title: Subject LST019,  biological rep1

tag: response

value: ER

tag: site

tag: allergen

value: Cat Hair (Lot)

tag: Sex

value: F

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)

value: whole blood


title: Subject LST014,  biological rep1

status: Public on Sep 20 2013

type: RNA

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

hyb_protocol: Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing:
Raw data normalization using the 'farms' package consisted of RMA background correction, quantile normalization and  summarization of probe-level data using Factor Analysis for Robust Microarray Summarization
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 10%.
All statistical analyses were performed in the statistical computing program R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pre

label_protocol: standard Affymetrix protocol

extract_protocol:
Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

value: Laval

value: Cat Pelt

value: Caucasian

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell volume (fl)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)

tag: tissue


title: Subject LST012,  biological rep1

tag: response

tag: site

tag: allergen

tag: Sex

tag: ethnicity

tag: age

tag: mch pc20 (mg/ml) at pre-challenge

tag: mch pc20 (mg/ml) at post-challenge

tag: % fall in fev1 (early)


title: Subject LST013,  biological rep1

value: DR

value: Cat Hair

tag: % fall in fev1 (late)

tag: erythrocytes (x10^12/l)

tag: hemoglobin (g/l)

tag: hematocrit (l/l)

tag: mean cell hb (pg)

tag: mean cell hb conc. (g/l)

tag: red cell distr. width (%)

tag: platelets (x10^9/l)

tag: leukocytes (x10^9/l)


title: Subject LST003,  biological rep1

tag: response

tag: site

tag: mean cell volume (fl)

tag: neutrophils (x10^9/l)

tag: lymphocytes (x10^9/l)

tag: monocytes (x10^9/l)

tag: eosinophils (x10^9/l)

tag: basophils (x10^9/l)

tag: tissue


title: Line_M061_Diet_C_Replicate_2_Slide_v_subarray_8

status: Public on Sep 19 2013

city: Tuscaloosa

first: Laura

middle: Katie

last: Reed

state: AL

address: 300 Hackberry Ln.

department: Biological Sciences

country: USA

institute: University of Alabama

description: Nimblegen Design: 090901_Dmr43_expr

hyb_protocol: Samples were prepared for hybridized to the Nimblegen 12 plex slide arrays per manufactures instructions.  Hybridization took place in a Maui Mixer maintained at 42 degrees C for 16-20 hours.

scan_protocol: Slides were scanned using an Axon Genepix Microarray Scanner at 532nm.  Gain was optimized for each slide individually to minimize saturation but maintain good low level signal.

data_processing:
Raw image files were processed using Nimblegen's DEVA software to extract the *.pair and *.calls files.  The *.calls files were generated using the Expression Robust Multi-Array (RMA) Analysis.
DEVA software was used to generate the signal intensity files with RMA analysis, these data were then log2 transformed in JMP Genomics.  Subsequent median normalization and statistical analyses were also conducted in JMP Genomics.  The data reported here have not been median normalized.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: pools of 30 whole Drosophila melanogaster 3rd instar larvae

label_protocol: Invitrogen SuperScript Double Stranded cDNA Synthesis Kit was used to synthesize double stranded cDNA and polyT primers per manufactures instructinos.  cDNA was then labeled using Cy3 labled random nonamer primers per following the Nimblegen labling protocol.

growth_protocol: Adult Drosophila melanogaster were allowed to oviposit onto apple juice/agar plates for 12 hours.  Eggs were allowed to hatch and larve were collect as 1st instars and place into dietary treatment at a density of 50 larvae per vial.  Larvae were allow to grow for 3 days to 3rd instar larvae and then separated from their food using 20% sucorse solution, washed with distilled water, then allowed to fast on water-agar plates for 6 hours before being collected in groups of 30 and flash frozen in liquid nitrogen.  All parental lines and test larvae were maintained at 25 degrees C and a 12:12 light:dark cycle.

extract_protocol: Total RNA was extracted using the Ambion MagMAX™-96 Total RNA Isolation Kit protocol including a DNAse treatment per manufactures instructions.

treatment_protocol: Frozen larvae samples were homogenized into 300 ul of Tri regeant (LifeTechnologies Inc).

tag: line

tag: diet

value: C

tag: biological replicate

tag: slide

value: v

tag: subarray

tag: larval survival

tag: pupal survival

tag: development time

tag: weight

tag: log trehalose

tag: log triglycerides

tag: developmental stage

value: 3rd instar larvae


title: DSB-pat1.as2

type: genomic

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

description: IP/Input scaling factor: 1.1

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.

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Dark spot and control probes were removed, as were custom probes for repetitive DNA.  To allow comparisons between strains in the same experiment (the same rad50 allele), log ratios were multiplied by a calibration factor ranging from 1.1-1.3 determined by comparing probes within six prominant DSB hotspots shown by Southern blot to be indistinguishable.  The resulting ratios were then median normalized.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: IP Rec12, pat1-as2, rad50+

label_protocol: Immunoprecipitated material and whole-cell extracts were PCR amplified to increase signal and Cy3/Cy5-labeled dUTPs were incorporated.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for 16-18 hours to synchronize cells; nitrogen was added and meiosis was induced by two different methods: addition of a chemical inhibitor (1-NM-PP1) of the pat1-as2 allele or the temperature was shifted to 34°C.

extract_protocol: Cells were collected at the indicated time points following induction of meiosis when DSBs were maximal.  No exogenous crosslinking agent was used; cells were treated with protease inhibitors, broken with a bead beater, chromatin sonicated to ~500-1000 bp, and Rec12-FLAG immunoprecipitated.

tag: time

value: 6.5 hours

tag: induction method

value: pat1-as2 inhibitor

source_name: Whole-cell input for induced pat1-as2, rad50+


title: Tg2576

city: Beijing

first: Subi

last: Wei

state: Beijing

address: Xueyuan Load

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua university

description: low-molecuar-weight RNA derived from total RNA

hyb_protocol: Standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using GenePix Pro 4.0 (Axon Instruments, California, United States). Data processing including local background subtraction, quantile normalization across multiple slides was performed in R package (version 2.5.0).

organism: Mus musculus

label_protocol: 5μg of the Low-molecular-weight RNAs were isolated from total RNAs by a PEG solution precipitation method and labelled with 5-phosphate-cytidyl-uridyl-Cy3-3(Dharmacon, Chicago, United States) using T4 RNA ligase (NEB, Beijing, China) at 4°C for 4 hours in the dark. Eight synthetic small RNAs were spiked in for exogenous control.

growth_protocol: APP/PS1M146V/+ mice were generated by crossed Tg2576 APP transgenic mice with PS1 M146V homozygous (PS1M146V/M146V) mice. All mice were feed and housed according to standard procedures.

extract_protocol: The bilateral hippocampus was dissected from groups of mice (n= 3), pooled, then stored in liquid nitrogen until use. Tissue was homogenized in liquid nitrogen and total RNAs was prepared using TRIzol™ reagent according to the protocol provided by the manufacturer, with an additional 2 h incubation step at -20 °C during isopropanol precipitation. The A260/A280 ratio as well as the banding pattern of RNAs by denaturing gel electrophoresis was used to estimate the quality of the RNAs.

treatment_protocol: No treatment

tag: disease state

value: alzheimer's disease

value: bilateral hippocampus

tag: genotype/variation


title: APP/PS1M146V/+

tag: tissue


title: DSB-pat1.114

description: IP/Input scaling factor: 1

value: 3.5 hours

value: temperature shift

source_name: Whole-cell input for induced pat1-114, rad50+


title: Line_M096_Diet_N_Replicate_1_Slide_v_subarray_6

description: Nimblegen Design: 090901_Dmr43_expr

tag: line

value: N

tag: ai


title: Line_M026_Diet_4_Replicate_3_Slide_v_subarray_7

description: Nimblegen Design: 090901_Dmr43_expr

tag: diet

tag: biological replicate


title: DSB-pat1.as2-2

description: IP/Input scaling factor: 1

source_name: IP Rec12, pat1-as2, rad50+, replicate

source_name: Whole-cell input for induced pat1-as2, rad50+, replicate


title: Line_M012_Diet_F_Replicate_2_Slide_v_subarray_10

description: Nimblegen Design: 090901_Dmr43_expr

value: F

tag: slide

tag: subarray


title: Line_M054_Diet_4_Replicate_3_Slide_v_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr

tag: larval survival

tag: pupal survival


title: Line_NC2 063_Diet_F_Replicate_2_Slide_v_subarray_3

description: Nimblegen Design: 090901_Dmr43_expr

tag: development time

tag: weight


title: Line_M019_Diet_F_Replicate_1_Slide_v_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr

tag: log trehalose

tag: log triglycerides


title: Line_M027_Diet_N_Replicate_1_Slide_v_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr

tag: developmental stage


title: Line_NC2 047_Diet_F_Replicate_1_Slide_u_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr

value: u


title: Line_M012_Diet_N_Replicate_2_Slide_u_subarray_10

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_C_Replicate_3_Slide_v_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_N_Replicate_2_Slide_u_subarray_9

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_C_Replicate_2_Slide_u_subarray_11

description: Nimblegen Design: 090901_Dmr43_expr


title: WT_LSK

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

country: Japan

institute: Kumamoto University

description: Gene expression in LSK cells from WT mice at 20 weeks old

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner (Agilent Technologies)

data_processing: Standard Agilent protocol

source_name: Bone marrow LSK cells, wild type, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: strain

value: wild type

tag: transplantation

value: no

tag: cell type

value: Bone marrow LSK cells (from mice at 20 weeks old)


title: Line_M092_Diet_F_Replicate_2_Slide_v_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_N_Replicate_1_Slide_u_subarray_7

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_F_Replicate_1_Slide_u_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M054_Diet_C_Replicate_1_Slide_u_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M027_Diet_F_Replicate_1_Slide_u_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M054_Diet_4_Replicate_1_Slide_u_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M012_Diet_F_Replicate_2_Slide_t_subarray_11

description: Nimblegen Design: 090901_Dmr43_expr

value: t


title: Line_M011_Diet_N_Replicate_1_Slide_t_subarray_10

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 090_Diet_N_Replicate_2_Slide_t_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M026_Diet_N_Replicate_1_Slide_u_subarray_8

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M026_Diet_4_Replicate_2_Slide_t_subarray_9

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_4_Replicate_2_Slide_t_subarray_6

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M077_Diet_F_Replicate_3_Slide_t_subarray_8

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_C_Replicate_2_Slide_t_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M096_Diet_F_Replicate_1_Slide_t_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M026_Diet_F_Replicate_2_Slide_t_subarray_7

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 047_Diet_4_Replicate_2_Slide_t_subarray_3

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M012_Diet_4_Replicate_2_Slide_s_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr

value: s


title: Line_NC2 081_Diet_N_Replicate_2_Slide_s_subarray_11

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M051_Diet_N_Replicate_2_Slide_t_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M011_Diet_4_Replicate_2_Slide_t_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M051_Diet_N_Replicate_2_Slide_s_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M052_Diet_N_Replicate_3_Slide_s_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 005_Diet_C_Replicate_2_Slide_s_subarray_6

description: Nimblegen Design: 090901_Dmr43_expr

value: C


title: Line_M054_Diet_N_Replicate_2_Slide_s_subarray_7

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M012_Diet_4_Replicate_1_Slide_s_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M077_Diet_4_Replicate_1_Slide_r_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr

value: r


title: Line_M077_Diet_F_Replicate_3_Slide_r_subarray_9

description: Nimblegen Design: 090901_Dmr43_expr

value: 3rd instar larvae


title: Line_M052_Diet_C_Replicate_2_Slide_r_subarray_10

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M054_Diet_N_Replicate_1_Slide_s_subarray_8

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M092_Diet_F_Replicate_3_Slide_s_subarray_10

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M026_Diet_N_Replicate_3_Slide_s_subarray_9

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_F_Replicate_2_Slide_s_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 005_Diet_C_Replicate_3_Slide_r_subarray_8

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M051_Diet_N_Replicate_3_Slide_r_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_F_Replicate_3_Slide_q_subarray_6

description: Nimblegen Design: 090901_Dmr43_expr

value: q


title: Line_M011_Diet_C_Replicate_2_Slide_r_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 038_Diet_F_Replicate_2_Slide_r_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M051_Diet_F_Replicate_3_Slide_r_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M061_Diet_N_Replicate_2_Slide_p_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr

value: p


title: Line_M012_Diet_4_Replicate_3_Slide_q_subarray_3

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_N_Replicate_2_Slide_q_subarray_4

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 047_Diet_F_Replicate_1_Slide_p_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 096_Diet_F_Replicate_3_Slide_p_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_C_Replicate_1_Slide_q_subarray_2

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M027_Diet_C_Replicate_1_Slide_q_subarray_12

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M027_Diet_C_Replicate_3_Slide_p_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 081_Diet_F_Replicate_2_Slide_p_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_C_Replicate_1_Slide_p_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_C_Replicate_3_Slide_p_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_N_Replicate_1_Slide_q_subarray_1

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M019_Diet_N_Replicate_1_Slide_q_subarray_8

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M054_Diet_4_Replicate_3_Slide_o_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr

value: o


title: Line_M077_Diet_C_Replicate_3_Slide_o_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_C_Replicate_2_Slide_r_subarray_6

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 005_Diet_4_Replicate_3_Slide_r_subarray_3

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_M073_Diet_F_Replicate_1_Slide_p_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_C_Replicate_3_Slide_p_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_4_Replicate_1_Slide_p_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_4_Replicate_2_Slide_q_subarray_5

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 096_Diet_N_Replicate_3_Slide_o_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_C_Replicate_3_Slide_o_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_C_Replicate_1_Slide_p_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_N_Replicate_3_Slide_o_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_C_Replicate_3_Slide_o_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 081_Diet_C_Replicate_1_Slide_p_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_C_Replicate_1_Slide_o_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_4_Replicate_2_Slide_o_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_F_Replicate_3_Slide_o_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_4_Replicate_1_Slide_o_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_C_Replicate_3_Slide_o_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_C_Replicate_3_Slide_n_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr

value: n


title: Line_M096_Diet_C_Replicate_1_Slide_n_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_F_Replicate_3_Slide_n_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_4_Replicate_1_Slide_m_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: m


title: Line_NC2 005_Diet_N_Replicate_1_Slide_n_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_4_Replicate_2_Slide_m_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_N_Replicate_3_Slide_m_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_F_Replicate_3_Slide_n_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_C_Replicate_2_Slide_n_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_4_Replicate_1_Slide_m_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_C_Replicate_2_Slide_n_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_F_Replicate_3_Slide_m_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_F_Replicate_3_Slide_m_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_C_Replicate_1_Slide_m_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_4_Replicate_3_Slide_n_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_C_Replicate_1_Slide_m_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_F_Replicate_1_Slide_m_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_4_Replicate_1_Slide_m_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_4_Replicate_1_Slide_m_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_C_Replicate_1_Slide_n_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_4_Replicate_2_Slide_l_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: l


title: Line_M011_Diet_C_Replicate_2_Slide_l_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_F_Replicate_2_Slide_n_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_C_Replicate_2_Slide_m_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_4_Replicate_1_Slide_n_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_4_Replicate_1_Slide_l_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_C_Replicate_1_Slide_l_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_C_Replicate_1_Slide_l_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_F_Replicate_2_Slide_l_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_N_Replicate_3_Slide_l_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr

value: N


title: Line_NC2 096_Diet_C_Replicate_3_Slide_l_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_4_Replicate_2_Slide_u_subarray_3

description: Nimblegen Design: 090901_Dmr43_expr


title: Line_NC2 005_Diet_N_Replicate_3_Slide_k_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: k


title: Line_NC2 081_Diet_F_Replicate_1_Slide_k_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr

value: F


title: Line_M019_Diet_4_Replicate_2_Slide_k_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_N_Replicate_1_Slide_l_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 081_Diet_4_Replicate_1_Slide_k_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 081_Diet_4_Replicate_2_Slide_k_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_F_Replicate_1_Slide_l_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_N_Replicate_3_Slide_j_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: j


title: Line_M096_Diet_F_Replicate_1_Slide_k_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_F_Replicate_2_Slide_l_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_C_Replicate_3_Slide_k_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_N_Replicate_3_Slide_k_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_N_Replicate_3_Slide_j_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_4_Replicate_2_Slide_j_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_F_Replicate_3_Slide_k_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_F_Replicate_2_Slide_j_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_C_Replicate_3_Slide_k_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_F_Replicate_2_Slide_j_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_F_Replicate_1_Slide_j_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_N_Replicate_3_Slide_j_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_4_Replicate_3_Slide_l_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_4_Replicate_1_Slide_j_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_C_Replicate_1_Slide_j_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_4_Replicate_3_Slide_j_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_C_Replicate_3_Slide_j_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_N_Replicate_2_Slide_i_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr

value: i


title: Line_NC2 090_Diet_N_Replicate_2_Slide_i_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_C_Replicate_3_Slide_i_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 096_Diet_4_Replicate_1_Slide_i_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_C_Replicate_3_Slide_i_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_4_Replicate_1_Slide_i_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_F_Replicate_2_Slide_i_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_4_Replicate_3_Slide_i_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_4_Replicate_3_Slide_h_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: h


title: Line_NC2 047_Diet_F_Replicate_2_Slide_h_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_N_Replicate_2_Slide_h_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_4_Replicate_3_Slide_g_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: g


title: Line_M052_Diet_F_Replicate_3_Slide_h_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_C_Replicate_2_Slide_g_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_F_Replicate_1_Slide_i_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_C_Replicate_1_Slide_i_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_C_Replicate_3_Slide_h_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_F_Replicate_3_Slide_j_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 096_Diet_F_Replicate_1_Slide_h_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_F_Replicate_1_Slide_h_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M051_Diet_4_Replicate_2_Slide_g_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_C_Replicate_1_Slide_i_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_4_Replicate_1_Slide_g_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_N_Replicate_3_Slide_i_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_N_Replicate_1_Slide_h_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_N_Replicate_3_Slide_h_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_N_Replicate_3_Slide_h_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_F_Replicate_2_Slide_g_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_4_Replicate_3_Slide_g_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_F_Replicate_1_Slide_g_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_4_Replicate_3_Slide_g_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_N_Replicate_1_Slide_g_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_4_Replicate_2_Slide_g_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_C_Replicate_2_Slide_f_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr

value: f


title: Line_NC2 090_Diet_N_Replicate_3_Slide_f_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_N_Replicate_1_Slide_f_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_C_Replicate_1_Slide_f_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr

value: C


title: Line_NC2 090_Diet_4_Replicate_2_Slide_f_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_N_Replicate_2_Slide_f_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_C_Replicate_3_Slide_f_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_N_Replicate_3_Slide_f_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_N_Replicate_1_Slide_f_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_C_Replicate_2_Slide_f_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 005_Diet_F_Replicate_1_Slide_f_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_N_Replicate_1_Slide_f_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_4_Replicate_2_Slide_d_subarray_10

description: Nimblegen Design: 080306_Dmr43_expr

value: d


title: Line_M051_Diet_4_Replicate_3_Slide_e_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr

value: e

value: 3rd instar larvae


title: Line_M077_Diet_F_Replicate_3_Slide_d_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_N_Replicate_3_Slide_e_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_F_Replicate_2_Slide_e_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_4_Replicate_2_Slide_e_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_F_Replicate_3_Slide_e_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_F_Replicate_1_Slide_d_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_N_Replicate_2_Slide_d_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M092_Diet_F_Replicate_1_Slide_d_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_N_Replicate_1_Slide_d_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 096_Diet_C_Replicate_1_Slide_d_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_4_Replicate_2_Slide_d_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_F_Replicate_2_Slide_c_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr

value: c


title: Line_NC2 005_Diet_F_Replicate_3_Slide_c_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_F_Replicate_1_Slide_c_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_F_Replicate_3_Slide_c_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_4_Replicate_3_Slide_d_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 081_Diet_N_Replicate_1_Slide_c_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M054_Diet_C_Replicate_3_Slide_c_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 047_Diet_4_Replicate_3_Slide_d_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_C_Replicate_1_Slide_c_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_4_Replicate_1_Slide_b_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr

value: b


title: Line_NC2 047_Diet_C_Replicate_2_Slide_c_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_4_Replicate_3_Slide_c_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M026_Diet_4_Replicate_3_Slide_b_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M061_Diet_F_Replicate_2_Slide_b_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_F_Replicate_3_Slide_b_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_N_Replicate_3_Slide_c_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_4_Replicate_1_Slide_b_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_4_Replicate_2_Slide_b_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_F_Replicate_2_Slide_a_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr

value: a


title: Line_M011_Diet_C_Replicate_1_Slide_b_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M073_Diet_N_Replicate_1_Slide_b_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_4_Replicate_1_Slide_b_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M019_Diet_N_Replicate_3_Slide_a_subarray_1

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_4_Replicate_3_Slide_a_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 090_Diet_F_Replicate_1_Slide_a_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 084_Diet_C_Replicate_3_Slide_1_subarray_4

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M096_Diet_C_Replicate_3_Slide_1_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M077_Diet_4_Replicate_3_Slide_1_subarray_9

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M012_Diet_N_Replicate_1_Slide_a_subarray_12

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M052_Diet_N_Replicate_2_Slide_1_subarray_7

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 063_Diet_N_Replicate_1_Slide_a_subarray_3

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_C_Replicate_2_Slide_a_subarray_2

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M027_Diet_F_Replicate_3_Slide_b_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_M011_Diet_4_Replicate_2_Slide_a_subarray_8

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 038_Diet_F_Replicate_2_Slide_a_subarray_11

description: Nimblegen Design: 080306_Dmr43_expr


title: Line_NC2 096_Diet_4_Replicate_3_Slide_1_subarray_6

description: Nimblegen Design: 080306_Dmr43_expr


title: Control- ind29 (sample 171)

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

institute: Laval university

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray scanner (Packard BioScience). Spots were localized and quantified with the QuantArray 3.0 software, using the histogram quantification method and keeping the mean value of intensity for each spot.

data_processing: Data were exported in text format and were analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000)

organism: Perca flavescens

source_name: fish from nickel experiment

label_protocol: For each sample, 12 µg total RNA was reverse-transcribed and the cDNA samples labeled using the Genisphere 3DNA Array 50 Kit, Invitrogen’s Superscript II retro-transcriptase and Cyanine3 and Cyanine5 fluorescent dyes (Genisphere), following the procedures described at http://genisphere.com/products/3dna-array-detection/support (Genisphere Array 50 Protocol)

extract_protocol: Total RNA was extracted with the PureLink TM Micro-to-Midi Total RNA Purification System Kit and then treated using Amplification Grade DNase I (3 unit/μl; Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Total RNA was stored in RNAse free water at -80 °C. Quality and integrity of the total RNA were controlled using an Experion Automated Electrophoresis Station and RNA HighSens Chips (Biorad, Hercules, CA).

tag: tissue

value: Liver

tag: experiment

value: Control


title: Control- ind2 (sample 174)


title: Highnickelconcentration- ind7 (sample 172)

value: Highnickelconcentration


title: Highnickelconcentration- ind4 (sample 176)


title: Highnickelconcentration- ind8 (sample 173)


title: Control- ind23 (sample 175)


title: Control- ind29 (sample 170)


title: Highnickelconcentration- ind8 (sample 168)


title: Lownickelconcentration- ind14 (sample 169)

value: Lownickelconcentration


title: Line_NC2 081_Diet_C_Replicate_2_Slide_1_subarray_5

description: Nimblegen Design: 080306_Dmr43_expr

tag: line

tag: ai


title: Control- ind22 (sample 166)


title: Lownickelconcentration- ind12 (sample 165)


title: Lownickelconcentration- ind13 (sample 161)


title: Control- ind21 (sample 164)


title: Control- ind23 (sample 162)


title: Lownickelconcentration- ind10 (sample 163)


title: Lownickelconcentration- ind12 (sample 160)


title: Highnickelconcentration- ind4 (sample 157)


title: Lownickelconcentration- ind13 (sample 158)


title: Lownickelconcentration- ind7 (sample 155)


title: Highnickelconcentration- ind3 (sample 159)


title: Lownickelconcentration- ind9 (sample 154)


title: Control- ind20 (sample 153)


title: Lownickelconcentration- ind1 (sample 167)


title: Highnickelconcentration- ind7 (sample 151)


title: Lownickelconcentration- ind14 (sample 152)


title: Highnickelconcentration- ind9 (sample 150)


title: Lownickelconcentration- ind2 (sample 149)


title: Highnickelconcentration- ind13 (sample 148)


title: Highnickelconcentration- ind15 (sample 146)


title: Lownickelconcentration- ind10 (sample 144)


title: Control- ind16 (sample 142)


title: Lownickelconcentration- ind9 (sample 145)


title: Control- ind18 (sample 156)


title: Control- ind18 (sample 138)


title: Highnickelconcentration- ind9 (sample 141)


title: Highnickelconcentration- ind1 (sample 140)


title: Highnickelconcentration- ind13 (sample 137)


title: Control- ind22 (sample 135)


title: Highnickelconcentration- ind3 (sample 136)


title: Highnickelconcentration- ind15 (sample 133)


title: Control- ind20 (sample 134)


title: Lowcadmiumconcentration- ind15 (sample 125)

source_name: fish from cadmium experiment

value: Lowcadmium concentration


title: Control- ind29 (sample 126)


title: Control- ind23 (sample 128)


title: Control- ind16 (sample 131)


title: Lownickelconcentration- ind1 (sample 130)


title: Control- ind2 (sample 129)


title: Lowcadmiumconcentration- ind14 (sample 127)


title: Lowcadmiumconcentration- ind5 (sample 124)


title: Lownickelconcentration- ind2 (sample 132)


title: Control- ind2 (sample 123)


title: Highnickelconcentration- ind1 (sample 143)


title: Highcadmiumconcentration- ind12 (sample 120)

value: Highcadmium concentration


title: Lowcadmiumconcentration- ind11 (sample 119)


title: Lowcadmiumconcentration- ind12 (sample 117)


title: Control- ind22 (sample 116)


title: Lowcadmiumconcentration- ind13 (sample 115)


title: Lowcadmiumconcentration- ind11 (sample 114)


title: Control- ind17 (sample 121)


title: Lowcadmiumconcentration- ind8 (sample 122)


title: Lowcadmiumconcentration- ind15 (sample 112)


title: Lowcadmiumconcentration- ind10 (sample 110)


title: Control- ind20 (sample 113)


title: Highcadmiumconcentration- ind4 (sample 111)


title: Lowcadmiumconcentration- ind12 (sample 108)


title: Control- ind18 (sample 109)


title: Highcadmiumconcentration- ind1 (sample 107)


title: Lowcadmiumconcentration- ind8 (sample 97)


title: Highcadmiumconcentration- ind9 (sample 98)


title: Highcadmiumconcentration- ind11 (sample 102)


title: Control- ind21 (sample 118)


title: Highcadmiumconcentration- ind3 (sample 105)


title: Highcadmiumconcentration- ind3 (sample 96)


title: Highcadmiumconcentration- ind8 (sample 100)


title: Lowcadmiumconcentration- ind14 (sample 106)


title: Control- ind23 (sample 95)


title: Highcadmiumconcentration- ind1 (sample 94)


title: Control- ind21 (sample 93)


title: Control- ind18 (sample 92)


title: Highcadmiumconcentration- ind11 (sample 91)


title: Control- ind2 (sample 90)


title: Highcadmiumconcentration- ind8 (sample 89)


title: Lowcadmiumconcentration- ind13 (sample 104)


title: Highcadmiumconcentration- ind2 (sample 103)


title: Highcadmiumconcentration- ind4 (sample 88)


title: Lowcadmiumconcentration- ind5 (sample 99)


title: Lowcadmiumconcentration- ind10 (sample 101)


title: Control- ind29 (sample 87)


title: Highcadmiumconcentration- ind12 (sample 83)


title: Control- ind20 (sample 84)


title: Control- ind17 (sample 86)


title: Control- ind18 (sample 80)

source_name: fish from diet level experiment


title: Control- ind22 (sample 81)


title: Diet restriction- ind21 (sample 79)

value: Diet restriction


title: Diet restriction- ind19 (sample 77)


title: Diet restriction- ind218 (sample 76)


title: Control- ind312 (sample 75)


title: Highcadmiumconcentration- ind9 (sample 85)


title: Diet restriction- ind116 (sample 69)


title: Control- ind28 (sample 72)


title: Diet restriction- ind111 (sample 74)


title: Control- ind419 (sample 73)


title: Diet restriction- ind123 (sample 71)


title: Highcadmiumconcentration- ind2 (sample 82)


title: Control- ind11 (sample 78)


title: Control- ind517 (sample 70)


title: Diet restriction- ind110 (sample 68)


title: Control- ind213 (sample 63)

source_name: fish from oxygen level experiment


title: Hypoxia- ind321 (sample 64)

value: Hypoxia


title: Diet restriction- ind214 (sample 66)


title: Control- ind13 (sample 67)


title: Control- ind47 (sample 65)


title: Control- ind414 (sample 62)


title: Control- ind424 (sample 56)


title: Control- ind47 (sample 57)


title: Hypoxia- ind118 (sample 58)


title: Hypoxia- ind212 (sample 60)


title: Control- ind22 (sample 59)


title: Hypoxia- ind35 (sample 55)


title: Hypoxia- ind22 (sample 61)


title: Hypoxia- ind221 (sample 54)


title: Control- ind225 (sample 52)


title: Control- ind419 (sample 50)


title: Hypoxia- ind314 (sample 51)


title: Temperature 11- ind1-6 (sample 48)

source_name: fish from temperature experiment

value: Temperature 11


title: Hypoxia- ind214 (sample 49)


title: Control- ind518 (sample 53)


title: Temperature 11- ind3-16 (sample 46)


title: Temperature 11- ind3-12 (sample 44)


title: Temperature 28- ind2-12 (sample 41)

value: Temperature 28


title: Temperature 20- ind2-15 (sample 42)

value: Temperature 20


title: Temperature 20- ind4-18 (sample 47)


title: Temperature 28- ind2-18 (sample 40)


title: Temperature 20- ind2-15 (sample 43)


title: Temperature 11- ind3-16 (sample 39)


title: Temperature 11- ind1-7 (sample 38)


title: Temperature 20- ind4-17 (sample 37)


title: Temperature 11- ind1-7 (sample 35)


title: Temperature 28- ind3-24 (sample 34)


title: Temperature 20- ind4-17 (sample 32)


title: Temperature 11- ind1-6 (sample 33)


title: Temperature 20- ind5-21 (sample 45)


title: Temperature 28- ind2-4 (sample 31)


title: Temperature 20- ind2-2 (sample 30)


title: Temperature 28- ind2-4 (sample 36)


title: Temperature 20- ind4-18 (sample 28)


title: Temperature 28- ind1-19 (sample 29)


title: Temperature 28- ind3-24 (sample 27)


title: M9-without nickel-log phase-rep3

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

description: Nickel-resistant Saccharomyces cerevisiae, log phase, replicate 3

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Fresh precultures of yeast cells were diluted to an OD600 of 0.1 in fresh minimal medium. They were cultivated at 30°C and 150 rpm untill they reach the OD600 value of about 1.00. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Yeast cells were not treated with any special agent.

tag: phenotype

value: nickel-resistant mutant


title: M9-without nickel-log phase-rep2

description: Nickel-resistant Saccharomyces cerevisiae, log phase, replicate 2


title: Wild Type-without nickel-log phase-rep1

description: Saccharomyces cerevisiae, log phase, replicate 1

source_name: Saccharomyces cerevisiae, log phase

value: wild type


title: M9-without nickel-log phase-rep1

description: Nickel-resistant Saccharomyces cerevisiae, log phase, replicate 1


title: Temperature 20- ind5-21 (sample 26)


title: Temperature 28- ind2-12 (sample 24)


title: Temperature 11- ind3-12 (sample 23)


title: Temperature 28- ind2-20 (sample 22)


title: Wild Type-without nickel-log phase-rep3

description: Saccharomyces cerevisiae, log phase, replicate 3


title: Wild Type-without nickel-log phase-rep2

description: Saccharomyces cerevisiae, log phase, replicate 2


title: Temperature 11- ind3-20 (sample 21)


title: Temperature 28- ind2-20 (sample 19)


title: Temperature 28- ind2-18 (sample 25)


title: Temperature 11- ind2-3 (sample 17)


title: Temperature 28- ind1-19 (sample 16)


title: Temperature 20- ind3-6 (sample 14)


title: Temperature 11- ind3-7 (sample 15)


title: Temperature 20- ind4-1 (sample 20)


title: Temperature 11- ind3-7 (sample 10)


title: Temperature 20- ind2-2 (sample 9)


title: Lactobacillus rhamnosus GG tagatose.

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

description: Biological replication 1 of 1

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).

organism: Lacticaseibacillus rhamnosus GG

source_name: Lactobacillus rhamnosus GG with glucose

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP or Cy3-dUTP.

growth_protocol: Overnight cultured Lactobacillus rhamnosus GG cells were inoculated in prebiotic minimum media containing 2% glucose or tagatose and incubated at 37°C for 24 h without shaking.

extract_protocol: After culturing Lactobacillus rhamnosus GG cells, bacterial cells were distrupted with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) and Rnase free-DNase I treatment (Qiagen)

tag: patent

tag: treatment

value: glucose

source_name: Lactobacillus rhamnosus GG with tagatose

treatment_protocol: For replacing carbohydrate source, tagatose was supplemented into prebiotic minimum medium with final 2% concentrations.

value: tagatose


title: Temperature 20- ind4-1 (sample 11)


title: Temperature 11- ind3-20 (sample 12)


title: RJ17-9

city: baltimore

first: chris

last: cheadle

state: MD

address: 5200 Eastern Ave

department: SOM

institute: JHU

description: rIL-4 (50 ng/mL)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The  expression values for all the probes for each sample were scaled to have median 256 (2^8) and then log (base 2) transformed before performing statistical analysis.

source_name: endothelial cells

label_protocol: Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.

growth_protocol: WT and IL-4 KO (C57BL/6 background; male, 8–12 weeks old) were were placed in a Plexiglas chamber maintained at 10% O2 (hypoxic group) or in a chamber open to room air (normoxic group) for 4 days (d) with a 12:12-hours (h) light-dark cycle. After exposure to hypoxia or normoxia, mice were sacrificed and the lungs were harvested for RNA extraction.  Mouse PMVEC were isolated from 4–6-week-old female C57BL/6 mice.  Cells were incubated at 37°C in a humidified atmosphere of 5% CO2 and were used at passages 3–5.

extract_protocol: Total lung RNA was isolated from each animal or from PMVEC and extracted using the Trizol Reagent method (Invitrogen). Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA).  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: For gene expression study, PMVEC cells were treated with recombinant IL-4 (rIL-4, 50 ng/mL, Sigma-Aldrich), or vehicle control for 24h (n=3).

value: pulmonary microvascular

tag: genotype

tag: age

tag: gender

value: female

tag: background strain

value: rIL-4 (50 ng/mL)


title: Temperature 28- ind1-16 (sample 18)

value: Liver


title: Temperature 11- ind2-7 (sample 7)


title: RJ17-8

description: rIL-4 (50 ng/mL)


title: Temperature 11- ind2-3 (sample 6)


title: RJ17-7

description: rIL-4 (50 ng/mL)


title: RJ17-3

description: vehicle

value: vehicle


title: RJ17-2

description: vehicle


title: Temperature 28- ind1-16 (sample 13)


title: RJ17-1

description: vehicle


title: RJ7-11

description: hypoxia

source_name: lung

value: lung

value: IL-4 KO

value: 8–12 weeks old

value: male


title: RJ7-12

description: hypoxia


title: Temperature 28- ind1-9 (sample 8)


title: RJ7-10

description: hypoxia


title: Temperature 20- ind3-5 (sample 4)


title: RJ7-8

description: normoxia

value: room air


title: RJ7-6

description: hypoxia


title: RJ7-9

description: normoxia


title: Temperature 28- ind1-9 (sample 3)


title: Temperature 20- ind3-5 (sample 1)


title: Temperature 11- ind2-7 (sample 2)

value: Temperature 11


title: Temperature 20- ind3-6 (sample 5)


title: RJ7-4

description: hypoxia


title: RJ7-5

description: hypoxia


title: Frozen – Vitrified 6 day old Embryos Replicate 3

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

country: Spain

institute: Universidad Politécnica Valencia

description: Biological Replicate 3 of 3, Frozen embryos vs. Vitrified embryos

hyb_protocol: Hibridization was done using Agilent Gene Expression Hybridization Kit, following manufacturer's instructions. After 17 hours at 65ºC on a , hybridised slides  were washed sequential.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

organism: Oryctolagus cuniculus

source_name: 6 day old embryos

label_protocol: Total RNA (100 ng) was labelled using QuickAmp Labelling Kit (Agilent Technologies) following manufacturer's instructions. Excess dye was removed with the  RNAeasy Mini Kit (QIAGEN) and dye incorporation and concentration were determined using the microarray setting on the Nanodrop 1000.

extract_protocol: Total RNBA was extracted using TRIZOL reagen, following manufacter's instructions.

treatment_protocol: Morulae were vitrified in two steps at 20ºC.  In the first step, embryos were placed for 2 min in a vitrification solution consisting of 12.5% dimethyl sulphoxide (DMSO) and 12.5% ethylene glycol (EG) in DPBS supplemented with 0.2% of BSA.  In the second step, embryos were suspended for 30 seconds in a solution of 20% DMSO and 20% EG in DPBS supplemented with 0.2% of BSA.  Then, embryos suspended in vitrification medium were loaded into 0.25 ml plastic straws and two sections of DPBS were added at either end of each straw, separated by air bubbles.  Finally, straws were sealed and plunged directly into liquid nitrogen.  Warming was performed by horizontally placing the straw 10 cm from liquid nitrogen for 20-30 seconds and when the crystallisation process began, the straws were immersed in a water bath at 20ºC for 10-15 seconds.  The vitrification medium was removed while loading the embryos into a solution containing DPBS and 0.33 M sucrose for 5 min, followed by one bath in a solution of DPBS for another 5 min.

tag: method

value: Vitrified

value: 6 day old embryos

value: Frozen


title: RJ7-3

description: normoxia

value: wild type


title: Frozen – Vitrified 6 day old Embryos Replicate 1

description: Biological Replicate 1 of 3, Frozen embryos vs. Vitrified embryos


title: Frozen – Vitrified 6 day old Embryos Replicate 2

description: Biological Replicate 2 of 3, dye swap, Frozen embryos vs. Vitrified embryos


title: Brain Metastasis 6

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
MBM-6
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array

hyb_protocol: Samples were hybridized with Human Exon 1.0 ST Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix).

data_processing:
Data were analyzed in Expression Console 1.1 software (Affymetrix) using the core transcript set and employing the robust multi-array average algorithm (RMA) for background correction and normalization of data.
Core exons; genome build hg18.

source_name: Melanoma brain metastasis

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted from melanoma-related specimens by using the miRNeasy Mini Kit (QIAGEN) including an on-column DNase digestion step following the protocol provided by the manufacturer. RNA concentration was quantified using the Quant-iT™ RiboGreen® RNA assay kit (Invitrogen). The quality of the RNA was assessed by RNA Integrity Number (RIN) score on the Agilent 2100 Bioanalyzer.

treatment_protocol: Not applicable.

value: brain metastasis

tag: disease

value: melanoma

tag: clinical stage

value: IV


title: Brain Metastasis 5

description:
MBM-5
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: RJ7-2

description: normoxia


title: Brain Metastasis 7

description:
MBM-7
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Brain Metastasis 8

description:
MBM-8
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Brain Metastasis 4

description:
MBM-4
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Brain Metastasis 3

description:
MBM-3
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: RJ7-7

description: normoxia


title: RJ7-1

description: normoxia


title: Brain Metastasis 2

description:
MBM-2
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 9

description:
LNM-9
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array

source_name: Melanoma lymph node metastasis

value: lymph node metastasis

value: III


title: Lymph Node Metastasis 12

description:
LNM-13
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 5

description:
LNM-5
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 11

description:
LNM-12
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 8

description:
LNM-8
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 7

description:
LNM-7
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 1

description:
LNM-1
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 6

description:
LNM-6
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 4

description:
LNM-4
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 10

description:
LNM-11
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 2

description:
LNM-2
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Lymph Node Metastasis 3

description:
LNM-3
Cell line derived from patient.
Affymetrix HuEx 1.0 ST Array


title: Melanocyte 3

description:
MNC-3
Cell line
Affymetrix HuEx 1.0 ST Array

source_name: Normal melanocytes, dark pigmentation

value: skin (dark pigmentation)


title: Melanocyte 2

description:
MNC-2
Cell line
Affymetrix HuEx 1.0 ST Array

source_name: Normal melanocytes, medium pigmentation

value: skin (medium pigmentation)


title: Zea mays 2nd leaf control 60 min distal

city: San Antonio

first: Jurgen

last: Engelberth

state: Texas

address: One UTSA Circle

institute: University of Texas at San Antonio

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning (http://ag.arizona.edu/microarray/Microarraymethod1.doc).

scan_protocol: Arrays were scanned using a GenePix Autoloader 4200AL.

data_processing: Raw data were extracted using Gene Pix Pro 6.0 program; then saved as gpr and txt files for each block individually (total 4 blocks on the chip resulting in 4 hybridizations). Within arrays, loess normalization was done using the Limma package in R (version R2.5.1) (Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30(4):e15). Between arrays, normalization was also done with the Limma package so that the scale the log-ratios to have the same median-absolute-deviation (MAD) across arrays (Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. In: METHODS: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience, D. Carter (ed.). Methods Volume 31, Issue 4, December 2003, pages 265-273).

organism: Zea mays

source_name: Zea mays 2nd leaf after 60min of volicitin treatment control

label_protocol: 1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://www.maizearray.org/files/cRNA_Target_Production_Using_RNA_Amplification.pdf

growth_protocol: Zea mays (inbred line B73) plants were grown in soil (Redi Earth Plug and Seedling Mix, Sun Gro) in a growth chamber with a 12 h photoperiod, 60% relative humidity at 26°C for three weeks (V2 stage). Light intensity was set at app. 150 mmol m2 s-1.

extract_protocol: The pooled leaf material (about 100mg) was used for RNA extraction. Total RNA was extracted with the Ultra Clean Plant RNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA) according to the manufacture’s instructions with the following modifications. Frozen plant samples were homogenized in 2 ml screw cap FastPrep tubes containing 0.5 g of Zirmil microbeads and 200 ml extraction buffer (PR1) for 20 sec at 6000 rpm in a Precellys tissue homogenizer (MO BIO Laboratories, Carlsbad, CA, USA). After this initial homogenization step the remaining 800 ml of PR1 were added and the sample again homogenized for 10 sec at 6000 rpm. The extract was then further processed as described in the manufacturer’s instructions.

treatment_protocol: Zea mays (B73, 3 week old) were treated with volicitin (0.1nmol/microliter) in potassium phosphate buffer (pH 8, 50 mM) for 60 min. 1 nmol was applied per plant. Controls were untreated. Leaves segments (1cm) comprising the volicitin application site (local) and about 3cm leaf upwards (distal, also 1 cm) were cut and frozen in liquid N2 and stored at -80 °C prior to RNA extraction. Per leaf site (local and distal) 3 segments from 3 individual were pooled for one biological replicate. 2 biological replicates were performed per leaf site (local and distal, respectively).

tag: developmental stage

value: 3 week-old seedling

value: 2nd leaf

source_name: Zea mays_2nd leaf_60min_ volicitin_distal


title: Zea mays_2nd leaf_60min_ volicitin_distal

source_name: Zea mays 2nd leaf control 60 min distal


title: Melanocyte 1

description:
MNC-1
Cell line
Affymetrix HuEx 1.0 ST Array

source_name: Normal melanocytes, light pigmentation

value: skin (light pigmentation)


title: 15min_RB3RT2_3

city: Rennes

first: Virginie

last: Dufour

address: 263 avenue du General Leclerc

institute: Université Rennes 1

description: 15 minutes treatment Biological replicate 3 technical replicate 2 column 3

hyb_protocol: Fluorescently labelled cDNA samples from the benzylisothiocyanate-treated or ethanol control samples were combined, vacuum dried, and resuspended in 36µl of hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 25µg salmon sperm DNA). NCTC11168 microarray slides (Palyada et al., 2004; Stintzi, 2003)  were prepared for hybridization by incubation in slide hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 1% BSA) for 45 minutes at 42°C. The fluorescently labelled, pooled cDNA samples were hybridized to the microarray slide a under glass coverslip which was placed in a humidified chamber (ArrayIt) overnight at 42°C protected from light. Following overnight incubation, the microarray slide was washed in 100mL of 2X SSC, 0.1% SDS solution for 5 min at 42°C. The slide was subsequently washed in 100mL of 0.1X SSC, 0.1% SDS at room temperature for 10 min and followed by an additional 4x 1 min washes in 0.1X SSC, 0.1% SDS solution. The slide was rinsed briefly in distilled H2O and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: Data collection was performed using the GenePix Pro 4.0 software (Axon Instruments) which determines the signal intensity for each spot on the microarray. Hybridization abnormalities or spots that were localized within regions of hybridization were removed from the analysis and the raw fluorescent intensities for each spot were subtracted from the background fluorescence of the microarray. Spots that had background-subtracted intensity values less than three times the standard deviation of the local background in both Cy3 and Cy5 channels were subsequently removed from data analysis. Next, MIDAS software (available from TIGR; http://www.tigr.org/software/) was used along with locally weighted linear regression (Lowess) to normalize the fluorescent intensity values for both Cy3 and Cy5 channels. The ratio of the fluorescent intensity values in the Cy3 channel to the Cy5 channel was calculated and converted into a log2 value.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: MEMα + Ethanol (control) (15 min)

label_protocol: Preparation of fluorescently labelled cDNA and microarray slide hybridization was performed as described previously (Palyada et al., 2004). Briefly, 16µg of C. jejuni (from benzylisothiocyanate treated samples or ethanol control samples) extracted RNA was reversed transcribed in presence of 10µg random hexamers, 0.5mM dGTP, dATP, dCTP, 0.16mM dTTP, and 0.34mM aminoallyl dUTP using SuperScript II (Invitrogen) for 2 hours at 42°C. The reaction was stopped by the addition of 50mM EDTA and 10 N NaOH and incubated at 65°C for 20 minutes. The reaction was neutralized by addition of 5M acetic acid and the aminoallyl-labelled cDNA was purified from non-incorporated aminoallyl dUTPs using Micron YM-30 spin columns (Millipore). The purified aminoallyl-labelled cDNA was coupled to Cy3 or Cy5 monoreactive fluors (Amersham) using the method described previously (Palyada et al., 2004). Following the coupling of fluorescent dyes to cDNA, the cDNA samples were purified using the PureLink PCR Purification Kit (Invitrogen) according to the manufacturer’s specifications.

growth_protocol: Overnight MH biphasic cultures were used to inoculate 25ml of MEMα (supplemented with 20mM pyruvate) to an OD600nm of 0.01. C. jejuni NCTC11168 cells were then grown to mid-log phase (OD600nm=0.2) at 37°C under microaerophilic conditions (10% O2, 5% CO2, 85% N2).

extract_protocol: After 10 or 15 min of benzylisothiocyanate or ethanol treatment,  2.5mL cold RNA degradation stop solution (10% buffer-saturated phenol pH 4.3 in ethanol) were added to prevent RNA decay. Bacterial cells were harvested by centrifugation, resuspended in TE buffer followed by total RNA isolation using the hot phenol-chloroform method as described previously (Tao et al., 1999). Extracted RNA samples were treated twice with DNase-I (Epicenter) and purified using the RNeasy kit (Qiagen) followed by PCR amplification to confirm the absence of contaminating genomic DNA in the samples. The Experion RNA STDsens Analysis Kit (Bio-Rad Laboratories) was used to quantify and confirm RNA integrity of the extracted RNA samples. RNA samples were stored at -80°C.

treatment_protocol: Benzylisothiocyanate (Sigma) stock solutions were prepared in absolute ethanol. Fresh dilutions were made in absolute ethanol. 500µL of diluted benzylisothiocyanate in ethanol was added to 25mL mid-log grown cells in dMEM culture media (treated sample), to achieve a final benzylisothiocyanate concentration of 2µg/mL in culture media. As a control, the same volume of absolute ethanol was added to 25mL cells mid-log grown cells in dMEM culture media. Total RNA extraction was carried out 10 min or 15 min after addition of diluted benzylisothiocyanate or ethanol.

tag: strain

tag: optical density 600nm

value: Ethanol (control)

source_name: MEMα + Benzylisothiocyanate 2µg/mL (15 min)

value: 15 min Benzylisothiocyanate 2µg/mL


title: Zea mays_2nd leaf_60min_ volicitin_local

tag: tissue

source_name: Zea mays 2nd leaf control 60 min local


title: 15min_RB3RT2_1

description: 15 minutes treatment Biological replicate 3 technical replicate 2 column 1


title: 15min_RB3RT2_2

description: 15 minutes treatment Biological replicate 3 technical replicate 2 column 2


title: Zea mays 2nd leaf control 60 min local

source_name: Zea mays_2nd leaf_60min_ volicitin_local


title: 15min_RB3RT1_3

description: 15 minutes treatment Biological replicate 3 technical replicate 1 column 3


title: heart-ko-1

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description: Hearts of 10 weeks old Jun delta mu, replicate 1

hyb_protocol: 5 μg of biotin-labeled cRNA was fragmented randomly to 35-200 bp and hybridized to GeneChip® GeneChip Mouse Genome 430 2.0 Arrays.

scan_protocol: The fluorescent intensity emitted by the labeled target was measure in Affymetrix GeneChip Scanner 3000 (Affymetrix).

data_processing: Expression data were RMA background corrected and quantile normalized using the oligo package in R.

source_name: Heart of 10 weeks old mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Briefly, cardiac ventricles were fragmented, digested with ADS buffer containing collagenase (Worthington Biochemical Corp.) and pancreatin (Sigma), and plated in plating medium containing 65% DMEM (Animed), 17% M199 (Animed), 10% Horse Serum (Invitrogen), 5% Fetal Calf Serum (Invitrogen), 2% L-Glutamine (Animed), 1% PS (Invitrogen). After 24h, medium was changed to maintenance medium (86% DMEM, 10% M199, 1% Horse Serum, 2% L-Glutamine, 1% PS).

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

value: mixed 129/Ola-C57BL/6 background

tag: genotype/variation

value: Jun delta mu


title: heart-ko-2

description: Hearts of 10 weeks old Jun delta mu, replicate 2


title: 15min_RB3RT1_2

description: 15 minutes treatment Biological replicate 3 technical replicate 1 column 2


title: heart-wt-2

description: Hearts of 10 weeks old Junf/f, replicate 2

value: Junf/f


title: 15min_RB3RT1_1

description: 15 minutes treatment Biological replicate 3 technical replicate 1 column 1


title: Rhodobacter capsulatus gtaI mutant logarithmic RCV 30 degree

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

institute: Memorial University

hyb_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 6: Prokaryotic Target Hybridization, page 119-126

scan_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 7: Prokaryotic Arrays: Washing, Staining and Scanning page 127-152.

data_processing: Raw data was RMA normalized after scanning using Affymetrix Expression Console v1.1

organism: Rhodobacter capsulatus

source_name: R. capsulatus logarithmic growth phase

label_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 5: Prokaryotic Target Preparation, page 101-118

growth_protocol:
Photoheterotrophic
RCV defined media
30 degrees C

extract_protocol: As per described in RNeasy Mini Handbook (Qiagen Inc.), Protocol for Isolation of Total RNA from Bacteria, pages 56-60.

value: gtaI mutant

tag: growth phase

value: logarithmic


title: 15min_RB2RT3_2

description: 15 minutes treatment Biological replicate 2 technical replicate 3 column 2


title: Rhodobacter capsulatus gtaI mutant stationary RCV 30 degree

source_name: R. capsulatus stationary growth phase

value: stationary


title: Control- ind21 (sample 139)

source_name: fish from nickel experiment

value: Liver

tag: experiment

value: Control


title: 15min_RB2RT2_3

description: 15 minutes treatment Biological replicate 2 technical replicate 2 column 3


title: Rhodobacter capsulatus wild type logarithmic RCV 30 degree

value: wild type


title: 15min_RB2RT3_3

description: 15 minutes treatment Biological replicate 2 technical replicate 3 column 3


title: Vivo_rep1

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

hyb_protocol: Standard Affymetrix lab protocol

scan_protocol: Standard Affymetrix lab protocol

data_processing: RMA background correction. Lowess normalization with JMP Genomics v3.0

organism: Aspergillus flavus

source_name: Pathogenic phase

label_protocol: Standard Affymetrix lab protocol

growth_protocol: The wild type (WT) used was Aspergillus flavus NRRL 3357, a producer of the aflatoxin B1. The isolates were incubated on Czapek Dox Agar (CDA) (Difco) for 7 days at 30°C, before use.

extract_protocol: For total RNA extraction the Qiagen RNeasy kit RNA cleanup protocol was typically used, for most samples a phenol chloroform extraction protocol preceeded use of the RNeasy kit. For some samples phenol chloroform extractions and LiCl precipitation was used to purify RNA, this protocol is available from http://www.aspergillusflavus.org/protocols/.

treatment_protocol: An amount of ~10000 conidia was used for infecting injured maize kernels directly onto maize ears in the field. The kernels were injured with the same needle used for inoculating the fungal conidia. This condition has been reported as vivo (i.e. the pathogenic phase).

value: NRRL 3357


title: Vivo_rep2


title: 15min_RB2RT1_3

description: 15 minutes treatment Biological replicate 2 technical replicate 1 column 3


title: 15min_RB2RT1_1

description: 15 minutes treatment Biological replicate 2 technical replicate 1 column 1


title: heart-wt-1

description: Hearts of 10 weeks old Junf/f, replicate 1


title: 15min_RB2RT1_2

description: 15 minutes treatment Biological replicate 2 technical replicate 1 column 2


title: 15min_RB2RT3_1

description: 15 minutes treatment Biological replicate 2 technical replicate 3 column 1


title: 15min_RB1RT3_3

description: 15 minutes treatment Biological replicate 1 technical replicate 3 column 3


title: Vivo_rep3


title: Chemo_rep3

source_name: Chemotrophic phase

treatment_protocol: 0.1 ml of conidial suspension of A. flavus were incubated into 100-ml Erlenmeyer flasks containing CDB (50ml) and a dialysis membrane (cut off 7000 Da) in which 5 injured viable kernels were placed. This condition is subsequently reported as chemo phase (i.e. the chemotrophic phase). The dialysis membrane should allow the passage of small molecules from the injured kernels to the CDB medium.


title: Chemo_rep1


title: Melanoma brain metastasis 7

description:
MBM-7
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

hyb_protocol: Following fragmentation, 3ug of gDNA was annealed for 16 hours at temperature of 50C to Affymetrix Genome-Wide Human SNP Array 6.0 at a pH of 6.6.

scan_protocol: Scanned on 7G 3000 manufactured by Affymetrix.

data_processing: SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 (Affymetrix). Sample table and .CNCHP data are based on genome build GRCh37 (hg19).

label: Biotin

source_name: Melanoma brain metastasis

label_protocol: Biotinylated gDNA was prepared according to the standard Affymetrix protocol from 3 ug of gDNA.

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA extraction from cell lines was carried out with the QIAamp DNA mini kit (QIAGEN, Valencia, CA). DNA quality and quantity were assessed using a UV Spectrophotometer and PicoGreen.

value: brain

tag: disease state

value: melanoma

value: IV

value: male


title: Melanoma brain metastasis 6

description:
MBM-6
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

value: female


title: Lymph node metastasis 13

description:
LNM-13
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

source_name: Lymph node metastasis

value: lymph node

value: III


title: Sapro_rep3

source_name: Saprophytic phase

treatment_protocol: An amount (10g) of dead maize kernels (by autoclaving) were inoculated with 10000 conidia of NRRL 3357 in a sterile Petri plate and incubated at 30°C for 4d. This condition has been named as sapro (i.e. the saprophytic phase).


title: Chemo_rep2


title: Rhodobacter capsulatus wild type stationary RCV 30 degree


title: 15min_RB1RT3_1

description: 15 minutes treatment Biological replicate 1 technical replicate 3 column 1

value: Ethanol (control)

value: 15 min Benzylisothiocyanate 2µg/mL


title: 15min_RB2RT2_2

description: 15 minutes treatment Biological replicate 2 technical replicate 2 column 2


title: Melanoma brain metastasis 2

description:
MBM-2
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: Lownickelconcentration- ind7 (sample 147)

value: Lownickelconcentration


title: MVIKK3

city: Stanford

first: HSU-PING

last: KUO

address: 265 Campus Dr.

institute: Stanford University

hyb_protocol: The array was placed in 45°C hybridization oven, at 60 rpm, and incubated for 17 hours ± 1 hour.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used for scanning. It takes approximately 10 minutes to scan each Gene Array.

data_processing: Affymetrix GeneChip Expression Console and Affymetrix GeneChip Command Console were used for data processing. dchip 2010 was used to normalize data.

source_name: MV4;11_IKK inhibitor

label_protocol: The Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay is  designed to generate amplified and biotinylated sense-strand DNA targets

growth_protocol: Cells were cultured in RPMI/10%FBS/NEAA medium

extract_protocol: RNeasy plus mini kit was used for total RNA extraction

treatment_protocol: Vehicle or 1µM IKK inhibitor was used for treatment

tag: cell line

tag: cell type

value: leukemia cells

tag: treated with

value: 1µM IKK inhibitor


title: MVIKK2


title: 15min_RB1RT3_2

description: 15 minutes treatment Biological replicate 1 technical replicate 3 column 2

tag: treatment


title: 15min_RB1RT2_3

description: 15 minutes treatment Biological replicate 1 technical replicate 2 column 3


title: Melanoma brain metastasis 4

description:
MBM-4
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

tag: gender


title: Lymph node metastasis 7

description:
LNM-7
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: Sapro_rep2


title: 15min_RB1RT2_2

description: 15 minutes treatment Biological replicate 1 technical replicate 2 column 2


title: MVIKK1


title: Sapro_rep1


title: 15min_RB1RT2_1

description: 15 minutes treatment Biological replicate 1 technical replicate 2 column 1


title: 15min_RB2RT2_1

description: 15 minutes treatment Biological replicate 2 technical replicate 2 column 1


title: MVC2

value: vehicle


title: MVC3


title: 15min_RB1RT1_3

description: 15 minutes treatment Biological replicate 1 technical replicate 1 column 3


title: Flask_rep3

source_name: In vitro phase

treatment_protocol: Fifty ml of Czapek Dox Broth (CDB) (Difco) (which is low-conducive for aflatoxins) in was inoculated with the WT using 0.1 ml of conidial suspension for each flask; incubation was performed at 30°C up to 4 days. This growth condition is indicated as flask (i.e. the in vitro phase).


title: Lymph node metastasis 11

description:
LNM-11
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: Melanoma brain metastasis 3

description:
MBM-3
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: Lymph node metastasis 6

description:
LNM-6
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: 15min_RB1RT1_2

description: 15 minutes treatment Biological replicate 1 technical replicate 1 column 2


title: Lymph node metastasis 3

description:
LNM-3
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: 15min_RB1RT1_1

description: 15 minutes treatment Biological replicate 1 technical replicate 1 column 1


title: Melanoma brain metastasis 8

description:
MBM-8
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: Flask_rep2


title: 10min_RB2RT3_2

description: 10 minutes treatment Biological replicate 2 technical replicate 3 column 2

source_name: MEMα + Ethanol (control) (10 min)

source_name: MEMα + Benzylisothiocyanate 2µg/mL (10 min)

value: 10 min Benzylisothiocyanate 2µg/mL


title: Flask_rep1


title: MVC1


title: Lymph node metastasis 12

description:
LNM-12
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.


title: 10min_RB2RT3_1

description: 10 minutes treatment Biological replicate 2 technical replicate 3 column 1


title: 10min_RB2RT2_3

description: 10 minutes treatment Biological replicate 2 technical replicate 2 column 3


title: 10min_RB2RT2_2

description: 10 minutes treatment Biological replicate 2 technical replicate 2 column 2


title: 10min_RB2RT2_1

description: 10 minutes treatment Biological replicate 2 technical replicate 2 column 1


title: 10min_RB2RT1_3

description: 10 minutes treatment Biological replicate 2 technical replicate 1 column 3


title: CCL17 positve rep4

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite 6.6 (v.6.12.1227)

source_name: lymph node_CCL17 positve

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: strain background

tag: age

value: 2-5 months

value: lymph node (LN) dendritic cell (DC)

tag: sorted cells

value: NK1.1-CD8alpha-CD11c+CD11b+ cells expressing CCL17/EGFP


title: CCL17 negative rep4

source_name: spleen_CCL17 negative

value: spleen

value: splenic dendritic cell (DC)

value: CCL17/EGFP-negative cells expressing NK1.1-CD8alpha-CD11c+CD11b+


title: CCL17 negative rep3


title: CCL17 positve rep2


title: CCL17 negative rep1


title: Lymph node metastasis 1

description:
LNM-1
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

value: melanoma

tag: clinical stage


title: CCL17 positve rep3


title: CCL17 positve rep1


title: Lymph node metastasis 2

description:
LNM-2
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

value: female


title: CCL17 negative rep2


title: MLL-AF10IKK2

source_name: MLL-AF10_IKK inhibitor

growth_protocol: Cells were cultured in RPMI/20%FBS/20% WEHI condition medium

treatment_protocol: Vehicle or 0.5µM IKK inhibitor was used for treatment

value: 0.5µM IKK inhibitor


title: 10min_RB1RT3_3

description: 10 minutes treatment Biological replicate 1 technical replicate 3 column 3


title: 10min_RB2RT1_1

description: 10 minutes treatment Biological replicate 2 technical replicate 1 column 1


title: 10min_RB2RT1_2

description: 10 minutes treatment Biological replicate 2 technical replicate 1 column 2


title: 10min_RB1RT3_2

description: 10 minutes treatment Biological replicate 1 technical replicate 3 column 2


title: 10min_RB1RT3_1

description: 10 minutes treatment Biological replicate 1 technical replicate 3 column 1


title: 10min_RB1RT2_3

description: 10 minutes treatment Biological replicate 1 technical replicate 2 column 3


title: 10min_RB2RT3_3

description: 10 minutes treatment Biological replicate 2 technical replicate 3 column 3


title: Pg(CSE) LPS treated macrophages

city: Chapel Hill

first: Afsar

middle: Raza

last: Naqvi

state: North Carolina

address: Brauer Hall 111

department: Periodontics

institute: University of North Carolina chapel Hill

description: two replicates

hyb_protocol: Hybridization reactions were performed according to the manufacturer’s instructions with 5 mL of the fivefold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString, Technologies, Seattle, WA, USA) at Lineberger Comprehensive Cancer Centre UNC, Chapel Hill following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed.

data_processing: Data normalization was performed according to manufacturer’s instructions. Briefly, NanoString nCounter miRNA raw data was normalized for lane-to-lane variation with a dilution series of six spike-in positive controls. The sum of the six positive controls for a given lane was divided by the average sum across lanes to yield a normalization factor, which was then multiplied by the raw counts in each lane to give normalized values. Further, the sum of five different endogenous controls were averaged and normalized across the samples. The values obtained were averaged for LPS treated and untreated samples. Fold change was calculated as the ratio of LPS treated versus untreated control sample.

label: Color coded beads

source_name: Pg(CSE) LPS treated macrophages (2 replicates)

label_protocol: 100 ng of total RNA was used as input for nCounter miRNA sample preparation reactions. Two biological replicates were used to generate cDNA library according to the manufacturer’s instructions. Ligation reactions, purification and dilution of probes were performed according to the manufacturer’s instructions (www.nanostring.com)

growth_protocol: The THP1 cell line was procured from the UNC Lineberger Comprehensive Cancer Center Tissue Culture Facility (UNC, Chapel Hill) and maintained at 2×105 cells/ml in RPMI 1640 medium supplemented with 10% FCS and 2 mmol/L L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). THP1 cells (2×105/ml) were differentiated using 50 ng/ml phorbol 12-myristate 13-acetate (PMA) for 3d.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) following manufacturer’s protocol. The RNA was quantitated using the NanoDrop (Thermo Scientific) and integrity assessed using the 2100 Bioanalyzer

treatment_protocol: Differentiation of PMA treated cells was enhanced after the initial 3d stimulus by removing the PMA-containing media and washing twice with PBS before adding fresh RPMI 1640 (10% FCS, 1% L-glutamine). The following day, media was replaced with complete RPMI containing purified LPS (1000ng/ml) of Aggregatibacter actinomycetemcomitans, Y4 serotype B, Porphyromonas gingivalis, strain W83 (Pg), or Pg grown in cigarette smoke extract at a concentration of 4000 ng nicotine equivalents/ml for 4 hours.

tag: source cell type

value: Human acute monocytic leukemia cells


title: 10min_RB1RT2_1

description: 10 minutes treatment Biological replicate 1 technical replicate 2 column 1

tag: strain

value: Ethanol (control)


title: 10min_RB1RT1_3

description: 10 minutes treatment Biological replicate 1 technical replicate 1 column 3

tag: optical density 600nm


title: 10min_RB1RT2_2

description: 10 minutes treatment Biological replicate 1 technical replicate 2 column 2


title: Pg LPS treated macrophages

description: two replicates

source_name: Pg LPS treated macrophages (2 replicates)


title: Untreated Macrophages

description: two replicates

source_name: Untreated Macrophages (2 replicates)


title: Aa LPS treated macrophages

description: two replicates

source_name: Aa LPS treated macrophages (2 replicates)


title: Lymph node metastasis 4

description:
LNM-5
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

tag: tissue

value: lymph node

value: III


title: 10min_RB1RT1_1

description: 10 minutes treatment Biological replicate 1 technical replicate 1 column 1


title: MLL-AF10IKK3

value: leukemia cells


title: MLL-AF10IKK1


title: Melanoma brain metastasis 5

description:
MBM-5
Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array.

value: brain

value: IV

value: male


title: 10min_RB1RT1_2

description: 10 minutes treatment Biological replicate 1 technical replicate 1 column 2

value: 10 min Benzylisothiocyanate 2µg/mL


title: MLL-AF10C3

value: vehicle


title: MLL-AF10C2


title: MLL-AF10C1


title: 7059 - Dysplasia

status: Public on Sep 18 2013

city: Vancouver

first: Rebecca

middle: M

last: Towle

department: Integrative Oncology

institute: British Columbia Cancer Research Centre

description: oral dysplasia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 BeadChip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy3 and Cy5

source_name: Dysplasia, 7059

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using standard phenol chloroform extraction and isopropanol precipitation procedure.

tag: patient identifier

value: tongue

value: dysplasia

tag: sample type

value: fresh frozen tissue


title: 5266 - SCC

description: oral squamous cell carcinoma

value: oral squamous cell carcinoma


title: 7057 - Normal

description: normal oral tissue

source_name: Normal, 7057

value: normal


title: 7057 - SCC

description: oral squamous cell carcinoma

value: female


title: 7059 - Normal

description: normal oral tissue

source_name: Normal, 7059


title: 7059 - SCC

description: oral squamous cell carcinoma


title: 5266 - Normal

description: normal oral tissue

source_name: Normal, 5266


title: 3002 - SCC

description: oral squamous cell carcinoma


title: 1999 - CIS

description: oral carcinoma in situ

value: carcinoma in situ


title: 7057 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 7057


title: 3002 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 3002


title: 1999 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1999


title: 1953 - Normal

description: normal oral tissue

source_name: Normal, 1953


title: 1979 - Normal

description: normal oral tissue

source_name: Normal, 1979

value: front of mouth


title: 1953 - CIS

description: oral carcinoma in situ


title: 5266 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 5266


title: 3002 - Normal

description: normal oral tissue

source_name: Normal, 3002


title: 1979 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1979


title: 1953 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1953


title: 1858 - SCC

description: oral squamous cell carcinoma


title: 1999 - Normal

description: normal oral tissue

source_name: Normal, 1999


title: 1878 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1878


title: 1979 - CIS

description: oral carcinoma in situ


title: 1878 - SCC

description: oral squamous cell carcinoma


title: 1878 - Normal

description: normal oral tissue

source_name: Normal, 1878


title: 1896 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1896


title: GRADE IV, 2

city: Messina

first: Alfredo

last: Conti

state: Sicily

address: via La Farina 15

institute: Alfredo

description:
GLIOBLASTOMA MULTIFORME, GRADE IV, HUMAN TISSUE SAMPLE
SAMPLE 7

scan_protocol: Real-time PCR was performed using a standard TaqMan PCR kit procedure on an “Real Time Fast 7900 HT” PCR System (Applied Biosystems). The 100 µl PCR included 50 µl RT product (before diluited 1:60) and 50 µl TaqMan Universal PCR Master Mix (2X) (Applied Biosystems). The total volume were loaded into Card TaqMan Low Density Array Human MicroRNA Panel (Applied Biosystem) including a total of 384 human microRNAs publicated on databases www.sanger.ac.uk. The reaction cards was runned at 50°C for 2 min and 95°C for 10 min, followed by 40 cycles of 97°C for 30s and 59,7°C for 1 min. All reactions were run in triplicate.

data_processing: Analysis of data was performed using the SDS 2.3 software using the 2-∆∆Ct (relative quantitative) method. The ∆Ct of every miRNA was determined in relation to the endogenous control RNA U6 that was invariably expressed in all samples.

label: FAM

source_name: ASTROCYTIC TUMOR

label_protocol: The miRNAs were first converted to cDNA using Multiplex RT for TaqMan Array Human MicroRNA Panel. The RT Master mix included 100 mM each of dNTPs , 50 U/ml MultiScrabe reverse transcriptase (Applied Biosystems), 20 U/µl RNase inhibitor (Applied Biosystems) and 10X RT Buffer. The 10 µl reactions, including 7 µl of RT master mix, 2 µl of purified microRNA and 1 µl of Multiplex RT Human primer pool (Applied Biosystem), were incubated in ice for 5 min and then in a thermal cycler for 30 min at 16°C, 30 min at 42°C, 5 min at 85°C, and then hold at 4°C. miRNA levels were normalized to the expression of small nucleolar RNAs, RNU44, RNU48 and RNU6B. All reverse transcriptase reactions, including no-template controls and RT controls, were run in duplicate.

extract_protocol: Total RNA, including small RNA, was isolated from tissue samples using the mirVanaTM miRNA Isolation Kit (Ambion) following the standard protocol. The quantity and quality of the purified RNA was evaluated by spectrophotometric analysis and electrophoresis on denaturing gel of acrylamide.

tag: grade

value: WHO GRADE 4


title: GRADE IV CULTURE

description:
PRIMARY CULTURE FORM HUMA GLIOBLASTOMA MULTIFORME
SAMPLE 8


title: GRADE IV, 1

description:
GLIOBLASTOMA MULTIFORME, GRADE IV, HUMAN TISSUE SAMPLE
SAMPLE 6


title: GRADE I, 1

description:
PILOCYTIC ASTROCYTOMA, GRADE I HUMAN TISSUE SAMPLE
SAMPLE 1

value: WHO GRADE 1


title: BJ_vector_rep2

city: Cleveland

first: HyeonJoo

last: Cheon

state: OH

address: 9500 Euclid Ave

department: Molecular Genetics

institute: Cleveland Clinic

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

source_name: BJ fibroblasts, empty vector transfected

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

growth_protocol: Cells were cultured in DMEM supplemented with 5% FBS, 100 U/ml penicillin, and 100 g/ml streptomycin. Lentiviral vector transfected cells were selected by puromycin treatment.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Nanodrop.

treatment_protocol: Cells were treated with 3 IU/ml of IFN beta for 6 hrs. Cells were transfected with empty lentiviral vector or vector containing Y701F STAT1 cDNA.

value: normal fibroblasts

value: empty vector


title: BJ_Y701F STAT1_rep1

source_name: BJ fibroblasts, Y701F STAT1 transfected

value: Y701F STAT1


title: 1858 - Dysplasia

description: oral dysplasia

source_name: Dysplasia, 1858

tag: disease state


title: 1896 - CIS

description: oral carcinoma in situ


title: BJ_IFNgamma_6h_rep1

source_name: BJ fibroblasts, IFN beta treated for 6 h

value: IFN gamma


title: GRADE II, 1

description:
FIBRILLARY DIFFUSE ASTROCYTOMA, GRADE II, HUMAN SAMPLE
SAMPLE 3

value: WHO GRADE 2


title: GRADE II, 2

description:
FIBRILLARY DIFFUSE ASTROCYTOMA, GRADE II, HUMAN SAMPLE
SAMPLE 4


title: BJ_vector_rep1


title: GRADE I, 2

description:
PILOCYTIC ASTROCYTOMA, GRADE I HUMAN TISSUE SAMPLE
SAMPLE 2


title: BJ_IFNgamma_6h_rep2


title: BJ_IFNbeta_6h_rep1

value: IFN beta


title: BJ_Y701F STAT1_rep2


title: BJ_IFNbeta_6h_rep2