title: W593

status: Public on Feb 29 2016

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

data_processing: Data were exported into text format for further analysis. If qRT-PCR amplification curves presented a “Tholdfail” error flag (i.e. the automatic thresholding algorithm failed), data were discarded. Subsequently, raw Ct values were normalized. In the case of techincal replicates, data were averaged after normalization procedure described hereafter. To run the miR-Test, data were normalized using mean CTs (HK-mean) of six “housekeeping” miRNAs genes (miR-197, miR-19b, miR-24, miR-146, miR-15b, miR-19a; (1)) using the following procedure: a scaling factor (SF) was calculated for each sample by subtracting the “HK-mean” to a constant value (K = 21.646). Data were then normalized by these SFs to eliminate technical fluctuations, using the formula: SF + miRNA CTraw = CTnormalized. If CT raw was greater than 30.01 or ‘undetermined’ by qRT-PCR, data was set to 30.01 and normalization skipped. This normalization strategy assures an independency from the original set of samples used to train the miR-Test, and allow new samples classification without the need of an internal reference.   The Calibration set was used to: i) refine DLDA weight coefficients (wi) of the miRNA signature by using diagonal linear discriminant analysis (DLDA) as class metric (BRB-ArrayTools version 4.3.0 - Beta_2 Release); ii) reduce the number of miRNAs in the signature. The leave–one-out (LOO) cross-validation procedure was used to cross-validate the classifier and estimate sensitivity and specificity in the calibration set. Parametric t-test set at 0.05 significance level was used for feature selection. Statistical significance of the performance of the classifier was assessed by performing 1000 permutations of class labels. Samples were then classified as positive or negative if the absolute value of the inner sum of weighted expressions (CTnorm*wi) was greater than the absolute value of the threshold. Since both weights and threshold are negative, the risk score was calculated as:     RS= - (∑i wi xi - THRES), for i=1…13 (13-miRNA signature).    Where THRES = -261.779, wi is the weight coefficient of the ith miRNA (Supplemental Table 2), and xi is the expression value (CT) of the ith miRNA.    All bioinformatical analyses were automated using a custom R script developed in-house using the R statistical software version 2.14.1. The script allows to read the information content of the output documents from the Applied Biosystems ViiA 7™ and provides miR-Test risk scores automatically.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: Reverse transcription (RT) and pre-amplification reaction (Pre-AMP) protocols were optimized by using a MicroLab Star Liquid Handling. RT was performed from a fixed volume (3 uL) of total RNA with TaqMan MicroRNA Reverse Transcription Kit and a custom pool of Human miRNA-specific stem-loop primers (Applied Biosystem) according to the manufacturer's instruction, in a 2720 Thermo Cycler (Applied Biosystem). RT product was then diluted 1:2 with water; 5 uL of diluted RT product were pre-amplified (12 cycles of PCR) with TaqMan PreAmp Master Mix (2X) and Megaplex PreAmp Primers Human PoolA (Applied Biosystem), according to the manufacturer's instruction. The pre-amplification reaction was diluted 1:4 with Tris-EDTA buffer 0.1X. Next, 6 uL of diluted pre-amplification reaction were combined with 46.5 uL of water and with 52.5 uL of TaqMan Universal Master Mix II (Applied Biosystem). The final solution (105 uL) was loaded into one lane of a custom TaqMan¨ Low Density Array microRNA Custom Panel (Applied Biosystem). RTQ-PCR was carried out on an Applied Biosystems 7900HT thermocycler using the manufacturer's recommended cycling conditions. We used a Hamilton MICROLAB¨ STAR liquid handling workstation to automate most of the described processes.

extract_protocol: Blood collection: Blood samples (10 ml) were collected by standard phlebotomy before any analysis or instrumental procedure. The first 3 mL of blood were not used for serum preparation to prevent contamination by skin. Serum was prepared by collecting blood in tubes with clot activator (S-Monovette 7.5ml REF01.1601 – Sarstedt), left at room temperature for 3 hours to clot, then spun at 3000 rpm (1000 g, Megafuge 2.0 Heraeus) for 10 minutes at RT. The serum was removed immediately after centrifugation, leaving a 0.5 cm leftover to avoid disturbing the serum-clot interface. Serum was then aliquoted in barcoded cryotubes and snap frozen in dry ice. Aliquots were stored in a dedicated -80°C fridge.  Serum miRNA purification: Total RNA purification, including miRNAs, was based on lysis with Guanidinium thiocyanate-phenol-chloroform extraction (TriZol-LS, Applied Biosystem) and Spin Column-based total RNA purification (MiRneasy Mini Kit, Qiagen). Briefly, 0.3 mL of serum were mixed with Trizol-LS in volumetric ratios of 3:1 for lysis. After denaturation, a spike of synthetic miRNA (5x108 copies of miR-34a) was added to the solution to monitor the extraction efficiency. A volume of 0.24 mL of Chloroform was added to the solution, which was then centrifuged for 15 min at 11,800g at 4°C. A fixed amount (0.35 mL; around 70% of the final volume of the sample) of aqueous phase was recovered. This choice was preferred to limit contamination from the interphase. The subsequent steps were performed in automation through a Qiacube machine (QIAGEN), according to the “miRNEASY Mini” standard protocol. RNA was eluted in 30 uL and stored at -80°C until further analysis.

tag: group

value: SCREENING

tag: sample type

value: Control


title: W592


title: W595


title: W590


title: W591


title: W59


title: W589


title: mutant 1 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 3

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description:
induced and exponentially growing
Biological replicate 3 of 3. constitutively active N119A CXCR4 mutants transfected human hematopoetic leukemic k562 cells.

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID:  27114)

scan_protocol: Scanned with GenePix scanner having 5µm resolution in a single pass scanning mode having a scan area of 61 * 21.6mm.

data_processing: The data was normalized by percentile shift normalization method using GeneSpring GX11 (Agilent technologies, India). Following normalization, gProcessed signal (dye normalized background subtracted signal intensity) of the probes showing at least 30% change in expression across the 3 donors were computed and ratios (treated/untreated) were log2 transformed. Statistical analysis of the data was performed using Cyber-T regularized t statistic due to small sample size (n= 3) since it takes into account Bayesian estimate of variance by pooling across genes with similar intensities.

source_name: N119A CAM CXCR4 gene transfected human hematopoetic leukemic k562 cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-4444).

extract_protocol: Total RNA was extracted using the RNA isolation kit following manufacturer's instructions

tag: cell line

tag: transfection

value: constitutively active mutant N119A CXCR4 gene


title: mutant 2 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 1

description:
induced and exponentially growing
Biological replicate 1 of 3. constitutively active N119S CXCR4 mutants transfected human hematopoetic leukemic k562 cells.

source_name: N119S CAM CXCR4 gene transfected human hematopoetic leukemic k562 cells

value: constitutively active mutant N119S CXCR4 gene


title: control human hematopoietic leukemic k562 cells replicate 2

description: Biological replicate 2 of 3. Control human hematopoietic leukemic k562  cells, untreated.

source_name: human hematopoietic leukemic k562 cells

value: control


title: W587


title: wild type CXCR4 transfected human hematopoietic leukemic k562 cells replicate 2

description:
induced and exponentially growing
Biological replicate 2 of 3. wild type CXCR4 transfected human hematopoietic leukemic k562 cells.

source_name: wild type CXCR4 gene transfected human hematopoietic leukemic k562 cells

value: wild type CXCR4 gene


title: control human hematopoietic leukemic k562 cells replicate 1

description: Biological replicate 1 of 3. Control human hematopoietic leukemic k562  cells, untreated.


title: mutant 1 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 2

description:
induced and exponentially growing
Biological replicate 2 of 3. constitutively active N119A CXCR4 mutants transfected human hematopoetic leukemic k562 cells.


title: W594


title: wild type CXCR4 transfected human hematopoietic leukemic k562 cells replicate 3

description:
induced and exponentially growing
Biological replicate 3 of 3. wild type CXCR4 transfected human hematopoietic leukemic k562 cells.


title: W586


title: mutant 1 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 1

description:
induced and exponentially growing
Biological replicate 1 of 3. constitutively active N119A CXCR4 mutants transfected human hematopoetic leukemic k562 cells.


title: control human hematopoietic leukemic k562 cells replicate 3

description: Biological replicate 3 of 3. Control human hematopoietic leukemic k562  cells, untreated.


title: W588


title: W582


title: W583


title: mutant 2 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 2

description:
induced and exponentially growing
Biological replicate 2 of 3. constitutively active N119S CXCR4 mutants transfected human hematopoetic leukemic k562 cells.


title: mutant 2 CXCR4 transfected human hematopoetic leukemic k562 cells replicate 3

description:
induced and exponentially growing
Biological replicate 3 of 3. constitutively active N119S CXCR4 mutants transfected human hematopoetic leukemic k562 cells.


title: W585


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title: W561


title: W563


title: W548


title: W549


title: W55


title: W547


title: W56


title: W550


title: wild type CXCR4 transfected human hematopoietic leukemic k562 cells replicate 1

description:
induced and exponentially growing
Biological replicate 1 of 3. wild type CXCR4 transfected human hematopoietic leukemic k562 cells.


title: W560


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title: W1003


title: W1001


title: PT9

value: TUMOR-SCREENING

value: Case

tag: tumor type

value: Lung Adenocarcinoma


title: W1


title: W10


title: W100


title: PT6


title: PT8


title: W1000


title: PT50

value: Lung Squamous Carcinoma


title: PT5

value: Lung Small Cell Carcinoma


title: PT3


title: PT26


title: PT4


title: PT250


title: PT213


title: PT2


title: PT141


title: PT148


title: PT16


title: PT1


title: T68


title: T63


title: T67


title: T64


title: T65


title: PT7


title: T66


title: T62


title: T60


title: T59


title: T61


title: T58


title: T56


title: T55


title: T57


title: T53


title: T54


title: T51


title: T52


title: B07


title: N16

value: NORMAL-CALIBRATION


title: T50


title: N14


title: N15


title: N13


title: N08


title: N11


title: N12


title: N07


title: N09


title: N04


title: N02


title: T14

value: TUMOR-CALIBRATION


title: T16


title: N01


title: T13


title: T12


title: 3D9_12_IL31_Dox_8h

city: Aachen

first: Bernhard

last: Luscher

address: Pauwelsstrasse 30

department: Biochemistry

country: Germany

institute: RWTH Aachen University

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

data_processing: Raw data were processed with GeneSpring 12.0 for background correction and normalization.

label: biotin

source_name: immortalized primary keratinocytes, treated with IL-31 for 8h

label_protocol: Samples were enzymatically fragmented and biotinylated using the Whole Transcripts (WT) sense Target labeling Assay (Ambion)

growth_protocol: To construct the dermis of the skin equivalent, collagen gels were prepared by mixing 8 volumes of ice-cold bovine collagen I solution with 1 volume of 10x concentrated Hank’s balanced salt solution. After neutralization with 1 M NaOH, 1 volume of fibroblasts suspended in FCS was added. The final concentration of fibroblasts in this gel solution was 10000 cells/ml. Four milliliters of this gel solution was poured into each polycarbonate membrane insert (0.4 µm pore size). Following complete polymerization, gels were covered with DMEM containing 10% FCS, 100 U/ml penicillin, and 100 mg/ml streptomycin and incubated in a humidified atmosphere at 37°C and 5% CO2. After 2 days, approximately 2 x 106 HaCaT cells were seeded on each dermis equivalent. The skin equivalents were cultured in a medium consisting of 47.5% keratinocyte growth medium and 47.5% DMEM supplemented with 5% FCS, 100 U/ml penicillin, 100 mg/ml streptomycin, and 50 mg/ml ascorbic acid. After 2-3 days of submerged culture, the skin equivalents were lifted to the air-liquid interface and the calcium concentration in the medium was raised to 1.2 mM.

extract_protocol: The models were mechanically disrupted in RNA extraction lysis buffer (Nucleo Spin II).

treatment_protocol: 1-2 days after the models were lifted to the air-liquid interphase, the models were treated with or without IL-31 (100 ng/ml) that was added to the medium. The models were harvested after 2, 8, 24, and 48 hours.

tag: gender

value: male

tag: age

tag: cell type

value: immortalized primary keratinocytes (HaCaT)


title: 3D9_12_IL31_Dox_24h

source_name: immortalized primary keratinocytes, treated with IL-31 for 24h


title: T15


title: 3D9_12_Control_8h

source_name: Human dermal fibroblasts, untreated 8h

value: female

value: human dermal fibroblasts (HDFs)


title: 3D9_12_IL31_Dox_48h

source_name: immortalized primary keratinocytes, treated with IL-31 for 48h


title: 3D9_12_IL31_Dox_2h

source_name: immortalized primary keratinocytes, treated with IL-31 for 2h


title: T11


title: 3D9_12_Control_2h

source_name: Human dermal fibroblasts, untreated 2h


title: 3D9_12_Control_48h

source_name: Human dermal fibroblasts, untreated 48h


title: T09


title: 3D9_12_Control_24h

source_name: Human dermal fibroblasts, untreated 24h


title: T07


title: T08


title: Card9‒/‒ Control Exp. #3

city: Budapest

first: Attila

last: Mocsai

address: Tuzolto utca 37-47

department: Department of Physiology

country: Hungary

institute: Semmelweis University

description: Gene expression data of mouse neutrophils

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: CHP files were generated using Affymetrix Expression Control.

organism: Mus musculus

source_name: Neutrophil

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

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

treatment_protocol: Mouse neutrophils were stimulated on immune complex (IC) surfaces for 4 hours at 37 °C.

tag: strain

value: Card9‒/‒ (C57BL/6)

tag: cell surafce marker

tag: treatment

tag: time

value: Experiment #3


title: T02


title: T04


title: Card9‒/‒ IC Exp. #3

value: IC


title: T01


title: Wild type IC Exp. #3

value: Wild type (C57BL/6)


title: W999

value: SCREENING

value: Control


title: W996


title: W994


title: W997


title: W995


title: W998


title: Wild type Control Exp. #3


title: W993


title: W992


title: W991


title: Card9‒/‒ Control Exp. #2

value: Experiment #2


title: Card9‒/‒ IC Exp. #2


title: Wild type IC Exp. #2


title: W990


title: Wild type IC Exp. #1

value: Experiment #1


title: Card9‒/‒ IC Exp. #1


title: Wild type Control Exp. #2


title: Card9‒/‒ Control Exp. #1


title: Liver lard germ free mouse 4

city: Gothenbrug

first: Robert

last: Caesar

address: Gothenburg University

department: Wallenberg Laboratory

country: Sweden

institute: Gothenburg University

hyb_protocol: not provided

scan_protocol: The samples were scanned using the GeneChip® Scanner 3000 7G according to the manufacturer’s manual (PN 702731 Rev 3, Affymetrix).

data_processing: The raw data were normalized using the robust multi-array average method (Li and Wong, 2001). Differential expression of microarray data was evaluated by Student's t-test followed by correction for false discovery rate. Analysis of interaction, using colonization status and diet as independent variables, was evaluated by two-way analysis of interaction followed by correction for false discovery rate.

source_name: Liver, germ free mouse fed lard

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit (P/N 4425209 Rev C 09/2009) and Affymetrix GeneChip® WT Terminal

growth_protocol: Mice were fed high fat diet for 11 weeks

extract_protocol: RNA was isolated usinr Rneasy Tissue Mini kit (Qiagen)

treatment_protocol: Mice were fasted for 4 hours before sac

value: 11 weeks

tag: tissue

value: Liver

tag: bacterial status

value: germ-free

tag: diet

value: lard


title: Wild type Control Exp. #1


title: Liver lard germ free mouse 3


title: Liver lard germ free mouse 6


title: Liver lard germ free mouse 2


title: W99


title: Liver lard germ free mouse 5


title: W988


title: Liver lard germ free mouse 1


title: Liver lard conventional mouse 6

source_name: Liver, conventional mouse fed lard

value: conventional


title: W986


title: W985


title: W987


title: Liver lard conventional mouse 5


title: W981


title: W982


title: W983


title: Liver lard conventional mouse 4


title: Liver lard conventional mouse 3


title: W989


title: Liver fish oil germ free mouse 6

source_name: Liver, germ free mouse fed fish oil

value: fish oil


title: W978

source_name: Serum


title: W984


title: Liver fish oil germ free mouse 4


title: Liver fish oil germ free mouse 2


title: Liver lard conventional mouse 1


title: Liver fish oil conventional mouse 5

source_name: Liver, conventional mouse fed fish oil


title: Liver lard conventional mouse 2


title: Liver fish oil conventional mouse 4


title: W980


title: Liver fish oil conventional mouse 3


title: Liver fish oil germ free mouse 3


title: Liver fish oil germ free mouse 5


title: W972


title: W979


title: W976


title: Liver fish oil conventional mouse 1


title: W97


title: Liver fish oil conventional mouse 6


title: W975


title: W969


title: Xenopus laevis expression data from larval inner ear tissue s56_2

city: Cleveland

first: Selene

last: Virk

state: OH

address: 2103 Cornell Road

country: USA

institute: Case Western Reserve University

description: Gene expression data from larval animals ranging from stage 56 to stage 58 based on Nieuwkoop and Faber (1994) Normal Table of Xenopus laevis (Daudin). Garland Publishing Inc, New York ISBN 0-8153-1896-0.

hyb_protocol: Fragmented cDNA was hybridized according to manufacture's protocol (Affymetrix)

scan_protocol: GeneChip Xenopus laevis 2.0 were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data processed using JMP Genomics software

organism: Xenopus laevis

source_name: Xenopus laevis larvae

label_protocol: Labeled antisense single-stranded cDNA was prepared from each RNA replicate (1 ug total RNA) using the Ovation RNA Amplification System V2 in conjunction with the FL-Ovation cDNA Biotin Module V2 (both from NuGEN)

growth_protocol: Larval Xenopus laevis (n=7) were aged 38-44 days post-fertilization with an average weight of 0.59 ± 0.10 g and an average length of 5.07 ± 0.29 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) as per Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E: RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20.

value: inner ear

tag: developmental stage

value: larval stages 56-58

value: larval animals 38-44 days post-fertilization


title: W973


title: Xenopus laevis expression data from larval inner ear tissue s56_1

growth_protocol: Larval Xenopus laevis (n=10) were aged 38-44 days post-fertilization with an average weight of 0.55 ± 0.11 g and an average length of 5.03 ± 0.30 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: Liver fish oil conventional mouse 2


title: W967


title: W966


title: W962


title: W964


title: W963


title: W971


title: W961


title: W96


title: W959


title: W970


title: W960


title: W958


title: W965


title: W957


title: W968


title: W955


title: W954


title: W953


title: Xenopus laevis expression data from larval inner ear tissue s56_3

growth_protocol: Larval Xenopus laevis (n=8) were aged 38-44 days post-fertilization with an average weight of 0.48 ± 0.05 g and an average length of 4.93 ± 0.29 cm and obtained from Nasco (Fort Atkinson, WI). Animal procedures and protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.


title: MCF-10A shCHK2_cyclin E overexpression set 2 replicate 1

city: Houston

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

description:
shCHK2-2_cycE-1
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized and log2 transformed by BRB ArrayTools (Biometric Research Branch, NCI)

label: Biotin

source_name: MCF-10A breast cell line

label_protocol: Biotinylated cRNA were prepared with illumina TotalPrep RNA Amplification Kit

growth_protocol: All cell were cultured in MCF-10A medium

extract_protocol: total RNA was extracted with ambion mirVara miRNA isolation kit.

treatment_protocol: cyclin E overexpression with shRNA stable knockdown

tag: protocol

value: cyclin E overexpression_shCHK2


title: MCF-10A shCHK2_cyclin E overexpression set 1 replicate 3

description:
shCHK2_cycE-3
replicate 3


title: MCF-10A shCHK2_cyclin E overexpression set 1 replicate 2

description:
shCHK2_cycE-2
replicate 2


title: MCF-10A shCHK1_cyclin E overexpression set 2 replicate 3

description:
shCHK1-2_cycE-3
replicate 3

value: cyclin E overexpression_shCHK1


title: W952

tag: group


title: MCF-10A shCHK2_cyclin E overexpression set 2 replicate 2

description:
shCHK2-2_cycE-2
replicate 2


title: MCF-10A shCHK2_cyclin E overexpression set 2 replicate 3

description:
shCHK2-2_cycE-3
replicate 3


title: MCF-10A shCHK1_cyclin E overexpression set 2 replicate 2

description:
shCHK1-2_cycE-2
replicate 2


title: MCF-10A shCHK1_cyclin E overexpression set 1 replicate 3

description:
shCHK1_cycE-3
replicate 3


title: MCF-10A shCHK2_cyclin E overexpression set 1 replicate 1

description:
shCHK2_cycE-1
replicate 1


title: MCF-10A shCHK1_cyclin E overexpression set 1 replicate 1

description:
shCHK1_cycE-1
replicate 1


title: MCF-10A shCHK1_cyclin E overexpression set 2 replicate 1

description:
shCHK1-2_cycE-1
replicate 1


title: MCF-10A shATR_cyclin E overexpression set 2 replicate 3

description:
shATR-2_cycE-3
replicate 3

value: cyclin E overexpression_shATR


title: W956

tag: sample type


title: W951


title: W950


title: W95


title: W948


title: W947


title: W946


title: MCF-10A shATR_cyclin E overexpression set 2 replicate 1

description:
shATR-2_cycE-1
replicate 1

tag: cell line


title: MCF-10A shCHK1_cyclin E overexpression set 1 replicate 2

description:
shCHK1_cycE-2
replicate 2


title: MCF-10A shATR_cyclin E overexpression set 1 replicate 1

description:
shATR_cycE-1
replicate 1


title: MCF-10A shATR_cyclin E overexpression set 2 replicate 2

description:
shATR-2_cycE-2
replicate 2


title: W949


title: W941


title: W940


title: W94


title: W939


title: W943


title: W942


title: MCF-10A shATR_cyclin E overexpression set 1 replicate 2

description:
shATR_cycE-2
replicate 2


title: MCF-10A shATM_cyclin E overexpression set 2 replicate 1

description:
shATM-2_cycE-1
replicate 1

value: cyclin E overexpression_shATM


title: MCF-10A shATM_cyclin E overexpression set 2 replicate 3

description:
shATM-2_cycE-3
replicate 3


title: MCF-10A shATM_cyclin E overexpression set 2 replicate 2

description:
shATM-2_cycE-2
replicate 2


title: W932

value: SCREENING


title: W936

value: Control


title: W937


title: W935


title: W938


title: W974


title: MCF-10A shATM_cyclin E overexpression set 1 replicate 1

description:
shATM_cycE-1
replicate 1


title: MCF-10A shATM_cyclin E overexpression set 1 replicate 3

description:
shATM_cycE-3
replicate 3


title: W934


title: W931


title: W930


title: E30N

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description:
frozen tissue extracted by Trizol  or Allprep kit (Qiagen) per the manufacturer’s instructions
Total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified. RNA from paired tumor and normal esophageal tissues were run together in parallel in the same experiment.  The protocol followed the manufacturer’s manual at http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042167.pdf.  Briefly, three uL of total RNA (350-1000ng) was added to 4.50uL of RT reaction mix, which consisted of 10x Megaplex RT Primers, 100mM dNTPs with dTTP, 50U/uL MultiScribe Reverse Transcriptase, 10x RT buffer, 25mM MgCl2, 20U/uL RNase Inhibitor, and nuclease-free H2O.  The samples were run on a thermal cycler using the following conditions:  40 cycles of 16oC for two min, 42oC for one min, and 50oC for one sec.  All reactions were completed with a final incubation of 85oC for five min.   Six uL of cDNA generated from the thermal cycler was mixed with 450uL of 2x TaqMan Universal PCR Master Mix with no AmpErase UNG, and 444uL of nuclease-free H2O.  100uL of the reaction mix was added to each of eight fill ports on the TaqMan MicroRNA Array.  The filled Array was centrifuged twice at 1200 rpm for one min, and then sealed with the eight fill ports removed.  The array was run on the 7900HT RT-PCR System with SDS software.  The comparative CT method was used to determine the expression levels of mature miRNAs.

data_processing: RQ Manager integrated in software from ABI was used to normalize the entire signal generated. Expression level (as fold change) was calculated when both tumor and normal samples had signals in the assays using DataAssist software v2.0 (Life Technologies, http://www.lifetechnologies.com/about-life-technologies.html).  Signals for miRNA that showed either in tumor only or normal only were dropped from analysis.  Fold change was calculated using the 2 -ΔΔCT method.  In the present study, the data are presented as fold change in the target gene expression in tumors normalized to the internal control gene (MammU6) and relative to the normal tissue control (matched normal as calibrator).  Results of the real-time PCR data are represented as CT values, with CT defined as the threshold cycle number of PCRs at which amplified product was first detected.  The average CT was calculated for both the target gene and MammU6 and the ΔCT was determined as (the mean of up to three CT values for the target gene) minus (the mean of the CT values for U6).  The ΔΔCT represented the difference between the paired tissue samples, as calculated by the formula ΔΔCT = (ΔCT of tumor - ΔCT of normal).  The N-fold differential expression in the target gene of a tumor sample compared to its normal sample counterpart was expressed as 2 -ΔΔCT.  For each case, the frequency of dysregulated miRNAs was calculated as the number of dysregulated miRNAs divided by the total number of miRNAs that showed signals in both tumor and normal.  The criteria used to call an miRNA dysregulated were fold changes ≥ 2 or ≤ 0.5.

source_name: adjacent normal tissue

label_protocol: As per manufacturer (ABI).

extract_protocol: Total RNA was extracted and purified by standard Trizol method and using the Allprep Kit (Qiagen). All RNA  quality and quantity were determined using RNA6000 labchip/Agilent 2100 bioanalyzer.

value: adjcent epithelium


title: W93


title: W929


title: MCF-10A shControl_cyclin E overexpression set 2 replicate 3

description:
shCtrl-2_cycE-3
replicate 3

value: cyclin E overexpression_shControl


title: W928


title: W944


title: W933


title: MCF-10A shATR_cyclin E overexpression set 1 replicate 3

description:
shATR_cycE-3
replicate 3


title: E29N


title: E29T

source_name: tumor tissue

value: esophageal squamous cell carcinoma


title: W927


title: E28T


title: MCF-10A shControl_cyclin E overexpression set 1 replicate 1

description:
shCtrl_cycE-1
replicate 1


title: E30T


title: Liver fish oil germ free mouse 1

value: 11 weeks

value: Liver


title: W925


title: W977


title: E27T


title: E27N


title: W923


title: W924


title: E28N


title: W926


title: W922


title: E26N


title: E26T


title: MCF-10A shATM_cyclin E overexpression set 1 replicate 2

description:
shATM_cycE-2
replicate 2


title: MCF-10A shControl_cyclin E overexpression set 1 replicate 2

description:
shCtrl_cycE-2
replicate 2


title: W921


title: MCF-10A shControl_cyclin E overexpression set 2 replicate 1

description:
shCtrl-2_cycE-1
replicate 1


title: MCF-10A shControl_cyclin E overexpression set 2 replicate 2

description:
shCtrl-2_cycE-2
replicate 2


title: MCF-10A shControl_cyclin E overexpression set 1 replicate 3

description:
shCtrl_cycE-3
replicate 3


title: E25N


title: W920


title: E24N


title: W92


title: E24T


title: E23N


title: W914


title: W918


title: W917


title: E23T


title: W916


title: W915


title: W919


title: E19T


title: E20T


title: E25T


title: E22T


title: E22N


title: E21N


title: W911


title: W912


title: W913


title: E18N


title: E19N


title: E20N


title: E21T


title: W908


title: W909


title: W910


title: E18T


title: W906


title: E17T


title: E16N


title: E17N


title: W903


title: W904


title: W901


title: E16T


title: E15N


title: E15T


title: E14N


title: W902


title: W898


title: E13N


title: E14T


title: W90


title: W9


title: E13T


title: E12N


title: E12T


title: W905


title: W900


title: W907


title: W896


title: W894


title: W895


title: E11N


title: E11T


title: JVE192_snp

type: genomic

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

country: Singapore

institute: Duke-NUS Medical School

description: Genomic DNA isolated from novel CRC cell lines was genotyped using the Illumina HumanExome-12 v1.0 BeadChip

hyb_protocol: Standard illumina protocol

scan_protocol: Standard illumina protocol

data_processing: Data were processed in GenomeStudio. The file HumanExome-12_v1.0_signal.txt contains the raw signals and is available on the series record.

molecule: genomic DNA

source_name: CRC

label_protocol: 200 ng of DNA was labelled according to the standard illumina protocol

extract_protocol: DNA was isolated using the Wizard genomic DNA isolation kit

value: colorectal cancer

value: F

tag: tumor location

value: Ascending colon

value: Mucinous adenocarcinoma

tag: tumor stage (dukes)


title: JVE017_snp

tag: gender

value: Cecum

tag: tumor type


title: W893


title: KP363T_snp

value: M

value: Left-sided colon

value: Adenocarcinoma


title: W897


title: W892


title: JVE114_snp

source_name: CRC-liver-metastasis

value: colorectal cancer-liver-metastasis

value: Liver metastasis

value: D


title: E10N


title: E10T


title: W890

value: SCREENING

value: Control


title: W89


title: W891


title: JVE044_snp

value: Rectum


title: E9N

value: adjcent epithelium


title: E8N


title: E7T

value: esophageal squamous cell carcinoma


title: W885


title: W886


title: W888


title: E6N


title: E8T


title: W883


title: W884


title: W882


title: E5N


title: E5T


title: E6T


title: E7N


title: E9T


title: W881


title: E4N


title: W880


title: E4T


title: W88


title: W879


title: E3T


title: W877


title: E2N


title: E2T


title: W876


title: W871


title: W875


title: W873


title: E3N


title: W870


title: E1N


title: W887


title: W868


title: W869


title: E1T


title: W874


title: W87


title: W878


title: W867


title: W865


title: W864


title: W872


title: W863


title: W862


title: W854


title: W855


title: W856


title: W853


title: W861


title: W86


title: W860


title: W858


title: W857


title: W852


title: W85


title: W849


title: W845


title: W851


title: W847


title: W846


title: W848


title: W843


title: W850


title: W844


title: W841


title: W840


title: W842


title: W84


title: W838


title: W836


title: W835


title: W839


title: W831


title: W833


title: W830


title: W832


title: W827


title: W829


title: W828


title: W83


title: W826


title: W866


title: W82


title: W824


title: W825


title: W837


title: W821


title: W816


title: W813


title: W819


title: W812


title: W823


title: W810


title: W811


title: W81


title: W809


title: W808


title: W807


title: W818


title: W804


title: W800


title: W802


title: W803


title: W815


title: W820


title: W80


title: W822


title: W817


title: W799


title: W797


title: W796


title: W795


title: W794


title: W790


title: W791


title: W792


title: W793


title: W805


title: W788


title: W784


title: W785


title: W786


title: W783


title: W78


title: W779


title: W782


title: W778


title: W789


title: W774


title: W79


title: W775


title: W780


title: W777


title: W776


title: W798


title: W772


title: W787


title: W771


title: W768


title: W77


title: W769


title: W766


title: W781


title: W765


title: W760


title: W762


title: W761


title: W763


title: W764


title: W76


title: W773


title: W759


title: W757


title: W756


title: W758


title: W755


title: W753


title: W750


title: W751


title: W752


title: W75


title: W749


title: W748


title: W754


title: W770


title: W742


title: W743


title: W740


title: W74


title: W736


title: W739


title: W745


title: W741


title: W734


title: W747


title: W732


title: W733


title: W730


title: W729


title: W726


title: W731


title: W723


title: W728


title: W722


title: W721


title: W725


title: W746


title: W744


title: W735


title: W720


title: W806


title: W719


title: W72


title: W718


title: W767


title: W716


title: W715


title: W73


title: W724


title: W713


title: W712


title: W709


title: W707


title: W710


title: W705


title: W706


title: W708


title: W704


title: W717


title: W703


title: W714


title: W697


title: W70


title: W699


title: W701


title: W7


title: W698


title: W711


title: W71


title: W695


title: W696


title: W694


title: W693


title: W692


title: W69


title: W702


title: W691


title: W684


title: W686


title: W687


title: W688


title: W700


title: W690


title: W685


title: W689


title: W680


title: W68


title: W681


title: W679


title: W673


title: W672


title: W671


title: W676


title: W677


title: W675


title: W67


title: W674


title: W668


title: W669


title: W670


title: W666


title: W683


title: W665


title: W664


title: W663


title: W661


title: W662


title: W660


title: W66


title: W658


title: W659


title: W678


title: W657


title: W656


title: W655


title: W653


title: W654


title: W667


title: W650


title: W65


title: W646


title: W645


title: W647


title: W651


title: W652


title: W642


title: W648


title: W641


title: W640


title: W644


title: W635


title: W632


title: W634


title: W637


title: W638


title: W633


title: W631


title: W64


title: W629


title: W630


title: W636


title: W63


title: W626


title: W627


title: W628


title: W643


title: W625


title: W622


title: W623


title: W624


title: W639


title: W620


title: W618


title: W619


title: W617


title: W616


title: W62


title: W615


title: W614


title: W613


title: W612


title: W607


title: W610


title: W611


title: W61


title: W609


title: W608


title: W604


title: W605


title: W603


title: W606


title: W600


title: W601


title: W602


title: W60


title: W6


title: W598


title: W597


title: W599


title: W596


title: hBM-MSC #3 P7 duplicate (II)

city: Vilnius

first: Gabrielis

last: Kundrotas

address: Santariškių str. 1

country: Lithuania

institute: National Cancer Institute

description: SAMPLE 12

data_processing:
All the data analysis were performed according to the manufacturer’s instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php
For the normalization it uses the geometric average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, and RPLP0
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)
The web-based software package automatically performs all ΔΔCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against the mean of housekeeping genes)
Fold Change worksheet reports test/control (i.e., late passage hBM-MSCs/ early passage hBM-MSCs) ratios

label: SYBR Green

source_name: Human bone marrow_Test

label_protocol: PCR assays were performed using the Human Cellular Senescence RT² Profiler™ PCR Array (SABiosciences, Qiagen) following the manufacturer’s instructions. Reverse transcription was performed from 800 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Rotor-Gene Q, Qiagen) with 40 cycles at 95 oC for 15 seconds and 60 oC for 30 seconds.

growth_protocol: hBM-MSCs were grown in medium containing 10 % FBS under the  standard conditions at 37°C with 5% CO2 and fully humidified atmosphere

extract_protocol: Total RNA was isolated from hBM-MSCs using miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions

treatment_protocol: Before total RNA isolation, the cells were harvested with 0.25% trypsin-EDTA and washed twice with PBS

value: Bone marrow

value: female

tag: age

value: 28 years

tag: cell type

value: Mesenchymal stem cells

tag: passages


title: hBM-MSC #3 P7 (II)

description: SAMPLE 11


title: hBM-MSC #2 P7 (II)

description: SAMPLE 9

value: male

value: 38 years


title: hBM-MSC #1 P6 (II)

description: SAMPLE 7

value: 24 years


title: hBM-MSC #1 P6 duplicate (II)

description: SAMPLE 8


title: hBM-MSC #2 P7 duplicate (II)

description: SAMPLE 10


title: hBM-MSC #3 P4 duplicate (II)

description: SAMPLE 6

source_name: Human bone marrow_Control


title: hBM-MSC #3 P4 (II)

description: SAMPLE 5


title: hBM-MSC #2 P4 duplicate (II)

description: SAMPLE 4


title: hBM-MSC #2 P4 (II)

description: SAMPLE 3


title: hBM-MSC #1 P3 duplicate (II)

description: SAMPLE 2


title: hBM-MSC #1 P3 (II)

description: SAMPLE 1


title: hBM-MSC #3 P7 duplicate (I)

description: SAMPLE 12

label_protocol: PCR assays were performed using the Human Mesenchymal Stem Cell RT² Profiler™ PCR Array (SABiosciences, Qiagen) following the manufacturer’s instructions. Reverse transcription was performed from 800 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (Rotor-Gene Q, Qiagen) with 40 cycles at 95 oC for 15 seconds and 60 oC for 30 seconds.


title: hBM-MSC #3 P7 (I)

description: SAMPLE 11


title: hBM-MSC #2 P7 (I)

description: SAMPLE 9


title: hBM-MSC #2 P7 duplicate (I)

description: SAMPLE 10


title: hBM-MSC #1 P6 (I)

description: SAMPLE 7


title: hBM-MSC #1 P6 duplicate (I)

description: SAMPLE 8


title: hBM-MSC #3 P4 duplicate (I)

description: SAMPLE 6


title: hBM-MSC #2 P4 duplicate (I)

description: SAMPLE 4


title: hBM-MSC #2 P4 (I)

description: SAMPLE 3


title: hBM-MSC #1 P3 (I)

description: SAMPLE 1


title: hBM-MSC #1 P3 duplicate (I)

description: SAMPLE 2


title: hBM-MSC #3 P4 (I)

description: SAMPLE 5


title: W682


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, treated with RA for 6 days, rep 1

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 125K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

scan_protocol: The array was scanned using NimbleGen MS 200 Microarray scanner.

data_processing: Data was analysed using Biocondutor 2.12 running on R3.0.0. Probe set expression measures were calculated using quantile normalisation of log2 transformed data.

label: Cyanine 3

source_name: CSB-depleted SH-SY5Y cells re-expressing SYT9_RA for 6 days

label_protocol: Double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit from 10-20 μg total RNA, up to 1 μg cDNA was labelled with Cy3 according to the standard Nimblegen protocol by using Nimblegen labeling kit.

growth_protocol: human neuroblastoma cell line SH-SY5Y was maintained in 1:1 E4/F12 + 10% FBS medium at 37ºC with 5% CO2

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions.

treatment_protocol: cells were transduced with lentiviruses expressing either empty vector pLKO.1 or SYT9 cDNA, 24 hr after transduction, cells were treated with 5 μM retinoic acid and cultured for the indicated time as described in the study before total RNA was isolated.

value: CSB-KD SH-SY5Y cells

value: human neuroblastoma

tag: transduced with

value: lentiviral vector expressing SYT9 cDNA

tag: treated with

value: 5 μM RA 24 hr after transduction

tag: harvest time

value: 6 days after treatment


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, rep 2

value: 48 hr after transduction


title: JVE774_snp

description: Genomic DNA isolated from novel CRC cell lines was genotyped using the Illumina HumanExome-12 v1.2 BeadChip

data_processing: Data were processed in GenomeStudio.The file HumanExome-12_v1.2_signal.txt contains the raw signals and is available on the series record.

value: Male

tag: tissue

value: colorectal cancer

value: Adenocarcinoma


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, rep 1


title: CSB-depleted SH-SY5Y cells, treated with RA for 6 days, rep 1

source_name: CSB-depleted SH-SY5Y cells_RA for 6 days

value: lentiviral vector pLKO.1


title: CSB-depleted SH-SY5Y cells, treated with RA for 3 days, rep 1

source_name: CSB-depleted SH-SY5Y cells_RA for 3 days

value: 3 days after treatment


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, treated with RA for 6 days, rep 2


title: CSB-depleted SH-SY5Y cells, treated with RA for 3 days, rep 2


title: GA19_180DPI_Chronic SIV

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Test

data_processing:
TLDA-SDS run files at all time points were loaded onto Applied Biosystems Relative Quantification (RQ) Manager Software v1.2.2 and analyzed using automatic baseline settings and a manual threshold of 0.2.
The results from the RQ manager analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the DataAssist version 3.01 software (Lifetech Corp), a data analysis tool designed to compare samples using the deltadelta CT method for relative quantification of gene expression.
MiRNA expression data were normalized to snoU6 and RNU48.
In all experiments, the CT upper limit was set to 33 meaning that all miRNA detectors with a CT value greater than or equal to 33 were excluded.
Multiple comparisons correction was not applied due to small sample size and exploratory nature of the study.
DataAssist software automatically performs global normalization including all deltadeltaCT based fold-change calculations from the uploaded raw threshold cycle values. Matrix normalized worksheet reports normalized signal (normalized to snoU6 and RNU48). Data were normalized within experimental group (Acute SIV, Set Point, Chronic SIV).  Fold Change files report test/control (e.g. Chronic SIV infected/uninfected control) ratios.

label: FAM

organism: Macaca mulatta

source_name: Intestinal lamina propria leukocytes_Chronic SIV

label_protocol: MicroRNA profiling was performed using the TaqMan® Array Human MicroRNA A+B Cards Set v3.0 (Life Tech, catalog number 4444913, based on MirBase release 18) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 8 animals were used in this study. Intestinal surgical resection segments (~6-8 cm) were collected before and at 21 and 90 days post intravenous infection with 100 TCID50 SIVmac251. Intestinal lamina propria leukocytes were isolated from these segments for miRNA profiling studies.

value: small intestine

value: leukocytes

tag: days post siv infection (dpi)

value: 180 DPI


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, treated with RA for 3 days, rep 2

source_name: CSB-depleted SH-SY5Y cells re-expressing SYT9_RA for 3 days


title: GK31_180DPI_Chronic SIV

description: Test


title: CSB-depleted SH-SY5Y cells, treated with RA for 6 days, rep 2


title: HB48_180DPI_Chronic SIV

description: Test


title: JVE015_snp

value: Female

value: Sigmoid


title: JVE222_snp

value: Ascending colon


title: CSB-depleted SH-SY5Y cells re-expressing SYT9, treated with RA for 3 days, rep 1

value: CSB-KD SH-SY5Y cells


title: HF27_180DPI_Chronic SIV

description: Test


title: HV95_90DPI_Set point

description: Test

source_name: Intestinal lamina propria leukocytes_Set point

value: 90 DPI


title: KP7038T_snp

value: Right-sided colon


title: HR57_90DPI_Set point

description: Test


title: JVE528_snp


title: HB31_180DPI_Chronic SIV

description: Test


title: GA19_90DPI_Set point

description: Test


title: HB48_90DPI_Set point

description: Test


title: CSB-depleted SH-SY5Y cells, rep 1

source_name: CSB-depleted SH-SY5Y cells

value: human neuroblastoma


title: CSB-depleted SH-SY5Y cells, rep 2


title: HF27_90DPI_Set point

description: Test


title: HB31_90DPI_Set point

description: Test


title: JVE109_snp

value: Hepatic flexure


title: HC36_90DPI_Set point

description: Test


title: JVE253_snp

value: colorectal cancer-liver-metastasis

value: Liver metastasis

value: Mucinous adenocarcinoma

value: D


title: JVE187_snp

value: Adenocarcinoma


title: HV95_21DPI_Acute SIV

description: Test

source_name: Intestinal lamina propria leukocytes_Acute SIV


title: JVE103_snp

value: Male


title: GA19_21DPI_Acute SIV

description: Test

value: small intestine

value: 21 DPI


title: JVE371_snp


title: GK31_21DPI_Acute SIV

description: Test

value: leukocytes


title: JVE207_snp

value: colorectal cancer

value: Descending colon


title: JVE241_snp

value: Cecum


title: HF27_21DPI_Acute SIV

description: Test


title: JVE367_snp

value: Female

value: Ileocecal junction

value: Large cell neuroendocrine carcinoma


title: KP283T_snp


title: HB48_21DPI_Acute SIV

description: Test


title: HB31_21DPI_Acute SIV

description: Test


title: JVE059_snp

value: Colon transversum


title: HR57_21DPI_Acute SIV

description: Test

value: 90 DPI


title: HR57_Preinfection

description: Control

source_name: Intestinal lamina propria leukocytes_Preinfection Control

value: Uninfected


title: HF27_Preinfection

description: Control


title: HC36_21DPI_Acute SIV

description: Test


title: HB31_Preinfection

description: Control


title: HC36_Preinfection

description: Control


title: JVE127_snp

value: Ascending colon


title: HB48_Preinfection

description: Control


title: TAX577036

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

institute: Lund University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

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

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes.

label: Cy5 and Cy3

source_name: breast tumor

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was was isolated from fresh frozen breast tissues in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.

tag: disease state

value: breast cancer


title: TAX577240


title: JVE367

hyb_protocol: DNA was bisulfite converted using the EZ DNA methylation gold kit. Hybridization was performed according to the illumina protocol.

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized using the BMIQ function from the wateRmelon package in R with nfit=5000. probes with detection pval. ## 1370 sites were removed as beadcount <3 in 5 % of samples ## 5118 sites having 1 % of samples with a detection p-value greater than 0.05 were removed ## final filtering: sites with total intensity (methylated + unmethylated) <2000 were removed. The Unmethylated and methylated signal intensities can be found in the file Matrix_signal_intensities.txt located on the series record.

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the DNA isolation was performed using the Wizard Genomic DNA Purification Kit (Promega

tag: braf mutation status


title: KP363T


title: TAX577788


title: TAX577712


title: TAX577223


title: JVE103

value: colorectal cancer- liver metastasis

value: BRAF-WT


title: KP7038T


title: TAX577234


title: JVE127


title: TAX577790


title: TAX577423


title: JVE114


title: JVE253


title: JVE059


title: JVE528


title: JVE774


title: JVE109


title: JVE241


title: JVE207


title: JVE222


title: JVE187


title: TAX577354


title: TAX577791


title: KP283T


title: JVE192


title: JVE371


title: TAX577424


title: A/J-12SM, biological rep3

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with MAS5 using Affymetrix GeneChip Operating Software 1.2 default analysis settings and global scaling as normalization method.

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. After that, RNA was performed a cleanup using the QIAGEN Rneasy Mini kit.

treatment_protocol: high fat diet for 7 weeks

tag: strain

value: liver


title: TAX577210


title: TAX577789


title: A/J-12SM, biological rep1


title: JVE044


title: A/J-12SM, biological rep2


title: A/J, biological rep1

value: A/J


title: A/J, biological rep2


title: A/J, biological rep3


title: non_EB-SAM_EB Rep.1

city: Quebec city

first: Habib

middle: A.

last: Shojaei Saadi

state: Quebec

address: 2440 bl hochelaga, pavillon inaf

country: Canada

institute: Laval University

description: Biological replicate 1 of 4. (non-treated expanded blastocysts vs. SAM-treated expanded blastocysts)

hyb_protocol: Hybridizations were performed according to the microarray manufacturer's instructions (Agilent Technologies, Santa Clara, USA). Briefly, 1 µg of labeled sample (in 40 µL) was mixed with 158 µL of hybridization master mix containing 25 µL of bovine Cot-1 DNA (1.0 mg/mL, Bovine Hybloc competitor DNA, Applied Genetics Laboratories, Melbourne, FL, USA), 2.6 µL of Agilent 100x Blocking Agent and 130 µL of Agilent 2x HI-RPM Hybridization Buffer (Agilent Technologies, Santa Clara, USA). Samples were held at 95 °C for 3 min and at 37 °C for 30 min followed by addition of 65 µL of Agilent-CGHBlock (final volume 260 µL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab, Cornelius, OR, USA) for 40 h at 65 °C and 20 rpm. Washing was carried out according to the microarray manufacturer's instructions

scan_protocol: Slides were scanned with the PowerScanner (Tecan, Männedorf, Switzerland)

data_processing: Intensity values were obtained from slide images using the Array-Pro Analyzer 6.3 software (MediaCybernetics, Bethesda, MD, USA). Raw intensities were subjected to within-array normalization(loess) followed by between-array normalization (quantile) using the limma library from Bioconductor.

organism: Bos taurus

source_name: non-treated EB

label_protocol: Extracted RNA from each sample (n=10 Blst.) of both SAM-treated (four replicates) and non-treated (four replicates)  groups were amplified through in vitro transcription by T7 RNA amplification using the RiboAmp HS Plus RNA Amplification Kit (Molecular Devices) and the anti-sense RNA (aRNA) was produced. Then the quantity of the aRNA were measured using NanoDrop ND-1000 (Nano- Drop Technologies, Wilmington, DE, USA) and 2 µg of aRNA were labeled (Cy3 and Cy5) using the ULS Fluorescent Labelling Kit for Agilent arrays  (Kreatech Diagnostics, Amsterdam, The Netherlands). Following purification with Pico-Pure RNA Isolation Kit (Molecular Devices, Sunnyvale, CA, USA) the labeling efficiency was evaluated using the Nano-Drop ND-1000 (Nano- Drop Technologies, Wilmington, DE, USA). Similar to DNA methylome analysis, four samples (10 Blst./sample) (biological replicates) of SAM-treated and control groups were hybridized on EmbryoGENE’s bovine transcriptome 44k Agilent microarray slides (V2) (Agilent Technologies) using a dye-swap design (technical replicates) for a total of eight arrays.

growth_protocol: Bovine blastocyst production in synthetic oviduct fluid (SOF) media was performed with some modifications. Dairy cattle ovaries were collected from a commercial slaughterhouse and were transported to the laboratory in saline (0.9% NaCl) containing 1% Antibiotic-Antimycotic 100X (Gibco. 15240, Invitrogen, Burlington, ON, CAN) agent. Cumulus oocyte complexes (COCs) were aspirated from 2–6 mm follicles within 2 h of reception. Only COCs with at least five layers of cumulus without fragmented cytoplasm, pyknotic cumulus, pale nuclei and abnormal morphology were selected for maturation. The collected COCs were washed three times in HEPES-buffered Tyrode’s medium (TLH) containing with 1.5 % bovine serum albumin (Fraction V, Sigma-Aldrich, Oakville, Canada), 200 µM/mL pyruvate and 50 µg/mL of gentamycin as the washing medium. Pools of 10 COCs were placed in 50 µL droplets of maturation medium comprising TCM199 (Gibco 11150–059; Invitrogen, Burlington, ON, CAN), 0.6% bovine serum albumin (Sigma fraction V), 200 µM/mL pyruvate, 50 µg/mL of gentamycin, 0.1 µg/mL of follicle stimulating hormone (FSH) (Gonal-f, Serono Canada Inc.,Mississauga, QC, CAN) and 1µg/mL Estradiol  (E2) covered with filtered mineral oil and incubated for 24 h at 38.5°C with 5% CO2, 20% O2 and high humidity. Matured COCs were washed three time in washing medium (TLH) and were transferred  (n=5) to 50 µL fertilization medium drops comprising modified Tyrode’s lactate medium, supplemented with 0.6% bovine serum albumin (Sigma fraction V), 200 µM/mL pyruvate and 50 µg/mL gentamycin, covered with filtered mineral oil. Then 2 µL of a solution containing 1 mM hypotaurine, 2 mM penicillamine and 250 mM epinephrine was added to the COCs-containing fertilization droplets. In vitro fertilization was performed through insemination of the COCs with 25 x 106 sperm/mL. Briefly, the cryo-preserved Holstein bulls semen obtained from L'Alliance Boviteq Inc (Saint-Hyacinthe, QC, Canada) were thawed (37 °C water bath for 30 s) and washed through discontinuous Percoll gradient  (45%-90% Percoll ; 700 × g for 30 min RT). After sperm motility assessment and the appropriate concentration adjustment the sperm were added to the COCs-contained fertilization drops and incubated for 15 –18 h at 38.5°C with 5% CO2, 20% O2 and high humidity.  Zygotes and unfertilized COCs were mechanically denuded by repeated pipetting and washed three times in TLH to ensure complete removal of cumulus cells and sperm. For standard culture conditions, groups of ten embryos were placed in 10 µL droplets of modified synthetic oviduct fluid (SOF) under filtered mineral oil. Sequential SOF media were used as following: the embryos were first placed in SOF#1 (6 mM lactate, 0.2 mM glucose). The embryo culture dishes were incubated 38.5°C with 6.5% CO2, 5% O2 and high humidity. Embryos were then transferred to 10 µL droplets of SOF#2 (1 mM lactate, 0.5 mM glucose) 96 h post-fertilization (hpf) and finally to 10 µL droplets of SOF#3 (1 mM lactate, 2.5 mM glucose) 144 hpf.

extract_protocol: Extraction of total RNA from the collected EB embryos was carried out using the AllPrep DNA/RNA Mini Kit (Qiagen Canada Inc., Mississauga, ON, Canada) according to the manufacture manual and the samples were eluted in 30 µL for extracted RNA. Quantity and quality of each pool of extracted RNA was veriﬁed on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada).  The extracted total RNA from blastocysts were appropriately labeled and immediately frozen at – 80 °C until use.

treatment_protocol: In order to treat the early embryos, 10 µM of S-(5′-Adenosyl)-L-methionine chloride dihydrochloride, SAM (Sigma-Aldrich, Oakville, Canada# A7007) were freshly prepared by dissolving in SOF medium for each IVF trial and were quickly aliquoted into 100 µL and kept frozen at -80 until being used for each SAM-treatment. For control, only SOF medium without SAM were prepared freshly and aliquots of 100 µL were frozen at -80 until being used for control group during each treatment. The treatment was initiated at ~ 72 hpf (8-cell stage) of in vitro produced bovine embryo. To do that, for each IVF trial, only the 8-cell early embryos were collected and randomly divided equally into SAM-treated and control groups. The SAM treatment were performed at the final concentration of 2 µM SAM  through adding 2 µL of 38.5°C frozen-thawed prepared aliquots of SAM (10 µM) into 8 µL of SOF droplets. For control group, similar treatment were performed with 2 µL of 38.5°C frozen-thawed prepared aliquot of SOF medium. The treatment was carried out every three hr, four times/day until blastocyst collection. For each treatment the embryos were transferred into a new SOF droplet (8 µL) and then 2 µL of SAM (10 µM) or SOF were added for SAM-treated or control group, respectively. For each IVF trial both groups were simultaneously treated and transferred into new droplets.  Only expanded-blastocyst-stage embryos were collected, in four pools of ten embryos (n=40) per each group for parallel DNA methylome and transcriptome study.

value: Expanded blastocyst

value: none (control)

source_name: SAM-treated EB

value: S-(5′-Adenosyl)-L-methionine chloride dihydrochloride (SAM)


title: non_EB-SAM_EB Rep.3

description: Biological replicate 3 of 4. (non-treated expanded blastocysts vs. SAM-treated expanded blastocysts)


title: non_EB-SAM_EB Rep.4

description: Biological replicate 4 of 4. (non-treated expanded blastocysts vs. SAM-treated expanded blastocysts)


title: SAM_EB-non_EB Rep.3

description: Biological replicate 3 of 4. (SAM-treated expanded blastocysts vs. non-treated expanded blastocysts)


title: SAM_EB-non_EB Rep.1

description: Biological replicate 1 of 4. (SAM-treated expanded blastocysts vs. non-treated expanded blastocysts)


title: Hypothalamus_Triclosan-Maternal Infusion_Replicate 1

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

description: Gene expression in fetal hypothalamus whose mother was infused with Triclosan-Replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity: 10.2 to 12.8 pmol Cy3/μg RNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least four arrays.

organism: Ovis aries

source_name: Fetal Hypothalamus, Maternal Triclosan infusion

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent, Newcastle DE) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from fetal hyothalamus with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: To evaluate the effect of direct TCS exposure, chronically catheterized late gestation fetal sheep were infused with vehicle (n=4) or TCS (250 μg/day; n=4) iv for two days. To evaluate the effect of indirect TCS exposure, TCS (100 μg/kg/day; n=3) or vehicle (n=3) was infused into the maternal circulation for two days.

value: hypothalamus

tag: developmental stage

value: Around 130 days of fetal age


title: Hypothalamus_Triclosan-Maternal Infusion_Replicate 2

description: Gene expression in fetal hypothalamus whose mother was infused with Triclosan-Replicate 2


title: JVE015

source_name: CRC

value: colorectal cancer


title: Hypothalamus_Triclosan-Maternal Infusion_Replicate 3

description: Gene expression in fetal hypothalamus whose mother was infused with Triclosan-Replicate 3


title: TAX577387


title: Hypothalamus_Triclosan-Fetal Infusion_Replicate 2

description: Gene expression in fetal hypothalamus infused with Triclosan-Replicate 2

source_name: Fetal Hypothalamus, Fetal Triclosan infusion


title: TAX577284


title: Hypothalamus_Triclosan-Fetal Infusion_Replicate 3

description: Gene expression in fetal hypothalamus infused with Triclosan-Replicate 3


title: JVE017


title: Hypothalamus_Triclosan-Fetal Infusion_Replicate 4

description: Gene expression in fetal hypothalamus infused with Triclosan-Replicate 4


title: TAX577158


title: TAX577334


title: TAX577554


title: Hypothalamus_Triclosan-Fetal Infusion_Replicate 1

description: Gene expression in fetal hypothalamus infused with Triclosan-Replicate 1


title: Hypothalamus_Control-Maternal Infusion_Replicate 3

description: Gene expression in fetal hypothalamus whose mother was infused with vehicle-Replicate 3

source_name: Fetal Hypothalamus, Maternal vehicle infusion


title: Hypothalamus_Control-Maternal Infusion_Replicate 1

description: Gene expression in fetal hypothalamus whose mother was infused with vehicle-Replicate 1


title: TAX577551


title: TAX577147


title: SAM_EB-non_EB Rep.2

description: Biological replicate 2 of 4. (SAM-treated expanded blastocysts vs. non-treated expanded blastocysts)


title: TAX577124


title: Hypothalamus_Control-Fetal Infusion_Replicate 2

description: Gene expression in fetal hypothalamus infused with vehicle-Replicate 2

source_name: Fetal Hypothalamus, Fetal vehicle infusion


title: Hypothalamus_Control-Maternal Infusion_Replicate 2

description: Gene expression in fetal hypothalamus whose mother was infused with vehicle-Replicate 2


title: Hypothalamus_Control-Fetal Infusion_Replicate 4

description: Gene expression in fetal hypothalamus infused with vehicle-Replicate 4


title: TAX577463


title: TAX577221


title: SAM_EB-non_EB Rep.4

description: Biological replicate 4 of 4. (SAM-treated expanded blastocysts vs. non-treated expanded blastocysts)


title: TAX577015


title: Hypothalamus_Control-Fetal Infusion_Replicate 3

description: Gene expression in fetal hypothalamus infused with vehicle-Replicate 3


title: TAX577289


title: Hypothalamus_Control-Fetal Infusion_Replicate 1

description: Gene expression in fetal hypothalamus infused with vehicle-Replicate 1


title: TAX577542


title: TAX577718


title: TAX577220


title: Day7 immortalized brown adipogenic cells transducted with non targeting control particles_2

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

description: gene expression of control cells

hyb_protocol: Genechip hybridization, wash, stain and scan were performed using standard Affymetrix procedures.

scan_protocol: GeneTitan instrument was used for scanning.

data_processing: Raw array data were normalized using RMA method implemented in CarmaWeb (https://carmaweb.genome.tugraz.at/carma/). A moderate t-test was used to compare ntc and siAspa. The p-values  were corrected for multiple testing using Benjamini-Hochberg's method. Corrected p-values <0.05 were considered differentially expressed.

source_name: immortalized brown adipogenic cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

growth_protocol: Immortalized brown adipogenic cells (iBACs) were grown in high glucose DMEM containing 10% FBS, 50 µg/ml streptomycin, 50 units/ml penicillin (P/S, Invitrogen), and 20mM Hepes at 37°C and 5% CO2. For differentiation medium of confluent cells was supplemented with 0.5 mM 3-isobutyl-1-methylxanthine (IBMX) (Calbiochem), 0.5 µM dexamethasone, 20 nM insulin , 1 nM triiodthyronine, and 125 µM indomethacin (all Sigma). Two days after induction, medium was changed to maintenance medium containing 20 nM insulin and 1 nM T3 and cells were kept in this medium until harvest on day 7.

extract_protocol: Total RNA was isolated with PeqGOLD total RNA isolation kit (Peqlab) according to manufacturers recommendations yielding a RIN of 9.5-10.

treatment_protocol: For stable knock-down of Aspa, lentiviral shRNA particles and a nontargeting control construct were obtained from Sigma (CSTVRS-TRCN0000098802). Infections of pre-confluent cells were followed by G418 (1.5 µg/µl) selection.

tag: shRNA

value: control


title: TAX577567


title: 13 drought b

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 216 slides were hybridized and scanned was Randomized to minimize the impact on differences between samples of any potential variation in the processing conditions. According to this Randomized experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Cy3 and Cy5 scans for each slide were combined and processed in ImaGene version 8.0 (BioDiscovery) to extract raw intensity and background corrected data values for each spot on the array
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using a modified version of R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy3 or Cy5

organism: Arabidopsis thaliana

source_name: Day:13 Treatment:drought  Biorep:B

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis thaliana plants (Col-0, agl22-3 [SALK_141674], and agl22-4 [SAIL_583_C08]) were obtained from the European Arabidopsis Stock Centre, and were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing individual seeds onto a soil mix (Scotts Levingtons F2+S compost : fine grade vermiculite in a ratio of 6:1:). For the drought time course experiment, pots (7cm x 7cm x 9 cm) were filled with the same amount of soil mix. Control pots, to determine 100% and 0% soil water content, were set up at the same time. Plants were transferred into individual pots 2 weeks after the sowing date and were kept well watered until the beginning of the drying episode at 5 weeks after sowing.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Half the plants were maintained at well watered conditions, while for the remaining half, water was withdrawn and pot weight was determined daily. Relative soil water content was calculated for each day and pots were left to dry until 17% rSWC was reached. 5 week old plants were saturated in water to reach 95% rSWC, and watering was stopped in the treatment plants until ~17% rSWC was reached. The control plants were maintained under well-watered conditions at ~95% rSWC. Due to the early flowering phenotype of both agl22 mutant alleles, drought experiments were carried out on 20 day old plants to ensure the experiments were carried out at similar rosette developmental stages and prior to the onset of flowering, as indicated in Supplemental Figure 5A. The drying rate was determined as the slope of the decline in relative soil water content, measured daily throughout the drying period.

tag: treatment

value: drought

tag: time (day)

tag: biological replicate

value: B


title: Day7 immortalized brown adipogenic cells transducted with Aspa shRNA particles_3

description: gene expression of Aspa knock-down cells

value: Aspa


title: Day7 immortalized brown adipogenic cells transducted with non targeting control particles_3

description: gene expression of control cells


title: 1 drought c

source_name: Day:1 Treatment:drought  Biorep:C

value: C


title: Day7 immortalized brown adipogenic cells transducted with non targeting control particles_1

description: gene expression of control cells


title: Day7 immortalized brown adipogenic cells transducted with Aspa shRNA particles_1


title: 10 drought b

source_name: Day:10 Treatment:drought  Biorep:B


title: 12 drought b

source_name: Day:12 Treatment:drought  Biorep:B


title: 9 drought b

source_name: Day:9 Treatment:drought  Biorep:B


title: TAX577422


title: TAX577490


title: TAX577584


title: 6 drought b

source_name: Day:6 Treatment:drought  Biorep:B


title: 5 drought b

source_name: Day:5 Treatment:drought  Biorep:B


title: 7 drought b

source_name: Day:7 Treatment:drought  Biorep:B


title: 1 drought b

source_name: Day:1 Treatment:drought  Biorep:B


title: 13 drought a

source_name: Day:13 Treatment:drought  Biorep:A

value: A


title: 3 drought b

source_name: Day:3 Treatment:drought  Biorep:B


title: 4 drought b

source_name: Day:4 Treatment:drought  Biorep:B


title: 11 drought a

source_name: Day:11 Treatment:drought  Biorep:A


title: TAX577327

source_name: breast tumor

value: breast cancer


title: 8 drought b

source_name: Day:8 Treatment:drought  Biorep:B


title: 12 drought a

source_name: Day:12 Treatment:drought  Biorep:A


title: 10 drought a

source_name: Day:10 Treatment:drought  Biorep:A


title: 9 drought a

source_name: Day:9 Treatment:drought  Biorep:A


title: TAX577433


title: TAX577161


title: 2 drought b

source_name: Day:2 Treatment:drought  Biorep:B


title: 7 drought a

source_name: Day:7 Treatment:drought  Biorep:A


title: 8 drought a

source_name: Day:8 Treatment:drought  Biorep:A


title: 6 drought a

source_name: Day:6 Treatment:drought  Biorep:A


title: TAX577357


title: hBM-MSC #3 P7 (III)

description: SAMPLE 11

data_processing:
All the data analysis were performed according to the manufacturer’s instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/mirna/arrayanalysis.php
For the normalization it uses the geometric average of six small RNAs: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, and RNU6-2
Target miRNAs signals normalized to reference miRNAs; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)
The web-based software package automatically performs all ΔΔCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against the mean of reference miRNAs)
Fold Change worksheet reports test/control (i.e., late passage hBM-MSCs/ early passage hBM-MSCs) ratios

source_name: Human bone marrow_Test

label_protocol: PCR assays were performed using the miRNome miScript miRNA PCR Array (SABiosciences, Qiagen) following the manufacturer’s instructions. Reverse transcription was performed from 600 ng total RNA using the miScript II RT Kit (Qiagen). Quantitative real-time PCR were performed (Rotor-Gene Q, Qiagen) with 40 cycles at 94 oC for 15 seconds, at 55 oC for 30 seconds, and 70 oC for 30 seconds.

value: Bone marrow

tag: gender

value: female

value: 28 years

value: Mesenchymal stem cells


title: TAX577128


title: 11 drought b

source_name: Day:11 Treatment:drought  Biorep:B


title: 5 drought a

source_name: Day:5 Treatment:drought  Biorep:A


title: TAX577370


title: TAX577112


title: hBM-MSC #2 P7 duplicate (III)

description: SAMPLE 10

value: male

tag: age

value: 38 years


title: TAX577012


title: hBM-MSC #2 P7 (III)

description: SAMPLE 9

tag: cell type


title: TAX577022


title: TAX577787


title: TAX577171


title: hBM-MSC #1 P6 (III)

description: SAMPLE 7

value: 24 years

tag: passages


title: hBM-MSC #1 P6 duplicate (III)

description: SAMPLE 8


title: TAX577350


title: TAX577786


title: hBM-MSC #3 P7 duplicate (III)

description: SAMPLE 12


title: hBM-MSC #3 P4 duplicate (III)

description: SAMPLE 6

source_name: Human bone marrow_Control


title: TAX577143


title: 3 drought a

source_name: Day:3 Treatment:drought  Biorep:A


title: hBM-MSC #2 P4 duplicate (III)

description: SAMPLE 4


title: non_EB-SAM_EB Rep.2

description: Biological replicate 2 of 4. (non-treated expanded blastocysts vs. SAM-treated expanded blastocysts)

source_name: non-treated EB

value: Expanded blastocyst

value: none (control)

source_name: SAM-treated EB

value: S-(5′-Adenosyl)-L-methionine chloride dihydrochloride (SAM)


title: 2 drought a

source_name: Day:2 Treatment:drought  Biorep:A


title: 4 drought a

source_name: Day:4 Treatment:drought  Biorep:A


title: 12 control d

source_name: Day:12 Treatment:control  Biorep:D

value: control

value: D


title: 1 drought a

source_name: Day:1 Treatment:drought  Biorep:A

value: drought


title: hBM-MSC #3 P4 (III)

description: SAMPLE 5


title: TAX577290

source_name: breast tumor


title: hBM-MSC #2 P4 (III)

description: SAMPLE 3


title: Day7 immortalized brown adipogenic cells transducted with Aspa shRNA particles_2

source_name: immortalized brown adipogenic cell line

value: Aspa


title: hBM-MSC #1 P3 duplicate (III)

description: SAMPLE 2


title: TAX577394


title: hBM-MSC #1 P3 (III)

description: SAMPLE 1


title: 10 control d

source_name: Day:10 Treatment:control  Biorep:D


title: 6 control d

source_name: Day:6 Treatment:control  Biorep:D


title: 7 control d

source_name: Day:7 Treatment:control  Biorep:D


title: TAX577413


title: TAX577545


title: 8 control d

source_name: Day:8 Treatment:control  Biorep:D


title: 4 control d

source_name: Day:4 Treatment:control  Biorep:D


title: 13 control d

source_name: Day:13 Treatment:control  Biorep:D


title: 11 control d

source_name: Day:11 Treatment:control  Biorep:D


title: 9 control d

source_name: Day:9 Treatment:control  Biorep:D


title: 5 control d

source_name: Day:5 Treatment:control  Biorep:D


title: 1 control d

source_name: Day:1 Treatment:control  Biorep:D


title: 2 control d

source_name: Day:2 Treatment:control  Biorep:D


title: 3 control d

source_name: Day:3 Treatment:control  Biorep:D


title: TAX577259


title: TAX577053


title: TAX577473


title: TAX577546


title: 10 control c

source_name: Day:10 Treatment:control  Biorep:C

value: C


title: TAX577404


title: 0 zero d

source_name: Day:0 Treatment:zero  Biorep:D

value: zero


title: TAX577432

value: breast cancer


title: 12 control c

source_name: Day:12 Treatment:control  Biorep:C


title: 11 control c

source_name: Day:11 Treatment:control  Biorep:C


title: TAX577406

source_name: breast tumor


title: 8 control c

source_name: Day:8 Treatment:control  Biorep:C


title: TAX577587


title: 13 control c

source_name: Day:13 Treatment:control  Biorep:C


title: 9 control c

source_name: Day:9 Treatment:control  Biorep:C


title: TAX577375


title: TAX577088


title: TAX577257


title: TAX577475


title: 6 control c

source_name: Day:6 Treatment:control  Biorep:C


title: TAX577526


title: 7 control c

source_name: Day:7 Treatment:control  Biorep:C


title: TAX577462


title: 4 control c

source_name: Day:4 Treatment:control  Biorep:C


title: 1 control c

source_name: Day:1 Treatment:control  Biorep:C


title: TAX577186


title: 5 control c

source_name: Day:5 Treatment:control  Biorep:C


title: 3 control c

source_name: Day:3 Treatment:control  Biorep:C


title: TAX577155


title: 2 control c

source_name: Day:2 Treatment:control  Biorep:C


title: G3BP1 Non Stress 3, biological replicate 3

city: Toronto

first: James

last: Rutka

state: Ontario

address: 686 Bay Street

department: Cell Biology

institute: Hospital for Sick Children

description: RNA immunopreciptation (RIP) using G3BP1 antibody from non-stressed cells. Biological replicate 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. CHECK WITH FACILITY

scan_protocol: GeneChips were scanned at The Centre for Applied Genomics (TCAG), SickKids Hospital Toronto, Canada

data_processing: The data were normalized with Affymetrix Expression Console Software using RMA analysis.

source_name: Human Brain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in DMEM media supplemented with 10% FBS

extract_protocol: RNA was extracted with the RNeasy Mini Kit (Qiagen, Cat#74104 ) using the manufacturer's protocol.

treatment_protocol: Cells were treated with 500uM aresenite to induce stress and RNA harvested after 30 minutes. Control cells (non stress) were treated with DMSO and RNA harvested from cells after 30 minutes.

tag: cell line

value: astrocytoma


title: 13 control b

source_name: Day:13 Treatment:control  Biorep:B

value: B


title: G3BP1 Non Stress 2, biological replicate 2

description: RNA immunopreciptation (RIP) using G3BP1 antibody from non-stressed cells. Biological replicate 2


title: G3BP1 Non Stress 1, biological replicate 1

description: RNA immunopreciptation (RIP) using G3BP1 antibody from non-stressed cells. Biological replicate 1


title: 0 zero c

source_name: Day:0 Treatment:zero  Biorep:C


title: TAX577496


title: G3BP1 Stress 3, biological replicate 3

description: RNA immunopreciptation (RIP) using G3BP1 antibody from cells treated with arsentite to induce stress granules. Biological replicate 3


title: 12 control b

source_name: Day:12 Treatment:control  Biorep:B


title: 11 control b

source_name: Day:11 Treatment:control  Biorep:B


title: TAX577419


title: 10 control b

source_name: Day:10 Treatment:control  Biorep:B


title: TAX577148

source_name: breast tumor


title: TAX577549


title: TAX577683


title: G3BP1 Stress 2, biological replicate 2

description: RNA immunopreciptation (RIP) using G3BP1 antibody from cells treated with arsentite to induce stress granules. Biological replicate 2


title: TAX577324


title: TAX577162


title: 8 control b

source_name: Day:8 Treatment:control  Biorep:B


title: TAX577052


title: TAX577388


title: Input Non-Stress 3, biological replicate 3

description: Input Non-Stress 3


title: Input Non-Stress 2, biological replicate 2

description: Input Non-Stress 2


title: 9 control b

source_name: Day:9 Treatment:control  Biorep:B


title: TAX577544


title: TAX577400


title: G3BP1 Stress 1, biological replicate 1

description: RNA immunopreciptation (RIP) using G3BP1 antibody from cells treated with arsentite to induce stress granules. Biological replicate 1


title: Input Non-Stress 1, biological replicate 1

description: Input Non-Stress 1


title: 7 control b

source_name: Day:7 Treatment:control  Biorep:B


title: Input Stress 3, biological replicate 3

description: Input Stress 3


title: 6 control b

source_name: Day:6 Treatment:control  Biorep:B


title: Input Stress 2, biological replicate 2

description: Input Stress 2


title: TAX577380


title: 5 control b

source_name: Day:5 Treatment:control  Biorep:B


title: TAX577421


title: TAX577001


title: TAX577325


title: TAX577532


title: TAX577569


title: 3 control b

source_name: Day:3 Treatment:control  Biorep:B


title: Tial Non Stress 3,biological rep3

description: RNA immunopreciptation (RIP) using TIAL antibody from non-stressed cells. Biological replicate 3


title: Tial Non Stress 1,biological rep1

description: RNA immunopreciptation (RIP) using TIAL antibody from non-stressed cells. Biological replicate 1


title: TAX577461


title: 1 control b

source_name: Day:1 Treatment:control  Biorep:B


title: 2 control b

source_name: Day:2 Treatment:control  Biorep:B


title: Tial Non Stress 2,biological rep2

description: RNA immunopreciptation (RIP) using TIAL antibody from non-stressed cells. Biological replicate 2


title: 0 zero b

source_name: Day:0 Treatment:zero  Biorep:B


title: Tial Stress 3, biological rep 3

description: RNA immunopreciptation (RIP) using TIAL antibody from cells treated with arsentite to induce stress granules. Biological replicate 3


title: TAX577585


title: 13 control a

source_name: Day:13 Treatment:control  Biorep:A

value: A


title: 11 control a

source_name: Day:11 Treatment:control  Biorep:A


title: TAX577539


title: 4 control b

source_name: Day:4 Treatment:control  Biorep:B


title: 12 control a

source_name: Day:12 Treatment:control  Biorep:A


title: Tial Stress 2, biological rep 2

description: RNA immunopreciptation (RIP) using TIAL antibody from cells treated with arsentite to induce stress granules. Biological replicate 2

source_name: Human Brain


title: TAX577034


title: TAX577784


title: DMSO treated activated CD4 cells, biological rep2

city: Frederick

first: Ven

last: Natarajan

institute: Leidos Biomedical Research Inc

description: In vitro activated CD4 cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was processed using Partek Pro. RMA normalization and mean gene summary was performed
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Peripheral blood mononuclear cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Human Peripheral blood mononuclear cells (PBMCs) were purified by Histopaque density gradient centrifugation from lymphapheresis of healthy donors. CD4 lymphocytes were isolated using Dynal beads and were maintained in RPMI medium supplemented with 10 mM HEPES buffer, 2 mM L-glutamine, 60 mg/ml gentamicin, rIL-2 (20 units/ml), and 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using Qiagen Rneast mini kit

treatment_protocol: Cells (10^6/ml) were treated with anti-CD3 antibodies immobilized (10 mg/ml in PBS) on polystyrene surfaces in presence or absence of 2 µM of all-trans-retinoic acid. After 48 h of incubation cells were harvested and total cellular RNA was isolated.

value: In vitro activated CD4 cells


title: 10 control a

source_name: Day:10 Treatment:control  Biorep:A


title: TAX577361

source_name: breast tumor


title: ATRA treated activated CD4 cells, biological rep1

description: In vitro activated CD4 cells


title: ATRA treated activated CD4 cells, biological rep2

description: In vitro activated CD4 cells


title: 9 control a

source_name: Day:9 Treatment:control  Biorep:A


title: TAX577113


title: DMSO treated activated CD4 cells, biological rep1

description: In vitro activated CD4 cells


title: 6 control a

source_name: Day:6 Treatment:control  Biorep:A


title: 7 control a

source_name: Day:7 Treatment:control  Biorep:A


title: Whole blood sample, healthy individual, no treatment (01-01-026)

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: The slides were washed and stained on a GeneChip® Fluidics Station (Affymetrix) and scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing: Fluorescence intensity data were normalized by robust multiarray analysis (RMA) using GeneSpring® (Agilent Technologies, Santa Clara, CA).

source_name: Healthy individual, in the absence of any treatment

label_protocol: RNA was labeled using a One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA)

extract_protocol: RNA was extracted from blood samples using a Paxgene Blood RNA kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integriti number (RIN) > 6

treatment_protocol:
28 patients with SLE (aged 18 - 50 years), according to the American College of Rheumatology criteria for SLE,[5] were recruited in a multicenter, randomized, double-blind placebo-controlled, phase I/II staggered dose-escalation trial of IFN-K (ClinicalTrials.gov registry number NCT01058343). Patients were randomized to receive 3 or 4 injections placebo (n=7), 30 microg (n=3), 60 microg (n=6), 120 microg (n=6) or 240 microg (n=6) IFN-K. Clinical and safety data, induction of anti-IFNalpha Ab, and gene expression profiling studies up to day 168 after the first IFN-K injection were reported previously (Lauwerys BR et al. Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon alpha-kinoid. Arthritis Rheum 2013; 65: 447-56)
In 6 patients, whole blood samples were collected in PAXgene Blood RNA tubes (Qiagen) every 6 months after completion of the initial study. RNA was extracted from these samples, and was also re-extracted from baseline (month 0) and day 168 (month 6) PAXgene tubes stored at -80° from the same patients, and from 10 healthy volunteers

tag: individual

value: Healthy

value: Female

tag: age at baseline

tag: anti-double stranded dna ab titers (farr units/ml)

value: ND

tag: serum c3 (mg/l)

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: sledai

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

tag: agent

value: untreated

value: whole blood


title: TAX577039

tag: disease state


title: TAX577785


title: TAX577564


title: Tial Stress 1, biological rep 1

description: RNA immunopreciptation (RIP) using TIAL antibody from cells treated with arsentite to induce stress granules. Biological replicate 1


title: Whole blood sample, healthy individual, no treatment (01-01-021)

tag: tissue


title: 3 control a

source_name: Day:3 Treatment:control  Biorep:A

tag: treatment

tag: time (day)

tag: biological replicate


title: TAX577524


title: TAX577783


title: TAX577495


title: Whole blood sample, healthy individual, no treatment (01-01-002)

tag: gender