title: Triton X100 vs S1P

city: Urayasu

first: Kazuhisa

last: Iwabuchi

state: Chiba

address: 2-1-1 Tomioka

department: Institute for Environmental and Gender-specific Medicine

institute: Juntendo University Graduate School of Medicine

description: Ultra-sensitive DNA chip for human genome wide gene expression analysis

hyb_protocol: Cy3- and Cy5-labeled aaRNA were concentrated using Microcon YM-30 centrifugal filter units (Nihon Millipore K.K., Tokyo, Japan), mixed with the hybridization buffer supplied with the kit, and denatured at 95 °C for 2 min. The hybridization mixture was applied to a “3D-Gene” human oligo chip 25k (Toray Industries Inc., Tokyo, Japan) and incubated according to the manufacturer’s instructions.

scan_protocol: Scanned on an GenePix 4400a scanner at PMTGain=498 (Cy5) 437 (Cy3) [low] or 628(Cy5)  558(Cy3) [high]

data_processing:
Any genes displaying signal intensities less than or equal to 10 were omitted from the data list. Subsequently, the obtained numerical data were normalized using the global median normalization per slide and per channel. Furthermore, the genes showing signal intensities less than or equal to 100 were omitted in order to define the credibility of the dataset.
The normalized Cy5 and Cy3 signal intensities were converted by taking logarithms of base two of the high PMTGain data set, and the Cy5/Cy3 ratio was calculated for each slide. If the data are more than 60,000, the data of the low PMTGain data set were used.
1_TXvsCD_normalized.txt: The combined normalized data file of 1_TXvsCD_low_res and 1_TXvsCD_high_res after ommiting the data of which signal intensities were less than or equal to 10
1_TXvsCD_anno_final.txt: The final data file after merging the low and high data in TXvsCD_normalized.txt
2_TXvsS1P_normalized.txt: The combined normalized data file of 2_TXvsS1P_low and 2_TXvsS1P_high after ommiting the data of which signal intensities were less than or equal to 10
2_TXvsS1P_final.txt: The final data file after merging the low and high data in 2_TXvsS1P_normalized.txt

source_name: Triton X100 treated three-dimensionally cultured keratinocytes

label_protocol: cDNA synthesis and production of aminoallyl-labeled RNA (aaRNA) were performed using the Amino Allyl Message Amp II™ aaRNA Amplification Kit (Applied Biosystems) according to the manufacturer’s protocol.

growth_protocol: The culture system used was the LabCyte EPI-Model (J-Tec Co., Gamagori, Japan), which consists of normal human epidermal keratinocytes cultured to form a multilayer and provides a highly differentiated model of the human epidermis.

extract_protocol: Total RNA was isolated using an Absolutely RNA Purification Kit (Agilent Technologies; Palo Alto, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Sterilized nitrocellulose filters were incubated with PaCDase or S1P in 25 mM Tris-buffered saline (pH 8.5), 2.5 mM CaCl2, with or without 0.1% (1.6 mM) Triton X-100 for 4 h at 4 °C. Excess liquid was removed by blotting with sterile filter paper, and the wetted filters were placed onto the stratum corneum of the EPI-Model in 10-mm diameter chambers and incubated in a CO2 incubator for 24 h.

tag: cell type

source_name: S1P, Triton X100-treated three-dimensionally cultured keratinocytes


title: Triton X100 vs PaCDase

status: Public on Dec 25 2014

type: RNA

country: Japan

molecule: total RNA

organism: Homo sapiens

source_name: PaCDase, Triton X100-treated three-dimensionally cultured keratinocytes


title: AIM2 TKO 4

type: protein

city: Worcester

first: Rebecca

last: Baum

state: MA

address: 55 N Lake Ave LRB 240D

department: Medicine

country: USA

institute: University of Massachusetts Medical School

description:
Serum samples pretreated with DNAse I were diluted 1:100 and incubated with autoantigen arrays bearing 125 autoantigens
raw data in: Slide 2.gpr

hyb_protocol: Autoantigen array protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX).

scan_protocol: Genepix Pro 7.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: Heatmap was generated using Cluster and treeview software (http://rana.lbl.gov/EisenSoftware.htm)

label: cy3-labeled anti-mouse IgG

molecule: protein

organism: Mus musculus

source_name: Sera

label_protocol: Autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG)

growth_protocol: not applicable

extract_protocol: Sera was isolated from blood that was centrifuged at 6000rpm for 10 minutes.

treatment_protocol: not applicable

tag: age

value: 10 months

tag: mouse strain

tag: gender

value: Male

tag: genotype

value: AIM2 TKO


title: Pdyn wt F Hypo Input2

city: New York

first: Zhiying

last: Li

state: NY

address: 1230 York ave.

institute: Rockefeller University

description:
total RNA
transcriptome data from total hypothalamic RNA of wild-type mice

hyb_protocol: 20ug of cRNA for each sample was fragmented according to manufacturer's instruction and hybridized to room temperature-equilibriated arrays according to kit instruction (Affymetrix 900720) in Hybridizatoin Oven 640 (Affymetrix 800138), following which the arrays were washed and stained according to manufacturer's instruction using GeneChip Fluidic Station 450 (Affymetrix, 00-0079).

scan_protocol: Mouse Genome 430 2.0 arrays were scanned using the GeneChip Sanner 3000 (Affymetrix, 00-00212).

data_processing: Data were processed using GeneSpring GX software. GC-RMA was used for normalization. Probesets with a minimum hybridization intensity of 100 in all sample of at least one condition were deemed expressed. Averaged values for each condition were used for further analyses.

label: biotin

source_name: wild-type hypothalamic Input sample 2

label_protocol: Biotinylated cRNA was prepared according to manufacturer's instructions (Affymetrix, 901230)

growth_protocol: Mice were housed under 12hr light-dark cycle at room temperature 68-72 °F and fed ad lib with regular rodent chow until 3-4 month of age.

extract_protocol: BAC TRAP procedure: pooled hypothalami were hypogenized, polysomal RNA was immuno-precipitated using antibodies against GFP after an aliquote for Input RNA was saved separately.

treatment_protocol: No treatment other than routine feeding and cleaning were done when mice were growing up. On the day of experiment, hypothalami were dissected on ice and immediately processed for IP and Input RNA purification

tag: strain

tag: tissue

value: hypothalamus

value: wildtype

tag: developmental stage

value: adult

tag: antibody

value: none (input)

tag: antibody source

value: The Rockefeller University Monoclonal Antibody Resource Center, HtzGFP-19F7 and HtzGFP-19C8


title: Pdyn wt M Hypo Input1

source_name: wild-type hypothalamic Input sample 1


title: Pdyn wt F Hypo IP2

description:
immunoprecipitated polysomal RNA
transcriptome data from hypothalamic Pdyn neurons-specific polysomal RNA of wild-type mice

source_name: wild-type hypothalamic IP sample 2

value: anti-GFP


title: AIM2 TKO 2

description:
Serum samples pretreated with DNAse I were diluted 1:100 and incubated with autoantigen arrays bearing 125 autoantigens
raw data in: Slide 1.gpr


title: AIM2 TKO 1

value: Female


title: STING TKO 7

value: STING TKO


title: Gonad_FF_rep3

city: Barcelona

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

country: Spain

institute: Institute of Marine Sciences (ICM-CSIC)

description: Fish that exhibited a fast growing rate and through overfeeding were forced to maintain a fast growing rate

hyb_protocol: Each sample (1.65 μg) was hybridized to D. labrax array (Agilent ID 023790) at 65 °C for 17 h using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. The microarray platform GPL13443 has been validated and uploaded to the Gene Expression Omnibus (GEO)-NCBI database.

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp (Ritchie et al., 2007) method. To assure comparability across samples quantile normalization (Bolstad, 2001) was used. A probe was considered reliable if its raw foreground intensity was at least two times higher than the respective background intensity and if it was neither saturated nor flagged by the Feature Extraction software. On our custom array design, most probes (78%) were represented in two (or in some cases more) identical copies. Median intensities of respective probe replicates were taken in order to yield only one expression value per probe. A probe was considered reliable if at least half of its replicates were reliable, as defined above. Differential expression analysis was carried out on all non-control probes with an empirical Bayes approach on linear models (limma) (Smyth, 2004). Results were corrected for multiple testing according to the False Discovery Rate (FDR) method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed if they had adjusted P-value < 0.05, absolute fold change > 1.2 and were reliable in all samples.  All statistical analyses were performed with the Bioconductor project (http://www.bioconductor.org/) in the R statistical environment (http://cran.rproject.org/) (Gentleman et al., 2004).

organism: Dicentrarchus labrax

source_name: Whole gonad,  332 days post fertilization, Fast growing-Fast growing fish from the population

label_protocol: RNA labelling, hybridizations, and scanning were performed according to manufacturer’s instructions. Briefly, total RNA (100 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen), quantified with the Nanodrop ND- 1000 and verified using the Bioanalyzer 2100.

growth_protocol: Rearing conditions and handling methods were as described at (Díaz et al., 2013). At the beginning of the experiment both experimental groups (F and S) followed the same feeding protocol; larvae were fed three times a day with Artemia AF and then with amino acid enriched Artemia EG (INVE Aquaculture, Belgium). Juveniles and adults were fed following each specific group feeding regime with dry food (ProAqua S.A., Spain) of different diameters according to fish size.

extract_protocol: Total RNA was purified from 170 dph European sea bass isolated gonads by homogenizing the tissue with Trizol reagent (Invitrogen- Live Technologies, Scotland, UK). Briefly, samples were then separated into phases by chloroform, precipitated with isopropanol and washed in 75% Ethanol. The quality and concentration of the RNA were assessed by ND-1000 spectrophotometer (NanoDrop Technologies) based on A260 absorbance and checked on a 1% agarose/formaldehyde gel. Integrity of the total RNA was then verified analyzing 1 µl/sample with a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent, Spain) before processing for microarrays to assure consistency across samples. RNA samples of 100-200 ng/µl and RINs higher than 7 were used to perform the hybridizations. Two hundred nanograms of total RNA were treated with E.coli RNAse H in order to remove complementary RNA. From this RNA 100 ng were used for the cDNA synthesis using SuperScript III RNase Transcriptase (Invitrogen, Spain) and Random hexamer (Invitrogen, Spain) following manufacturer’s instructions.

treatment_protocol: Larvae were divided in two tanks and maintained at 17ºC, a temperature known to avoid temperature effects on sex ratio (Piferrer et al., 2005; Navarro-Martín et al., 2009), for the first 20 dph and then raised and maintained at 21ºC to allow growth from the whole experiment until fall, when temperature followed natural fluctuations to allow gonad maturation. Different feeding regimes are described elsewhere (Díaz et al., 2013; Experiment 2).

value: Testis


title: STING TKO 6


title: Gonad_S_rep8

description: Fish that exhibited a slow growing rate (the ones with the lowest Standard Length SL)

source_name: Whole gonad,  133 days post fertilization, Slow growing fish from the population

value: Undifferentiated gonads


title: Gonad_FF_rep1


title: Gonad_FF_rep2


title: STING TKO 5


title: STING TKO 4


title: STING TKO 3


title: Gonad_S_rep7


title: Gonad_S_rep6


title: Gonad_S_rep4


title: DKO 5

value: DKO


title: M2_polarized_rep3

city: Ribeirão Preto

first: Jose

middle: Mauricio Segundo Correia

last: Mota

state: São Paulo

address: 3900 Bandeirantes Ave

department: Clinics

country: Brazil

institute: University of São Paulo

description: Gene expression in M2-polarized macrophage

hyb_protocol: For cRNA hybridization, 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were added with 0.5 μL 10X gene Expression Blocking Agent and 24 μL nuclease-free water. Then, 1 μL of 25X Fragmentation Buffer were added and incubated for 30 min at 60o C. On completion of the fragmentation reaction, 25 μL of 2x Hi-RPM Hybridization Buffer were carefully added to the fragmentation mixture and hybridized to Agilent microarray slides (Sure Print G3 Mouse Gene Expression 8x60k Microarray, G4852A, Agilent Technologies, Slide 1: 252800516673, Slide 2: 252800516674, Slide 3: 252800516788) for 17 hours at 65o C in a rotating Agiled hybridization oven. To avoid bias, the position of each sample was determined following two random and sequential lotteries. After hybridization, two sequential washes were made using Gene Expression Wash Buffer 1 followed by Gene Expression Wash Buffer, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on G4900DA SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: M2-polarized macrophage, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA according to the manufacturer's instructions, followed by RNAeasy Mini Kit column purification (Qiagen, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoVue spectrophotometer (GE Healthcare Life Sciences, Utah, USA).

extract_protocol: RNA was isolated using a specific kit (Quick-RNATM MicroPrep, Zymo Research, CA, USA), following manufacturer instructions. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoVue spectrophotometer (GE Healthcare Life Sciences, Utah, USA).

value: 10 weeks

tag: weight

value: weight 20-30 g

tag: Sex

value: male

tag: sepsis

value: naïve

value: bone marrow derived macrophage

tag: protocols (time of isolation)

value: not applicable

tag: protocols (isolation method)

value: Isolation of mononuclear progenitors by adhesion

tag: protocols (differentiation)

value: culture with RPMI + L929 supernatant 20% + FBS 10% for 7 days

tag: protocols (polarization)

value: Supplementation with IL-10 (20 ng/mL) at the 3rd day of culture


title: M1_polarized_rep3

description: Gene expression in M1-polarized macrophage

source_name: M1-polarized macrophage, replicate 3

tag: cell type

value: Supplementation with IFN-gamma (50 ng/mL) e LPS (10 ng/mL) at the 3rd day of culture


title: M2_polarized_rep1

source_name: M2-polarized macrophage, replicate 1

tag: age


title: BM_derived_M0_naïve_rep3

description: Gene expression in bone marrow derived macrophage from naïve

source_name: bone marrow derived macrophage, M0, naïve, replicate 3


title: M1_polarized_rep4

source_name: M1-polarized macrophage, replicate 4


title: M2_polarized_rep2

source_name: M2-polarized macrophage, replicate 2


title: BM_derived_M0_naïve_rep2

source_name: bone marrow derived macrophage, M0, naïve, replicate 2


title: DKO 4

value: 10 months

tag: mouse strain

value: Male


title: Gonad_S_rep3


title: M2_polarized_rep4

source_name: M2-polarized macrophage, replicate 4


title: M1_polarized_rep1

source_name: M1-polarized macrophage, replicate 1


title: Gonad_S_rep5


title: BM_derived_M0_naïve_rep4

source_name: bone marrow derived macrophage, M0, naïve, replicate 4


title: Gonad_F_rep7

description: Fish that exhibited a fast growing rate (the ones with the highest Standard Length SL)

source_name: Whole gonad,  133 days post fertilization, Fast growing fish from the population


title: DKO 3

source_name: Sera

tag: gender

value: Female


title: BM_derived_M0_naïve_rep1

source_name: bone marrow derived macrophage, M0, naïve, replicate 1


title: Gonad_S_rep2


title: STING TKO 2

value: 3 months

tag: genotype

value: STING TKO


title: Gonad_F_rep6

value: Undifferentiated gonads


title: BM_derived_M0_post-sepsis_rep4

description: Gene expression in bone marrow derived macrophage from post-sepsis

source_name: bone marrow derived macrophage, M0, post-sepsis, replicate 4

tag: strain

value: post-sepsis

value: 14 days after sepsis induction


title: M1_polarized_rep2

source_name: M1-polarized macrophage, replicate 2

value: 10 weeks

value: weight 20-30 g


title: STING TKO 1


title: Gonad_F_rep5

tag: tissue


title: Gonad_F_rep4


title: BM_derived_M0_post-sepsis_rep3

source_name: bone marrow derived macrophage, M0, post-sepsis, replicate 3

value: male


title: BM_derived_M0_post-sepsis_rep1

source_name: bone marrow derived macrophage, M0, post-sepsis, replicate 1

value: bone marrow derived macrophage


title: DKO 2

value: DKO


title: BM_derived_M0_post-sepsis_rep2

source_name: bone marrow derived macrophage, M0, post-sepsis, replicate 2

value: Isolation of mononuclear progenitors by adhesion

value: not applicable


title: TAM_naïve_rep1

description: Gene expression in TAM from naïve

source_name: TAM, naïve, replicate 1

value: naïve

value: TAM

value: Percoll (70/30) followed by 1 hour adhesion


title: TAM_naïve_rep2 &

description:
Gene expression in TAM from naïve
sample was excluded from analysis due to reduced RNA concentrations and low quality

source_name: TAM, naïve, replicate 2


title: Gonad_F_rep3


title: DKO 1


title: TAM_naïve_rep3

description: Gene expression in TAM from naïve

source_name: TAM, naïve, replicate 3


title: TAM_naïve_rep4

description: Gene expression in TAM from naïve

source_name: TAM, naïve, replicate 4


title: Gonad_F_rep2


title: TAM_post-sepsis_rep1

description: Gene expression in TAM from post-sepsis

source_name: TAM, post-sepsis, replicate 1


title: Gonad_S_rep1

source_name: Whole gonad,  133 days post fertilization, Slow growing fish from the population


title: TAM_post-sepsis_rep2

description: Gene expression in TAM from post-sepsis

source_name: TAM, post-sepsis, replicate 2


title: TAM_post-sepsis_rep4

description: Gene expression in TAM from post-sepsis

source_name: TAM, post-sepsis, replicate 4


title: TAM_post-sepsis_rep3

description: Gene expression in TAM from post-sepsis

source_name: TAM, post-sepsis, replicate 3


title: Vehicle, biological rep2

status: Public on Dec 24 2014

city: Salisbury

first: Philip

middle: D

last: Anderson

state: Maryland

address: 1101 Camden Avenue

department: Biological Sciences

institute: Salisbury University

description: Vehicle, biological rep2

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix GeneChip Mouse gene 2.0 ST arrays.

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

data_processing: Raw microarray data was imported to R/Bioconductor and pre-processed using the oligo package. Arrays were background-corrected by rma, normalized by quantiles and summarized by median-polish. See the Supplemental Methods in the manuscript for full details.

source_name: Vehicle-DHT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Cells were harvested into Trizol reagent (Life Technologies) and RNA was extracted using the manufacturer’s protocol.

tag: cell line

value: MYCCaP

tag: agent

value: Vehicle-DHT


title: AZD1208, biological rep2

description: AZD1208, biological rep2


title: Gonad_F_rep1

source_name: Whole gonad,  133 days post fertilization, Fast growing fish from the population


title: Vehicle, biological rep1

description: Vehicle, biological rep1


title: AZD1208, biological rep1

description: AZD1208, biological rep1


title: Vehicle, biological rep3

description: Vehicle, biological rep3


title: MYCCaP, rep3

description: MYCCaP, technical rep3

source_name: MYCCaP+DHT

value: +DHT


title: AZD1208, biological rep3

description: AZD1208, biological rep3


title: Sertoli cells 2

type: genomic

city: Warsaw

first: Marta

last: Smyk

address: Kasprzaka 17A

department: Medical Genetics

country: Poland

institute: Intitute of Mother and Child

hyb_protocol: Hybridization of 4C DNA libraries was done according NimbleGen Array User’s Guide v8.1 for ChIP-chip arrays.

scan_protocol: The arrays were scanned on Agilent DNA Microarray Scanner, and analyzed using Agilent Scan Control

data_processing:
Arrays were processed using NimbleGen software DEVA v1.1
scaled, log2 (ChIP/Input) ratio in gff files

molecule: genomic DNA

source_name: cross-linked genomic DNA from Sertoli cells

label_protocol: Labeling of 4C DNA libraries was done according NimbleGen Array User’s Guide v8.1 for ChIP-chip arrays.

extract_protocol: 4C experiments were performed as described (Smyk et al., 2013). Primers used for amplification were: 5´-TACTTCTTATGCACAGGCAAGTTTGGA-3´ and 5´- GAGTTTCATGCAAGCCTCTTCCTACTT-3´ for NR0B1. The primers were designed within the EcoRI and DpnII fragments, containing PolII binding site of the NR0B1 promoter.

treatment_protocol: cross-linked DNA from Sertoli cells digested overnight with EcoRI and DpnII

value: Sertoli cells

source_name: reference Sertoli cells

treatment_protocol: uncross-linked DNA isolated from Sertoli cells and digested with EcoRI and DpnII


title: Sertoli cells 3


title: Lymphoblasts 2

source_name: cross-linked genomic DNA from lymphoblasts

treatment_protocol: cross-linked DNA from lymphoblasts digested overnight with EcoRI and DpnII

value: EBV-transformed lymphoblasts

source_name: reference EBV-transformed lymphoblasts

treatment_protocol: uncross-linked DNA isolated from lymphoblasts and digested with EcoRI and DpnII


title: Lymphoblasts 1


title: MYCCaP, rep1

description: MYCCaP, technical rep1


title: SF4 meDIP

city: KARNAL

first: TIRTHA

middle: KUMAR

last: DATTA

state: HARYANA

address: NDRI

department: ANIMAL BIOTECHNOLOGY

country: India

institute: NATIONAL DAIRY RESEARCH INSTITUTE

description:
Comparison between high fertile and subfertile groups.
ch1-cy3 (WCE) and ch2-cy5(IP)

hyb_protocol: Cy3-labeled Input was mixed with Cy5-labeled IP DNA.  Hybridizations were done using the Hybridization kit of Agilent (Part Number : 5188-5380 ). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 24 hours. The hybridized slides were washed using Agilent wash buffers (Part No: 5188-5226)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction done using Agilent Feature extraction software and Feature extracted raw data was analyzed using Agilent Genomic Workbench Lite Edition 6.5 (Methylation Application-Linear Normalization)

organism: Bubalus bubalis

source_name: input DNA from SF4

label_protocol: Two micrograms of WCE / input DNA and IP DNA was then labeled with Cy3 and Cy5 dUTP using Agilent Genomic DNA Labeling Kit PLUS ( Part No: 5190-0453) and   DNA yield and incorporation of labeled dye (specific activity) was measured using NanoDrop spectrophotometer.

extract_protocol: DNA was isolated from the cryopreserved semen samples using QIAamp® DNA Mini Kit (Qiagen, Valencia, CA) protocol, sheared by sonication (Bioruptor, Diagenode Cat No:UCD-200TM-EX) to get fragment length of 300 -1000bp. For immunoprecipitation of methylated CpG regions, antibody against 5- methylcytosine (Eurogentec, cat no. BI-MECY-0100) was used. Before this 5 μg of Dynabeads® Pan Mouse IgG (cat. No. 11041) were prepared for immunoprecipitation. The sheared DNA was immunoprecipitated and methylated DNA was eluted from the magnetic beads, cleaned using Phenol:Chloroform:isoamylalcohol extraction followed by ethanol precipitation. Genomic DNA integrity was assessed by running it on a 0.8% Agarose Gel, purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). Genomic DNA with OD260/OD280>1.8 and OD260/OD230 ≥ 1.3 was used for microarray experiments.

value: Subfertile bull sperm

tag: chip antibody

value: none, input DNA

tag: cell

value: Sperm

source_name: meDIP DNA from SF4

value: 5- methylcytosine


title: SF5 meDIP

source_name: input DNA from SF5

source_name: meDIP DNA from SF5


title: SF1 H3K4

description:
SF1_H3K4 vs SF1_WCE
Comparison between high fertile and subfertile groups of H3K4

hyb_protocol: The labeled DNA samples were hybridized on a Genotypic designed Human Bovine ChIP-on-Chip , 4X180K  (AMADID: 040096). 5 micrograms of cy3 and cy5 labeled samples were hybridized. Hybridizations were done using the Agilent Hybridization kit of (Part Number: 5188-6420) Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours. The hybridized slides were washed using Agilent aCGH wash buffers

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent. Feature extracted raw data was analyzed using Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5 (Chip-on-Chip Application) and Microsoft Excel.

source_name: input DNA from SF1

label_protocol: The DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol of Agilent Technologies. The blunted DNA was cleaned, precipitated and resuspended in 25 microlitres of water. The entire DNA was then ligated to linkers. The linker-ligated DNA was subjected to two rounds of LMPCR and resuspended in water. Two micrograms of each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS with Cy3 or Cy5 dUTP( 5190-0453). DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

extract_protocol: ChIP experiment from cryopreserved semen samples was done as per the protocol of Magna ChIP G/A kit. The crosslinked chromatin was sheared using Micrococcal enzyme NEB (Cat no. MO247S). The antibodies against H3K4me2 and H3K27me3 were obtained from MILLIPORE (ChIPAb + Dimethyl-Histone H3 (Lys4), Cat. No. 17-677 and ChIPAb + Trimethyl-Histone H3 (Lys27), Cat. No. 17-622). 3µl of each of immunoprecipitating antibody was used in 100µl of sperm chromatin preparation. The precipitated chromatin was decrosslinked using 1µl proteinaseK  by incubating at 62°C for 2 hours with shaking. Then it was incubated at 95°C for 10 minutes for deactivation of enzyme. The samples were cooled down to room temperature and magnetic beads were separated with the help of magnetic separator and proceeded further for purification of DNA using Magna ChIP columns. The purified DNA samples were  assessed for purity by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). Genomic DNA with OD260/OD280>1.8 and OD260/OD230 ≥ 1.3 was used for microarray experiments.

source_name: H3K4 ChIP DNA from SF1


title: MYCCaP, rep2

description: MYCCaP, technical rep2


title: SF5 H3K27

description:
SF5_H3K27 vs SF5_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from SF5


title: HF5 H3K4

description:
HF5_H3K4 vs HF5_WCE
Comparison between high fertile and subfertile groups of H3K4

source_name: input DNA from HF5

value: High fertile bull sperm

source_name: H3K4 ChIP DNA from HF5


title: HF3 meDIP

source_name: input DNA from HF3

source_name: meDIP DNA from HF3


title: SF1 meDIP

source_name: meDIP DNA from SF1


title: Lymphoblasts 3

value: male


title: PBS whole lung 1

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

hyb_protocol: hybridized to the SurePrint G3 Mouse GE 8X60K microarray (Agilent Technologies)

scan_protocol: Arrays were scanned with a DNA Microarray Scanner with SureScan High-Resolution Technology, (G2565CA; Agilent Technologies)

data_processing: Data were acquired using Agilent Feature Extraction software ver. 10.7.3.1. (Agilent Technologies). Probe annotations were provided by Agilent Technologies (AMADID 028005).

source_name: PBS whole lung

label_protocol: RNA amplification was performed using the Arcturus Riboamp Plus RNA Amplification Kit (Life technologies) in accordance with the manufacturer’s instructions. RNA was labeled by using the Agilent Low Input Quick Amp Labeling kit, one color (Agilent Technologies, Santa Clara, CA)

extract_protocol: Total RNA of sorted macrophages was extracted using TRIzol reagent (Life Technologies, Carlsbad, CA) and precipitated with isopropanol.

treatment_protocol: Lungs were fixed in 4% paraformaldehyde (PFA) phosphate buffer solution. Fixed tissues were embedded in OCT compound (Sakura Finetek, Tokyo, Japan), frozen by liquid N2 and stored at -80°C.

tag: tissue/cell type

value: whole lung

tag: venus detected

tag: infection

value: PBS

tag: dose


title: PBS whole lung 2


title: SF4 H3K27

description:
SF4_H3K27 vs SF4_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from SF4


title: SF1 H3K27

description:
SF1_H3K27 vs SF1_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from SF1


title: HF5 H3K27

description:
HF5_H3K27 vs HF5_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from HF5


title: Venus whole lung 1

source_name: Venus whole lung


title: Venus whole lung 2


title: PBS whole lung 3


title: Venus negative macrophages 3

source_name: Venus negative macrophages

value: lung macrophage

value: Neg


title: HF2 meDIP

source_name: input DNA from HF2

source_name: meDIP DNA from HF2


title: PBS macrophages 3

source_name: PBS macrophages


title: HF3 H3K27

description:
HF3_H3K27 vs HF3_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from HF3


title: PBS macrophages 1


title: Venus negative macrophages 2


title: HF5 meDIP

source_name: meDIP DNA from HF5


title: Sertoli cells 1

source_name: cross-linked genomic DNA from Sertoli cells

source_name: reference Sertoli cells


title: Venus whole lung 3


title: HF3 H3K4

description:
HF3_H3K4 vs HF3_WCE
Comparison between high fertile and subfertile groups of H3K4

source_name: H3K4 ChIP DNA from HF3


title: HF2 H3K27

description:
HF2_H3K27 vs HF2_WCE
Comparison between high fertile and subfertile groups of H3K27

source_name: H3K27 ChIP DNA from HF2


title: SF5 H3K4

description:
SF5_H3K4 vs SF5_WCE
Comparison between high fertile and subfertile groups of H3K4

source_name: input DNA from SF5

source_name: H3K4 ChIP DNA from SF5


title: SF4 H3K4

description:
SF4_H3K4 vs SF4_WCE
Comparison between high fertile and subfertile groups of H3K4

source_name: input DNA from SF4

source_name: H3K4 ChIP DNA from SF4


title: PBS macrophages 2


title: HF2 H3K4

description:
HF2_H3K4 vs HF2_WCE
Comparison between high fertile and subfertile groups of H3K4

source_name: H3K4 ChIP DNA from HF2


title: Venus positive macrophages 1

source_name: Venus positive macrophages

value: Pos


title: Venus positive macrophages 2


title: Venus positive macrophages 3


title: FLO8 Microgravity rep3.

city: Brussel

first: Katty

last: Goossens

address: Pleinlaan 2

department: DBIT

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Each sample was hybridized onto an Affymetrix Yeast Genome 2.0 array for the gene expression profiling. The extraction of RNA, cDNA synthesis, cRNA synthesis and labelling, as well as array hybridisation to Affymetrix Yeast Genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were performed as described in the Affymetrix manual.  Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual. (Affymetrix, Santa Clara, CA).

data_processing: The analysis is based on the RMA expression values (Irizarry et al. (2003)) as obtained with the affy package (version 1.26.1) of Bioconductor (www.bioconductor.org). All non-Saccharomyces cerevisiae probe sets were removed during the RMA normalization and summarization processing. Furthermore, all Affymetrix control probes were removed prior to analysis. To decide whether a signal was significantly above background, the MAS 5.0 detection calls (Affymetrix (2001)) were used.

organism: Saccharomyces cerevisiae

source_name: BY4742::FLO8 strain grown in microgravity

growth_protocol: The yeast cells were inserted in the experiment module in isotonic saline (0.9% (w/v) NaCl) solution at a concentration of 20 x 106 cells/ml and activated automatically by injecting 2 x YPD 5 days after the launch. The cells were grown for 3 days in liquid YPD medium at a temperature of 23°C in the International Space Station (ISS). A postflight ground experiment was set up in a programmable incubator with use of the logged temperature data.

extract_protocol: The RNA extraction protocol was optimised for small quantities of ~108 cells from 1 ml liquid cell cultures and has been successfully carried out on all samples. The total RNA yield and purity was determined spectrophotometrically using a Nanodrop ND1000. The RNA integrity was measured using the Agilent Bioanalyzer 2100.

treatment_protocol: After 72 hours of growth in microgravity and 1-g, the cells were filtrated and immediately fixated with RNALater™, which proved to be a suitable fixating agent to preserve the RNA in S. cerevisiae under extreme temperature conditions and under extreme temperature cycle conditions.

tag: strain/genotype

tag: growth conditions

value: in microgravity


title: FLO1 Ground rep1.

scan_protocol: The extraction of RNA, cDNA synthesis, cRNA synthesis and labelling, as well as array hybridisation to Affymetrix Yeast Genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were performed as described in the Affymetrix manual.  Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual. (Affymetrix, Santa Clara, CA).

source_name: BY4742 FLO1 overexpression strain grown on ground

value: BY4742 FLO1 overexpression

value: on ground


title: WT Microgravity rep3.

source_name: BY4742 WT strain grown in microgravity

label_protocol: The extraction of RNA, cDNA synthesis, cRNA synthesis and labelling, as well as array hybridisation to Affymetrix Yeast Genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were performed as described in the Affymetrix manual.  Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual. (Affymetrix, Santa Clara, CA).

value: BY4742 WT


title: FLO8 Ground rep1.

source_name: BY4742::FLO8 strain grown on ground


title: FLO8 Microgravity rep2.


title: WT Microgravity rep1.


title: FLO1 Ground rep2.


title: FLO8 Ground rep3.


title: FLO1 Ground rep3.


title: FLO8 Ground rep2.


title: WT Microgravity rep2.


title: WT Ground rep2.

source_name: BY4742 WT strain grown on ground


title: FLO1 Microgravity rep2.

source_name: BY4742 FLO1 overexpression strain grown in microgravity


title: WT Ground rep3.


title: WT Ground rep1.


title: FLO1 Microgravity rep1.


title: Pericarp, biological rep2

city: Lethbridge

first: Carolyn

last: Penniket

state: Alberta

country: Canada

institute: Agriculture & Agri-Food Canada

description:
Pericarp_2
Triticale (x Triticosecale Wittmack cv. Certa) Pericarp_2

hyb_protocol: Chip hybridization for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com).

scan_protocol: Wheat GeneChips were scanned by the McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com).

data_processing: The data was normalized using the Robust Multichip Average (RMA) normalization algorithm which include background correction, quantile normalization, and a median polish summarization.  The data was analyzed using FlexArray software package from Genome Quebec (Blazejczyk et al., 2007).

organism: Secale cereale x Triticum turgidum subsp. durum

source_name: Pericarp - Seed coat tissue layer between endosperm and epiderm disected from seed at the soft dough stage of seed development, Zadoks' stage 85

label_protocol: Biotinylated cRNA was synthesized according to standard Affymetrix protocol using the two-cycle Eukaryotic Target labeling kit from 50-100ng total RNA.  Labelling for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com).

growth_protocol: Plants were maintained in temperature controlled growth chamber with 16 h photoperiods at 18°C and 8 h dark periods at 15°C.

extract_protocol: Total RNA was extracted from crease, epiderm and all leaf and stem tissues using QIAGEN RNeasy® Plant Mini Kit with on column digestion of DNA using the QIAGEN RNase-Free DNase Set according to manufacturer's protocol.  Total RNA from stem tissues was further purified using the RNA cleanup protocol in the QIAGEN RNeasy® Mini Kit to remove carbohydrates.  For embryo, endosperm and pericarp tissues, total RNA was isolated using the method described by Singh et al. (2003) using a guanidine hydrochloride buffer system then further purified using the RNA cleanup protocol for the QIAGEN RNeasy® Mini Kit with on-column digestion of DNA.  For root and coleoptile tissues, total RNA was extracted using a guanidine isothiocyanate/cesium chloride ultracentrifugation method (Wang et al., 2010).

tag: cultivar

value: AC Certa

value: Pericarp

tag: zadoks' growth scale


title: Endosperm, biological rep3

description:
Endosperm_3
Triticale (x Triticosecale Wittmack cv. Certa) Endosperm_3

source_name: Endosperm - disected from seed at the soft dough stage of seed development, Zadoks' stage 85

value: Endosperm


title: Pericarp, biological rep1

description:
Pericarp_1
Triticale (x Triticosecale Wittmack cv. Certa) Pericarp_1


title: Embryo, biological rep3

description:
Embryo_3
Triticale (x Triticosecale Wittmack cv. Certa) Embryo_3

source_name: Embryo with attached scutellum disected from seed at the soft dough stage of seed development, Zadoks' stage 85

value: Embryo


title: 30DPA, biological rep3

description:
30DPA_3
Triticale (x Triticosecale Wittmack cv. Certa) 30DPA_3

source_name: Flag leaf tissue at late senescence, 30 days post anthesis, Zadoks' stage 85

value: Flag Leaf


title: Embryo, biological rep2

description:
Embryo_2
Triticale (x Triticosecale Wittmack cv. Certa) Embryo_2


title: Crease, biological rep1

description:
Crease_1
Triticale (x Triticosecale Wittmack cv. Certa) Crease_1

source_name: Crease - vascular bundle from ventral groove with most seed coat tissue removed, disected from seed at the soft dough stage of seed development, Zadoks' stage 85

value: Crease


title: Endosperm, biological rep1

description:
Endosperm_1
Triticale (x Triticosecale Wittmack cv. Certa) Endosperm_1


title: Embryo, biological rep1

description:
Embryo_1
Triticale (x Triticosecale Wittmack cv. Certa) Embryo_1


title: 30DPA, biological rep2

description:
30DPA_2
Triticale (x Triticosecale Wittmack cv. Certa) 30DPA_2


title: Epiderm, biological rep2

description:
Epiderm_2
Triticale (x Triticosecale Wittmack cv. Certa) Epiderm_2

source_name: Epiderm - outermost seed coat tissue layer disected from seed at the soft dough stage of seed development, Zadoks' stage 85

value: Epiderm


title: 22DPA, biological rep3

description:
22DPA_3
Triticale (x Triticosecale Wittmack cv. Certa) 22DPA_3

source_name: Flag leaf tissue at early senescence, 22 days post anthesis, Zadoks' stage 75


title: 30DPA, biological rep1

description:
30DPA_1
Triticale (x Triticosecale Wittmack cv. Certa) 30DPA_1


title: Tillering, biological rep2

description:
Tillering_2
Triticale (x Triticosecale Wittmack cv. Certa) Tillering_2

source_name: Leaf tissue at the tillering stage, Zadoks' stage 23

value: Leaf


title: Flag Leaf, biological rep3

description:
Flag Leaf_3
Triticale (x Triticosecale Wittmack cv. Certa) Flag Leaf_3

source_name: Flag Leaf tissue at the early booting stage, Zadoks' stage 49


title: Flag Leaf, biological rep5

description:
Flag Leaf_5
Triticale (x Triticosecale Wittmack cv. Certa) Flag Leaf_5


title: Seedling, biological rep3

description:
Seedling_3
Triticale (x Triticosecale Wittmack cv. Certa) Seedling_3

source_name: Leaf tissue at the seedling stage, Zadoks' stage 13


title: 22DPA, biological rep2

description:
22DPA_2
Triticale (x Triticosecale Wittmack cv. Certa) 22DPA_2


title: 22DPA, biological rep1

description:
22DPA_1
Triticale (x Triticosecale Wittmack cv. Certa) 22DPA_1


title: Crease, biological rep2

description:
Crease_2
Triticale (x Triticosecale Wittmack cv. Certa) Crease_2


title: Endosperm, biological rep2

description:
Endosperm_2
Triticale (x Triticosecale Wittmack cv. Certa) Endosperm_2


title: Crease, biological rep3

description:
Crease_3
Triticale (x Triticosecale Wittmack cv. Certa) Crease_3


title: Flag Leaf, biological rep4

description:
Flag Leaf_4
Triticale (x Triticosecale Wittmack cv. Certa) Flag Leaf_4


title: Flag Leaf, biological rep1

description:
Flag Leaf_1
Triticale (x Triticosecale Wittmack cv. Certa) Flag Leaf_1


title: Tillering, biological rep3

description:
Tillering_3
Triticale (x Triticosecale Wittmack cv. Certa) Tillering_3


title: Tillering, biological rep1

description:
Tillering_1
Triticale (x Triticosecale Wittmack cv. Certa) Tillering_1


title: Flag Leaf, biological rep2

description:
Flag Leaf_2
Triticale (x Triticosecale Wittmack cv. Certa) Flag Leaf_2


title: Venus negative macrophages 1

source_name: Venus negative macrophages


title: Epiderm, biological rep1

description:
Epiderm_1
Triticale (x Triticosecale Wittmack cv. Certa) Epiderm_1


title: Seedling, biological rep2

description:
Seedling_2
Triticale (x Triticosecale Wittmack cv. Certa) Seedling_2


title: FLO8 Microgravity rep1.

source_name: BY4742::FLO8 strain grown in microgravity


title: Stem75, biological rep1

description:
Stem75_1
Triticale (x Triticosecale Wittmack cv. Certa) Stem75_1

source_name: Internode stem tissue between crown and second node, Zadoks' stage 75

value: Stem


title: Stem45, biological rep1

description:
Stem45_1
Triticale (x Triticosecale Wittmack cv. Certa) Stem45_1

source_name: Internode stem tissue between crown and second node, Zadoks' stage 45


title: Stem21, biological rep3

description:
Stem21_3
Triticale (x Triticosecale Wittmack cv. Certa) Stem21_3

source_name: Internode stem tissue between crown and second node, Zadoks' stage 21


title: Stem21, biological rep2

description:
Stem21_2
Triticale (x Triticosecale Wittmack cv. Certa) Stem21_2


title: Stem59, biological rep3

description:
Stem59_3
Triticale (x Triticosecale Wittmack cv. Certa) Stem59_3

source_name: Internode stem tissue between crown and second node, Zadoks' stage 59


title: Seedling, biological rep1

description:
Seedling_1
Triticale (x Triticosecale Wittmack cv. Certa) Seedling_1


title: Coleoptile, biological rep3

description:
Coleoptile_3
Triticale (x Triticosecale Wittmack cv. Alta) Coleoptile_3

source_name: emerged coleoptile tissue collected 7 days after being sewn, Zadoks' stage 7

value: AC Alta

value: Coleoptile


title: Stem21, biological rep1

description:
Stem21_1
Triticale (x Triticosecale Wittmack cv. Certa) Stem21_1


title: Stem75, biological rep3

description:
Stem75_3
Triticale (x Triticosecale Wittmack cv. Certa) Stem75_3


title: Stem59, biological rep1

description:
Stem59_1
Triticale (x Triticosecale Wittmack cv. Certa) Stem59_1


title: Root, biological rep2

description:
Root_2
Triticale (x Triticosecale Wittmack cv. Alta) Root_2

source_name: root tissue collected 7 days after being sewn, Zadoks' stage 7

value: Root


title: Coleoptile, biological rep1

description:
Coleoptile_1
Triticale (x Triticosecale Wittmack cv. Alta) Coleoptile_1


title: Stem59, biological rep2

description:
Stem59_2
Triticale (x Triticosecale Wittmack cv. Certa) Stem59_2


title: Coleoptile, biological rep2

description:
Coleoptile_2
Triticale (x Triticosecale Wittmack cv. Alta) Coleoptile_2


title: Stem45, biological rep2

description:
Stem45_2
Triticale (x Triticosecale Wittmack cv. Certa) Stem45_2


title: Root, biological rep3

description:
Root_3
Triticale (x Triticosecale Wittmack cv. Alta) Root_3


title: ESC biological rep2

city: Rotterdam

first: Dorota

last: Kurek

address: Dr Molewaterplein 50

country: Netherlands

institute: ErasmusMC

description: Gene expression data from ESC

hyb_protocol: RNA was converted to biotin-labeled cRNA, hybridized on the Affymetrix Mouse Genome 430 2.0 Array, and analyzed with the Affymetrix GeneChip Scanner 3000 at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands) according to manufacturer’s instructions.

scan_protocol: Arrays were analyzed with the Affymetrix GeneChip Scanner 3000

data_processing:
Raw probe values were normalized into probesets by calling Variance Stabilization (VSN) and calculating the summaries with the medianpolish algorithm of the Robust Multi-Array Average (RMA) expression. The resulting expression estimates were converted to log2 ratios. Quality control was investigated using the qc function from the simpleaffy R package. A filter was applied to the normalized values consisting of a cutoff ratio of maximal/minimal intensity of at least 1.5 and an intensity of 100 or above in one third of the samples. Differentially expressed genes were called with the limma package, using a threshold of 0.05 for FDR adjusted p-value and minimal fold change of 2. Heatmaps were clustered using the Spotfire software.
Differentially expressed genes were called with the limma package, using a threshold of 0.05 for FDR adjusted p-value and minimal fold change of 2.

source_name: ESC

growth_protocol: EpiSCs were cultured on gelatine and FCS-coated plates in N2B27 medium supplemented with 20 ng/ml ActivinA and 12 ng/ml bFGF (Peprotech) (EpiSC medium). ESC  were cultured on gelatine-coated plates in N2B27 medium supplemented with 1000 U/ml LIF and 250ng/ml Wnt3a

extract_protocol: Total RNA was prepared using TriPure (Roche) according to the manufacturer’s protocol.

treatment_protocol: EpiSCs were cultured with IWP2 prior addition of Wnt3a. 2h before addition of wnt3a the medium was changed in all samples.

tag: cell type

value: ESC


title: EpiSC with IWP2, biological rep3

description: Gene expression data from EpiSC cultured with IWP2

source_name: EpiSC with IWP2

label_protocol: RNA was converted to biotin-labeled cRNA, hybridized on the Affymetrix Mouse Genome 430 2.0 Array, and analyzed with the Affymetrix GeneChip Scanner 3000 at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands) according to manufacturer’s instructions.

value: EpiSC

tag: treatment


title: EpiSC with Vehicle, biological rep3

description: Gene expression data from EpiSC cultured with Vehicle

source_name: EpiSC with Vehicle

value: Vehicle


title: ESC biological rep1

description: Gene expression data from ESC


title: EpiSC with Vehicle, biological rep2


title: Root, biological rep1

description:
Root_1
Triticale (x Triticosecale Wittmack cv. Alta) Root_1


title: Stem45, biological rep3

description:
Stem45_3
Triticale (x Triticosecale Wittmack cv. Certa) Stem45_3


title: EpiSC with IWP2, biological rep2


title: ESC biological rep3

description: Gene expression data from ESC


title: EpiSC with IWP2, biological rep1


title: 2297_177_1_Cerebellum

city: London

first: Dervis

middle: A

last: Salih

address: Gower St

department: Dementia Research Institute

country: United Kingdom

institute: University College London

hyb_protocol: The IVT products were hybridized to the Illumina MouseRef-8 V2 BeadArrays and incubated overnight at 48 C.

scan_protocol: The arrays were scanned in an Illumina BeadStation Scanner using a standard protocol.

data_processing: Data was quantile normalised and corrected for batch effect. Raw data provided.

source_name: Cerebellum

label_protocol: 100 ng total RNA starting material. cDNA and in vitro transcription was performed using the Ambion Illumina total prep kit (cat#: AMIL1791) according to the manufacturer's instructions.

extract_protocol: Total RNA from the hippocampus was isolated using the RNeasy Mini Kit (Qiagen). The quality and concentration of the total RNA was determined using a NanoDrop Spectrophotometer (A260:A280 and A260:A230 ratios).

tag: sample section

value: C

tag: hybridisation day

tag: age(weeks)

tag: grown with

value: TPM

tag: genotype


title: 2155_222_1_Cortex

source_name: Cortex

value: H

value: WILD


title: 2359_129_2_Cortex

value: B


title: 1461_130_1_Cortex

value: A

value: TAU


title: 2351_135_1_Cerebellum

value: F


title: 2425_251_1_Cortex

value: G


title: 1149_91_1_Cerebellum


title: 2339_132_1_Cerebellum


title: 2338_132_1_Cerebellum


title: EpiSC with Vehicle, biological rep1

tag: strain


title: 832_59_1_Cerebellum

value: E


title: 460_29_1_Cerebellum


title: 835_59_1_Cerebellum


title: 1473_132_1_Cortex


title: 1817_156_2_Cerebellum

value: D


title: 2443_255_1_Cerebellum


title: 1474_132_1_Cortex


title: 2376_133_2_Cortex


title: 2357_129_2_Cortex


title: 509_35_1_Cerebellum


title: 1462_130_1_Cerebellum


title: 451_52_1_Cerebellum


title: 1808_Cortex


title: 1150_91_1_Cerebellum


title: 2306_178_1_Cortex


title: 1108_118_1_Cortex


title: 2393_135_2_Cortex


title: Stem75, biological rep2

description:
Stem75_2
Triticale (x Triticosecale Wittmack cv. Certa) Stem75_2

value: AC Certa

tag: tissue

value: Stem


title: 809_86_1_Cerebellum


title: 493_23_1_Cerebellum


title: 1494_136_1_Cortex


title: 1838_149_2_Cortex


title: 1818_156_2_Cerebellum


title: 810_86_1_Cerebellum


title: 1804_Cortex


title: 478_27_1_Cortex


title: 2424_251_1_Cerebellum


title: 2125_215_1_Cortex


title: 2306_178_1_Cerebellum


title: 1473_132_1_Cerebellum


title: 2391_247_1_Cortex


title: 1463_130_1_Cortex


title: 2187_210_1_Cortex


title: 2374_133_2_Cortex


title: 2152_222_1_Cortex


title: 2423_Cerebellum


title: 2331_131_1_Cerebellum


title: 1809_153_3_Cortex


title: 454_52_1_Cerebellum


title: 2337_132_1_Cerebellum


title: 2440_255_1_Cerebellum


title: 154_Cortex


title: 2297_177_1_Cortex


title: 833_59_1_Cerebellum


title: 966_94_1_Cerebellum


title: 2330_131_1_Cerebellum


title: 1811_153_3_Cortex


title: 809_86_1_Cortex


title: 2431_254_1_Cortex


title: 510_35_1_Cerebellum


title: 452_52_1_Cerebellum


title: 97_9_1_Cortex


title: 1810_Cortex


title: 476_27_1_Cerebellum


title: 2438_Cerebellum


title: 2399_Cortex


title: 475_27_1_Cerebellum


title: 510_35_1_Cortex


title: 2320_129_1_Cortex


title: 2336_132_1_Cerebellum


title: 2153_222_1_Cortex


title: 2423_Cortex


title: 2357_129_2_Cerebellum


title: 1461_130_1_Cerebellum


title: 2341_133_1_Cerebellum


title: 1816_156_2_Cerebellum


title: 834_59_1_Cerebellum


title: 2418_250_1_Cerebellum


title: 2393_247_1_Cortex


title: 1472_132_1_Cortex


title: 2417_250_1_Cerebellum


title: 1824_Cortex


title: 2335_132_1_Cerebellum


title: 2442_255_1_Cortex


title: 113_13_1_Cortex


title: 2350_135_1_Cerebellum


title: 2392_247_1_Cortex


title: 2415_250_1_Cortex


title: 1462_130_1_Cortex


title: 1826_158_4_Cortex


title: 1160_94_1_Cerebellum


title: 2416_250_1_Cerebellum


title: 1825_158_4_Cortex


title: 810_86_1_Cortex


title: 2443_255_1_Cortex


title: 2342_133_1_Cerebellum


title: 967_94_1_Cerebellum


title: 2434_254_1_Cortex


title: 2424_251_1_Cortex


title: 2360_129_2_Cerebellum


title: 2343_133_1_Cerebellum


title: 492_23_1_Cortex


title: 116194_1_Cerebellum


title: 968_94_1_Cerebellum


title: 2319_129_1_Cortex


title: 2376_133_2_Cerebellum


title: 2314_179_1_Cortex


title: 812_86_1_Cortex


title: 2154_222_1_Cerebellum


title: 2344_133_1_Cerebellum


title: 2398_Cortex


title: 811_86_1_Cortex


title: 969_94_1_Cerebellum


title: 2351_135_1_Cortex


title: 1106_118_1_Cerebellum


title: 1145_90_1_Cerebellum


title: 2439_255_1_Cortex


title: 493_23_1_Cortex


title: 2350_135_1_Cortex


title: 1475_132_1_Cerebellum


title: 1150_91_1_Cortex


title: 2418_250_1_Cortex


title: 2375_133_2_Cerebellum


title: 509_35_1_Cortex


title: 2337_132_1_Cortex


title: 1809_153_3_Cerebellum


title: 2416_250_1_Cortex


title: 835_59_1_Cortex


title: 2398_Cerebellum


title: 2335_132_1_Cortex


title: 1160_94_1_Cortex


title: 1819_156_2_Cerebellum


title: 2154_222_1_Cortex


title: 2374_133_2_

source_name: HIP


title: 1106_118_1_Cortex


title: 1475_132_1_Cortex


title: 1107_118_1_Cerebellum


title: 2417_250_1_Cortex


title: 1839_149_2_Cortex


title: 2099_211_1_Cerebellum


title: 2358_129_2_Cortex


title: 811_86_1_Cerebellum


title: 2434_254_1_Cerebellum


title: 1105_118_1_Cortex


title: 1804_Cerebellum


title: 1494_136_1_Cerebellum


title: 2314_179_1_Cerebellum


title: 834_59_1_Cortex


title: 454_52_1_Cortex


title: 1474_132_1_Cerebellum


title: 2152_222_1_Cerebellum


title: 2425_251_1_Cerebellum


title: 492_23_1_Cerebellum


title: 966_94_1_Cortex


title: 2336_132_1_Cortex


title: 1808_Cerebellum


title: 1108_118_1_Cerebellum


title: 2359_129_2_Cerebellum


title: 2341_133_1_Cortex


title: 2375_133_2_Cortex


title: 2391_247_1_Cerebellum


title: 1816_156_2_Cortex


title: 2393_135_2_Cerebellum


title: 2440_255_1_Cortex


title: 451_52_1_Cortex


title: 2331_131_1_Cortex


title: 2330_131_1_Cortex


title: 2443


title: 1151_91_1_Cerebellum


title: 2098_211_1_Cerebellum


title: 2297


title: 1826


title: 1804


title: 969


title: 2376


title: 2393TPM


title: 834_H


title: 2320


title: 2391


title: 2424


title: 1473


title: 812


title: 2341


title: 2423


title: 2337


title: 509


title: 2392


title: 2319


title: 1838


title: 1474


title: 2338_H


title: 2417


title: 510


title: 2350


title: 1150


title: 2125


title: 966


title: 451


title: 2153


title: 2351_H


title: 1811


title: 453


title: 2152


title: 1107


title: 452


title: 1161


title: 475


title: 2339


title: 1817


title: 460


title: 2434_H


title: 1108


title: 1160


title: 2442


title: 1494


title: 2399


title: 2398


title: 1816


title: 2431


title: 2306


title: 2418


title: 968


title: 833_H


title: 832_H


title: 967


title: 1475


title: 116194_1_Cortex


title: 967_94_1_Cortex


title: 2314


title: 1811_153_3_Cerebellum


title: 968_94_1_Cortex


title: 1839


title: 2431_254_1_Cerebellum


title: 1151


title: 2342_133_1_Cortex


title: 475_27_1_Cortex


title: 1810_Cerebellum


title: 2155_222_1_Cerebellum


title: 2415_250_1_Cerebellum


title: 2343_133_1_Cortex


title: 460_29_1_Cortex


title: 1145_90_1_Cortex


title: 2392_247_1_Cerebellum


title: 969_94_1_Cortex


title: 97_9_1_Cerebellum


title: 2153_222_1_Cerebellum


title: 154_Cerebellum


title: 1826_158_4_Cerebellum


title: 1817_156_2_Cortex


title: 476_27_1_Cortex


title: 2442_255_1_Cerebellum


title: 2438_Cortex


title: 1819_156_2_Cortex


title: 832_59_1_Cortex


title: 2358_129_2_Cerebellum


title: 1463_130_1_Cerebellum


title: 2339_132_1_Cortex


title: 1105_118_1_Cerebellum


title: 1839_149_2_Cerebellum


title: 2338_132_1_Cortex


title: 1149_91_1_Cortex


title: 1824_Cerebellum


title: 1825_158_4_Cerebellum


title: 2360_129_2_Cortex


title: 1838_149_2_Cerebellum


title: 452_52_1_Cortex


title: 2438


title: 2359


title: 1818_156_2_Cortex


title: 2125_215_1_Cerebellum


title: 453_52_1_Cortex


title: 113_13_1_Cerebellum


title: 2335


title: 833_59_1_Cortex


title: 1824


title: 2187


title: 2374_133_2_Cerebellum


title: Japanese flounder_PBS_12h_2

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was scanned with a Agilent G2565CA scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.5.1 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: kidney, 12 hours, PBS

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

extract_protocol: Total RNA was extracted from fish kidneys using the RNeasy Mini Kit.

treatment_protocol: Fish were treated with E. tarda FKC, S. iniae FKC and PBS (control).

value: kidney


title: 1463


title: Japanese flounder_PBS_12h_4


title: 810


title: 2344_133_1_Cortex


title: Japanese flounder_PBS_12h_3


title: 2098


title: Japanese flounder_PBS_12h_1


title: 2343


title: Japanese flounder_PBS_6h_3

source_name: kidney, 6 hours, PBS


title: 1809


title: Japanese flounder_S. iniae FKC_12h_2

source_name: kidney, 12 hours, S. iniae FKC


title: Japanese flounder_S. iniae FKC_12h_4


title: Japanese flounder_PBS_6h_2


title: Japanese flounder_PBS_6h_1


title: 2415


title: Japanese flounder_PBS_6h_4


title: 492


title: 1818


title: 2357


title: Japanese flounder_S. iniae FKC_12h_1


title: 2440


title: Japanese flounder_S. iniae FKC_6h_3

source_name: kidney, 6 hours, S. iniae FKC


title: 1105


title: 1461


title: 2154


title: 2336


title: 454


title: 2330


title: Japanese flounder_E. tarda FKC_12h_3

source_name: kidney, 12 hours, E. tarda FKC


title: 476


title: Japanese flounder_E. tarda FKC_6h_2

source_name: kidney, 6 hours, E. tarda FKC


title: Japanese flounder_S. iniae FKC_12h_3


title: Japanese flounder_S. iniae FKC_6h_1


title: 1145


title: 2360


title: Japanese flounder_E. tarda FKC_12h_2


title: 2425


title: Japanese flounder_E. tarda FKC_12h_1


title: Japanese flounder_E. tarda FKC_12h_4


title: 113


title: Japanese flounder_E. tarda FKC_6h_1


title: 1825


title: 2416


title: 493


title: 811


title: 2099


title: 1810


title: Japanese flounder_S. iniae FKC_6h_2


title: 1149


title: Japanese flounder_E. tarda FKC_6h_3


title: MelCLRefMixB vs. WM2664 MelCL

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

institute: UCLA

hyb_protocol: In comparison of expression between each melanoma cell line and a reference mix pool composed of equal amount of selected 47 different melanoma cell line (refer to ch2: Sample included in Reference Yes/No column). 825 ng each of labeled reference mix  (Mel-RefMixB,cy3 label) and individual melanoma cell  line(cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent G2505C scanner with extended dynamic range Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing:
Agilent Feature Extraction Software (v10.7.3.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging

source_name: MelCLRefMixB

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

growth_protocol:
Melanoma cell lines were cultured in RPMI (Life Technologies) supplemented with penicillin/streptomycin and fetal bovine serum (FBS).
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were characterized using mtDNA sequence prior to use

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol

tag: ref

value: mixed reference pool containing equal amounts of 47 melanoma cell lines.

tag: cell line

value: Melanoma Cell line

tag: sample included in reference yes/no

value: Yes


title: MelCLRefMixB vs. WM1366 MelCL


title: 1472

value: C


title: MelCLRefMixB vs. SKMEL31 MelCL

value: No


title: MelCLRefMixB vs. WM115 MelCL


title: MelCLRefMixB vs. SKMEL5 MelCL


title: MelCLRefMixB vs. TE353SK MelCL


title: 2344

value: TPM


title: MelCLRefMixB vs. SKMEL173 MelCL


title: MelCLRefMixB vs. SKMEL24 MelCL


title: 2375


title: 1106


title: MelCLRefMixB vs. SKMEL1 MelCL


title: MelCLRefMixB vs. SBCL2 MelCL


title: 2393TAS10

value: H

value: WILD


title: 154

value: B


title: MelCLRefMixB vs. SKMEL2 MelCL


title: MelCLRefMixB vs. SKMEL28 MelCL


title: MelCLRefMixB vs. S117 MelCL


title: MelCLRefMixB vs. S19 MelCL


title: MelCLRefMixB vs. SKMEL3 MelCL


title: 2342


title: MelCLRefMixB vs. M375 MelCL


title: 1808

value: TAU


title: MelCLRefMixB vs. Malme 3M MelCL

description: Malme 3M

source_name: Malme 3M

value: Malme 3M


title: 2439


title: 97


title: 2358

value: G


title: MelCLRefMixB vs. M368 MelCL


title: MelCLRefMixB vs. M299 MelCL


title: MelCLRefMixB vs. M321 MelCL


title: MelCLRefMixB vs. M328 MelCL


title: 2331

value: F


title: 835_H


title: MelCLRefMixB vs. M318 MelCL


title: Tumor_LP_WT_2

city: Iowa City

first: Weizhou

last: Zhang

state: IA

address: 100 Medical Laboratories

department: Pathology

institute: The University of Iowa

description:
CD24hiCD49flowCD61+
Z-12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: tumor from WT LP

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tumor initiating cells

value: WT luminal progenitors

value: FVB/N


title: 2155

value: E


title: Tumor_MYO_WT_2

description:
CD24lowCD49flow
Z-11

source_name: tumor from WT MYO

value: WT myoepithelial cells


title: MelCLRefMixB vs. M297 MelCL

value: mixed reference pool containing equal amounts of 47 melanoma cell lines.


title: Tumor_MSC_WT_1

description:
CD24lowCD49fhi
Z-10

source_name: tumor from WT MSC

value: WT mammary stem cells


title: MelCLRefMixB vs. M308 MelCL

value: Melanoma Cell line

value: Yes


title: Tumor_MSC_WT_5

description:
CD24lowCD49fhi
Z-09


title: MelCLRefMixB vs. M296 MelCL


title: MelCLRefMixB vs. M263 MelCL


title: MelCLRefMixB vs. M260 MelCL


title: MelCLRefMixB vs. M285 MelCL


title: Tumor_MSC_WT_2

description:
CD24lowCD49fhi
Z-07


title: MelCLRefMixB vs. M262 MelCL


title: MelCLRefMixB vs. M275 MelCL


title: Tumor_LP_AA_1

description:
CD24hiCD49flowCD61+
Z-08

source_name: tumor from AA LP

value: Luminal progenitors from IKKa-AA mice


title: Tumor_LP_AA_2

description:
CD24hiCD49flowCD61+
Z-06


title: MelCLRefMixB vs. M288 MelCL


title: 1819

value: D


title: MelCLRefMixB vs. M257 MelCL


title: Tumor_MYO_WT_1

description:
CD24lowCD49flow
Z-05


title: 1462

value: C


title: MelCLRefMixB vs. M249 MelCL


title: MelCLRefMixB vs. M255 MelCL

value: No


title: 809

value: B


title: 1107_118_1_Cortex


title: MelCLRefMixB vs. M245 MelCL


title: Tumor_MYO_WT_5

description:
CD24lowCD49flow
Z-04


title: MelCLRefMixB vs. M243 MelCL


title: 2399_Cerebellum

value: WILD


title: Tumor_LP_WT_5

description:
CD24hiCD49flowCD61+
Z-03


title: 478

value: A


title: MelCLRefMixB vs. M233 MelCL


title: Tumor_LP_AA_4

description:
CD24hiCD49flowCD61+
Z-02


title: MelCLRefMixB vs. M230 MelCL


title: 812_86_1_Cerebellum

value: H


title: MelCLRefMixB vs. M202 MelCL


title: MelCLRefMixB vs. M229 MelCL


title: MelCLRefMixB vs. M238 MelCL


title: MelCLRefMixB vs. M14 MelCL


title: 2320_129_1_Cerebellum

value: TPM


title: MelCLRefMixB vs. M207 MelCL


title: 2319_129_1_Cerebellum


title: MelCLRefMixB vs. G361 MelCL


title: MelCLRefMixB vs. M244 MelCL


title: MelCLRefMixB vs. HS895SK MelCL


title: 2439_255_1_Cerebellum


title: MelCLRefMixB vs. A375 MelCL


title: Tumor_LP_WT_1

description:
CD24hiCD49flowCD61+
Z-01

value: WT luminal progenitors


title: MelCLRefMixB vs. Colo829 MelCL


title: MelCLRefMixB vs. CHL MelCL

description: CHL

source_name: CHL

value: CHL


title: Donor 3 TLR8 agonist

city: Columbus

first: Jonathan

middle: P

last: Butchar

state: OH

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

hyb_protocol: Affymetrix hybridization

scan_protocol: Affymetrix scanning

data_processing: R and BioConductor, using gcrma to calculate expression values on all chips simultaneously, and limma to test for differential expression

source_name: monocytes

label_protocol: Affymetrix labeling

growth_protocol: Human monocytes isolated from Red Cross Leukopacks using CD14+ MACS, incubated in RPMI-1640 with 10% FBS, plus Pen/Strep and L-glutamine

extract_protocol: Trizol-based RNA extraction followed by Qiagen column cleanup

treatment_protocol: Overnight treatment with Vehicle (H20), with TLR7 agonist from 3M, or with TLR8 agonist (VTX-2337) from VentiRx, Seattle, WA

value: TLR8 agonist

tag: individual

value: deidentified donor 3

value: monocytes


title: Donor 3 untreated

value: untreated


title: Donor 3 TLR7 agonist

value: TLR7 agonist


title: 2099_211_1_Cortex


title: 1472_132_1_Cerebellum

source_name: Cerebellum

value: TAU


title: MelCLRefMixB vs. HS688(B)T MelCL

value: mixed reference pool containing equal amounts of 47 melanoma cell lines.

value: Melanoma Cell line

value: Yes


title: 2098_211_1_Cortex

source_name: Cortex

value: E


title: Donor 1 TLR7 agonist

value: deidentified donor 1


title: MODE-K cells_LPS_exo.r1

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

hyb_protocol: RNA-loaded BeadChips were placed into Hyb Chamber inserts and these were incubated in the Illumina Hybridization Oven for 18 hours at 58°C. BeadChips were then washed as follows: High Temperature wash, 1st Room Temp Wash, Ethanol Wash, 2nd Room Temp Wash, Block with E1 Buffer, *Detect Signal and 3rd Room Temp Wash. BeadChips were then centrifuged immediately to prevent surface evaporation, 1,400rpm at room temperature for 4 minutes.

scan_protocol: BeadChips were scanned on the iScan System (HiScan H166)

data_processing: The raw SampleProbeProfile file was processed within R, using ‘lumi’ and ‘lumiMouseAll.db’ Bioconductor packages.Raw expression values were processed with the Variance Stabilizing Transformation and the Robust Spline Normalization. An InterQuartile Range was calculated across all samples for each probe, and used to select the most variable probe of those that mapped to the same transcript. Probes without a gene or transcript annotation were excluded, leaving a total of 30,708 non-redundant annotated probes.

source_name: MODE-K in medium + LPS + exosomes

label_protocol: RNA was prepared for microarray analysis using the Ambion Illumina TotalPrep RNA Amplification kit.

growth_protocol: MODE-K cells were obtained from Dominique Kaiserlian (INSERM) and grown following standard protocol in DMEM (Invitrogen) medium supplemented with 10% Foetal Bovine Serum (Invitrogen), 1% penicillin-streptomycin (Lonza), 1% L-glutamine (Lonza), 1% non essential amino acids/sodium pyruvate  (Gibco).

extract_protocol: Total RNA was extracted using the miRNAeasy kit.

treatment_protocol: MODE-K cells were grown in DMEM media as described above and seeded into 24-well plates at 20,000 cells per well. The following day, cells were left untreated or treated with H. polygyrus-derived exosomes (5 ug total protein per well) in DMEM media for 20 hours in the absence or presence of 1 ug/mL LPS, after which cells were washed twice with PBS.

tag: cell-line

value: MODE-K cells

value: LPS+exosomes


title: MODE-K cells_LPS.r1

source_name: MODE-K in medium + LPS

value: LPS


title: MelCLRefMixB vs. A2058 MelCL


title: MODE-K cells_LPS_exo.r3


title: 2393_247_1_Cerebellum

value: D

value: WILD


title: MODE-K cells_exo.r3

source_name: MODE-K in medium + exosomes

value: exosomes


title: Donor 2 untreated

value: deidentified donor 2


title: 1151_91_1_Cortex

value: F


title: Donor 1 untreated

value: monocytes


title: MODE-K cells_LPS.r3


title: Donor 2 TLR7 agonist


title: MODE-K cells_LPS_exo.r2


title: MODE-K cells_exo.r1


title: MODE-K cells_LPS.r2


title: MODE-K cells_exo.r2


title: MODE-K cells_med.r3

source_name: MODE-K in medium


title: Donor 1 TLR8 agonist

value: TLR8 agonist


title: MODE-K cells_med.r2


title: Macrophages infected with Mtb H37Rv: 24h post-infection (replicate) vs. untreated

status: Public on Dec 23 2014

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

institute: Bose Institute

hyb_protocol: Agilent's In situ Microarray Hybridization Chamber Kit (G2534A)

scan_protocol: Microarray slides were scanned using an Agilent microarray scanner at 3 micron resolution.

data_processing: Microarray data was normalized and analysed using using GeneSpring GX version 11.0 and Microsoft Excel.

source_name: treated RAW264.7 with H37Rv, 24 hr post-infection

label_protocol: T7 RNA polymerase amplification to generate labeled complementary RNA. Treated: Cy5; Untreated: Cy3

growth_protocol: RAW264.7 cells were grown in DMEM supplemented with 10% FBS at 37 degrees C in 5% CO2.

extract_protocol: RNA was isolated using the Ambion miRVana RNA isolation kit.

treatment_protocol: Cells were infected with Mtb H37Rv at an MOI of 10 for 4 h, washed and RNA was isolated 4 and 24 h post-infection.

tag: infected with

value: M. tuberculosis H37Rv (Mtb)

tag: time point

value: 24hr post infection

source_name: Untreated RAW264.7 cells

value: none (untreated control)


title: Exercised biol.replicate 8

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

description: Exercised: Biological replicate 8

hyb_protocol: Overnight hybridization (17 hrs, 65ºC and 10 rpm rotation) was performed in a Microrarray Hybridization Oven (Agilent Technologies). After hybridization, microrarrays were washed with Gene Expression Wash Buffers 1 and 2 (Agilent Technologies).

scan_protocol: Microrarrays were scanned using the High-Resolution Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction Software 10.7.3.1 (Agilent Technologies) was used for spot to grid alignment, feature extraction and quantification. Processed data were subsequently imported into GeneSpring GX 11.5 (Agilent Technologies).

organism: Danio rerio

source_name: Fast muscle_exercised_8

label_protocol: RNA was amplified and labeled with Cy3 dye using the single color Low Input Quick Amp Labeling kit (Agilent Technologies) following the manufacturer’s indications using 200 ng of RNA in each reaction. Next, 1,65 ng of labeled cRNA were hybridized to the arrays.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Experiments complied with the current laws of the Netherlands and were approved by the animal experimental committee (DEC number 09161).

extract_protocol: After 20 experimental days, fish were anesthetised with 1 ml clove oil (10% in absolute ethanol) in 1 liter of fresh water and euthanized by decapitation. Dorsal epaxial fast muscle filets were dissected and either immediately stored at -20ºC in RNA later (Ambion) for microarray analyses. Total RNA from fast skeletal muscle samples of individual adult zebrafish was isolated with TRIzol (Invitrogen, Spain) according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Exercised adult zebrafish swam at Uopt (0.4 m/s) for 6 hours per day during 20 experimental days while non-exercised zebrafish rested at a lower swimming speed of 0.1 m/s.

value: fast muscle

tag: developmental stage

value: Adult

tag: groups

value: Exercised


title: Macrophages infected with Mtb H37Rv: 24 h post-infection vs. untreated


title: Exercised biol.replicate 5

description: Exercised: Biological replicate 5

source_name: Fast muscle_exercised_5


title: Exercised biol.replicate 1

description: Exercised: Biological replicate 1

source_name: Fast muscle_exercised_1


title: Non-exercised  biol. replicate 8

description: Non-exercised: Biological replicate 8

source_name: Fast muscle_non-exercised_8

value: Non-exercised


title: Exercised biol.replicate 6

description: Exercised: Biological replicate 6

source_name: Fast muscle_exercised_6


title: Exercised biol.replicate 2

description: Exercised: Biological replicate 2

source_name: Fast muscle_exercised_2


title: Exercised biol.replicate 7

description: Exercised: Biological replicate 7

source_name: Fast muscle_exercised_7


title: Non-exercised  biol. replicate 4

description: Non-exercised: Biological replicate 4

source_name: Fast muscle_non-exercised_4


title: Macrophages infected with Mtb H37Rv: 4 h post-infection (replicate) vs. untreated

source_name: treated RAW264.7 with H37Rv, 4 hr post-infection

value: 4hr post infection


title: Han/Wistar_Hypothalamus_CornOil_rep4

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

data_processing: Quantitated array data (CEL files) were loaded into the R statistical environment (v3.1.0) using the affy package (v1.42.2) of the BioConductor library. Data was pre-processed with the RMA algorithm (Irizarry et al. NAR) and probes were mapped to Entrez Gene Ids using the rat2302rnentrezgcdf (v18.0.0) package in R.

organism: Rattus norvegicus

growth_protocol: Animals were grown in a 12h/12h light/dark cycle, housed singly in suspended stainless-steel wire-mesh cages with pelleted R36 feed and tap water. The housing environment was maintained at 21 +/- 1 degree Celcius with relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Lipid Tissue Mini kits according to the manufacturer's instructions. Total RNA was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with either 100 ug/kg TCDD in corn oil vehicle or corn oil alone by oral gavage.

value: Han/Wistar

tag: gender

value: male

tag: age

value: 15-16 weeks

tag: tcdd dose

value: 0 ug/kg

tag: vehicle

value: corn oil

tag: exposure length

value: 23 hours


title: Control embryos replicate 1

city: Barcelona

description: Control: Biological replicate 1

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were injected at the single cell stage with 3.1 ng of zfglut2 translational start site blocking morpholino (5'-ACTGCTTCTCCATTTTGCATGAAGT-3') in 1× Danieau buffer (58mM NaCl, 0.7mM KCl, 0.4mM MgSO4, 0.6mM Ca(NO3)2, 5.0mM N-2-hydroxyethylpiperazine-N ́-2-ethanesulfonic acid; pH 7.6) containing 1% phenol red (Sigma-Aldrich). A standard control morpholino (5′-CCTCTTACCTCAGTTACAATTTATA-3′) (Gene Tools LLC) was used as negative control.  At 72 hpf pools of 20 embryos per treatment group were snap-frozen in liquid nitrogen.

value: Embryo (24 hpf)

value: Control


title: Han/Wistar_Hypothalamus_CornOil_rep1

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

tag: strain


title: Non-exercised  biol. replicate 6

description: Non-exercised: Biological replicate 6

source_name: Fast muscle_non-exercised_6

tag: tissue


title: Morphant embryos replicate 2

description: Morphant: Biological replicate 2

value: Morphant


title: Exercised biol.replicate 4

description: Exercised: Biological replicate 4

source_name: Fast muscle_exercised_4


title: Non-exercised  biol. replicate 2

description: Non-exercised: Biological replicate 2

source_name: Fast muscle_non-exercised_2


title: Non-exercised  biol. replicate 5

description: Non-exercised: Biological replicate 5

source_name: Fast muscle_non-exercised_5


title: Control embryos replicate 3

description: Control: Biological replicate 3


title: Morphant embryos replicate 3

description: Morphant: Biological replicate 3


title: Non-exercised  biol. replicate 7

description: Non-exercised: Biological replicate 7

source_name: Fast muscle_non-exercised_7


title: Control embryos replicate 2

description: Control: Biological replicate 2


title: Non-exercised  biol. replicate 1

description: Non-exercised: Biological replicate 1

source_name: Fast muscle_non-exercised_1


title: Macrophages infected with Mtb H37Rv: 4 h post-infection vs. untreated

value: M. tuberculosis H37Rv (Mtb)


title: Han/Wistar_Hypothalamus_TCDD_rep1

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

value: 100 ug/kg


title: Donor 2 TLR8 agonist

source_name: monocytes

tag: treatment

value: TLR8 agonist

value: deidentified donor 2

tag: cell type

value: monocytes


title: Han/Wistar_Hypothalamus_CornOil_rep2


title: Han/Wistar_Hypothalamus_TCDD_rep3


title: Han/Wistar_Hypothalamus_TCDD_rep2


title: Han/Wistar_Hypothalamus_TCDD_rep4


title: Long-Evans_Hypothalamus_CornOil_rep4

value: Long-Evans

value: 16-22 weeks


title: Non-exercised  biol. replicate 3

description: Non-exercised: Biological replicate 3

source_name: Fast muscle_non-exercised_3

value: fast muscle

value: Adult

value: Non-exercised


title: Han/Wistar_Hypothalamus_CornOil_rep3

value: Han/Wistar

value: male

value: 15-16 weeks


title: Long-Evans_Hypothalamus_TCDD_rep2

value: corn oil

value: 23 hours


title: Exercised biol.replicate 3

description: Exercised: Biological replicate 3

source_name: Fast muscle_exercised_3

value: Exercised


title: Long-Evans_Hypothalamus_TCDD_rep3


title: Long-Evans_Hypothalamus_TCDD_rep4


title: Long-Evans_Hypothalamus_TCDD_rep1


title: A549_IP_mivaRNAI-137(G)_rep2

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description:
RNA isolated from immunopurified RISC
Adherent human lung cancer cell line (ATCC CCL-185)

hyb_protocol: Between 0.6 and 3.0 µg fragmented and labeled DNA was hybridized to an Affymetrix Human Gene 1.1 ST Array. Hybridization and washing was performed according to the instructions of the manufacturer.

scan_protocol: Scanning was performed on an Affymetrix GeneTitan® system.

data_processing: Normalization was done using the RMA algorithm with the Affymetrix GeneChip Expression Console Software

label_protocol: 2 µg RNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by terminal labeling with biotin using the “WT Terminal Labeling Kit” (Affymetrix, Inc., Santa Clara, CA, USA) according to the instructions of the manufacturer.

growth_protocol: Adherent monolayers, maintained in DMEM supplemented with 10% fetal calf serum at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was extrated using TRIzol according to the manufacturer's instructions (Life Technologies).

treatment_protocol: Cells were transfected with 10 nM mivaRNAI(G)-137 mimic and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 24h.

tag: cell line

tag: cell origin

value: lung epithelial cell


title: Morphant embryos replicate 1

description: Morphant: Biological replicate 1

value: Embryo (24 hpf)

value: Morphant


title: A549_Ad5_IP_rep1

treatment_protocol: Cells were infected with human adenovirus 5 at an MOI of 30 TCID50/cell and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 30h.


title: A549_mock_IP_rep2

description: Adherent human lung cancer cell line (ATCC CCL-185)

treatment_protocol: Cells were mock-infected and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 30h.


title: A549_IP_control_rep2

treatment_protocol: Cells were transfected with 10 nM negative control siRNA and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 24h.


title: A549_IP_mivaRNAI-137(G)_rep1


title: A549_IP_mivaRNAI-137(A)_rep2

treatment_protocol: Cells were transfected with 10 nM mivaRNAI(A)-137 mimic and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 24h.


title: A549_IP_mivaRNAI-137(G)_rep3


title: A549_IP_control_rep3


title: A549_Ad5_input_rep2


title: A549_mock_IP_rep1


title: A549_input_mivaRNAI-137(G)_rep2


title: A549_input_mivaRNAI-137(A)_rep2


title: A549_input_mivaRNAI-137(A)_rep1


title: Long-Evans_Hypothalamus_CornOil_rep1

value: 0 ug/kg


title: A549_input_mivaRNAI-137(G)_rep1


title: A549_Ad5_input_rep1


title: A549_input_mivaRNAI-137(A)_rep3


title: Long-Evans_Hypothalamus_CornOil_rep2


title: A549_IP_mivaRNAI-137(A)_rep1


title: A549_input_control_rep2


title: Long-Evans_Hypothalamus_CornOil_rep3


title: A549_IP_control_rep1


title: A549_input_control_rep3


title: A549_input_mivaRNAI-137(G)_rep3


title: A549_IP_mivaRNAI-137(A)_rep3


title: A549_input_control_rep1


title: A549_Ad5_IP_rep2


title: TNF_6D_biological rep1

city: Boston

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) with Background correction using default analysis settings with log2 transformation and quantile normalization. Linear model is fit to normalized data to obtain expression measure for each probe set on each array.

source_name: Differentiated 3T3-L1 adipocytes, TNF-alpha, 6d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3T3-L1 preadipocytes were differentiated for 14 days.

extract_protocol: Total RNA was extracted from cells or tissues using TRIzol Reagent according to the manufacturer’s instructions.

treatment_protocol: Treatment was started 2H, 24H, 6D, or 0h (CTL) prior to harvesting for RNA.

value: in vitro cultured adipocytes

value: tumor necrosis factor-alpha


title: TNF_2H_biological rep3

source_name: Differentiated 3T3-L1 adipocytes, TNF-alpha, 2h


title: TNF_2H_biological rep1


title: TNF_6D_biological rep2


title: TNF_24H_biological rep3

source_name: Differentiated 3T3-L1 adipocytes, TNF-alpha, 24h


title: TNF_24H_biological rep2


title: TNF_2H_biological rep2


title: Dex_6D_biological rep1

source_name: Differentiated 3T3-L1 adipocytes, Dex, 6d

value: dexamethasone


title: Dex_24H_biological rep2

source_name: Differentiated 3T3-L1 adipocytes, Dex, 24h


title: Dex_24H_biological rep3


title: Dex_6D_biological rep3


title: Dex_6D_biological rep2


title: TNF_24H_biological rep1


title: CTL, biological rep3

source_name: Differentiated 3T3-L1 adipocytes, control, 0h

value: control


title: Dex_24H_biological rep1


title: TNF_6D_biological rep3


title: Dex_2H_biological rep1

source_name: Differentiated 3T3-L1 adipocytes, Dex, 2h


title: Dex_2H_biological rep3


title: Dex_2H_biological rep2


title: Tooth Germs at E50

city: Beijing

first: Fu

last: Wang

address: Tian Tan Xi Li No.4, P. R. China

country: China

institute: Capital Medical University

description: Gene expression data from tooth germs at E50

hyb_protocol: Array hybridization and washes were performed as detailed in the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the GeneChip® scanner 3000 (Affymetrix, CA, US).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Sus scrofa

source_name: Last tooth germs in mandible at embryos E50

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (GeneChip®3'IVT Express Kit user manual,  Affymetrix).

growth_protocol: The staged miniature pig embryos were obtained at room temperature (RT) by cesarean section at E40, E50, and E60.  The last deciduous molar germs, including the dental lamina in mandibles from the same litter were isolated and pooled at 4C

extract_protocol: Total RNA was extracted from samples at specific stages using TRIZOL Reagent following the manufacturer’s instructions.

treatment_protocol: last deciduous molar germs, including the dental lamina in mandibles from the same litter were isolated and pooled, then immerged in 5–10 volumes of RNAlater solution (Ambion, USA) and incubated overnight at 4°C, and then stored at –20°C until needed for total RNA extraction

value: Primary molar germ at bell stage with secondary dental lamina initiation

tag: breed

value: Wuzhishan miniature pigs


title: CTL, biological rep1


title: Tooth Germs at E40

description: Gene expression data from tooth germs at E40

source_name: Last tooth germs in mandible at embryos E40

value: Primary molar germ at cap stage without secondary dental lamina


title: Sulfodoxine-Pyrimethamine_treated_kidney_R

city: Lucknow

first: Shrawan

middle: Kumar

last: Mishra

address: MG Marg,Chattar Manzil Palace

department: Toxicology

institute: CDRI

description: Mice (Mus musculus) were sacrificed and kidney were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Kidney samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 µg of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit (Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

hyb_protocol: The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer (Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA. The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0 at default settings.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Vehicle (DMSO)-treated control

label_protocol: CyScribe First Strand cDNA Labeling Kit Protocol.

growth_protocol: The animals were housed in plastic cages and acclimated to controlled conditions of light and dark (12 h each), and temperature (23±2ºC) for next 24 hrs. after drug administration. Access to food and water was ‘ad libitum’ before and after drug treatment.

extract_protocol: TRI Reagent protocol.

treatment_protocol: Vehicle (DMSO) treated.

value: Swiss albino

value: 8-10 weeks

value: kidney

value: vehicle (DMSO) control

source_name: Sulfodoxine-Pyrimethamine

treatment_protocol: Mice were treated with 300mg/kg bw of Sulfodoxine followed with 15 mg/kg bw of Pyrimethamine.

value: Sulfodoxine-Pyrimethamine


title: Amodiaquine+Sulfodoxine-Pyrimethamine_treated_kidney_R

value: male

source_name: Amodiaquine+Sulfodoxine-Pyrimethamine

treatment_protocol: Mice were treated with 120 mg/kg bw of Amodiaquine and 300mg/kg bw of Sulfodoxine followed with 15 mg/kg bw of Pyrimethamine.


title: Amodiaquine_treated_kidney_F

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. All the experiments were performed in duplicate. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data belonging to all the three doses to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Amodiaquine

treatment_protocol: Mice were treated with 120mg/kg bw of Amodiaquine.

value: Amodiaquine


title: CTL, biological rep2


title: Sulfodoxine-Pyrimethamine_treated_kidney_F


title: Tooth Germs at E60

description: Gene expression data from tooth germs at E60

source_name: Last tooth germs in mandible at embryos E60

value: Primary molar germ at secretory stage with secondary dental lamina


title: Amodiaquine+Sulfodoxine-Pyrimethamine_treated_kidney_F


title: Amodiaquine_treated_kidney_R

hyb_protocol: The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer (Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA. The samples were heated at 95 degree C for 3 minutes and  immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. All the experiments were performed in duplicate. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data to find probes with statistically significant p values (uncorrected) and fold-changes.


title: 13281

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description: 25W DEN + 5W αPlGF (treatment) tumour tissue

hyb_protocol: Purified and labeled cRNA (600 ng of Cy3 labeled cRNA) was hybridised on Agilent Sureprint G3 Mouse GE 8x60k Microarrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.7.3.1) after an additional quantile normalization. Intensities were base 2 log-transformed.

source_name: 25W DEN + 5W αPlGF tumour tissue

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Qiagen

value: 210 days

value: liver tumor

tag: induction

value: 25W diethylnitrosamine

value: 5 weeks αPlGF-treatment


title: Whole DRG tissue, biological replicate 1

first: Isaac

middle: M

last: Chiu

address: 3 Blackfan Circle

department: Neurology

institute: Boston Children's Hospital

description: RNA from whole homogenized tissue of pooled lumbar DRG samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr on Affymetrix mouse Gene ST version 1.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix CEL files were analyzed with the Robust Mutli-array Average (RMA) algorithm as the normalization method with quantile normalization, background correction, and median scalin. using the GenePattern (http://www.broadinstitute.org/cancer/software/genepattern) software platform.

source_name: DRG from WT C57BL/6 mice

label_protocol: 100 ng total RNA was amplified using the GeneChip WT cDNA syntehsis and amplification kit (Affymetrix).  cDNA synthsis, biotinylation of cRNA, fragmentation, and labeling was according to standard Affymetrix protocols.

growth_protocol: SNS-Cre mice were bred with Rosa26-TdTomato mice to generate SNS-Cre/TdTomato reporter mice.   Parv-Cre mice were bred with Rosa26-TdTomato mice to generate Parv-Cre/TdTomato mice. These strains of mice were used for FACS sorting of distinct DRG sensory neurons.  We also used WT C57BL/6 mice as a source of total DRG tissue RNA.

extract_protocol: RNA was extraced by sequential Qiazol extraction and Qiagen Rneasy micro column purification with genomic DNA digest.

treatment_protocol: Dorsal root ganglia (DRG) were dissected from adult mice (7-20 week old) of different fluorescent strains, treated with Collagenase/Dispase enzyme digestion for cell dissociation.   Total dorsal root ganglia (lumbar to thoracic segments) were dissected from mice and pooled for FACS sorting (3 mice were pooled/sample).  Flow cytometry and fluorescent gating strategies were used to isolate distinct subtypes of DRG somatosensory neurons, utilizing IB4-FITC surface staining, SNS-Cre/TdTomato, and/or Parv-TdTomato staining to set gates (TdTomato high expressing cells were sorted to obtain just cell bodies).  Ssurface IB4-FITC in combination with SNS-Cre/TdTomato labels non-peptidergic neurons (IB4+SNS-Cre/TdT+), with concurrent sorting of IB4- SNS-Cre lineage neurons (IB4-SNS-Cre/TdT+).

tag: genotype/variation

value: naïve C57BL/6

value: Whole DRG tissue


title: Whole DRG tissue, biological replicate 2


title: 13285


title: Isolectin B4 negative SNS-Cre/Tdtomato+ DRG neurons, biological replicate 3

description: RNA from Isolectin B4-FITC negative SNS-Cre/TdTomato FACS sorted neurons from pooled DRG samples

source_name: DRG from SNS-Cre/R26TdTomato mice

value: SNS-Cre/TdTomato+

value: FACS purified IB4 negative Dorsal root ganglia sensory neurons


title: 13284

description: 25W DEN + 5W IgG (control) tumour tissue

source_name: 25W DEN + 5W IgG tumour tissue

value: 5 weeks IgG-control


title: 13283

description: 25W DEN + 5W αPlGF (treatment) surrounding (non tumour) tissue

source_name: 25W DEN + 5W αPlGF surrounding tissue

value: liver (non-tumor)


title: 13280