
CD4+CD8+ thymocytes were isolated from thymuses of Flvcr+/+ mice and FACS sorted
WT3


title: Blood-P084

status: Public on Feb 16 2015

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R-bioconductor/minfi
The non_normalized.txt contains unmethylated and methylated signal intensities. The beta values were obtained before raw data normalization; we used Subset-quantile Within Array Normalization (SWAN)(available in the minfi Bioconductor package).

label: Cy3, Cy5

source_name: no prenatal tobacco exposure

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was extracted from venous umbilical cord blood with the RealPure kit (REALPURE, REAL, DURVIZ, Ref: RBMEG01) and was quantified with the Nanodrop-2000C Spectrophotometer. A DNA quality check was performed with Quant-iT PicoGreen dsDNA reagent.

treatment_protocol: Umbilical cord blood was collected in EDTA-tubes, centrifuged to yield plasma, stored at -80ºC and thawed before use.

tag: prenatal tobacco exposure

value: NO

tag: newborn gender

value: female

value: Umbilical cord blood


title: Blood-P068


title: Blood-P054


title: Blood-P124


title: Blood-P058


title: Blood-P096


title: Harvard Sib female CHB1000005676

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: Harvard.Sib.female

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: group

tag: gender

value: F

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Black

value: leukocyte


title: Blood-P044


title: Harvard Sib female CHB1000005840

description: Harvard.Sib.female

hyb_protocol: Followed the manufacturer's (Illumina) specifications


title: Blood-P052


title: Blood-N03

source_name: prenatal tobacco exposure

value: YES


title: Harvard Sib female CHB1000005862

description: Harvard.Sib.female

value: Unknown


title: Harvard Sib female CHB1000005922

description: Harvard.Sib.female

value: Other


title: Ctrl CTL91

description: Ctrl

value: Ctrl


title: Harvard Sib female CHB1000005876

description: Harvard.Sib.female


title: Ctrl CTL93

description: Ctrl


title: Ctrl CTL92

description: Ctrl


title: Blood-N04


title: Harvard Sib female CHB1000005686

description: Harvard.Sib.female


title: Blood-P012

value: male


title: Blood-N02


title: Blood-N13


title: Blood-N14


title: Blood-P056


title: Blood-N09


title: Blood-N06


title: Blood-P062


title: Blood-N10


title: Blood-N12


title: Harvard Sib female CHB1000005928

description: Harvard.Sib.female

value: Asian


title: Harvard Sib female CHB1000005706

description: Harvard.Sib.female


title: Harvard Sib female CHB1000005678

description: Harvard.Sib.female


title: Harvard Sib female CHB1000005712

description: Harvard.Sib.female


title: MDS-2.13C II

city: New York

first: Eirini

last: Papapetrou

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing: The complete set of data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi. The dataset was initially filtered by flagging probes that were below a signal “noise floor,” which was established using the 75th percentile of the negative control probe signals within each array. The dataset was subsequently filtered by employing a variance filter using the “shorth” function of the Bioconductor package genefilter.  Statistical analyses between donor-paired samples (hTERT+Vector versus hTERT+MEG3) were performed using the Bioconductor package limma, and a false discovery rate (FDR) method was used to correct for multiple testing. Differential gene expression was defined as |log2 (ratio) | ≥ 0.485 (± 1.4-fold) with the FDR set to 5%,

growth_protocol: hPSCs were kept in an undifferentiated, pluripotent state by using 6 ng/ml FGF2 (Recombinant Human FGF basic (146 aa), R and D systems, 233-FB-001MG/CF) and grown on top of murine embryonic fibroblasts feeder layer inactivated by mitomycin C

extract_protocol: Total RNA extracted using Trizol and RNA was further cleaned with QIAGEN Rneasy mini kit following manufacturer's instructions    RNeasy Mini Kit     RNeasy Mini Kit  following manufacturer's instructions

treatment_protocol: no treatment

value: human induced pluripotent stem cells

tag: cell line

value: MDS 206.13.diploid


title: MDS-2.13C III


title: MDS-2.13C I


title: ART ART_GB089481

description: ART

value: ART


title: ART ART_GB079981

description: ART


title: Harvard Sib female CHB1000007295

description: Harvard.Sib.female


title: Ctrl CTL90

description: Ctrl


title: Harvard Sib female CHB1000006525

description: Harvard.Sib.female


title: ART ART_GB083741

description: ART


title: Harvard Sib female CHB1000007265

description: Harvard.Sib.female


title: Harvard Sib female CHB1000006547

description: Harvard.Sib.female


title: ART ART_GB943281

description: ART


title: ART ART_GB091191

description: ART


title: Harvard Sib female CHB1000006541

description: Harvard.Sib.female


title: Ctrl CTL_88

description: Ctrl


title: ART ART_GB088781

description: ART


title: Harvard Sib female CHB1000009617

description: Harvard.Sib.female


title: ART ART_GB077051A

description: ART


title: Harvard Sib female CHB1000007249

description: Harvard.Sib.female


title: Ctrl CTL_87

description: Ctrl


title: Harvard Sib female CHB1000009607

description: Harvard.Sib.female


title: ART ART_GB0677261

description: ART


title: ART ART_GB800161

description: ART


title: ART ART_GB0134201

description: ART


title: ART ART_GB080431

description: ART


title: Harvard Sib female CHB1000006551

description: Harvard.Sib.female


title: Harvard Sib female CHB1000006545

description: Harvard.Sib.female


title: Ctrl CTL_89

description: Ctrl


title: ART ART_GB035991

description: ART


title: MDS-2.13 III


title: ART ART_GB096251

description: ART


title: MDS-2.13 II


title: N-2.12 I


title: ART ART_GB086561

description: ART


title: N-2.12 II


title: N-2.12 III


title: ART ART_GB80061

description: ART


title: Liver from control exposed rats, biological rep 1

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

description: Gene expression data from rat treated with monuron

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: Signal condensation and normalization was performed using GC-RMA (Robust Multiarray Analysis algorithm) using GeneSpring GX11.

organism: Rattus norvegicus

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

growth_protocol: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal calf serum, penicillin 100 I.U./ml, and streptomycin solution 100 µg/ml in a humidified 5% CO2 incubator at 370C. Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University. The rats were housed in plastic cages in a room maintained at 20ºC ± 2ºC and a relative humidity of 50% ± 5% with a 12h light-dark cycle starting at 04.00h. Rats were allowed food (rat expanded diet), and water ad libitum.

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

treatment_protocol: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to CHL dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 μM CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point. All animal procedures were performed in accordance with a license issued under the animals (Scientific Procedures) Act, 1986.  Male rats (190-240g) 7-9 weeks of age were used, four rats being dosed with MON at 40mg/kg body weight on day 1 and 400mg/kg body weight on days 2 and 3, at 5ml/kg in corn oil. Four control animals were dosed with corn oil at 5ml/kg. Seventy two hours after the last dose all rats were killed by a rising concentration of carbon dioxide, the liver and kidneys quickly removed and immersed in RNAlater.

value: liver

tag: genotype

value: Male, Wistar-derived-Liverpool John Moores University rats

tag: age

value: 7-9 weeks of age

tag: treatment

value: control 72 hr


title: Liver from control exposed rats, biological rep 2

source_name: Wistar-derived-Liverpool John Moores University rats


title: Liver from MON exposed rats, biological rep 3

value: monuron 72 hr


title: Liver from MON exposed rats, biological rep 4


title: Liver from MON exposed rats, biological rep 2


title: Liver from control exposed rats, biological rep 3


title: Liver from control exposed rats, biological rep 4


title: Kidney from control rats, biological rep 4

value: kidney


title: Liver from MON exposed rats, biological rep 1


title: MDS-2.13 I


title: ART ART_GB083691

description: ART


title: Harvard Sib female CHB1000006527

description: Harvard.Sib.female

value: F

value: Black


title: Harvard Sib female CHB1000007247

description: Harvard.Sib.female

value: leukocyte


title: Harvard Sib female CHB1000009605

description: Harvard.Sib.female


title: ART ART_GB987461

description: ART


title: Kidney from control rats, biological rep 3


title: Kidney from control rats, biological rep 2


title: Kidney from MON exposed rats, biological rep 4


title: Kidney from control rats, biological rep 1


title: Kidney from MON exposed rats, biological rep 3


title: Harvard Sib female CHB1000006549

description: Harvard.Sib.female


title: Kidney from MON exposed rats, biological rep 1


title: Kidney from MON exposed rats, biological rep 2


title: DMSO-treated NRK-52E cells at 72h, biological rep 3

description: Gene expression data from cells treated with monuron

source_name: NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571)

value: kidney epithelial proximal tubule cells

value: Osborne-Mendel

value: DMSO 72 hr


title: ART ART_GB067761

description: ART


title: FX FX_BL

description: FX

value: FX


title: ART ART_GB0416251

description: ART


title: Harvard Sib female CHB1000005900

description: Harvard.Sib.female

value: Unknown


title: Harvard Sib female CHB1000007271

description: Harvard.Sib.female


title: DMSO-treated NRK-52E cells at 72h, biological rep 1


title: Monuron-treated NRK-52E cells at 72h, biological rep 3


title: ART ART_GB086661

description: ART


title: DMSO-treated NRK-52E cells at 72h, biological rep 2


title: ART ART_GB077051B

description: ART


title: Monuron-treated NRK-52E cells at 72h, biological rep 2


title: Ctrl CTL_86

description: Ctrl

value: Ctrl


title: Monuron-treated NRK-52E cells at 72h, biological rep 1


title: ART ART_GB0279131B

description: ART


title: Ctrl CTL85

description: Ctrl


title: Monuron-treated NRK-52E cells at 24h, biological rep 2

value: monuron 24 hr


title: DMSO-treated NRK-52E cells at 24h, biological rep 1

value: DMSO 24 hr


title: DMSO-treated NRK-52E cells at 24h, biological rep 3


title: Harvard Sib female CHB1000006553

description: Harvard.Sib.female

value: White


title: Harvard Sib female CHB1000006537

description: Harvard.Sib.female


title: ART ART_GB076981

description: ART

value: ART


title: Monuron-treated NRK-52E cells at 24h, biological rep 3


title: Harvard Sib female CHB1000005672

description: Harvard.Sib.female


title: DMSO-treated NRK-52E cells at 6h, biological rep 2

value: DMSO 6 hr


title: Monuron-treated NRK-52E cells at 24h, biological rep 1


title: ART ART_GB093971

description: ART


title: Harvard Sib female CHB1000007267

description: Harvard.Sib.female

value: Other


title: DMSO-treated NRK-52E cells at 6h, biological rep 3


title: Harvard Sib female CHB1000006531

description: Harvard.Sib.female


title: DMSO-treated NRK-52E cells at 6h, biological rep 1


title: Monuron-treated NRK-52E cells at 6h, biological rep 3

value: monuron 6 hr


title: ART ART_GB090561

description: ART


title: ART ART_GB057581

description: ART


title: Harvard Sib female CHB1000007259

description: Harvard.Sib.female


title: Monuron-treated NRK-52E cells at 6h, biological rep 2


title: FVPTC 6

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description:
Sample name: TM-2646-10R
Gene expression data from FVPTC

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings. Data were RMA normalized and analyzed with Partek Genomics Suite 6.5.

source_name: FVPTC histology

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

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

tag: braf status

value: BRAF wild type

value: FVPTC


title: Monuron-treated NRK-52E cells at 6h, biological rep 1


title: ART ART_GB092871

description: ART


title: ART ART_GB083081

description: ART


title: Harvard Sib female CHB1000005940

description: Harvard.Sib.female

value: F


title: FVPTC 5

description:
Sample name: TM-1188-12R
Gene expression data from FVPTC

tag: tissue


title: Harvard Sib female CHB1000005948

description: Harvard.Sib.female

tag: cell type

value: leukocyte


title: ART ART_GB0660121

description: ART


title: Ctrl CTL84

description: Ctrl


title: FVPTC 3

description:
Sample name: TM-557-13R
Gene expression data from FVPTC


title: FVPTC 1

description:
Sample name: TM-134-10R
Gene expression data from FVPTC


title: FA 7

description:
Sample name: TM-110-11R
Gene expression data from FA

source_name: FA histology variant Huerthle cell

value: not determined

value: FA


title: FA 6

description:
Sample name: TM-2647-10R
Gene expression data from FA

source_name: FA histology


title: FA 5

description:
Sample name: TM-1163-11R
Gene expression data from FA


title: DMSO-treated NRK-52E cells at 24h, biological rep 2

value: kidney epithelial proximal tubule cells

value: Osborne-Mendel


title: ART ART_GB018852

description: ART


title: Harvard Sib female CHB1000005936

description: Harvard.Sib.female


title: FA 1

description:
Sample name: TM-116-12R
Gene expression data from FA


title: ART ART_GB089561

description: ART


title: Ctrl CTL83

description: Ctrl


title: TN 7

description:
Sample name: TN-1109-11R
Gene expression data from normal thyroid tissue

source_name: normal thyroid

value: normal thyroid tissue


title: TN 6

description:
Sample name: TN-879-11R
Gene expression data from normal thyroid tissue


title: Harvard Sib female CHB1000006533

description: Harvard.Sib.female

value: Unknown


title: ART ART_GB073021A

description: ART


title: ART ART_GB086161

description: ART


title: FA 2

description:
Sample name: TM-214-09R
Gene expression data from FA


title: ART ART_GB0188261A

description: ART


title: ART ART_GB097351B

description: ART


title: ART ART_GB0575221

description: ART


title: ART ART_GB0652211

description: ART


title: TN 5

description:
Sample name: TN-769-11R
Gene expression data from normal thyroid tissue


title: ART ART_GB0188261B

description: ART


title: ART ART_GB0748151

description: ART


title: Harvard Sib female CHB1000005950

description: Harvard.Sib.female

value: Black


title: Harvard Sib female CHB1000007263

description: Harvard.Sib.female


title: Harvard Sib female CHB1000005944

description: Harvard.Sib.female


title: TN 1

description:
Sample name: TN-157-12R
Gene expression data from normal thyroid tissue


title: Harvard Sib female CHB1000009611

description: Harvard.Sib.female


title: TN 3

description:
Sample name: TN-720-11R
Gene expression data from normal thyroid tissue


title: Ctrl CTL82

description: Ctrl

value: Ctrl


title: TN 4

description:
Sample name: TN-726-11R
Gene expression data from normal thyroid tissue


title: FA 3

description:
Sample name: TM-269-11R
Gene expression data from FA


title: FA 4

description:
Sample name: TM-601-11R
Gene expression data from FA


title: Harvard Sib female CHB1000005822

description: Harvard.Sib.female


title: ART ART_GB097351A

description: ART


title: Ctrl CTL81

description: Ctrl


title: ART ART_GB091891

description: ART


title: PTC BRAF mut 11

description:
Sample name: TM-857-12R
Gene expression data from PTC with a BRAF mutation

source_name: PTC histology

value: BRAFmutant

value: PTC with a BRAF mutation


title: Harvard Sib female CHB1000005692

description: Harvard.Sib.female


title: Rad51_HU

city: Milan

first: Madhusoodanan

last: Urulangodi

state: Milan

address: Via Adamello 16

institute: IFOM

description: WT  cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.1M for 20 minutes

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YPD

extract_protocol: Extraction was performed as described in Bermejo et al., 2009.

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml).For HU experiments, cells were released in hydroxyurea (HU) 0.1M for 20 minutes

tag: strain

tag: genotype/variation

value: W303 Elg1-10FLAG (WT)

tag: antibody

value: Anti-Rad51 antibody

tag: antibody vendor

value: Santa cruz

tag: antibody cat. #

tag: sample type

value: input DNA


title: esc2_Rad51_HU

description: esc2 cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.1M for 20 minutes

value: W303 esc2 Elg1-10FLAG (esc2delta)


title: TN 2

description:
Sample name: TN-247-13R
Gene expression data from normal thyroid tissue


title: Harvard Sib female CHB1000006539

description: Harvard.Sib.female

tag: group

tag: gender

value: F

tag: sentrix id

tag: sentrix position


title: esc2_Elg1_FLAG_HU

description: esc2 (Elg1-FLAG) cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.1M for 20 minutes

value: Anti-FLAG M2 antibody

value: Sigma


title: Harvard Sib female CHB1000005918

description: Harvard.Sib.female

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

value: leukocyte


title: ExtractNoRnt1p_rep1

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

description: Cells were harvested and washed twice in AGK buffer containing protease inhibitors. Cell pellet was resuspended in 1 volume of the same buffer and the slurry was quickly frozen in liquid nitrogen. About 12g of the frozen cell suspension was lysed in a 6870 Freezer Mill. Grinded powder was then thawed on ice and spun at 20 000g for 30 min. The supernatant (S20 fraction) was collected. Incubated in buffer without purified Rnt1p and then treated with Xrn1p

hyb_protocol: Array hybridization was performed at the Centre for Applied Genomics at University of Toronto according to the protocols supplied with Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (Affymetrix; PN: 900645).

scan_protocol: Scanning was done according to the Affymetrix tiling array manufacturer instructions

data_processing: Probes were annotated using the S. cerevisiae S288c reference genome (SGD, http://www.yeastgenome.org, August 10th, 2007). The raw microarray data was treated as described in David et al., 2006 with the following modifications. Variations in probe intensity were corrected based on predicted ∆G. The top 5% of the probes with high ∆G was removed and the intensities of the remaining probes adjusted to obtain a null slope and a null average variation. Regions with less than 12 unique probes were ignored. The variation in intensity between untreated and treated samples was analyzed using segmentation algorithm (Huber et al., 2006) with consideration of the BIC optimal number of segment.

source_name: rnt1d whole cell extract, treated with Xrn1p

label_protocol: Preparation of the cDNA and biotin labeling was performed at the Centre for Applied Genomics at University of Toronto according to the protocols supplied with Affymetrix GeneChip WT Double-Stranded Target Assay (without amplification).

growth_protocol: Yeast cells were grown and manipulated using standard procedures in YEP media supplemented with 2% dextrose at 26°C

extract_protocol: 50 µg of rnt1∆ RNA was incubated with 6 pmol of purified Rnt1p (Lamontagne Methods 2001) for 20 min at 30 °C in 100 ml of reaction buffer [30mM Tris–HCl (pH 7.5), 5mM spermidine, 0.1mM DTT, 0.1mM EDTA (pH7.5), 10mM MgCl2, 150mM Kcl]. Fifty µg of total RNA (cleaved with recombinant Rnt1p or untreated) was incubated with 8 µl Terminator™ 5´-Phosphate-Dependent Exoribonuclease (Xrn1p; Epicentre Biotechnologies) for 90 min in the supplied buffer. The reactions were stopped by Phenol phenol : Chloroform chloroform extraction, and the RNA recuperated using 95% salted ethanol precipitation.

treatment_protocol: Exponentially growing yeast cells were collected


title: Harvard Sib female CHB1000005828

description: Harvard.Sib.female

value: White


title: Harvard Sib female CHB1000005842

description: Harvard.Sib.female


title: Elg1_FLAG_HU

description: WT (Elg1-FLAG) cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.1M for 20 minutes


title: MDS-2.A3C

hyb_protocol: hybridization was performed according to manufacturer's instructions

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

data_processing: Median background subtracted signal intensities from Feature Extraction results files were imported into R and loess normalized.  The data was further normalized by mean centering the logFC values, where the mean was calculated from all autosomes, except chromosome 7.

source_name: 206.A1-3C  induced pluripotent stem cells

label_protocol: labeling was performed according to manufacturer's instructions

extract_protocol: gDNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions

tag: cell line

value: iPSCs

value: del7q iPS line


title: Harvard Sib female CHB1000005824

description: Harvard.Sib.female

value: Black


title: ExtractWithRnt1p_rep1

description: Cells were harvested and washed twice in AGK buffer containing protease inhibitors. Cell pellet was resuspended in 1 volume of the same buffer and the slurry was quickly frozen in liquid nitrogen. About 12g of the frozen cell suspension was lysed in a 6870 Freezer Mill. Grinded powder was then thawed on ice and spun at 20 000g for 30 min. The supernatant (S20 fraction) was collected. Incubated in buffer with purified Rnt1p and then treated with Xrn1p

source_name: rnt1d whole cell extract, treated with Rnt1p and Xrn1p


title: H1-D-Cre7

source_name: H1-D-Cre7 embryonic stem cells

value: hESCs

value: Normal diploid line


title: H1-D-2Cre6

source_name: H1-D-2Cre6 embryonic stem cells


title: Harvard Sib female CHB1000005886

description: Harvard.Sib.female


title: Ctrl CTL80

description: Ctrl

value: Ctrl


title: WithRnt1p_rep1

description: Cells were lysed by vortexing in presence of glass beads and phenol and the total RNA extracted using standard phenol:chloroform extraction. Incubated in buffer with purified Rnt1p and then treated with Xrn1p

source_name: rnt1d total RNA, treated with Rnt1p and Xrn1p


title: Harvard Sib female CHB1000005680 1

description: Harvard.Sib.female


title: Harvard Sib dup CHB1000005680 2

description: Harvard.Sib.dup


title: Harvard Sib female CHB1000005848

description: Harvard.Sib.female


title: H1-D-Cre1

source_name: H1-D-Cre1 embryonic stem cells


title: NoRnt1p_rep1

description: Cells were lysed by vortexing in presence of glass beads and phenol and the total RNA extracted using standard phenol:chloroform extraction. Incubated in buffer without purified Rnt1p and then treated with Xrn1p

source_name: rnt1d total RNA, treated with Xrn1p


title: N-2.12-D-6Cre6

source_name: 206.12 D1-16Cre6 induced pluripotent stem cells


title: Harvard Sib female CHB1000005838

description: Harvard.Sib.female

source_name: leukocyte


title: Harvard Sib Failed CHB1000005698

description: Harvard.Sib.Failed

value: M


title: Harvard Sib female CHB1000005710

description: Harvard.Sib.female


title: wildtype_rep1

data_processing: Probes were annotated using the S. cerevisiae S288c reference genome (SGD, http://www.yeastgenome.org, August 10th, 2007). The raw microarray data was treated as described in David et al., 2006 with the following modifications. Variations in probe intensity were corrected based on predicted ∆G. The top 5% of the probes with high ∆G was removed and the intensities of the remaining probes adjusted to obtain a null slope and a null average variation. Expression was defined as the median level of all probes within the region and adjusted so the median of two deleted genes is 0. Regions with less than 12 unique probes were ignored. The variation in intensity between RNT1 and rnt1∆ samples was analyzed using segmentation algorithm (Huber et al., 2006) with consideration of the BIC optimal number of segment.

source_name: wild type cells

label_protocol: The cDNA preparations and biotin end labeling were performed by the University of Wisconsin Gene Expression Center according to the protocols supplied with Affymetrix GeneChip WT Double-Stranded Target Assay (without amplification).

extract_protocol: Cells were lysed by vortexing in presence of glass beads and phenol and the total RNA extracted using standard phenol:chloroform extraction

value: wild type

value: wild-type haploid strain 10H3


title: N-2.12-D-2Cre4

source_name: 206.12 D1-12Cre4 induced pluripotent stem cells


title: N-2.12-D-8Cre23

source_name: 206.12 D1-18Cre23 induced pluripotent stem cells


title: Harvard Sib female CHB1000005674

description: Harvard.Sib.female


title: N-2.12-D-8Cre21

source_name: 206.12 D1-18Cre21 induced pluripotent stem cells


title: Harvard Sib female CHB1000005934

description: Harvard.Sib.female


title: N-2.12-D-Cre44

source_name: 206.12 D1-1Cre44 induced pluripotent stem cells


title: Streptococcus mutans fabM mutant strain glucose shock replicate 2

status: Public on Feb 15 2015

city: Rochester

first: Roberta

middle: C

last: Faustoferri

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

organism: Streptococcus mutans UA159

source_name: RNA from fabM mutant strain, glucose shock

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.  Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 (parent strain) and UR117 (fabM mutant) were grown in continuous culture to a steady-state pH value of 7.  The pH control (2N KOH) was removed and then cultures were exposed to a glucose shock (200mM).  Samples were collected upon achieving culture pH value of 5.5.  pH control was re-established and cultures were allowed to grow to a steady-state pH value of 5 (for UA159) and 5.5 (for fabM mutant).  Growth was in a BioFlo2000 fermentor at a dilution rate of 0.24h-1.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose medium to steady-state pH values of 7 and 5 and from glucose-shock samples by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

tag: genotype-variation

value: fabM mutant

tag: protocol

value: glucose shock

source_name: RNA from parent strain, mid-log

value: wildtype

value: mid-log


title: MDS-2.13

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The CGH workflow in NimbleGen’s DEVA v1.1 software was used to preprocess the data, consisting of  loess normalization, background subtraction, qspline normalization, and waviness correction.  This was followed by mean centering, where the mean was calculated using the normalized log2 ratios from the probes on 7p.

source_name: MDS 206.13 induced pluripotent stem cells

growth_protocol: iPSCs were kept in an undifferentiated, pluripotent state by using 6 ng/ml FGF2 (Recombinant Human FGF basic (146 aa), R and D systems, 233-FB-001MG/CF) and grown on top of murine embryonic fibroblasts feeder layer inactivated by mitomycin C

source_name: 206.12 induced pluripotent stem cells

value: 206.12 Normal diploid line


title: Streptococcus mutans fabM mutant strain glucose shock replicate 4


title: Ctrl CTL79

description: Ctrl

tag: cell type


title: Streptococcus mutans fabM mutant strain glucose shock replicate 3


title: Vehicle control, id, 6hr, spleen, biological replicate 2, slice no.1

city: Ibaraki-shi

first: Yoshinobu

last: Igarashi

state: Osaka

address: 7-6-8 Asagi Saito

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition

description: sample name: PBSid06h_2_SP1_1007_03

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) in Bioconductor/R Affy package. Median normalization was used. The customized PA call for fold change value was applied.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: After a 7-day quarantine and acclimatization period, the adjuvants were injected to the C57BL/6J mice (6 week old, male) at 10 AM.

extract_protocol: The total RNA was isolated and purified from the sample homogenates with an RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: After 6 h, the inguinal LNs, liver, and spleen were removed and stored in RNAlater RNA Stabilization Reagent (Life Technologies, CA). Each sample in RNAlater was homogenized in Buffer RLT (Qiagen, Germany) by adding a 5 mm diameter zirconium bead (AS ONE Corporation, Japan) and shaking with a MixerMill 300 (Qiagen GmbH) at 20 Hz for 5 min.

tag: agent

value: Vehicle control

tag: administration route

value: id

tag: organ

value: spleen

value: male

tag: age

tag: strain


title: Streptococcus mutans fabM mutant strain glucose shock replicate 1


title: rrp6d_rep1

source_name: rrp6 delta cells

tag: genotype/variation

value: RRP6 deletion

value: MATa, his3Δ1 leu2Δ0, met15Δ0, ura3Δ0, rrp6Δ::KMX4 haploid from the Yeast knock out collection obtained from Open Biosystems


title: bCD, id, 6hr, spleen, biological replicate 1, slice no.1

description: sample name: bCDid06h_1_SP1_1007_03

value: bCD


title: bCD, id, 6hr, liver, biological replicate 3, slice no.1

description: sample name: bCDid06h_3_LV1_1007_02

value: liver


title: N-2.12-D-Cre32

source_name: 206.12 D1-1Cre32 induced pluripotent stem cells

value: iPSCs

value: Normal diploid line


title: Ctrl CTL78

description: Ctrl

tag: group

value: Ctrl

value: leukocyte


title: MDS-3.1

source_name: MDS L1-B2a2 induced pluripotent stem cells

value: MDS L1-B2a2

source_name: L1S8 induced pluripotent stem cells

value: L1S8 normal diploid line


title: Vehicle control, id, 6hr, liver, biological replicate 3, slice no.1

description: sample name: PBSid06h_3_LV1_1007_02

tag: gender


title: Vehicle control, id, 6hr, spleen, biological replicate 3, slice no.1

description: sample name: PBSid06h_3_SP1_1007_03


title: bCD, id, 6hr, spleen, biological replicate 2, slice no.1

description: sample name: bCDid06h_2_SP1_1007_03


title: Streptococcus mutans fabM mutant strain pH5.5 replicate 4

source_name: RNA from fabM mutant strain, steady-state pH5.5

value: fabM mutant

value: steady-state pH5.5

value: wildtype


title: bCD, id, 6hr, spleen, biological replicate 3, slice no.1

description: sample name: bCDid06h_3_SP1_1007_03


title: bCD, id, 6hr, liver, biological replicate 1, slice no.1

description: sample name: bCDid06h_1_LV1_1007_02


title: Streptococcus mutans fabM mutant strain pH5.5 replicate 3

value: mid-log


title: PTC BRAF wt 1

description:
Sample name: LN-163-11R
Gene expression data from PTC without a BRAF mutation

source_name: PTC histology

tag: braf status

value: BRAF wild type

tag: tissue

value: PTC without a BRAF mutation


title: N-2.12-D-Cre10

source_name: 206.12 D1-1Cre10 induced pluripotent stem cells


title: bCD, id, 6hr, liver, biological replicate 2, slice no.1

description: sample name: bCDid06h_2_LV1_1007_02

value: id

value: male


title: Vehicle control, id, 6hr, spleen, biological replicate 1, slice no.1

description: sample name: PBSid06h_1_SP1_1007_03

value: Vehicle control

value: spleen


title: Vehicle control, id, 6hr, liver, biological replicate 2, slice no.1

description: sample name: PBSid06h_2_LV1_1007_02

value: liver


title: bCD, id, 6hr, lymph node, biological replicate 3, slice no.1

description: sample name: bCDid06h_3_LN1_1007_01

value: bCD

value: lymph node


title: Streptococcus mutans fabM mutant strain pH5.5 replicate 1


title: Streptococcus mutans fabM mutant strain pH5.5 replicate 2


title: Streptococcus mutans fabM mutant strain pH7 replicate 4

source_name: RNA from fabM mutant strain, steady-state pH7

value: steady-state pH7


title: Streptococcus mutans fabM mutant strain pH7 replicate 3


title: Streptococcus mutans fabM mutant strain pH7 replicate 2


title: Streptococcus mutans UA159 parent strain glucose shock replicate 4

source_name: RNA from parent strain, glucose shock

value: glucose shock


title: Streptococcus mutans fabM mutant strain pH7 replicate 1


title: Vehicle control, id, 6hr, liver, biological replicate 1, slice no.1

description: sample name: PBSid06h_1_LV1_1007_02


title: Streptococcus mutans UA159 parent strain glucose shock replicate 3


title: Streptococcus mutans UA159 parent strain glucose shock replicate 2


title: bCD, id, 6hr, lymph node, biological replicate 2, slice no.1

description: sample name: bCDid06h_2_LN1_1007_01


title: bCD, id, 6hr, lymph node, biological replicate 1, slice no.1

description: sample name: bCDid06h_1_LN1_1007_01


title: Vehicle control, id, 6hr, lymph node, biological replicate 2, slice no.1

description: sample name: PBSid06h_2_LN1_1007_01


title: Streptococcus mutans UA159 parent strain glucose shock replicate 1


title: Vehicle control, id, 6hr, lymph node, biological replicate 3, slice no.1

description: sample name: PBSid06h_3_LN1_1007_01


title: bCD, ip, 6hr, liver, biological replicate 2, slice no.1

description: sample name: bCDip06h_2_LV1_1006_02

value: ip


title: Dicer KO CD4 T cells 3

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description: Gene expression data from Dicer KO CD4 T cells

hyb_protocol: Fragmented and labelled cDNA from three biological replicates was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Software used: Genespring GX 9. Processing algorithm: MAS5. Intensity values were log2 transformed and median normalised

source_name: Resting CD4 T cells

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) for hybridization on MoGene 1.0 ST v1 arrays was used according to Affymetrix protocol.

growth_protocol: Lymph node single cell suspension were obtained and the CD4+CD62L- resting T cells were sorted by flow cytometry.

extract_protocol: Cells were pelleted by centrifugation and lysed in RNAbee. Total RNA was then purified by phenol/chloroforme extraction according to manufacturer instructions.

treatment_protocol: No treatment was performed.

tag: genotype

value: Dicer KO

value: CD4+CD62L- resting T cells


title: bCD, ip, 6hr, liver, biological replicate 3, slice no.1

description: sample name: bCDip06h_3_LV1_1006_02


title: Vehicle control, id, 6hr, lymph node, biological replicate 1, slice no.1

description: sample name: PBSid06h_1_LN1_1007_01


title: rnt1d_rep1

source_name: rnt1 delta cells

value: RNT1 deletion

value: MATa, lys2∆0, ura3∆0, his3∆200, leu2∆0, rnt1::HIS3 haploid strain


title: Dicer KO CD4 T cells 2


title: Streptococcus mutans UA159 parent strain pH5 replicate 4

source_name: RNA from parent strain, steady-state pH5

value: wildtype

value: steady-state pH5

value: mid-log


title: bCD, ip, 6hr, liver, biological replicate 1, slice no.1

description: sample name: bCDip06h_1_LV1_1006_02


title: Dicer KO CD4 T cells 1


title: Streptococcus mutans UA159 parent strain pH5 replicate 2


title: Streptococcus mutans UA159 parent strain pH5 replicate 3


title: Dicer WT CD4 T cells 3

description: Gene expression data from Dicer WT CD4 T cells

value: Dicer WT


title: Vehicle control, ip, 6hr, liver, biological replicate 3, slice no.1

description: sample name: PBSip06h_3_LV1_1006_02

value: male


title: Dicer WT CD4 T cells 2


title: Dicer WT CD4 T cells 1


title: bCD, ip, 6hr, spleen, biological replicate 2, slice no.1

description: sample name: bCDip06h_2_SP1_1006_01


title: bCD, ip, 6hr, spleen, biological replicate 3, slice no.1

description: sample name: bCDip06h_3_SP1_1006_01


title: Vehicle control, ip, 6hr, liver, biological replicate 2, slice no.1

description: sample name: PBSip06h_2_LV1_1006_02

value: Vehicle control


title: bCD, ip, 6hr, spleen, biological replicate 1, slice no.1

description: sample name: bCDip06h_1_SP1_1006_01

value: spleen


title: Streptococcus mutans UA159 parent strain pH7 replicate 4

source_name: RNA from parent strain, steady-state pH7


title: Streptococcus mutans UA159 parent strain pH5 replicate 1


title: Sox2-shRNA-3

first: Alka

last: Mansukhani

address: 550 First Avenue

department: Microbiology

institute: New York University Medical Center

description: from spontaneous tumor in RB p53 null

hyb_protocol: 2.5 ug cRNA samples were hybridized to mouse A430-2 Affymetrix chips which contain 22,290 entities.

scan_protocol: Gene Array Scanner (Affymetrix) at NYU School of Medicine Genome Technology Center according to manufacturer's protocol.

data_processing:
CEL files were generated using GCOS 1.4 software (Affymetrix) and normalized using GeneSpring GX11 software (Agilent, Santa Clara, CA).  Probe level  normalization was by RMA (Robust Mutichip Average) algorithm and principal component analysis was used to examine variances in the data.
Gene expression changes >1.66 fold were determined to be statistically significant by t test (p<=0.05) of relative intensity signal values of triplicate samples using GeneSpring software.

molecule: polyA RNA

source_name: 482 cells Sox2shRNA-rep3

label_protocol: Fragmented, biotinylated cRNA was prepared from 100 ng RNA using Affymetrix 3' IVT Express labelling kit and array prcessing protocol (Affymetrix).

growth_protocol: Mouse osteosarcoma cells 482 expressing either scrambled or Sox2shRNA900 (A)  were selected in DMEM and 10%FBS + 200ug/ml hygromycin.  These cells are described in BasuRoy et al,S Oncogene 2010: http://www.ncbi.nlm.nih.gov/pubmed/21927024

extract_protocol: Total cellular RNA from OS 482 scrambled and OS-482 Sox2shRNA cells  was extracted by RNEASY. RNA quality was assessed using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000.  cRNA was prepared from 100 ng RNA using the Affymetrix 3’ IVT Express labeling kit and array processing protocol (Affymetrix).   cRNAs were hybridized to mouse genome  430A 2.0 arrays (Affymetrix) which contain 22690 gene probes.  Arrays were processed and scanned according to procedures recommended by the manufacturer (Affymetrix)

treatment_protocol: Stably-infected control or Sox2shRNA cells cells were grown in triplicate plates to 80% confluence.

value: osteosarcoma


title: Sox2-shRNA-2

description: from spontaneous tumor in RB p53 null

source_name: 482 cells Sox2shRNA-rep2


title: Vehicle control, ip, 6hr, liver, biological replicate 1, slice no.1

description: sample name: PBSip06h_1_LV1_1006_02

value: liver


title: Streptococcus mutans UA159 parent strain pH7 replicate 3

source_name: RNA from parent strain, mid-log


title: Streptococcus mutans UA159 parent strain pH7 replicate 2


title: Sox2-ShRNA-1

description: from spontaneous tumor in RB p53 null

source_name: 482 cells Sox2shRNA-rep1


title: Streptococcus mutans UA159 parent strain pH7 replicate 1


title: Sh-control-2

description: from spontaneous tumor in RB p53 null

source_name: 482 cells scrambledshRNA rep2


title: Vehicle control, ip, 6hr, spleen, biological replicate 2, slice no.1

description: sample name: PBSip06h_2_SP1_1006_01


title: Vehicle control, ip, 6hr, spleen, biological replicate 3, slice no.1

description: sample name: PBSip06h_3_SP1_1006_01


title: Sh-control-3

description: from spontaneous tumor in RB p53 null

source_name: 482 cells scrambledshRNA rep3


title: Sh-control-1

description: from spontaneous tumor in RB p53 null

source_name: 482 cells scrambledshRNA rep1


title: Vehicle control, ip, 6hr, spleen, biological replicate 1, slice no.1

description: sample name: PBSip06h_1_SP1_1006_01


title: 557284A05 - col_0µMFe_BR3 vs fit-3_0µMFe_BR3

status: Public on Feb 14 2015

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Analyse the responses to bHLH39 overexpression. bHLH39 is one of the transcription factors regulating iron homeostasis responses.

hyb_protocol: fit-3_0µMFe_BR3 Cy5 / col_0µMFe_BR3 Cy3 : 30pmol.

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: roots - Media=Hoagland-agar hygrometry Temperature=21°C Light=16 hours light

treatment_protocol: Name:0µM Fe - abiotic stress - compound starvation,fe:quantity 0uM . Col-0 (wild type, named C), HA-FIT 8 (a strong 2xpCAMV35S-driven HA7-tagged FIT overexpressor, named H) and fit-3 (fit knock-out mutant, named F) plants were grown as follows: Seeds were sterilized and stratified for two days at 4 °C in the dark. Hydroponic growth was carried out as previously described (Klatte et al., 2009). Plants were hydroponically grown for five weeks in ¼ Hoagland medium with 10 µM Fe under long-day conditions. The medium was refreshed every seven days. The fit-3 mutants were weekly sprayed with iron. Then the rosettes were showered intensively with ddH2O and the roots were rinsed with quarter-strength Hoagland medium with 0 μM Fe to remove residual iron and then the plants of each line were split into two fractions. During the sixth week half of the plants were exposed to the same medium (+Fe control, named +) while the other half was exposed to iron-sufficient conditions (-Fe, ¼ Hoagland, 0 Fe, named -).

value: seedling

tag: treatment

value: 0 µMFe

tag: genetic background

tag: arabidopsis thaliana (columbia)  mutant (col-0) -  dev.stage (boyes et al. plant cell 2001)

extract_protocol: col_0µMFe_BR3:10ug. (Qiagen_RNeasy.pdf)

value: wild type

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)


title: 557284A02 - fit-3_0µMFe_BR1 vs col_0µMFe_BR1

hyb_protocol: col_0µMFe_BR1 Cy5 / fit-3_0µMFe_BR1 Cy3 : 30pmol.

extract_protocol: col_0µMFe_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 557283A10 - fit-3_10µMFe_BR2 vs col_10µMFe_BR2

hyb_protocol: col_10µMFe_BR2 Cy5 / fit-3_10µMFe_BR2 Cy3 : 30pmol.

value: 10 µMFe


title: 557247A09 - col_0µMFe_BR2 vs HA-FIT-8_0µMFe_BR2

hyb_protocol: HA-FIT-8_0µMFe_BR2 Cy5 / col_0µMFe_BR2 Cy3 : 30pmol.

extract_protocol: col_0µMFe_BR2:10ug. (Qiagen_RNeasy.pdf)


title: 557284A04 - fit-3_0µMFe_BR2 vs col_0µMFe_BR2

hyb_protocol: col_0µMFe_BR2 Cy5 / fit-3_0µMFe_BR2 Cy3 : 30pmol.


title: 557283A11 - col_10µMFe_BR3 vs fit-3_10µMFe_BR3

hyb_protocol: fit-3_10µMFe_BR3 Cy5 / col_10µMFe_BR3 Cy3 : 30pmol.


title: 557283A08 - fit-3_10µMFe_BR1 vs col_10µMFe_BR1

hyb_protocol: col_10µMFe_BR1 Cy5 / fit-3_10µMFe_BR1 Cy3 : 30pmol.


title: 557283A12 - fit-3_10µMFe_BR3 vs col_10µMFe_BR3

hyb_protocol: col_10µMFe_BR3 Cy5 / fit-3_10µMFe_BR3 Cy3 : 30pmol.


title: 557284A06 - fit-3_0µMFe_BR3 vs col_0µMFe_BR3

hyb_protocol: col_0µMFe_BR3 Cy5 / fit-3_0µMFe_BR3 Cy3 : 30pmol.


title: 0186_rep3

city: Vicksburg

first: Dawn

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

description:
0186 C
This sample is of Gordonia sp. KTR9 0186 Mutant under carbon starvation conditions. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Two micrograms of the labeled DNA was used for subsequent hybridization to custom Nimblegen Bacterial Gene Expression Arrays for Gordonia sp. KTR9. The hybridized arrays were washed using the Nimblegen Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Microarray Scanner

data_processing: Microarray images were analyzed using Nimblescan v2.5.26 software (Nimblegen) and ArrayStar v4.0.0 (DNAstar, Madison, WI) software. Expression data were log2 transformed and statistical significance was determined using a moderated t-test for binary transcriptome comparisons (i.e. control vs. experimental). The P-value was set at 0.05 and only those genes induced or repressed at least fivefold were considered in this paper.  Differentially expressed transcripts were assigned to their functional classifications based on the Comprehensive Microbial Resource genome annotation from the J. Craig Venter Institute.

organism: Gordonia sp. KTR9

source_name: 0186 under carbon starvation rep3

label_protocol: The cDNA was labeled with the One-Color DNA Labeling Kit (Nimblegen, Madison, WI) and the concentration verified using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA).

growth_protocol:
Gordonia sp. KTR9 and KTR9 mutant 0186 were grown in mineral salts media supplemented with succinate (10 mM), gluconate (10 mM), fructose (10 mM) and ammonium chloride (18 mM) for 72 h at 30°C shaking at 150 rpm. This was used as a starter culture to inoculate triplicates of KTR9 and KTR9 mutant 0186.
Triplicates of KTR9 and KTR9 mutant 0186 were inoculated at an OD600 of 0.015 and grown in mineral salts media  supplemented with succinate (10 mM), gluconate (10 mM), fructose (10 mM) and ammonium chloride (18 mM) for 72 h at 30°C shaking at 150 rpm.
For nitrogen starvation, cultures were spun down, rinsed in PBS buffer, and resuspended in mineral salts media with succinate (10 mM), gluconate (10 mM), and fructose (10 mM) and incubated at 30C for 48h.
After nitrogen starvation, cultures were exposed to carbon starvation. Cultures were spun down, rinsed in PBS buffer, and resuspended in mineral salts media with ammonium chloride (18 mM) and incubated at 30C for 72h.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and bead beating for 30s. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer. The RNA was used to generate cDNA using the Superscript II Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s directions. At each step the quality of the RNA and cDNA was analyzed using the Agilent 2100 Bioanalyzer and DNA 1000 Kit (Agilent).

value: KTR9_0186 disruptant

tag: exposed to

value: carbon starvation


title: 557283A01 - fit-3_0µMFe_BR1 vs fit-3_10µMFe_BR1

hyb_protocol: fit-3_10µMFe_BR1 Cy5 / fit-3_0µMFe_BR1 Cy3 : 30pmol.


title: 557284A01 - col_0µMFe_BR1 vs fit-3_0µMFe_BR1

hyb_protocol: fit-3_0µMFe_BR1 Cy5 / col_0µMFe_BR1 Cy3 : 30pmol.


title: Ovol2 BT, biological rep1 (E17.5)

city: Irvine

first: Xing

last: Dai

state: Ca

address: Med Sci I D288

institute: UC Irvine

description:
Gene expression data from isolated skin
TRE-Ovol2-Flag or TRE-Ovol2-Flag;K5-tTA

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: skin from mice

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Littermates were raised in the same cages.

extract_protocol: Trizol extraction of total RNA followed by column purification (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Control (TRE-Ovol2-Flag, or wild type 2 mice/array) and Ovol2 overexpression in epidermis (TRE-Ovol2-Flag;K5-tTA (Ovol2 BT), 2 mice/array)

value: FVB/N

value: Skin

value: female

value: Ovol2 overexpression (Ovol2 BT)


title: 0186_rep2

description:
0186 B
This sample is of Gordonia sp. KTR9 0186 Mutant under carbon starvation conditions. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: 0186 under carbon starvation rep2


title: Ovol2 BT, biological rep2 (E17.5)


title: 557283A05 - fit-3_0µMFe_BR3 vs fit-3_10µMFe_BR3

hyb_protocol: fit-3_10µMFe_BR3 Cy5 / fit-3_0µMFe_BR3 Cy3 : 30pmol.


title: 557283A09 - col_10µMFe_BR2 vs fit-3_10µMFe_BR2

hyb_protocol: fit-3_10µMFe_BR2 Cy5 / col_10µMFe_BR2 Cy3 : 30pmol.


title: 557283A03 - fit-3_0µMFe_BR2 vs fit-3_10µMFe_BR2

hyb_protocol: fit-3_10µMFe_BR2 Cy5 / fit-3_0µMFe_BR2 Cy3 : 30pmol.


title: 557247A10 - HA-FIT-8_0µMFe_BR2 vs col_0µMFe_BR2

hyb_protocol: col_0µMFe_BR2 Cy5 / HA-FIT-8_0µMFe_BR2 Cy3 : 30pmol.


title: 557283A07 - col_10µMFe_BR1 vs fit-3_10µMFe_BR1

hyb_protocol: fit-3_10µMFe_BR1 Cy5 / col_10µMFe_BR1 Cy3 : 30pmol.


title: 557283A04 - fit-3_10µMFe_BR2 vs fit-3_0µMFe_BR2

hyb_protocol: fit-3_0µMFe_BR2 Cy5 / fit-3_10µMFe_BR2 Cy3 : 30pmol.


title: 557247A12 - HA-FIT-8_0µMFe_BR3 vs col_0µMFe_BR3

hyb_protocol: col_0µMFe_BR3 Cy5 / HA-FIT-8_0µMFe_BR3 Cy3 : 30pmol.


title: 557284A03 - col_0µMFe_BR2 vs fit-3_0µMFe_BR2

hyb_protocol: fit-3_0µMFe_BR2 Cy5 / col_0µMFe_BR2 Cy3 : 30pmol.


title: 557283A06 - fit-3_10µMFe_BR3 vs fit-3_0µMFe_BR3

hyb_protocol: fit-3_0µMFe_BR3 Cy5 / fit-3_10µMFe_BR3 Cy3 : 30pmol.


title: 557247A11 - col_0µMFe_BR3 vs HA-FIT-8_0µMFe_BR3

hyb_protocol: HA-FIT-8_0µMFe_BR3 Cy5 / col_0µMFe_BR3 Cy3 : 30pmol.


title: Control, biological rep2 (E17.5)

value: Control


title: 557283A02 - fit-3_10µMFe_BR1 vs fit-3_0µMFe_BR1

hyb_protocol: fit-3_0µMFe_BR1 Cy5 / fit-3_10µMFe_BR1 Cy3 : 30pmol.