title: Input Stau1 rep2

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

institute: Université de Montréal

description:
Replicate 2
LDS202

scan_protocol: Standard Illumina hybridization protocol

data_processing:
The data were normalized using robust spline normalization
The data were processed with the FlexArray 1.6.2 software

source_name: Prometaphase cells

label_protocol: Biotinylated cRNA were prepared with the TotalPrep RNA labelling kit (Ambion) for Illumina arrays

growth_protocol: Cells were cultured in Dulbecco modified Eagle's medium (Invitrogen) supplemented with 10% cosmic calf serum (HyClone), 100 µg/ml streptomycin and 100 units/ml penicillin (Wisent)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment using the TURBO DNA-free kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with 50 ng/ml Nocodazole for 15 h.

tag: treatment

value: Nocodazole

tag: phase

value: Prometaphase

tag: transfection

value: plasmids coding for Stau155-FLAG


title: IP Control rep 3

status: Public on Jul 03 2014

type: RNA

country: Canada

description:
Replicate 3
LDS206

hyb_protocol: Standard Illumina hybridization protocol

label: Biotin

molecule: total RNA

organism: Homo sapiens

extract_protocol: Stau1-containing complexes were immunoprecipitated with anti-FLAG antibody, RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment using the TURBO DNA-free kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: empty vector

tag: antibody

value: anti-FLAG


title: Input Control rep 1

description:
Replicate 1
LDS198


title: Input Stau1 rep3

description:
Replicate 3
LDS203


title: IP Stau1 rep1

description:
Replicate 1
LDS207


title: IP Control rep 2

description:
Replicate 2
LDS205


title: Input Control rep 2

description:
Replicate 2
LDS199


title: Input Stau1 rep1

description:
Replicate 1
LDS201


title: IP Stau1 rep3

description:
Replicate 3
LDS209


title: IP Control rep 1

description:
Replicate 1
LDS204


title: MEF2CA replicate3

city: San Diego

first: xiayu

last: huang

state: CA

address: 3010 Science Park Road

country: USA

institute: Sanford|Burnham Medical Research Institute

hyb_protocol: We then hybridized the labeled cRNA (750 ng) overnight, at 58 °C, to Sentrix® humanHT-12 Expression BeadChips (> 46,000 gene transcripts; Illumina), following the manufacturer's instructions.

scan_protocol: We subsequently washed and developed BeadChips with fluorolink streptavidin- Cy3 (GE Healthcare), and used an Illumina BeadArray Reader to scan the BeadChips.

data_processing: Microarray data were collected and analyzed in three steps. First, we obtained the sample probe file of all samples using illumina’s GenomeStudio software after expression intensities were calculated and quality controlled with a detection p value set to < 0.05 for each gene probed on the array for all hybridizations. Second, we used hierarchical clustering methods to detect outliers in all samples. From this analysis, no outliers were detected. Finally, we further analyzed the expression data for differentially expressed genes using Agilent’s GeneSpring GX 11.5 software with quantile normalization, log transformation, and statistical analysis. We determined differentially expressed genes on the basis of t tests with the Benjamini-Hochberg correction (corrected P value ≤ 0.05) and fold-change difference in expression level (fold change ≥ 1.5), as is customary for this analysis (Bolstad et al., 2003).

label_protocol: We prepared and labeled cRNA from 500 ng of RNA using the Illumina® RNA amplification kit from Ambion (Life technology).

growth_protocol: We cultured and induced neural differentiation of H9 hESCs (WiCell Research Institute) as previously described (Cho et al., 2011).

extract_protocol: We extracted total RNA from NSCs using Trizol Reagent and the PureLink™ RNA Mini Kit (Invitrogen).

treatment_protocol: We transfected the cells with MEF2CA-tdTomato mammalian-expression constructs or vector controls by electroporation using the human stem cell nucleofector® kit, according to the manufacturer's instructions (Lonza/Amaxa Biosystem).

tag: cell type

value: human neural stem cell (NSCs) derived from H9 ESCs

tag: transfected with

value: constitutively-active MEF2 (MEF2CA)


title: MEF2CA replicate2


title: IP Stau1 rep2

description:
Replicate 2
LDS208


title: MEF2CA replicate1


title: Vector controls replicate 3

source_name: NSC_vector control

value: vector control (ptd-Tomato)


title: Input Control rep 3

description:
Replicate 3
LDS200


title: Vector controls replicate 2


title: AR-K2R_R1881_16h_rep2

city: Kuopio

first: Päivi

last: Sutinen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was analyzed using the Bioconductor associated packages (lumi, limma).  Data were preprocessed (bgAdjust), variance stabilizing transformed (VST) and robust spline normalized (RSN) with lumi package and analyzed using LIMMA to identify statistically significant genes.

label: biotin

source_name: PC-3-cells (AR-K2R), R1881 treated, 16 h

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

growth_protocol: PC-3 cells were grown in F-12 (10% FBS, 1% penicillin/streptomycin) under G418 selection (400 µg/ml).

extract_protocol: Total RNA of biological triplicates was extracted with TriPure isolation reagent (Roche Diagnostics GmbH, Mannheim, Germany), Dnase I treated and quality control was performed with Agilent Bioanalyzer

treatment_protocol: PC-3 cells were seeded onto 6-well plates and growth 48h in transfection medium (5% stripped FBS in F-12) before treating 16h with 10 nM R1881 or vehicle (EtOH).

value: PC-3 prostate cancer cells

tag: genotype/variation

value: SUMOylation-defective AR


title: AR-K2R_EtOH_16h_rep3

source_name: PC-3-cells (AR-K2R), vehicle treated, 16 h

value: EtOH


title: GHTMM-miR133

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: GMTMM/miR-133 transduced-HCFs

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.

source_name: HCFs

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: 24 h after transduction, the medium was replaced with D-MEM (high glucose) with L-Glutamate and Phenol Red (Wako, 044-29765) /Medium199 with Earle’s Salts, L-Glutamate and 22g/L Sodium Bicarbonate (Gibco, 11150-059)/10% Hyclone Characterized FBS (Thermo Scientific, SV30014.03) medium and changed every 2-3 days.

extract_protocol: RNA samples were extracted from cells using ReliaPrep™ RNA Cell Miniprep System (Promega).

treatment_protocol: CSII-CMV lentivirus were used for transduction with Polybrene (Miilopore). Synthetic mimics of mature miRNA-133a (Thermo Scientific) were transfected simultaneously into cells with Lipofectamine 2000 (Invitrogen)

value: HCFs (induced toward a cardiac-like phenotype (iCM))

value: GMTMM/miR-133 transduced

tag: time

value: day 7


title: Vector controls replicate 1


title: D7 GMT/miR-133/Snai1-iCMs

description: a-MHC-GFP+ cells induced by GMT/miR-133/Snai1 transduction were sorted at D7

organism: Mus musculus

source_name: MEFs

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

treatment_protocol: pMx retrovirus were used for transduction with Polybrene (Miilopore). Synthetic mimics of mature miRNA-133a (Thermo Scientific) were transfected simultaneously into cells with Lipofectamine 2000 (Invitrogen)

value: MEFs (induced toward a cardiac-like phenotype (iCM))

value: GMT/miR/Snai1 transduced


title: GHTMM-miR133-Snai1

description: GMTMM/miR-133/Snai1 transduced-HCFs

value: GMTMM/miR-133/Snai1 transduced


title: D7 GMT/miR-133-iCMs-2

description: a-MHC-GFP+ cells induced by GMT transduction were sorted at D7

value: GMT/miR transduced


title: wtAR_EtOH_16h_rep1

source_name: PC-3-cells (wtAR), vehicle treated, 16 h

value: wild-type AR


title: GMTMM

description: GMTMM transduced-HCFs

value: GMTMM transduced


title: wtAR_R1881_16h_rep2

source_name: PC-3-cells (wtAR), R1881 treated, 16 h


title: AR-K2R_EtOH_16h_rep1


title: D18-GMT/miR-133-iCMs

description: a-MHC-GFP+ cells induced by GMT/miR-133 transduction were sorted at D18

value: day 18


title: D7-GMT/miR-133-iCMs

description: a-MHC-GFP+ cells induced by GMT/miR-133 transduction were sorted at D7


title: AR-K2R_R1881_16h_rep3


title: AR-K2R_EtOH_16h_rep2


title: wtAR_EtOH_16h_rep2


title: AR-K2R_R1881_16h_rep1


title: D18-GMT-iCMs

description: a-MHC-GFP+ cells induced by GMT transduction were sorted at D18

value: GMT transduced


title: D3-GMT/miR-133-iCMs

description: a-MHC-GFP+ cells induced by GMT/miR-133 transduction were sorted at D3

value: day 3


title: Heart

description: Human heart

source_name: Human heart tissue

tag: tissue

value: Heart

value: without any treatment

value: control


title: Heart

description: Mouse hearts

source_name: Mouse heart tissue


title: wtAR_R1881_16h_rep1

value: PC-3 prostate cancer cells


title: wtAR_R1881_16h_rep3


title: HCF

description: Human fibroblasts

value: HCFs


title: wtAR_EtOH_16h_rep3

value: EtOH


title: D3-GMT-iCMs

description: a-MHC-GFP+ cells induced by GMT transduction were sorted at D3


title: Experiment 2, A549 cells treated with Ent+Fe, replicate 2

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: Following fragmentation, approximately 5 ug of cDNA were hybridized for 20 hr at 48C to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed in the R-statistical environment using RMA to estimate log2 transformed expression values for each probe-set. We analyzed 29096 non-control probe-sets according to Affymetrix annotation.

source_name: Experiment 2_A549_Ent+Fe

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 150 ng total RNA.

growth_protocol: A549 (ATCC CCL-185) cells, a human type II pneumocyte cell line, were cultured in F12K (Invitrogen, Carlsbad, CA) media supplemented with 10% fetal bovine serum (Invitrogen) and 1:100 penicillin streptomycin (Invitrogen).  24-well plates were seeded with A549 cells at a concentration of 35000 cells/well. After two days, cells were weaned from serum and antibiotics overnight.

extract_protocol: Total RNA was extracted using an miRneasy kit (Qiagen).

treatment_protocol: Cells were stimulated overnight with the indicated combinations of 50 uM Ferric ammonium citrate (FAC) (Sigma, St. Louis, MO), 50 uM Ent (Sigma or EMC Microcollections, Tubingen, Germany), and/or 25 uM lipocalin 2 (Lcn2) in F12K media lacking serum or antibiotics.

value: human type II pneumocyte cells

tag: treated with

value: 50 uM Ferric Ammonium Citrate, and 50 uM Enterobactin


title: Experiment 2, A549 cells treated with Fe, replicate 4

source_name: Experiment 2_A549_Fe

value: 50 uM Ferric Ammonium Citrate


title: Experiment 2, A549 cells treated with Fe, replicate 2


title: Experiment 2, A549 cells treated with Ent, replicate 4

source_name: Experiment 2_A549_Ent

value: 50 uM Enterobactin


title: Experiment 2, A549 cells treated with Ent, replicate 3


title: Experiment 2, A549 cells treated with Ent+Fe, replicate 4


title: Experiment 2, A549 cells treated with Ent, replicate 1


title: Experiment 2, A549 cells treated with Ent+Fe, replicate 3


title: Experiment 2, A549 cells treated with Ent+Fe, replicate 1


title: Experiment 1, A549 cells treated with Lcn2+Ent, replicate 2

source_name: Experiment 1_A549_Lcn2+Ent

value: 25 uM Lcn2, and 50 uM Enterobactin


title: Experiment 2, A549 cells treated with Fe, replicate 3


title: Experiment 2, A549 cells treated with PBS (control), replicate 3

source_name: Experiment 2_A549_PBS (control)

value: PBS (control)


title: Experiment 2, A549 cells treated with PBS (control), replicate 2


title: Experiment 2, A549 cells treated with Fe, replicate 1


title: Experiment 2, A549 cells treated with PBS (control), replicate 4


title: Experiment 2, A549 cells treated with PBS (control), replicate 1


title: Experiment 1, A549 cells treated with Lcn2+Ent, replicate 1


title: Experiment 1, A549 cells treated with Lcn2+Ent+Fe, replicate 2

source_name: Experiment 1_A549_Lcn2+Ent+Fe

value: 25 uM Lcn2, 50 uM Enterobactin, 50 uM Ferric Ammonium Citrate


title: BMDM treated vs no treated replicate1

city: Madrid

first: Susana

last: Alemany

state: Madrid

address: Arturo DUperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas ALberto Sols

description:
Biological replicates 1 of 3
Mice were sacrificed by CO2 chamber euthanasia. Total bone marrow was obtained from mice by flushing femurs and tibiae with DMEM. Bone marrow mononuclear phagocytic precursor cells were maturated maturation with 30% L929 cells -conditioned medium (a source of CSF-1), and the cells were cultured in bacteria culture plates. Three days later a 30% L929-conditioned medium was added and incubated for 4 days. Adherent cells bone marrow-derived macrophages (BMDM) were scraped and plated in tissues plates.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

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

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: WT control

label_protocol: Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)

extract_protocol: Total RNA was isolated from BMDM (1.5 x 106 cells) stimulated or not for 18 h with adiponectin (12 mg/ml), using the miRNeasy mini Kit and according to the manufacturer’s instructions (Quiagen).

treatment_protocol: Bone marrow derived macrophages (1.5 x106) were cultured in p12 multiwell plates in DMEM with 0.1%FBS. Twenty four hours later cells were stimulated or not for 18 h with adiponectin ( 12 ug/ml). Cells were then washed twice with PBS and lysed with 1 ml of Trizol.

tag: strain

value: bone marrow derived macrophage

source_name: WT APN 18h

value: APN 12ug/ml 18h


title: BMDM treated vs no treated replicate2

description:
Biological replicates 2 of 3
Mice were sacrificed by CO2 chamber euthanasia. Total bone marrow was obtained from mice by flushing femurs and tibiae with DMEM. Bone marrow mononuclear phagocytic precursor cells were maturated maturation with 30% L929 cells -conditioned medium (a source of CSF-1), and the cells were cultured in bacteria culture plates. Three days later a 30% L929-conditioned medium was added and incubated for 4 days. Adherent cells bone marrow-derived macrophages (BMDM) were scraped and plated in tissues plates.


title: 10 treatments by polarized macrophages (M11)

city: Nantong

first: Xingmin

last: Wang

state: Jiangsu

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

country: China

institute: Nantong Maternity and Child Healthcare Hospital

description:
M11
replicate 1

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: cell line

extract_protocol: Total RNA was extracted from clones and YAMC cells using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) with  DNase I treatment in accordance with the manufacturer's protocolt. Quality control was performed with Agilent Bioanalyser.

value: CBA/Ca X C57BL/10

tag: age

value: 10 weeks

value: colon

value: YAMC

value: 10 treatments by polarized macrophages


title: D7-GMT-iCMs

value: MEFs (induced toward a cardiac-like phenotype (iCM))

value: GMT transduced

value: day 7


title: Experiment 1, A549 cells treated with Lcn2+Ent+Fe, replicate 1

value: human type II pneumocyte cells


title: Experiment 1, A549 cells treated with Lcn2, replicate 2

source_name: Experiment 1_A549_Lcn2

value: 25 uM Lcn2


title: Experiment 1, A549 cells treated with PBS (control), replicate 1

source_name: Experiment 1_A549_PBS (control)


title: Experiment 1, A549 cells treated with Lcn2, replicate 1


title: 10 treatments by 4-HNE (H2)

description:
H2
replicate 1

value: 10 treatments by 4-HNE


title: Experiment 1, A549 cells treated with PBS (control), replicate 2


title: 10 treatments by polarized macrophages (37M10-3)

description:
37M10-3
replicate 1


title: 10 treatments by polarized macrophages (M3)

description:
M3
replicate 1


title: 10 treatments by 4-HNE (H3)

description:
H3
replicate 1


title: BMDM treated vs no treated replicate3

description:
Biological replicates 3 of 3
Mice were sacrificed by CO2 chamber euthanasia. Total bone marrow was obtained from mice by flushing femurs and tibiae with DMEM. Bone marrow mononuclear phagocytic precursor cells were maturated maturation with 30% L929 cells -conditioned medium (a source of CSF-1), and the cells were cultured in bacteria culture plates. Three days later a 30% L929-conditioned medium was added and incubated for 4 days. Adherent cells bone marrow-derived macrophages (BMDM) were scraped and plated in tissues plates.


title: 10 treatments by polarized macrophages (M15)

description:
M15
replicate 1


title: 10 treatments by polarized macrophages (M13)

description:
M13
replicate 1


title: 10 treatments by polarized macrophages (M17)

description:
M17
replicate 1


title: untreated control (YAMC Ctrl2)

description:
YAMC Ctrl2
replicate 2

value: untreated control


title: Gamma_70mGy_rep 1

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description:
M2
Gene expression after 48 h in 70 mGy gamma radiation exposed fish liver

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Salmo salar

source_name: 70 mGy gamma radiation exposed replicate 1

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 200 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted from 20-30 mg snap-frozen liver tissue using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/230 > 2.0, 260/280>1.8, yield >200 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>8.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Atlantic salmon parr were transferred to lake water (Maridalsvannet, Norway) for 72 h acclimation prior to being exposed to 0 mGy (control), 15 mGy, 70 mGy and 280 mGy external gamma radiation emitted from a cobalt-60 source in the dark for 48 h. Fish were exposed in a flow-through system supplied with air pumps. No feeding was performed during the acclimation and exposure period.

value: Liver


title: 10 treatments by 4-HNE (H7)

description:
H7
replicate 1


title: 10 treatments by 4-HNE (H5)

description:
H5
replicate 1


title: Gamma_280mGy_rep 3

description:
H1
Gene expression after 48 h in 280 mGy gamma radiation exposed fish liver

source_name: 280 mGy gamma radiation exposed replicate 3


title: Gamma_280mGy_rep 4

description:
H4
Gene expression after 48 h in 280 mGy gamma radiation exposed fish liver

source_name: 280 mGy gamma radiation exposed replicate 4


title: Gamma_15mGy_rep 1

description:
L4
Gene expression after 48 h in 15 mGy gamma radiation exposed fish liver

source_name: 15 mGy gamma radiation exposed replicate 1


title: Gamma_280mGy_rep 2

description:
H6
Gene expression after 48 h in 280 mGy gamma radiation exposed fish liver

source_name: 280 mGy gamma radiation exposed replicate 2


title: Gamma_70mGy_rep 4

description:
M3
Gene expression after 48 h in 70 mGy gamma radiation exposed fish liver

source_name: 70 mGy gamma radiation exposed replicate 4


title: Experiment 2, A549 cells treated with Ent, replicate 2

value: 50 uM Enterobactin


title: untreated control (YAMC Ctrl1)

description:
YAMC Ctrl1
replicate 1


title: Gamma_15mGy_rep 3

description:
L6
Gene expression after 48 h in 15 mGy gamma radiation exposed fish liver

source_name: 15 mGy gamma radiation exposed replicate 3


title: Control_rep 3

description:
C2
Gene expression after 48 h in control fish liver

source_name: Control replicate 3


title: Control_rep 1

description:
C3
Gene expression after 48 h in control fish liver

source_name: Control replicate 1


title: Gamma_280mGy_rep 1

description:
H3
Gene expression after 48 h in 280 mGy gamma radiation exposed fish liver

source_name: 280 mGy gamma radiation exposed replicate 1


title: Gamma_15mGy_rep 2

description:
L2
Gene expression after 48 h in 15 mGy gamma radiation exposed fish liver

source_name: 15 mGy gamma radiation exposed replicate 2


title: Gamma_15mGy_rep 4

description:
L5
Gene expression after 48 h in 15 mGy gamma radiation exposed fish liver

source_name: 15 mGy gamma radiation exposed replicate 4


title: Gamma_70mGy_rep 3

description:
M4
Gene expression after 48 h in 70 mGy gamma radiation exposed fish liver

source_name: 70 mGy gamma radiation exposed replicate 3


title: Gamma_70mGy_rep 2

description:
M5
Gene expression after 48 h in 70 mGy gamma radiation exposed fish liver

source_name: 70 mGy gamma radiation exposed replicate 2


title: Control_rep 4

description:
C6
Gene expression after 48 h in control fish liver

source_name: Control replicate 4


title: Empty vector (line3)-rep3

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

institute: Center for Research in Agricultural Genomics (CRAG)

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 2 of 2; Technical replicate 3 of 3.

hyb_protocol: Cy3- and Cy5-labelled cRNAs were combined and hybridized to the microarray for 17 h at 60°C using Agilent's gaskets G2534-60002, G2534A hybridization chambers and DNA Hybridization Oven G2545A.

scan_protocol: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B and Feature Extraction software (v10.1).

data_processing: The raw fluorescence intensity data were processed using the Polyphemus™ software, developed at Oryzon Genomics. Microarray data was normalized by the median-centering method. TIGR MIDAS software was used for data normalization.

organism: Oryza sativa Japonica Group

source_name: Empty vector, line 3, roots grown hydroponic culture

label_protocol: Total RNA (0.5 μg) amplification and labelling with Cy3 (Empty Vector samples) or Cy5 (OsCPK4-rice samples) was carried out using the MessageAmp™ RNA amplification kit from Ambion (Applied Biosystems).

growth_protocol: Roots of OsCPK4 and vector control plants were grown hydroponically in Yoshida liquid medium for 15 days.

extract_protocol: RNAs were extracted by using the Plant total RNA extraction kit (Qiagen). The quality and concentration of the RNA were analysed using the Agilent 2100 Bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific). Samples with RNA integrity number (RIN) < 6.0 were discarded.

treatment_protocol: No treatment.

tag: cultivar

value: Nipponbare

value: empty vector

tag: line

value: 15 days

value: roots

tag: growth condition

value: hydroponic culture


title: Empty vector (line3)-rep2

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 2 of 2; Technical replicate 2 of 3.


title: PC3 over-expressing MAOA xenograft tumor 2 treated with docetaxel

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the GE2_105_Jan09 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of NA to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  Data was further normalized using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA was extracted from frozen tumor sections using the RNeasy Mini RNA isolation kit (Qiagen, Valencia, CA) according to the manufactures protocol followed by two rounds of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: model

value: Mouse xenograft models were generated via subcutaneous injections into the right flank of 8-10 week old male CB17 SCID mice (Taconic, Hudson, NY). Specifically, subcutaneous xenografts were derived utilizing either PC3 cells engineered to stably overexpress MAOA or empty vector controls. Prior to injection cells were grown to 90% confluence, washed once with PBS and resuspended in ice-cold PBS. Animals were anesthetized and 1.0x106 cells were implanted subcutaneously in 200 microliters of 1:1 PBS:Matrigel solution. Once tumors were established, mice were dosed with 5 mg/kg docetaxel weekly by IP injection. For both treatment arms (MAOA and Control) xenografts were generated and tumor growth was monitored for a period of 4 weeks post injection at which point tumors were excised and snap frozen.

value: tumor xenograft

value: Once tumors were established, mice were dosed with 5 mg/kg docetaxel weekly by IP injection for a period of 4 weeks.

tag: overexpression

value: MAOA


title: PC3 over-expressing MAOA xenograft tumor 1 treated with docetaxel

tag: treatment


title: AR-K2R_R1881_24h_rep1

hyb_protocol: Standart Illumina hybridization protocol

scan_protocol: Standart Illumina scanning protocol

data_processing: The data was analyzed using the Bioconductor associated packages (lumi, limma).  Data were preprocessed (bgAdjust), variance stabilizing transformed (VST) and robust spline normalized (RSN) with lumi package and analyzed using LIMMA  to identify statistically significant genes.

source_name: Isogenic HEK293 Cells, R1881 treated, 24 h

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

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B,  and kept at 37 °C in a humidified 95% air/ 5% CO2

tag: cell line

value: Isogenic Human Embryonal Kidney (HEK293) Cells

value: SUMOylation-defective AR


title: PC3 empty vector control xenograft tumor 2 treated with docetaxel

value: control


title: AR-K2R_EtOH_24h_rep2

source_name: Isogenic HEK293 Cells, vehicle treated, 24 h

value: vehicle


title: WT vs. Wip1 KO tissues after Partial Hepatectomy at 24h

city: hangzhou

first: Hu

address: wenyixi road 1378

institute: hangzhou normal university

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Wip1 KO mice liver tissues after Partial Hepatectomy at 24h

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

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

treatment_protocol: Partial Hepatectomy Experiments following manufacturer's instructions

value: Wip1 KO

value: 3 months

source_name: WT mice liver tissues after Partial Hepatectomy at 24h

value: wild type


title: AR-K2R_EtOH_24h_rep1


title: Empty vector (line11)-rep3

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 1 of 2; Technical replicate 3 of 3.

source_name: Empty vector, line 11, roots grown hydroponic culture

value: Nipponbare

value: empty vector


title: Ce 0.4 mM Se

city: Madison

first: Roger

middle: A

last: Sunde

state: WI

address: 1415 Linden Dr

department: Nutritional Sciences

institute: University of Wisconsin

hyb_protocol: A 12 ug cocktail was made up for each sample. aRNA Hybridization cocktail prepared according to protocols & procedures in the AFX Expression Analysis Technical Manual with Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit (P/N 702232 Rev. 3). 10 ug of aRNA applied to AFX C.elegans arrays & hybridized ON at 45°C for 16 hours in AFX 640 Hyb oven

scan_protocol: C.elegans GeneChips post processed on the AFX 450 Fluidics Station according to all AFX protocols and procedures defined for the C.elegans array (FS450_0004). All GC’s scanned on AFX GC3000 G7 scanner. Data extracted from GC3000 G7 scanned images using the AFX Expression Console v 1.2.0.20 software

data_processing: Resulting .cel files were analyzed using GeneSpring version 12.0. Raw data was filtered on Expression >100 (100.0 - 32455.01), and then normalized.

organism: Caenorhabditis elegans

source_name: cultured in 0.4 mM Se axenic media

label_protocol: RNA wasprocessed and labeled using the Ambion MessageAmp™ Premier RNA Amplification Kit

growth_protocol: Synchronous C. elegans N2 Bristol were grown in 10 ml of low Se axenic media to the mid-L4 stage in development

extract_protocol: Total RNA was isolated with TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol from pelleted cells washed in M9 buffer

treatment_protocol: The low Se (0.000125 mM Se) axenic media was supplemented with 0, 0.05, 0.1, 0.2, or 0.4 mM Se as sodium selenite

value: N2 Bristol

tag: development stage

value: mid L4-larva stage


title: AR-K2R_R1881_24h_rep3


title: OsCPK4-rice (line13)-rep3

source_name: OsCPK4-rice, line 13, roots grown hydroponic culture

value: OsCPK4 transgenic

value: 15 days

value: roots

value: hydroponic culture


title: Control_rep 2

description:
C1
Gene expression after 48 h in control fish liver

source_name: Control replicate 2

value: Liver


title: OsCPK4-rice (line13)-rep2


title: Empty vector (line3)-rep1

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 2 of 2; Technical replicate 1 of 3.


title: Empty vector (line11)-rep2

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 1 of 2; Technical replicate 2 of 3.


title: wtAR_R1881_24h_rep2

value: wild-type AR


title: wtAR_R1881_24h_rep1

value: Isogenic Human Embryonal Kidney (HEK293) Cells


title: AR-K2R_EtOH_24h_rep3

value: SUMOylation-defective AR


title: Ce 0.1 mM Se

source_name: cultured in 0.1 mM Se axenic media


title: Ce 0.2 mM Se

source_name: cultured in 0.2 mM Se axenic media


title: wtAR_EtOH_24h_rep3


title: OsCPK4-rice (line13)-rep1


title: AR-K2R_R1881_24h_rep2


title: Empty vector (line11)-rep1

description:
Each array includes 3 different specific oligonucleotides recognizing the same locus. These are used as technical replicates.
Biological replicate 1 of 2; Technical replicate 1 of 3.


title: WT vs. Wip1 KO tissues after Partial Hepatectomy at 36 h

description: liver tissues after Partial Hepatectomy at 36h

source_name: Wip1 KO mice liver tissues after Partial Hepatectomy at 36 h

source_name: WT mice liver tissues after Partial Hepatectomy at 36 h


title: OsCPK4-rice (line 1)-rep2

source_name: OsCPK4-rice, line 1, roots grown hydroponic culture


title: wtAR_R1881_24h_rep3


title: OsCPK4-rice (line 1)-rep3


title: 2 Ctrl 2

status: Public on Jul 02 2014

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

description: 2 Ctrl 2.CEL

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Mouse Genome 430 2.0 GeneChips were scanned using the Affymetrix 3000 scanner/AGCC.

data_processing: Data were analyzed by GeneSpring GX.

organism: Rattus norvegicus

source_name: Alveolar type 2 cells_control

label_protocol: Biotinylation of RNA was completed as described in the Affymetrix user manual.

growth_protocol: Male Spargue Dawley rats were fed the liquid Lieber-DeCarlie diet containg EtOH for 6 wk or an isocaloric control diet without EtOH.

extract_protocol: RNA was extracted by Trizol.

treatment_protocol: Alveolar type 2 cells were isolated using an immunoabsorption technique.

tag: strain background

value: Sprague Dawley

value: male

tag: diet

value: isocaloric control diet without EtOH for 6wks

tag: sample group

value: Control

tag: cell type

value: Alveolar type 2 cells


title: 7 Etoh 3

description: 7 Etoh 3.CEL

source_name: Alveolar type 2 cells_Alcohol ingestion

value: Lieber-DeCarlie diet containg EtOH for 6 wk

value: Alcohol ingestion


title: 1 Ctrl 1

description: 1 Ctrl 1.CEL


title: wtAR_EtOH_24h_rep2

value: vehicle

tag: genotype/variation


title: 8 Etoh 4

description: 8 Etoh 4.CEL


title: Ce 0 mM Se

source_name: cultured in 0 mM Se axenic media

value: N2 Bristol

value: mid L4-larva stage


title: Ce 0.05 mM Se

source_name: cultured in 0.05 mM Se axenic media


title: PC3 empty vector control xenograft tumor 1 treated with docetaxel

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Mouse xenograft models were generated via subcutaneous injections into the right flank of 8-10 week old male CB17 SCID mice (Taconic, Hudson, NY). Specifically, subcutaneous xenografts were derived utilizing either PC3 cells engineered to stably overexpress MAOA or empty vector controls. Prior to injection cells were grown to 90% confluence, washed once with PBS and resuspended in ice-cold PBS. Animals were anesthetized and 1.0x106 cells were implanted subcutaneously in 200 microliters of 1:1 PBS:Matrigel solution. Once tumors were established, mice were dosed with 5 mg/kg docetaxel weekly by IP injection. For both treatment arms (MAOA and Control) xenografts were generated and tumor growth was monitored for a period of 4 weeks post injection at which point tumors were excised and snap frozen.

tag: tissue

value: tumor xenograft

value: Once tumors were established, mice were dosed with 5 mg/kg docetaxel weekly by IP injection for a period of 4 weeks.

value: control


title: SW480 cell-transfected-pBabe-rep3

city: Guangzhou

first: Yan-Qing

last: Ding

address: 1838#, Northern Guangzhou Dadao Road

institute: Southern Medical University

description: This sample is of SW480 cells transfected with control vector pBabe. It is the third of three control cells replicates used in this experiment, each from separate cultures.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.  All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.

source_name: SW480 cell-transfectedpBabe

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA)

growth_protocol: SW480/pBabe or SW480/FOXC2 cells were grown in RPMI 1640 culture medium containing 10% fetal bovine serum (PAA Laboratories, Pasching, Austria) and 1% penicillin/streptomycin (Invitrogen) at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA Quantification and Quality Assurance by NanoDrop ND-1000.

treatment_protocol: SW480 cells were transfected with pBabe control vector or FOXC2 construct by a retroviruse system, and then selected using 0.5 μg/mL puromycin for 3 to 5 days. Cells were harvest when reaching to 90% confluence.

tag: genotype

value: expressing control vector pBabe

value: colorectal cancer cell line


title: OsCPK4-rice (line 1)-rep1

value: Nipponbare

value: OsCPK4 transgenic

tag: age

value: 15 days

value: roots

value: hydroponic culture


title: SW480 cell-transfected-FOXC2-rep2

description: This sample is of SW480 cells transfected with FOXC2 construct. It is the second of three FOXC2-overexpressing cells replicates used in this experiment, each from separate cultures.

source_name: SW480 cell-transfected FOXC2

value: FOXC2 ectopic expression


title: SW480 cell-transfected-FOXC2-rep1

description: This sample is of SW480 cells transfected with FOXC2 construct. It is the first of three FOXC2-overexpressing cells replicates used in this experiment, each from separate cultures.


title: SW480 cell-transfected-FOXC2-rep3

description: This sample is of SW480 cells transfected with FOXC2 construct. It is the third of three FOXC2-overexpressing cells replicates used in this experiment, each from separate cultures.


title: gubernaculum-GD19-b

city: Wilmington

first: Julia

middle: S.

last: Barthold

state: DE

address: 1600 Rockland Road

department: Urology

institute: Nemours/AI duPont Hospital for Children

description:
OP19d
hybridization batch: 2

hyb_protocol: Biotin-labeled cRNA was hybridized to GeneChip Rat Genome 230 v2 Affymetrix Arrays GeneChip System 3000 w/autoloader which includes 640 hyb oven and FS450 fluidics station .

scan_protocol: For scanning  the GC30007G scanner was used according to manufacturers instructions

data_processing: Raw signal intensities for each probeset were background-corrected, normalized and summarized using GC Robust Multiarray Analysis (GC-RMA)  withn the affylmGUI (v.1.13.1) Bioconductor package of R (v.2.6.2).

source_name: gubernaculum at GD19

label_protocol: Total Gubernaculum RNA was labeled using GeneChip 3' IVT Express from Affymetrix according to manufacturers instructions.

extract_protocol: Gubernaculum total RNA extraction was carried using Qiagen Micro RNAeasy kit according to manufacturers instructions.

tag: strain

value: unknown

value: gestational day 19

value: gubernaculum


title: 6 Etoh 2

description: 6 Etoh 2.CEL

value: Sprague Dawley

value: male

value: Lieber-DeCarlie diet containg EtOH for 6 wk

value: Alcohol ingestion

value: Alveolar type 2 cells


title: SW480 cell-transfected-pBabe-rep1

description: This sample is of SW480 cells transfected with control vector pBabe. It is the first of three control cells replicates used in this experiment, each from separate cultures.

source_name: SW480 cell-transfected pBabe


title: ORL gubernaculum-GD19-biological rep3

description:
OP19c
hybridization batch: 1

source_name: ORL gubernaculum at GD19

value: ORL


title: ORL gubernaculum-GD19-biological rep6

description:
OP19g
hybridization batch: 2


title: 3 Ctrl 3

description: 3 Ctrl 3.CEL

value: isocaloric control diet without EtOH for 6wks

value: Control


title: wtAR_EtOH_24h_rep1

source_name: Isogenic HEK293 Cells, vehicle treated, 24 h

value: Isogenic Human Embryonal Kidney (HEK293) Cells

value: vehicle

value: wild-type AR


title: 4 Ctrl 4

description: 4 Ctrl 4.CEL


title: SW480 cell-transfected-pBabe-rep2

description: This sample is of SW480 cells transfected with control vector pBabe. It is the second of three control cells replicates used in this experiment, each from separate cultures.

value: expressing control vector pBabe

value: colorectal cancer cell line


title: ORL gubernaculum-GD19-biological rep5

description:
OP19f
hybridization batch: 2


title: ORL gubernaculum-GD19-biological rep2

description:
OP19b
hybridization batch: 1


title: AvrRpt2 treated Col-0 at 6hpi, biological rep1

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX default analysis settings

organism: Arabidopsis thaliana

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Arabidopsis plants (Columbia-0) were grown on soil (Metro Mix 360) at 22˚C under a 12/12 hr light/dark cycle for 4 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: Mature leaves were infiltrated with Psm carrying AvrRpt2 at OD 0.01 in 10mM MgSO4 solution

tag: ecotype

value: WT

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 6h

value: mature leaf


title: AvrRpt2 treated Col-0 at 6hpi, biological rep3


title: AvrRpt2 treated Col-0 at 0hpi, biological rep3

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 0h


title: LE gubernaculum-GD19-biological rep6

description:
WP19g
hybridization batch: 2

source_name: LE gubernaculum at GD19

value: Long Evans

value: gestational day 19

value: gubernaculum


title: AvrRpt2 treated Col-0 at 0hpi, biological rep2


title: ORL gubernaculum-GD19-biological rep4

description:
OP19e
hybridization batch: 2


title: LE gubernaculum-GD19-biological rep5

description:
WP19f
hybridization batch: 2


title: LE gubernaculum-GD19-biological rep4

description:
WP19d
hybridization batch: 2


title: AvrRpt2 treated Col-0 at 6hpi, biological rep2


title: LE gubernaculum-GD19-biological rep2

description:
WP19b
hybridization batch: 1


title: LE gubernaculum-GD19-biological rep3

description:
WP19c
hybridization batch: 1


title: leukocytes_COPD_old_female_180min_rep4

city: Barcelona

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

description:
* This sample has not been included in related publications, detected as outlier
$ This sample has not been analyzed in the first publication.

hyb_protocol: Following cRNA fragmentation, the sample was hybridized on the GeneChip HT HG-U219 Array Plate.

scan_protocol: Hybridization, washes and scanning were processed in the Gene Titan instrument, a fully automated array system.

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the Expression Console™ Software 1.2.1.20. Batch effect (by plates) was corrected using Partek® Software

source_name: Total leukocytes

label_protocol: Sample preparation for microarray hybridization was performed following Affymetrix's protocols. The GeneChip 3'IVT Express Protocol was used for sample labeling. Briefly, from 150 ng total RNA a biotin-labeled cRNA was generated by reverse transcription, followed by an IVT.

extract_protocol:
Erythrocytes were lysed from whole blood, total leukocytes were washed twice and total RNA was extracted.
Total RNA was extracted using QIAamp RNA Blood Mini Kit.

value: female

value: leukocyte

tag: smoking status

value: Smoker

tag: disease status

value: COPD


title: ORL gubernaculum-GD17-biological rep6

description:
OP17f
hybridization batch: 2

source_name: ORL gubernaculum at GD17

value: ORL

value: gestational day 17


title: leukocytes_COPD_old_female_180min_rep2

tag: gender


title: ORL gubernaculum-GD17-biological rep5

description:
OP17e
hybridization batch: 2


title: ORL gubernaculum-GD17-biological rep7

description:
OP17g
hybridization batch: 2


title: gubernaculum-GD19-a

description:
WP19e
hybridization batch: 2

value: unknown


title: ORL gubernaculum-GD17-biological rep3

description:
OP17c
hybridization batch: 1


title: LE gubernaculum-GD19-biological rep1

description:
WP19a
hybridization batch: 1


title: leukocytes_COPD_old_female_0min_rep4


title: AvrRpt2 treated Col-0 at 0hpi, biological rep1


title: * leukocytes_COPD_old_female_0min_rep5


title: ORL gubernaculum-GD17-biological rep4

description:
OP17d
hybridization batch: 2


title: * leukocytes_COPD_old_female_180min_rep5


title: leukocytes_COPD_old_female_0min_rep2


title: leukocytes_COPD_old_female_180min_rep3


title: ORL gubernaculum-GD17-biological rep2

description:
OP17b
hybridization batch: 1


title: ORL gubernaculum-GD19-biological rep1

description:
OP19a
hybridization batch: 1


title: leukocytes_COPD_old_female_0min_rep3


title: leukocytes_COPD_old_male_180min_rep6

value: male


title: LE gubernaculum-GD17-biological rep4

description:
WP17d
hybridization batch: 2

source_name: LE gubernaculum at GD17


title: LE gubernaculum-GD17-biological rep5

description:
WP17e
hybridization batch: 2


title: leukocytes_COPD_old_male_0min_rep6


title: ORL gubernaculum-GD17-biological rep1

description:
OP17a
hybridization batch: 1


title: leukocytes_COPD_old_female_180min_rep1


title: leukocytes_COPD_old_male_180min_rep7


title: leukocytes_COPD_old_male_0min_rep7


title: LE gubernaculum-GD17-biological rep3

description:
WP17c
hybridization batch: 1


title: * leukocytes_COPD_old_male_180min_rep5


title: LE gubernaculum-GD17-biological rep2

description:
WP17b
hybridization batch: 1


title: leukocytes_COPD_old_female_0min_rep1


title: LE gubernaculum-GD17-biological rep1

description:
WP17a
hybridization batch: 1


title: leukocytes_COPD_old_male_180min_rep4


title: * leukocytes_COPD_old_male_0min_rep5


title: Sox4fl/fl SE-Cre HA-Sox4 rep 1

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: The University of Texas MD Anderson Cancer Center

description: Gain-of-function array-2

hyb_protocol: Standard Illumina hybridization protocol was used.

scan_protocol: Standard Illumina scanning protocol was used.

data_processing: Data was normalized by quantile normalization method in the Linear Models for Microarray Data package in R 3.0.1 program.

source_name: p190 Bcr-Abl immortalized progenitor B cells

label_protocol: Biotinylated cRNA was prepared as per standard protocol provided in Illumina TotalPrep RNA Amplification Kit .

extract_protocol: RNA was isolated from >95% pure progenitor B cells with the TRI Reagent (Ambion). During RNA precipitation, 20 µg of linear polyacrylamide (Ambion) was added to isopropanol (Sigma), and precipitated RNA was gently washed once with n-butanol (Sigma) and twice with 70% alcohol before air-dried RNA pellets were dissolved in diethylpyrocarbonate-treated water.

value: Sox4fl/fl SE-Cre HA-Sox4

value: Embryonic fetal liver

tag: developmental stage

value: Progenitor B cells


title: leukocytes_COPD_old_male_0min_rep3


title: leukocytes_COPD_old_male_0min_rep4


title: Sox4fl/fl SE-Cre HA-Sox4 rep 2

description: Gain-of-function array-2

value: p190 Bcr-Abl immortalized progenitor B cells


title: Sox4fl/fl SE-Cre HA rep 3

description: Gain-of-function array-2

value: Sox4fl/fl SE-Cre HA


title: Sox4fl/fl SE-Cre HA rep 2

description: Gain-of-function array-2


title: Sox4fl/fl SE-Cre rep 2

description: Loss-of-function array-1

source_name: Progenitor B cells

value: Sox4fl/fl SE-Cre


title: Sox4fl/fl SE-Cre HA rep 1

description: Gain-of-function array-2


title: leukocytes_COPD_old_male_0min_rep1


title: Sox4fl/fl SE-Cre rep 3

description: Loss-of-function array-1


title: leukocytes_smoker_old_male_0min_rep6

value: Healthy


title: * leukocytes_COPD_old_male_0min_rep2


title: Sox4fl/fl SE-Cre HA-Sox4 rep 3

description: Gain-of-function array-2


title: leukocytes_COPD_old_male_180min_rep3


title: leukocytes_COPD_old_male_180min_rep1


title: * leukocytes_COPD_old_male_180min_rep2


title: Sox4fl/fl rep 3

description: Loss-of-function array-1


title: leukocytes_smoker_old_male_180min_rep4


title: leukocytes_smoker_old_male_0min_rep5


title: leukocytes_smoker_old_male_180min_rep3


title: Sox4fl/fl rep 2

description: Loss-of-function array-1


title: Sox4fl/fl rep 1

description: Loss-of-function array-1


title: leukocytes_smoker_old_male_0min_rep4


title: leukocytes_smoker_old_male_0min_rep3


title: leukocytes_smoker_old_male_180min_rep6


title: myocardium-postnatal-failing-DCM-rep3

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The raw data were read into the R statistical software package and processed with the functions implemented in the Bioconductor beadarray (2.12.0) and lumi (2.14.0) package. The data was transformed using variance stabilizing transformation.

source_name: failing myocardium_before LVAD support

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp Premier RNA Amplification Kit.

extract_protocol: Total RNA was extracted with the Trizol reagent, followed by a DNase I and proteinase K treatment and another phenol chloroform extraction. The RNA was recovered by ethanol precipitation, and column treated with the QIagen miRNeasy kit according to the manufacturers instructions. Quality control was performed with the Agilent Bioanalyser.

tag: sample id

tag: disease

value: Dilated Cardiomyopathy

value: Female

tag: race

value: Caucasian

tag: nyha

tag: ejection fraction

tag: treatment

value: LVAD Implantation

value: left ventricular myocardium


title: leukocytes_smoker_old_male_180min_rep5

tag: cell type

value: leukocyte

value: Smoker


title: Sox4fl/fl SE-Cre rep 1

description: Loss-of-function array-1


title: myocardium-postnatal-failing-DCM-rep4

description:
7018861008_K
This is a technical replicate of array 7018861004_J which was replaced by this array because of a low signal to noise ratio. The RNA used for the replicate was from the same initial isolation, but before column treatment. All chips were processed at the same time.

value: Male

value: African American


title: leukocytes_smoker_old_male_180min_rep1

value: male


title: myocardium-postnatal-failing-ICM-VAD-treatment-rep3

source_name: failing myocardium_after LVAD support

value: Ischemic Cardiomyopathy

value: LVAD Explantation


title: leukocytes_smoker_old_male_0min_rep2


title: myocardium-postnatal-failing-ICM-VAD-treatment-rep4


title: leukocytes_smoker_old_male_0min_rep1


title: myocardium-postnatal-failing-DCM-rep2


title: leukocytes_smoker_old_female_180min_rep5

value: female


title: leukocytes_smoker_old_male_180min_rep2


title: myocardium-postnatal-non-failing-rep4

source_name: non-failing postnatal myocardium


title: leukocytes_smoker_old_female_0min_rep4


title: leukocytes_smoker_old_female_0min_rep3


title: myocardium-postnatal-failing-DCM-VAD-treatment-rep3


title: myocardium-fetal-non-failing-rep4

source_name: fetal myocardium


title: myocardium-postnatal-failing-ICM-rep3


title: myocardium-postnatal-failing-DCM-VAD-treatment-rep4


title: myocardium-postnatal-failing-ICM-rep2


title: myocardium-postnatal-non-failing-rep3

value: Asian


title: leukocytes_smoker_old_female_0min_rep1


title: myocardium-postnatal-failing-ICM-VAD-treatment-rep2


title: leukocytes_smoker_old_female_180min_rep4


title: myocardium-postnatal-failing-DCM-rep1


title: leukocytes_smoker_old_female_180min_rep2


title: myocardium-postnatal-failing-DCM-VAD-treatment-rep2


title: myocardium-postnatal-non-failing-rep2


title: leukocytes_smoker_old_female_180min_rep1


title: leukocytes_smoker_old_female_0min_rep2


title: $ leukocytes_smoker_young_male_0min_rep4


title: leukocytes_smoker_old_female_0min_rep5


title: $ leukocytes_smoker_young_male_180min_rep5


title: myocardium-fetal-non-failing-rep3


title: myocardium-postnatal-failing-ICM-rep1


title: myocardium-fetal-non-failing-rep1


title: leukocytes_smoker_old_female_180min_rep3


title: myocardium-postnatal-failing-ICM-rep4


title: $ leukocytes_smoker_young_male_0min_rep5


title: myocardium-fetal-non-failing-rep2


title: myocardium-postnatal-non-failing-rep1


title: $ leukocytes_smoker_young_male_180min_rep3


title: myocardium-postnatal-failing-DCM-VAD-treatment-rep1


title: miR-542-3p-rep3

first: Yemin

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Centre

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

source_name: U2OS cells

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

extract_protocol: RNA was extracted with Qiagen RNeasy kit, followed by DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: miR-542-3p mimic

value: ostesarcoma


title: $ leukocytes_smoker_young_male_0min_rep2

value: Healthy


title: $ leukocytes_smoker_young_male_180min_rep4


title: miR-neg_rep1

value: miR-negative

tag: tissue


title: $ leukocytes_smoker_young_female_180min_rep5


title: miR-542-3p-rep2


title: myocardium-postnatal-failing-ICM-VAD-treatment-rep1


title: miR-neg_rep2


title: $ leukocytes_smoker_young_female_0min_rep3


title: $ leukocytes_smoker_young_male_180min_rep1


title: $ leukocytes_smoker_young_male_0min_rep1


title: $ leukocytes_smoker_young_male_180min_rep2


title: $ leukocytes_smoker_young_female_180min_rep4


title: miR-neg_rep3


title: $ leukocytes_smoker_young_female_0min_rep5


title: $ leukocytes_smoker_young_female_0min_rep2


title: $ leukocytes_smoker_young_male_0min_rep3


title: $ leukocytes_smoker_young_female_180min_rep3


title: $ leukocytes_smoker_young_female_180min_rep2


title: leukocytes_non smoker_old_male_0min_rep3

value: Non-smoker


title: miR-542-3p-rep1


title: leukocytes_non smoker_old_male_180min_rep2


title: $ leukocytes_smoker_young_female_0min_rep1


title: $ leukocytes_smoker_young_female_0min_rep4


title: leukocytes_non smoker_old_male_180min_rep3


title: leukocytes_non smoker_old_male_180min_rep4


title: leukocytes_non smoker_old_male_0min_rep4


title: leukocytes_non smoker_old_male_0min_rep5


title: $ leukocytes_smoker_young_female_180min_rep1


title: leukocytes_non smoker_old_female_0min_rep3


title: leukocytes_non smoker_old_female_180min_rep2


title: leukocytes_non smoker_old_female_180min_rep3


title: leukocytes_non smoker_old_male_0min_rep1


title: leukocytes_non smoker_old_female_0min_rep5


title: leukocytes_non smoker_old_male_180min_rep1


title: $ leukocytes_non smoker_young_male_0min_rep4


title: leukocytes_non smoker_old_male_0min_rep2


title: leukocytes_non smoker_old_male_180min_rep5


title: leukocytes_non smoker_old_female_180min_rep5


title: leukocytes_non smoker_old_female_180min_rep4


title: leukocytes_non smoker_old_female_0min_rep4


title: $ leukocytes_non smoker_young_male_180min_rep3


title: leukocytes_non smoker_old_female_0min_rep1


title: $ leukocytes_non smoker_young_male_0min_rep5


title: leukocytes_non smoker_old_female_180min_rep1


title: leukocytes_non smoker_old_female_0min_rep2


title: $ leukocytes_non smoker_young_male_180min_rep4


title: $ leukocytes_non smoker_young_male_0min_rep3


title: $ leukocytes_non smoker_young_male_180min_rep2


title: $ leukocytes_non smoker_young_male_0min_rep2


title: $ leukocytes_non smoker_young_male_180min_rep1


title: $ leukocytes_non smoker_young_female_180min_rep5


title: $ leukocytes_non smoker_young_female_180min_rep4


title: $ leukocytes_non smoker_young_male_180min_rep5


title: $ leukocytes_non smoker_young_female_180min_rep3


title: $ leukocytes_non smoker_young_female_0min_rep3


title: $ leukocytes_non smoker_young_female_0min_rep5


title: $ leukocytes_non smoker_young_female_180min_rep2


title: $ leukocytes_non smoker_young_female_0min_rep1


title: $ leukocytes_non smoker_young_female_180min_rep1


title: $ leukocytes_non smoker_young_female_0min_rep4


title: Peripheral blood sample from anaphylaxis patient # 6 at timepoint 1

city: Subiaco

first: Anthony

last: Bosco

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: 5.5 μg of fragmented, biotin labeled ssDNA was hybridized to each Human Gene 1.0ST microarras according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data was preprocessed in R employing the qFarms algorithm (laplacian prior). A custom CDF file was used (hugene10sthsentrezg, version 16). The data was filtered using the Informative/non-informative (I/NI) calls algorithm.

label_protocol: 250ng of total RNA was amplified (Ambion WT kit), labeled with biotin (Affymetrix terminal labelling kit) and fragmented according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).

growth_protocol: Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

extract_protocol: RNA was extracted with the PAXgene Blood RNA Extraction Kits (PreAnalytiX GmbH, Switzerland) by automation with the Qiacube instrument (Qiagen, Australia).

treatment_protocol: Blood samples were colected and stabilized in PAXgene tubes. The PAXgene tubes were placed immediately at 4°C then transferred to -20°C within 72 hours, before final storage at -80°C.

tag: phenotype

value: Anaphylaxis patient

tag: timepoint

value: 1 hr after arrival


title: Peripheral blood sample from anaphylaxis patient # 5 at timepoint 1


title: Peripheral blood sample from anaphylaxis patient # 3 at timepoint 2

value: 3 hrs after arrival


title: Peripheral blood sample from anaphylaxis patient # 5 at timepoint 0

value: at arrival


title: Peripheral blood sample from anaphylaxis patient # 3 at timepoint 1


title: Peripheral blood sample from anaphylaxis patient # 4 at timepoint 2


title: Peripheral blood sample from anaphylaxis patient # 4 at timepoint 1


title: Peripheral blood sample from anaphylaxis patient # 3 at timepoint 0


title: Peripheral blood sample from anaphylaxis patient # 5 at timepoint 2


title: Peripheral blood sample from anaphylaxis patient # 2 at timepoint 2


title: Peripheral blood sample from anaphylaxis patient # 4 at timepoint 0


title: $ leukocytes_non smoker_young_female_0min_rep2

value: leukocyte

tag: age


title: liver from Sco1fl/fl mouse_3

city: Saskatoon

first: Scot

last: Leary

state: SK

address: 107 Wiggins Road

department: Biochemistry

institute: University of Saskatchewan

hyb_protocol: The fragmented and labeled DNA target was hybridized on Mouse Gene 2.0 ST (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: Raw intensities in the CEL files were read background corrected, normalized, log2 transformed and summarized at the transcript cluster level using the rma function in the Bioconductor package oligo 1.24

source_name: wild-type

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  Sense-strand cDNA was synthesized from 250ng of total RNA using the Ambion® WT Expression Kit according to the manufacturer’s instructions (Life Technologies Corporation). The cDNA was fragmented and labeled with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).

growth_protocol: Mouse livers were dissected at day 27

extract_protocol: Mice were identified as wild-type or mutants by PCR.  Liver samples were snap frozen in liquid N2. Total RNA was extracted using the Qiagen RNeasy kit, with an on column DNase treatment, according to the manufacturer's specifications.

tag: strain

value: 27 days

value: Liver

tag: genotype


title: liver from Sco1fl/fl mouse_2


title: liver from Sco1fl/fl mouse_1


title: $ leukocytes_non smoker_young_male_0min_rep1

value: male

tag: smoking status

tag: disease status


title: liver from Sco1fl/fl mouse_4


title: liver from Alb-Cre Sco1fl/fl mouse_3


title: Peripheral blood sample from anaphylaxis patient # 2 at timepoint 1


title: liver from Alb-Cre Sco1fl/fl mouse_4


title: liver from Alb-Cre Sco1fl/fl mouse_1


title: Peripheral blood sample from anaphylaxis patient # 2 at timepoint 0


title: Peripheral blood sample from anaphylaxis patient # 1 at timepoint 2


title: Peripheral blood sample from anaphylaxis patient # 1 at timepoint 1


title: Peripheral blood sample from anaphylaxis patient # 1 at timepoint 0


title: liver from Alb-Cre Sco1fl/fl mouse_2


title: PBMC from Donor C at 12h with HIV-2

city: London

first: Adriano

last: Boasso

address: 369 Fulham road

department: Immunology at Chelsea and Westminster Hospital

country: United Kingdom

institute: Imperial College London

description: Single donor (C) PBMC cultured with HIV-2 for 12 hours

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute, (N.B. this deviates from Affy SOP) • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm in GeneChip Hybridisation Oven 645• Fluidics washing is FS450_0002

scan_protocol: Affymetrix GeneChiP Scanner 3000 7G

data_processing:
Partek Genomics 6.6 (Partek Inc., Saint Louis, MO, USA) was used for data processing and analysis.
probe group file: HuGene-2_0-st.pgf
meta-probeset file: HuGene-2_0-st.mps

source_name: C 12hrs HIV-2

label_protocol: Ambion WT Expression kit was used to prepare the cDNA, which was then labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, High Wycombe, UK).

growth_protocol: PBMC from healthy volunteers cultured in RPMI164 supplemented with 10% FBS, 2mM L-Glutamine, 100U/ml Penicillin and 0.1mg/ml Streptomycin

extract_protocol: Cells were collected after 6 and 12 hours. Total RNA was extracted using the RNeasy Mini extraction kit (QIAGEN) and subsequently concentrated using the RNeasy MinElute Cleanup kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Media only (negative control); 13x10^9 RNA copies/ml HIV-1MNgrown in H9 cells; 13x10^9 RNA copies/ml HIV-2NIH-Zgrown in HuT78 cells; or 0.5uM CpG oligonucleotide type A - cultured for 6 or 12 hours

tag: donor

value: C

tag: time

value: 12 hours

value: HIV-2 NIH-Z


title: Peripheral blood sample from healthy subject # 6 at timepoint 2

value: Healthy control subject


title: PBMC from Donor C at 12h with CpG-A

description: Single donor (C) PBMC cultured with CpG-A for 12 hours

label: Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, High Wycombe, UK)

source_name: C 12hrs CpG

value: CpG-A ODN


title: PBMC from Donor B at 12h with CpG-A

description: Single donor (B) PBMC cultured with CpG-A for 12 hours

source_name: B 12hrs CpG

value: B


title: PBMC from Donor B at 12h in Media

description: Single donor (B) PBMC cultured in Media for 12 hours

source_name: B 12hrs media

value: Media


title: PBMC from Donor A at 12h with CpG-A

description: Single donor (A) PBMC cultured with CpG-A for 12 hours

source_name: A 12hrs CpG

value: A


title: Peripheral blood sample from healthy subject # 6 at timepoint 1


title: PBMC from Donor B at 12h with HIV-2

description: Single donor (B) PBMC cultured with HIV-2 for 12 hours

source_name: B 12hrs HIV-2


title: PBMC from Donor A at 12h with HIV-2

description: Single donor (A) PBMC cultured with HIV-2 for 12 hours

source_name: A 12hrs HIV-2


title: Peripheral blood sample from healthy subject # 6 at timepoint 0


title: PBMC from Donor C at 12h in Media

description: Single donor (C) PBMC cultured in Media for 12 hours

source_name: C 12hrs media


title: PBMC from Donor A at 12h with HIV-1

description: Single donor (A) PBMC cultured with HIV-1 for 12 hours

source_name: A 12hrs HIV-1

value: HIV-1 MN


title: Peripheral blood sample from healthy subject # 5 at timepoint 2


title: skeletal_muscle_UASmnt_rep2

city: Boston

first: William

middle: R

last: Swindell

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description:
skeletal muscle from UAS-Mnt flies
NP2012053047_14DT_mnt_rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA) signals were calculated using the R statistical software.

organism: Drosophila melanogaster

source_name: skeletal muscle

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: Flies were collected within 24 hours from eclosion and reared at standard density (20 per vial) on cornmeal/soy flour/yeast fly food at 25C

extract_protocol: Total RNA was extracted from at least 15 male flies per group with the Trizol reagent followed by cleanup with the RNeasy mini kit (Qiagen). Samples for three independent biological replicates per genotype were collected. RNA integrity was assessed with an Agilent 2100 Bioanalyzer before cRNA synthesis and hybridization to Affymetrix Drosophila Genome 2.0 Arrays.

treatment_protocol: The UAS-FOXO and UAS-Mnt stocks have been described by Zheng et al. 2007 and Loo et al. 2005 (Zheng, X., Yang, Z., Yue, Z., Alvarez, J. D., and Sehgal, A. (2007). FOXO and insulin signaling regulate sensitivity of the circadian clock to oxidative stress. Proc Natl Acad Sci U S A 104, 15899-15904; Loo, L. W., Secombe, J., Little, J. T., Carlos, L. S., Yost, C., Cheng, P. F., Flynn, E. M., Edgar, B. A., and Eisenman, R. N. (2005). The transcriptional repressor dMnt is a regulator of growth in Drosophila melanogaster. Mol Cell Biol 25, 7078-7091.)

tag: gender

value: UAS-Mnt

value: skeletal muscle


title: PBMC from Donor A at 12h in Media

description: Single donor (A) PBMC cultured in Media for 12 hours

source_name: A 12hrs media


title: PBMC from Donor B at 12h with HIV-1

description: Single donor (B) PBMC cultured with HIV-1 for 12 hours

source_name: B 12hrs HIV-1


title: skeletal_muscle_UASmnt_rep3

description:
skeletal muscle from UAS-Mnt flies
NP2012053048_16DT_mnt_rep3


title: PBMC from Donor C at 6h with CpG-A

description: Single donor (C) PBMC cultured with CpG-A for 6 hours

source_name: C 6hrs CpG

value: 6 hours


title: skeletal_muscle_UASfoxo_rep3

description:
skeletal muscle from UAS-FOXO flies
NP2012053039_3FX_foxo_rep3

value: UAS-Foxo


title: skeletal_muscle_UASmnt_rep1

description:
skeletal muscle from UAS-Mnt flies
NP2012053046_12DT_mnt_rep1


title: Peripheral blood sample from healthy subject # 4 at timepoint 2

value: 3 hrs after arrival


title: Peripheral blood sample from healthy subject # 5 at timepoint 1

value: 1 hr after arrival


title: Peripheral blood sample from healthy subject # 5 at timepoint 0

value: at arrival


title: skeletal_muscle_UASfoxo_rep2

description:
skeletal muscle from UAS-FOXO flies
NP2012053038_2FX_foxo_rep2

value: male


title: PBMC from Donor C at 6h with HIV-2

description: Single donor (C) PBMC cultured with HIV-2 for 6 hours

source_name: C 6hrs HIV-2

value: C


title: PBMC from Donor C at 6h with HIV-1

description: Single donor (C) PBMC cultured with HIV-1 for 6 hours

source_name: C 6hrs HIV-1


title: skeletal_muscle_control_rep3

description:
skeletal muscle from control flies
NP2012053042_6NC_control_rep3

value: control


title: PBMC from Donor C at 6h in Media

description: Single donor (C) PBMC cultured in Media for 6 hours

source_name: C 6hrs media


title: skeletal_muscle_UASfoxo_rep1

description:
skeletal muscle from UAS-FOXO flies
NP2012053037_1FX_foxo_rep1


title: Peripheral blood sample from healthy subject # 4 at timepoint 1


title: skeletal_muscle_control_rep1

description:
skeletal muscle from control flies
NP2012053040_4NC_control_rep1


title: Peripheral blood sample from healthy subject # 3 at timepoint 1


title: Peripheral blood sample from healthy subject # 4 at timepoint 0


title: Peripheral blood sample from healthy subject # 3 at timepoint 0


title: Peripheral blood sample from healthy subject # 3 at timepoint 2


title: skeletal_muscle_control_rep2

description:
skeletal muscle from control flies
NP2012053041_15NC_control_rep2


title: Peripheral blood sample from healthy subject # 2 at timepoint 1


title: Peripheral blood sample from healthy subject # 2 at timepoint 2


title: PBMC from Donor B at 6h with CpG-A

description: Single donor (B) PBMC cultured with CpG-A for 6 hours

source_name: B 6hrs CpG


title: PBMC from Donor B at 6h with HIV-2

description: Single donor (B) PBMC cultured with HIV-2 for 6 hours

source_name: B 6hrs HIV-2

value: HIV-2 NIH-Z


title: PBMC from Donor A at 6h with CpG-A

description: Single donor (A) PBMC cultured with CpG-A for 6 hours

source_name: A 6hrs CpG


title: PBMC from Donor B at 6h in Media

description: Single donor (B) PBMC cultured in Media for 6 hours

source_name: B 6hrs media


title: PBMC from Donor A at 6h with HIV-2

description: Single donor (A) PBMC cultured with HIV-2 for 6 hours

source_name: A 6hrs HIV-2


title: M18MSP1P2_cell_rep2

city: Shanghai

first: yaqian

last: Li

address: Dongchuan Road

institute: Shanghai Jiaotong University

description: gene expression without PCA

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US)Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit( Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

organism: Pseudomonas aeruginosa

source_name: Cells, no PCA,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the  Low RNA Input Linear Amplification  kit (Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions,and purified by RNeasy mini kit ( QIAGEN, GmBH, Germany).

growth_protocol: Cells were grown to OD600=5.0 (exponential phase) in PPM medium at 28℃.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen,Carlsbad, CA, USA).

tag: pca status


title: PBMC from Donor B at 6h with HIV-1

description: Single donor (B) PBMC cultured with HIV-1 for 6 hours

source_name: B 6hrs HIV-1


title: Peripheral blood sample from healthy subject # 1 at timepoint 0

value: Healthy control subject


title: Peripheral blood sample from healthy subject # 2 at timepoint 0


title: PBMC from Donor A at 6h in Media

description: Single donor (A) PBMC cultured in Media for 6 hours

source_name: A 6hrs media


title: Peripheral blood sample from healthy subject # 1 at timepoint 1


title: PBMC from Donor A at 6h with HIV-1

description: Single donor (A) PBMC cultured with HIV-1 for 6 hours

source_name: A 6hrs HIV-1


title: BCat_KO-MLL-AF9-rep1

first: Amit

last: Sinha

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

description:
SA2012080854
MLL-AF9 murine leukemia; loss of beta-catenin

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: Bcat-/-MLL-AF9 secondary AML cells from mouse bone marrow

label_protocol: Standard Affymetrix protocol

growth_protocol: Secondary leukemias were generated by injecting 10,000 MLL-AF9 or KRasG12DMLL-AF9 primary leukemia cells into B6129 recpieints. Bulk leukemia cells from the bone marrow were isolated from leukemic mice.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Lin-Kit+GFP+ leukemia cells from the bone marrow from leukemic mice were sorted from secondary transplant recipients

value: secondary AML cells

value: bone marrow


title: M18MSP1P2_cell_rep3

description: gene expression without PCA

source_name: Cells, no PCA,replicate 3


title: BCat_KO-MLL-AF9-rep3

description:
SA2012080856
MLL-AF9 murine leukemia; loss of beta-catenin


title: PBMC from Donor C at 12h with HIV-1

description: Single donor (C) PBMC cultured with HIV-1 for 12 hours

source_name: C 12hrs HIV-1

value: 12 hours


title: Peripheral blood sample from healthy subject # 1 at timepoint 2


title: M18MSP1P2_cell_rep1

description: gene expression without PCA

source_name: Cells, no PCA,replicate 1


title: M18MSU1_cell_rep2

description: gene expression with higher amount of PCA

source_name: Cells, higher amount of PCA,replicate 2

value: higher amount


title: M18MSU1_cell_rep1

source_name: Cells, higher amount of PCA,replicate 1


title: M18MSU1_cell_rep3

source_name: Cells, higher amount of PCA,replicate 3


title: BCat_WT-MLL-AF9-rep3

description:
SA2012080853
MLL-AF9 murine leukemia; WT beta-catenin

source_name: Bcat+/+MLL-AF9 secondary AML cells from mouse bone marrow


title: BCat_WT-MLL-AF9-rep2

description:
SA2012080852
MLL-AF9 murine leukemia; WT beta-catenin


title: BCat_WT-MLL-AF9-rep1

description:
SA2012080851
MLL-AF9 murine leukemia; WT beta-catenin


title: BCat_KO-Kras-MLL-AF9-rep2

description:
SA2012080849
KRasG12DMLL-AF9 murine leukemia; loss of beta-catenin

source_name: Bcat-/-KRasG12DMLL-AF9 secondary AML cells from mouse bone marrow


title: BCat_KO-Kras-MLL-AF9-rep3

description:
SA2012080850
KRasG12DMLL-AF9 murine leukemia; loss of beta-catenin


title: BCat_KO-MLL-AF9-rep2

description:
SA2012080855
MLL-AF9 murine leukemia; loss of beta-catenin


title: M18MS_cell_rep2

description: gene expression with lower amount of PCA

source_name: Cells, lower amount of PCA,replicate 2

value: lower amount


title: M18MS_cell_rep1

source_name: Cells, lower amount of PCA,replicate 1


title: Peripheral blood sample from anaphylaxis patient # 6 at timepoint 2

value: Anaphylaxis patient


title: M18MS_cell_rep3

source_name: Cells, lower amount of PCA,replicate 3


title: Peripheral blood sample from anaphylaxis patient # 6 at timepoint 0


title: BCat_WT-Kras-MLL-AF9-rep3

description:
SA2012080847
KRasG12DMLL-AF9 murine leukemia; WT beta-catenin

source_name: Bcat+/+KRasG12DMLL-AF9 secondary AML cells from mouse bone marrow


title: Multi-fractionated radiation 24hr 2Gyx5, Rep2 [miRNA]

status: Public on Jul 01 2014

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: Labeled target was applied to Agilent-021827 miRNA 8x15K arrays (Design ID #021827) and hybridized overnight.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction), and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: HCAECs, MF, 24hr

label_protocol: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

growth_protocol: Cryopreserved human coronary artery endothelial cells (HCAEC) and the media were purchased from Lonza Walkersville Inc. (Walkersville, MD). Cells were thawed and maintained in EBM-2 basal medium supplemented with fetal bovine serum and growth factors (EGM-2 MV BulletKit CC-3202) according to the supplier's instructions. Cells from passages P1 to P3 were used. Cells were plated into T75cm2 flasks (1-1.5 x 10^6 for single-dose radiation and 0.6-0.8 x 10^6 for fractionated radiation).

extract_protocol: Total RNA was extracted and purified using Ribopure (Ambion) RNA isolation and confirmed for quality (Agilent 2100 Bioanalyzer, Agilent Technologies, Inc., Santa Clara, CA) following the manufacturers' instructions.

treatment_protocol: Cells were irradiated in a PANTAK high frequency X-ray generator (Precision X-ray Inc., N. Bedford, CT), operated at 300kV and 10MA. The dose rate was 1.6 Gy per min. Cells were plated into T75cm2 flasks (1-1.5 x 10^6 for single-dose radiation and 0.6-0.8 x 10^6 for fractionated radiation). After 24h, cells were exposed to a total of 10 Gy radiation administered either as a single-dose radiation (SD), or as multi-fractionated radiation of 2 Gy x 5 (MF). These non-isoeffective doses were selected to simulate clinical hypofractionated and conventionally fractionated radiotherapy regimens. For the MF protocol, cells were exposed to 2 Gy radiation twice a day, at 6h interval. The cells were approximately 90% confluent at the time of harvesting. For both protocols, radiation-induced changes were analyzed at 6h and 24h after a SD and 6h and 24h after the final dose of fractionated irradiation. Separate controls were maintained for SD and MF radiation protocols.

value: human coronary artery endothelial cells (HCAECs)

value: multi-fractionated radiation (2Gyx5)

tag: time point


title: Multi-fractionated radiation 24hr 2Gyx5, Rep3 [miRNA]


title: Multi-fractionated radiation 6hr 2Gyx5, Rep3 [miRNA]

source_name: HCAECs, MF, 6hr


title: Multi-fractionated radiation 24hr Control, Rep3 [miRNA]

source_name: HCAECs, control (MF), 24hr

value: control (multi-fractionated radiation)


title: Multi-fractionated radiation 24hr Control, Rep1 [miRNA]


title: Multi-fractionated radiation 24hr Control, Rep2 [miRNA]


title: Multi-fractionated radiation 6hr 2Gyx5, Rep2 [miRNA]


title: Multi-fractionated radiation 24hr 2Gyx5, Rep1 [miRNA]


title: BCat_KO-Kras-MLL-AF9-rep1

description:
SA2012080848
KRasG12DMLL-AF9 murine leukemia; loss of beta-catenin


title: Multi-fractionated radiation 6hr 2Gyx5, Rep1 [miRNA]


title: Multi-fractionated radiation 6hr Control, Rep3 [miRNA]

source_name: HCAECs, control (MF), 6hr


title: Single-dose radiation 24hr 10Gy, Rep1 [miRNA]

source_name: HCAECs, SD, 24hr

value: single-dose radiation (10Gy)


title: BCat_WT-Kras-MLL-AF9-rep2

description:
SA2012080846
KRasG12DMLL-AF9 murine leukemia; WT beta-catenin


title: Single-dose radiation 24hr 10Gy, Rep3 [miRNA]


title: Single-dose radiation 24hr 10Gy, Rep4 [miRNA]


title: Multi-fractionated radiation 6hr Control, Rep1 [miRNA]


title: Single-dose radiation 24hr Control, Rep4 [miRNA]

source_name: HCAECs, control (SD), 24hr

value: control (single-dose radiation)


title: Multi-fractionated radiation 6hr Control, Rep2 [miRNA]


title: Single-dose radiation 24hr Control, Rep1 [miRNA]


title: Single-dose radiation 6hr 10Gy, Rep4 [miRNA]

source_name: HCAECs, SD, 6hr


title: Single-dose radiation 6hr 10Gy, Rep3 [miRNA]


title: Single-dose radiation 6hr Control, Rep4 [miRNA]

source_name: HCAECs, control (SD), 6hr


title: BCat_WT-Kras-MLL-AF9-rep1

description:
SA2012080845
KRasG12DMLL-AF9 murine leukemia; WT beta-catenin


title: Single-dose radiation 6hr Control, Rep3 [miRNA]


title: Single-dose radiation 24hr Control, Rep3 [miRNA]


title: Single-dose radiation 6hr Control, Rep1 [miRNA]


title: Single-dose radiation 6hr 10Gy, Rep1 [miRNA]


title: BM05

city: Kuala Lumpur

first: Moon

middle: Nian

last: Lim

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

description: US83503546_252800412749_S01_GE1_107_Sep09_1_1

hyb_protocol: The labeled cRNA was purified and quantitated before subjected to hybridization in a hybridization oven at 65 °C for 17 hr.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Dye channel is set to Green and Green PMT).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal. Data analysis was done by using GeneSpring 11.5 (Agilent Technologies, Santa Clara, CA). The threshold was set to intensity value of 1.0. Log base 2 transformation was carried out for threshold data. Normalization was done by 75th percentile shift. Baseline transformation was based on the median of samples. The data were futher filtered by probeset on flags and expression less than 20. Unpaired Student’s T test was used for statistical analysis. Genes up- or down-regulated by two-fold change were selected for further analysis.

source_name: Cultured bone marrow mesenchymal stem cells (Millipore)

label_protocol: Prior to Cy3 labeling, 2uL of Agilent One-Colour Spike Mix dilution was added to 100ng of total RNA for each sample. The total RNA was converted to cDNA and then to Cy3-labeled cRNA by using the Agilent One-Colour RNA Spike-In Kit as per the manufacturer's protocol.

growth_protocol: Cell culturing methods.

extract_protocol: Total RNA was extracted when the culture was near confluent. About 2-3 x 10^6 cells from each sample were lysed and total RNA was isolated using the RNeasy kit (Qiagen Hamburg GmbH, Hamburg, Germany) according to the manufacturer's protocol.

treatment_protocol: No specific treatment.

value: bone marrow mesenchymal stem cells


title: BM06

description: US83503546_252800412750_S01_GE1_107_Sep09_1_1


title: HFF02

description: US83503546_252800412749_S01_GE1_107_Sep09_2_4

source_name: Cultured human foreskin fibroblasts

value: foreskin fibroblasts


title: HFF01

description: US83503546_252800412748_S01_GE1_107_Sep09_2_4


title: HFF03

description: US83503546_252800412750_S01_GE1_107_Sep09_2_4


title: AD001

description: US83503546_252800412748_S01_GE1_107_Sep09_1_4

source_name: Cultured adipose stromal cells

value: adipose stromal cells


title: AD003

description: US83503546_252800412750_S01_GE1_107_Sep09_1_4


title: S1-P6 (matrigel)

description:
LS-matrigel
US83503546_252800412748_S01_GE1_107_Sep09_1_3

source_name: Ex vivo derived limbal stromal cells from donor S1, cultured on matrigel, passage 6

value: limbal stromal cells

tag: culture conditions

value: matrigel


title: AD002

description: US83503546_252800412749_S01_GE1_107_Sep09_1_4


title: 18B

type: SRA

city: Leiden

first: Elmar

middle: Wouter

last: Tobi

address: Einthovenweg 20

department: Medical Statistics and Bioinformatics

country: Netherlands

institute: Leiden University Medical Center

description: control family 18

library_source: genomic

data_processing:
Data was aligned as detailed in Meissner A. et al. Nature 2008, this is a custom version of MAQ in bisulfite mode
The number of unmethylated and methylated cytosines per measured CpG dinucleotide was determined from the .BAM alignment files using a custom python script detailed and available for download in Meissner A. et al. Nature 2008
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing the genomic coordinates of CpG sites, the number of methylated reads for this CpG dinucleotide, the total number of reads for this CpG dinucleotide, the methylation fraction for this CpG dinucleotide x 1000. The .bed files correspond to EGA .BAM files (see EGA accession numbers in 'Characteristics' field).

molecule: genomic DNA

source_name: genomic DNA from whole blood

extract_protocol:
genomic DNA was isolated using the salting out method
libraries were generated using the protocol as detailed by Gu H. et al. Nat Methods 2010

tag: tissue collection

value: whole blood drawn in EDTA tubes

tag: ega study id

tag: ega dataset id

tag: ega sample id

tag: ega raw file (run accession id that links to the actual .bam file)

tag: famine exposure

value: CONTROL

value: Male

tag: family


title: 23B

description: control family 23


title: 17B

description: control family 17

value: Female


title: S3-P4 (FBS)

description:
LS-FBS
US83503546_252800412749_S01_GE1_107_Sep09_1_2

source_name: Ex vivo derived limbal stromal cells from donor S3, cultured in FBS, passage 4

tag: cell type

value: FBS


title: S6-P5 (matrigel)

description:
LS-matrigel
US83503546_252800412750_S01_GE1_107_Sep09_1_3

source_name: Ex vivo derived limbal stromal cells from donor S6, cultured on matrigel, passage 5


title: 20B

description: control family 20


title: 24B

description: control family 24


title: 22B

description: control family 22


title: S6-P3 (FBS)

description:
LS-FBS
US83503546_252800412750_S01_GE1_107_Sep09_1_2

source_name: Ex vivo derived limbal stromal cells from donor S6, cultured in FBS, passage 3


title: 16B

description: control family 16


title: 21B

description: control family 21


title: 15B

description: control family 15


title: S1-P3 (FBS)

description:
LS-FBS
US83503546_252800412748_S01_GE1_107_Sep09_1_2

source_name: Ex vivo derived limbal stromal cells from donor S1, cultured in FBS, passage 3


title: 14B

description: control family 14


title: 13B

description: control family 13


title: BM01

description: US83503546_252800412748_S01_GE1_107_Sep09_1_1


title: 7B

description: control family 7


title: 9B

description: control family 9


title: 11B

description: control family 11


title: 10B

description: control family 10


title: 8B

description: control family 8


title: 6B

description: control family 6


title: 2B

description: control family 2


title: 5B

description: control family 5


title: 1B

description: control family 1


title: 3B

description: control family 3


title: 24A

description: exposed individual family 24

value: EXPOSED


title: 23A

description: exposed individual family 23


title: 22A

description: exposed individual family 22


title: 4B

description: control family 4


title: 20A

description: exposed individual family 20


title: S3-P6 (matrigel)

description:
LS-matrigel
US83503546_252800412749_S01_GE1_107_Sep09_1_3

source_name: Ex vivo derived limbal stromal cells from donor S3, cultured on matrigel, passage 6


title: 18A

description: exposed individual family 18


title: 19A

description: exposed individual family 19


title: 21A

description: exposed individual family 21


title: 12B

description: control family 12


title: 17A

description: exposed individual family 17


title: 16A

description: exposed individual family 16


title: 15A

description: exposed individual family 15


title: 14A

description: exposed individual family 14


title: 13A

description: exposed individual family 13


title: 12A

description: exposed individual family 12


title: 6A

description: exposed individual family 6


title: 9A

description: exposed individual family 9


title: 3A

description: exposed individual family 3


title: 5A

description: exposed individual family 5


title: 4A

description: exposed individual family 4


title: 11A

description: exposed individual family 11


title: 7A

description: exposed individual family 7


title: 8A

description: exposed individual family 8


title: 1A

description: exposed individual family 1


title: 2A

description: exposed individual family 2


title: IMR90 Apoptosis (GPL9777)

type: genomic

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Regional preferences in apoptotic DNA degradation were determined by co-hybridizing high molecular (> 48 kb) and degraded apoptotic DNA (~4 kb), which we have extracted from 1% low melting agarose and amplified by means of the GenomePlex Whole Genome Amplification Kit .

scan_protocol: scanned on an Agilent DNA Microarray Scanner G2565BA, Scan resolution: 2µm, Scan region: 61 x 21.6 mm, Green PMT: 100%, Red PMT: 100%

data_processing: TIFF image processing with Agilent Feature Extraction v10.5.1.1, CGH_105_Dec08 protocol. Data visualization and further analysis was performed with GenomeCATPro 1.3.1 (Tebel et al., manuscript in preparation; http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/CGHPRO.html) and the UCSC genome browser (https://genome.ucsc.edu/index.html).

source_name: fetal lung fibroblast

label_protocol: Agilent Genomic DNA Enzymatic Labeling Kit

growth_protocol: Both cell lines were cultured in Eagle´s minimum essential medium (EMEM) supplemented  with 10% fetal bovine serum, 2 mM UltraGlutamine 1, 1 mM sodium pyruvate and 100units/ml penicillin/streptomycin. The fibroblasts were maintained at 37°C with a humidified atmosphere of 5% CO2 and ambient oxygen.

extract_protocol: ChIP was done according to the Transcription Factor ChIP kit protocol (Diagenode, Liège, Belgium). In brief, lysed cells were sonicated  for 60 minutes using the Bioruptor UCD-200 device (Diagenode, Liège, Belgium), followed by overnight incubation of 1x106 cells with 5 µg of antibodies against unmodified histone H3 (ab1791; Abcam, Cambridge, UK) and histone H4 lysine 8 acetylation (pAb-103-050; Diagenode, Liège, Belgium), respectively. The subsequent chromatin reverse crosslinking, elution and purification of ChIP and input DNA were done employing the IPure Kit (Diagenode, Liège, Belgium). Analysis of apoptotic DNA: after treatment cells were washed once in PBS, detached by five minutes treatment with trypsin-EDTA and the cell pellets were stored at -80°. For DNA isolation cells were treated with lysis buffer (0.40 M Tris-HCl pH 8.0, 0.06 M Na-EDTA, 0.15 M NaCl, 1% SDS) and RNA was digested for 1 hour at 37°C using 15 µg/mL RNase A. 1 M sodium perchlorate and one volume chloroform were added to deproteinize cell lysates. After phase separation and collection of the aqueous phase DNA was precipitated. 3 µg of genomic DNA were loaded onto a 1% low melt agarose gel, electrophoresed for 90 minutes at 120 V and stained with ethidium bromide for 30 minutes. DNA bands responding to non-fragmented (> 48 kb) and fragmented DNA (approximately 4 kb) were cut with a scalpel and collected. For the extraction of DNA from the gel pieces β-Agarase I (New England Biolabs, Ipswich, USA) was used according to the manufacturer´s protocol.

treatment_protocol: Apoptosis  was induced by staurosporine (Cell Signaling Technology, Inc., Danvers, USA), which was dissolved in dimethyl sulfoxide (DMSO, Sigma, Saint Louis, USA) to a stock concentration of 1 mmol/L. About 2 x 10^6 cells were exposed to either 1 µmol/L staurosporine/0.1%DMSO or 0.1% DMSO alone as a control for 4 hours at 37°C.

value: female

tag: cell line

tag: sample type

value: DNA fragment ~ 4 kb

value: DNA fragment > 48 kb


title: 26B

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: carcinoma

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalised using lumi library in R 3.0.2

source_name: prostate

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted with MirVana Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: malignacy type

value: Prostate carcinoma

tag: carcinoma percentage

tag: paired sample status

value: control


title: 21BK

description: carcinoma

value: carcinoma


title: 25B

description: carcinoma


title: 26BK

description: carcinoma


title: 23B

description: carcinoma


title: IMR90 H4K8ac (GPL9777)

tag: gender

value: IP DNA

tag: chip antibody

tag: chip antibody manufacturer

value: Diagenode

tag: chip antibody catalog #

value: Input DNA


title: 23BK

description: carcinoma


title: 20B

description: carcinoma


title: 21B

description: carcinoma


title: 25BK

description: carcinoma


title: 19BK

description: carcinoma


title: 13BK

description: carcinoma


title: 14BK

description: carcinoma


title: 14B

description: carcinoma


title: 15B

description: carcinoma


title: IMR90 H3

value: Abcam


title: 15BK

description: carcinoma


title: 20BK

description: carcinoma


title: IMR91L H4K8ac

value: male


title: 19B

description: control family 19

tag: tissue collection

value: whole blood drawn in EDTA tubes


title: 18BK

description: carcinoma


title: 13B

description: carcinoma


title: 8B

description: carcinoma


title: 19B

description: carcinoma


title: 5BK

description: carcinoma


title: 7BK

description: carcinoma


title: 7B

description: carcinoma


title: 10A

description: exposed individual family 10

tag: ega study id