title: Me13_AZD6244+ BEZ235+sTRAIL_8hrs_rep3

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: SAMPLE 24

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: Me13_AZD6244+ BEZ235+sTRAIL_8hrs

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

value: human Melanoma

tag: treated with

value: AZD6244+ BEZ235+sTRAIL

tag: drug concentration

tag: exposure time


title: Sac3-Flag ChIP

status: Public on Oct 08 2014

type: genomic

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: Asynchronous cultures growing in rich YPD medium

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated (IP) fraction with the supernatant (SUP) fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P < 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log2 ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Sac3-Flag ChIP DNA from SAC3-FLAG, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 30°C

extract_protocol: ChIP was carried out as previously described (Katou et al., 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-FLAG monoclonal antibody M2 (Sigma-Aldrich) was used for ChIP.

tag: chip antibody

value: FLAG

tag: strain

tag: genotype

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 SAC3::FLAG::KanMX trp1-1 ura3-1

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from SAC3-FLAG

value: input


title: Thp1-Flag ChIP

source_name: Thp1-Flag ChIP DNA from THP1-FLAG, asynchronous culture

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 THP1::FLAG::KanMX trp1-1 ura3-1

source_name: Input DNA from THP1-FLAG


title: Naïve CD8+ CD5hi 2

type: RNA

city: Minneapolis

first: Stephen

last: Jameson

state: MN

address: 2101 6th St. SE

department: Center for Immunology

country: USA

institute: University of Minnesota

hyb_protocol: 20 ug of fragmented cRNA was hybridized for 16h at 45oC to Affymetrix Mouse430A_2 arrays at the University of Minnesota Biomedical Genomics Center.  Washing was performed using a GeneChip Fluidics Station 400

scan_protocol: Scanning used an Agilent GeneArray Scanner (Affymetrix).

data_processing: Genespring software was used:  Data was MAS5 normalized and filtered for present/absent calls in at least one group, and for statistically significant (p<0.05) fold change of >1.4 fold

molecule: total RNA

organism: Mus musculus

source_name: Naïve CD8+ T cells_CD5_hi

label_protocol: biotinylated cRNA was made using MessageAmpIII Amplification kit (Ambion), following manufacturer's recommendations

extract_protocol: Sorted cells were extracted using an RNeasy micro kit (Qiagen), following manufacturer's recommendations

tag: tissue

value: spleen and lymph nodes

tag: cell type

value: Naïve CD8+ T cells


title: Me13_AZD6244+ BEZ235+sTRAIL_8hrs_rep2

description: SAMPLE 23

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

organism: Homo sapiens

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

tag: cell line


title: WSN-230_8hpi_rep1

city: Helsinki

first: Maria

last: Anastasina

address: Tukholmankatu 8

department: Institute for Molecular Medicine, Finland

country: Finland

institute: University of Helsinki

data_processing: quantile normalized using Limma package for R from Bioconductor

source_name: Macrophages

label_protocol: Standard Illumina label protocol

growth_protocol: Peripheral blood mononuclear cells were isolated form Buffy coats obtained from healthy donors. Macrophages were differentiated from PBMCs in serum-free medium containing granulocyte-macrophage colony stimulating factor for 7 days.

extract_protocol: Total RNA was isolated from infected and non-infected macrophages after 8 hours of infection using Qiagen Rneasy Plus mini kit.

treatment_protocol: Macrohages were infected with Influenza A viruses at multiplicity of infection = 2 in serum-free medium.

tag: time post infection, h

tag: infection

value: wild type NS1 protein


title: Naïve CD8+ CD5lo 3

source_name: Naïve CD8+ T cells_CD5_lo


title: Naïve CD8+ CD5lo 1


title: Naïve CD8+ CD5hi 3


title: WSN-230_8hpi_rep3


title: Rrm3-Flag sac3∆ exp1

source_name: Rrm3-Flag ChIP DNA from S3RBb-5B, asynchronous culture

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG bar1Δ sac3::KanMX

source_name: Input DNA from S3RBb-5B


title: ICAM-1-/- control (ND-KO)

city: Okayama

first: Satoshi

last: Miyamoto

address: 2-5-1 Shikata-cho

country: Japan

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical sciences

hyb_protocol: In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5x fragmentation buffer and incubate at 94 C for 20 min. Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90C for 5 min and immediately chill on ice for 5 min. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18 hours at 37C in an Innove 4080 shaker. Remove the Flex Chamber using the hybridization removal tool. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75xTNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75xTNT, and incubate at 46 C for exactly 1 hour. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir in to the small reagent reservoir and incubate bioarrays at RT for 30 min. Wash the bioarrays four times with 1xTNT at RT for 5 min. Rinse the bioarrays in 0.1xSSC/0.05%Tween by moving rack up and down 5 times in 5 seconds. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark.

scan_protocol: We scanned bioarrays with Axon GenePix 4000B and analyzed with CodeLink Expression Analysis software version 2.3.2.

data_processing: The 10,000 spot intensities on the scanned microarray image were normalized to a median value of 1 and data were exported for analysis with CodeLink Expression Analysis software version 2.3.2.

source_name: kidney (renal cortex)

label_protocol: The concentration and the quality of the total RNA sample were assessed by Agilent Bioanalyzer. Biotin-labeled target cRNA was prepared using First and Second strand cDNA Synthesis Kit (Amersham Biosciences, No. 320000) and In Vitro Transcription Kit (Amersham Biosciences, No.320001). Incubate total RNA (5 μg), diluted bacterial mRNA spike controls and T7 oligo (dT) primer for 10 min at 70 C. Add first-strand reaction components and incubate 1 hour at 42C. Add the first-strand cDNA product to the second-strand reaction components and incubate for 2 hours at 16 C. Double-strand cDNA was purified using QIAquick purification kit (Qiagen), eluted twice, each time with 30μl of nuclease-free water then dried in a SpeedVac concentrator. Prepare IVT mix of biotinylated UTP, ribonucleotides, and the 10x T7 enzyme mix and add to the resuspended cDNA. Incubate at 37C for 14 hours. Purify cRNA using RNeasy Mini Kit (Qiagen) and elute the cRNA twice, each time with 50 μl nuclease-free water. Measure the absorbance at 260 nm and 280 nm to determine the ratio (A260:A280=2).

growth_protocol: All mice had free access to standard diet and tap water. All procedures were performed according to the Guidelines for Animal Experiments at Okayama University Medical School, Japanese Government Animal Protection and Management Law (no. 105), and Japanese Government Notification on Feeding and Safekeeping of Animals (no. 6).

extract_protocol: 12 weeks after the injection of citrate buffer, all mice were killed, and the kidneys were harvested. Total RNA was extracted from each specimen of renal cortex using standard protocol from RNeasy midi kit (Qiagen, Valencia, CA).

treatment_protocol: ICAM-1-/- mice aged 8 weeks (n=5) were received an intraperitoneal injection of citrate buffer (pH 4.5).

tag: genotype/variation

tag: gender

value: male

value: Kidney cortex

tag: age

value: 20 weeks of age

tag: treatment group

value: 12 weeks after peritoneal injection of citrate buffer


title: Me13_AZD6244+ BEZ235+sTRAIL_8hrs_rep1

description: SAMPLE 22


title: ICAM-1-/- DM (DM-KO)

extract_protocol: 12 weeks after the injection of STZ, all mice were killed, and the kidneys were harvested. Total RNA was extracted from each specimen of renal cortex using standard protocol from RNeasy midi kit (Qiagen, Valencia, CA).

treatment_protocol: ICAM-1-/- mice aged 8 weeks (n=5) were received an intraperitoneal injection of streptozotocin (STZ) at 200mg/kg in citrate buffer (pH 4.5).

value: 12 weeks after peritoneal injection of streptozotocin


title: Naïve CD8+ CD5hi 1


title: ICAM-1+/+ control (ND-WT)

hyb_protocol: In 25 µl total volume, add 10 µg of cRNA to 5 µl of 5x fragmentation buffer and incubate at 94 C for 20 min. Bring 10 µg of fragmented cRNA, 78 µl of hybridization buffer component A, and 130 µl of hybridization buffer component B to a final volume of 260 µl with water. Incubate at 90C for 5 min and immediately chill on ice for 5 min. Slowly inject 250 µl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18 hours at 37C in an Innove 4080 shaker. Remove the Flex Chamber using the hybridization removal tool. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75xTNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75xTNT, and incubate at 46 C for exactly 1 hour. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir in to the small reagent reservoir and incubate bioarrays at RT for 30 min. Wash the bioarrays four times with 1xTNT at RT for 5 min. Rinse the bioarrays in 0.1xSSC/0.05%Tween by moving rack up and down 5 times in 5 seconds. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark.

label_protocol: The concentration and the quality of the total RNA sample were assessed by Agilent Bioanalyzer. Biotin-labeled target cRNA was prepared using First and Second strand cDNA Synthesis Kit (Amersham Biosciences, No. 320000) and In Vitro Transcription Kit (Amersham Biosciences, No.320001). Incubate total RNA (5 µg), diluted bacterial mRNA spike controls and T7 oligo (dT) primer for 10 min at 70 C. Add first-strand reaction components and incubate 1 hour at 42C. Add the first-strand cDNA product to the second-strand reaction components and incubate for 2 hours at 16 C. Double-strand cDNA was purified using QIAquick purification kit (Qiagen), eluted twice, each time with 30µl of nuclease-free water then dried in a SpeedVac concentrator. Prepare IVT mix of biotinylated UTP, ribonucleotides, and the 10x T7 enzyme mix and add to the resuspended cDNA. Incubate at 37C for 14 hours. Purify cRNA using RNeasy Mini Kit (Qiagen) and elute the cRNA twice, each time with 50 µl nuclease-free water. Measure the absorbance at 260 nm and 280 nm to determine the ratio (A260:A280=2).

treatment_protocol: C57BL/6J (ICAM-1+/+) mice aged 8 weeks (n=5) were received an intraperitoneal injection of citrate buffer (pH 4.5).


title: Me13_BEZ235+ sTRAIL_8hrs_rep3

description: SAMPLE 21

source_name: Me13_BEZ235+ sTRAIL_8hrs

value: BEZ235+ sTRAIL


title: Me13_BEZ235+ sTRAIL_8hrs_rep2

description: SAMPLE 20

value: human Melanoma


title: ICAM-1+/+ DM (DM-WT)

treatment_protocol: C57BL/6J (ICAM-1+/+) mice aged 8 weeks (n=5) were received an intraperitoneal injection of streptozotocin (STZ) at 200mg/kg in citrate buffer (pH 4.5).


title: C2aV72cys3_ N72cys5R3

city: Saint-Genès Champanelle

first: Sabine

last: Leroy

address: Clermont-Ferrand Theix Research Center

department: MICA

country: France

institute: INRA

hyb_protocol: The experimentation was realized in dye swap. Cyanine 3/cDNA and cyanine 5/cDNA were mixed with  Agilent hybridization buffer, and hybridized at a temperature of 60°C for 18 hours in a dedicated hybridization oven.

scan_protocol: Microarrays were scanned in a SYS-SN-ARRAY Agilent Microarray Scanner (5-µm resolution) with a coefficient of photomultiplication of 30%.

data_processing: Global lowess within array normalization.

organism: Staphylococcus xylosus

source_name: Without nitrate and nitrite at 72hours of incubation, repetition 3

label_protocol: RNA from each sample was reverse transcribed to cDNA according to the manufacturer’s instructions (Invitrogen, Superscript Reverse Transcriptase). The RNA was digested by RNAse H (Invitrogen). The cDNA was labeled by cyanine 3 or cyanine 5 by the kit Bioprime DNA according to the manufacturer’s instructions (Invitrogen). Unincorporated Cy-dye was removed using CentriSep column (Applied Biosystem).

growth_protocol: S.xylosus was precultured 24 h in a minimum media Mx, cultured 21 h in Mx and then inoculated at 107 CFU/g of meat. S. xylosus was finally incubated in meat during 24 or 72hours.

extract_protocol: Bacteria were lysed in 1.25 ml of Trizol reagent (Invitrogen Life Technologie) with 800mg of zirconia-silica beads (0.1 mm-diameter) in a FastPrep instrument (MP Biomedicals). RNA was purified with the kit Nucleospin RNA II (Macherey Nagel) according to the manufacturer’s instructions. A supplementary treatment is performed with Turbo DNAse (Ambion) to remove all traces of contaminated DNA.

treatment_protocol: S.xylosus was incubated in a meat matrix containing per kg: 5 g of glucose, 27.7 g of NaCl and with or without 0.18 g of KNO3 and 0.06 g of NaNO2

source_name: With nitrate and nitrite at 72hours of incubation, repetition 3


title: Me13_BEZ235+ sTRAIL_8hrs_rep1

description: SAMPLE 19


title: C2aN72cys3_V72cys5R3


title: C2aV24cys3_ N24cys5R3

source_name: Without nitrate and nitrite at 24hours of incubation, repetition 3

source_name: With nitrate and nitrite at 24hours of incubation, repetition 3


title: C2aV72cys3_ N72cys5R1

source_name: Without nitrate and nitrite at 72hours of incubation, repetition 1

source_name: With nitrate and nitrite at 72hours of incubation, repetition 1


title: Me13_AZD6244+ sTRAIL_8hrs_rep1

description: SAMPLE 16

source_name: Me13_AZD6244+ sTRAIL_8hrs

value: AZD6244+ sTRAIL


title: HEK293_siControl_1 (RNA)

city: Huddinge

first: Milica

last: Putnik

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Sample name: AW13_H_siCtrl

hyb_protocol: Array plates were washed and stained in the Affymetrix Gene Titan system.

scan_protocol: Array plates were scanned according to Affymetrix Gene Titan standard procedure.

data_processing: RMA

source_name: HEK293 cells, siControl knock-down, rep 1

label_protocol: GeneChip 3' IVT Express kit starting with 200 ng of total RNA.

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (all from Gibco, Life Technologies).

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: The MAML1 cell lines were constructed by transfecting human embryonic kidney HEK293 cells (ATCC, Manassas, VA, USA) with the pcDNA3.1-MAML1 vector, and stable clones were selected with geneticin. For siRNA experiments, HEK293 cells were transiently transfected with 100 nM MAML1 siRNA (a predesigned MAML1 SMARTpool set of 4 siRNAs; Dharmacon, Lafayette Colorado, USA) or control siRNA using DharmaFECT 1 siRNA reagents (Dharmacon)  in 6-well plates. RNA was collected 72 hours post-transfection.

value: HEK293 human embryonic kidney cells

tag: treatment

value: siControl knock-down


title: Me13_AZD6244+BEZ235_8hrs_rep1

description: SAMPLE 13

tag: treated with


title: Me13_AZD6244+BEZ235_8hrs_rep3

description: SAMPLE 15

tag: drug concentration


title: Me13_AZD6244+ sTRAIL_8hrs_rep3

description: SAMPLE 18

tag: exposure time


title: Me13_BEZ235_8hrs_rep3

description: SAMPLE 9


title: HEK293_siControl_2 (RNA)

description: Sample name: AW14_H_siCtr

source_name: HEK293 cells, siControl knock-down, rep 2


title: C2aN72cys3_V72cys5R2

source_name: With nitrate and nitrite at 72hours of incubation, repetition 2

source_name: Without nitrate and nitrite at 72hours of incubation, repetition 2


title: C2aV72cys3_ N72cys5R2


title: C2aV24cys3_ N24cys5R1

source_name: Without nitrate and nitrite at 24hours of incubation, repetition 1

source_name: With nitrate and nitrite at 24hours of incubation, repetition 1


title: HEK293_siMAML1_1 (RNA)

description: Sample name: AW15_H_siMAML1

source_name: HEK293 cells, siMAML1 knock-down, rep 1

value: siMAML1 knock-down


title: C2aN24cys3_V24cys5R3


title: Me13_sTRAIL_8hrs_rep1

description: SAMPLE 10

value: sTRAIL

value: 25 ng/ml


title: Me13_AZD6244+ sTRAIL_8hrs_rep2

description: SAMPLE 17


title: HEK293_MAML1_3 (RNA)

description: Sample name: AW06_H_MAML1_F05

source_name: HEK293 cells, MAML1 stable overexpression, rep 3

value: MAML1 stable overexpression


title: C2aN24cys3_V24cys5R1


title: C2aN24cys3_V24cys5R2

source_name: With nitrate and nitrite at 24hours of incubation, repetition 2

source_name: Without nitrate and nitrite at 24hours of incubation, repetition 2


title: Me13_AZD6244+BEZ235_8hrs_rep2

description: SAMPLE 14


title: C2aN72cys3_V72cys5R1


title: Me13_BEZ235_8hrs_rep1

description: SAMPLE 7


title: Me13_sTRAIL_8hrs_rep3

description: SAMPLE 12


title: C2aV24cys3_ N24cys5R2


title: Me13_sTRAIL_8hrs_rep2

description: SAMPLE 11


title: Me13_BEZ235_8hrs_rep2

description: SAMPLE 8


title: HEK293_siMAML1_2 (RNA)

description: Sample name: AW16_H_siMAML1

source_name: HEK293 cells, siMAML1 knock-down, rep 2


title: HEK293_control_3 (RNA)

description: Sample name: AW03_H

source_name: HEK293 cells, no treatment, rep 3

value: no treatment


title: HEK293_MAML1_1 (RNA)

description: Sample name: AW04_H_MAML1

source_name: HEK293 cells, MAML1 stable overexpression, rep 1


title: Me13_AZD6244_8hrs_rep1

description: SAMPLE 4


title: HEK293_MAML1_2 (RNA)

description: Sample name: AW05_H_MAML1

source_name: HEK293 cells, MAML1 stable overexpression, rep 2


title: HEK293_control_2 (RNA)

description: Sample name: AW02_H

source_name: HEK293 cells, no treatment, rep 2


title: Me13_AZD6244_8hrs_rep2

description: SAMPLE 5


title: Me13_untreated_8hrs_rep2

description: SAMPLE 2

value: none (untreated control)


title: H1299_4 h_direct bystander positive_rep4

status: Public on Oct 07 2014

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression in H1299 RAD9 normal, 4hr, irradiated corresponding to bystander positive

hyb_protocol: 1.6 mg of cRNA (>9 pmol Cy3 per mg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) using the Gene Expression Hybridization Kit as recommended by Agilent

scan_protocol: Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 11.5 (Agilent)

data_processing: Background corrected intensities were log2 transformed in BRB-ArrayTools, Version 4.3.2. Background corrected intensities were log2 transformed and median-normalized, probes were averaged over replicates and then filtered. Non-uniform outliers or features not significantly above background intensity in 25% or more of the hybridizations were filtered out, leaving 15859 features.  A further filter requiring a minimum 1.3-fold change in at least 20% of the hybridizations was then applied yielding a final set of 9502 features that were used for subsequent analyses.

source_name: NSCLC H1299, direct irradiated bystander positive, 4 h, rep4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions

growth_protocol: H1299, a human non-small cell lung carcinoma cell line, were used in this study. Cells were cultured in DMEM containing 10% FBS plus penicillin/streptomycin, at final concentrations of 50 ug/ml at 37ºC in a humidified 95% air+5% CO2 incubator. To obtain cells with decreased levels of RAD9 protein, H1299 cells were infected with pSUPER.retro.puro.siRNA viral vector expressing a short hairpin RAD9 RNA for RNA silencing.

extract_protocol: RNA was isolated using Exiqon Mircury (Exiqon), according to the manufacturer’s instructions

treatment_protocol: Cells were exposed to 0 (sham irradiated) or 1 Gy 4He ions (125 KeV per micron) using the track segment mode of the 5.5-MeV Singletron accelerator

value: Non small cell lung cancer cell line, H1299

tag: rad9 status

value: RAD9 normal


title: H1299_4 h_ bystander positive_rep1

description: Gene expression in H1299 RAD9 normal, 4hr, bystander positive

source_name: NSCLC H1299, irradiated bystander positive, 4 h, rep1


title: H1299_4 h_ bystander positive_rep5

source_name: NSCLC H1299, irradiated bystander positive, 4 h, rep5


title: Me13_untreated_8hrs_rep3

description: SAMPLE 3


title: HEK293_control_1 (RNA)

description: Sample name: AW01_H

source_name: HEK293 cells, no treatment, rep 1


title: H1299_4 h_ bystander positive_rep3

source_name: NSCLC H1299, irradiated bystander positive, 4 h, rep3


title: Me13_AZD6244_8hrs_rep3

description: SAMPLE 6


title: H1299_4 h_ bystander positive_rep4

source_name: NSCLC H1299, irradiated bystander positive, 4 h, rep4


title: H1299_4 h_direct bystander positive_rep2

source_name: NSCLC H1299, direct irradiated bystander positive, 4 h, rep2


title: H1299_4 h_direct bystander positive_rep3

source_name: NSCLC H1299, direct irradiated bystander positive, 4 h, rep3


title: H1299_4 h_ bystander negative_rep5

description: Gene expression in H1299 RAD9 normal, 4hr, bystander negative

source_name: NSCLC H1299, irradiated bystander negative, 4 h, rep5


title: H1299_4 h_direct bystander positive_rep1

source_name: NSCLC H1299, direct irradiated bystander positive, 4 h, rep1


title: H1299_4 h_ bystander negative_rep2

source_name: NSCLC H1299, irradiated bystander negative, 4 h, rep2


title: H1299_4 h_ bystander negative_rep4

source_name: NSCLC H1299, irradiated bystander negative, 4 h, rep4


title: H1299_4 h_ bystander negative_rep3

source_name: NSCLC H1299, irradiated bystander negative, 4 h, rep3


title: H1299_4 h_ bystander negative_rep1

source_name: NSCLC H1299, irradiated bystander negative, 4 h, rep1


title: H1299_4 h_direct bystander negative_rep4

description: Gene expression in H1299 RAD9 normal, 4hr, irradiated corresponding to bystander negative

source_name: NSCLC H1299, direct irradiated bystander negative, 4 h, rep4


title: H1299_4 h_direct bystander negative_rep3

source_name: NSCLC H1299, direct irradiated bystander negative, 4 h, rep3


title: H1299_4 h_direct bystander negative_rep5

source_name: NSCLC H1299, direct irradiated bystander negative, 4 h, rep5


title: H1299_4 h_direct bystander negative_rep1

source_name: NSCLC H1299, direct irradiated bystander negative, 4 h, rep1


title: H1299_4 h_ control_rep5

description: Gene expression in H1299 RAD9 normal, 4hr, sham irradiated control

source_name: NSCLC H1299, control, 4 h, rep5


title: H1299_4 h_direct bystander negative_rep2

source_name: NSCLC H1299, direct irradiated bystander negative, 4 h, rep2


title: A.niger grown without B.subtilis rep 3

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: centre of fungal biodiversity, Utrecht, KNAW

description: Gene expression data from A.niger grow without B.subtilis 4h

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned according to Affymetrix protocol.

data_processing: Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus niger

source_name: A.niger grown without B.subtilis at 4 hours

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: Aspergillus niger CB 119.1 was inoculated at 104 spores/ml and cultivated in TY medium  (1% Bacto tryptone, 0.5% Bacto yeast, 0.5% NaCl, and 0.1 mM MnCl2) at 30 ºC, 250 rpm for 15 hours. For co-cultivation, B. subtilis was subsequently added the pre-cultures at a final concentration of 5•106 cfu/mL. The shaken co-cultivations were incubated at 30 ºC, 150 rpm for 2-40 hours before samples were taken at 4h for Microarray.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer. RNA quantity and quality were determined on a Nanodrop spectrophotometer, and integrity was tested on an Agilent 2100 Bioanalyser.

treatment_protocol: Mycelium from three A. niger cultures in absence and in presence of B. subtilis was pooled on Miracloth and immediately frozen in liquid nitrogen.

tag: strain


title: HEK293_siMAML1 (DNA)

description: Sample name: HEK293_siMAML

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio software (v. 2010.2)

label: Cy5 and Cy3

source_name: HEK293 cells, siMAML1 knock-down, rep 1

label_protocol: Standard Illumina Protocol

extract_protocol: Invisorb Spin Tissue Mini Kit (Invitek, Nordic Biolabs)

treatment_protocol: The MAML1 cell lines were constructed by transfecting human embryonic kidney HEK293 cells (ATCC, Manassas, VA, USA) with the pcDNA3.1-MAML1 vector, and stable clones were selected with geneticin. For siRNA experiments, HEK293 cells were transiently transfected with 100 nM MAML1 siRNA (a predesigned MAML1 SMARTpool set of 4 siRNAs; Dharmacon, Lafayette Colorado, USA) or control siRNA using DharmaFECT 1 siRNA reagents (Dharmacon) in 6-well plates. DNA was collected 72 hours post-transfection.


title: HEK293_control_2 (DNA)

description: Sample name: HEK293 2

source_name: HEK293 cells, no treatment, rep 2


title: A.niger grown without B.subtilis rep 2


title: HEK293_siControl (DNA)

description: Sample name: HEK293_siControl

source_name: HEK293 cells, siControl knock-down, rep 1


title: HEK293_MAML1_2 (DNA)

description: Sample name: HEK293_MAML1 2

source_name: HEK293 cells, MAML1 stable overexpression, rep 2


title: H1299_4 h_ control_rep3

source_name: NSCLC H1299, control, 4 h, rep3


title: H1299_4 h_ control_rep4

source_name: NSCLC H1299, control, 4 h, rep4


title: HEK293_control_1 (DNA)

description: Sample name: HEK293 1

source_name: HEK293 cells, no treatment, rep 1


title: H1299_4 h_ control_rep2

source_name: NSCLC H1299, control, 4 h, rep2


title: A.niger grown with B.subtilis rep 2

description: Gene expression data from A.niger grow with B.subtilis 4h

source_name: A.niger grown with B.subtilis at 4 hours


title: FTC14

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: FTC

hyb_protocol: Hybridization was carried out according to the manufacturer’s instructions (Illumina, San Diego, CA, USA)

scan_protocol: Scanning was performed with BeadArray Reader

data_processing: All of the data sets were normalized with quantile normalization in R/Bioconductor by preprocessCore library. log2 transformation was applied to diminish the effect of skewed microarray intensity distributions. For our data we additionally applied centering around mean miRNA expression values of FTC samples to diminish technical differences between chips. All miRNAs in all four data sets were annotated with miRBase version 20. 2 versions of normalized file are available: one with miRNA annotation and other with probe sequence annotation.

label: oligonucleotide beads

source_name: thyroid tumor

label_protocol: Labeling was carried out according to the manufacturer’s instructions (Illumina, San Diego, CA, USA)

growth_protocol: miRNA expression profiling was performed for 17 freshly frozen FTC samples and 8 freshly frozen FA samples, macrodisected from primary tumor

extract_protocol: Before miRNA expression profiling, the FTC samples were reviewed by two independent pathologists for the occurrence of capsular- or vascular invasion, the histopathological hallmarks of FTCs

tag: malignity

value: malignant

tag: sample type

value: snap frozen

tag: tumor type

value: follicular carcinoma


title: FTC16

description: FTC


title: FTC17

description: FTC


title: FTC15

description: FTC


title: H1299shRAD9_4 h_ bystander positive_rep4

description: Gene expression in H1299 RAD9 depleted, 4hr, bystander positive

source_name: NSCLC H1299shRAD9, irradiated bystander positive, 4 h, rep4

value: RAD9 depleted


title: FTC13

description: FTC


title: FTC12

description: FTC


title: HEK293_MAML1_1 (DNA)

description: Sample name: HEK293_MAML1 1

source_name: HEK293 cells, MAML1 stable overexpression, rep 1


title: H1299shRAD9_4 h_ bystander positive_rep5

source_name: NSCLC H1299shRAD9, irradiated bystander positive, 4 h, rep5


title: A.niger grown with B.subtilis rep 3


title: H1299_4 h_ control_rep1

source_name: NSCLC H1299, control, 4 h, rep1


title: H1299shRAD9_4 h_ bystander positive_rep1

source_name: NSCLC H1299shRAD9, irradiated bystander positive, 4 h, rep1


title: FTC11

description: FTC


title: FTC10

description: FTC


title: A.niger grown with B.subtilis rep 1


title: H1299shRAD9_4 h_ bystander positive_rep2

source_name: NSCLC H1299shRAD9, irradiated bystander positive, 4 h, rep2


title: A.niger grown without B.subtilis rep 1

source_name: A.niger grown without B.subtilis at 4 hours


title: H1299shRAD9_4 h_ bystander positive_rep3

source_name: NSCLC H1299shRAD9, irradiated bystander positive, 4 h, rep3


title: H1299shRAD9_4 h_direct bystander positive_rep5

description: Gene expression in H1299 RAD9 depleted, 4hr, irradiated corresponding to bystander positive

source_name: NSCLC H1299shRAD9, direct irradiated bystander positive, 4 h, rep5


title: H1299shRAD9_4 h_direct bystander positive_rep3

source_name: NSCLC H1299shRAD9, direct irradiated bystander positive, 4 h, rep3


title: H1299shRAD9_4 h_direct bystander positive_rep4

source_name: NSCLC H1299shRAD9, direct irradiated bystander positive, 4 h, rep4


title: FTC7

description: FTC


title: FTC9

description: FTC


title: FTC6

description: FTC


title: H1299shRAD9_4 h_direct bystander positive_rep2

source_name: NSCLC H1299shRAD9, direct irradiated bystander positive, 4 h, rep2


title: FTC5

description: FTC


title: H1299shRAD9_4 h_ bystander negative_rep4

description: Gene expression in H1299 RAD9 depleted, 4hr, bystander negative

source_name: NSCLC H1299shRAD9, irradiated bystander negative, 4 h, rep4


title: FTC4

description: FTC


title: H1299shRAD9_4 h_ bystander negative_rep3

source_name: NSCLC H1299shRAD9, irradiated bystander negative, 4 h, rep3


title: FTC8

description: FTC


title: H1299_4 h_ bystander positive_rep2

source_name: NSCLC H1299, irradiated bystander positive, 4 h, rep2


title: FTC3

description: FTC


title: H1299shRAD9_4 h_direct bystander positive_rep1

source_name: NSCLC H1299shRAD9, direct irradiated bystander positive, 4 h, rep1


title: FTC2

description: FTC

source_name: thyroid tumor


title: FTC1

description: FTC


title: H1299shRAD9_4 h_ bystander negative_rep2

source_name: NSCLC H1299shRAD9, irradiated bystander negative, 4 h, rep2


title: H1299shRAD9_4 h_ bystander negative_rep1

source_name: NSCLC H1299shRAD9, irradiated bystander negative, 4 h, rep1


title: FA8

description: FA

value: benign

value: follicular adenoma


title: H1299shRAD9_4 h_ bystander negative_rep5

source_name: NSCLC H1299shRAD9, irradiated bystander negative, 4 h, rep5


title: HIV/HCV coinfected patient 8 at baseline

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from peripheral blood mononuclear cells of HIV/HCV infected patient prior to combination antiretroviral therapy

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Microarray quality was examined using the Affymetrix Expression Console Program.  CEL files were analyzed using the RMA noralization and expression level quantitation algorithm.  Probesets were filtered to identify those with absolute expression at RMA>=5.5 in at least 2 samples.  Differential expression was based on treated versus baseline per patient using Benjamini Hochberg corrected p<0.05.

source_name: Periperal blood mononuclear cells from an HIV/HCV coinfected patient before combination antiretroviral therapy

label_protocol: Affymetrix-specified 3'UTR-based labeling method

extract_protocol: Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation and were either used immediately or cryoperserved in cell-freezing medium.  RNA was extracted using Qiagen's Rneasy Mini Kit spin-column technology.

treatment_protocol: Combined antiretroviral therapy for 24 weeks

tag: tissue

value: Peripheral blood mononuclear cells

tag: timepoint

value: baseline


title: FA7

description: FA


title: HIV/HCV coinfected patient 8 at followup

description: Gene expression data from peripheral blood mononuclear cells of HIV/HCV infected patient after 24 weeks of combination antiretroviral therapy

source_name: Periperal blood mononuclear cells from an HIV/HCV coinfected patient after 24 weeks of combination antiretroviral therapy

value: Combination antiretroviral therapy

value: 24 weeks


title: H1299shRAD9_4 h_direct bystander negative_rep4

description: Gene expression in H1299 RAD9 depleted, 4hr, irradiated corresponding to bystander negative

source_name: NSCLC H1299shRAD9, direct irradiated bystander negative, 4 h, rep4

tag: cell line


title: HIV/HCV coinfected patient 7 at baseline


title: HIV/HCV coinfected patient 5 at followup


title: HIV/HCV coinfected patient 6 at baseline


title: H1299shRAD9_4 h_direct bystander negative_rep3

source_name: NSCLC H1299shRAD9, direct irradiated bystander negative, 4 h, rep3


title: HIV/HCV coinfected patient 4 at followup


title: H1299shRAD9_4 h_direct bystander negative_rep2

source_name: NSCLC H1299shRAD9, direct irradiated bystander negative, 4 h, rep2


title: FA5

description: FA


title: H1299shRAD9_4 h_direct bystander negative_rep5

source_name: NSCLC H1299shRAD9, direct irradiated bystander negative, 4 h, rep5


title: H1299_4 h_direct bystander positive_rep5

source_name: NSCLC H1299, direct irradiated bystander positive, 4 h, rep5


title: HIV/HCV coinfected patient 6 at followup


title: HIV/HCV coinfected patient 5 at baseline


title: Cal-27-resistant 0.01% dmso 48hr replicate 2

city: Iowa City

first: Aditya

last: Stanam

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was quantile normalized in GenomeStudio.

source_name: erlotinib-resistant tongue squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays.

growth_protocol: Sensitive (i.e. parental) Cal-27 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 4 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate and 4.5 g/L glucose with 10% Fetal Bovine Serum (FBS; Hyclone, Logan, UT). SCC-25 cells were cultured in a 1:1 mixture of Dulbecco’s modified Eagle’s medium and Ham’s F12 medium containing 1.2 g/L sodium bicarbonate, 2.5 mM L-glutamine, 15 mM HEPES, 0.5 mM sodium pyruvate, 4.5 g/L glucose, and 400 ng/mL hydrocortisone with 10% FBS. However the both types of resistant cells were cultured in their relevant culture media supplemented with erlotinib.

extract_protocol: RNA was extracted using RNeasy® Plus Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: To the cell lines, 0.01% DMSO (vehicle) was added 48 hours prior to RNA harvest.

value: Erlotinib-resistant Cal-27 tongue squamous cell carcinoma 200,000 cells (ATCC #CRL-20950


title: HIV/HCV coinfected patient 4 at baseline


title: HIV/HCV coinfected patient 3 at baseline


title: Me13_untreated_8hrs_rep1

description: SAMPLE 1

tag: cell type

value: human Melanoma


title: H1299shRAD9_4 h_ control_rep5

description: Gene expression in H1299 RAD9 depleted, 4hr, sham irradiated control

source_name: NSCLC H1299shRAD9, control, 4 h, rep5


title: Cal-27-resistant 0.01% dmso 48hr replicate 1

description: replicate 1


title: HIV/HCV coinfected patient 2 at followup


title: FA2

description: FA


title: H1299shRAD9_4 h_direct bystander negative_rep1

source_name: NSCLC H1299shRAD9, direct irradiated bystander negative, 4 h, rep1


title: HIV/HCV coinfected patient 3 at followup


title: Cal-27-resistant 0.01% dmso 48hr replicate 3

description: replicate 3


title: FA4

description: FA


title: Cal-27-sensitive 0.01% dmso 48 hr-replicate 3

description: replicate 3

source_name: erlotinib-sensitive tongue squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

value: ATCC #CRL-2095 erlotinib-sensitive Cal-27 tongue squamous cell carcinoma 200,000 cells


title: FA3

description: FA


title: H1299shRAD9_4 h_ control_rep4

source_name: NSCLC H1299shRAD9, control, 4 h, rep4


title: HIV/HCV coinfected patient 2 at baseline


title: FA1

description: FA


title: H1299shRAD9_4 h_ control_rep3

source_name: NSCLC H1299shRAD9, control, 4 h, rep3


title: Cal-27-sensitive 0.01% dmso 48 hr-replicate 1

description: replicate 1


title: FA(FTC)2

description: FA

source_name: thyroid tumor


title: HIV/HCV coinfected patient 1 at followup


title: H1299shRAD9_4 h_ control_rep2

source_name: NSCLC H1299shRAD9, control, 4 h, rep2


title: SCC-25-resistant 0.01% dmso 48hr replicate 3

description: replicate 3

value: Erlotinib-resistant SCC-25 tongue squamous cell carcinoma 200,000 cells (developed from ATCC #CRL-1628)


title: Cal-27-sensitive 0.01% dmso 48 hr-replicate 2

description: replicate 2


title: Cj_cellulose_staphase_biorep2

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description: This sample is of wild-type Cellvibrio japonicus during stationary growth in cellulose It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed at the UW-Madison Biotechnology Center following NimbleGen standard operating protocol.

scan_protocol: Scanning was performed at the UW-Madison Biotechnology Center following NimbleGen standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software package.

organism: Cellvibrio japonicus Ueda107

source_name: Cellvibrio japonicus sp. nov. strain Ueda107

label_protocol: Labeling was performed at the UW-Madison Biotechnology Center following NimbleGen standard operating protocol.

growth_protocol:
Cellvibrio japonicus was grown to mid-log phase (O.D.600nm = 0.3) anerobically at 30°C in MOPS defined media (Gardner, et al. AEM (2010) 76(15):5079-5087).
Cellvibrio japonicus was grown to stationary phase (O.D.600nm = 1.2) anerobically at 30°C in MOPS defined media (Gardner, et al. AEM (2010) 76(15):5079-5087).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent bioanalyzer at the UW-Madison Biotechnology Center.

value: cellulose stationary phase

tag: genotype

value: wild-type


title: Cj_cellulose_logphase_biorep2

description: This sample is of wild-type Cellvibrio japonicus during exponential growth in cellulose It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

value: cellulose log phase


title: Cj_cellulose_staphase_biorep1

description: This sample is of wild-type Cellvibrio japonicus during stationary growth in cellulose It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: SCC-25-resistant 0.01% dmso 48hr replicate 2

description: replicate 2


title: HIV/HCV coinfected patient 1 at baseline


title: SCC-25-sensitive 0.01% dmso 48 hr-replicate 3

description: replicate 3

value: ATCC #CRL-1628 erlotinib-sensitive SCC-25 tongue squamous cell carcinoma 200,000 cells


title: SCC-25-resistant 0.01% dmso 48hr replicate 1

description: replicate 1


title: Cj_glucose_staphase_biorep2

description: This sample is of wild-type Cellvibrio japonicus during stationary growth in glucose. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

value: glucose stationay phase


title: H1299shRAD9_4 h_ control_rep1

source_name: NSCLC H1299shRAD9, control, 4 h, rep1

value: Non small cell lung cancer cell line, H1299


title: HIV/HCV coinfected patient 7 at followup


title: Cj_glucose_staphase_biorep1

description: This sample is of wild-type Cellvibrio japonicus during stationary growth in glucose. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Cj_glucose_logphase_biorep2

description: This sample is of wild-type Cellvibrio japonicus during exponential growth in glucose. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

value: glucose log phase


title: Cj_cellulose_logphase_biorep1

description: This sample is of wild-type Cellvibrio japonicus during exponential growth in cellulose It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Cj_glucose_logphase_biorep1

description: This sample is of wild-type Cellvibrio japonicus during exponential growth in glucose. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: E9.5 trunk, wt, replicate3

city: Madrid

first: Juan Jose

last: Sanz-Ezquerro

address: Darwin, 3

department: Biologia Molecular y Celular

institute: Centro Nacional dde Biotecnologia

description: Gene expression in E9.5 trunks

hyb_protocol: Samples were hybridised to Whole Mouse Genome Microarray 4 x 44K ( G4846A, Agilent Technologies). 1.65 µg of Cy3 labelled aRNA were hybridised for 17 hours at 65ºC in a hybridisation oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5µm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analysed using Feature Extraction software version 9.5.3.1 (Agilent Technologies).

data_processing: Data were filtered at a probe level according to the following criteria. We demanded that at least 75% of the probes in at least one experimental condition had a quantification flag denoting that the signal is distinguishable from background. The same criterion is applied independently for the saturation of the signal. In addition, we filtered out those probes that had more than 25% of the replicates in at least one experimental condition with a flag indicating presence of outliers in the quantification of the signal probe.

source_name: E9.5 trunk, wt, replicate3

label_protocol: The One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. Briefly, 200-800 ng of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was then converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

extract_protocol: E9.5 embryos were dissected in cold PBS. The trunk was isolated (including the body from the otic vesicle to somite 15 and forelimbs). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates. RNA was extracted with the Qiagen extraction kit and RNA quality was checked by Nanodrop spectrophotometer measure and gel electrophoresis.

tag: developmental stage

value: trunk

tag: phenotype

value: wild type


title: E9.5 trunk, Arid3b-null, replicate1

description: Gene expression in E9.5 trunks

source_name: E9.5 trunk, Arid3b-null, replicate1


title: E9.5 trunk, Arid3b-null, replicate2

description: Gene expression in E9.5 trunks

source_name: E9.5 trunk, Arid3b-null, replicate2


title: E9.5 trunk, Arid3b-null, replicate3

description: Gene expression in E9.5 trunks

source_name: E9.5 trunk, Arid3b-null, replicate3


title: E9.5 trunk, wt, replicate2

description: Gene expression in E9.5 trunks

source_name: E9.5 trunk, wt, replicate2


title: SCC-25-sensitive 0.01% dmso 48 hr-replicate 2

description: replicate 2


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 3 by dye-swap color

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

description: Biological replicate 3 of 3

hyb_protocol: Hybridization was performed in 40% formamide, 5x Denhardt’s solution, 0.1% SDS, 1 mM Sodium pyrophosphate and 5x SSC during 14-16h at 52°C under agitation in rotating oven. Slides were then washed sequentially in 2× SSC/0.2% SDS during 5 min, 0.5× SSC during 10 min, 0.05x SSC during 5 min and 0.01x SSC during 1 min at room temperature before drying.

scan_protocol: Scanned on an Innoscan 700 scanner (Innopsys), images were segmented using Mapix Software (version 3.2.1).

data_processing: A specific script on R was used (limma package) for LOWESS normalization within slide and between slides.

organism: Bordetella pertussis

source_name: pellet of bacteria

label_protocol: 15 µg of total RNA was reverse transcribed with 400 units of SuperScript III (Invitrogen) in presence of 100µM Cy3-dCTP or Cy5-dCTP (GE) and 300 mM of hexanucleotide random (Roche) during 2 hours à 42°C. The labelled cDNA was then NaOH treated to degrade RNA and purified on Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: Bordetella pertussis strains were first grown on Bordet-Gengou (BG) agar plates and in Stainer-Scholte (SS) liquid medium supplemented with  10 µg/ml gentamicin, 100 µg/ml streptomycin

extract_protocol: Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions

tag: genotype/variaton

value: Delta KpsT mutant

tag: genotype/variation

value: Wild type


title: E9.5 trunk, wt, replicate1

description: Gene expression in E9.5 trunks

source_name: E9.5 trunk, wt, replicate1


title: E9.5 head, Arid3b-null, replicate2

description: Gene expression in E9.5 heads

source_name: E9.5 head, Arid3b-null, replicate2

extract_protocol: E9.5 embryos were dissected in cold PBS. The head was isolated (including head and first branchial arch). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates. RNA was extracted with the Qiagen extraction kit and RNA quality was checked by Nanodrop spectrophotometer measure and gel electrophoresis.

value: head


title: SCC-25-sensitive 0.01% dmso 48 hr-replicate 1

description: replicate 1


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2 by dye-swap color

description: Biological replicate 2 of 3


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 3

description: Biological replicate 3 of 3


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 2

description: Biological replicate 2 of 3


title: E9.5 head, Arid3b-null, replicate3

description: Gene expression in E9.5 heads

source_name: E9.5 head, Arid3b-null, replicate3


title: E9.5 head, wt, replicate2

description: Gene expression in E9.5 heads

source_name: E9.5 head, wt, replicate2


title: E9.5 head, wt, replicate3

description: Gene expression in E9.5 heads

source_name: E9.5 head, wt, replicate3


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1

description: Biological replicate 1 of 3


title: Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicat 1 by dye-swap color

description: Biological replicate 1 of 3


title: E9.5 heart, Arid3b-null, replicate3

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, Arid3b-null, replicate3

extract_protocol: E9.5 embryos were dissected in cold PBS. The heart was isolated (including the heart tube and the pharyngeal mesoderm and endoderm located beneath). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates. RNA was extracted with the Qiagen extraction kit and RNA quality was checked by Nanodrop spectrophotometer measure and gel electrophoresis.

value: heart


title: E9.5 head, wt, replicate1

description: Gene expression in E9.5 heads

source_name: E9.5 head, wt, replicate1


title: E9.5 heart, Arid3b-null, replicate2

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, Arid3b-null, replicate2


title: E9.5 head, Arid3b-null, replicate1

description: Gene expression in E9.5 heads

source_name: E9.5 head, Arid3b-null, replicate1


title: A724_24_RAV39+Sunutinib+GF

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

hyb_protocol: 3 μg of labelled products were hybridized, washed and stained in an Affymetrix GeneTitan system.

scan_protocol: Arrays were scanned in an Affymetrix GeneTitan system.

data_processing:
Raw intensities were quantile normalized and summarized with the RMA (Robust Multichip Average) expression measure described in Irizarry et al, Biostatistics (2003)
For the final analysis, only those features were used that could be mapped to EntrezIDs.

source_name: brain tumor initiating cells (BTIC)

label_protocol: cRNA and ssDNA were prepared from 0.3 µg totalRNA according to the Ambion WT Expression Kit manual. Fragmentation and terminal biotinylation were performed using the Affymetrix Terminal Labeling Kit.

growth_protocol: BTICs were cultured in stem-cell permissive RHB-A media (Stem Cell, Cambridge, UK) supplemented with 20 ng/ml of each human recombinant epidermal growth factor (EGF; R&D Systems, Minneapolis, USA) and human recombinant basic fibroblast growth factor (FGF; Peprotech, Hamburg, Germany).

extract_protocol: Cells were washed twice with ice-cold PBS and harvested in RLT-lysis buffer (provided in the RNeasy Kit, Qiagen, Hilden, Germany) for subsequent RNA-extraction

treatment_protocol: Cells were cultured in growth factor free medium for 16 hours prior to treatment. After starvation, cells were treated with 1 µM Sunitinib in the treatment groups or 0.00025 % DMSO in the control groups either with or without supplementation of recombinant growth factors PDGF-A/B and VEGFA (25 ng/ml) for 6 hours before harvest.

value: brain tumor initiating cells (BTIC)

tag: treatment

value: Sunitinib

tag: gf

value: yes

tag: btic culture

tag: treatment response of glioma in vitro_proliferation.score

tag: treatment response of glioma in vitro_proliferation.label

value: moderate induction

tag: treatment response of glioma in vitro_migration.score

tag: treatment response of glioma in vitro_migration.label

value: moderate inhibition


title: A724_21_RAV39+DMSO

value: DMSO

value: no


title: E9.5 heart, Arid3b-null, replicate1

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, Arid3b-null, replicate1


title: E9.5 heart, wt, replicate3

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, wt, replicate3


title: A724_22_RAV39+DMSO+GF


title: A724_23_RAV39+Sunutinib


title: A724_20_RAV57+Sunutinib+GF


title: A724_17_RAV57+DMSO


title: E9.5 heart, wt, replicate2

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, wt, replicate2


title: MMTV-Cre:Rbp53 primary tumor TMCPR-1014

city: Guelph

first: Robert

last: Jones

address: 50 Stone Rd

department: Biomedical Sciences

country: Canada

institute: University of Guelph

description: Tumor DNA is being compared to pooled tail DNA from animals of same mixed background

hyb_protocol: 2 ug of each DNA sample was hybridized according to the 40-hour manual protocol described by the manufacturer

scan_protocol: The arrays were scanned at 5 micron resolution in an Agilent scanner

data_processing: The images were processed with Agilent feature extraction version 9.5.1.1

source_name: pooled mouse tail DNA

label_protocol: The Invitrogen BioPrime CGH labeling kit was used (Cat#18094011) according to manufacturer's protocol

growth_protocol: Samples from independent primary mammary tumors from MMTV-Cre:Rbp53,MMTV-Cre:p53 and Ad-Cre:Rbp53 models were frozen and kept in -80 degree.

extract_protocol: Genomic DNAs were purified using DNAeasy kits (Qiagen)

treatment_protocol: Genomic DNA obtained from primary tumors were used for aCGH analysis to determine copy number alterations following combined loss of Rb/p53

tag: strain background

value: mixed

value: tail

tag: source

value: reference DNA (non-tumor bearing)

source_name: Primary mammary tumor Rbp53 deleted

value: Primary mammary tumor

tag: tumor model

value: MMTV-Cre (Transplant)


title: A724_18_RAV57+DMSO+GF


title: Ad-Cre:Rbp53 primary tumor ACRP-1

tag: tissue

value: Ad-CMVcre (Transplant)


title: MMTV-Cre:Rbp53 primary tumor TMCRP-1123


title: MMTV-Cre:Rbp53 primary tumor TMCRP-3


title: A724_19_RAV57+Sunutinib

tag: cell type


title: A724_13_RAV28+DMSO


title: CD161++_Patient3

city: Oxford

first: Joannah

middle: R

last: Fergusson

state: select a state

address: South Parks Road

department: Peter Medawar Building for Pathogen Research

country: United Kingdom

institute: University of Oxford

description: Gene expression in FACS sorted CD161++ CD8+ T cells

hyb_protocol: A total of 750ng of biotin-labeled cRNA from each sample was used in the hybridization process at 58C for 18 h. The hybridized BeadChip was washed and labeled with streptavidin-Cy3 according to the Illumina protocols.

scan_protocol: Chips were scanned with Illumina BeadArray Reader accordingly

data_processing: GenomeStudio (Illumina Inc) was used for data extraction accordingly

source_name: CD8+ T cells

label_protocol: Biotinylated cRNA Probes were prepared using illumina TotalPrep-96  Ambion # 4393543

growth_protocol: Cells taken ex vivo from healthy donors and separated using Ficoll centrifugation

extract_protocol: RNA was extracted from cells using a Qiagen Rneasy kit

treatment_protocol: CD8+ T cell subsets were sorted using a FACS sorter

value: Peripheral Blood cells

value: CD8+ T cells


title: A724_16_RAV28+Sunutinib+GF

value: strong inhibition


title: MMTV-Cre:Rbp53 primary tumor TMCRP-1


title: A724_15_RAV28+Sunutinib


title: Ad-Cre:Rbp53 primary tumor ACRP-2


title: CD161+_Patient4

description: Gene expression in FACS sorted CD161+ CD8+ T cells


title: CD161++_Patient4


title: CD161+_Patient3


title: A724_14_RAV28+DMSO+GF


title: A724_12_RAV42+Sunutinib+GF


title: CD161-_Patient4

description: Gene expression in FACS sorted CD161- CD8+ T cells


title: E9.5 heart, wt, replicate1

description: Gene expression in E9.5 hearts

source_name: E9.5 heart, wt, replicate1

value: heart

value: wild type


title: CD161-_Patient3


title: MMTV-Cre:Rbp53 primary tumor TMCRP-985


title: MMTV-Cre:Rbp53 primary tumor MCRP-1175

value: MMTV-Cre (nulliparous)


title: MMTV-Cre:Rbp53 primary tumor MCRP-1241

value: MMTV-Cre (Parous)


title: CD161++_Patient2


title: A724_10_RAV42+DMSO+GF

value: brain tumor initiating cells (BTIC)

value: yes


title: A724_04_RAV20+Sunutinib+GF

value: Sunitinib

value: moderate inhibition

value: moderate induction


title: CD161-_Patient2


title: A724_09_RAV42+DMSO

value: DMSO

value: no


title: CD161+_Patient1


title: A724_11_RAV42+Sunutinib


title: A724_06_RAV1+DMSO+GF


title: A724_01_RAV20+DMSO


title: A724_01b_RAV20+DMSO


title: CD161++_Patient1


title: CD161+_Patient2


title: CD161+_3

description: Gene expression in CD161+ CD4+ T cells

source_name: CD4 T cells

treatment_protocol: CD4+ T cells were enriched using EasySep human CD4 enrichment kit, and CD161+ and CD161- cells then selected by anti-PE microbeads (Miltenyi Biotec)

value: CD4+ T cells


title: A724_03_RAV20+Sunutinib


title: A724_05_RAV1+DMSO


title: A724_02_RAV20+DMSO+GF


title: CD161-_3

description: Gene expression in CD161- CD4+ T cells


title: CD161-_2

description: Gene expression in CD161- CD4+ T cells


title: A724_08_RAV1+Sunutinib+GF


title: CD161+_2

description: Gene expression in CD161+ CD4+ T cells


title: CD161-_Patient1


title: A612b_23_RAV26_1uM_Sunitinib_2


title: A612b_24_RAV26_1uM_Sunitinib_GF


title: ExVivoTCRgd_CD161-_Donor4

description: Gene expression in FACS sorted CD161- TCRgd T cells

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).  Briefly, 600ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17hrs, 65degrees celsius) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).  The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing: Raw data microarray features were normalised using variance stabilising normalisation (vsn) using R and Bioconductor packages.

source_name: Peripheral Blood, FACS sorted TCRgd+ T cells

label_protocol: 10ng of each total RNA sample was used to produce Cy3-labeled cRNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol.  Yields of cRNA and dye-incorporation rate were measured with the ND-100 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Rneasy® Mini Kit, Qiagen following manufacturer's protocol.  RNA samples were quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)

treatment_protocol: TCRgd+ T cell subsets were sorted using a FACS sorter

tag: cd161 subtype

value: negative

tag: donor

value: TCRgd T cells


title: CD161-_1

description: Gene expression in CD161- CD4+ T cells

value: Peripheral Blood cells


title: CD161+_1

description: Gene expression in CD161+ CD4+ T cells


title: E9.0 mouse embryos, Arid3b-null, replicate4

description: Gene expression in E9.0 whole embryos

hyb_protocol: Samples were hybridised to Whole Mouse Genome Microarray 4 x 44K (G4122F, Agilent Technologies). 1.65 µg of Cy3 labelled aRNA were hybridised for 17 hours at 65ºC in a hybridisation oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

extract_protocol: E9.0 embryos were dissected in cold PBS. Four wild-type and four mutant samples consisting of 3-4 embryos each were used. RNA was extracted with the Qiagen extraction kit and RNA quality was checked by Nanodrop spectrophotometer measure and gel electrophoresis.

tag: developmental stage

value: whole embryo

tag: phenotype


title: E9.0 mouse embryos, Arid3b-null, replicate1

description: Gene expression in E9.0 whole embryos


title: E9.0 mouse embryos, wt, replicate4

description: Gene expression in E9.0 whole embryos

source_name: E9.0 mouse embryos, wt, replicate4


title: E9.0 mouse embryos, Arid3b-null, replicate3

description: Gene expression in E9.0 whole embryos


title: A612b_19_RAV19_1uM_Sunitinib


title: A612b_22_RAV26_DMSO_GF


title: ExVivoTCRgd_CD161-_Donor3


title: ExVivoTCRgd_CD161+_Donor4

description: Gene expression in FACS sorted CD161+ TCRgd T cells

value: positive


title: ExVivoTCRgd_CD161-_Donor1


title: ExVivoTCRgd_CD161+_Donor2


title: ExVivoTCRgd_CD161+_Donor3


title: A612b_21_RAV26_DMSO_2


title: A612b_16_RAV17_1uM_Sunitinib_GF_2

value: strong inhibition


title: A612b_18_RAV19_DMSO_GF


title: E9.0 mouse embryos, Arid3b-null, replicate2

description: Gene expression in E9.0 whole embryos


title: E9.0 mouse embryos, wt, replicate1

description: Gene expression in E9.0 whole embryos

source_name: E9.0 mouse embryos, wt, replicate1

value: wild type


title: ExVivoTCRgd_CD161+_Donor1


title: A612b_20_RAV19_1uM_Sunitinib_GF


title: E. coli ∆patZ_chemostat_repl3

city: Murcia

first: Sara

last: Castaño Cerezo

address: Faculty of Chemistry. Campus de Espinardo. University of Murcia

department: Dpt. Biochemistry and Molecular Biology B and Immunology

institute: University of Murcia

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip E. Coli Genome 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software

organism: Escherichia coli K-12

source_name: E. coli ∆patZ grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep3

label_protocol: Labelling was performed according to the Affymetrix protocol (Affymetrix, Santa Clara, CA, US)

growth_protocol: E. coli wt and its mutants deficient in cobB or patZ genes were grown in aerobic batch 20 mM glucose minimal media, cell were harvested at exponential phase for analysis. Also this strain and mutants were grown in glucose limited chemostat cultures (5 mM glucose) at a dilution rate of 0.2 h-1.

extract_protocol: Total RNA extraction using Vantage™ RNA Purification Kit was performed according with the manufacter instructions.

tag: strain

value: E. coli ∆patZ (JW2568)


title: E9.0 mouse embryos, wt, replicate2

description: Gene expression in E9.0 whole embryos

source_name: E9.0 mouse embryos, wt, replicate2


title: A612b_17_RAV19_DMSO

tag: treatment


title: ExVivoTCRgd_CD161-_Donor2


title: E9.0 mouse embryos, wt, replicate3

description: Gene expression in E9.0 whole embryos

source_name: E9.0 mouse embryos, wt, replicate3


title: A612b_14_RAV17_DMSO_GF

tag: gf


title: E. coli ∆patZ_chemostat_repl2

source_name: E. coli ∆patZ grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep2


title: E. coli ∆patZ_chemostat_repl1

source_name: E. coli ∆patZ grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep1


title: E. coli ∆cobB_chemostat_repl2

source_name: E. coli ∆cobB grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep2

value: E. coli ∆cobB (JW1106)


title: E. coli ∆cobB_chemostat_repl1

source_name: E. coli ∆cobB grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep1


title: Treg_LN_6A

city: London

first: Lucy

last: Walker

address: Royal Free Campus

department: Institute of Immunity & Transplantation

institute: University College London

description: Gene expression data from sorted cells

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

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

data_processing: The data were analysed with Robust Multi-array Average (RMA) procedure using the Bioconductor package affy.

source_name: CD4+CD25+CD69- Tregs from lymph nodes

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA using the standard protocols of two cycle cDNA synthesis (GeneChip Expression 3’-Amplification Reagents Two Cycle cDNA Synthesis Kit) and IVT amplification (MEGAscript T7 kit [Ambion Inc]).

growth_protocol: Freshly sorted cells

extract_protocol: RNA was isolated using the RNeasy micro kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: No treatment

value: CD4+CD25+CD69- Tregs

tag: tissue origin

value: lymph nodes


title: A612b_11_RAV24_1uM_Sunitinib

source_name: brain tumor initiating cells (BTIC)

value: brain tumor initiating cells (BTIC)

value: Sunitinib

tag: btic culture


title: A612b_15_RAV17_1uM_Sunitinib


title: E. coli wt_chemostat_repl3

source_name: E. coli wt grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep3

value: E. coli BW25113 wt


title: Treg_LN_5A

description: Gene expression data from sorted cells


title: E. coli ∆cobB_chemostat_repl3

source_name: E. coli ∆cobB grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep3


title: Tcell_LN_4B

description: Gene expression data from sorted cells

source_name: CD4+CD25-CD69- Tcells from lymph nodes

value: CD4+CD25-CD69- Tcells


title: Treg_panLN_5C

description: Gene expression data from sorted cells

source_name: CD4+CD25+CD69+ Tregs from pancreatic lymph nodes

value: CD4+CD25+CD69+ Tregs

value: pancreatic lymph nodes


title: Treg_panLN_4C

description: Gene expression data from sorted cells


title: A612b_13_RAV17_DMSO

value: DMSO

value: no


title: A612b_12_RAV24_1uM_Sunitinib_GF

value: yes

tag: treatment response of glioma in vitro_proliferation.score

tag: treatment response of glioma in vitro_proliferation.label

value: moderate inhibition

value: moderate induction


title: Whole bone marrow_MD253

city: Badalona

first: Vera

last: Adema

address: Carretera de Can Ruti, Cami de les Escoles s/n

department: MDS Group

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to 6.0 Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

data_processing:
CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis.

label: Biotin

source_name: Whole bone marrow from MDS_5q-

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from whole bone marrow, whole peripheral blood or CD3 lymphocytes isolated from peripheral blood prior to treatment with lenalidomide, at the individual centers participating in the study. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Whole bone marrow from MDS 5q-

tag: disease state

value: Myelodysplastic syndrome


title: A612b_08_RAV33_1uM_Sunitinib_GF_2

tag: treatment response of glioma in vitro_migration.score

tag: treatment response of glioma in vitro_migration.label


title: Treg_LN_4A

description: Gene expression data from sorted cells


title: A612b_09_RAV24_DMSO


title: E. coli ∆patZ_batch_repl3

source_name: E. coli ∆patZ grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep3

value: E. coli ∆patZ (JW2568)


title: E. coli wt_chemostat_repl1

source_name: E. coli wt grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep1


title: A612b_06_RAV33_DMSO_GF


title: Treg_panLN_3C

description: Gene expression data from sorted cells


title: Whole bone marrow_MD27

description: Hybridized to 6.0 Array


title: A612b_05_RAV33_DMSO


title: E. coli ∆patZ_batch_repl2

source_name: E. coli ∆patZ grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli ∆patZ_batch_repl1

source_name: E. coli ∆patZ grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: A612b_04_RAV27_1uM_Sunitinib_GF


title: CD3+_CD3_27

description: Hybridized to 6.0 Array

source_name: CD3+ lymphocytes from peripheral blood

value: CD3+ lymphocytes from peripheral blood


title: Treg_LN_2A

description: Gene expression data from sorted cells

value: CD4+CD25+CD69- Tregs


title: Treg_LN_3A

description: Gene expression data from sorted cells

value: lymph nodes


title: CD3+_CD3_253

description: Hybridized to 6.0 Array


title: Tcell_LN_6B

description: Gene expression data from sorted cells


title: Tcell_panLN_3D

description: Gene expression data from sorted cells

source_name: CD4+CD25-CD69+ Tcells from pancreatic lymph nodes

value: CD4+CD25-CD69+ Tcells


title: Tcell_panLN_2D

description: Gene expression data from sorted cells


title: E. coli ∆cobB_batch_repl3

source_name: E. coli ∆cobB grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep3

value: E. coli ∆cobB (JW1106)


title: E. coli wt_batch_repl3

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep3

value: E. coli BW25113 wt


title: A612b_01_RAV27_DMSO_2

value: brain tumor initiating cells (BTIC)


title: E. coli ∆cobB_batch_repl2

source_name: E. coli ∆cobB grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2


title: E. coli ∆cobB_batch_repl1

source_name: E. coli ∆cobB grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: Treg_LN_1A

description: Gene expression data from sorted cells

source_name: CD4+CD25+CD69- Tregs from lymph nodes


title: Tcell_panLN_5D

description: Gene expression data from sorted cells


title: A612b_02_RAV27_DMSO_GF

source_name: brain tumor initiating cells (BTIC)


title: A612b_03_RAV27_1uM_Sunitinib

value: Sunitinib


title: A612_24_RAV21_Sunitinib_GF

value: strong inhibition


title: A612_23_RAV21_Sunitinib


title: Treg_Pan_LN_3

description: Gene expression data from sorted cells

value: CD4+CD25+CD69+ Tregs

value: pancreatic lymph nodes


title: A612_22_RAV21_DMSO_GF

value: DMSO

value: yes


title: Tcell_LN_1B

description: Gene expression data from sorted cells

value: CD4+CD25-CD69- Tcells


title: A612_20_R11_1uM_Sunitinib_GF

value: moderate inhibition


title: CD4_TOL_rep2

city: Glasgow

first: Agapitos

last: Patakas

state: Lanarkshire

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

description: Gene expression data from CD4+ T cells from orally tolerised mice

hyb_protocol: 2.5 ug of labeled cDNA was hybridized on Affymetrix GeneChip HT MG-430 PM array according to the manufacturer’s recommendations.

scan_protocol: GeneChips were scanned using Affymetrix HT Array Plate and scanned images were subjected to visual inspection and a chip quality report was generated by Expression console (Affymetrix).

data_processing: The data were analyzed with the robust multi-array analysis (RMA) algorithm, obtained from www.bioconductor.org

source_name: MACS sorted CD4+ T cells from orally tolerised mice

label_protocol: 50 ng of total RNA was amplified and labeled with Ovation® Pico WTA System and Encore™ Biotin Module assay (NuGEN Technologies Inc , San Carlos, CA), target labeling process was performed according to the manufacturer's recommendation.

growth_protocol: DO11.10 RAG2-/- mice were kept in ivc cages under home office regulation

extract_protocol: Total mRNA was isolated using the RNEASY mini kit (Qiagen, UK) according to the manufacturer's instructions.

treatment_protocol: The study included 5 experimenta groups: Unimmunised mice, mice primed with CFA/OVA (100ug/mouse), mice primed and treated with control IgG (10mg/kg), mice primed and treated with abatacept (10mg/kg), and orally tolerised mice that were generated by feeding with OVA in the drinking water (50mg/ml). For CD4+ T cells draining LNs were used (unimmunised: pooled LNs and spleeen, primed: axillary, orally tolerised: mesenteric LNs) CD4+ T cells were isolated using MACS negative selection with over 90% purity. CD11c+ cells were isolated from pooled LNs and spleen using CD11c microbeads and MACS with over 90% purity.

value: mesenteric lymph nodes

tag: genotype

value: DO11.10 RAG2-/- BALB/c

tag: age

value: 8-10 weeks

value: CD4+ T


title: CD11c_naïve_rep1

description: Gene expression data from CD11c+ cells from unimmunised mice

source_name: MACS sorted CD11c+ cells from unimmunised mice

tag: tissue

value: pooled spleen and lymph nodes

tag: cell type


title: CD4_TOL_rep1


title: E. coli wt_batch_repl1

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1


title: CD11c_TOL_rep2

description: Gene expression data from CD11c+ cells from orally tolerised mice

source_name: MACS sorted CD11c+ cells from orally tolerised mice


title: KO_MEF_un.2

city: Boston

first: Jillian

middle: Leigh

last: Astarita

state: MA

address: 450 Brookline Ave

department: Cancer Immunology and AIDS

institute: Dana Farber Cancer Institute

description: PDPN KO MEF, biological replicate 2

hyb_protocol: Fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45C. The chips are then washed to remove unhybridized cDNA. Bound cDNA is fluorescently labeled using phycoerythrin-conjugated streptavidin, additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. From http://macf-web.dfci.harvard.edu/

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. From http://macf-web.dfci.harvard.edu/

data_processing: Data were processed using GenePattern (Broad Institute). Data were RMA normalized.

source_name: KO MEF

label_protocol: Single stranded cDNA is synthesised and purified, then fragmented using uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I. Fragmented cDNA is end-labeled with a biotinylated nucleotide analogue

growth_protocol: WT and PDPN-deficient embryos were collected from pregnant females between E9.5 and 13.5. MEFs were grown in aMEM with 10% batch-selected fetal calf serum for 7-10 days. MEFs were then purified from any contaminanting endothelial and hematopoietic cells by negative MACS selection with biotinylated anti-CD31 and anti-CD45 antibodies.

extract_protocol: A Qiagen Rneasy kit was used to isolate total RNA, according to the manufacturer's instructions.

treatment_protocol: not applicable

tag: Sex

value: female

value: Pdpn-/-

value: mouse embryonic fibroblasts


title: A612_18_R11_DMSO_GF_2

value: brain tumor initiating cells (BTIC)


title: A612_19_R11_1uM_Sunitinib

value: Sunitinib

value: no


title: KO_MEF_un.1

description: PDPN KO MEF, biological replicate 1


title: CD4_ABA_rep3

description: Gene expression data from CD4+ T cells from primed mice treated with abatacept

source_name: MACS sorted CD4+ T cells from primed mice treated in the presence of abatacept

value: axillary lymph nodes


title: A612_21_RAV21_DMSO


title: CD11c_TOL_rep3

description: Gene expression data CD11c+ cells from orally tolerised mice


title: WT_MEF_un.2

description: WT MEF, biological replicate 2

source_name: WT MEF

value: WT


title: A612b_10_RAV24_DMSO_GF_2

value: DMSO


title: smc_wt_rep3

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The samples were scanned using the Illumina iScan array scanner

data_processing: Data were retrieved using Illumina's Genomestudio v. 2011.1 software. Analyses were carried out with Bioconductor packages in the statistical software package R (version 2.14.0). Normexp-by-control background correction, quantile normalization, and log2 transformation (Shi et al, NAR, 2010) were performed on the Illumina sample and control probe profiles using the limma package (version 3.10.2), function neqc.

source_name: aortic smooth muscle cells_wt

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate biotin-labeled (biotin-16-UTP) amplified cRNA

growth_protocol: Aortic SMCs were isolated from WT and FHL2-knockout mice as described previously (Kurakula et al, 2014, PLOS One).

extract_protocol: RNA was isolated using the Aurum total RNA isolation kit (Bio-Rad)

treatment_protocol: Aortic SMCs were grown to confluency and made quiescent in serum-free medium for 48hrs.

value: Wild-type

value: aorta

value: smooth muscle


title: smc_wt_rep2


title: CD4_ABA_rep2

source_name: MACS sorted CD4+ T cells from primed mice treated with abatacept


title: A612_16_R28_1uM_Sunitinib_GF

value: yes

value: moderate inhibition

value: no effect


title: A612b_07_RAV33_1uM_Sunitinib


title: CD4_CFA_OVA_rep3

description: Gene expression data from CD4+ T cells from primed mice

source_name: MACS sorted CD4+ T cells from primed mice

value: DO11.10 RAG2-/- BALB/c

value: 8-10 weeks

value: CD4+ T


title: A612_13_R28_DMSO


title: A612_12_R65_1uM_Sunitinib_GF

value: strong inhibition


title: CD11c_CFA_OVA_rep3

description: Gene expression data from CD11c cells from primed mice

source_name: MACS sorted CD11c+ cells from primed mice

value: pooled spleen and lymph nodes


title: A612_14_R28 _DMSO_GF_2

value: brain tumor initiating cells (BTIC)


title: WT_MEF_un.1

description: WT MEF, biological replicate 1

value: female

value: mouse embryonic fibroblasts


title: A612_15_R28_1uM_Sunitinib

value: Sunitinib

value: no


title: CD4_ABA_rep1

value: axillary lymph nodes


title: A612_17_R11_DMSO

value: DMSO


title: CD4_CFA_OVA_rep2


title: A612_11_R65_1uM_Sunitinib


title: smc_wt_rep1

value: Wild-type

value: aorta


title: smc_fhl2ko_rep3

source_name: aortic smooth muscle cells_fhl2ko

value: smooth muscle


title: smc_fhl2ko_rep1


title: Whole cortex, input RNA, biological rep2

city: New York

first: Miho

last: Nakajima

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

description:
TRAP RNA
Cortex_input2

hyb_protocol: Standard Affymetric protocol for mouse 430 2.0 platform.

data_processing: GCRMA normlalization within biological replicate groups was performed with R/Bioconductor

source_name: TRAP RNA

label_protocol: Affymetrix two cycle amplification kit, starting with 20 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol-LS extraction, DNAse treatement, and RNeasy Minelute Cleanup.

tag: genetic background

value: C57BL/6 / FVB

tag: expression

value: Cort

value: whole cortex

tag: line

value: Cort GM130

tag: area

value: Cortex


title: A612_10_R65_DMSO_GF_2

tag: treatment

tag: gf

value: yes


title: CD4_IgG_rep3

description: Gene expression data from CD4+ cells from primed mice treated with control IgG

source_name: MACS sorted CD4+ T cells from primed mice treated with control IgG

value: DO11.10 RAG2-/- BALB/c

value: 8-10 weeks


title: A612_09_R65_DMSO

value: brain tumor initiating cells (BTIC)

tag: btic culture


title: A612_08_R49_1uM_Sunitinib_GF_2

tag: treatment response of glioma in vitro_proliferation.score

value: moderate inhibition


title: Whole cortex, input RNA, biological rep3

description:
TRAP RNA
Cortex_input3

scan_protocol: Standard Affymetric protocol for mouse 430 2.0 platform.

value: Htr3a GM433


title: CD11c_CFA_OVA_rep2

description: Gene expression data from CD11c+ cells from primed mice

value: pooled spleen and lymph nodes


title: E. coli wt_chemostat_repl2

source_name: E. coli wt grown in minimal media glucose limited chemostat at dilution rate of 0.2 h-1, biological rep2

tag: strain

value: E. coli BW25113 wt


title: CD4_CFA_OVA_rep1

description: Gene expression data from CD4+T cells  from primed mice

value: axillary lymph nodes


title: Oxtr cells, cortex, TRAP RNA, biological rep3

description:
TRAP RNA
Oxtr_ctx_ip3

value: Oxtr

value: cortical interneuron


title: CD11c_naïve_rep3


title: CD11c_CFA_OVA_rep1


title: CD4_IgG_rep2

description: Gene expression data from CD4+ T cells from primed mice treated with control IgG

value: CD4+ T


title: CD4_IgG_rep1


title: Whole cortex, input RNA, biological rep1

description:
TRAP RNA
Cortex_input1

value: C57BL/6 / FVB

value: Dlx1 GM520


title: Oxtr cells, cortex, TRAP RNA, biological rep1

description:
TRAP RNA
Oxtr_ctx_ip1


title: Oxtr cells, cortex, TRAP RNA, biological rep2

description:
TRAP RNA
Oxtr_ctx_ip2


title: CD4_naïve_rep3

description: Gene expression data from CD4+ T cells from unimmunised mice

source_name: MACS sorted CD4+ T cells from unimmunised mice


title: A612_07_R49_1uM_Sunitinib

source_name: brain tumor initiating cells (BTIC)

value: Sunitinib

value: no


title: Htr3a cells, cortex, TRAP RNA, biological rep2

description:
TRAP RNA
Htr3a_ctx_ip2

value: Cortex


title: Htr3a cells, cortex, TRAP RNA, biological rep3

description:
TRAP RNA
Htr3a_ctx_ip3


title: Nek7 cells, cortex, TRAP RNA, biological rep3

description:
TRAP RNA
Nek7_ctx_ip3

value: Nek7 MN733


title: A612_03_R40_1uM_Sunitinib


title: Htr3a cells, cortex, TRAP RNA, biological rep1

description:
TRAP RNA
Htr3a_ctx_ip1


title: A612_04_R40_1uM_Sunitinib_GF

value: yes

tag: treatment response of glioma in vitro_proliferation.label

value: strong inhibition


title: A612_06_R49_DMSO_GF

value: brain tumor initiating cells (BTIC)

value: DMSO


title: CD11c_naïve_rep2

value: DO11.10 RAG2-/- BALB/c

value: 8-10 weeks


title: A612_05_R49_DMSO


title: Nek7 cells, cortex, TRAP RNA, biological rep2

description:
TRAP RNA
Nek7_ctx_ip2


title: CD4_naïve_rep2

value: pooled spleen and lymph nodes


title: HSRA-C kidney at week4, biological rep4

city: Jackson

first: Michael

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat Gene 1.1 ST Array.  Arrays were automatically washed and stained in the Affymetrix GeneAtlast Fluidics Station.

scan_protocol: Rat Gene 1.1 ST Array were scanned using the GeneAtlast Imaging Station

data_processing:
Analysis of microarray data was performed  using CEL files, followed by RMA normalization, using software provided by Affymetrix and Array Star 5 (DNASTAR, Inc, WI);
program-name = ArrayStar
program-version = 11.2.2.3
affymetrix-algorithm-name = RMA
affymetrix-algorithm-version = 1.0
HSRA-C (two-kidney) samples were set as the control.

organism: Rattus norvegicus

source_name: HSRA-C kidney at week4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat Gene 1.1 ST Array

growth_protocol: HSRA-S (congenital solitary kidney) and HSRA-C (two-kidney) were grown to 4 weeks of age, at which point animals were euthanized and whole kidney was removed for RNA isolation.

extract_protocol: RNA was isolated using TRIzol® and Invitrogen PureLink Kit (Life Technologies) and evaluated for quality and integrity (Bio-Rad Experion™ System)

treatment_protocol: Whole genome transcript analysis was performed using Affymetrix GeneAtlast platform on  kidney tissue collected from HSRA-S (congenital solitary kidney) and HSRA-C (two-kidney) using n=4 per group

tag: genotype/variation

value: HSRA; heterogeneous stock derived model of unilateral renal agenesis

value: 4 weeks

value: kidney

tag: tissue subtype

value: two-kidney; control


title: Nek7 cells, cortex, TRAP RNA, biological rep1

description:
TRAP RNA
Nek7_ctx_ip1

value: C57BL/6 / FVB

value: cortical interneuron


title: CD4_TOL_rep3

description: Gene expression data from CD4+ cells from orally tolerised mice

source_name: MACS sorted CD4+ T cells from orally tolerised mice

value: mesenteric lymph nodes

tag: genotype


title: A612_01_R40_DMSO

value: no


title: A612_02_R40_DMSO_GF


title: HSRA-C kidney at week4, biological rep3

tag: age


title: Cort cells, cortex, TRAP RNA, biological rep3

description:
TRAP RNA
Cort_ctx_ip3

value: Cort

value: Cort GM130

value: Cortex


title: HSRA-C kidney at week4, biological rep1

tag: tissue


title: CD4_naïve_rep1

description: Gene expression data from CD4+ cells from unimmunised mice

tag: cell type


title: HSRA-S kidney at week4, biological rep4

source_name: HSRA-S kidney at week4

value: congenital solitary kidney


title: HSRA-C kidney at week4, biological rep2


title: Cort cells, cortex, TRAP RNA, biological rep2

description:
TRAP RNA
Cort_ctx_ip2


title: Dlx1 cells, cortex, TRAP RNA, biological rep3

description:
TRAP RNA
Dlx1_ctx_ip3

value: Dlx1 GM520


title: Dlx1 cells, cortex, TRAP RNA, biological rep2

description:
TRAP RNA
Dlx1_ctx_ip2


title: CD11c_ABA_rep3

description: Gene expression data from CD11c+ cells from primed mice treated with abatacept

source_name: MACS sorted CD11c+ cells from primed mice treated with abatacept


title: Cort cells, cortex, TRAP RNA, biological rep1

description:
TRAP RNA
Cort_ctx_ip1


title: CD11c_ABA_rep1


title: CD11c_IgG_rep2

description: Gene expression data from CD11c+ cells from primed mice treated with control IgG

source_name: MACS sorted CD11c+ cells from primed mice treated with control IgG


title: CD11c_IgG_rep3


title: CD11c_ABA_rep2


title: CD11c_IgG_rep1


title: Dlx1 cells, cortex, TRAP RNA, biological rep1

description:
TRAP RNA
Dlx1_ctx_ip1


title: HSRA-S kidney at week4, biological rep2


title: CD11c_TOL_rep1

source_name: MACS sorted CD11c+ cells from orally tolerised mice


title: HSRA-S kidney at week4, biological rep1


title: HSRA-S kidney at week4, biological rep3


title: PMEIox B

status: Public on Oct 06 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: PMEIox transformant in Col-0 background

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of  aragene10st-type from Affymetrix. A Custom CDF Version 16 (Brainarray-CDF) with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Arabidopsis thaliana

source_name: PMEIox transformant in Col-0 background

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

growth_protocol: Arabidopsis thaliana seedlings were plated on half-strength MS medium without sugars, kept in the coldroom for 48 hours, and were then exposed to white light (100 µmol m-2 s-1) for 6 hours. Plates were wrapped in three layers of aluminium foil and incubated for 4 days at 22 degrees. MAterial was harvested under a green safe light and flash frozen in liquid nitrogen.

extract_protocol: RNA was extracted using GeneMATRIX Universal RNA purification kit (EURX)

value: Col-0 background

value: seedling

value: PMEIox transformant in Col-0 background


title: PMEIox A

description: PMEIox transformant in Col-0 background


title: Col-0 B

description: wild-type

source_name: wild-type

value: wild-type


title: Col-0 C

description: wild-type


title: cnu2 B

description: cnu2 suppressor mutant of PMEIox

source_name: cnu2 suppressor mutant of PMEIox

value: cnu2 suppressor mutant of PMEIox


title: PMEIox C

description: PMEIox transformant in Col-0 background


title: smc_fhl2ko_rep2

value: aorta

value: smooth muscle


title: Col-0 A

description: wild-type


title: cnu1 A

description: cnu1 suppressor mutant of PMEIox

source_name: cnu1 suppressor mutant of PMEIox

value: cnu1 suppressor mutant of PMEIox


title: cnu2 C

description: cnu2 suppressor mutant of PMEIox


title: cnu2 A

description: cnu2 suppressor mutant of PMEIox


title: melanoma_AJCCstageIII_TumourID360

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

hyb_protocol: Labelled material was hybridised to the arrays at 55C for 20hrs, rotating at 20rpm. Slides were washed with agilent wash buffers.

scan_protocol: Agilent High Resolution Scanner, G2505B was used. Agilent Feature Extractiob version 10.7.3.1. software was used for data extraction and protocol used by Fe software: miRNA 107 Sep09

data_processing: Data has been quantile normalised with no background subtraction.

source_name: melanoma lymph node, fresh frozen tissue (>80% tumor cell content, <30% necrosis)

label_protocol: 100ng of total RNA was used. miRNAs were fluorescently labelled by lagation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule

growth_protocol: All the tumour tissues were stored in liquid nitrogen untill extraction.

extract_protocol: Total RNA was extracted from fresh frozen tissues using the Roche High Pure miRNA Isolation kit (Cat No 05080576001, Roche Diagnostic, Indiana, IN, USA) in accordance with the manufacturer’s protocol. The quality and quantity of small RNAs present in the total RNA extract was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: lymph node

tag: diagnosis

value: melanoma

tag: patient age at primary dignosis (years)

tag: patient sex

value: Female

tag: patient age at stage iii sample banked (years)

tag: survival from stage iii tumour banked (months)

tag: survival from primary melanoma (months)

tag: number of primary melanomas

tag: stage at primary diagnosis 5th edition

value: Stage II

tag: patient last status

value: Dead Melanoma


title: melanoma_AJCCstageIII_TumourID351

value: Male

value: Stage I


title: melanoma_AJCCstageIII_TumourID343


title: cnu1 C

description: cnu1 suppressor mutant of PMEIox

tag: strain


title: E. coli wt_batch_repl2

source_name: E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2

value: E. coli BW25113 wt


title: melanoma_AJCCstageIII_TumourID356

value: Dead Not Melanoma


title: melanoma_AJCCstageIII_TumourID385

value: Alive NSR


title: melanoma_AJCCstageIII_TumourID333


title: melanoma_AJCCstageIII_TumourID278

value: Stage III


title: melanoma_AJCCstageIII_TumourID387


title: melanoma_AJCCstageIII_TumourID349

value: Stage Unknown


title: melanoma_AJCCstageIII_TumourID334


title: melanoma_AJCCstageIII_TumourID366

value: Alive with Melanoma


title: melanoma_AJCCstageIII_TumourID259


title: melanoma_AJCCstageIII_TumourID322


title: cnu1 B

description: cnu1 suppressor mutant of PMEIox

value: Col-0 background

value: seedling


title: melanoma_AJCCstageIII_TumourID237


title: melanoma_AJCCstageIII_TumourID277


title: melanoma_AJCCstageIII_TumourID350


title: melanoma_AJCCstageIII_TumourID340


title: melanoma_AJCCstageIII_TumourID249


title: melanoma_AJCCstageIII_TumourID242


title: melanoma_AJCCstageIII_TumourID234


title: melanoma_AJCCstageIII_TumourID394


title: melanoma_AJCCstageIII_TumourID273


title: melanoma_AJCCstageIII_TumourID205


title: melanoma_AJCCstageIII_TumourID232


title: melanoma_AJCCstageIII_TumourID179


title: melanoma_AJCCstageIII_TumourID288


title: melanoma_AJCCstageIII_TumourID233


title: melanoma_AJCCstageIII_TumourID194


title: melanoma_AJCCstageIII_TumourID217


title: melanoma_AJCCstageIII_TumourID142


title: melanoma_AJCCstageIII_TumourID196


title: melanoma_AJCCstageIII_TumourID201


title: melanoma_AJCCstageIII_TumourID139


title: melanoma_AJCCstageIII_TumourID102


title: melanoma_AJCCstageIII_TumourID172


title: melanoma_AJCCstageIII_TumourID152


title: melanoma_AJCCstageIII_TumourID219


title: melanoma_AJCCstageIII_TumourID125


title: melanoma_AJCCstageIII_TumourID149


title: melanoma_AJCCstageIII_TumourID126


title: melanoma_AJCCstageIII_TumourID119


title: melanoma_AJCCstageIII_TumourID173


title: melanoma_AJCCstageIII_TumourID100


title: melanoma_AJCCstageIII_TumourID94

value: Dead Cause Unknown


title: melanoma_AJCCstageIII_TumourID74


title: melanoma_AJCCstageIII_TumourID83


title: melanoma_AJCCstageIII_TumourID103


title: melanoma_AJCCstageIII_TumourID120


title: melanoma_AJCCstageIII_TumourID93


title: melanoma_AJCCstageIII_TumourID88


title: melanoma_AJCCstageIII_TumourID61


title: melanoma_AJCCstageIII_TumourID62


title: melanoma_AJCCstageIII_TumourID52


title: melanoma_AJCCstageIII_TumourID23


title: melanoma_AJCCstageIII_TumourID37


title: melanoma_AJCCstageIII_TumourID53


title: melanoma_AJCCstageIII_TumourID47


title: melanoma_AJCCstageIII_TumourID13


title: melanoma_AJCCstageIII_TumourID45


title: melanoma_AJCCstageIII_TumourID66


title: melanoma_AJCCstageIII_TumourID51


title: melanoma_AJCCstageIII_TumourID43

value: Alive Status Unknown


title: melanoma_AJCCstageIII_TumourID17

value: lymph node


title: melanoma_AJCCstageIII_TumourID32

value: melanoma


title: melanoma_AJCCstageIII_TumourID54


title: melanoma_AJCCstageIII_TumourID30


title: melanoma_AJCCstageIII_TumourID25


title: SMC_4h_M4

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: SAMPLE 12

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols from Affymetrix.

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

data_processing: The microarray data were preprocessed in Expression Consol software (Affymetrix) employing the probe logarithmic intensity error algorithm (PLIER, parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization)

source_name: pBSMCs_PDGF 24hr

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s instructions (Affymetrix)

growth_protocol: Human primary bladder smooth muscle cells (pBSMCs) were cultured in smooth muscle cell medium (SMCM, Sciencell Research Laboratories, Carlsbad, CA) at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from pBSMCs was extracted using the TRIzol reagent followed by RNeasy (QIAgen) method. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: pBSMCs were serum starved overnight and treated with 1 nM PDGF for 0, 4, and 24 h.

value: bladder

tag: treated with

value: 1 nM PDGF-BB for 24hrs


title: melanoma_AJCCstageIII_TumourID5

value: Stage II


title: SMC_4h_M1

description: SAMPLE 9

value: Human primary bladder smooth muscle cells (pBSMCs)