title: Han Chinese American [GM17824]

description: healthy sample


title: Han Chinese American [GM17826]

status: Public on Jul 22 2013

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: healthy sample

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: The intensities of the images were extracted using GenomeStudio (V2011.2) Methylation module (1.8.5) software. The methylation score of each CpG is represented as a beta value.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel.

tag: cell line

tag: gender

value: Male

tag: health state

value: Healthy donor


title: Han Chinese American [GM17812]

description: healthy sample


title: Han Chinese American [GM17816]

description: healthy sample

value: Female


title: Han Chinese American [GM17813]

description: healthy sample


title: Han Chinese American [GM17817]

description: healthy sample


title: Han Chinese American [GM17814]

description: healthy sample


title: Han Chinese American [GM17810]

description: healthy sample


title: Han Chinese American [GM17815]

description: healthy sample


title: Han Chinese American [GM17809]

description: healthy sample


title: Han Chinese American [GM17808]

description: healthy sample


title: Han Chinese American [GM17811]

description: healthy sample


title: Han Chinese American [GM17804]

description: healthy sample


title: Han Chinese American [GM17806]

description: healthy sample


title: Han Chinese American [GM17807]

description: healthy sample


title: Han Chinese American [GM17803]

description: healthy sample


title: Han Chinese American [GM17800]

description: healthy sample


title: Han Chinese American [GM17805]

description: healthy sample


title: Han Chinese American [GM17798]

description: healthy sample


title: Han Chinese American [GM17795]

description: healthy sample


title: Han Chinese American [GM17799]

description: healthy sample


title: Han Chinese American [GM17801]

description: healthy sample


title: Han Chinese American [GM17802]

description: healthy sample


title: Han Chinese American [GM17796]

description: healthy sample


title: Han Chinese American [GM17797]

description: healthy sample


title: Han Chinese American [GM17791]

description: healthy sample


title: Han Chinese American [GM17789]

description: healthy sample


title: Han Chinese American [GM17793]

description: healthy sample


title: Han Chinese American [GM17785]

description: healthy sample


title: Han Chinese American [GM17782]

description: healthy sample


title: Han Chinese American [GM17790]

description: healthy sample


title: Han Chinese American [GM17774]

description: healthy sample


title: Han Chinese American [GM17794]

description: healthy sample


title: Han Chinese American [GM17823]

description: healthy sample


title: Han Chinese American [GM17775]

description: healthy sample


title: Han Chinese American [GM17783]

description: healthy sample


title: Han Chinese American [GM17780]

description: healthy sample


title: Han Chinese American [GM17773]

description: healthy sample


title: Han Chinese American [GM17766]

description: healthy sample


title: Han Chinese American [GM17771]

description: healthy sample


title: Han Chinese American [GM17770]

description: healthy sample


title: Han Chinese American [GM17779]

description: healthy sample


title: Han Chinese American [GM17761]

description: healthy sample


title: Han Chinese American [GM17787]

description: healthy sample


title: Han Chinese American [GM17765]

description: healthy sample


title: Han Chinese American [GM17759]

description: healthy sample


title: Han Chinese American [GM17745]

description: healthy sample


title: Han Chinese American [GM17754]

description: healthy sample


title: Han Chinese American [GM17753]

description: healthy sample


title: Han Chinese American [GM17756]

description: healthy sample


title: Han Chinese American [GM17758]

description: healthy sample


title: Han Chinese American [GM17767]

description: healthy sample


title: Han Chinese American [GM17742]

description: healthy sample


title: Han Chinese American [GM17746]

description: healthy sample


title: Han Chinese American [GM17744]

description: healthy sample


title: Han Chinese American [GM17739]

description: healthy sample


title: Han Chinese American [GM17747]

description: healthy sample


title: Han Chinese American [GM17755]

description: healthy sample


title: Han Chinese American [GM17762]

description: healthy sample


title: Han Chinese American [GM17741]

description: healthy sample


title: Han Chinese American [GM17749]

description: healthy sample


title: Han Chinese American [GM17737]

description: healthy sample


title: Han Chinese American [GM17752]

description: healthy sample


title: Han Chinese American [GM17740]

description: healthy sample


title: Han Chinese American [GM17743]

description: healthy sample


title: Han Chinese American [GM17736]

description: healthy sample


title: Han Chinese American [GM17734]

description: healthy sample


title: Han Chinese American [GM17768]

description: healthy sample


title: Han Chinese American [GM17733]

description: healthy sample


title: Han Chinese American [GM17738]

description: healthy sample


title: Han Chinese American [GM17735]

description: healthy sample


title: African American [GM17194]

description: healthy sample


title: African American [GM17192]

description: healthy sample


title: African American [GM14496]

description: healthy sample


title: African American [GM17189]

description: healthy sample


title: African American [GM17196]

description: healthy sample


title: Han Chinese American [GM17776]

description: healthy sample


title: African American [GM17180]

description: healthy sample


title: African American [GM17188]

description: healthy sample


title: Han Chinese American [GM17792]

description: healthy sample


title: African American [GM17190]

description: healthy sample


title: African American [GM17181]

description: healthy sample


title: Han Chinese American [GM17757]

description: healthy sample


title: African American [GM17186]

description: healthy sample


title: African American [GM17184]

description: healthy sample


title: African American [GM17185]

description: healthy sample


title: African American [GM17182]

description: healthy sample


title: Han Chinese American [GM17764]

description: healthy sample


title: African American [GM17179]

description: healthy sample


title: African American [GM17193]

description: healthy sample


title: African American [GM17187]

description: healthy sample


title: Han Chinese American [GM17769]

description: healthy sample


title: African American [GM17178]

description: healthy sample


title: African American [GM17183]

description: healthy sample


title: African American [GM17191]

description: healthy sample


title: African American [GM17174]

description: healthy sample


title: African American [GM17173]

description: healthy sample


title: wild_37_4a

type: RNA

city: beijing

first: jianghong

last: yan

state: beijing

address: NO.1 West Beichen Road

country: China

institute: Institute of Microbiology

description: w_37_4a@252368110008_S01_GE1_105_Dec08_1_4

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent). After fragmentation, 1 mg of cRNA was hybridized at 65°C for 17 h with a rotation at 10 rpm.

scan_protocol: arrays were scanned using an Agilent Microarray Scanner System (G2565BA) (Agilent) with a resolution of 5 µm, 100% and 10% PTM respectively and the two data sets were combined automatically.

data_processing: The signal intensities were normalized using the Feature Extraction Software (Agilent). Data were analyzed using Genespring Software 5.0. Genes with all signals present (flag=P) were selected for analysis. Different genes were selected with P≤0.05, FC≥1.5 by T-test methods.

molecule: total RNA

organism: Aspergillus fumigatus

source_name: mycelia

label_protocol: 2 mg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After purification, 4 mg cRNA was labeled with Cy3 NHS ester and purified.

growth_protocol: 2×108 conidia were inoculated in 200 ml of liquid CM and incubated at 37°C for 36h with shaking at 200 rpm.

extract_protocol: Mycelia were ground by hand using liquid nitrogen.The powder was used to extract total RNA using Trizol according to the manufacturer’s instructions.

treatment_protocol: afpig-a mutant was constructed by replacing the native promoter of the afpig-a gene with alcA promoter which is repressed in CM media

tag: genotype/variation

value: wild-type

tag: inoculation density

tag: temperature

tag: rotation speed

tag: cultivated time


title: African American [GM17175]

description: healthy sample


title: wild_37_3a

description: w_37_3a@252368110008_S01_GE1_105_Dec08_1_3

value: 2×108 conidia were inoculated in 200 ml of liquid CM


title: African American [GM17171]

description: healthy sample


title: African American [GM17166]

description: healthy sample


title: African American [GM17165]

description: healthy sample


title: African American [GM14544]

description: healthy sample


title: African American [GM17164]

description: healthy sample


title: African American [GM17172]

description: healthy sample


title: African American [GM17170]

description: healthy sample


title: African American [GM17154]

description: healthy sample


title: wild_37_2a

description: w_37_2a@252368110008_S01_GE1_105_Dec08_1_2


title: African American [GM17168]

description: healthy sample


title: African American [GM17161]

description: healthy sample


title: wild_37_1a

description: w_37_1a@252368110008_S01_GE1_105_Dec08_1_1


title: African American [GM17162]

description: healthy sample


title: African American [GM17157]

description: healthy sample


title: African American [GM17153]

description: healthy sample


title: African American [GM17176]

description: healthy sample


title: African American [GM17152]

description: healthy sample


title: African American [GM17151]

description: healthy sample


title: African American [GM17177]

description: healthy sample


title: mutant_37_3a

description: afpiga_37_3a@252368110008_S01_GE1_105_Dec08_2_3

value: conditional afpig-a mutant


title: African American [GM17156]

description: healthy sample


title: African American [GM17167]

description: healthy sample


title: African American [GM17169]

description: healthy sample


title: African American [GM17149]

description: healthy sample


title: mutant_37_4a

description: afpiga_37_4a@252368110008_S01_GE1_105_Dec08_2_4


title: African American [GM17158]

description: healthy sample


title: African American [GM17159]

description: healthy sample


title: African American [GM17148]

description: healthy sample


title: African American [GM17150]

description: healthy sample


title: African American [GM17160]

description: healthy sample


title: African American [GM17155]

description: healthy sample


title: African American [GM17147]

description: healthy sample


title: mutant_37_2a

description: afpiga_37_2a@252368110008_S01_GE1_105_Dec08_2_2


title: African American [GM17146]

description: healthy sample


title: African American [GM17145]

description: healthy sample


title: African American [GM17143]

description: healthy sample


title: Rice seedlings roots_FA long exposures Replicate 3

city: Tainan

first: Wen-Chang

last: Chi

state: Taiwan

address: No.1, University Road, Tainan City

department: Life Science

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 3 of 3. Rice seedling roots with or without 50 ppm ferulic acid during long (24 h) exposures

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 50 ppm ferulic acid during long (24 h) exposures

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after ferulic acid treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.

growth_protocol: 6-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Control and rice seedlings were exposed to to 50 ppm ferulic acid during short (pooled from 1- and 3-h treatments) exposures or long (24 h) exposures

tag: cultivar

value: cv. TN-67

tag: agent

value: 50 ppm ferulic acid

tag: time point

value: long (24 h)

tag: age

value: 6 day

source_name: Rice seedlings roots were exposed to water

value: water


title: Rice seedlings roots_FA short exposures Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 50 ppm ferulic acid short (pooled from 1- and 3-h treatments) exposures

source_name: Roots of rice seedlings were exposed to 50 ppm ferulic acid during short (pooled from 1- and 3-h treatments) exposures


title: Rice seedlings roots_FA long exposures Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 50 ppm ferulic acid during long (24 h) exposures


title: A2780CBNDXL vs A2780CC

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

country: Canada

institute: Advanced Medical Research Institute of Canada

description:
A2780CBNDXL US83003524_251485049378_S01_GE2_107_Sep09_1_1:technical replicate 1 of 4
A2780CBNDXL US83003524_251485049378_S01_GE2_107_Sep09_1_2:technical replicate 2 of 4
A2780CBNDXL US83003524_251485055720_S01_GE2_107_Sep09_1_1:technical replicate 3 of 4
A2780CBNDXL US83003524_251485055720_S01_GE2_107_Sep09_1_2:technical replicate 4 of 4

hyb_protocol: Microarray hybridization process was conducted as per description by Agilent Two-clour Microarray-based gene expression Analysis

scan_protocol: After hybridization, the microarray slides were scanned by using an Agilent G2505C scanner as discribed in Agilent manual.

data_processing:
Images were quantified and background subtraction was performed using Agilent Feature Extraction Software (version A.10_7_3).
Normalized log2 ratio (Cy5/Cy3) was used to represent the ratio of test/reference, which means A2780CBN/A2780CC and A2780CBNDXL/A2780CC. Data analysis was done using Partek Genomic suite after feature extraction.  A 3-way ANOVA model was performed by using Method of Moments (Eisenhart, 1947) as outlined below :  Model: Yijkl = μ + (Cell lines)i+Dyesj+Arraysk+ εijkl  Where Yijkl represents the lth observation on the ith Cell lines jth Dyes kth Arrays   μ is the common effect for the whole experiment.  εijkl represents the random error present in the lth observation on the ith Cell lines jth Dyes kth Arrays. The errors εijkl are assumed to be normally and independently distributed with mean 0 and standard deviation δ for all measurements. Arrays is a random effect.    Fold changes of the differentially expressed genes between drug resistant and parental cells were calculated and genes with more than two-fold difference were selected with FDR at either 0.05 or 0.01. (Tamhane, Ajit C., & Dunlop, Dorothy D. 2000)

source_name: human ovarian cancer cells

label_protocol: Agilent 4×44k oligonucleotide arrays (Agilent, Product #: G4112F.) were used in our microarray experiments to compare the expression of genes between drug-selected docetaxel resistant cells and its parental cells. 500 ng of RNA  was used. Labelling was done using the Quick Amp labeling kit (Agilent, #5190-0444) as described in Agilent manual.

growth_protocol: Cells were grown in tissue culture flucks with RPMI 1640 medium at 37C with 5% of CO2, and subcultured when cell density reached 80-90% confluence.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen), and quantity and quality were assessed using Agilent BioAnalyizer. 3 separate isolations with RIN at 10 were pooled together for labelling.

treatment_protocol: Cell were cultured and selected for survival in increasing doses of docetaxel or carboplatin or combination of two drugs as previously described (Guo B, Villeneuve DJ, Hembruff SLet al. Breast Cancer Res Treat. 2004;85(1):31-5126;27).  A2780 cells selected to terminally tolerated dose at 405 nM of docetacel (A2780DXL, GSE26129), 22.2 uM of carboplatin (A2780CBN), and at 8.02 uM of a combination of both carboplatin and docetaxel (A2780CBNDXL) were used in this microarray study.


title: Rice seedlings roots_FA short exposures Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 50 ppm ferulic acid short (pooled from 1- and 3-h treatments) exposures


title: African American [GM17144]

description: healthy sample


title: Rice seedlings roots_FA short exposures Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 50 ppm ferulic acid short (pooled from 1- and 3-h treatments) exposures


title: Rice seedlings roots_FA long exposures Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 50 ppm ferulic acid during long (24 h) exposures


title: African American [GM17141]

description: healthy sample


title: African American [GM17142]

description: healthy sample


title: African American [GM17138]

description: healthy sample


title: African American [GM17139]

description: healthy sample


title: African American [GM17133]

description: healthy sample


title: A2780CBN vs A2780CC

description:
A2780CBN US83003524_251485049378_S01_GE2_107_Sep09_1_3:technical replicate 1 of 4
A2780CBN US83003524_251485049378_S01_GE2_107_Sep09_1_4:technical replicate 2 of 4
A2780CBN US83003524_251485055720_S01_GE2_107_Sep09_1_3:technical replicate 3 of 4
A2780CBN US83003524_251485055720_S01_GE2_107_Sep09_1_4:technical replicate 4 of 4


title: HBL-1 DMSO 12h R1

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

hyb_protocol: Hybridization was performed with HumanHT-12 v4 Expression BeadChip kit (Illumina) according to manufacturer's protocol.

scan_protocol: Scan was performed according to manufacturer's protocol.

data_processing: Data were imported on raw bead level (see supplementary data files) and subsequently a bead level spotfilter was applied for each microarray based on the fitted density mode for the background intensities. Afterwards, bead intensities of all measured microarrays were quantile-normalized and beads were grouped by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations.

label: biotin

source_name: male ABC DLBCL cell line HBL-1, DMSO, 12hr

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol.

growth_protocol: Cell line HBL-1 was maintained in RPMI medium with 10%FBS at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted with NucleoSpin RNAII kit (Illumina) according to manufacturer's protocol.

treatment_protocol: Cell line HBL-1 was treated with MLN120b or carrier (DMSO).

tag: treatment

value: DMSO

tag: duration in hours

tag: replicate


title: HBL-1 DMSO 24h R1

source_name: male ABC DLBCL cell line HBL-1, DMSO, 24hr


title: mutant_37_1a

description: afpiga_37_1a@252368110008_S01_GE1_105_Dec08_2_1


title: African American [GM17130]

description: healthy sample


title: African American [GM17125]

description: healthy sample


title: African American [GM17140]

description: healthy sample


title: African American [GM17132]

description: healthy sample


title: African American [GM17137]

description: healthy sample


title: HBL-1 DMSO 12h R2


title: HBL-1 DMSO 24h R2


title: African American [GM17129]

description: healthy sample


title: African American [GM17136]

description: healthy sample


title: African American [GM17135]

description: healthy sample


title: African American [GM17131]

description: healthy sample


title: African American [GM17128]

description: healthy sample


title: African American [GM17126]

description: healthy sample


title: African American [GM17123]

description: healthy sample


title: African American [GM17127]

description: healthy sample


title: HBL-1 DMSO 6h R1

source_name: male ABC DLBCL cell line HBL-1, DMSO, 6hr


title: HBL-1 DMSO 6h R2


title: African American [GM17124]

description: healthy sample


title: HBL-1 MLN 24h R2

source_name: male ABC DLBCL cell line HBL-1, MLN120b, 24hr

value: 20 µM MLN120b


title: HBL-1 MLN 24h R1


title: HBL-1 MLN 12h R1

source_name: male ABC DLBCL cell line HBL-1, MLN120b, 12hr


title: HBL-1 MLN 6h R2

source_name: male ABC DLBCL cell line HBL-1, MLN120b, 6hr


title: African American [GM17122]

description: healthy sample


title: HBL-1 NFKBIZshRNA-Dox72h R2

scan_protocol: Scanning was performed according to manufacturer's protocol.

data_processing: Data were imported on raw bead level (see supplementary data files) and subsequently a bead level spotfilter was applied for each microarray based on the fitted density mode for the background intensities. Afterwards, bead intensities of all measured microarrays were quantile-normalized and beads were grouped by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer's annotations.

source_name: male ABC DLBCL cell line HBL-1, 72hr

treatment_protocol: Cell line HBL-1 was retrovirally transduced with NFKBIZ shRNA. Transduced cells were selected by puromycin and NFKBIZ shRNA expression was induced by doxycyline.

tag: nfkbiz shrna expression

value: not induced


title: HBL-1 MLN 6h R1


title: HBL-1 MLN 12h R2


title: African American [GM17119]

description: healthy sample


title: HBL-1 NFKBIZshRNA-Dox48h R2

source_name: male ABC DLBCL cell line HBL-1, 48hr


title: African American [GM17118]

description: healthy sample


title: HBL-1 NFKBIZshRNA-Dox96h R2

source_name: male ABC DLBCL cell line HBL-1, 96hr


title: HBL-1 NFKBIZshRNA-Dox72h R1


title: HBL-1 NFKBIZshRNA-Dox48h R1


title: African American [GM17121]

description: healthy sample


title: African American [GM17117]

description: healthy sample


title: HBL-1 NFKBIZshRNA-Dox24h R2

source_name: male ABC DLBCL cell line HBL-1, 24hr


title: African American [GM17113]

description: healthy sample


title: HBL-1 NFKBIZshRNA-Dox24h R1


title: Sinorhizobium meliloti CL150 pF1084, biological replicate 3

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

country: USA

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: RpoE2 overexpression strain

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Cultures were inoculated to OD600=0.05 in 20 ml M9 glycerol medium and allowed to grow to mid exponential phase (OD600=0.50-0.55), at which time melibiose was added to a final concentration of 0.4%. Cells were harvested after 30 minutes induction with melibiose.  The reference for the pCAP11 vector is: Arango Pinedo et al., J Bacteriol. 2008 April; 190(8): 2947–2956

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: strain

tag: growth condition

value: Grown to mid exponential phase in M9 glycerol medium, then induced with melibiose for 30 minutes

value: RpoE2 overexpression


title: HBL-1 NFKBIZshRNA+Dox96h R2

source_name: male ABC DLBCL cell line HBL-1, NFKBIZ shRNA, 96hr

tag: cell line

value: induced by doxycycline


title: Sinorhizobium meliloti CL150 pF1084, biological replicate 2


title: HBL-1 NFKBIZshRNA-Dox96h R1


title: African American [GM17120]

description: healthy sample

tag: gender

tag: health state


title: African American [GM17115]

description: healthy sample

value: Male


title: African American [GM17111]

description: healthy sample

value: Healthy donor


title: African American [GM17109]

description: healthy sample


title: African American [GM17112]

description: healthy sample

value: Female


title: African American [GM17106]

description: healthy sample


title: African American [GM17104]

description: healthy sample


title: HBL-1 NFKBIZshRNA+Dox72h R1

source_name: male ABC DLBCL cell line HBL-1, NFKBIZ shRNA, 72hr


title: Sinorhizobium meliloti CL150 pF1084, biological replicate 1


title: African American [GM17134]

description: healthy sample


title: HBL-1 NFKBIZshRNA+Dox72h R2


title: Sinorhizobium meliloti CL150 pCAP11, biological replicate 3

source_name: Control strain

value: CL150 pCAP11

value: control


title: Sinorhizobium meliloti CL150 pCAP11, biological replicate 2


title: HBL-1 NFKBIZshRNA+Dox24h R2

source_name: male ABC DLBCL cell line HBL-1, NFKBIZ shRNA, 24hr


title: simGal4 UAS Dichaete WT vs UAS GFP control rep 1

city: Cambridge

first: Steve

last: Russell

address: Tennis Court Road

department: Genetics

country: United Kingdom

institute: University of Cambridge

description:
DWT1
Biological replicate 1 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

source_name: simgal4 DWT

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: simGal4 females were crossed to UAS construct carrying males. 3.5 - 4.5h Drosophila embryos (stage 8-9) grown at 25˚C were collected.

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes 4 °C to pellet debris and transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, vortex for 60 seconds. Centrifuge at 13,000 rpm for 15 minutes. Remove upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.4 µl GeneElute Linear Polyacrylamide (Sigma) (25 µg / µl stock diluted 1:10 in DEPC MilliQ water) and 0.8 volumes of isopropanol, invert and then incubate for 1 hour at -20 °C. Pellet the RNA by centrifugation at 13,000 rpm for 30 minutes. Discard the supernatant and wash the RNA pellet with 500 µl 70% ethanol/DEPC MilliQ water. Air-dry the pellet. Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 5 µl. Verify quality of RNA on a 0.8 % agarose gel stained with SYBR-gold (Molecular Probes).

treatment_protocol: The embryos were stored in Trizol.

tag: developmental stage

value: Stage 8-9 (3.5-4.5h) embryos

tag: genotype/variation

value: The collected embryos have a simGal4 driver and a UAS construct. Sample embryos are expressing a UAS Dichaete wild type construct.

tag: tissue

value: Whole embryos

source_name: simGal4 GFP

value: The collected embryos have a simGal4 driver and a UAS construct. The control embryos are expressing a UAS GFP construct.


title: simGal4 UAS Dichaete WT vs UAS GFP control rep 3

description:
DWT3
Biological replicate 3 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: simGal4 UAS HMG- vs UAS GFP control rep 3

description:
HMG3
Biological replicate 3 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.

source_name: simgal4 HMG-

value: The collected embryos have a simGal4 driver and a UAS construct. Sample embryos are expressing a UAS HMG- construct.


title: African American [GM17102]

description: healthy sample


title: simGal4 UAS Dichaete WT vs UAS GFP control rep 2

description:
DWT2
Biological replicate 2 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: simGal4 UAS HMG- vs UAS GFP control rep 2

description:
HMG2
Biological replicate 2 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: simGal4 UAS HMG- vs UAS GFP control rep 4

description:
HMG4
Biological replicate 4 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: simGal4 UAS Dichaete WT vs UAS GFP control rep 4

description:
DWT4
Biological replicate 4 of 4. Sample embryos are expressing a UAS Dichaete wild type construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: simGal4 UAS HMG- vs UAS GFP control rep 1

description:
HMG1
Biological replicate 1 of 4. Sample embryos are expressing a UAS HMG- construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: Sinorhizobium meliloti CL150 pCAP11, biological replicate 1


title: African American [GM17108]

description: healthy sample


title: HBL-1 NFKBIZshRNA+Dox96h R1


title: African American [GM17114]

description: healthy sample


title: HBL-1 NFKBIZshRNA+Dox48h R1

source_name: male ABC DLBCL cell line HBL-1, NFKBIZ shRNA, 48hr


title: HBL-1 NFKBIZshRNA+Dox48h R2


title: African American [GM17107]

description: healthy sample


title: Control sample 19

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: According to the manufacturer's instructions (febit biomed).

scan_protocol: Geniom Realtime Analyzer (GRTA, febit gmbh, Heidelberg, Germany). Wizard software on standard Microsoft Windows Workstation PC.

data_processing: Data were normalized using the quantile normalization function normalize.quantiles from the R package preprocessCore. Summarization of technical replica by median.

source_name: RNA from blood, normal control

label_protocol: MPEA, microfluidic primer extension assay, biotin labeling.

extract_protocol: Blood of controls and long-lived individuals was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood was obtained. The content of blood sampling tubes of each patient and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase-free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore, the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform was added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1.5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture was placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT was added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL was added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL was added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase-free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: Stored at -20C degrees.

value: peripheral blood

tag: disease state

value: healthy


title: Control sample 18


title: Control sample 17


title: Control sample 16


title: African American [GM17116]

description: healthy sample


title: HBL-1 NFKBIZshRNA+Dox24h R1


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 38

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affymetrix- 20 ug biotin-labeled cRNA was applied to a rat RGU34A GeneChip (Affymetrix) for hybridization (one chip per animal).

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed for quality control with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Robust Multi-Chip Analysis (RMA) was used to generate signal intensity values using the standard settings in Bioconductor (2.2) operating in the R programming environment (R 2.7.1) with the 'justRMA' command.

organism: Rattus norvegicus

source_name: rat hippocampus (CA1 region)_LowInj

label_protocol: For each sample, 20 ug of biotin-labeled cRNA was generated from 5 ug of total RNA according to manufacturer’s instructions (Standard Affymetrix).

extract_protocol: RNA was extracted from each CA1 tissue block, as described previously (Blalock et al., 2003; Kadish et al., 2009; Rowe et al., 2007) using TRIzol (Invitrogen) followed by ethanol precipitation, and was reconstituted in RNase-free water (Standard Affymetrix)

value: Fisher 344

value: male

value: 18 months

value: hippocampal CA1 brain

tag: treament group

value: Low-CORT (ADX) + short-term high-dose injected


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 36


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 39


title: Control sample 13


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 35


title: Control sample 14


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 37


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 34


title: simGal4 UAS EnRep vs UAS GFP control rep 3

description:
EnRep3
Biological replicate 3 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.

source_name: simgal4 En

value: The collected embryos have a simGal4 driver and a UAS construct. Sample embryos are expressing a UAS EnRep construct.


title: African American [GM17103]

description: healthy sample

value: Male

value: Healthy donor


title: simGal4 UAS EnRep vs UAS GFP control rep 2

description:
EnRep2
Biological replicate 2 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.


title: Control sample 12


title: HBL1 cells treated with MALT inhibitor Z-VRPR-FMK for 24h

hyb_protocol: Hybridization was performed according to Agilent Technologies protocol (Two-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling v.6.5).

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US11163898. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization. An additional spot filter based on the linear intensity was applied requiring Cy3>20 & Cy5>20 | Cy3>100 | Cy5>100.

source_name: male ABC DLBCL cell line HBL-1, MALT inhibitor, 24h

label_protocol: Cy3 and Cy5 labeling was performed according to Agilent Technologies protocol (Two-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labeling v.6.5).

growth_protocol: Cell line HBL-1 was maintained in RPMI medium with 10% FBS at 37°C with 5% CO2

extract_protocol: RNA extraction from the cells was performed with the RNeasy Mini Kit (Qiagen) and genomic DNA was eliminated with the RQ1 RNase-free DNase (Promega) according to the manufacturer's protocol.

treatment_protocol: Cell line HBL-1 was treated with Z-VRPR-FMK or carrier (DMSO).

value: 50 µM of MALT inhibitor Z-VRPR-FMK

tag: treatment duration

tag: date of measurement

source_name: male ABC DLBCL cell line HBL-1, DMSO, 24h

value: DMSO


title: HBL1 cells treated with MALT inhibitor Z-VRPR-FMK for 48h

source_name: male ABC DLBCL cell line HBL-1, MALT inhibitor, 48h

source_name: male ABC DLBCL cell line HBL-1, DMSO, 48h


title: HBL1 cells treated with MALT inhibitor Z-VRPR-FMK for 12h

source_name: male ABC DLBCL cell line HBL-1, MALT inhibitor, 12h

source_name: male ABC DLBCL cell line HBL-1, DMSO, 12h


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 32

tag: age


title: Control sample 11


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 33


title: simGal4 UAS EnRep vs UAS GFP control rep 1

description:
EnRep1
Biological replicate 1 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.

value: Stage 8-9 (3.5-4.5h) embryos


title: HBL1 cells treated with MALT inhibitor Z-VRPR-FMK for 6h

source_name: male ABC DLBCL cell line HBL-1, MALT inhibitor, 6h

tag: treatment

source_name: male ABC DLBCL cell line HBL-1, DMSO, 6h


title: Control sample 10


title: Control sample 9


title: Control sample 7


title: Control sample 4


title: Control sample 5


title: Control sample 6


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 29

source_name: rat hippocampus (CA1 region)_LowCort

value: Low-CORT (ADX)


title: Control sample 2


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 30


title: Control sample 1


title: rat hippocampus (CA1 region), LowInj, 18 months old, subject 31


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 26


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 27


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 28


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 23


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 25


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 24


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 22


title: African American [GM17110]

description: healthy sample

value: Female


title: Tumor sample 23

source_name: RNA from blood, Wilms tumor

value: Wilms tumor


title: African American [GM17101]

description: healthy sample


title: Control sample 3


title: African American [GM17105]

description: healthy sample


title: Tumor sample 21


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 19

source_name: rat hippocampus (CA1 region)_IntermediateCort

value: Intermediate-CORT (ADX)


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 18


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 20


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 17


title: rat hippocampus (CA1 region), LowCort, 18 months old, subject 21


title: Control sample 8

value: peripheral blood


title: Tumor sample 12


title: Tumor sample 22


title: Tumor sample 15


title: Tumor sample 19


title: Tumor sample 16


title: Tumor sample 20


title: Tumor sample 17


title: Tumor sample 14


title: Tumor sample 13


title: Tumor sample 18


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 16


title: Tumor sample 11


title: rat hippocampus (CA1 region), sham, 18 months old, subject 10

source_name: rat hippocampus (CA1 region)_sham

value: Sham (intact) control


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 13

value: Fisher 344


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 14

value: male


title: rat hippocampus (CA1 region), sham, 18 months old, subject 8

value: 18 months


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 12

value: hippocampal CA1 brain


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 15


title: Tumor sample 10


title: Tumor sample 8


title: Tumor sample 7


title: rat hippocampus (CA1 region), sham, 18 months old, subject 9

description: hippocampus CA1 region

value: sham


title: rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 11


title: rat hippocampus (CA1 region), sham, 18 months old, subject 5


title: Tumor sample 6


title: rat hippocampus (CA1 region), sham, 18 months old, subject 4


title: rat hippocampus (CA1 region), sham, 18 months old, subject 6


title: rat hippocampus (CA1 region), sham, 18 months old, subject 3


title: simGal4 UAS EnRep vs UAS GFP control rep 4

description:
EnRep4
Biological replicate 4 of 4. Sample embryos are expressing a UAS EnRep construct, while the control embryos are expressing a UAS GFP construct. Both were expressed in the midline using a simGal4 driver.

value: The collected embryos have a simGal4 driver and a UAS construct. Sample embryos are expressing a UAS EnRep construct.

value: Whole embryos

source_name: simGal4 GFP

value: The collected embryos have a simGal4 driver and a UAS construct. The control embryos are expressing a UAS GFP construct.


title: Tumor sample 4


title: Tumor sample 3


title: rat hippocampus (CA1 region), sham, 18 months old, subject 2


title: Tumor sample 5


title: Tumor sample 9


title: MCF10A.B2, control, biological replicate 5 (ErbB2-E)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

country: Italy

institute: University of Padova

description: miRNA expression profiling of MCF10A.B2 cells with activation of ErbB2 (control-E)

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93).

source_name: MCF10A.B2 cells transduced with pBabe retroviral empty vector.

label_protocol: We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad).

growth_protocol: MCF10A.B2 cells were maintained in DMEM/F12 (Gibco, BRL) supplemented with 5% horse serum, 20 ng/ml EGF, 10 μg/ml insulin, 1 ng/ml cholera toxin, 100 μg/ml hydrocortisone, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from 107 ErbB2 (control) and Cas/ErbB2 cells by using Trizol® Reagent (Life Technologies) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% were used for microarray analysis.

treatment_protocol: To generate 10A.B2 ErbB2 (control) and 10A.B2 Cas/ErbB2 cells, we transduced MCF10A.B2 with pBabe retroviral empty vector or carrying p130Cas cDNA fused with GFP.

value: MCF10A.B2 (breast cancer)

value: ErbB2 (control)


title: Control sample 15

source_name: RNA from blood, normal control

value: healthy


title: MCF10A.B2, over-expressing p130Cas, biological replicate 4 (Cas/ErbB2-D)

description: miRNA expression profiling of MCF10A.B2 over-expressing p130Cas cells with activation of ErbB2 (Cas/ErbB2-D)

source_name: MCF10A.B2 cells transduced with pBabe retroviral vector carrying p130Cas cDNA fused with GFP.


title: Tumor sample 1


title: Tumor sample 2


title: rat hippocampus (CA1 region), sham, 18 months old, subject 1


title: rat hippocampus (CA1 region), sham, 18 months old, subject 7


title: MCF10A.B2, control, biological replicate 4 (ErbB2-D)

description: miRNA expression profiling of MCF10A.B2 cells with activation of ErbB2 (control-D)


title: MCF10A.B2, over-expressing p130Cas, biological replicate 3 (Cas/ErbB2-C)

description: miRNA expression profiling of MCF10A.B2 over-expressing p130Cas cells with activation of ErbB2 (Cas/ErbB2-C)


title: MCF10A.B2, control, biological replicate 2 (ErbB2-B)

description: miRNA expression profiling of MCF10A.B2 cells with activation of ErbB2 (control-B)


title: MCF10A.B2, control, biological replicate 3 (ErbB2-C)

description: miRNA expression profiling of MCF10A.B2 cells with activation of ErbB2 (control-C)


title: MCF10A.B2, control, biological replicate 1 (ErbB2-A)

description: miRNA expression profiling of MCF10A.B2 cells with activation of ErbB2 (control-A)


title: MCF10A.B2, over-expressing p130Cas, biological replicate 1 (Cas/ErbB2-A)

description: miRNA expression profiling of MCF10A.B2 over-expressing p130Cas cells with activation of ErbB2 (Cas/ErbB2-A)


title: MCF10A.B2, over-expressing p130Cas, biological replicate 2 (Cas/ErbB2-B)

description: miRNA expression profiling of MCF10A.B2 over-expressing p130Cas cells with activation of ErbB2 (Cas/ErbB2-B)


title: Pericyte PDGF-BB treated, rep1

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Pericytes were isolated and treated with PDGF-BB for 5 days.

hyb_protocol: Samples were hybridized with the Affymetrix Mouse Gene 1.0 ST Array according to the instructions of the manufacturer.

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data were extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label: Biotin

organism: Mus musculus

source_name: Mouse pericytes, PDGF-BB

label_protocol: Single round labeling recommended by manufacturer.

growth_protocol: Pericytes were isolated and maintained as described (Cao, R., et al. VEGFR1-mediated pericyte ablation links VEGF and PlGF to cancer-associated retinopathy. Proc Natl Acad Sci U S A 107, 856-861 (2010)).

extract_protocol: RNeasy (Qiagen).

treatment_protocol: Treatment with PDGF-BB (100 ng/ml) for 5 days or control.

tag: strain/background

tag: cell type

value: pericyte

value: PDGF-BB for 5 days


title: Pericyte control, rep3

description: Pericytes were isolated and treated with control for 5 days.

source_name: Mouse pericytes, control

value: control


title: Pericyte control, rep1


title: Pericyte PDGF-BB treated, rep2


title: Pericyte PDGF-BB treated, rep3


title: HepG2 treated with BF

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

description:
HepG2-BF
miRNA expression after 48 h in BF treated human cells

hyb_protocol: Each sample was placed on an Agilent Human miRNA microarray and hybridized for 20 h at 55°C in the Agilent hybridization system.

scan_protocol: Hybridization images on the slides were scanned by GenePix 4000B (Axon instruments, Forster city, CA, USA). Scanned images were analyzed with GenePix 4.1 software (Axon Instruments) to obtain gene expression ratios.

data_processing: Fold After Log2 transform, inter-array normalization of expression levels was performed with Variance Stabilization Normalization for gene expression profiling to correct possible experimental distortions. We used GeneSpring GX V.11.1 software (Agilent Technologies, CA) for analysis.

source_name: HepG2_48 h_IC20 value

label_protocol: Total RNA samples containing miRNA were labelled with Cyanine Cy3 using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: The HCC cell line HepG2 was purchased from Korean Cell Line Bank (KCLB, Seoul, Korea) and was maintained under a humidified atmosphere of 5% CO2 and 95% air at 37°C. The culture medium was 90% Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, sodium bicarbonate (Sigma), sodium pyruvate (GIBCO), and penicillin and streptomycin (GIBCO). The culture medium was refreshed every 2 to 3 days.

extract_protocol: Total RNA was extracted from BA- and BF-treated HepG2 cells using TRIzol reagent.

treatment_protocol: The cells were treated with each compounds at 1.0% of final solvent (DMSO) concentration in dish. The HepG2 cells were seeded at a density of 6 × 106 cells/mL for RNA extraction. After incubation for 24 h at 37°C, the cells were treated with each compounds for 48 h.

value: hepatocellular carcinoma cells

tag: treated with

value: benzo[k]fluoranthene for 48 h

tag: molecule subtype

value: microRNA


title: HepG2 treated with BA

description:
HepG2-BA
miRNA expression after 48 h in BA treated human cells

value: benzo[a]anthracene for 48hr


title: Pericyte control, rep2


title: HepG2 treated with DMSO (control for BA)

description:
HepG2-Control for BA
miRNA expression after 48 h in DMSO (vehicle control) treated human cells

source_name: HepG2_48 h_1% of total volume

value: DMSO for 48hr


title: HepG2 treated with DMSO (control for BF)

description:
HepG2-Control for BF
miRNA expression after 48 h in DMSO (vehicle control) treated human cells


title: Piri_PNM_3dpi_R2

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).

organism: Serendipita indica

source_name: P. indica grown on 1/10 PNM, 3 days post inoculation, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica was cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Barley seeds (Hordeum vulgare cv. Golden Promise) were surface sterilized with 70% ethanol for 1 minute, 12% sodium hypochlorite for 1.5 hours and sterile distilled water for 3 hours. Sterilized seeds were kept in the dark for 3 days on sterile wet filter paper at room temperature. Incubation was performed in a Conviron phytochamber with a day/night cycle of 16/8 hours (light intensity: 110 µmol m-2 s-1) and temperature 22/18°C. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4‹C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23‹C (350 µmol/m-2s-1); night: 8 h, 18‹C; 60% humidity).

extract_protocol: Barley root samples from four to five plants per jar were collected 14 dpi and carefully washed in distilled water. The differentiation zone (four cm below the seed) of the roots was excised and immediately frozen in liquid nitrogen. Arabidopsis root material was harvested in liquid nitrogen 3 and 14 dpi. For each time point roots from 80 to 100 plants were pooled. P. indica hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturerfs instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For barley studies, three-day-old barley germlings were transferred into sterile jars containing 1/10 PNM medium and inoculated with 3 ml chlamydospore suspension (5×105 ml-1 in 0.002% TWEEN20). For inoculation of Arabidopsis roots with P. indica chlamydospores, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or mock treated.

tag: host

tag: host tissue

value: hyphae

tag: time (dpi)

tag: sample type

value: P. indica grown on 1/10 PNM medium


title: Piri_PNM_3dpi_R3

source_name: P. indica grown on 1/10 PNM, 3 days post inoculation, replicate 3


title: Piri_Hvulg_14dpi_R3

description: H. vulgare plants were pre-grown for 3 days prior to inoculation

source_name: H. vulgare root, P. indica inoculated, 14 days post inoculation, replicate 3

value: H. vulgare

value: root

tag: symbiont

value: P. indica


title: MCF7_RocA-10nM_Rep1

status: Public on Jul 21 2013

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from MCF7 cells treated with 10 nM RocA for 6 Hours

hyb_protocol: Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.

scan_protocol: The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.

data_processing: Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.

source_name: MCF7 cells, 10 nM RocA treated, 6H

label_protocol: As per Affymetrix instructions

growth_protocol: In vitro cultured according to published conditions

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

value: breast cancer cell line


title: Piri_PNM_3dpi_R1

source_name: P. indica grown on 1/10 PNM, 3 days post inoculation, replicate 1


title: MCF7_RocA-10nM_Rep2


title: MCF7_RocA-30nM_Rep2

description: Gene expression data from MCF7 cells treated with 30 nM RocA for 6 Hours

source_name: MCF7 cells, 30 nM RocA treated, 6H


title: Piri_Hvulg_14dpi_R2

source_name: H. vulgare root, P. indica inoculated, 14 days post inoculation, replicate 2


title: Piri_Hvulg_14dpi_R1

source_name: H. vulgare root, P. indica inoculated, 14 days post inoculation, replicate 1


title: MCF7_RocA-200nM_Rep2

description: Gene expression data from MCF7 cells treated with 200 nM RocA for 6 Hours

source_name: MCF7 cells, 200 nM RocA treated, 6H


title: MCF7_RocA-30nM_Rep1


title: MCF7_27A-50nM_Rep1

description: Gene expression data from MCF7 cells treated with 50 nM 27A for 6 Hours

source_name: MCF7 cells, 50 nM 27A treated, 6H


title: MCF7_27A-25nM_Rep2

description: Gene expression data from MCF7 cells treated with 25 nM 27A for 6 Hours

source_name: MCF7 cells, 25 nM 27A treated, 6H


title: MCF7_RocA-200nM_Rep1


title: Oregon-R-whole l3 larval homegenate replicate-1

city: Fairfax

first: Daniel

middle: N

last: Cox

state: VA

address: 4400 University Drive, MSN 2A1

department: School of Systems Biology, Krasnow Institute

institute: George Mason University

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Drosophila Melanogaster Genome Oligo Microarrays 4 x 44K (table 3) using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES, v.10.5.1.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. GeneSpring (Agilent) was used to normalize and analyze raw dataset. The raw data was quantile normalized, and the values were thresholded to 1.

source_name: Oregon-R larval total RNA L3 Stage

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Drosophila stocks were raised on standard cornmeal-molasses-agar media at 25˚C.

extract_protocol: The isolation and purification of C-IV da neurons was performed as previously described (Iyer et al., 2009).  Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL4ppk.1.9 or ppk-GAL80;GAL4221 driver were collected and washed several times in ddH20. The larvae were rinsed in RNAse away followed by ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate was incubated with magnetic beads coupled with rat anti-CD8 antibody (Invitrogen) for 60 minutes. Finally the C-I and C-IV neurons attached to the magnetic beads were separated using a powerful magnetic field. The cells were washed 5 times, before lysing them in SuperAmp™ (Miltenyi Biotec) RNA lysis buffer followed by storage of the RNA at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

tag: strain background

value: Oregon-R

tag: genotype/variation

value: wild type

tag: developmental stage

value: Larval L3

value: Whole Larvae


title: Oregon-R-whole l3 larval homegenate replicate-2

tag: tissue


title: MCF7_27A-25nM_Rep1


title: Class-IV da neuron replicate-2

source_name: Class-IV da neuron-Larval L3 Stage

value: GAL4ppk.1.9, UAS-mcd8::GFP

value: Class-IV da neuron


title: Class-IV da neuron replicate-1


title: MCF7_DMSO_Rep2

description: Gene expression data from MCF7 cells treated with DMSO for 6 Hours

source_name: MCF7 cells, DMSO treated, 6H


title: Oregon-R-whole l3 larval homegenate replicate-3


title: MCF7_27A-50nM_Rep2


title: Class-I da neuron replicate-2

source_name: Class-I da neuron-Larval L3 Stage

value: ppk-GAL80;GAL4221, UAS-mcd8::GFP

value: Class-I da neuron


title: MCF7_DMSO_Rep1


title: Class-I da neuron replicate-1


title: E1_H006

status: Public on Jul 20 2013

city: Taichung Ciy

first: Hao-Teng

last: Chang

address: No.91, Hsueh-shih Rd. N. Dist.

institute: China Medical University

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve. Rosetta Resolver System (Rosetta Biosoftware) was used to normalize the data.

source_name: normal bronchial epithelial cell

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. RNA was extracted using Trizol.


title: svb -/- embryos, replicate 4

city: Toulouse

first: serge

last: plaza

address: 118 route de Narbonne

department: Developmental Biology Center

country: France

institute: toulouseII University

description:
SPA_R4
Gene expression data from genotyped svb -/- embryos at stage 13-15h.

hyb_protocol: Hybridizations were performed as recommended by the manufacturer's instruction for GeneChip Drosophila 2.0 Array.

scan_protocol: Chips were scanned with the GeneArray Scanner 3000.

data_processing: Data were analyzed with the Microarray Suite version 5.0 (MAS5.0) algorithm using Affymetrix Expression Console software version 1.1.

source_name: svb -/- Drosophila embryos 13-15h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Data Analysis Manual, 2003, Affymetrix).

growth_protocol: wt, svb +/- or pri +/- flies developed in 2h window at 25°C and aged at 18°C for 13-15h stage.

extract_protocol: Total RNA extraction was performed according to the instructions given by the manufacturer of Trizol.

treatment_protocol: Embryos were dechorionated with 50% bleach and further genotyped using GFP balancer for homozygote embryos. Selected embryos were rinsed with PBS 0.1% Triton and placed in Trizol solution.

value: dechorionated embryos

value: 13-15h after egg laying

value: svb -/-


title: E2_H007


title: pri -/- embryos, replicate 1

description:
SPA_P1
Gene expression data from genotyped pri -/- embryos at stage 13-15h.

source_name: pri -/- Drosophila embryos 13-15h

value: pri -/-


title: svb -/- embryos, replicate 3

description:
SPA_R3
Gene expression data from genotyped svb -/- embryos at stage 13-15h.


title: E2_H008


title: pri -/- embryos, replicate 4

description:
SPA_P4
Gene expression data from genotyped pri -/- embryos at stage 13-15h.


title: pri -/- embryos, replicate 5

description:
SPA_P5
Gene expression data from genotyped pri -/- embryos at stage 13-15h.


title: pri -/- embryos, replicate 3

description:
SPA_P3
Gene expression data from genotyped pri -/- embryos at stage 13-15h.


title: svb -/- embryos, replicate 2

description:
SPA_R2
Gene expression data from genotyped svb -/- embryos at stage 13-15h.


title: svb -/- embryos, replicate 1

description:
SPA_R1
Gene expression data from genotyped svb -/- embryos at stage 13-15h.


title: pri -/- embryos, replicate 2

description:
SPA_P2
Gene expression data from genotyped pri -/- embryos at stage 13-15h.


title: C2_H004


title: wt embryos, replicate 5

description:
SPA_W5
Gene expression data from genotyped wt embryos at stage 13-15h.

source_name: wt Drosophila embryos 13-15h

value: wt


title: svb -/- embryos, replicate 5

description:
SPA_R5
Gene expression data from genotyped svb -/- embryos at stage 13-15h.


title: C1_H001


title: wt embryos, replicate 4

description:
SPA_W4
Gene expression data from genotyped wt embryos at stage 13-15h.


title: wt embryos, replicate 3

description:
SPA_W3
Gene expression data from genotyped wt embryos at stage 13-15h.


title: wt embryos, replicate 2

description:
SPA_W2
Gene expression data from genotyped wt embryos at stage 13-15h.


title: C2_H003


title: E1_H005


title: Lineage I wildtype compared to sigma B null mutant_replicates

city: Sao Paulo

first: Vinicius

middle: Buccelli

last: Ribeiro

state: Sao Paulo

address: 580 Lineu Prestes Ave

country: Brazil

institute: University of Sao Paulo

hyb_protocol: Briefly, microarray slides were blocked in a prehybridization buffer supplemented with bovine serum albumen (BSA) (Sigma-Aldrich), washed with deionized water then isopropyl alcohol. Dried Cy3- and Cy5-labeled cDNA was hydrated with hybridization buffer containing 0.6 mg/ml sheared salmon sperm DNA (Invitrogen), denatured twice at 95ºC for 5 minutes and briefly centrifuged. cDNA was hybridized to the microarray at 42ºC for 16 hours. Following hybridization, slides were washed according to the PFGRC/JCVI M008 protocol and dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.) using the following general scanning parameters: pixel size=10, focus position=20, lines to average=1, laser power=100%. The auto-PMT function was used to scan the slides with an acceptable PMT range of 400-900. Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis. The PFGRC/JCVI L. monocytogenes microarray contained multiple probes for certain loci that lacked a 70mer consensus sequence for a given locus among the four strains represented on the microarray. In instances where multiple probes were present for a single locus, the probe that best matched the sequence for a given strain used in the present study was selected as the representative probe for subsequent analyses for that strain. BLASTN was used to calculate the hybridization index (HI), the percent identity between each probe and each strain; BLASTN results were parsed to compare percent identity between each strain and the probes. EGD-e locus names were used to describe the corresponding open reading frames (ORFs) in the lineage I, IIIA, and IIIB strains as these genomes have not yet been annotated; EGD-e locus names were also used in lieu of 10403S locus names to facilitate comparisons among all strains in this study. Genes unique to F2365, F6852 and H7858 (i.e. genes with no EGD-e homologue) maintained their locus names. Genes with higher transcript levels in a wildtype strain compared to its isogenic ΔsigB mutant (fold change > 1.5) and adjusted p-values < 0.05 were considered positively differentially expressed, and thus σB-dependent. The IDs (genes/spots) described as obsolete and blank were removed from the averaged, normalized data.

organism: Listeria monocytogenes

source_name: delta sigB

label_protocol: The Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (PFGRC/JCVI) L. monocytogenes microarray version 2 was used to identify mRNA transcript level differences between wildtype strains and their respective ∆sigB mutants. The PFGRC/JCVI microbial RNA aminoallyl labeling for microarray standard operating procedure M007 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to reverse transcribe and label the total RNA. Spectrophotometry was used to quantify cDNA and total picomoles of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ) incorporation. Cy3- and Cy5-labeled cDNA was combined and thoroughly dehydrated prior to hybridization. PFGRC/JCVI standard operating procedure M008 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to hybridize the Cy-dye labeled cDNA to the microarray.

extract_protocol: RNAProtect bacterial reagent (Qiagen, Valencia, CA) was added to the cultures according to manufacturer’s instructions to stabilize the mRNA; pellets were stored at -80°C prior to RNA isolation. RNA was isolated as previously described. Briefly, bacterial cells were lysed enzymatically with lysozyme (Fisher Scientific, Pittsburg, PA), and mechanically, using 6 sonication bursts (Misonix, Farmingdale, NY) at 18W on ice for 30 seconds. Total RNA was isolated and purified using the RNeasy Midi kit (Qiagen) according to the manufacturer’s protocol. RNA was eluted from the column using RNase-free water. Total RNA was incubated with RNasin (Promega, Madison, WI) to inhibit RNases, and RQ1 DNase (Promega) to remove DNA contamination. After phenol:chloroform extraction, UV spectrophotometry (Nanodrop, Wilmington, DE) was used to quantify and assess purity of the RNA. RNA integrity was assessed by agarose gel electrophoresis. Purified RNA was stored in RNase-free water at -80°C prior to reverse transcription.

tag: serotype

value: serotype 1/2b

value: delta sigB

value: Lag phase cells in osmotic stress

source_name: parent wild type

value: parent wild type


title: C1_H002


title: Animal-AMAS-20-Treatment-C (Acb-sh)

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain nucleus accumbens shell (Acb-sh)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol using GCOS (GeneChip Operating System) and the Genechip Scanner 3000.

data_processing: The data were analyzed with RMA

source_name: Accumbens-shell from P rat

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3' IVT express kit from 50ng total RNA.

extract_protocol: RNA was extracted using Trizol using twice the volume, followed by Qiagen RNeasy mini kit.

value: Accumbens-shell

value: water


title: Animal-AMAS-21-Treatment-C (Acb-sh)


title: CD133_negative_0h_rep2

city: Pohang

first: Taek-Kyun

last: Kim

state: Gyeongbuk

address: San 31, Hyoja-dong, Nam-gu

department: Interdisciplinary Bioscience and Bioengineering

institute: POSTECH

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalized using quantile normalization method with beadarray version 1.10 and lumi version 1.8.3 in R/Bioconductor package.

source_name: CD133 negative cell

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: Dulbecco’s modified Eagle medium (DMEM, invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 µg /ml penicillin and 0.25 µg/ml streptomycin and maintained in a humidified 37℃ incubator with 5% CO2.

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

treatment_protocol: Cells irradiated using a caesium-137 source delivering 3.42 Gy/min using a Gammacell irradiator (Gammacell 3000 Elan Irradiation System, Canada) at the indicated doses and times.

tag: cell line

value: Human HCC cell line Huh-7

tag: treatment protocol

value: untreated

tag: time


title: Animal-AMAS-17-Treatment-C (Acb-sh)

tag: treatment


title: Animal-AMAS-19-Treatment-C (Acb-sh)


title: Animal-AMAS-18-Treatment-C (Acb-sh)


title: Animal-AMAS-8-Treatment-E (Acb-sh)

value: ethanol


title: CD133_negative_12h_rep2

tag: cell type

value: radiation exposure


title: Animal-AMAS-16-Treatment-C (Acb-sh)


title: CD133_positive_0h_rep2


title: Animal-AMAS-9-Treatment-E (Acb-sh)


title: CD133_positive_12h_rep2


title: CD133_negative_24h_rep2


title: Animal-AMAS-6-Treatment-E (Acb-sh)


title: MCF10A.B2, over-expressing p130Cas, biological replicate 5 (Cas/ErbB2-E)

description: miRNA expression profiling of MCF10A.B2 over-expressing p130Cas cells with activation of ErbB2 (Cas/ErbB2-E)

source_name: MCF10A.B2 cells transduced with pBabe retroviral vector carrying p130Cas cDNA fused with GFP.

value: MCF10A.B2 (breast cancer)


title: CD133_negative_24h_rep1

source_name: CD133 positive cell


title: CD133_negative_12h_rep1


title: CD133_positive_12h_rep1


title: wt embryos, replicate 1

description:
SPA_W1
Gene expression data from genotyped wt embryos at stage 13-15h.


title: Animal-AMAS-5-Treatment-E (Acb-sh)


title: CD133_negative_0h_rep1


title: Animal-AMAS-15-Treatment-C (Acb-sh)


title: Animal-AMAS-7-Treatment-E (Acb-sh)


title: CD133_positive_0h_rep1


title: CD133_positive_24h_rep2


title: Animal-AMAS-14-Treatment-C (Acb-sh)


title: Animal-AMAS-12-Treatment-C (Acb-sh)


title: Animal-AMAS-13-Treatment-C (Acb-sh)


title: Animal-AMAS-1-Treatment-E (Acb-sh)


title: Animal-AMAS-2-Treatment-E (Acb-sh)


title: Animal-AMAS-21-Treatment-C (CeA)

description: Gene expression data from brain central nucleus of amygdala (CeA)

source_name: Central nucleus of amygdala from P rat

value: Central nucleus of amygdala


title: Animal-AMAS-10-Treatment-E (CeA)


title: Animal-AMAS-4-Treatment-E (Acb-sh)


title: Animal-AMAS-9-Treatment-E (CeA)


title: Animal-AMAS-3-Treatment-E (Acb-sh)


title: Animal-AMAS-20-Treatment-C (CeA)


title: CD133_positive_24h_rep1


title: RWPE SChLAP1 Isoform2 Replicate 2

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

description:
Technical replicate 2 of 2 (Isoform 2)
06162012_251485072628_S01_GE2-v5_95_Feb07_1_2.txt

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio and PValueLogRatio columns from each feature file were then merged into a single processed data matrix.  The LogRatio was converted to base 2 from its default base 10.

source_name: RWPE_SChLAP1 Isoform2

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

growth_protocol: Cells were grown in RPMI 1640 (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer’s instructions.

treatment_protocol: SChLAP-1 or control-expressing cell lines were generated by cloning SChLAP-1 or control into the pLenti6 vector (Invitrogen).  Stably-transfected RWPE cells were selected using blasticidin (Invitrogen). Overexpression efficacy was determined by qPCR.

value: RWPE

value: benign immortalized prostate cancer cells

value: overexpressing SChLAP-1 isoform 2

source_name: RWPE_overexpressing LACZ

value: overexpressing LACZ


title: RWPE SChLAP1 Isoform1 Replicate 2

description:
Technical replicate 2 of 2 (Isoform 1)
06162012_251485072628_S01_GE2-v5_95_Feb07_1_1.txt

source_name: RWPE_SChLAP1 Isoform1

value: overexpressing SChLAP-1 isoform 1


title: Animal-AMAS-18-Treatment-C (CeA)


title: Animal-AMAS-16-Treatment-C (CeA)


title: Animal-AMAS-17-Treatment-C (CeA)


title: Animal-AMAS-5-Treatment-E (CeA)


title: Animal-AMAS-19-Treatment-C (CeA)


title: Animal-AMAS-6-Treatment-E (CeA)


title: Animal-AMAS-8-Treatment-E (CeA)


title: Animal-AMAS-15-Treatment-C (CeA)


title: Animal-AMAS-7-Treatment-E (CeA)


title: LNCaP SMARCA4 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485070031_S01_GE2-v5_95_Feb07_1_2.txt

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control features were removed. A merged processed data file was created by aggregating the logFoldChange and PValueLogFoldChange columns from each of the feature files

molecule: polyA RNA

source_name: LNCaP_non-targeting siRNA

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and transfected with 20uM experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating.  Knockdowns were performed with Oligofectamine and Optimem.  Knockdown efficiency was determined by qPCR.

value: LNCaP

value: prostate cancer cells

tag: transfected with

value: 20uM non-targeting control-siRNA oligos at 12 hr and 36 hr post-plating

source_name: LNCaP_SMARCA4 siRNA

value: 20uM SMARCA4 siRNA oligos at 12 hr and 36 hr post-plating

tag: sirna sequence

value: GCGACUCACUGACGGAGAA


title: Animal-AMAS-14-Treatment-C (CeA)

value: water


title: 22RV1 SMARCA2 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485064520_S01_GE2-v5_95_Feb07_1_3.txt

source_name: 22Rv1_non-targeting siRNA

source_name: 22Rv1_SMARCA2 siRNA

value: 20uM SMARCA2 siRNA oligos at 12 hr and 36 hr post-plating

value: CAAAGCAGAUGAACGCUAU


title: Animal-AMAS-12-Treatment-C (CeA)


title: RWPE SChLAP1 Isoform1 Replicate 1

description:
Technical replicate 1 of 2 (Isoform 1)
06162012_251485072627_S01_GE2-v5_95_Feb07_1_1.txt


title: LNCaP SMARCA2 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485070031_S01_GE2-v5_95_Feb07_1_3.txt

source_name: LNCaP_SMARCA2 siRNA


title: 22RV1 SMARCA2 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485064520_S01_GE2-v5_95_Feb07_1_4.txt

value: GAAAGGAGGUGCUAAGACA


title: LNCaP SMARCB1 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485064520_S01_GE2-v5_95_Feb07_1_1.txt

source_name: LNCaP_SMARCB1 siRNA

value: 20uM SMARCB1 siRNA oligos at 12 hr and 36 hr post-plating

value: GUGACGAUCUGGAUUUGAA


title: RWPE SChLAP1 Isoform2 Replicate 1

description:
Technical replicate 1 of 2 (Isoform 2)
06162012_251485072627_S01_GE2-v5_95_Feb07_1_2.txt


title: LNCaP SMARCB1 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485064520_S01_GE2-v5_95_Feb07_1_2.txt

value: GAUGACGCCUGAGAUGUUU


title: LNCaP SMARCA2 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485070031_S01_GE2-v5_95_Feb07_1_4.txt


title: Animal-AMAS-13-Treatment-C (CeA)

value: Central nucleus of amygdala


title: Animal-AMAS-4-Treatment-E (CeA)

value: ethanol


title: LNCaP SMARCA4 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485070031_S01_GE2-v5_95_Feb07_1_1.txt

value: GCACACCGCUGCAGAACAA


title: [reference]_[high exposed_male_rep2]

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

description:
Total RNA extraction: Trizol method
Fluorescently labeled cRNA: Quick Amp labeling kit Agilent
Hybridization: Agilent’s two-color microarray-based gene expression analysis protocol
Scanning: Genepix Personal 4100A confocal scanner

hyb_protocol: The hybridization was performed according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Two probe volumes (Cy3 vs. Cy5) corresponding with 300ng cRNA were mixed and applied onto every microarray. The microarray slides were incubated at 65°C for 17 hours in a hybridization chamber which was placed in a rotating (10rpm) Agilent hybridization oven. The slides were washed with Agilent wash buffers and acetonitrile and finally submersed in Agilent stabilization and drying solution to protect against ozone-induced degradation of the cyanine dyes.

scan_protocol: Microarrays were scanned at 532 and 635 nm using the Genepix Personal 4100A confocal scanner (Axon instruments, Union City, USA) at a resolution of 5µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing: Statistical analysis was performed in the open source statistical programming environment R, using the Bioconductor package limma (Linear Models for Microarray Data) (Smyth, 2005). Briefly, spots for which the mean foreground signal was lower than the mean local BG+2SD (BG: background signal, SD: standard deviation of the background) and spots with oversaturated signal intensities on all microarrays were filtered out before analysis. Intensity data were corrected using a normal-exponential convolution model (Ritchie et al., 2007) and normalized using the lowess method (Smyth and Speed, 2003). An empirical Bayes method was used to estimate contrasts of interest from the normalized and linear model-fitted data (Smyth, 2004). The different exposure concentrations of males and females were contrasted against their respective controls. Gene transcripts were considered significantly different if the log2 ratio of a contrast was ≤-0.75 or ≥+0.75 and the p-value was <0.05.

organism: Danio rerio

source_name: reference

label_protocol: Fluorescently labelled cRNA was constructed using the Quick Amp labelling kit (Agilent Technologies, Diegem, Belgium) according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Briefly, total RNA was reverse transcribed into first and second strand cDNA. Using T7 RNA polymerase, the second strand cDNA was converted in cRNA while either Cy3-CTP or Cy5-CTP was incorporated. The labelled cRNA was purified using the Qiagen RNeasy mini spin column kit (Qiagen, Venlo, The Netherlands) and labelling efficiency was determined by spectrophotometry at 550nm (Cy3) and 650nm (Cy5) (NanoDrop, NanoDrop Technologies, Rockland, USA).

extract_protocol: The livers of the fish were homogenized in liquid nitrogen and total liver RNA was extracted applying the Trizol-RNA extraction procedure (Gibco BRL, Life Technologies, Merelbeke, Belgium). The extracted RNA was purified using Dnase I and RNase inhibitor (Fermentas, St. Leon-Rot, Germany) followed by a phenol/chloroform extraction. RNA integrity was checked by denaturing formaldehyde-agarose gel electrophoresis. RNA quality was measured using spectrophotometry (NanoDrop, NanoDrop Technologies, Rockland, DE, USA): absorbance at 260nm (RNA), 280nm (proteins) and 230nm (organic contaminants and solvents) was determined and all RNA samples had 260/280 and 260/230 ratios >1.8.

treatment_protocol: The liver of the fish was dissected on ice and the livers from 6 fish per biological replicate (males and females separately) were pooled and snap frozen in liquid nitrogen. All samples were stored at -80°C until further analysis.

tag: reference

value: equal amounts of pooled RNA from all samples of the experiment

source_name: high exposed_male_rep2

tag: gender

value: male

value: liver

tag: exposure condition

value: exposed to 1mg/l PFOA


title: Animal-AMAS-10-Treatment-E (Acb-sh)

description: Gene expression data from brain nucleus accumbens shell (Acb-sh)

value: Accumbens-shell


title: [control_male_rep2]_[reference]

value: control


title: 22RV1 SMARCA4 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485064519_S01_GE2-v5_95_Feb07_1_4.txt

value: prostate cancer cells

value: 20uM non-targeting control-siRNA oligos at 12 hr and 36 hr post-plating

source_name: 22Rv1_SMARCA4 siRNA

value: 20uM SMARCA4 siRNA oligos at 12 hr and 36 hr post-plating

value: GCGACUCACUGACGGAGAA


title: [control_male_rep2]_[high exposed_male_rep2]


title: Animal-AMAS-3-Treatment-E (CeA)


title: 22RV1 SMARCB1 siRNA-2

description:
Biological replicate 2 of 2 (siRNA 2)
10122011_251485064519_S01_GE2-v5_95_Feb07_1_2.txt

source_name: 22Rv1_SMARCB1 siRNA


title: Animal-AMAS-1-Treatment-E (CeA)

description: Gene expression data from brain central nucleus of amygdala (CeA)


title: 22RV1 SMARCA4 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485064519_S01_GE2-v5_95_Feb07_1_3.txt


title: [high exposed_male_rep1]_[reference]

source_name: high exposed_male_rep1


title: [low exposed_male_rep2]_[control_male_rep2]

source_name: low exposed_male_rep2

value: exposed to 0.1mg/l PFOA


title: [high exposed_male_rep1]_[low exposed_male_rep2]


title: [low exposed_male_rep1]_[reference]

source_name: low exposed_male_rep1


title: Animal-AMAS-2-Treatment-E (CeA)

source_name: Central nucleus of amygdala from P rat


title: [low exposed_male_rep1]_[control_male_rep1]


title: [reference]_[low exposed_male_rep2]


title: LNCaP siRNA-J Replicate 3

description:
Biological replicate 2 of 2 (siRNA J)
07262011_251485068650_S01_GE2-v5_95_Feb07_1_4.txt

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio and PValueLogRatio columns from each feature file were then merged into a single processed data matrix

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

value: LNCaP

value: 20uM SChLAP1-siRNA oligos at 12 hr and 36 hr post-plating


title: 22RV1 SMARCB1 siRNA-1

description:
Biological replicate 1 of 2 (siRNA 1)
10122011_251485064519_S01_GE2-v5_95_Feb07_1_1.txt

value: 20uM SMARCB1 siRNA oligos at 12 hr and 36 hr post-plating

value: GUGACGAUCUGGAUUUGAA


title: [control_female_rep1]_[low exposed_female_rep1]

value: female

source_name: low exposed_female_rep1


title: LNCaP siRNA-H Replicate 2

description:
Biological replicate 1 of 2 (siRNA H)
07262011_251485068650_S01_GE2-v5_95_Feb07_1_1.txt


title: LNCaP siRNA-J Replicate 2

description:
Biological replicate 2 of 2 (siRNA J)
07262011_251485068650_S01_GE2-v5_95_Feb07_1_3.txt


title: LNCaP siRNA-J Replicate 1

description:
Biological replicate 2 of 2 (siRNA J)
07012011_251485068573_S01_GE2-v5_95_Feb07_1_4.txt


title: [low exposed_female_rep1]_[low exposed_male_rep1]


title: LeafBlade_125DAT_12:00_2010

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression of leaf blade at daytime 125 days after transplanting in 2010

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX12(Agilent).

organism: Oryza sativa Japonica Group

source_name: Leaf blade, 125 days after transplanting, 12:00, 2010

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2010.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

tag: organ/tissue

value: Leaf Blade

tag: growth/development stage

value: 125 days after transplanting

tag: sampling time

value: Daytime 12:00


title: LeafBlade_111DAT_12:00_2010

description: Gene expression of leaf blade at daytime 111 days after transplanting in 2010

source_name: Leaf blade, 111 days after transplanting, 12:00, 2010

value: 111 days after transplanting


title: LeafBlade_118DAT_12:00_2010

description: Gene expression of leaf blade at daytime 118 days after transplanting in 2010

source_name: Leaf blade, 118 days after transplanting, 12:00, 2010

value: 118 days after transplanting


title: [low exposed_female_rep1]_[reference]

value: liver

value: equal amounts of pooled RNA from all samples of the experiment


title: LeafBlade_104DAT_12:00_2010

description: Gene expression of leaf blade at daytime 104 days after transplanting in 2010

source_name: Leaf blade, 104 days after transplanting, 12:00, 2010

value: 104 days after transplanting


title: LeafBlade_97DAT_12:00_2010

description: Gene expression of leaf blade at daytime 97 days after transplanting in 2010

source_name: Leaf blade, 97 days after transplanting, 12:00, 2010

value: 97 days after transplanting