title: Sample 20 DAY

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description: 20 DAY B.napus inoculated with Plasmodiophora brassicae

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Brassica napus

source_name: 20 DAY B.napus (Plasmodiophora brassicae)

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 0.5 µg total RNA samples that were first subject to dephosphorylation reaction to remove 5’ phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3’ end of sample (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contains a tag segment for capturing fluorescent dye during a later Cy3 dye staining process.

growth_protocol: Seeds of Brassica napus were germinated on moist filter paper in petri dishes and placed under a light/dark (16h/8 h) regime for 7 days at 22±1 º C.

extract_protocol: One-week old seedlings of B. napus cv. Westar were divided into two groups; one was inoculated with P. brassicae while the other, uninoculated group, served as controls in the experiment. Tissues were harvested at 10 and 20-days-post inoculation (dpi) for RNA isolation. Plant roots from these groups were pooled separately and total RNA was isolated using the TRI-Reagent (Ambion, USA) and used in microarray experiments.

treatment_protocol: Clubroot gall pathotype SACAN03-1 (St. Albert, Canada type 03-1), was isolated from infected tissues stored at -20 ºC (collected from Southern Alberta region), [71]. Resting spores were extracted by homogenizing mature clubroot galls of Chinese cabbage, followed by filtration through six layers of cheesecloth and two subsequent centrifugation steps (2,500 x g) for 10 min [72]. The resting spores of P. brassicae were resuspended in autoclaved, deionized water and the number of spores in the suspension was counted using a haemocytometer. One week-old seedlings were individually dipped into the spore suspensions (1x107  spores/mL) for 1-2 seconds and planted in flats (3 × 3 cm, one seed per insert) containing LA4 Aggregate Plus (Sunshine Professional Peat-Lite Mix; Sungro Horticulture, Vancouver, BC, Canada). Plants were placed in a growth chamber with an 18 h photoperiod (light intensity of 130 µmol m-2 s-1) with a day (21 ± 1oC)/ night (18 ± 1oC) temperature cycle for 1 week, with a water tray underneath.

value: root

tag: inoculant

value: Plasmodiophora brassicae


title: D20 replicate 2

status: Public on Nov 28 2013

type: RNA

city: Sheffield

first: Keith

middle: David

last: Hunter

state: South Yorkshire

address: Claremont Crescent

department: School of Clinical Dentistry

country: United Kingdom

institute: University of Sheffield

description: miRNA expression data precancerous oral keratinocytes

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the miRNA-1.0 Affymetrix miRNA Array in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were normalised using RMAExpress before further anlaysis in TIGR MeV

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: oral precancer cell line D20

label_protocol: Biotinylation of antisense miRNA carried out according to Affymetrix protocol

growth_protocol: All cells were grown in KGM/Greens medium, as per standard protocols, to 60% confluence before trypsinisation

extract_protocol: Total RNA was extracted from cell pellets using RNEasy minikit (Qiagen)

tag: cell type

value: oral precancer cell line D20

tag: cell line


title: D20 replicate 1


title: Control 20 DAY

country: USA

description: 20 DAY B.napus plants serves as control

source_name: 20 DAY B.napus (Uninoculated)

tag: tissue

value: uninoculated


title: allantoin limited clone2 in allantoin limited media vs FY4 in ammonium limited media

city: New York

first: Jungeui

last: Hong

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: Evolved clone2 in allantoin limited media vs Ancestor (FY4) strain ammonium limited media

hyb_protocol: Cy3 and Cy5 labeled cRNA was co-hybridized to an Agilent 60-mer DNA microarray at 65C for 16 hours.  DNA microarrays were washed using the standard Agilent wash protocol.

scan_protocol: DNA microarrays were scanned using an Agilent Technologies Scanner G2505B

data_processing: Probe intensities were determined using the Feature Exractor software and normalized between the Cy5 and Cy3 channel using a linear-loess normalization

organism: Saccharomyces cerevisiae

label_protocol: cDNA from each sample was generated using MMLV reverse transcriptase primed with a poly-dT primer containing the promoter sequence for T7 RNA polymerase.  Labeled cRNA was generated using T7 RNA polymerase and UTPs labeled with either Cy3 or Cy5.

growth_protocol: Chemostat cultures were maintained for 250 generations using Sixfors fermentors (Infors) at 30°C, constantly stirred at 400 rpm in aerobic conditions and diluted at a rate of 0.12 hr-1 (population doubling time 5.8 hr).

extract_protocol: mRNA from evolved clones and the ancestor (FY4) was prepared using hot acid phenol exatraction followed by purification using a QIAGEN RNeasy mini kit

treatment_protocol: All nitrogen-limiting media contained 800µM nitrogen regardless of the molecular form of the nitrogen and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins

value: allantoin

source_name: Ancestor (FY4) in ammonium limited media

value: ammonium


title: allantoin limited clone3 in allantoin limited media vs FY4 in ammonium limited media

description: Evolved clone3 in allantoin limited media vs Ancestor (FY4) strain ammonium limited media


title: allantoin limited clone1 in allantoin limited media vs FY4 in ammonium limited media

description: Evolved clone1 in allantoin limited media vs Ancestor (FY4) strain ammonium limited media


title: urea limited clone1 in urea limited media vs FY4 in ammonium limited media

description: Evolved clone1 in urea limited media vs Ancestor (FY4) strain ammonium limited media

source_name: Evolved clone1 in urea limited media

value: urea


title: NOK, replicate 2

description: miRNA expression data normal oral keratinocytes

source_name: normal oral keratinocyte primary culture


title: Sample 10 DAY

description: 10 DAY B.napus inoculated with Plasmodiophora brassicae

source_name: 10 DAY B.napus (Plasmodiophora brassicae)


title: proline limited clone2 in proline limited media vs FY4 in ammonium limited media

description: Evolved clone2 in proline limited media vs Ancestor (FY4) strain ammonium limited media

source_name: Evolved clone2 in proline limited media

value: proline


title: glutamate limited clone1 in glutamate limited media vs FY4 in ammonium limited media

description: Evolved clone1 in glutamate limited media vs Ancestor (FY4) strain ammonium limited media

value: glutamate


title: Control 10 DAY

description: 10 DAY B.napus plants serves as control

source_name: 10 DAY B.napus (Uninoculated)


title: NOK, replicate 1

value: normal oral keratinocyte primary culture


title: proline limited clone1 in proline limited media vs FY4 in ammonium limited media

description: Evolved clone1 in proline limited media vs Ancestor (FY4) strain ammonium limited media

source_name: Evolved clone1 in proline limited media


title: 7970042

city: New Orleans

first: Reza

last: Izadpanah

state: Louisiana

address: 1430 Tulane Avenue

department: Heart and Vascular Institute

institute: Tulane University

hyb_protocol: Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification was done using ImaGene software version 9.0 (BioDiscovery, Los Angeles, MA). Normalization was performed using the calibration oligos

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: 2 µg of respective total RNA as well as 2 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

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

tag: sample type

value: syntethic miRNA pool of 950 miRNA sequences from human, mouse, rat, and virus

source_name: MDA-MB 231

value: MDA-MB 231


title: glutamine limited clone3 in glutamine limited media vs FY4 in ammonium limited media

description: Evolved clone3 in glutamine limited media vs Ancestor (FY4) strain ammonium limited media

value: glutamine


title: 7970041


title: glutamine limited clone2 in glutamine limited media vs FY4 in ammonium limited media

description: Evolved clone2 in glutamine limited media vs Ancestor (FY4) strain ammonium limited media


title: nasal mucosa_4week after last OVA challenge_rep3

city: Beijing

first: wang

last: min

state: Beijing

address: No. 17, HouGouHuTong, DongCheng District

country: China

institute: Beijing Institute of Otolaryngology

description: Gene expression data from mouse nasal mucusa_4week after last OVA challenge

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

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: nasal mucosa,4week after last OVA challenge

label_protocol: cRNA was generated using a WT Expression Kit (Ambion; Austin, TX) and labeled using a GeneChip WT Terminal Labeling Kit (Affymetrix; Santa Clara, CA)

growth_protocol: The animals were housed in horizontal laminar flow cabinets and provided sterile food and water in a specific pathogen-free facility.

extract_protocol: Total RNA was isolated from nasal mucosa of mice using the RNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol: (a) control group mice sensitized and challenged with saline; (b) OVA group mice sensitized and challenged with ovalbumin (OVA) and sacrificed 2 hours after the last challenge; (c) 4w-after group mice sensitized and challenged with OVA and sacrificed 4 weeks after the last challenge.

value: nasal mucosa

tag: treatment

value: 4week after last OVA challenge

tag: gender

value: Male

tag: strain

value: BALB/c

tag: age


title: nasal mucosa_4week after last OVA challenge_rep2


title: glutamine limited clone1 in glutamine limited media vs FY4 in ammonium limited media

description: Evolved clone1 in glutamine limited media vs Ancestor (FY4) strain ammonium limited media


title: nasal mucosa_4week after last OVA challenge_rep1


title: 7970040


title: 7970039


title: arginine limited clone1 in arginine limited media vs FY4 in ammonium limited media

description: Evolved clone1 in arginine limited media vs Ancestor (FY4) strain ammonium limited media

value: arginine


title: nasal mucosa_OVA_rep3

description: Gene expression data from mouse nasal mucusa_OVA sensitized and challenged with OVA

source_name: nasal mucosa,OVA,sensitized and challenged with OVA

value: OVA, sensitized and challenged with OVA


title: nasal mucosa_OVA_rep2


title: nasal mucosa_OVA_rep1


title: ammonium limited clone1 in ammonium limited media vs FY4 in ammonium limited media

description: Evolved clone1 in ammonium limited media vs Ancestor (FY4) strain in ammonium limited media


title: nasal mucosa_control_rep3

description: Gene expression data from mouse nasal mucusa_control sensitized and challenged with saline

source_name: nasal mucosa,control,sensitized and challenged with saline

value: control, sensitized and challenged with saline


title: arginine limited clone2 in arginine limited media vs FY4 in ammonium limited media

description: Evolved clone2 in arginine limited media vs Ancestor (FY4) strain ammonium limited media


title: AIMAH Patient 22 Nodule

type: genomic

city: PARIS

first: Guillaume

last: Assié

address: 24 rue du Fg Saint Jacques

department: Endocrinology Metabolism Cancer

country: France

institute: Institut Cochin

description: Hybridized to SNP6

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not.
primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs)

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: AIMAH nodules DNA was extracted with Qiagen QIAamp MinElute. Leucocyte DNA was extracted with the Roche DNA isolation kit for mammalian blood. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

value: AIMAH nodule

tag: patient

value: Patient 22


title: ammonium limited clone2 in ammonium limited media vs FY4 in ammonium limited media

description: Evolved clone2 in ammonium limited media vs Ancestor (FY4) strain in ammonium limited media

value: ammonium


title: AIMAH Patient 27 Leucocyte

description: Hybridized to SNP6

value: Leucocyte

value: Patient 27


title: nasal mucosa_control_rep2


title: AIMAH Patient 44 Nodule 1

description: Hybridized to SNP6

value: Patient 44


title: AIMAH Patient 24 Nodule

description: Hybridized to SNP6

value: Patient 24


title: AIMAH Patient 23 Nodule

description: Hybridized to SNP6

value: Patient 23


title: nasal mucosa_control_rep1


title: AIMAH Patient 44 Leucocyte

description: Hybridized to SNP6


title: AIMAH Patient 44 Nodule 2

description: Hybridized to SNP6


title: AIMAH Patient 21 Nodule

description: Hybridized to SNP6

value: Patient 21


title: AIMAH Patient 25 Nodule

description: Hybridized to SNP6

value: Patient 25


title: gln-pro limited clone1

description: Evolved clone1 in gln-pro limited media vs Ancestor (FY4) strain

hyb_protocol: Array Comparative Genomic Hybridization (aCGH) was performed using Agilent 60mer DNA microarrays.  Hybridization reactions were performed at 65C for 17 hours after which microarrays were washed using the standard Agilent wash protocol.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B

data_processing: DNA microarrays were analyzed using Agilent Feature Extractor.  Data were normalized using a linear-loess normalization.

source_name: Evolved clone1 in gln-pro limited media

label_protocol: Sonicated DNA from each evolved clone or population was labeled with Cy3 and DNA from the ancestral strain was labeled with Cy5 using random hexamers and Klenow-mediated incorporation of label

extract_protocol: Genomic DNA (gDNA) from evolved clones and entire populations was prepared using the QIAGEN genomic DNA extraction kit

value: 250 generation

source_name: FY4 ancestor

value: 0 generataions


title: gln-pro limited clone3

description: Evolved clone3 in gln-pro limited media vs Ancestor (FY4) strain

source_name: Evolved clone3 in gln-pro limited media


title: AIMAH Patient 20 Nodule

description: Hybridized to SNP6

value: Patient 20


title: AIMAH Patient 16 Nodule

description: Hybridized to SNP6

value: Patient 16


title: AIMAH Patient 26 Nodule

description: Hybridized to SNP6

value: Patient 26


title: AIMAH Patient 44 Nodule 3

description: Hybridized to SNP6


title: gln-pro-alla limited clone2

description: Evolved clone2 in gln-pro-alla limited media vs Ancestor (FY4) strain


title: gln-pro-alla limited clone3

description: Evolved clone3 in gln-pro-alla limited media vs Ancestor (FY4) strain


title: AIMAH Patient 16 Leucocyte

description: Hybridized to SNP6


title: AIMAH Patient 15 Leucocyte

description: Hybridized to SNP6

value: Patient 15


title: AIMAH Patient 17 Leucocyte

description: Hybridized to SNP6

value: Patient 17


title: AIMAH Patient 15 Nodule

description: Hybridized to SNP6

value: AIMAH nodule


title: AIMAH Patient 17 Nodule 2

description: Hybridized to SNP6


title: AIMAH Patient 27 Nodule

description: Hybridized to SNP6


title: gln-pro-alla limited clone1

description: Evolved clone1 in gln-pro-alla limited media vs Ancestor (FY4) strain


title: AIMAH Patient 13 Nodule

description: Hybridized to SNP6

value: Patient 13


title: gln-pro limited clone2

description: Evolved clone2 in gln-pro limited media vs Ancestor (FY4) strain

source_name: Evolved clone2 in gln-pro limited media


title: gln-pro limited population

description: Evolved population in gln-pro limited media vs Ancestor (FY4) strain


title: AIMAH Patient 14 Nodule

description: Hybridized to SNP6

value: Patient 14


title: gln-pro-alla limited population

description: Evolved population in gln-pro-alla limited media vs Ancestor (FY4) strain


title: gln-alla limited clone3

description: Evolved clone3 in gln-alla limited media vs Ancestor (FY4) strain


title: gln-pro-alla-urea limited clone1

description: Evolved clone1 in gln-pro-alla-urea limited media vs Ancestor (FY4) strain


title: AIMAH Patient 17 Nodule 1

description: Hybridized to SNP6


title: gln-pro-alla-urea limited population

description: Evolved population in gln-pro-alla-urea limited media vs Ancestor (FY4) strain


title: gln-alla limited population

description: Evolved population in gln-alla limited media vs Ancestor (FY4) strain


title: non-CF subject 41

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University, Heidelberg, Germany

description: experimental design: Collect rectal mucosal epithelia by suction biopsy from CF-patients, homocygous for the CFTR D508 mutation and from non CF-individuals; monitor activity of mucosal epithelia by ICM; analysis of gene expression profiles.

hyb_protocol: The Human GeneChip HG-U133A was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite version 5.0.

scan_protocol: standard Affymetrix protocol

data_processing: Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data were normalized using a rank based normalization algorithm (rank mean) in MatLab.

source_name: rectal suction specimens

label_protocol: Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT-T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo).  For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).

extract_protocol: Total RNA was extracted from rectal suction biopsies of CF patients and non-CF individuals using the RNAeasy mini kit (Qiagen, Hilden, D). Quality of total RNA was monitored by gel electorphoresis.

value: rectal mucosal epithelia

tag: genotype

value: non-CF


title: gln-alla limited clone1

description: Evolved clone1 in gln-alla limited media vs Ancestor (FY4) strain


title: gln-alla limited clone2

description: Evolved clone2 in gln-alla limited media vs Ancestor (FY4) strain


title: non-CF subject 40


title: gln-pro-alla-urea limited clone3

description: Evolved clone3 in gln-pro-alla-urea limited media vs Ancestor (FY4) strain


title: AIMAH Patient 14 Leucocyte

description: Hybridized to SNP6

value: Leucocyte


title: AIMAH Patient 12 Nodule

description: Hybridized to SNP6

value: Patient 12


title: allantoin limited clone3

description: Evolved clone3 in allantoin limited media vs Ancestor (FY4) strain


title: allantoin limited clone1

description: Evolved clone1 in allantoin limited media vs Ancestor (FY4) strain


title: non-CF subject 39


title: non-CF subject 36


title: allantoin limited clone2

description: Evolved clone2 in allantoin limited media vs Ancestor (FY4) strain


title: non-CF subject 37


title: AIMAH Patient 12 Leucocyte

description: Hybridized to SNP6


title: gln-pro-alla-urea limited clone2

description: Evolved clone2 in gln-pro-alla-urea limited media vs Ancestor (FY4) strain


title: non-CF subject 38


title: AIMAH Patient 13 Leucocyte

description: Hybridized to SNP6


title: allantoin limited population

description: Evolved population in allantoin limited media vs Ancestor (FY4) strain


title: urea limited clone3

description: Evolved clone3 in urea limited media vs Ancestor (FY4) strain

source_name: Evolved clone3 in urea limited media


title: non-CF subject 35


title: urea limited clone2

description: Evolved clone2 in urea limited media vs Ancestor (FY4) strain

source_name: Evolved clone2 in urea limited media


title: AIMAH Patient 11 Nodule

description: Hybridized to SNP6

value: Patient 11


title: urea limited clone1

description: Evolved clone1 in urea limited media vs Ancestor (FY4) strain

source_name: Evolved clone1 in urea limited media


title: non-CF subject 33


title: non-CF subject 34


title: AIMAH Patient 10 Nodule

description: Hybridized to SNP6

value: Patient 10


title: urea limited population

description: Evolved population in urea limited media vs Ancestor (FY4) strain


title: AIMAH Patient 10 Leucocyte

description: Hybridized to SNP6


title: non-CF subject 32


title: AIMAH Patient 9 Leucocyte

description: Hybridized to SNP6

value: Patient 9


title: glutamate limited clone2

description: Evolved clone2 in glutamate limited media vs Ancestor (FY4) strain

value: 250 generation


title: glutamate limited clone3

description: Evolved clone3 in glutamate limited media vs Ancestor (FY4) strain

value: 0 generataions


title: AIMAH Patient 9 Nodule

description: Hybridized to SNP6


title: AIMAH Patient 8 Nodule

description: Hybridized to SNP6

value: Patient 8


title: non-CF subject 30


title: AIMAH Patient 8 Leucocyte

description: Hybridized to SNP6


title: non-CF subject 31


title: AIMAH Patient 7 Leucocyte

description: Hybridized to SNP6

value: Patient 7


title: AIMAH Patient 7 Nodule

description: Hybridized to SNP6


title: glutamate limited clone1

description: Evolved clone1 in glutamate limited media vs Ancestor (FY4) strain


title: AIMAH Patient 6 Nodule 4

description: Hybridized to SNP6

value: Patient 6


title: 20wk old NOD-Replicate 6

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Biological replicate of gene expression in the isolated pancreatic islets of individual 20 week old NOD mice vs. a pool of age-matched NOD.B10 controls

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Data were processed using Genespring 11.5.  Samples were filtered for detected entities.

source_name: Pancreatic islets

label_protocol: 300 ng of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility.  All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.

extract_protocol: Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Micro Kit.

treatment_protocol: pancreatic islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion, and placed in Trizol Reagent.

value: 20 week old

tag: Sex

value: female

value: NOD/LtJ (NOD)

source_name: Pancreatic Islets (pool of 6 age-matched NOD.B10 mice)

value: Female

value: NOD.B10Sn-H2b/J  (NOD.B10)


title: AIMAH Patient 6 Nodule 3

description: Hybridized to SNP6

value: AIMAH nodule


title: AIMAH Patient 6 Nodule 1

description: Hybridized to SNP6


title: 20wk old NOD-Replicate 5


title: glutamate limited population

description: Evolved population in glutamate limited media vs Ancestor (FY4) strain


title: 20wk old NOD-Replicate 4


title: proline limited clone2

description: Evolved clone2 in proline limited media vs Ancestor (FY4) strain

source_name: Evolved clone2 in proline limited media


title: proline limited population

description: Evolved population in proline limited media vs Ancestor (FY4) strain


title: AIMAH Patient 6 Leucocyte

description: Hybridized to SNP6


title: CF (D508) subject14

description: experimental design: Collect rectal mucosal epithelia by suction biopsy from CF-patients, homocygous for the CFTR D508 mutation and from non CF-individuals; monitor activity of mucosal epithelia by ICM; analysis of gene expression profiles.

value: rectal mucosal epithelia

value: CFTR D508


title: 20wk old NOD-Replicate 3


title: CF (D508) subject16


title: AIMAH Patient 3 Nodule

description: Hybridized to SNP6

value: Patient 3


title: CF (D508) subject13


title: glutamine limited clone3

description: Evolved clone3 in glutamine limited media vs Ancestor (FY4) strain


title: CF (D508) subject11


title: CF (D508) subject12


title: AIMAH Patient 4 Leucocyte

description: Hybridized to SNP6

value: Leucocyte

value: Patient 4


title: 20wk old NOD-Replicate 1


title: 20wk old NOD-Replicate 2


title: glutamine limited clone2

description: Evolved clone2 in glutamine limited media vs Ancestor (FY4) strain


title: kaiCEE at LL96

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

description: Gene expression data from Synechococcus elongatus PCC 7942

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings to obtain raw data.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: kaiCEE mutant cells_continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (40 micromol/m^2/sec)

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: genotype/variation

value: kaiCEE strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

tag: collection time point

value: 96h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: AIMAH Patient 5 Nodule

description: Hybridized to SNP6

value: Patient 5


title: CF (D508) subject10


title: kaiCEE at LL88

value: 88h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: glutamine limited clone1

description: Evolved clone1 in glutamine limited media vs Ancestor (FY4) strain

value: 250 generation

value: 0 generataions


title: 12wk old NOD-Replicate 6

description: Biological replicate of gene expression in the isolated pancreatic islets of individual 12 week old NOD mice vs. a pool of age-matched NOD.B10 controls

value: 12 week old


title: AIMAH Patient 4 Nodule

description: Hybridized to SNP6


title: kaiCEE at LL80

value: 80h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: CF (D508) subject9


title: glutamine limited population

description: Evolved population in glutamine limited media vs Ancestor (FY4) strain


title: 12wk old NOD-Replicate 5

value: female

value: NOD/LtJ (NOD)


title: AIMAH Patient 3 Leucocyte

description: Hybridized to SNP6


title: kaiCEE at LL72

value: 72h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: CF (D508) subject8


title: proline limited clone1

description: Evolved clone1 in proline limited media vs Ancestor (FY4) strain

source_name: Evolved clone1 in proline limited media


title: AIMAH Patient 2 Nodule 2

description: Hybridized to SNP6

value: AIMAH nodule

value: Patient 2


title: kaiCEE at LL64

value: 64h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: kaiCEE at LL56

value: 56h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: CF (D508) subject7

value: rectal mucosal epithelia

value: CFTR D508


title: arginine limited clone3

description: Evolved clone3 in arginine limited media vs Ancestor (FY4) strain


title: arginine limited clone2

description: Evolved clone2 in arginine limited media vs Ancestor (FY4) strain


title: arginine limited clone1

description: Evolved clone1 in arginine limited media vs Ancestor (FY4) strain


title: kaiCEE at LL48

value: kaiCEE strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 48h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: 12wk old NOD-Replicate 2

value: Female

value: NOD.B10Sn-H2b/J  (NOD.B10)


title: 12wk old NOD-Replicate 1


title: CF (D508) subject15


title: AIMAH Patient 2 Nodule 3

description: Hybridized to SNP6


title: AIMAH Patient 6 Nodule 2

description: Hybridized to SNP6

value: Patient 6


title: AIMAH Patient 2 Nodule 1

description: Hybridized to SNP6


title: arginine limited population

description: Evolved population in arginine limited media vs Ancestor (FY4) strain

value: 250 generation

value: 0 generataions


title: AIMAH Patient 11 Leucocyte

description: Hybridized to SNP6

value: Leucocyte

value: Patient 11


title: 4wk old NOD-Replicate 6

description: Biological replicate of gene expression in the isolated pancreatic islets of individual 4 week old NOD mice vs. a pool of age-matched NOD.B10 controls

value: 4 week old

value: female

value: NOD/LtJ (NOD)


title: kaiCEE at LL32

value: 32h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: ammonium limited clone2

description: Evolved clone2 in ammonium limited media vs Ancestor (FY4) strain


title: ammonium limited clone3

description: Evolved clone3 in ammonium limited media vs Ancestor (FY4) strain


title: CF (D508) subject3


title: CF (D508) subject4


title: CF (D508) subject5


title: kaiCEE at LL24

value: 24h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: kaiCEE at LL16

value: 16h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: AIMAH Patient 1 Nodule

description: Hybridized to SNP6

value: AIMAH nodule

value: Patient 1


title: CF (D508) subject2

value: rectal mucosal epithelia

value: CFTR D508


title: BS_KS400_2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description:
Bacillus subtilis KS400
gFG_527538A11

hyb_protocol: Each hybridization mixture was made up from 1.1 µg test (Cy3) and 1.1 µg reference (Cy5) sample.  Samples were dried and 1.98 µl of the appropriate sample tracking control (STC, Roche Nimblegen) was added. The hybridization cocktail was prepared according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen) and 5.22 µl was added to each sample. The samples were incubated for 5 min at 95°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto a XXXXXXXXXXX microarray (Design ………… EXP HX12). Microarrays were hybridized for 20 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: Afterwards, the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies).

data_processing: Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

organism: Bacillus subtilis

source_name: Bacillus subtilis KS400

label_protocol: For each sample, 5 µg total RNA was combined with 1 µg random octamers (Biolegio) in a total volume of 4.5 µl, heat-denatured at 65°C for 10 min and immediately transferred to ice-water for 10 min. Subsequently, 10 µl of a first-strand mastermix was added containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test sample) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, RNA was hydrolyzed by adding 1.5 µl 2.5 M NaOH and incubating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 8 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled with Cy5 as described above.

growth_protocol: Bacterial cultures were grown at 30ºC or 37ºC in liquid LB medium, or on solid nutrient agar (Oxoid).

extract_protocol: Cell pellets were flash frozen in liquid nitrogen immediately after harvesting and stored at -80°C prior to RNA extraction. Frozen pellets were ground using a mortar and pestle before immersion in 300 μl Qiazol reagent (Qiagen). RNA was isolated using the manufacturer’s Qiazol protocol, with the exception that the RNA-containing water phase was further purified using the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek), including an on-column treatment with the RNase-free DNase set (Life Technologies) to remove DNA contamination. The amount of RNA was measured on a NanoDrop ND-1000 (Thermo Scientific). RNA integrity was measured with a BioAnalyzer (Agilent Technolgies) using the RNA nano 6000 kit (Agilent Technologies) yielding RIN-values ≥ 9.7.

treatment_protocol: DNA manipulations were carried by standard techniques, chromosomal DNA was purified using a phenol chloroform extraction. Transformations of cells were carried out as described previously {Inoue, 1990 #1033;Anagnostopoulos, 1961 #1416;Hamoen, 2002 #1417}, and plated on nutrient agar supplemented with ampicillin (100 ug/ml), chloramphenicol (5 ug/ml), erythromycin (1 ug/ml), glucose (0.4 0.8%), kanamycin (5 ug/ml), spectinomycin (50 ug/ml), tetracycline (12 ug/ml), X gal (160 mg/ml), IPTG (0.5 1 mM), xylose (0.025 1 %).


title: AIMAH Patient 2 Leucocyte

description: Hybridized to SNP6

value: Patient 2


title: 4wk old NOD-Replicate 4

value: Female

value: NOD.B10Sn-H2b/J  (NOD.B10)


title: CF (D508) subject1


title: kaiCEE at LL8

value: kaiCEE strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 8h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: ammonium limited clone1

description: Evolved clone1 in ammonium limited media vs Ancestor (FY4) strain

value: 250 generation

value: 0 generataions


title: 4wk old NOD-Replicate 5

value: 4 week old


title: 4wk old NOD-Replicate 3

value: female


title: non-CF subject 29

value: non-CF


title: FY4 in allantoin limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in allantoin limited media vs Ancestor (FY4) strain ammonium limited media

value: allantoin

source_name: Ancestor (FY4) in ammonium limited media

value: ammonium


title: 12wk old NOD-Replicate 3

value: 12 week old

value: NOD/LtJ (NOD)


title: 4wk old NOD-Replicate 1


title: 4wk old NOD-Replicate 2


title: ammonium limited population

description: Evolved population in ammonium limited media vs Ancestor (FY4) strain


title: FY4 in urea limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in urea limited media vs Ancestor (FY4) strain ammonium limited media

source_name: Ancestor (FY4) in urea limited media

value: urea


title: BS_KS696_2

description:
Bacillus subtilis KS696
gFG_527538A09

source_name: Bacillus subtilis KS696


title: CF (D508) subject6

description: experimental design: Collect rectal mucosal epithelia by suction biopsy from CF-patients, homocygous for the CFTR D508 mutation and from non CF-individuals; monitor activity of mucosal epithelia by ICM; analysis of gene expression profiles.

value: rectal mucosal epithelia


title: AIMAH Patient 1 Leucocyte

description: Hybridized to SNP6

value: Leucocyte

value: Patient 1


title: BS_WT_3

description:
Bacillus subtilis wild type
gFG_527538A10

source_name: Bacillus subtilis WT

value: WT


title: WWOX–silenced subline B, replicate 2

city: Smithville

first: C. Marcelo

last: Aldaz

address: POB 389

department: Molecular Carcinogenesis

institute: The University of TX M.D. Anderson Cancer Center

description: Biological replicate 2 of 3, WWOX–silenced subline B.

hyb_protocol: The hybridization steps were carried out according to the Agilent protocol.

scan_protocol: Scanned on a Genepix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

data_processing:
Image analysis and initial quality control were performed using Agilent Feature Extraction Software v10.2.
We used the limma Bioconductor package for background adjustment (normexp method), within (Loess algorithm) and between (quantiles method) arrays normalization.

source_name: MCF10 shWWOX-B

label_protocol: 2 µg of total RNA from each of WWOX–silenced sublines labeled with Cy5 were individually hybridized on Agilent Whole Human Genome 4X44K microarrays to analyze ~40000 transcripts (Agilent Technologies, Palo Alto, CA, USA) using the RNA derived from the corresponding MCF10 Scr sample (labeled with Cy3) as reference. For RNA labeling, we used the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) by following the manufacturer's protocol.

growth_protocol: MCF10 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum, 100 μg/mL hydrocortisone, 10 μg/mL insulin, 20 ng/mL EGF, 1 ng/mL cholera toxin and 1% penicillin-streptomycin.

extract_protocol: Total RNA was extracted from 3 biological replicates each of MCF10 Scr, MCF10 shWWOX-A and MCF10 shWWOX-B using the RNeasy Mini kit (Qiagen).

treatment_protocol: Cells were infected with the following shRNA-expressing GIPZ lentiviruses (Open Biosystems) at an MOI of 5:  Scrambled control shRNA (#RHS4348), shWWOX-A (#V2LHS_255213 ) or shWWOX-B (#V2LHS_255229).  Co-infection of shWWOX-A and shWWOX-B was indicated as “shWWOX”. Cells were infected according to manufacturer’s instructions. Cells were selected for three days with 2 μg/ml puromycin and WWOX protein level was assayed by western blot.

value: MCF10F mammary epithelial cells

value: WWOX–silenced subline B

source_name: MCF10 scrambled control shRNA

value: scrambled control shRNA


title: WWOX–silenced subline B, replicate 3

description: Biological replicate 3 of 3, WWOX–silenced subline B.


title: 10 day old NOD-Replicate 6

description: Biological replicate of gene expression in the isolated pancreatic islets of individual 10 day old NOD mice vs. a pool of age-matched NOD.B10 controls

value: 10 day old

value: Female

value: NOD.B10Sn-H2b/J  (NOD.B10)


title: BS_WT_2

description:
Bacillus subtilis wild type
gFG_527538A08


title: BS_KS696_1

description:
Bacillus subtilis KS696
gFG_527538A07


title: urea limited clone3 in urea limited media vs FY4 in ammonium limited media

description: Evolved clone3 in urea limited media vs Ancestor (FY4) strain ammonium limited media


title: 10 day old NOD-Replicate 5

value: female


title: FY4 in glutamate limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in glutamate limited media vs Ancestor (FY4) strain ammonium limited media

value: glutamate


title: BS_WT_1

description:
Bacillus subtilis wild type
gFG_527538A06


title: WWOX–silenced subline B, replicate 1

description: Biological replicate 1 of 3, WWOX–silenced subline B.


title: FY4 in proline limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in proline limited media vs Ancestor (FY4) strain ammonium limited media

source_name: Ancestor (FY4) in proline limited media

value: proline


title: BS_KS400_1

description:
Bacillus subtilis KS400
gFG_527538A05


title: WWOX–silenced subline A, replicate 3

description: Biological replicate 3 of 3, WWOX–silenced subline A.

source_name: MCF10 shWWOX-A

value: WWOX–silenced subline A


title: 10 day old NOD-Replicate 4


title: FY4 in arginine limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in arginine limited media vs Ancestor (FY4) strain ammonium limited media

value: arginine

value: ammonium


title: FY4 in glutamine limited media vs FY4 in ammonium limited media

description: Ancestor (FY4) in glutamine limited media vs Ancestor (FY4) strain ammonium limited media

value: glutamine


title: 10 day old NOD-Replicate 2

value: NOD/LtJ (NOD)


title: 10 day old NOD-Replicate 3


title: urea limited clone2 in urea limited media vs FY4 in ammonium limited media

description: Evolved clone2 in urea limited media vs Ancestor (FY4) strain ammonium limited media

value: urea


title: 10 day old NOD-Replicate 1


title: WWOX–silenced subline A, replicate 2

description: Biological replicate 2 of 3, WWOX–silenced subline A.


title: WWOX–silenced subline A, replicate 1

description: Biological replicate 1 of 3, WWOX–silenced subline A.


title: 12wk old NOD-Replicate 4

description: Biological replicate of gene expression in the isolated pancreatic islets of individual 12 week old NOD mice vs. a pool of age-matched NOD.B10 controls

value: 12 week old


title: kaiCEE at LL40

description: Gene expression data from Synechococcus elongatus PCC 7942

value: kaiCEE strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 40h under continuous light (LL) under two 12-h:12-h light/dark cycles from a continuous culture


title: 3weeks injury + treadmill, biological rep 3

status: Public on Nov 27 2013

city: Suwon

first: Hae young

last: Shin

address: Wonchoen dong

department: Brain disease research center

country: South Korea

institute: Hae young Shin

description:
3W injury + TM(10F06)
Gene expression data from 3weeks injury after spinal cord injury with treadmill training

hyb_protocol: Fragmentation was checked on Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies) and hybridized to the arrays containing over 22,500 probe sets.

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

data_processing: The data were analyzed with Affymetrix's Expression Console software v.1.0 (GC-RMA).

label: biotinylated-psudoURidine

organism: Rattus norvegicus

source_name: lumbar spinal cord_3weeks injury only + treadmill

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

growth_protocol: Adult (8weeks) female Sprague-Dawley rats (250-300g) were used.

extract_protocol: Total RNA was isolated using an Rneasy Microarray Tissue Mini kit (Qiagen) in accordance with the manufacturer's instructions.

value: Sprague-Dawley

value: 8 weeks (adult)

value: lumbar spinal cord

tag: time point

value: 3 wks after contusive spinal cord injury with treadmill training


title: sham + treadmill, biological rep 3

description:
sham + TM(10F10)
Gene expression data from sham sample with only laminectomy and 2weeks treadmill training

source_name: lumbar spinal cord_sham + treadmill

value: laminectomy (sham) and 2 wks of treadmill training


title: 3weeks injury + treadmill, biological rep 2

description:
3W injury + TM(10F02)
Gene expression data from 3weeks injury after spinal cord injury with treadmill training

value: female


title: 3weeks injury + treadmill, biological rep 4

description:
3W injury + TM(10F07)
Gene expression data from 3weeks injury after spinal cord injury with treadmill training


title: 1week injury only, biological rep 3

description:
1W injury only(10J7)
Gene expression data from 1week injury after spinal cord injury

source_name: lumbar spinal cord_1week injury only

value: 1 wk after contusive spinal cord injury


title: 3weeks injury + treadmill, biological rep 1

description:
3W injury + TM(10F01)
Gene expression data from 3weeks injury after spinal cord injury with treadmill training


title: Fractured Day 6 αSMA-labeled cells rep3

city: Grafton

first: Brya

last: Matthews

state: Auckland

address: 85 Park Rd

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

description: Dissected tissue was digested in PBS containing 0.125% trypsin, 0.1% collagenase A, 0.1% hyaluronadase for 1 h at 37°C with agitation prior to cell sorting. Mice were given 2 doses of tamoxifen, 75ug/g, fractures were performed, then mice were sacrificed six days later.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: Tibial periosteum/soft callus cells from Day 6 fracture after digestion and cell sorting

label_protocol: RNA was amplified and biotinylated using the Ambion MessageAmp Premier RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent according to the manufacturer's instructions

treatment_protocol: Mice were given 2 doses of tamoxifen (75ug/g) on 2 consecutive days before fracture, or 2 days before collection of control samples.

value: Female

value: 4-5.5 months

tag: n animals


title: 3weeks injury only, biological rep 1

description:
3W injury only(10F03)
Gene expression data from 3weeks injury after spinal cord injury

source_name: lumbar spinal cord_3weeks injury only

value: 3 wks after contusive spinal cord injury


title: 1week injury only, biological rep 4

description:
1W injury only(10J8)
Gene expression data from 1week injury after spinal cord injury


title: 3weeks injury only, biological rep 4

description:
3W injury only(10J2)
Gene expression data from 3weeks injury after spinal cord injury


title: sham + treadmill, biological rep 2

description:
sham + TM(10F09)
Gene expression data from sham sample with only laminectomy and 2weeks treadmill training


title: sham + treadmill, biological rep 1

description:
sham + TM(10F08)
Gene expression data from sham sample with only laminectomy and 2weeks treadmill training


title: 1week injury only, biological rep 2

description:
1W injury only(10G02)
Gene expression data from 1week injury after spinal cord injury


title: Fractured Day 2 αSMA-labeled cells rep3

description: Dissected tissue was digested in PBS containing 0.125% trypsin, 0.1% collagenase A, 0.1% hyaluronadase for 1 h at 37°C with agitation prior to cell sorting. Mice were given 2 doses of tamoxifen, 75ug/g, fractures were performed, then mice were sacrificed two days later.

source_name: Tibial periosteum cells from Day 2 fracture after digestion and cell sorting

value: 4-5 months


title: Kn_DamID_3

city: Kyoto

first: Yukako

last: Hattori

address: Sakyo-ku

department: Graduate School of Biostudies

institute: Kyoto University

hyb_protocol: Hybridisation performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Scanning performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP-Chip data extraction.

organism: Drosophila melanogaster

source_name: DamID processed gDNA from UAS-Dam-Kn embryos

label_protocol: Labelling performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Embryos developed at 25oC.

extract_protocol: gDNA was extracted from embryos using the Qiagen DNeasy kit, 2.5ug of gDNA was precipitated and then digested with DpnI O/N. DpnI-digested DNA was ligated to an adaptor and then digested with DpnII. DpnII-digested DNA was PCR amplified and purified using a Qiagen PCR purification kit.

treatment_protocol: gDNA was extracted from embryos, DpnI digested and amplified using LM-PCR.

value: UAS-Dam-Kn

value: whole embryo

tag: developmental stage

value: embryo stage 17 (17-20 h AEL)

source_name: DamID processed gDNA from UAS-Dam embryos

value: UAS-Dam


title: 3weeks injury only, biological rep 2

description:
3W injury only(10F04)
Gene expression data from 3weeks injury after spinal cord injury


title: Fractured Day 6 αSMA-labeled cells rep2

value: Male

value: 3-5 months


title: Fractured Day 6 αSMA-labeled cells rep1

value: 4 months


title: 1week injury only, biological rep 1

description:
1W injury only(10G01)
Gene expression data from 1week injury after spinal cord injury

value: Sprague-Dawley

value: 8 weeks (adult)


title: 3weeks injury only, biological rep 3

description:
3W injury only(10J1)
Gene expression data from 3weeks injury after spinal cord injury

value: lumbar spinal cord


title: Ab_DamID_1

source_name: DamID processed gDNA from UAS-Dam-Ab embryos

value: UAS-Dam-Ab


title: 1week sham, biological rep 3

description:
1W sham(10G06)
Gene expression data from sham sample with only laminectomy

source_name: lumbar spinal cord_sham

value: female

value: 1 wk after laminectomy (sham)


title: 1week sham, biological rep 2

description:
1W sham(10G05)
Gene expression data from sham sample with only laminectomy


title: Fractured Day 2 αSMA-labeled cells rep2


title: Kn_DamID_4


title: Ab_DamID_2


title: Kn_DamID_2


title: Ab_DamID_3


title: Kn_DamID_1


title: Ab_DamID_4


title: Unfractured Day 2 αSMA-labeled cells rep1

description: Dissected tissue was digested in PBS containing 0.125% trypsin, 0.1% collagenase A, 0.1% hyaluronadase for 1 h at 37°C with agitation prior to cell sorting. Mice were given 2 doses of tamoxifen, 75ug/g, then sacrificed two days later.

source_name: Tibial periosteum cells after digestion and cell sorting


title: Fractured Day 2 αSMA-labeled cells rep1

value: 2-5 months


title: R48 cells, technical replicate 3

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for normalization, BRB Array Tools for statistical analysis

source_name: Kasumi-1 cells, dasatinib-treated for 12 weeks

growth_protocol: Kasumi-1 cells were grown at 0.5 x 10^6 cells/ml Gibco RPMI 1640 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 20% fetal calf serum in a humidified incubator at 37°C with 5% CO2 atmosphere.

extract_protocol: Extraction of total mRNA was performed using Trizol (Invitrogen) according to manufacturer's intructions.

treatment_protocol: R48 cells were derived from Kasumi-1 (K) cells by continuiously co-culture with dasatinib for 12 weeks. Treatment was initiated at 12 nM for 4 weeks and subsequently increased to 24 nM and 48 nM after 4 weeks, respectively. PR48 cells were derived from R48 cells by withdrawal of dasatinib and cessation of treatment for 1 week.


title: R48 cells, technical replicate 2

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: PR48 cells, technical replicate 1

source_name: Kasumi-1 cells, dasatinib-treated for 12 weeks, treatment discontinued for 1 week


title: PR48 cells, technical replicate 2


title: Unfractured Day 2 αSMA-labeled cells rep2

value: Female


title: 1week sham, biological rep 1

description:
1W sham(10G04)
Gene expression data from sham sample with only laminectomy


title: Unfractured Day 2 αSMA-labeled cells rep3


title: K cells, technical replicate 1

source_name: Kasumi-1 cells, left untreated


title: K cells, technical replicate 2


title: KA45 vs CD41SP

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: ES cells were indeuced to differentiate on the OP9 stromal cell line

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

treatment_protocol: Samples were FACS-sorted on day 5 (CD41SP) or day 7 (KA45) of differenation


title: R48 cells, technical replicate 1


title: Bone marrow 12h after phlebotomy 154397

city: Los Angeles

first: Léon

last: Kautz

department: Medicine/Pulmonary and critical care

institute: UCLA

hyb_protocol: Samples were hybridized with GeneChip® Mouse Gene 1.0 ST Array and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). Raw data were processed using Affymetrix Expression Console™ Software

data_processing: RMA

source_name: Bone marrow 12h after phlebotomy

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Six week-old C57BL/6 male mice were maintained on a standard chow. 500μL of blood was withdrawn by retro-orbital puncture for the phlebotomized mice

extract_protocol: Total RNA from mouse bone marrow was extracted using Trizol (Invitrogen) and purified using RNeasy Micro kit (Qiagen)

treatment_protocol: Femurs were collected at baseline and 4h, 9h, 12h, 15h and 48 hours after phlebotomy

value: Bone marrow

tag: time

value: 6 week-old

value: male


title: Bone marrow 9h after phlebotomy 154404

source_name: Bone marrow 9h after phlebotomy


title: Bone marrow 15h after phlebotomy 154399

source_name: Bone marrow 15h after phlebotomy


title: Bone marrow 48h after phlebotomy 154400

source_name: Bone marrow 48h after phlebotomy


title: Bone marrow control 154394

source_name: Bone marrow control

value: control


title: Bone marrow 9h after phlebotomy 154935


title: Bone marrow 15h after phlebotomy 154398


title: Bone marrow 4h after phlebotomy 154395

source_name: Bone marrow 4h after phlebotomy


title: Bone marrow 9h after phlebotomy 154934


title: Bone marrow control 154393


title: K cells, technical replicate 3


title: Bone marrow 12h after phlebotomy 154396


title: Bone marrow control 154933


title: Bone marrow 48h after phlebotomy 154401


title: Oocyte-XX_Zfy2-rep3

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

description:
Replicate 3
5665141081_C

data_processing: Data were normalized using Illumina GenomeStudio

source_name: Mouse oocyte, single copy Zfy2 transgene

label_protocol: cDNAs were amplified using Ovation Pico WTA System 2 kit (NuGen) and biotin labeled using Encore biotinIL (NuGen).

growth_protocol: Fully grown cumulus-enclosed oocytes at germinal vesicle (GV) stage for RNA extraction were collected in M2 medium (Sigma-Aldrich) from ovaries of 4 week-old females 45 48 hours after intraperitoneal injection of PMSG (Intervet), denuded of cumulus cells using a drawn-out pasteur pipette, frozen in liquid nitrogen with a minimal volume of M2 medium, and pooled in batches of around 100 cells coming from at least 2 females per genotype.

extract_protocol: Total RNA was extracted from frozen GV oocytes with RNAqueous-Micro Kit (Ambion) according to the manufacturer's protocols.

tag: background strain

value: MF1 outbred albino from the NIMR colony

value: GV oocyte

tag: batch


title: Oocyte-XX_Zfy2+E-rep2

description:
Replicate 2
5539777024_D

source_name: Mouse oocyte, single copy Zfy2 transgene, multiple copy Eif2s3y transgene

tag: tissue


title: Oocyte-XX_Zfy2_nf-rep1

description:
Replicate 1
5539777005_C

source_name: Mouse oocyte, nonfunctional Zfy2 transgene


title: Oocyte-XX_Zfy2+E-rep3

description:
Replicate 3
5539777024_F


title: PR48 cells, technical replicate 3

tag: cell line


title: Oocyte-XX_Zfy2+E-rep1

description:
Replicate 1
5539777024_B


title: Oocyte-XX_Zfy1_lo-rep1

description:
Replicate 1
5539777005_B

source_name: Mouse oocyte, single copy Zfy1 transgene


title: Oocyte-XX_Zfy1_hi-rep3

description:
Replicate 3
5665141081_F

source_name: Mouse oocyte, high copy Zfy1 transgene


title: Oocyte-XX_WT-rep3

description:
Replicate 3
5539777005_D

source_name: Mouse oocyte, wild type

value: XX


title: Oocyte-XX_Zfy1_lo-rep2

description:
Replicate 2
5539777005_E


title: Oocyte-XX_Zfy2-rep2

description:
Replicate 2
5665141081_B


title: Oocyte-XX_Zfy1_hi-rep2

description:
Replicate 2
5665141081_E


title: MCL23-1-2 (Puromycin-resistant empty vector), technical rep2

city: Salamanca

first: Alicia

middle: Ginel

last: Picardo

state: Select a State or Province

address: Campus Miguel de Unamuno

country: Spain

institute: Cic, Salamanca

description:
28. Puromycin-resistant control_miR
miRNA Expression data from K-Raslox cells transfected with puromycin-resistant empty vector

hyb_protocol: For mRNA expression analysis, labeled cRNAs were fragmented and hybridized to the GeneChip Mouse Genome 430 2.0 (Affymetrix) using the Genechip Fluidics Station 450 (Affymetrix). Hybridized arrays were stained with streptavidin–phycoerythrin, rewashed, treated with biotinylated antistreptavidin–phycoerythrin antibodies and restained with streptavidin–phycoerythrin, according to the manufacturer’s protocols. For miRNA samples, hybridizations were performed using the GeneChip miRNA Array (Affymetrix) according to protocols from Affymetrix.

scan_protocol: The stained mRNA expression microarrays were finally scanned in a GeneArray Scanner (Hewlett Packard). For miRNA hybridizations, washing and scanning were performed using the Affymetrix GeneChip System (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The RMA function (Irizarry, Hobbs et al. 2003) provided by the package Affy from R/Bioconductor was applied to both mRNA and miRNA raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php

label: Biotin

source_name: Control MEFs transfected with puromycin-resistant empty vector (control for MEK1 construct)

label_protocol: Total RNA was reverse transcribed into double-stranded complementary DNA (cDNA) using an oligo(dT)24 primer containing a T7 polymerase promoterbinding site (Genset). cDNA was then used as a template to synthesize cRNA by in vitro transcription (Ambion T7 Megascript), with incorporation of biotinylated nucleotides (Enzo Diagnostics). For miRNA samples, 1000 ng of total RNA were labeled using the Flash Tag Biotin HSR Labeling kit (Genisphere, P/N HSR10FTA) according to the manufacturer´s instructions.

growth_protocol: Cultures of different cell lines were grown in a humidified CO2 (5%) atmosphere at 37°C, in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with fetal bovine serum (10% FBS; Hyclone, Logan, Utah, USA), glutamine (2mM), penicillin (100 U/ml) and streptomycin (100 mg/ml). Hygromycin (200μg/ml, Sigma-Aldrich) or puromycin (2μg/ml, Sigma-Aldrich) was also added as appropriate to MEF cultures expressing BRAF or MEK1, respectively.

extract_protocol: For mRNA expression analysis, total RNA was isolated using the TRIzol reagent and protocol as described by the manufacturer (Ambion, Life Technologies). RNA samples were purified using the RNeasy® Mini Kit (Qiagen) and their concentration, purity and integrity was measured in an “Agilent 2100 Bioanalyzer” (Agilent Technologies). For microRNA studies, total RNA was extracted from two 10cm culture dishes per individual sample by using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol. RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For tamoxifen induction, cultures were treated as appropriate with 4-Hydroxy-tamoxifen (4-OHT, H7904, Sigma-Aldrich) for 6 or 12 days at final concentration 0.6μM to promote the K-Ras locus disruption. Subconfluent cultures of untreated or 4-OHT-treated cell lines were used for RNA extraction.

tag: treatment

tag: cell type

value: Mouse Embryonic Fibroblasts (MEFs)

value: Inmortalized MEFs cultures


title: Oocyte-XX_Zfy2-rep1

description:
Replicate 1
5665141081_A


title: Oocyte-XX_Zfy2_nf-rep3

description:
Replicate 3
5539777024_C


title: Oocyte-XX_Zfy2_nf-rep2

description:
Replicate 2
5539777005_F


title: Oocyte-XX_Zfy1_hi-rep1

description:
Replicate 1
5665141081_D


title: Oocyte-XX_Zfy1_lo-rep3

description:
Replicate 3
5539777024_E


title: Oocyte-XX_WT-rep1

description:
Replicate 1
5539777024_A


title: MCL23-1-5 (Puromycin-resistant empty vector), technical rep1

description:
26. Puromycin-resistant control_miR
miRNA Expression data from K-Raslox cells transfected with puromycin-resistant empty vector

value: transfected with puromycin-resistant empty vector (control for MEK1 construct)


title: MCL1-6-18 (MEK1-transfected), technical rep1

description:
22. MEK1-rescued MEFs_miR
miRNA Expression data from MEK1-rescued sample: MEK1-transfected Rasless cells (rescued ability for proliferation)

source_name: Rasless cells transfected with activated MEK1 construct


title: MCL1-6-18 (MEK1-transfected), biological rep1

description:
21. MEK1-rescued MEFs_miR
miRNA Expression data from MEK1-rescued sample: MEK1-transfected Rasless cells (rescued ability for proliferation)

value: Rasless cells transfected with activated MEK1 construct


title: MCL1-6-25 (MEK1-transfected), technical rep2

description:
24. MEK1-rescued MEFs_miR
miRNA Expression data from MEK1-rescued sample: MEK1-transfected Rasless cells (rescued ability for proliferation)


title: MCL1-6-25 (MEK1-transfected), biological rep2

description:
23. MEK1-rescued MEFs_miR
miRNA Expression data from MEK1-rescued sample: MEK1-transfected Rasless cells (rescued ability for proliferation)


title: MCL23-1-2 (Puromycin-resistant empty vector), biological rep2

description:
27. Puromycin-resistant control_miR
miRNA Expression data from K-Raslox cells transfected with puromycin-resistant empty vector


title: LG7-6-9 (BRAF-transfected), biological rep2

description:
15. BRAF-rescued MEFs_miR
miRNA Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

source_name: Rasless cells transfected with activated BRAF construct


title: LG7-6-9 (BRAF-transfected), technical rep2

description:
16. BRAF-rescued MEFs_miR
miRNA Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

value: Rasless cells transfected with activated BRAF construct


title: MCL23-1-5 (Puromycin-resistant empty vector), biological rep1

description:
25. Puromycin-resistant control_miR
miRNA Expression data from K-Raslox cells transfected with puromycin-resistant empty vector


title: LG7-6-5 (BRAF-transfected), biological rep1

description:
13. BRAF-rescued MEFs_miR
miRNA Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)


title: LG7-6-5 (BRAF-transfected), technical rep1

description:
14. BRAF-rescued MEFs_miR
miRNA Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)


title: DU315-6-12d-4OHT (Rasless), technical rep1

description:
10. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)

source_name: Control cells after 12 days of 4OHT treatment becaming Rasless MEFs


title: DU244-1-12d-4OHT (Rasless), biological rep2

description:
11. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)

value: 12 days of 4OHT treatment becaming Rasless MEFs


title: DU315-6-12d-4OHT (Rasless), biological rep1

description:
09. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: DU244-1-6d-4OHT (Rasless), technical rep2

description:
08. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 6 days (non-proliferating cells)

source_name: Control cells after 6 days of 4OHT treatment becaming Rasless MEFs


title: DU244-1 (K-Raslox). biological rep2

description:
03. K-Raslox MEFs, Control_miR
miRNA Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

source_name: MEFs expressing only K-Ras (H-Ras/N-Ras double knockout); Control


title: DU244-1-6d-4OHT (Rasless), biological rep2

description:
07. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 6 days (non-proliferating cells)

value: 6 days of 4OHT treatment becaming Rasless MEFs


title: DU315-6-6d-4OHT (Rasless), technical rep1

description:
06. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 6 days (non-proliferating cells)


title: DU244-1 (K-Raslox). technical rep2

description:
04. K-Raslox MEFs, Control_miR
miRNA Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: DU315-6 (K-Raslox), technical rep1

description:
02. K-Raslox MEFs, Control_miR
miRNA Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: DU315-6-6d-4OHT (Rasless), biological rep1

description:
05. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 6 days (non-proliferating cells)


title: DU244-1-12d-4OHT (Rasless), technical rep2

description:
12. Rasless MEFs_miR
miRNA Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: Oocyte-XX_WT-rep2

description:
Replicate 2
5539777005_A


title: DU315-6 (K-Raslox), biological rep1

description:
01. K-Raslox MEFs, Control_miR
miRNA Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: Liver_female_maternal_WSD_2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

source_name: female 2-weeks old offspring_maternal Western-style high fat diet

label_protocol: 100 ng of purified RNA was used for the preparation of labelled cDNA, applying the Ambion Whole Transcript (WT) Expression kit (Life Technologies, Carlsbad, USA) in combination with the Affymetrix GeneChip WT Terminal Labelling kit (Affymetrix, Santa Clara, USA).

growth_protocol: Female C57BL/6J mice (Harlan, Horst, The Netherlands), five weeks of age, were housed  in a light- and temperature-controlled facility (lights on 7:00 a.m. to 7:00 p.m., 21 °C). The mice had free access to drinking water and were randomly assigned to either a semi-synthetic low fat control diet (LFD) based on Research Diets’ formulations D12450B or a semi-synthetic energy rich Western-style high fat diet (WSD) based on Research Diets’ formulations D12451. After 6 weeks on their respective diets (pre-treatment period), the female mice were mated with males on control diet. Throughout pregnancy and lactation, the dams received the same diets as during pre-treatment. Mice were allowed to deliver spontaneously and were left undisturbed with their litters for 24 h. Litter sizes were standardized to 5-7 pups, to ensure no litter was nutritionally biased.

extract_protocol: Total RNA was isolated from liver samples using TRIzol reagent (Invitrogen, Breda, The Netherlands), treated with DNAse, and purified on columns (RNAeasy microkit, Qiagen, Venlo, the Netherlands). RNA concentration was determined using the NanoDrop ND-1000 UV-vis spectrophotometer (Isogen, Maarsen, The Netherlands). RNA integrity was verified on an Agilent 2100 Bioanalyzer with the 6000 Nano Kit using the Eukaryote Total RNA Nano assay according to the manufacturer’s instructions (Agilent Technologies, Amsterdam, The Netherlands). Samples were considered suitable for hybridization when they showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: For 6 weeks pre-treatment, as well as during gestation and lactation, dams of offspring received either a semi-synthetic low fat control diet (LFD, 3.85 kcal/g; 10 E% fat, 20 E% protein, 70 E% carbohydrate; containing 18.0 mg cholesterol/kg from lard) that  based on Research Diets’ formulations D12450B or a semi-synthetic energy rich Western-style high fat diet  (WSD, 4.73 kcal/g; 45 E% fat, 20 E% protein, 35 E% carbohydrate; containing 196.5 mg cholesterol/kg from lard) based on Research Diets’ formulations D12451. Mating  took place with males on control diet. Mice were allowed to deliver spontaneously and were left undisturbed with their litters for 24 h. Litter sizes were standardized to 5-7 pups, to ensure no litter was nutritionally biased. Two weeks into lactation, offspring were terminated by heart puncture under isoflurane anaesthesia. Livers were dissected, snap-frozen in liquid nitrogen, and stored at -80C until RNA isolation.

tag: strain

tag: gender

value: female

value: 2 week-old offspring

value: liver

tag: sample group

value: maternal Western-style high fat diet (for 6 wks pre-treatment, during pregnancy and lactation)


title: 996-P-20min-1

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

institute: Hunan Agricultural University

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rice Genome Oligo Microarrays (015241) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, respectively), and the scan data with 100% and 10% PMT were merged automatically.

data_processing: The above hybridization signal data files in text format from the Feature Extraction Software were imported into GeneSpring GX (Agilent Technologies). The data were marked with specific flag such as P, A, M (representing detected, not detected and compromised, respectively) using the default parameter and algorithm, and then normalized by Quantile algorithm followed by the process of baseline to median of all samples. The normalized data from two replicates of each sample were log2 transformed, and the correlation coefficient of replicates was determined through hierarchical clustering using complete linkage algorithm as implemented TIGR MeV version 4.0.

organism: Oryza sativa

source_name: rice panicle, 20min after 40 degree centigrade, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by QIAGEN RNeasy Mini Kit (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Heat-tolerant rice cultivar 996 was cultivated in the field until reproductive stage

extract_protocol: The rice panicle of post-meiosis was collected at the time point of 0 min (as control), 10min, 20 min, 60min, 2 hr, respectively, after heat treatment, and frozen in liquid nitrogen immediately, and stored at -80°C for microarray hybridization.

treatment_protocol: The proper rice plants transplanted into pots were moved in a growth chamber (Binder, Tuttlingen, Germany) under the condition of 32°C with 80% humidity at day, and 28°C with 80% relative humidity at night for one day, and then at 40°C with 80% relative humidity and 600 μmol m-2 s-1 of photosynthetically active radiation for 8hr.

value: rice panicle

value: 20min after 40 degree


title: 996-P-2hr-1

source_name: rice panicle, 2hr after 40 degree centigrade, replicate 1

value: 2hr after 40 degree


title: 996-P-60min-2

source_name: rice panicle, 60min after 40 degree centigrade, replicate 2

value: 60min after 40 degree


title: 996-P-CK-2

source_name: rice panicle, 0min after 40 degree centigrade, replicate 2

value: 0min after 40 degree


title: Liver_female_maternal_WSD_6

tag: age


title: Liver_female_maternal_WSD_1


title: Liver_female_maternal_LFD_7

source_name: female 2-weeks old offspring_maternal low fat diet

value: maternal low fat diet (for 6 wks pre-treatment, during pregnancy and lactation)


title: 996-P-2hr-2

source_name: rice panicle, 2hr after 40 degree centigrade, replicate 2


title: Liver_female_maternal_WSD_5


title: Liver_female_maternal_WSD_3


title: 996-P-20min-2

source_name: rice panicle, 20min after 40 degree centigrade, replicate 2


title: 996-P-60min-1

source_name: rice panicle, 60min after 40 degree centigrade, replicate 1


title: Liver_female_maternal_WSD_4


title: Liver_female_maternal_LFD_8


title: Liver_female_maternal_LFD_6


title: TES2b vs Cell Line pool

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

institute: University of Otago, Dunedin School of Medicine

hyb_protocol: Each Cy3-labeled cRNA sample probe was co-hybridized with Cy5-labeled cRNA reference probe to Agilent 4x44K (V1) expression microarrays following Agilent protocols. Details for μg of cRNA probes co-hybridized are provided.

scan_protocol: Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). Build hg18.

data_processing: Array control features and control targets were removed. Data transformed from Log10 to Log2.

source_name: Breast cancer cell line

label_protocol: Cy3-labeled cRNA probes were generated from 250 ng of RNA from each cell line using  Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA, Catalog# 5190-2306) following manufacturer's instructions. Probe Incorporation efficiency (pmoL cy dye/μg cRNA) provided. For the reference pool, 200 ng of total RNA from each cell line was combined. 10 batches of Cy5-labeled cRNA reference pool (500 ng total RNA input each) were prepared using Agilent's Low Input Quick Amp Labeling Kit. Each batch with Cy5 incorporation efficiency >8.0 pmoL cy dye/μg cRNA was combined and aliquotted to facilitate controlled batch hybridization. Cy dye incorporation efficiency was calculated with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE) following Agilent-recommended protocols. Details for incorporation efficiency (pmoL cy dye/μg cRNA) are provided.

growth_protocol: Cell lines from ATCC and Asterand were cultured using conditions recommended by the supplier. TES cell lines were cultured in media optimized by Drs. Felding Habermann and Smider at the Scripps Research Institute, San Diego, CA. Publication pending. Refer to conference proceeding: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-07 for details of cell line development.

extract_protocol: Cell monolayers were washed onle with PBS (calcium and magnesium free) and lysed at room temperature by addition of TRIzol reagent (Invitrogen; Carlsbad, CA). Organic lysate was homogenized by manual pipetting and stored at -80oC. Total RNA was purified from 200 μl TRIzol lysate using the RNeasy micro kit (Qiagen; Valencia, CA) following manufacturer's instructions including the optional DNAse treatment step. Total RNA concentration and purity was measured using a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). Average total RNA concentration 770 ng/μl. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA). All samples had an RNA integrity # (RIN#) of 9.4 or higher (median was 9.9).

treatment_protocol: Cells were grown to exponential growth phase prior to harvesting.

tag: tumor cell line

tag: tumor type

value: Metaplastic Inflammatory carcinoma

tag: tumor source

value: local recurrence

tag: biomaterial provider

value: Dr. Felding-Habermann, Scripps Research Institute

tag: pmol cy3/μg crna

tag: μg cy3 probe hybridized

source_name: reference pool

tag: sample type

value: Pool from all cell lines (reference)

tag: pmol cy5/μg crna

tag: μg cy5 probe hybridized


title: Liver_female_maternal_LFD_9

tag: tissue


title: SUM149PT vs Cell Line pool

value: Inflammatory breast carcinoma

value: Primary breast

value: Asterand


title: TESPE vs Cell Line pool

value: TESPE

value: Pleural effusion


title: TES1 vs Cell Line pool


title: 996-P-10min-2

source_name: rice panicle, 10min after 40 degree centigrade, replicate 2

tag: time point

value: 10min after 40 degree


title: 996-P-10min-1

source_name: rice panicle, 10min after 40 degree centigrade, replicate 1


title: 996-P-CK-1

source_name: rice panicle, 0min after 40 degree centigrade, replicate 1


title: SUM190PT vs Cell Line pool


title: MDAMB157 vs Cell Line pool

value: Metaplastic carcinoma

value: ATCC


title: Liver_female_maternal_LFD_5

value: female

value: 2 week-old offspring

value: liver


title: T47D vs Cell Line pool

value: Invasive ductal carcinoma


title: ZR751 vs Cell Line pool

value: Ascites fluid


title: ZR7530 vs Cell Line pool


title: MDAMB436 vs Cell Line pool


title: Liver_female_maternal_LFD_4

value: maternal low fat diet (for 6 wks pre-treatment, during pregnancy and lactation)


title: MDAMB175VII vs Cell Line pool

value: MDAMB175 VII


title: Liver_male_maternal_WSD_6

source_name: male 2-weeks old offspring_maternal Western-style high fat diet

value: male

value: maternal Western-style high fat diet (for 6 wks pre-treatment, during pregnancy and lactation)


title: Liver_female_maternal_LFD_2


title: Liver_female_maternal_LFD_1


title: Hs578T vs Cell Line pool

value: Pool from all cell lines (reference)


title: BT483 vs Cell Line pool

value: Primary breast


title: Liver_female_maternal_LFD_3


title: MDAMB134VI vs Cell Line pool

value: MDAMB134 VI


title: BT20 vs Cell Line pool


title: Liver_male_maternal_WSD_5


title: UACC893 vs Cell Line pool

value: Ductal carcinoma


title: MDAMB468 vs Cell Line pool

value: Adenocarcinoma

value: Pleural effusion


title: MDAMB361 vs Cell Line pool


title: MCF7 vs Cell Line pool


title: CAMA1 vs Cell Line pool


title: BT474 vs Cell Line pool


title: SKBR3 vs Cell Line pool


title: Liver_male_maternal_WSD_2


title: HCC1937 vs Cell Line pool


title: Liver_male_maternal_WSD_3


title: MDAMB231 vs Cell Line pool


title: Liver_male_maternal_WSD_4


title: MDAMB415 vs Cell Line pool


title: BT549 vs Cell Line pool


title: MCF10A vs Cell Line pool

value: Fibrocystic disease


title: Liver_male_maternal_WSD_1


title: AU565 vs Cell Line pool

value: ATCC


title: MCF12A vs Cell Line pool


title: Liver_male_maternal_LFD_6

source_name: male 2-weeks old offspring_maternal low fat diet


title: Liver_male_maternal_LFD_4


title: MCL1-6-25 (MEK1-transfected), biological rep3

description:
27. MEK1-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

source_name: Rasless cells transfected with activated MEK1 construct

tag: treatment

value: Mouse Embryonic Fibroblasts (MEFs)

tag: genotype

value: Inmortalized MEFs cultures

tag: cell line


description:
23. BRAF-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

source_name: Rasless cells transfected with activated BRAF construct

tag: cell type


title: LG7-6-13 (BRAF-transfected), biological rep3

description:
24. BRAF-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

value: transfected with activated BRAF construct


title: MCL23-1-2.r. (Puromycin-resistant empty vector), technical rep2

description:
31. Puromycin-resistant control
Gene Expression data from K-Raslox cells transfected with puromycin-resistant empty vector

source_name: Control MEFs transfected with puromycin-resistant empty vector (control for MEK1 construct)


title: Liver_male_maternal_LFD_3

tag: strain

tag: gender

value: 2 week-old offspring

value: liver

tag: sample group


title: DU244-1-12d-4OHT-N.r. (Rasless), technical rep4

description:
17. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)

source_name: Control cells after 12 days of 4OHT treatment becaming Rasless MEFs

tag: age


title: JU10-2-2 (Hygromycin-resistant empty vector), biological rep1

description:
32. Hygromycin-resistant control
Gene Expression data from K-Raslox cells transfected with hygromycin-resistant empty vector

source_name: Control MEFs transfected with Hygromycin-resistant empty vector (control for BRAF construct)

value: transfected with puromycin-resistant empty vector (control for BRAF construct)


description:
28. Puromycin-resistant control
Gene Expression data from K-Raslox cells transfected with puromycin-resistant empty vector

value: transfected with puromycin-resistant empty vector (control for MEK1 construct)


title: MCL23-1-5.r. (Puromycin-resistant empty vector), technical rep1

description:
29. Puromycin-resistant control
Gene Expression data from K-Raslox cells transfected with puromycin-resistant empty vector


title: MCL23-1-2 (Puromycin-resistant empty vector), biological rep2

description:
30. Puromycin-resistant control
Gene Expression data from K-Raslox cells transfected with puromycin-resistant empty vector


title: JU10-2-3 (Hygromycin-resistant empty vector), biological rep2

description:
33. Hygromycin-resistant control
Gene Expression data from K-Raslox cells transfected with hygromycin-resistant empty vector


title: Liver_male_maternal_LFD_5

value: male

value: maternal low fat diet (for 6 wks pre-treatment, during pregnancy and lactation)


title: MCL1-6-14 (MEK1-transfected), biological rep1

description:
25. MEK1-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)

value: transfected with activated MEK1 construct


title: DU244-1-12d-4OHT-N (Rasless), biological rep4

description:
16. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)

value: 12 days of 4OHT treatment becaming Rasless MEFs


title: Liver_male_maternal_LFD_1


title: DU315-6-12d-4OHT-S.r. (Rasless), technical rep2

description:
14. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: DU315-6-12d-4OHT-M.r. (Rasless), technical rep1

description:
12. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: DU315-6-12d-4OHT-S (Rasless), biological rep2

description:
13. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: MCL1-6-18 (MEK1-transfected), biological rep2

description:
26. MEK1-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)


title: DU315-6-12d-4OHT-N (Rasless), biological rep3

description:
15. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: Con sham 48h rep2

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST peg arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: liver from control [JNK1f/f] mice, 48 hrs after sham (control) treatment

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: JNK1-deficient mice were purchased from Harlan Laboratories (Bar Harbor, ME). JNK1f/f (C57BL/6 background) mice were kindly donated by Dr. Roger J. Davis (Howard Hughes Medical Institute, Chevy Chase, MD) and crossed with transgenic animals expressing the Cre transgene under control of a postnatal activated albumin promoter by crossing giving yield to the JNK1Δhepa strain, mice with specific deletion of JNK1 only in hepatocytes. Mice were maintained on standard laboratory chow.

extract_protocol: Total RNA was prepared from the liver using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Induction of liver fibrosis was performed in 7-8 weeks old age-matched male mice (n = 9-10 per group) by ligating the common bile duct (BDL). Control treated animals were opened and immediately closed (sham).  Mice were sacrificed 48h and 28days later.

value: sham

tag: time

tag: genetic background

value: JNK1f/f (control)

value: 8 weeks


title: LG7-6-5 (BRAF-transfected), biological rep1

description:
22. BRAF-rescued MEFs
Gene Expression data from BRAF-rescued sample: BRAF-transfected Rasless cells (rescued ability for proliferation)


title: Liver_male_maternal_LFD_2


title: JNK1dhepa BDL 48h rep3

source_name: liver from hepatocyte-specifik JNK1 null [JNK1Δhepa] mice, 48 hrs after bile duct ligation

value: bile duct ligation

value: hepatocyte-specific JNK1 null (JNK1Δhepa)


title: Con sham 48h rep1


title: DU315-6-12d-4OHT-M (Rasless), biological rep1

description:
11. Rasless MEFs
Gene Expression data from Rasless sample: 4-OHT-treated K-Raslox cells during 12 days (non-proliferating cells)


title: DU244-1-N2 (K-Raslox). technical rep4

description:
08. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

source_name: MEFs expressing only K-Ras (H-Ras/N-Ras double knockout); Control

value: control


title: Con sham 48h rep3


title: DU244-1-N (K-Raslox). biological rep4

description:
07. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

value: Mouse Embryonic Fibroblasts (MEFs)


title: JNK1dhepa BDL 48h rep1


title: DU315-6-S.r. (K-Raslox), technical rep2

description:
04. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

value: Inmortalized MEFs cultures


title: DU315-6-N (K-Raslox), biological rep3

description:
05. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: JNK1dhepa BDL 48h rep2


title: JNK1KO BDL 48h rep3

source_name: liver from JNK1 null [JNK1-/-] mice, 48 hrs after bile duct ligation

value: JNK1 null (JNK1-/-)


title: Control

city: Guangzhou

first: Hong-Ling

last: Jia

state: Guangdong

address: Huangpu Road

institute: Jinan University

description: miRNA expression after 6hr in 0Gy-irradiated human blood

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent miRNA Spike- In kit and miRNA Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).
Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and quantile normalization.

source_name: serum samples

label_protocol: 100 ng of total RNA(including miRNA) were dephosphorylated and denaturated,then ligated with Cyanine 3-pCp at 16℃ for 2 hours using T4 RNA Ligase.

extract_protocol: We isolated exosomes of sera from all participants by using ExoQuick precipitation following manufacturer′s instructions, Total RNA extracted using Trizol following manufacturer′s instructions

treatment_protocol: Blood samples from five mild  Hand,foot and mouth disease and five extremely severe Hand,foot and mouth disease children according to the ‘hand,foot and mouth disease prevention control guide’(2008 Edition) issued by the Ministry of Health, China(http://www.moh.gov.cn/publicfiles/business/htmlfiles/mohbgt/s9511/200805/34775.htm), were randomly collected for experiments and clinical symptoms and laboratory test(EV71 nucleic acid detection kit) confirmed that the EV71infections caused all these hand,foot and mouth disease cases. In addition to meeting the above symptoms, extremely severe Hand,foot and mouth disease patients all had encephalitis, pulmonary hemorrhage, and mechanical ventilation and other clinical symptoms.They were proven to have no other disease after a systematic check in the hospital.Five blood samples from healthy children were collected as controls

tag: diseaste state

value: healthy children


title: Con BDL 48h rep2

source_name: liver from control [JNK1f/f] mice, 48 hrs after bile duct ligation

value: liver


title: JNK1KO BDL 48h rep2


value: extremely severe hand,foot and mouth disease patients


title: Con BDL 48h rep1