title: BL cell line-5

description: Biological replicate 1 of 5. BL cell line Ramos harvested in exponential phase of growth

source_name: BL cell line Ramos, harvested in their exponential growth phase

value: PMID:181343; Epstein-Barr virus negative


title: BL cell line-3

status: Public on Sep 30 2015

type: RNA

city: Madrid

first: Miguel

middle: R

last: Campanero

address: Calle Arturo Duperier 4

department: Instituto de Investigaciones Biomedicas Alberto Sols

country: Spain

institute: Consejo Superior de Investigaciones Cientificas

description: Biological replicate 1 of 5. BL cell line DG-75 harvested in exponential phase of growth

hyb_protocol: Each of the 5 BL samples was mixed with the control pool and hybridized over night at 42ºC on Capital Bio 22K oligonucleotide arrays (Capitalbio V2.0). After hybridization, slides were washed following standard protocols.

scan_protocol: The arrays were scanned using a Capital Bio Luxscan 10K Scanner. From the raw tiff image the data was extracted using the software supplied with the scanner (Luxscan3 software)

data_processing: The analysis has been carried out on R statistical framework using the packages “marray” and “limma” for both stages of this analysis: preprocessing and quality control of the data and detection of differently expressed genes.    Data Pre-processing  All the arrays intensities, these are: sample, control, sample background and control background, were visualized to asset possible background irregularities. Background intensities were not homogeneous throughout the microarrays grids and the level of these intensities also varied between microarrays. To eliminate this effect and to make the 5 microarrays comparable, the following transformations have been applied:    1. Background correction. Method: subtraction.  2. Within array normalization. Method: print-tip normalization.  3. Between array normalization. Method: MAD scale transformation.    Statistical analysis  Lineal models as implemented by the “limma” package to find genes differentially expressed between the conditions were used.

molecule: total RNA

organism: Homo sapiens

source_name: BL cell line DG-75, harvested in their exponential growth phase

label_protocol: The RNA of the LCL cell lines X50-7, IB-4 and Dana were pooled in equimolar amount and labeled in Cy-3 as a universal control. The RNA from each BL cell line was labeled in Cy-5. All samples were labeled using the Ambion Aminoallyl Labeling kit, starting from 1 µg of total RNA.

growth_protocol: All cell lines were grown at 37ºC, 5% CO2 in RPMI supplemented with 10% FCS, 2mM glutamine, 100U/ml penicillin, and 100µg/ml streptomycin

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

tag: cell line

value: PMID:188769; Epstein-Barr virus negative

source_name: Pool of 3 LCL cell lines harvested in their exponential growth phase

value: Pool of Epstein-Barr virus positive cell lines X50-7 (PMID:3027963), IB-4 (PMID:6253674) and Dana (PMID:9001242)


title: distant normal_stage 4_#2

city: Changsha

first: xiayu

last: li

state: Hunan

address: Yuelu district, Tongzipo road #138

department: department of gastroenterology

country: China

institute: Xiangya third hospital

description: matched distant normal mucosa come from the same patient marked with identical sample name(I,II,III and IV stands for TNM stage 1,2,3 and 4,respectively, ca stands for tumor, n stands for normal mucosa);sample name with identical stage and number represent the same patient(for example, I-n-2 and I-ca-2 represent the normal mucosa and tumor from patient #2 of stage I,respectively).

hyb_protocol: Chips with labeled samples were hybridized at 56°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed using a miRCURY LNA™ washing buffer kit (Exiqon).

scan_protocol: Slides were scanned using a Genepix 4000B laser scanner (Axon, New York) and fluorescent intensities were extracted from the generated images by Genepix Pro 6.0 software (Axon).

data_processing: The repeatability of the microarray within each class ( normal, stage1,2,3 and 4) were examined by correlation analysis. Only those data with over 50% of intra-class correlation coefficient greater than 0.8 were selected for further analysis(Chen et al., 2007). Data filter: > 50% of the arrays and gene signal > 50 were selected. Normalization was done using per chip median normalization and median array method(Liu et al.,2004) .RVM F-test was applied to screen the dynamic differentially expressed miRNA for the normal and different TNM group(Wright et al., 2003).

source_name: colorectal distant normal mucosa, stage 4

label_protocol: 1 μg total RNA was labeled using a miRCURY LNA™ microRNA Hy3/Hy5 power labeling kit (Exiqon).

extract_protocol: On average, 100-150mg of flash frozen sample tissue were prepared for the extraction of total RNA. TRIZOL Reagent (Invitrogen ) were used to extract total RNA according to manufacturer's protocol

tag: tissue

value: colorectal distant normal mucosa

tag: histology

value: Normal mucosa

tag: age

tag: Sex

value: Female


title: distant normal_stage 4_#1

value: Male


title: distant normal_stage 3_#4

source_name: colorectal distant normal mucosa, stage 3


title: distant normal_stage 2_#5

source_name: colorectal distant normal mucosa, stage 2


title: distant normal_stage 1_#4

source_name: colorectal distant normal mucosa, stage 1


title: distant normal_stage 3_#2


title: distant normal_stage 2_#2


title: distant normal_stage 1_#2


title: distant normal_stage 3_#1


title: distant normal_stage 3_#3


title: distant normal_stage 2_#4


title: distant normal_stage 1_#3


title: distant normal_stage 2_#1


title: LCL_lowNMR_pair10242_rep3

city: Menlo Park

first: Aaron

last: Wacholder

state: CA

address: 333 Ravenswood Ave

department: Molecular Genetics Program

country: USA

institute: SRI International

hyb_protocol: Samples hybridized according to standard Affymetrix protocol using Affymetrix hybridization kit

scan_protocol: Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.  Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.  Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.  Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.  Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.

data_processing:
Probe data was generated using the RMA function in the Oligo R package from Bioconductor.  Probe data was generated using the RMA function in the Oligo R package from Bioconductor.
probe group file: HuGene-1_1-st-v1.r4.pgf
meta-probeset file: HuGene-1_1-st-v1.r4.mps

label: biotin

source_name: Lymphoblastoid cell line, low NMR

label_protocol: The cDNAs were fragmented with uracil DNA-deglycosylase and terminal labelled with biotin using Ambion® WT Expression Kit

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted from LCLs using Qiagen solid phase chemistry, treated with DNAse

treatment_protocol: Not applicable

tag: subject id

tag: twin pair id

tag: cell type

value: lymphoblastoid


title: LCL_lowNMR_pair10370_rep3


title: LCL_lowNMR_pair10242_rep2


title: LCL_highNMR_pair10821_rep3

source_name: Lymphoblastoid cell line, high NMR


title: LCL_lowNMR_pair10821_rep2


title: LCL_lowNMR_pair10821_rep3


title: LCL_highNMR_pair10242_rep2


title: LCL_highNMR_pair10242_rep3


title: LCL_highNMR_pair10821_rep2


title: LCL_highNMR_pair10402_rep2


title: LCL_lowNMR_pair10402_rep3


title: LCL_highNMR_pair10370_rep3


title: LCL_highNMR_pair10402_rep3


title: LCL_lowNMR_pair10402_rep2


title: LCL_lowNMR_pair10370_rep2


title: LCL_lowNMR_pair10402_rep1


title: LCL_highNMR_pair10370_rep2


title: LCL_highNMR_pair10821_rep1


title: LCL_lowNMR_pair10821_rep1


title: LCL_highNMR_pair10402_rep1


title: LCL_highNMR_pair10242_rep1


title: LCL_lowNMR_pair10242_rep1


title: overexpression DUSP2 vs. Ctrl_Replicate 1

city: Tainan

first: Shaw-Jenq

last: Tsai

address: 1 , University Road

department: Department of Physiology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 1 of 4

hyb_protocol: Base on Agilent two-color microarray-based gene expression analysis v5, samples were applied to microarrays enclosed in Agilent microarray hybridization chambers

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and rank consistant LOWESS normalization.

source_name: overexpression DUSP2_Replicate 1

label_protocol: 0.2mg RNA labeled with Cy3-CTP/ Cy5-CTP by Agilent low input qiuck amp labeling kit

growth_protocol: Hela cells grown on DMEM/F12 with 10%FBS

treatment_protocol: transient transfection of DUSP2-GFP or GFP-alone for 48 hours in HeLa cell

value: HeLa

value: cervical epithelioid carcinoma

source_name: control_Replicate 1


title: LCL_lowNMR_pair10370_rep1


title: overexpression DUSP2 vs. Ctrl_Replicate 4

description: Biological replicate 4 of 4

source_name: overexpression DUSP2_Replicate 4

source_name: control_Replicate 4


title: overexpression DUSP2 vs. Ctrl_Replicate 2

description: Biological replicate 2 of 4

source_name: overexpression DUSP2_Replicate 2

source_name: control_Replicate 2


title: LCL_highNMR_pair10370_rep1


title: T-ALL_Patient_16_ Givinostat_4

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

country: Italy

institute: University of Padua

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Microarray data (.CEL files) were normalized using the justRMA algorithm and analyzed using R-Bioconductor (Version 2.15.3).

label: Biotin

source_name: T-ALL,Givinostat, 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT Express Kit Technical Manual, 2008, Affymetrix).

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

treatment_protocol: Spleen extraction after 6 hour of tratment with Givinostat or Vehicle

value: T-ALL

tag: xenograft

tag: treatment

value: Givinostat


title: T-ALL_Patient_16_ Vehicle_5

source_name: T-ALL,vehicle, 6 hours

value: Vehicle


title: T-ALL_Patient_16_ Vehicle_3


title: T-ALL_Patient_16_ Givinostat_2


title: T-ALL_Patient_16_ Givinostat_3


title: overexpression DUSP2 vs. Ctrl_Replicate 3

description: Biological replicate 3 of 4

source_name: overexpression DUSP2_Replicate 3

source_name: control_Replicate 3


title: T-ALL_Patient_8_ Givinostat_4


title: T-ALL_Patient_16_ Givinostat_5


title: T-ALL_Patient_16_ Givinostat_1


title: T-ALL_Patient_8_ Givinostat_3


title: T-ALL_Patient_8_ Givinostat_2


title: T-ALL_Patient_16_ Vehicle_1


title: PC3+SostKO OB_2

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

description: gene expression data from PC3 cells co-cultured with SostKO osteoblasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array or Rat 230.2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Microarray data analysis was conducted using Bioconductor. Data preprocessing and normalization were performed using Robust Multi-chip Average (RMA) protocol. Genes differentially expressed between different conditions were identified using the empirical Bayes method implemented in Linear Models for MicroArray package.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PC3 cells, UMR-106 cells and primary osteoblasts were cultured in either a 12 well plate or a 3.0 µm pore transwell insert until cells reached 50% confluency in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. Then the media was changed to serum-free DMEM/F-12 media and the cells were cultured for 48 hours prior to RNA isolation.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini columns performed according to the manufacturer's instructions.

value: PC3 Prostate cancer cells


title: T-ALL_Patient_16_ Vehicle_2


title: PC3_control

description: gene expression data from PC3 cells cultured alone

source_name: PC3 cells cultured alone


title: T-ALL_Patient_16_ Vehicle_6


title: PC3+SostKO OB_1

source_name: PC3 cells co-cultured with SostKO osteoblasts


title: T-ALL_Patient_8_ Givinostat_5


title: T-ALL_Patient_8_ Givinostat_1


title: T-ALL_Patient_8_ Vehicle_5


title: T-ALL_Patient_16_ Vehicle_4


title: T-ALL_Patient_8_ Vehicle_6


title: T-ALL_Patient_8_ Givinostat_6


title: PC3+WT OB_2

description: gene expression data from PC3 cells co-cultured with WT osteoblasts

growth_protocol: PC3 cells, UMR-106 cells and primary osteoblasts were cultured in either a 12 well plate or a 3.0 µm pore transwell insert until cells reached 50% confluency in DMEM/F-12 media supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin.Then the media was changed to serum-free DMEM/F-12 media and the cells were cultured for 48 hours prior to RNA isolation.


title: PC3+WT OB_1

source_name: PC3 cells co-cultured with WT osteoblasts


title: T-ALL_Patient_8_ Vehicle_3


title: T-ALL_Patient_8_ Vehicle_4


title: T-ALL_Patient_9_ Givinostat_1


title: T-ALL_Patient_8_ Vehicle_1


title: T-ALL_Patient_9_ Vehicle_5


title: T-ALL_Patient_9_ Givinostat_5


title: T-ALL_Patient_9_ Vehicle_1


title: T-ALL_Patient_9_ Vehicle_4


title: T-ALL_Patient_9_ Givinostat_3


title: SOX2 expressing Biological Replicate 1

city: La Jolla

first: George

last: Sen

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

description: Cell transduced with SOX2

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing: Plier

source_name: SOX2 overexpressing cells used to regenerate human epidermis

growth_protocol: Human Primary Keratinocytes were grown in self-renewing condition using KSF-M (GIBCO-BRL) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: Keratinocytes were transduced with retroviral vectors to overexpress control LACZ or SOX2. These cells were then used to regenerate human epidermis.

value: SOX overexpression

value: Human Primary Keratinocytes


title: T-ALL_Patient_9_ Givinostat_2


title: T-ALL_Patient_9_ Givinostat_4


title: T-ALL_Patient_9_ Vehicle_3


title: T-ALL_Patient_8_ Vehicle_2


title: LACZ expressing control, Biological Replicate 2

description: Cell transduced with LACZ

source_name: Control Cells used to regenerate human epidermis

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

value: control


title: Ak3

city: omaha

first: Paras

middle: Kumar

last: Mishra

state: Nebraska

address: DRC1 Room 5047

department: Cellular and Integrative Physiology

institute: University of Nebraska medical center

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

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

data_processing: The data were analyzed with expression console and TAC software from Affymetrix using default analysis settings.

organism: Mus musculus

source_name: Heart tissue (Akita)

label_protocol: 150ng RNA was used from each sample. WT plus labelling kit from affymetrix was used for labelling the RNA.

extract_protocol: RNA was isolated from fresh heart tissue using mirVana kit.

tag: genotype

value: Mutation in Insulin 2 gene. Type 1 diabetic model.

value: heart

value: Male (12 week)

tag: genetic background


title: LACZ expressing Control, Biological Replicate 1

description: Cell transduced with LACZ


title: WT3

source_name: Heart tissue (Wild type)

value: Wild type


title: WT4


title: T-ALL_Patient_9_ Vehicle_2


title: SOX2 expressing Biological Replicate 2

description: Cell transduced with SOX2


title: KPAC-MGH87GSC-3

city: Columbus

first: Kamalakannan

last: Palanichamy

state: OHIO

address: 400 W. 12th Ave., Rm#385E, Wiseman Hall

department: Radiation Oncology

institute: The Ohio State University Medical Center

description: GSC from 2nd tumor serial implantation

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA (50mg/mL), Bioarray Eukaryotic hybridization controls (Enzo Life Sciences) Heat 65oC for 5 minutes, 99oC for 5 min, 45oC for 5 minutes. Hybridize for 16 hours at 45oC at 60 rpm.

scan_protocol: Affymetrix Gene CHIP Scanner 3000 7G using command console

data_processing: The data was analyzed using PARTEK Genomic suite. The data was normalized using GCRMA, appropriate statistical parameters such as Bonferroni correction and Benjamini and Hochberg False Discovery Rate corrections were used

source_name: Brain Tumor

label_protocol: Samples were enzymatically labeled using BioArray High Yield RNA transcript Labeling kit (Enzo)

growth_protocol: U87 Cell line and GSC spheres (MGH87GSC) obtained from U87 tumors harvested from NOD-SCID mouse.

extract_protocol: RNA was isolated using Qiagen kit, RIN was > 8.9 for all the samples used.

treatment_protocol: Intracranial tumor implantation

value: glioma stem cells

value: Tumor tissue


title: KPAC-MGH87GSC-4

description: GSC from 2nd tumor serial implantation


title: KPAC-MGH87GSC-1

description: GSC from 1st tumor


title: WT5


title: 35-day-old weaned piglet replicate 3

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

country: Japan

institute: Kyoto Prefectural University

description:
Gene expression data from porcine ileal mucosa
21W35D-3

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

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

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA.

organism: Sus scrofa

source_name: age of 35days weaned piglet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip 3'IVT Express Kit, Affymetrix).

growth_protocol: All animals were crossbred (Landrace × Large white × Duroc) piglets and were bred at a commercial farm in Japan. Weaning piglets received a typical commercial diet for weaning.

extract_protocol: leal tissue (75% in length from the pyloric sphincter) was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: Collected ileal mucosa was immersed into RNAlate. The samples were kept at 4°C overnight and then stored at −80°C until use.

value: ileal mucosa

tag: weaning

value: at 21days


title: KPAC-U87-3

description: U87 cells

source_name: GBM cells

value: glioblastoma


title: Ak1


title: Ak2


title: KPAC-U87-2

description: U87 cells


title: KPAC-MGH87GSC-2

description: GSC from 2nd tumor serial implantation


title: Sebastian leaves_H2O_drought stress_T3_rep2

city: Poznań

first: Małgorzata

last: Kaczmarek

address: Strzeszyńska 34

department: Department of Environmental Stress Biology

country: Poland

institute: Institute of Plant Genetics

hyb_protocol: Hybridization to the Barley1 Gene Chip were conducted at EMBL GeneCore Facility (Heidelberg, Austria) following the manufacturer recommendation’s (Affymetrix, Santa Clara, CA).Hybridization was done in Genechip Hybridization oven 640, hybridization time was 16 h. Washing and staining was done in Affymetrix Fluidic station 450.

scan_protocol: Scanning was done in Genechip Scanner 3000 7G.

data_processing: Row expression data were processed by the Affymetrix MAS5 algorithm; the expression detection calls P/M/A were used to select genes (contigs), for which there was at least one (genotype x treatment x time point x drought) combination with calls M or P in all three replications (17078 genes). Then RMA algorithm (Irizarry et al., 2003) was used to obtain expression values. Pearson correlation coefficients between biological replications were calculated. For each gene independently, analysis of variance was performed using the model with all main factor effects, first- and second-order interactions; the third-order interaction was pooled with error. F-test P-values for all model effects were saved for all genes; effects were declared as significant if their q-values, computed within the family of effects for all genes according to the method of Storey (2002), were smaller than 0.0001. Based on significant effects a model consisting of the significant highest-order interactions was selected. All considered genes were grouped into non-exclusive “model classes” according to the presence of significant effects. Drought effects (Drought – Control) were computed for all combinations and their significance was declared at P < 0.001 by the t test. Homogeneity of distribution of genes representing all model classes over 1st and 2nd order BINs (MapMan Thimm et al. 2004) was tested by the χ2 test; significantly enriched model classes in individual bins were identified by considering standardized residuals from the homogeneity model and their significance according to approximate Normal distribution, at FWER (family-wise error rate) < 0.01 with Bonferroni approximation (effective significance thresholds equal to 0.0004 and 0.00005 for 1st and 2nd order bins, respectively). Similarly, within model classes, the homogeneity of distribution of genes with a particular pattern of drought effects over bins was tested and enrichment of individual categories was found. For this analysis, only bins with at least 10 annotated genes were considered; for model classes D, GD, TD and MD the analysis was performed by a simple χ2 homogeneity test, and for model classes GTD and GMD by fitting an appropriate generalized linear model with Poisson distribution and logarithmic link function. All statistical analyses were performed in Genstat 15 (VSN Int.). Functional analysis of DEGs and their GO terms categorization was performed using Blast2Go (Conesa et al. 2005). MapMan and PageMan (Thimm et al. 2004; Usadel et al. 2005) was used to visualize the results of concerted analysis.

organism: Hordeum vulgare

source_name: Sebastian, leaves, H2O, drought, time point 3

label_protocol: Samples were biotin labelled  at EMBL GeneCore Facility (Heidelberg, Austria) following the manufacturer recommendation’s (GeneChip 3'IVT Express kit, Affymetrix, Santa Clara, CA). Starting amount was 500 ng of total RNA.

growth_protocol: The experiment was carried out on two spring barley (Hordeum vulgare L.) varieties differing in the response to drought stress:  Sebastian and Georgia.  The plants were grown in a growth chamber in 1 dm3 pots (ten plants each) filled with a mixture of sand  and soil (2:7, w/w). Initially, fifteen seeds were sown to each pot and then thinned to ten. The following parameters were maintained: 22/18°C day/night, 30% RH and the photoperiod of 16h during the growth stage. The optimal soil moisture related to field water capacity (pF)  between 2.4 and 3.0 was kept by every-day weighting and watering of pots. Three-week-old plants were exposed to drought stress by withstanding of water to ensure a water content corresponding to field water capacity (pF) of 3.2, 3.6, and 4.2 in the following days.

extract_protocol: RNA was extracted using Trizol® (Invitrogen) according to manufacturer's  instructions and then further purified using Rneasy Plant Mini kit (QIAGEN) or SV total RNA isolation system (Promega).

treatment_protocol: The initial seed moisture content were 7.36  and 11.6 % (on dry weight basis) for Georgia and Sebastian, respectively. The seeds were surface treated with JOCKEY 201FS for 5 min. to avoid fungal invasion. The seeds were primed with  50 mM CaCl2 concentrations versus water-treated control for 24 h at 23±2°C with continuous shaking of 400 rpm. The ratio of seed weight to solution volume was 1:25 (g/ml). After osmopriming the seeds were given three surfaces washings with distilled water then re-dried to approximately original weight and sown the next day.

tag: variety

value: Sebastian


title: 35-day-old weaned piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
21W35D-2


title: 28-day-old weaned piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
21W28D-2

source_name: age of 28days weaned piglet


title: Sebastian leaves_H2O_drought stress_T3_rep1


title: 28-day-old weaned piglet replicate 3

description:
Gene expression data from porcine ileal mucosa
21W28D-3


title: 28-day-old weaned piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
21W28D-1


title: KPAC-U87-1

description: U87 cells


title: 35-day-old suckling piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
S35D-2

source_name: age of 35days suckling piglet

value: no


title: Sebastian leaves_H2O_drought stress_T1_rep3

source_name: Sebastian, leaves, H2O, drought, time point 1


title: Sebastian leaves_H2O_drought stress_T2_rep2

source_name: Sebastian, leaves, H2O, drought, time point 2


title: Sebastian leaves_H2O_drought stress_T2_rep3


title: 35-day-old suckling piglet replicate 3

description:
Gene expression data from porcine ileal mucosa
S35D-3


title: Sebastian leaves_H2O_drought stress_T3_rep3


title: 35-day-old weaned piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
21W35D-1


title: 35-day-old suckling piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
S35D-1


title: Sebastian leaves_H2O_drought stress_T2_rep1


title: Sebastian leaves_H2O_drought stress_T1_rep2


title: 28-day-old suckling piglet replicate 4

description:
Gene expression data from porcine ileal mucosa
S28D-4

source_name: age of 28days suckling piglet


title: Sebastian leaves_H2O_control water regime_T3_rep3

source_name: Sebastian, leaves, H2O, control, time point 3


title: 28-day-old suckling piglet replicate 3

description:
Gene expression data from porcine ileal mucosa
S28D-3


title: Sebastian leaves_H2O_drought stress_T1_rep1


title: 28-day-old suckling piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
S28D-2


title: 21-day-old suckling piglet replicate 3

description:
Gene expression data from porcine ileal mucosa
S21D-3

source_name: age of 21days suckling piglet


title: Sebastian leaves_H2O_control water regime_T3_rep1


title: Sebastian leaves_H2O_control water regime_T3_rep2


title: 21-day-old suckling piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
S21D-2


title: Sebastian leaves_H2O_control water regime_T2_rep2

source_name: Sebastian, leaves, H2O, control, time point 2


title: 21-day-old suckling piglet replicate 4

description:
Gene expression data from porcine ileal mucosa
S21D-4


title: 28-day-old suckling piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
S28D-1


title: Sebastian leaves_H2O_control water regime_T2_rep3


title: 21-day-old suckling piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
S21D-1


title: Sebastian leaves_H2O_control water regime_T1_rep3

source_name: Sebastian, leaves, H2O, control, time point 1


title: Sebastian leaves_H2O_control water regime_T2_rep1


title: Neg CD5- CD43-_4

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

description: cord blood 269

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

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

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

source_name: CD5 negative B lymphoyctes

label_protocol: 10 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: freshly isolated cells, no culture

extract_protocol: RNA was extracted using the NucleoSpin® RNA II kit (Macherey & Nagel) following manufacturer's instructions

treatment_protocol: Mononuclear cells were isolated by Ficoll from heparinized cord blood, and then sorted by FACS to purify B lymphocytes, and cell pellet directly snap frozen

tag: phenotype

value: CD5 negative B lymphoyctes


title: Neg CD5- CD43-_3

description: cord blood 26F


title: Sebastian leaves_H2O_control water regime_T1_rep1


title: Sebastian leaves_H2O_control water regime_T1_rep2


title: High CD5+ CD43+_4

description: cord blood 269

source_name: CD5 positive B lymphocytes

value: CD5 positive B lymphocytes


title: 14-day-old suckling piglet replicate 3

description:
Gene expression data from porcine ileal mucosa
S14D-3

source_name: age of 14days suckling piglet


title: Wt26

city: Chicago

first: Andrew

last: Nesterovitch

state: IL

address: 707 S. Wood Street, Annex Bldg, Suite 220

department: Dermatology

institute: Rush University Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: bone marrow

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

tag: disease state

value: wild-type, healthy


title: High CD5+ CD43+_3

description: cord blood 26M


title: Wt27


title: 14-day-old suckling piglet replicate 2

description:
Gene expression data from porcine ileal mucosa
S14D-2


title: 14-day-old suckling piglet replicate 1

description:
Gene expression data from porcine ileal mucosa
S14D-1


title: Sebastian leaves_CaCl2_drought stress_T3_rep2

source_name: Sebastian, leaves, CaCl2, drought, time point 3


title: Sebastian leaves_CaCl2_drought stress_T2_rep3

source_name: Sebastian, leaves, CaCl2, drought, time point 2


title: Wt25


title: High CD5+ CD43+_1

description: cord blood 262


title: High CD5+ CD43+_2

description: cord blood 26F


title: Neg CD5- CD43-_2

description: cord blood 26M


title: Wt23


title: Sebastian leaves_CaCl2_drought stress_T3_rep1


title: Sebastian leaves_CaCl2_drought stress_T3_rep3


title: Wt24


title: Sebastian leaves_CaCl2_drought stress_T1_rep3

source_name: Sebastian, leaves, CaCl2, drought, time point 1


title: Sick15

value: NDLD, sick


title: Neg CD5- CD43-_1

description: cord blood 262


title: Sebastian leaves_CaCl2_drought stress_T2_rep1


title: Sick11


title: Sebastian leaves_CaCl2_drought stress_T2_rep2


title: Sick16


title: Sebastian leaves_CaCl2_drought stress_T1_rep1


title: Sick12


title: Calu_control1

city: Aurora

first: Viola

last: Dengler

state: CO

address: 12700 E 19th Avenue, Mailstop B112, Research Complex 2, Room 7124

department: Anesthesiology

institute: UC Denver

description: SAMPLE 3

hyb_protocol: Following fragmentation, 5.5ug of cDNA (not cRNA) was labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix terminal labeling kit that was covalently linked to biotin.Biotinylated cDNA was hybridized for 16 hours at 45C on Human Gene1.0ST arrays. Arrays were washed and stained on Genechip Fluidics Station 450 instrument.

scan_protocol: GeneChip arrays were scanned using the GeneChip Scanner.

data_processing: For each array CEL files were imported into Partek Genomic Suite software (v.6.6, Agilent), and data were normalized using the RMA (Robust Multichip Averaging) algorithm

source_name: pulmonary epithelial_control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: pulmonary epithelial cells

tag: genotype/variation

value: control-lentivirus


title: Sebastian leaves_CaCl2_control water regime_T3_rep3

source_name: Sebastian, leaves, CaCl2, control, time point 3


title: Sebastian leaves_CaCl2_drought stress_T1_rep2


title: miR-709-D

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

hyb_protocol: each sample was hybridized to a mouse Gene 1.0 array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS30007G using Affymetrix Command Console (AGCC)

data_processing: Cel files were generated by AGCC and imported into Partek Genomics Suite  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed, only core probesets (as defined by Affymetrix) were generated.

source_name: primary hepatocytes_miR-709

label_protocol: 100ng of RNA from each sample was labeled using the Ambion WT Expression kit and the Affymetrix WT Terminal Labeling kit

extract_protocol: Total RNA was isolated from 1x10^6 cells 24 hours post-transfection using RNeasy Midi kit (Qiagen) following the manufacturer’s protocol. The quality of RNA was determined by Agilent 600 Nanobioanalyzer.

treatment_protocol: miRNA-709 mimic or control miRNA (Cel-239b)

value: hepatocytes

tag: strain


title: miR-709-B


title: Calu_223_2

description: SAMPLE 2

source_name: pulmonary epithelial_hsa-miR-223

value: hsa-miR-223-overexpressing lentivirus


title: miR-709-C


title: Calu_223_1

description: SAMPLE 1


title: Sebastian leaves_CaCl2_control water regime_T3_rep2


title: miR-709-A


title: Sick14


title: Calu_control2

description: SAMPLE 4


title: Sebastian leaves_CaCl2_control water regime_T3_rep1


title: Sebastian leaves_CaCl2_control water regime_T2_rep3

source_name: Sebastian, leaves, CaCl2, control, time point 2


title: 2-12

city: Farmington

first: Anthony

middle: T

last: Vella

state: CT

address: 263 Farmington Avenue

department: Immunology

institute: University of Connecticut Health Center

hyb_protocol: Affymetrix GeneChip Mouse Genome 430 2.0 Array

scan_protocol: GeneChip Scanner 3000 7G, enabled for High-Resolution Scanning

data_processing: GeneChip Operating Software (GCOS) v1.1.1. The processed data on the Series record contains summarized data, not directly from the EC data. The first few columns show differential expression comparing conditions, ie. Fold change. The other columns show normalized signal intensity in linear form, ie the signal of that probeset for that sample, in linear form, after the MAS normalization and summarization algorithm MAS 5 is run. All analysis was performed by Yale Center for Genome Analysis (YCGA).

source_name: CD8 T cell

label_protocol: Extracted RNA from treated cells were shipped to Yale Center fpr Genome Analysis (UCGA), who performed the labeling, hybridization, scanning and data processing.

growth_protocol: Adoptively transferred OT-I CD8 T cells were primed in vivo with SIINFEKL peptide and CD134 plus CD137 costimulatory agonists and FACS sorted from spleen 4

extract_protocol: QIAGEN RNAeasy extraction of total RNA was used according to the manufacturer's instructions.

treatment_protocol: The sorted cells were treated in vitro with or without 1 ng/ml IL-12 or IL-33 or both cytokines for 2 hours.

value: effector CD8 T cell

tag: stimulated


title: 2-33-12

value: IL-12 and IL-33


title: 2-NONE


title: 2-33


title: Sebastian leaves_CaCl2_control water regime_T2_rep1


title: Sebastian leaves_CaCl2_control water regime_T2_rep2


title: Sebastian leaves_CaCl2_control water regime_T1_rep3

source_name: Sebastian, leaves, CaCl2, control, time point 1


title: 1-NONE


title: Cel-miR-239b-B


title: Cel-miR-239b-D


title: late CD62L high, rep3

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Affymetrix Model 7G upgraded scanner, and data were collected using the GeneChip Operating Software

data_processing: The data were analyzed with Partek Genomics suite (www.partek.com) using RMA background correction.

source_name: CD8+ P14 cells from spleen isolated after 8 months following LCMV infection

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

growth_protocol: All studies were performed on the C57BL/6 background.

extract_protocol: RNA was extracted using the RNEasy Kit (QIAGEN), and 1-5ng of mRNA was used for microarray analysis

treatment_protocol: P14 cells were transferred retro-orbitally into 6-12 week old naïve C57BL/6 mice, and recipients were infected 24hrs later intraperitoneally (i.p.) with 2x10^5 plaque forming units (PFU) of LCMV Armstrong

tag: tissue

value: spleen

tag: time point

value: 8 months following LCMV infection

value: late memory P14 cells that are CD62L+


title: Sebastian leaves_CaCl2_control water regime_T1_rep2


title: Sebastian leaves_CaCl2_control water regime_T1_rep1


title: 1-12


title: 1-33-12


title: Total RNA

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description:
total RNA
3t3

hyb_protocol: 11 µg of this amplified material of each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: Total RNA from myc-AUF1 p42-expressing cells

label_protocol: 50 ng of immunoprecipitated RNA or of the total RNA control sample were processed with the two-cycle target labelling protocol (Technical Manual; Gene Expression Analysis 701021 Rv.3 of Affymetrix) to produce biotinylated cRNA target.

growth_protocol: NIH-3T3 cells were stably transfected with pBSwitch and inducible pSLHGC-MYC-AUF1 p42 vectors, and grown exponentially

extract_protocol: Cells were lysed in 750 µl CelLytic-M lysis reagent (C-2978; Sigma, St. Louis, MO), cleared by centrifugation at 10,000xg and the supernatant incubated at 4°C for 4 h with anti-c-myc agarose beads (A-7470; Sigma) according to the manufacturer’s protocol. Immunoprecipitates were harvested by 15 sec centrifugation at 10,000xg and the beads washed twice with 1 x IP buffer (I-5779; Sigma), and resuspended in 100 µl of 0.1 x IP buffer. RNA was isolated using Qiagen RNeasy minikit (Qiagen, Hilden, Germany) after DNAse I digestion according to the Qiagen manual.

treatment_protocol: About 2.5 x 10^6 logarithmically growing NIH-3T3 transfected cells were induced for myc-AUF1 expression with 1 nM mifepristone for 24 h.

tag: cell line


title: late CD62L low, rep2

value: late memory P14 cells that are CD62L-


title: Georgia leaves_H2O_dorught sterss_T3_rep3

source_name: Georgia, leaves, H2O, drought, time point 3

value: Georgia


title: Cel-miR-239b-C


title: Georgia leaves_H2O_dorught sterss_T3_rep1


title: Georgia leaves_H2O_dorught sterss_T3_rep2


title: No induction control rep1

description:
RNA-IP
ctrl_A

molecule: polyA RNA

source_name: RNP-IPs of myc-AUF1 p42-expressing cells without AUF1 induction

tag: antibody

value: anti-c-myc agarose beads (A-7470; Sigma)


title: No induction control rep2

description:
RNA-IP
ctrl_B


title: late CD62L high, rep1


title: Georgia leaves_H2O_drought stress_T2_rep3

source_name: Georgia, leaves, H2O, drought, time point 2


title: AUF1 induction rep1

description:
RNA-IP
p42_A

source_name: RNP-IPs of myc-AUF1 p42-expressing cells with AUF1 induction


title: late CD62L low, rep3


title: late CD62L high, rep2


title: Georgia leaves_H2O_drought stress_T2_rep2


title: late CD62L low, rep1


title: Georgia leaves_H2O_drought sterss__T1_rep3

source_name: Georgia, leaves, H2O, drought, time point 1


title: early CD62L low, rep3

source_name: CD8+ P14 cells from spleen isolated at 30-45 days after LCMV infection

value: 30-45 days after LCMV infection

value: early memory P14 cells that are CD62L-


title: 1-33


title: AUF1 induction rep2

description:
RNA-IP
p42_B


title: Georgia leaves_H2O_drought stress_T2_rep1


title: Control_biological rep1

city: Wako

first: Kentaro

last: Ishida

state: Saitama

address: Hirosawa

institute: RIKEN

hyb_protocol: 10 ug of cRNA were hybridized for 16h at 45C on mouse genome 430 2.0 Array. GeneChips were washed and stained in the Affimetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix scanner 3000 7G.

data_processing: The data ware analyzed with GeneSpring version 10.0 (MAS 5.0) using Affymetrix default analysis setting and global scaling as normalization method.

source_name: Neuro2A cytoplasm_control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protcol from 200 ng poly(A)+ RNA.

growth_protocol: Neuro2A cells were cultured in a 1:1mixture of DMEM and HamF12 supplemented with 10% FCS.

extract_protocol: For subcellular fraction, cells were incubated for 5 minutes at 4 C in CSK buffer.Forrowing centrifuge at 700 g, the supernatant was collected as cytoplasmic fraction and  pellet was collected as nuclear faction. Total RNA was isolated using Trizol accoding to the manufacturer's instructions

treatment_protocol: For transfection with the antisense oligonucleotides, 2.5 x 106 cells plated in a 10 cm dish were transfected with 30 nM oligonucleotides using lipofectamine 2000 according to the manufacturer's instuuctions.

value: neuroblastoma

value: control


title: early CD62L low, rep2


title: Control_biological rep2


title: early CD62L high, rep3

value: early memory P14 cells that are CD62L+


title: early CD62L high, rep2


title: 4.5SH_KD_biological rep2

source_name: Neuro2A cytoplasm_4.5SH_KD

value: depletion of endogenous 4.5SH (4.5SH KD)


title: early CD62L high, rep1


title: Georgia leaves_H2O_control water regime_T3_rep3

source_name: Georgia, leaves, H2O, control, time point 3


title: early CD62L low, rep1


title: 4.5SH_KD_biological rep1


title: Georgia leaves_H2O_drought sterss__T1_rep1


title: Georgia leaves_H2O_control water regime_T3_rep1


title: Georgia leaves_H2O_control water regime_T3_rep2


title: Melanoma cell line T1

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

country: France

institute: Institut Gustave Roussy

description: Melanoma cell line T1 vs the Pool of the 23 melanoma cell lines total RNA

hyb_protocol: The labeled RNA was hybridized in dual-color on the Agilent Whole Human Genome 4x44K Microarray (AMADID 014850).

scan_protocol: After hybridization and washing, slides were scanned on an Agilent G2505B DNA microarray scanner at a resolution of 5 µm and a color depth of 20 bits.

data_processing: Signal acquisition was performed with Feature Extraction software (Agilent) v10.2.1.3.

source_name: melanoma cell line

label_protocol: Total RNA was labeled using the manufacturer's default protocol (Agilent Low Fluorescent Low Input Linear Amplification Kit).

growth_protocol: Melanoma cell lines were cultured at 37°C  in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% glutamine, under a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from melanoma cell lines with the miRNeasy Mini Kit (Qiagen).

treatment_protocol: None.

tag: gender

value: male

tag: nrasq61k mutation status

value: wt

tag: nrasq61l mutation status

tag: nrasq61r mutation status

tag: brafv600e mutation status

value: melanoma

value: mixed


title: Georgia leaves_H2O_drought sterss__T1_rep2


title: KO_rep1

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description:
Sample name: M244-05
Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® MoGene 1.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.5. RMA16 algorithm was used for normalization

source_name: Extensor digitorum longus muscles

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion)

extract_protocol: TRIzol extraction

value: C57/Bl6 and SV129 mixed background

value: AMPKα1α2 double knockout

value: Extensor digitorum longus muscles


title: Georgia leaves_H2O_control water regime_T2_rep3

source_name: Georgia, leaves, H2O, control, time point 2


title: Melanoma cell line G1

description: Melanoma cell line G1 vs the Pool of the 23 melanoma cell lines total RNA

tag: cell type


title: Melanoma cell line 888mel

description: Melanoma cell line 888mel vs the Pool of the 23 melanoma cell lines total RNA

value: female

value: mut


title: Georgia leaves_H2O_control water regime_T2_rep2

value: Georgia


title: Melanoma cell line 501mel

description: Melanoma cell line 501mel vs the Pool of the 23 melanoma cell lines total RNA


title: WT_rep4

description:
Sample name: M244-04
Gene expression data

value: Wild type


title: Georgia leaves_H2O_control water regime_T2_rep1


title: KO_rep3

description:
Sample name: M244-07
Gene expression data


title: KO_rep2

description:
Sample name: M244-06
Gene expression data


title: WT_rep3

description:
Sample name: M244-03
Gene expression data


title: Melanoma cell line Gerlach

description: Melanoma cell line Gerlach vs the Pool of the 23 melanoma cell lines total RNA

value: Gerlach


title: Georgia leaves_H2O_control water regime_T1_rep3

source_name: Georgia, leaves, H2O, control, time point 1


title: Melanoma cell line Lyse

description: Melanoma cell line Lyse vs the Pool of the 23 melanoma cell lines total RNA

value: Lyse


title: Melanoma cell line Mull

description: Melanoma cell line Mull vs the Pool of the 23 melanoma cell lines total RNA

value: Mull


title: Georgia leaves_H2O_control water regime_T1_rep2


title: WT_rep2

description:
Sample name: M244-02
Gene expression data


title: Melanoma cell line Dauv-1

description: Melanoma cell line Dauv-1 vs the Pool of the 23 melanoma cell lines total RNA


title: WT_rep1

description:
Sample name: M244-01
Gene expression data


title: Georgia leaves_H2O_control water regime_T1_rep1


title: Melanoma cell line Rosi

description: Melanoma cell line Rosi vs the Pool of the 23 melanoma cell lines total RNA

value: Rosi


title: Georgia leaves_CaCl2_drought stress_T3_rep2

source_name: Georgia, leaves, CaCl2,drought, time point 3


title: Melanoma cell line Daju

description: Melanoma cell line Daju vs the Pool of the 23 melanoma cell lines total RNA

value: Daju


title: Georgia leaves_CaCl2_drought stress_T3_rep3

source_name: Georgia, leaves,CaCl2, drought, time point 3


title: Melanoma cell line SK29

description: Melanoma cell line SK29 vs the Pool of the 23 melanoma cell lines total RNA


title: Amino acid treated cells 16h

city: Uppsala

first: Robert

last: Fredriksson

address: Husargatan 3

department: Neurosceince

country: Sweden

institute: Uppsala University

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 16 hours

hyb_protocol: GeneChip® ST Arrays ( GeneChip® Mouse Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: Gene chips were scanned using the GeneChip® Scanner 3000 7G

data_processing: Analysis of the gene expression data was carried out in the statistical computing language R. The raw data was normalized using the robust multi-array average (RMA) method. In order to search for the differentially expressed genes between the X samples and the Y samples group an empirical Bayes moderated t-test was used, using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg.

source_name: mouse N25/2 hypothalamic cells

label_protocol: 250ng of total RNA from each sample was used to produce amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit( P/N 4425209 Rev C 09/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 3, Affymetrix Inc., Santa Clara, CA).

growth_protocol: The immortalized embryonic mouse hypothalamic cell line  N25/2  was cultured in Dulbecco’s modified Eagles medium (DMEM) (Invitrogen, USA) supplemented with 50 ml Fetal Bovine serum (FBS), (Gibco, Life technologies, USA),  5 ml Penicillin-Streptomycin, liquid (Pen-Strep) (Gibco, Life technologies, USA) and 5 ml amphotericin (Gibco, Life technologies, USA) at 37°C in a humidified atmosphere of 5% CO2, 95% air.

extract_protocol: Total RNA was extraced with RNeasy Midi Kit (qiagen) following the manufactures protocol.

treatment_protocol: The cells were treated with medium containing amino acids or medium lacking amino acids for 1,2,3,5 or 16 hours.


title: Amino acid deprived cells 16h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 16 hours

value: immortalized embryonic mouse hypothalamic cell line  N25/2


title: Georgia leaves_CaCl2_drought stress_T2_rep2

source_name: Georgia, leaves, CaCl2,drought, time point 2


title: Amino acid deprived cells 5h sample 4

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 5 hours sample 4


title: Melanoma cell line WM1366

description: Melanoma cell line WM1366 vs the Pool of the 23 melanoma cell lines total RNA


title: Amino acid treated cells 5h sample4

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 5 hours sample 4


title: Georgia leaves_CaCl2_drought stress_T2_rep1


title: Amino acid deprived cells 5h sample 1

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 5 hours sample 1


title: Georgia leaves_CaCl2_drought stress_T3_rep1


title: Melanoma cell line WM983B

description: Melanoma cell line WM983B vs the Pool of the 23 melanoma cell lines total RNA

value: male


title: Georgia leaves_CaCl2_drought stress_T2_rep3


title: Melanoma cell line WM983A

description: Melanoma cell line WM983A vs the Pool of the 23 melanoma cell lines total RNA

value: wt


title: Amino acid deprived cells 5h sample 3

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 5 hours sample 3


title: Amino acid deprived cells 5h sample 2

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 5 hours sample 2


title: Melanoma cell line SK28

description: Melanoma cell line SK28 vs the Pool of the 23 melanoma cell lines total RNA

value: melanoma


title: Melanoma cell line MNT-1

description: Melanoma cell line MNT-1 vs the Pool of the 23 melanoma cell lines total RNA

value: mixed


title: Amino acid treated cells 5h sample3

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 5 hours sample 3


title: Melanoma cell line WM793

description: Melanoma cell line WM793 vs the Pool of the 23 melanoma cell lines total RNA


title: Amino acid treated cells 5h sample1

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 5 hours sample 1


title: Amino acid treated cells 5h sample2

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 5 hours sample 2


title: Melanoma cell line Quar

description: Melanoma cell line Quar vs the Pool of the 23 melanoma cell lines total RNA

value: Quar


title: Georgia leaves_CaCl2_drought stress_T1_rep3

source_name: Georgia, leaves, CaCl2,drought, time point 1


title: Georgia leaves_CaCl2_drought stress_T1_rep2


title: Georgia leaves_CaCl2_control water regime_T3_rep3

source_name: Georgia, leaves, CaCl2,control, time point 3


title: Melanoma cell line MeWo

description: Melanoma cell line MeWo vs the Pool of the 23 melanoma cell lines total RNA

value: MeWo


title: Georgia leaves_CaCl2_control water regime_T3_rep2


title: Melanoma cell line SKMel3

description: Melanoma cell line SKMel3 vs the Pool of the 23 melanoma cell lines total RNA


title: Georgia leaves_CaCl2_drought stress_T1_rep1


title: Amino acid deprived cells 3h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 3 hours


title: Melanoma cell line WM852

description: Melanoma cell line WM852 vs the Pool of the 23 melanoma cell lines total RNA


title: Melanoma cell line A375M

description: Melanoma cell line A375M vs the Pool of the 23 melanoma cell lines total RNA


title: Melanoma cell line Lu1205

description: Melanoma cell line Lu1205 vs the Pool of the 23 melanoma cell lines total RNA


title: Georgia leaves_CaCl2_control water regime_T2_rep2

source_name: Georgia, leaves, CaCl2,control, time point 2


title: Amino acid treated cells 3h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 3 hours


title: Amino acid deprived cells 2h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 2 hours


title: Georgia leaves_CaCl2_control water regime_T2_rep3


title: Georgia leaves_CaCl2_control water regime_T2_rep1


title: Georgia leaves_CaCl2_control water regime_T3_rep1


title: Amino acid treated cells 2h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 2 hours


title: CDM_S_DA_rep3

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

description: biological replicate 3 of 3 for A. pleuropneumoniae cultured in CDM plus serum and DA

hyb_protocol: Each  Slide  was  hybridized  with  600ng  Cy3-labeled  cRNA  using  Gene  Expression Hybridization  Kit  (Cat#5188-5242,  Agilent  technologies,  Santa  Clara,  CA,  US)  in Hybridization   Oven   (Cat#G2545A,   Agilent   technologies,   Santa   Clara,   CA,   US), according  to  the  manufacturer’s  instructions.  After  17  hours  hybridization,  slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene  Expression  Wash  Buffer  Kit(Cat#5188-5327,  Agilent  technologies,  Santa  Clara,   CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides  were  scanned  by  Agilent  Microarray  Scanner  (Cat#G2565CA,  Agilent technologies,  Santa  Clara,  CA,  US)  with  default  settings,  Dye  channel:  Green,  Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

source_name: A. pleuropneumoniae 4074 cultured in chemically defined medium (CDM) supplemented with serum(S) and dopamine (DA) to mid-log phase

label_protocol: Total  RNA  was  amplified  and  labeled  by  Low  Input  Quick  Amp  Labeling  Kit, One-Color  (Cat#5190-2305,  Agilent  technologies,  Santa  Clara,  CA,  US),  following  the manufacturer’s   instructions.   Labeled   cRNA   were   purified   by   RNeasy   mini   kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: A. pleuropneumoniae 4074  were cultured in chemically defined medium (CDM) at 37°C with rotation at 200 rpm.

extract_protocol: Total RNA was extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions, then purified using QIAGEN RNeasy Mini Kit (QIAGEN).

treatment_protocol: For serum treated A. pleuropneumoniae samples, filtered cattle serum at the concentration of 1/40 was added into CDM, for catecholamines treated A. pleuropneumoniae samples, epinephrine (Epi), norepinephrine (NE) and dopamine (DA) at 50μM were added respectively into CDM containing 1/40 serum.

tag: growth condition


title: Amino acid deprived cells 1h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium lacking amino acids for 1 hour


title: KRAS_Week20_S3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: KRAS

hyb_protocol: Following fragmentation, 15 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip MoGene-1.0-st-v1 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 GeneChip scanner with GCOS 1.4.

data_processing: The data were analysed using BRB-array tools. Background correction, normalization and probe summarization were performed with JustRMA for each tissue separately using the core transcript annotation.

source_name: KRAS, 20 weeks

label_protocol: Biotinylated cDNA was prepared according to the Affymetrix Whole Transcript Sense Labelling protocol from 100 ng total RNA according to the manufacturer.

extract_protocol: RNA was extracted by using the RNAqueous-Micro kit (Ambion) following the manufacturer's instructions for animal tissues.

value: pancreatic ductal and duct-like cells (DBA lectin positive)

tag: age

value: 20 weeks

tag: treatment


title: CDM_S_DA_rep1

description: biological replicate 1 of 3 for A. pleuropneumoniae cultured in CDM plus serum and DA

value: cultured in chemically defined medium (CDM) supplemented with serum(S) and dopamine (DA) to mid-log phase


title: Amino acid treated cells 1h

description: Gene expression data from entire mouse genome when mouse hypothalamic cells were treated in medium containing amino acids for 1 hour


title: KRAS_Control_S3

description: Control

source_name: KRAS control, 20 weeks


title: CDM_S_DA_rep2

description: biological replicate 2 of 3 for A. pleuropneumoniae cultured in CDM plus serum and DA


title: plaque

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

hyb_protocol: Probes generated from plaque tissue and mamaria were hybridized to the Ambion mirVanaTM miR Bioarray (1566 v.1, www.ambion.com/techlib/prot) according to manufactory instruction. Probes generated from human monocytes were hybridized to GenoExplorer human microRNA array by BIOCAT service also according to manufactory instruction.

scan_protocol: Scanning of the Ambion mirVana Bioarrays was performed using a dual-laser scanner Affymetrix 428 (affymetrx, CA) at various amplification settings (gains) above and below saturation of the most intensely fluorescent spots on each array. GenoExplorer human microRNA arrays scanning were provided by BIOCAT service.

data_processing: ImaGene 5.5.4 (BioDiscovery, CA) software was used to quantify the scanned Ambion mirVana Bioarray images. GenoExplorer human microRNA arrays were quatified BIOCAT service. Median pixel intensities of the spots were taken and normalized based on control spot intensities. Spots with intensities lower than negative control intensities were defined as 0, spots with intensities higher than negative controls get a relative expression value by comparing to positive control intensities.

source_name: plaque

label_protocol: RNA from plaque tissue  and mamaria were labeled using the mirVanaTM miR Labeling Kit (Ambion) and fluorescent Cy3 (Molecular Probes). RNA from human monocytes were labeled with GenoExplorer™ miRNA Labeling Kit.

extract_protocol: Human monocytes were isolated from buffy coats from healthy donors, and  sorted by FACS analysis using specific antibodies. Human advanced atherosclerotic plaques were collected during carotid endarterectomy. Aa. mammariae internae excised from patients undergoing elective by-pass surgery. Total RNA was isolated using the TRIzol kit (Invitrogen). miR was purified using the mirVanaTM miR Isolation Kit (Ambion).

value: Carotid plaque tissue


title: mammaria

source_name: mammaria

value: Ae. mammaria interna


title: Georgia leaves_CaCl2_control water regime_T1_rep1

source_name: Georgia, leaves, CaCl2,control, time point 1

tag: variety

value: Georgia


title: Georgia leaves_CaCl2_control water regime_T1_rep3


title: Georgia leaves_CaCl2_control water regime_T1_rep2


title: KRAS_Week10_S3

description: KRAS

source_name: KRAS, 10 weeks

tag: genotype/variation

value: 10 weeks


title: KRAS_Week20_S2

description: KRAS


title: CDM_S_NE_rep2

description: biological replicate 2 of 3 for A. pleuropneumoniae cultured in CDM plus serum and NE

source_name: A. pleuropneumoniae 4074 cultured in chemically defined medium (CDM) supplemented with serum(S) and norepinephrine (NE) to mid-log phase


title: KRAS_Control_S2

description: Control

source_name: KRAS control, 10 weeks


title: primary tumor_stage 4_#5

city: Changsha

first: xiayu

last: li

address: Yuelu district, Tongzipo road #138

department: department of gastroenterology

institute: Xiangya third hospital

hyb_protocol: Chips with labeled samples were hybridized at 50°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed successively with 2×SSPE/0.2% SDS at 42°C for 5 min, 2×SSC at 42°C for 5 min, 2×SSC at room temperature for 5 min and 0.2×SSC at room temperature for 15 min.

scan_protocol: Slides were scanned using a Genepix 4000B laser scanner (Axon, New York) and fluorescent intensities were extracted from the generated images by Genepix Pro 6.0 software (Axon).

data_processing: The repeatability of the microarray within each class ( normal, stageI,II,II and IV) were examined by correlation analysis. Only those data with over 50% of intra-class correlation coefficient greater than 0.8 were selected for further analysis(Chen et al., 2007). Data filter: > 50% of the arrays and gene signal > 0 were selected. Normalization was done using per chip median normalization and median array method(Liu et al.,2004) .RVM F-test was applied to screen the dynamic differentially expressed miRNA for the normal and different TNM group(Wright et al., 2003).

source_name: colorectal primary tumor, stage 4

label_protocol: 5-μg total RNA was used for Cy5-labeled aRNA preparation using a MessageAmp™ aRNA amplification kit (Ambion, Austin, TX).

extract_protocol: On average, 100-150mg of flash frozen sample tissue were prepared for the extraction of total RNA. TRIZOL Reagent (Invitrogen ) were used to extract total RNA according to manufacturer's protocol

value: colorectal primary tumor

tag: histology

value: G2,Moderately differentiated

tag: Sex

tag: Stage


title: primary tumor_stage 4_#4

tag: tissue

value: female


title: CDM_S_NE_rep1

description: biological replicate 1 of 3 for A. pleuropneumoniae cultured in CDM plus serum and NE

value: cultured in chemically defined medium (CDM) supplemented with serum(S) and norepinephrine (NE) to mid-log phase


title: CDM_S_Epi_rep3

description: biological replicate 3 of 3 for A. pleuropneumoniae cultured in CDM plus serum and Epi

source_name: A. pleuropneumoniae 4074 cultured in chemically defined medium (CDM) supplemented with serum(S) and epinephrine (Epi) to mid-log phase


title: KRAS_Week20_S1

description: KRAS


title: KRAS_Week10_S2

description: KRAS


title: CDM_S_Epi_rep2

description: biological replicate 2 of 3 for A. pleuropneumoniae cultured in CDM plus serum and Epi

value: cultured in chemically defined medium (CDM) supplemented with serum(S) and epinephrine (Epi) to mid-log phase


title: primary tumor_stage 4_#2


title: primary tumor_stage 4_#3


title: KRAS_Week10_S1

description: KRAS


title: CDM_S_Epi_rep1

description: biological replicate 1 of 3 for A. pleuropneumoniae cultured in CDM plus serum and Epi


title: KRAS_Control_S1

description: Control


title: CDM_S_rep3

description: biological replicate 3 of 3 for A. pleuropneumoniae cultured in CDM plus serum

source_name: A. pleuropneumoniae 4074 cultured in chemically defined medium (CDM) supplemented with serum (S) to mid-log phase


title: primary tumor_stage 4_#1

value: G1,Well differentiated

value: male


title: Embryo_P01_S2

description: Postnatal

source_name: Postnatal day 1

tag: strain/background

value: wild type

value: postnatal day 1


title: primary tumor_stage 3_#5

source_name: colorectal primary tumor, stage 3


title: CDM_S_rep2

description: biological replicate 2 of 3 for A. pleuropneumoniae cultured in CDM plus serum

value: cultured in chemically defined medium (CDM) supplemented with serum (S) to mid-log phase


title: Embryo_E16_S2

description: Embryo

source_name: Embryo, day 16.5

value: pancreatic ductal and duct-like cells (DBA lectin positive)

value: embryonic day 16.5


title: primary tumor_stage 3_#4

value: G3,Poorly differentiated


title: Embryo_P01_S1

description: Postnatal


title: CDM_S_rep1

description: biological replicate 1 of 3 for A. pleuropneumoniae cultured in CDM plus serum


title: primary tumor_stage 3_#2


title: Melanoma cell line SKMel3

hyb_protocol: The labeled RNAs were hybridized to Agilent Unrestricted Human miRNA microarrays (V3) for 20h at 55°C, with rotation.

scan_protocol: Slides were scanned with an Agilent 2565 AB DNA microarray scanner, with high dynamic range settings and 100% of the photomultiplier power, as recommend by the manufacturer.

data_processing: Agilent Probe Extraction Software (10.5.5.1) was used for data extraction. After quality control analysis, 2 melanoma cell lines (Quar and WM793) were detected as outliers and excluded from the panel of 23. The remaining 21 cell lines intensity profiles were log2-transformed and normalized using quantiles.

source_name: melanoma cell line

label_protocol: Total RNA (100ng) was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3, using T4 RNA ligase (GE Healthcare Europe GmbH).

extract_protocol: Total RNA was isolated from melanoma cell lines with the miRNeasy Mini Kit (Qiagen)

tag: cell line

value: wt

value: mut


title: CDM_S_NE_rep3

description: biological replicate 3 of 3 for A. pleuropneumoniae cultured in CDM plus serum and NE


title: Embryo_E16_S1

description: Embryo


title: primary tumor_stage 3_#3


title: primary tumor_stage 3_#1


title: CDM_rep2

description: biological replicate 2 of 3 for A. pleuropneumoniae cultured in CDM (control)

source_name: A. pleuropneumoniae 4074 cultured in chemically defined medium (CDM) to mid-log phase


title: CDM_rep3

description: biological replicate 3 of 3 for A. pleuropneumoniae cultured in CDM (control)

value: cultured in chemically defined medium (CDM) to mid-log phase


title: primary tumor_stage 2_#5

source_name: colorectal primary tumor, stage 2


title: CDM_rep1

description: biological replicate 1 of 3 for A. pleuropneumoniae cultured in CDM (control)


title: Melanoma cell line MNT-1

tag: gender


title: Embryo_E14_S2

description: Embryo

source_name: Embryo, day 14.5

value: embryonic day 14.5


title: Embryo_E15_S1

description: Embryo

source_name: Embryo, day 15.5

value: embryonic day 15.5


title: Embryo_E14_S1

description: Embryo


title: Melanoma cell line 888mel

tag: nrasq61k mutation status


title: primary tumor_stage 2_#2

value: colorectal primary tumor


title: primary tumor_stage 2_#4

value: G2,Moderately differentiated

value: female


title: primary tumor_stage 2_#3


title: Control_Day_5_S2

description: Control

source_name: Control, day 5

value: saline

tag: time

value: day 5


title: Control_Day_5_S1

description: Control


title: Control_Day_5_S3

description: Control


title: Pancreatitis_Day_5_S3

description: Pancreatitis

source_name: Pancreatitis, day 5

value: cerulein-induced acute pancreatitis


title: Pancreatitis_Day_5_S2

description: Pancreatitis

value: wild type


title: primary tumor_stage 1_#5

source_name: colorectal primary tumor, stage 1


title: primary tumor_stage 1_#4

value: G1,Well differentiated


title: Melanoma cell line T1

value: male

tag: nrasq61l mutation status

tag: nrasq61r mutation status


title: primary tumor_stage 1_#3


title: Melanoma cell line G1

tag: brafv600e mutation status


title: Control_Day_3_S3

description: Control

source_name: Control, day 3

tag: cell type

value: pancreatic ductal and duct-like cells (DBA lectin positive)

value: day 3


title: Pancreatitis_Day_5_S1

description: Pancreatitis


title: primary tumor_stage 1_#2

tag: age


title: Melanoma cell line 501mel


title: Melanoma cell line Gerlach

value: Gerlach


title: Melanoma cell line Lyse

value: Lyse

value: wt


title: Melanoma cell line Mull

value: Mull

value: mut


title: Melanoma cell line Daju

value: Daju


title: Melanoma cell line Dauv-1


title: Melanoma cell line Rosi

value: Rosi


title: Melanoma cell line SK29


title: primary tumor_stage 1_#1

value: colorectal primary tumor

value: G2,Moderately differentiated


title: Melanoma cell line SK28


title: distant normal_stage 3_#3

description: matched distant normal mucosa come from the same patient marked with identical sample name(I,II,III and IV stands for TNM stage 1,2,3 and 4,respectively, ca stands for tumor, n stands for normal mucosa);sample name with identical stage and number represent the same patient(for example, I-n-2 and I-ca-2 represent the normal mucosa and tumor from patient #2 of stage I,respectively).

source_name: colorectal distant normal mucosa, stage 3

value: colorectal distant normal mucosa

value: Normal mucosa

value: female


title: distant normal_stage 3_#2


title: distant normal_stage 4_#1

source_name: colorectal distant normal mucosa, stage 4


title: Pancreatitis_Day_3_S3

description: Pancreatitis

source_name: Pancreatitis, day 3

value: wild type

tag: treatment

value: cerulein-induced acute pancreatitis


title: distant normal_stage 3_#4


title: distant normal_stage 3_#1

value: male


title: distant normal_stage 2_#4

source_name: colorectal distant normal mucosa, stage 2


title: Control_Day_3_S1

description: Control

value: pancreatic ductal and duct-like cells (DBA lectin positive)

value: saline


title: Control_Day_3_S2

description: Control

value: day 3


title: distant normal_stage 2_#3


title: Control_Day_1_S3

description: Control

source_name: Control, day 1

value: day 1


title: Melanoma cell line WM983B

value: wt


title: distant normal_stage 2_#2


title: Pancreatitis_Day_3_S1

description: Pancreatitis


title: Melanoma cell line WM983A


title: classical monocytes

source_name: classical monocytes


title: distant normal_stage 2_#1


title: non-classical monocytes

source_name: non-classical monocytes


title: Pancreatitis_Day_3_S2

description: Pancreatitis


title: Control_Day_1_S1

description: Control


title: Pancreatitis_Day_1_S3

description: Pancreatitis

source_name: Pancreatitis, day 1


title: Pancreatitis_Day_1_S2

description: Pancreatitis


title: Control_Day_1_S2

description: Control


title: distant normal_stage 1_#4

source_name: colorectal distant normal mucosa, stage 1


title: Pancreatitis_Day_1_S1

description: Pancreatitis


title: Melanoma cell line WM1366

source_name: melanoma cell line


title: Melanoma cell line A375M


title: Control_Day0_S3

description: Control

source_name: Control, day 0

value: day 0


title: Control vs FSH Replicate 3

city: Charlestown

first: Petr

last: Vodicka

state: Massachusetts

address: 114 16th Street

department: Department of Neurology

institute: Massachusetts General Hospital

description: biological replicate 3

hyb_protocol: Microarray slides were rehydrated for 10 sec above water bath at 50 °C, dried on the heat block for 5 sec at 65 °C and cooled for 1 min at room temperature. This procedure was repeated 4 times. UV cross-linking was performed by exposing rehydrated slides to 180mJ of UV radiation. After crosslinking the slides were washed in 0.1% SDS with constant gently mixing for 5 min followed by rinsing in ddH2O and 3 min incubation in 100% ethanol with constant gently mixing, all steps at room temperature. Slides were dried by centrifugation for 4 min at 200 g. Just before use the microarray slides were pre-hybridized at 42 °C for 1 h in pre-hybridization buffer (5xSSC, 0.1%SDS, 1%BSA) using Tecan HS400Pro hybridization station (TECAN, Austria). Pre-mixed labeled aRNA probes were fragmented using Fragmentation buffer (Ambion Austin, Texas, USA) according to the manufacturer’s instructions. After fragmentation, probes were denatured for 5 min at 90 °C, mixed with 130 µl of SlideHyb Glass Array Hybridization Buffer # 1 (Ambion Austin, Texas, USA) preheated to 68 °C and hybridized for 15 h at 42 °C in the Tecan HS400Pro to pre-hybridized microarray slides. After hybridization, slides were washed and dried automatically in Tecan HS400Pro instrument and stored in dark until scanned (the same day).

scan_protocol: Slides were scanned using High-Resolution Microarray Scanner (Agilent) at 5 µm resolution on 20-bit dynamic range setting. Agilent Feature Extraction Software (v10.7) was used for image analysis.

data_processing: Microarray data background correction, normalization and statistical inference of changes in gene expression were performed using Bioconductor package Limma in R statistical environment. Briefly, spot and background median signals were imported into R data-frame and normex background correction was applied. After print-tip loess within array normalization A-quantile normalization was used to make signal intensities more comparable across arrays.

label: AlexaFluor 555

source_name: cumulus cells_untreated control

label_protocol: aRNA was prepared with one-round amplification using AminoAllyl MessageAmp II Kit (Ambion, Austin, Texas, USA). Time of in vitro transcription was 14 h. Five µg of aRNA were conjugated with either Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, California, USA). Labeled aRNAs were purified using PicoPure RNA isolation kit (Arcturus) according to the manufacturer’s instructions; 2 µg of each labeled aRNA (Alexa Fluor 555 and Alexa Fluor 647 conjugated aRNA samples according to the experimental design) were mixed together and stored at −80 °C.

growth_protocol: Ovaries of slaughtered gilts were collected at a local abattoir and transported to the laboratory in a thermos at 37°C. The contents of the medium size follicles (3-6 mm in diameter) was aspirated by a syringe connected with a 20 G needle, pooled in a Petri-dish and washed twice with PBS. COCs were isolated from the diluted aspirate and washed in PBS. Only COCs surrounded by compact multi-layered cumulus were selected for experiments. About 30 COCs were cultured in 0.5 ml of medium M-199 (#31150; Gibco, Life Technologies, Rockville, USA) supplemented with 0.91 mM sodium pyruvate, 0.57 mM cysteine, 4.2 mM Hepes, antibiotics and 5% fetal calf serum (FCS; #F2442). The COCs were cultured in 4-well dishes (Nunclon, Roskilde, Denmark) at 38.5 °C in a humidified atmosphere of 5% CO2 in the air for 3 h.

extract_protocol: At the end of the culture period, about 150 COCs were transferred in a Petri dish with 2 ml of PBS supplemented with 5 % FCS. The cumulus cells were stripped of oocytes mechanically by pipetting. The oocytes were removed and PBS with a suspension of the separated cumulus cells was transferred in a microtube and briefly centrifuged in a microcentrifuge. The supernatant was discarded and the pellet of cumulus cells was lysed in 300 µl of RTL buffer (Qiagen, Hilden, Germany) and stored at −80 °C. Total RNA from all nine samples was isolated using an RNeasy PLUS mini kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was verified by using RNA 6000 Nano LabChip by Agilent 2100 Bioanalyzer. Only RNA samples with resulting RNA integrity number (RIN) between 8.2–9.1 were used for amplification of aRNA.

treatment_protocol: Culture of COCs in control conditions (see growth protocol below).

value: Cumulus cells from cumulus-oocyte complexes

tag: treated with

value: none (untreated control)

tag: in vitro culture time

value: 3 h

label: AlexaFluor 647

source_name: cumulus cells_FSH

treatment_protocol: The maturation of COCs was stimulated by the addition of human recombinant FSH (100 ng/ml; Gonal F; Merck Serono Europe, London, GB) into the culture medium.

value: FSH


title: distant normal_stage 1_#3

tag: histology


title: Melanoma cell line Lu1205

value: mut


title: Melanoma cell line MeWo

value: MeWo


title: TOL, ITN010AD_687298_0V1

city: Bethesda

first: Adam

last: Asare

state: MD

address: 7500 Old Georgetown Road, Suite 800

department: Bioinformatics Group

institute: Immune Tolerance Network

description:
ITN010AD_687298 Visit V1
cDNA

scan_protocol: Products were resolved on a linear MALDI-TOF mass spectrometer (MassARRAY Compact, Sequenom, San Diego, CA.). Signal acquisition, allele assignment and peak area integration per spectrum were conducted with the MassARRAY RT Workstation v3.4 (Sequenom, San Diego, CA).

data_processing:
Data was analyzed using MassARRAY QGE Analyzer v3.4 (Sequenom, San Diego, CA.) with copy numbers for each transcript per sample determined based on the EC50 of standard curve titrations of known competitor amounts per assay vs. a fixed amount of cDNA template.
Normalization of copy numbers between samples for the different assays was conducted using a multiplexed set of ten well-characterized human housekeeping (normalization) transcripts plus an 18s RNA assay and geNorm software. Normalization factors per sample were calculated using the geometric mean of the most stable combination of these normalization assays, determined by the measure of their pairwise variation as calculated by geNorm.

source_name: TOL, cohort ITN010

label_protocol: Multiplexed primer and competitive template designs were created using the MassARRAY quantitative gene expression (MassARRAY QGE) Assay Design software for random hexamer priming, such that at least 1 PCR primer spanned an exonic boundary per transcript assayed.

extract_protocol: RNA was extracted from whole blood collected in ABI Tempus tubes. Extraction was performed using the ABI6100 instrument.

treatment_protocol: Participants in this study received no protocol related treatment.

value: peripheral whole blood

tag: disease state

value: renal transplant

tag: group

value: tolerant

tag: patient id

tag: visit

tag: cohort


title: FSH vs AREG/EREG Replicate 3

description: biological replicate 3

source_name: cumulus cells_AREG/EREG

treatment_protocol: The maturation of COCs was stimulated by the addition of recombinant human AREG (100 ng/ml, Sigma) and EREG (100 ng/ml; R&D Systems, Minneapolis, MN, USA) into the culture medium.

value: AREG/EREG


title: Melanoma cell line WM852

tag: cell line

tag: gender

value: male


title: Control_Day0_S2

description: Control

tag: strain/background

tag: genotype/variation

value: wild type

value: pancreatic ductal and duct-like cells (DBA lectin positive)

tag: time


title: AREG/EREG vs Control Replicate 3

description: biological replicate 3


title: Control_Day0_S1

description: Control

value: saline


title: FSH vs AREG/EREG Replicate 2

description: biological replicate 2 (dye-swap)


title: Control vs FSH Replicate 2

description: biological replicate 2 (dye-swap)


title: TOL, ITN036ST_968123_022

description:
ITN036ST_968123 Visit 22
cDNA

source_name: TOL, cohort ITN036

tag: tissue


title: TOL, ITN036ST_968123_018

description:
ITN036ST_968123 Visit 18
cDNA


title: TOL, ITN010AD_564051_0V1

description:
ITN010AD_564051 Visit V1
cDNA


title: TOL, ITN010AD_093464_0V1

description:
ITN010AD_093464 Visit V1
cDNA


title: TOL, ITN036ST_464831_022

description:
ITN036ST_464831 Visit 22
cDNA


title: TOL, ITN010AD_014804_0V1

description:
ITN010AD_014804 Visit V1
cDNA


title: Control vs FSH Replicate 1

description: biological replicate 1

tag: cell type


title: AREG/EREG vs Control Replicate 1

description: biological replicate 1


title: FSH vs AREG/EREG Replicate 1

description: biological replicate 1


title: Myocardium_MI+Val_4w_rep5

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

description:
8324341119_F
remote non-infarcted LV posterior and inferior wall

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol for iSCAN.

data_processing: Data variance stabilizing transformation (VST) and robust spline normalization (RSN) were conducted with the lumi R package implemented in BRB-ArrayTools 4.3.2, Bioconductor v. 2.12, and R v. 3.0.1.

source_name: Left ventricle, Valsartan-treated myocardial infarction, 4 weeks

label_protocol: RNA was used to generate biotinylated, linearly amplified RNA (cRNA) by Total Prep RNA Amplification Kit (Life Technologies), according to manufacturer’s manual.

growth_protocol: Animals were fed ad libitum with standard chow and water.

extract_protocol: Total RNA was extracted using silica-membrane RNeasy spin columns (Qiagen) following recommended manufacturer's instructions. RNA was treated with Turbo RNase-free DNase (Life Technologies) as described by the manufacturer's protocol. RNA quantity and purity were assessed by micro-volume spectrophotometry using an Infinite 200 PRO plate reader (Tecan). The quality and integrity of the total RNA were checked by the RNA 6000 Nano Assay kit in a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Infarcted mice with an ejection fraction (EF), obtained by CMR at 24 h, within the range 35-45% were randomized to 1:1 to Valsartan 1 mg/Kg/die in drinking water or water only for 4 weeks.

value: female

tag: strain

tag: age

value: 8-10 weeks

tag: stress

value: myocardial infarction

tag: agent

value: Valsartan

value: cardiac muscle (non-infarcted left ventricle)


title: AREG/EREG vs Control Replicate 2

description: biological replicate 2 (dye-swap)

value: Cumulus cells from cumulus-oocyte complexes

tag: treated with

value: none (untreated control)

tag: in vitro culture time

value: 3 h


title: Myocardium_sham_4w_rep6

description:
8324341119_D
remote non-infarcted LV posterior and inferior wall

source_name: Left ventricle, sham operated control, 4 weeks

value: sham operation

value: control


title: distant normal_stage 1_#1

value: colorectal distant normal mucosa

tag: histology

value: Normal mucosa

tag: Sex


title: 23S rRNA from Rhodococcus (AE4)

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
transfected with AE4
Raw data in Cy3 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_1.txt

hyb_protocol: The cRNA samples were then hybridized at 65uC for 17 h.

scan_protocol: Signal intensity was calculated from digitized images captured by a scanner from Agilent (Santa Clara, CA)

data_processing: Data analysis was performed by using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Cy5/Cy3 channels processed separately (no ratio data).

source_name: Fibroblast cell line

label_protocol: Both Cy3 and Cy5-labeled cRNA samples were prepared with two color labeling kit (Agilent Technologies, Santa Clara, CA)

extract_protocol: Total RNAs were isolated with an miRNeasy column (Qiagen, Valencia, CA)

treatment_protocol: The mouse Dicer deficient (DCR -/-) fibroblast cell line was generated from a conditional cre-lox Dicer allele, transgenic mouse available from JAX (http://jaxmice.jax.org/strain/006001.html) kindly provided by Dr. Jacques Peschon. Part of the RNase III domain encoded in the exon 23 of dicer gene was deleted following cre excision. DCR 2/2 cells were maintained in Dubecco’s modified Eagle’s medium with high glucose. The media was supplemented with 10% FBS, 1% non-essential amino acid, 1% Glutamax. The cells were routinely incubated at 37uC in a humidified atmosphere with 5% CO2. LipofectamineRNAiMAX was purchased from Invitrogen (Life Technologies, Carlsbad, CA). Exogenous RNA for transfection was obtained from Ambion (Life Technologies, Carlsbad, CA) and followed their custom miRNA design protocol. DCR2/2 cells were seeded at a density of 16105 cells in 6-well tissue culture plates 24 h prior to transfect with 10 nM of synthetic RNAs. Cells exposed to transfection reagents only were used as control. After 24 hours in the transfection media, the cells were harvested for RNA isolation and the transfection efficiency was validated with QPCR.

tag: transfection


title: Myocardium_MI+Val_4w_rep4

description:
8324341119_E
remote non-infarcted LV posterior and inferior wall


title: 23S rRNA from Rhodococcus (AE2)

description:
transfected with AE2
Raw data in Cy3 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_3.txt

growth_protocol: The cells were routinely incubated at 37uC in a humidified atmosphere with 5% CO2.

value: Dicer deficient (DCR -/-) fibroblast cell line


title: 23S rRNA from Rhodococcus (AE3)

description:
transfected with AE3
Raw data in Cy3 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_2.txt


title: 16S rRNA from Pseudomonas (AE1)

description:
transfected with AE1
Raw data in Cy3 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_4.txt


title: TOL, ITN036ST_456317_022

description:
ITN036ST_456317 Visit 22
cDNA

value: peripheral whole blood

tag: disease state

value: renal transplant

tag: group

value: tolerant

tag: patient id

tag: visit

tag: cohort


title: miR-263a from mosquito

description:
transfected with tca_miR-263
Raw data in Cy5 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_3.txt


title: TOL, ITN036ST_456317_018

description:
ITN036ST_456317 Visit 18
cDNA


title: Control1

description:
transfected with control1
Raw data in Cy5 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_4.txt


title: Myocardium_sham_4w_rep5

description:
8324341119_C
remote non-infarcted LV posterior and inferior wall

tag: gender


title: Myocardium_MI_4w_rep6

description:
8324341119_B
remote non-infarcted LV posterior and inferior wall

source_name: Left ventricle, untreated myocardial infarction, 4 weeks

tag: tissue


title: Bantam from house fly

description:
transfected with nvi_bantam
Raw data in Cy5 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_2.txt

tag: cell type


title: TOL, ITN036ST_464831_018

description:
ITN036ST_464831 Visit 18
cDNA


title: Fg_Barley_2d_BR3_cy5 vs mock

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description: Barley infected with Fusarium graminearum for 48hrs vs mock infected barley

hyb_protocol: Hybridizations were incubated overnight at 65ºC in a Robbins 400 oven outfitted with a Hybridization Oven Rotator (Agilent G2530-60029). Slides were washed as recommended by Agilent: Wash with Stabilization and Drying Solution.

scan_protocol: Slides were scanned on the Genepix 4200a (Molecular Devices) at 5µ resolution. Images were quantified using Genepix Pro 6.0 (Molecular Devices)

data_processing: Array results files (.gpr) were imported in Acuity 4.0 and normalized by ratio-based method using spike-in control (+)E1A_r60_1, which has a cy5:cy3 ratio of 1:1. There are 20 copies of (+)E1A_r60_1 on each array. Two datasets were formed with all arrays and the datatypes were changed to F532-B532 and F635-B635 respectively to remove false signals from dust or other contaminants. After the removal of false signals, for each dataset, features that did not have intensities higher than 250 in at least 1 of 8 replicates were removed. A new dataset was formed with the remaining features from each , and the datatype was changed to Ratio of Medians. Spike-in controls were removed. Cy3 test array data were swapped to cy5. Technical replicates were combined.

label_protocol: 500ng of total RNA was labelled using reagents and procedure described in the Two-color Quick Amp Labeling protocol version 5.7 (Agilent Technologies) except only half the amounts of reagents were used in Step 2 of the labelling reaction.

growth_protocol: Maize inbred B73 was grown in the field on the Central Experimental Farm, Ottawa, ON in 2004 and 2006. Wheat cultivar Roblin and barley cultivar Encore were grown in the greenhouse under conditons of 16 h light (20oC) and 8h dark (16oC).

extract_protocol: Total RNA was extracted using a guanidine isothiocyanate-cesium chloride method (Ohan and Heikkila 1995).

treatment_protocol: All three plant species were inoculated with F. graminearum strain DAOM180378 (15ADON-producer). Field-grown maize (Zea mays) inbred B73 ears were sib-crossed and developing kernels (eleven days post-fertilization) were inoculated through the husks with 0.1 ml of macroconidia suspension (5 x 105  spores/ml) (between 8 am and 10 am) and fields were irrigated for 15 min every afternoon during the inoculation period. The spring wheat (Triticum aestivum) cultivar Roblin and barley (Hordeum vulgare) cultivar Encore were grown in a controlled-environment cabinet with 16h light (20°C) and 8h dark (16°C).  At mid-anthesis, each biological replicate of six wheat heads were point inoculated by pipetting 10 µl of a 10,000 spores/mL F. graminearum macroconidia suspension between lemma and plea of two primary florets in each spikelet. All fully developed spikelets on each head were inoculated.  In the case of barley, at mid-anthesis, each fully developed floret of only two central rows was inoculated and florets from laterals rows were stripped from the rachis. In each inoculated barley floret, the tip of the lemma that includes the awn was excised and 1000 F. graminearum macroconidia were pipetted inside the lemma.  A mock inoculation using water was carried out in parallel. Inoculated wheat and barley plants were misted overhead for 20 sec every 30 min for 2 days to maintain high humidity during the initial infection period and then moved to a non-misted bench in the same cabinet. Infected ears or spikelets were harvested 1, 2 and 4 days post inoculation, flash-frozen in liquid nitrogen, and stored at -80oC.

tag: time

value: 2 days

tag: biorep

tag: growth condition

value: Greenhouse

tag: cultivar

value: Encore


title: Return to SI, ITN036ST_264166_022

description:
ITN036ST_264166 Visit 22
cDNA

source_name: Return to SI, cohort ITN036

value: return to standard immunosuppression


title: Return to SI, ITN036ST_264166_018

description:
ITN036ST_264166 Visit 18
cDNA


title: Fg_Barley_2d_BR3_cy3 vs mock


title: Sirolimus Monotherapy, ITN013ST_877664_062

description:
ITN013ST_877664 Visit 62
cDNA

source_name: Sirolimus Monotherapy, cohort ITN013

value: Sirolimus monotherapy


title: Sirolimus Monotherapy, ITN013ST_805828_062

description:
ITN013ST_805828 Visit 62
cDNA


title: Sirolimus Monotherapy, ITN013ST_597519_062

description:
ITN013ST_597519 Visit 62
cDNA


title: Myocardium_MI+Val_4w_rep2

description:
8324341115_D
remote non-infarcted LV posterior and inferior wall

value: female

tag: strain

tag: age

value: 8-10 weeks

tag: stress

value: myocardial infarction

tag: agent

value: Valsartan

value: cardiac muscle (non-infarcted left ventricle)


title: Sirolimus Monotherapy, ITN013ST_561464_062

description:
ITN013ST_561464 Visit 62
cDNA


title: Control2

description:
transfected with control2
Raw data in Cy5 channel of file:
252665512178_201202090928_S01_GE2_107_Sep09_1_1.txt

tag: transfection


title: Myocardium_sham_4w_rep4

description:
8324341115_F
remote non-infarcted LV posterior and inferior wall

value: sham operation

value: control


title: Fg_Barley_4d_BR2_cy3 vs mock

description: Barley infected with Fusarium graminearum for 96hrs vs mock infected barley

value: 4 days


title: Myocardium_MI+Val_4w_rep3

description:
8324341115_E
remote non-infarcted LV posterior and inferior wall


title: Myocardium_sham_4w_rep2

description:
8324341115_B
remote non-infarcted LV posterior and inferior wall


title: T B6 475 X LOW male

city: Madrid

first: Javier

last: Santos

address: Nicolás Cabrera, 1,

institute: Department of Cellular Biology and Immunology. Severo Ochoa Molecular Biology Center. Autonomous University (CBMSO-UAM)

description:
475Xlow-m
Independent sample 2 of 3

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing:
Data from hybridized microarray images were quantitated, backgound subtracted, corrected by additive detrending and submitted to intra-array Lowess global normalization with Agilent FeatureExtraction (FE) Software.
Lowess normalization reduces spurious bias by merging two-color data, and applying a smoothing adjustment that corrects non-linear dye-specific variation.
Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalized signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12 software.
Thresholding is a simple substitution step that removes very small expression values or negative values, so that there would not be large negative values or missing values in the log transformed data.
Normalization involves Log2 data transformation, which generates a roughly normal distribution and allows to use statistical parametric tests (student’s t-test, etc).

source_name: thymocyte sample

label_protocol:
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.
Labeled samples are purified with silica-based spin columns.
Microarray: Mouse Gene Expression G3 60K (Agilent microarray design ID 028005, P/N G4852A). Microarray sequences and annotations are listed in sheet '028005_mm9_20121126'.

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

treatment_protocol: Thymocytes were irradiated under three different radiation conditions: (1) priming low dose radiation (0.075 Gy of X-rays) 6 hour before high dose radiation (1.75 Gy of gamma rays); (2) low dose radiation (0.075 Gy of X-rays); (3) high dose radiation (1.75 Gy of gamma rays).

value: primary thymocytes

value: male

value: treated with low dose irradiation

source_name: Universal Mouse RNA (Stratagene)

tag: reference

value: Pool of amplified RNAs


title: Fg_Barley_4d_BR2_cy5 vs mock

value: 2 days


title: Myocardium_sham_4w_rep3

description:
8324341115_C
remote non-infarcted LV posterior and inferior wall


title: Myocardium_MI_4w_rep4

description:
8324341055_F
remote non-infarcted LV posterior and inferior wall


title: Fg_Barley_1d_BR3_cy3 vs mock

description: Barley infected with Fusarium graminearum for 24hrs vs mock infected barley

value: Greenhouse

value: 1 day


title: SI Multiagent, ITN013ST_492821_062

description:
ITN013ST_492821 Visit 62
cDNA

source_name: SI Multiagent, cohort ITN013

value: peripheral whole blood

tag: disease state

value: renal transplant

tag: group

value: standard immunosuppression multiagent


title: T B6 464 X+G male

description:
464X+G-m
Independent sample 3 of 3

value: radio-adapted


title: Fg_Barley_2d_BR2_cy3 vs mock

value: Encore


title: Fg_Barley_1d_BR3_cy5 vs mock


title: Fg_Barley_2d_BR2_cy5 vs mock