title: A549-2 weeks-0.08-rep 1

description: Sample name: 522529

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 1

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 1


title: A549-1 week-0.4-rep 1

status: Public on Sep 17 2014

type: genomic

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

description: Sample name: 522534

hyb_protocol: The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing:
Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal/Input signal) for each array. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA (Roche NimbleGen) leverages the “neighbor effect” characteristics of Methylation Dependent ImmunoPrecipitation on chip (MeDIP-chip) data from high density oligonucleotide arrays, where enriched fragments sizes far exceed the spacing between probes. In other words, probes within close proximity have a greater likelihood of reporting signals derived from the same enriched fragment during MeDIP procedure. PSW-ANOVA uses a sliding window approach to identify potential sites of differential enrichment and then assigns probability scores (p values) to each probe on the array using a repeated measure ANOVA model. PSW-ANOVA is implemented in the R statistical programming environment as a custom script and was provided by Roche NimbleGen in collaboration.
Briefly, for each probe, a sliding window is determined based on the sliding window size parameter, centering on the probe in question. Within each sliding window, a repeated measures ANOVA is used to assess the difference between the various experimental groups for all probes located within the sliding window, using the probe ID as the reference to reduce the amount of error arising from different probes within a sliding window. It is assumed that the background and non-specific hybridization behavior of adjacent probes within a sliding window can be larger than the changes in intensity difference between the two channels, but within the sliding window, the log ratios will still be proportional to the intensity difference between groups of samples.
PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR adjusted p- value < 0.05) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment. Peaks were identified in the DMR by searching for the number of probes (default = 2) above a p-value minimum cutoff (-log10, default = 1.3) within 150 bp distance of each other. Peaks within 500 bp were merged. Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site) and CpG islands of genes using the NimbleScan v2.6 software.

molecule: genomic DNA

organism: Homo sapiens

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 1

label_protocol:
Genomic DNAs were sonicated to obtain fragments ranging from 200 bp to 1000 bp, cleaned up using silica columns (Zymo Research) and eluted in TE buffer. 4.4 µg of each sonicated sample was dissolved in a total volume of 495 µL TE buffer. Ten percent of such prepared mixtures was kept as Input sample (Input) at 4°C, while the remaining was immunoprecipitated with 12 µL of a monoclonal antibody against 5’-methylcytidine (Eurogentec) as described by Weber et al (Weber M, JJ Davies, D Wittig, EJ Oakeley, M Haase, WL Lam and D Schubeler. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853-862.). Immunoprecipitated DNAs (MeDIP) were purified using silica columns (Zymo Research) and eluted in TE buffer. Forty ng of both Input and MeDIP samples were whole genome amplified (WGA) using the WGA2 kit (Sigma Aldrich) following the manufacturer’s instruction, but omitting the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water.
Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000.

extract_protocol: Cells were washed twice with Hank's Buffered Salt Solution (Invitrogen) and trypsinized. Cell pellets were resuspended in 500 µl digestion buffer (1 mM EDTA; 50 mM Tris–HCl, pH 8.0; 5% SDS) and proteinase K (1 mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated at 80 °C. RNAse A (400 µg/ml) (Qiagen) treatment was performed for 1 hour at 37 °C. An equal amount of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added and shaked manually for 5 min. After centrifugation, the upper phase was again treated with PCI until no protein was visible at the interphase. The upper phase was precipitated with 50 µl 3M NaAc pH 5.6 and 1250 µl cold 100% ethanol. The DNA pellet was washed with cold 70% ETOH, dissolved in 50µl nuclease free water and quantified spectrophotometrically using the NanoDrop 1000 (Thermo Scientific, Waltham, MA). The total amount was at least 10 µg DNA, the 260/280 ratio laid between 1.7-1.9, and the 260/230 was higher than 1.6.

tag: cell type

value: A549 human epithelial lung carcinoma cells

tag: treatment

value: 0.4 µM of sodium arsenite

tag: time

value: 1 week

tag: sample type

value: input DNA

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 1

tag: antibody

value: monoclonal antibody against 5’-methylcytidine (Eurogentec, Weber et al (2005), PMID:16007088)

value: immunoprecipitated methyl-DNA (MeDIP)


title: Tumor PV092TT1

status: Public on Sep 16 2014

type: RNA

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Laser capture microdissection sample

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

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

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

label: Biotin

molecule: total RNA

source_name: Mammary Gland Cell

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

extract_protocol: Total RNA was extracted by Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Mammary grand cells were isolated from frozen tissue sections using laser capture microdissection.

tag: tumor/nontumor

value: Tumor

value: Mammary Gland Cell from Tumor

tag: scan date (yymmdd)


title: Tumor PV085TT1

description: Laser capture microdissection sample


title: Tumor PV090TT1

description: Laser capture microdissection sample


title: Tumor PV093TT1

description: Laser capture microdissection sample


title: Tumor PV094TT1

description: Laser capture microdissection sample


title: Tumor PV084TT1

description: Laser capture microdissection sample


title: A549-1 week-2-rep 1

description: Sample name: 522553

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 1

value: 2 µM of sodium arsenite

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 1


title: Tumor PV091TT1

description: Laser capture microdissection sample


title: Tumor PV103TT1

description: Laser capture microdissection sample


title: Tumor PV100TT1

description: Laser capture microdissection sample


title: Tumor PV078TT1

description: Laser capture microdissection sample


title: Tumor PV088TT1

description: Laser capture microdissection sample


title: Tumor PV080TT1

description: Laser capture microdissection sample


title: Tumor PV086TT1

description: Laser capture microdissection sample


title: Tumor PV079TT1

description: Laser capture microdissection sample


title: Tumor PV077TT1

description: Laser capture microdissection sample


title: Tumor PV095TT1

description: Laser capture microdissection sample


title: Tumor PV101TT1

description: Laser capture microdissection sample


title: Tumor PV098TT1

description: Laser capture microdissection sample


title: Tumor PV074TT1

description: Laser capture microdissection sample


title: Tumor PV071TT1

description: Laser capture microdissection sample


title: Tumor PV072TT1

description: Laser capture microdissection sample


title: Tumor PV073TT1

description: Laser capture microdissection sample


title: Tumor PX015TT1

description: Laser capture microdissection sample


title: Tumor PV076TT1

description: Laser capture microdissection sample


title: Tumor PV047TT1

description: Laser capture microdissection sample


title: Tumor PV067TT1

description: Laser capture microdissection sample


title: Tumor PV070TT1

description: Laser capture microdissection sample


title: Tumor PV051TT1

description: Laser capture microdissection sample


title: Tumor PV057TT1

description: Laser capture microdissection sample


title: Tumor PV066TT1

description: Laser capture microdissection sample


title: Tumor PV055TT1

description: Laser capture microdissection sample


title: Tumor PV061TT1

description: Laser capture microdissection sample


title: Tumor PV058TT1

description: Laser capture microdissection sample


title: Tumor PV065TT1

description: Laser capture microdissection sample


title: Tumor PV041TT1

description: Laser capture microdissection sample


title: Tumor PV040TT1

description: Laser capture microdissection sample


title: Tumor PV054TT1

description: Laser capture microdissection sample


title: Tumor PV052TT1

description: Laser capture microdissection sample


title: Tumor PV060TT1

description: Laser capture microdissection sample


title: Tumor PV046TT1

description: Laser capture microdissection sample


title: Tumor PV050TT1

description: Laser capture microdissection sample


title: Tumor PV069TT1

description: Laser capture microdissection sample


title: Tumor PV056TT1

description: Laser capture microdissection sample


title: Tumor PV083TT1

description: Laser capture microdissection sample


title: Tumor PV064TT1

description: Laser capture microdissection sample


title: Tumor PV043TT1

description: Laser capture microdissection sample


title: Tumor PV044TT1

description: Laser capture microdissection sample


title: Tumor PV039TT1

description: Laser capture microdissection sample


title: Tumor PV053TT1

description: Laser capture microdissection sample


title: Tumor PV038TT1

description: Laser capture microdissection sample


title: Tumor PV062TT1

description: Laser capture microdissection sample


title: Tumor PV045TT1

description: Laser capture microdissection sample


title: Tumor PV037TT1

description: Laser capture microdissection sample


title: Tumor PV099TT1

description: Laser capture microdissection sample


title: Tumor PV026TT1

description: Laser capture microdissection sample


title: Tumor PV035TT1

description: Laser capture microdissection sample


title: Tumor PV025TT1

description: Laser capture microdissection sample


title: Tumor PV011TT1

description: Laser capture microdissection sample


title: Tumor PV010TT1

description: Laser capture microdissection sample


title: Tumor PV027TT1

description: Laser capture microdissection sample


title: Tumor PV023TT1

description: Laser capture microdissection sample


title: Tumor PV031TT1

description: Laser capture microdissection sample


title: Tumor PV021TT1

description: Laser capture microdissection sample


title: Tumor PV036TT1

description: Laser capture microdissection sample


title: Tumor PV013TT1

description: Laser capture microdissection sample


title: Tumor PV012TT1

description: Laser capture microdissection sample


title: Tumor PV014TT1

description: Laser capture microdissection sample


title: Tumor PV032TT1

description: Laser capture microdissection sample


title: Tumor PV016TT1

description: Laser capture microdissection sample


title: Tumor PV007TT1

description: Laser capture microdissection sample


title: Tumor PV024TT1

description: Laser capture microdissection sample


title: Tumor PV005TT1

description: Laser capture microdissection sample


title: Tumor PV001TT1

description: Laser capture microdissection sample


title: Tumor PV004TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC9

description: Laser capture microdissection sample

value: Non-tumor

value: Mammary Gland Cell from Non-tumor


title: Tumor PV006TT1

description: Laser capture microdissection sample


title: Tumor PV002TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC7

description: Laser capture microdissection sample


title: Tumor PV009TT1

description: Laser capture microdissection sample


title: Tumor PV033TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC8

description: Laser capture microdissection sample


title: Non-tumor NMEC6

description: Laser capture microdissection sample


title: Non-tumor NMEC2

description: Laser capture microdissection sample


title: Non-tumor NMEC11

description: Laser capture microdissection sample


title: Tumor MM390TT1

description: Laser capture microdissection sample


title: Tumor MM303TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC10

description: Laser capture microdissection sample


title: Non-tumor NMEC16

description: Laser capture microdissection sample


title: Non-tumor NMEC18

description: Laser capture microdissection sample


title: Non-tumor NMEC4

description: Laser capture microdissection sample


title: Non-tumor NMEC14

description: Laser capture microdissection sample


title: Tumor MM247TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC1

description: Laser capture microdissection sample


title: Tumor MM338TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC15

description: Laser capture microdissection sample


title: Tumor MM259TT1

description: Laser capture microdissection sample


title: Tumor MM230TT1

description: Laser capture microdissection sample


title: Tumor MM241TT1

description: Laser capture microdissection sample


title: Tumor MM226TT1

description: Laser capture microdissection sample


title: Tumor MM316TT1

description: Laser capture microdissection sample


title: Tumor MM328TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC3

description: Laser capture microdissection sample


title: Tumor MM367TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC17

description: Laser capture microdissection sample


title: Tumor MM312TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC12

description: Laser capture microdissection sample


title: Tumor MM237TT1

description: Laser capture microdissection sample


title: Tumor MM232TT1

description: Laser capture microdissection sample


title: Tumor MM225TT1

description: Laser capture microdissection sample


title: Tumor MM227TT1

description: Laser capture microdissection sample


title: Tumor MM235TT1

description: Laser capture microdissection sample


title: Tumor MM234TT1

description: Laser capture microdissection sample


title: Tumor MM219TT1

description: Laser capture microdissection sample


title: Tumor MM223TT1

description: Laser capture microdissection sample


title: Tumor MM218TT1

description: Laser capture microdissection sample


title: Tumor MM216TT1

description: Laser capture microdissection sample


title: Tumor MM222TT1

description: Laser capture microdissection sample


title: Tumor MM193TT1

description: Laser capture microdissection sample


title: Tumor MM200TT1

description: Laser capture microdissection sample


title: Tumor MM217TT1

description: Laser capture microdissection sample


title: Tumor MM198TT1

description: Laser capture microdissection sample


title: Tumor MM212TT1

description: Laser capture microdissection sample


title: Tumor MM189TT1

description: Laser capture microdissection sample


title: Tumor MM201TT1

description: Laser capture microdissection sample


title: Tumor MM186TT1

description: Laser capture microdissection sample


title: Tumor MM210TT1

description: Laser capture microdissection sample


title: Tumor MM185TT1

description: Laser capture microdissection sample


title: Tumor MM209TT1

description: Laser capture microdissection sample


title: Tumor MM194TT1

description: Laser capture microdissection sample


title: Tumor MM190TT1

description: Laser capture microdissection sample


title: Tumor MM192TT1

description: Laser capture microdissection sample


title: Tumor MM187TT1

description: Laser capture microdissection sample


title: Tumor MM208TT1

description: Laser capture microdissection sample


title: Tumor MM205TT1

description: Laser capture microdissection sample


title: Tumor MM196TT1

description: Laser capture microdissection sample


title: Tumor MM181TT1

description: Laser capture microdissection sample


title: Tumor MM213TT1

description: Laser capture microdissection sample


title: Tumor MM183TT1

description: Laser capture microdissection sample


title: Tumor MM207TT1

description: Laser capture microdissection sample


title: Tumor MM177TT1

description: Laser capture microdissection sample


title: Tumor MM180TT1

description: Laser capture microdissection sample


title: Tumor MM182TT1

description: Laser capture microdissection sample


title: Tumor MM176TT1

description: Laser capture microdissection sample


title: ctl vs Heme replic. 3 dye swap

city: College Park

first: Yoann

last: Le Breton

state: Maryland

address: 3217 Bioscience Research Building (413)

department: Cell Biology and Molecular Genetics

country: USA

institute: University of Maryland

description: biological replicate 3 control vs Heme treatment dye swap

hyb_protocol: Labeled probes were resuspended in hybridization buffer (30% formamide, 5X SSC, 0.1% SDS, 0.6 μg/μL salmon sperm DNA) and hybridized to the microarray slides in a 42°C water bath for 16–20 h

scan_protocol: Slides were scanned using an Axon 4100A personal array scanner and GenePixPro 6.0 software (Molecular Devices)

data_processing: Data from the output GenePix results file (gpr file) were analyzed using Acuity 4.0 software (Axon Instruments). Microarray data were normalized using the ratio of the means. Data sets were then generated by analyzing data points whose mean of the ratio (635/532) was ≥2.0 or ≤0.50, followed by removal of samples for which four of the six microarray hybridization experiments (67%) did not show significance.

organism: Streptococcus pyogenes

source_name: MGAS5005 1.5h 4 uM Heme

label_protocol: 10 μg of DNase I-treated total RNAs to be compared were used for reverse transcription into single-stranded cDNA using 200 U Superscript II reverse transcriptase (Life Technologies), 6 μg random hexamers, 1X first strand buffer, 10 mM dithiothreitol (DTT), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP and 0.2 mM of amino-allyl dUTP. The mixture was incubated at 42°C for 2 h and the reaction stopped by addition of 10 μl 0.5 M EDTA and 1 M NaOH. Amine-modified cDNA was purified by ethanol precipitation followed by chemical labeling with Cy3- or Cy5-NHS-ester fluorescent dyes (GE Healthcare) in a final step. Yield and incorporation of dye was determined using a Nanodrop ND-1000 (Thermo Scientific)

growth_protocol: The C-media was inoculated with an equal number of cells from an overnight culture of MGAS5005 cells. The cells were grown at 37 °C and growth was monitored hourly using a colorimeter.

extract_protocol: RNA was extracted from the cell pellet using the RiboPure™ RNA purification kit (Ambion) followed by DNaseI digestion (Ambion) performed according to manufacturer's instructions

treatment_protocol: The MGAS5005 cells were treated with 4 μM heme (dissolved in 0.035% DMSO) and a control (0.035% DMSO) at an early log phase. The cells were harvested 90 min. post-treatment and subjected to RNA extraction.

tag: strain

source_name: MGAS5005 1.5h DMSO


title: Tumor MM169TT1

description: Laser capture microdissection sample


title: Tumor MM167TT1

description: Laser capture microdissection sample


title: ctl vs Heme replic. 2 dye swap

description: biological replicate 2 control vs Heme treatment dye swap


title: Tumor MM173TT1

description: Laser capture microdissection sample


title: ctl vs Heme replic. 2

description: biological replicate 2 control vs Heme treatment


title: ctl vs Heme replic. 1 dye swap

description: biological replicate 1 control vs Heme treatment dye swap


title: Tumor MM163TT1

description: Laser capture microdissection sample


title: ctl vs Heme replic. 3

description: biological replicate 3 control vs Heme treatment


title: Tumor MM170TT1

description: Laser capture microdissection sample


title: Tumor MM175TT1

description: Laser capture microdissection sample


title: Tumor MM166TT1

description: Laser capture microdissection sample


title: ctl vs Heme replic. 1

description: biological replicate 1 control vs Heme treatment


title: Tumor MM160TT1

description: Laser capture microdissection sample


title: Tumor MM158TT1

description: Laser capture microdissection sample


title: Tumor MM159TT1

description: Laser capture microdissection sample


title: Tumor MM164TT1

description: Laser capture microdissection sample


title: Tumor MM172TT1

description: Laser capture microdissection sample


title: Tumor MM155TT1

description: Laser capture microdissection sample


title: Tumor MM156TT1

description: Laser capture microdissection sample


title: Tumor MM152TT1

description: Laser capture microdissection sample


title: Tumor MM154TT1

description: Laser capture microdissection sample


title: Tumor MM153TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#9)

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridization probes were prepared by combining 6 mg of Alexa Fluor® 3 labeled sample and 1 mg Alexa Fluor® 5 labeled reference and denatured at 95°C and hybridized at 63°C on Agilent Human 4x44K microarrays and processed following the manufacturer’s specifications.

scan_protocol: Fluorescence array images were collected for Alexa Fluor® 3 and Alexa Fluor® 5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the GE2_105_Jan09 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of NA to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  Data was further normalized using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label: Alexa Fluor® 5

label_protocol: Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen) (reference cDNA was labeled with Alexa Fluor® 5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications. The second round amplified amino-allyl RNA was then converted to first strand cDNA and labeled with Alexa Fluor® 5 using the BioPrime® Total Genomic labeling kit (Invitrogen).

tag: gender

value: male

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

label: Alexa Fluor® 3

extract_protocol:
A single DTC was isolated from bone marrow (BM) samples of PCa patient. Essentially, a two-step selection process was employed, in which anti-CD45 and anti-CD61 conjugated to immunomagnetic beads were used for negative selection, and anti-HEA was used for positive selection.  Cells were then fluorescently stained for BerEP4, counter stained with RPE anti-CD45, and individually selected under fluorescent light using a micropipette system for further analysis.
Total RNA was amplified from each sample using the WT-OviationTM one-direct system (NuGEN) according to the manufacturer’s directions. Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen).

tag: patient status

value: ADV


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#8)

value: A single DTC was isolated from bone marrow (BM) samples of PCa patient.


title: Tumor MM151TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#6)


title: Tumor MM161TT1

description: Laser capture microdissection sample


title: Tumor MM150TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#5)


title: Tumor MM138TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#8)


title: Tumor MM149TT1

description: Laser capture microdissection sample


title: Tumor MM147TT1

description: Laser capture microdissection sample


title: Tumor MM141TT1

description: Laser capture microdissection sample


title: Tumor MM143TT1

description: Laser capture microdissection sample


title: Tumor MM144TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#5)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#10)


title: Tumor MM146TT1

description: Laser capture microdissection sample


title: Tumor MM134TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#4)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#6)


title: Tumor MM140TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#1)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#10)


title: Tumor MM133TT1

description: Laser capture microdissection sample


title: Tumor MM132TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#2)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2680 (#2)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2678 (#2)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2678 (#9)


title: Tumor MM128TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2679 (#7)


title: Tumor MM131TT1

description: Laser capture microdissection sample


title: Tumor MM130TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2678 (#7)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#8)


title: Tumor MM126TT1

description: Laser capture microdissection sample


title: Tumor MM129TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2678 (#10)


title: Tumor MM124TT1

description: Laser capture microdissection sample


title: Tumor MM116TT1

description: Laser capture microdissection sample


title: Tumor MM111TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#6)


title: Tumor MM113TT1

description: Laser capture microdissection sample


title: Tumor MM121TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#1)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#10)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#4)


title: Tumor MM123TT1

description: Laser capture microdissection sample


title: Tumor MM122TT1

description: Laser capture microdissection sample


title: Tumor MM120TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#6)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#3)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#5)


title: Tumor MM117TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#2)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2677 (#3)


title: Tumor MM102TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#8)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#2)


title: Tumor MM103TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#5)


title: Tumor MM107TT1

description: Laser capture microdissection sample


title: Tumor MM100TT1

description: Laser capture microdissection sample


title: Tumor MM101TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2665 (#1)


title: Tumor MM099TT1

description: Laser capture microdissection sample


title: Tumor MM097TT1

description: Laser capture microdissection sample


title: Tumor MM091TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2613 (#7)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2613 (#5)


title: Tumor MM092TT1

description: Laser capture microdissection sample


title: Tumor MM085TT1

description: Laser capture microdissection sample


title: Tumor MM095TT1

description: Laser capture microdissection sample


title: Tumor MM084TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2613 (#2)


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2676 (#4)

value: NED


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2676 (#X)


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2613 (#3)


title: Tumor MM083TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2695 (#3)


title: Tumor MM082TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of ADV PCa patient 2613 (#0)


title: Tumor MM088TT1

description: Laser capture microdissection sample


title: Tumor MM078TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2687 (#5)


title: Tumor MM086TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2690 (#7)


title: Tumor MM089TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2690 (#8)


title: Tumor MM079TT1

description: Laser capture microdissection sample


title: single DTC isolated from bone marrow (BM) of NED PCa patient 2687 (#3)


title: Tumor MM075TT1

description: Laser capture microdissection sample


title: Tumor MM072TT1

description: Laser capture microdissection sample


title: Tumor MM070TT1

description: Laser capture microdissection sample


title: Tumor MM068TT1

description: Laser capture microdissection sample


title: Tumor MM066TT1

description: Laser capture microdissection sample


title: Tumor MM067TT1

description: Laser capture microdissection sample


title: Tumor MM077TT1

description: Laser capture microdissection sample


title: Tumor MM074TT1

description: Laser capture microdissection sample


title: Tumor MM059TT1

description: Laser capture microdissection sample


title: Tumor MM063TT1

description: Laser capture microdissection sample


title: Tumor MM062TT1

description: Laser capture microdissection sample


title: Tumor MM051TT1

description: Laser capture microdissection sample


title: Tumor MM057TT1

description: Laser capture microdissection sample


title: Tumor MM044TT1

description: Laser capture microdissection sample


title: Tumor MM053TT1

description: Laser capture microdissection sample


title: Tumor MM050TT1

description: Laser capture microdissection sample


title: Tumor MM031TT1

description: Laser capture microdissection sample


title: Tumor MM056TT1

description: Laser capture microdissection sample


title: Tumor MM027TT1

description: Laser capture microdissection sample


title: Tumor MM040TT1

description: Laser capture microdissection sample


title: Tumor MM032TT1

description: Laser capture microdissection sample


title: Tumor MM058TT1

description: Laser capture microdissection sample


title: Tumor MM034TT1

description: Laser capture microdissection sample


title: Tumor MM038TT1

description: Laser capture microdissection sample


title: Tumor MM047TT1

description: Laser capture microdissection sample


title: Tumor MM036TT1

description: Laser capture microdissection sample


title: Tumor MM035TT1

description: Laser capture microdissection sample


title: Tumor MM022TT1

description: Laser capture microdissection sample


title: Tumor MM026TT1

description: Laser capture microdissection sample


title: Tumor MM025TT1

description: Laser capture microdissection sample


title: Tumor MM016TT1

description: Laser capture microdissection sample


title: Tumor MM028TT1

description: Laser capture microdissection sample


title: Tumor MM049TT1

description: Laser capture microdissection sample


title: Tumor MM012TT1

description: Laser capture microdissection sample


title: Tumor MM023TT1

description: Laser capture microdissection sample


title: Tumor MM015TT1

description: Laser capture microdissection sample


title: Tumor MM017TT1

description: Laser capture microdissection sample


title: Tumor MM011TT1

description: Laser capture microdissection sample


title: Tumor MM014TT1

description: Laser capture microdissection sample


title: Tumor MM024TT1

description: Laser capture microdissection sample


title: Tumor MM013TT1

description: Laser capture microdissection sample


title: Tumor EP036TT1

description: Laser capture microdissection sample


title: Tumor EP042TT1

description: Laser capture microdissection sample


title: Tumor EP046TT1

description: Laser capture microdissection sample


title: Tumor MM010TT1

description: Laser capture microdissection sample


title: Tumor MM019TT1

description: Laser capture microdissection sample


title: Tumor EP047TT1

description: Laser capture microdissection sample


title: Tumor MM007TT1

description: Laser capture microdissection sample


title: Tumor EP052TT1

description: Laser capture microdissection sample


title: Tumor EP041TT1

description: Laser capture microdissection sample


title: Tumor MM006TT1

description: Laser capture microdissection sample


title: Tumor EP037TT1

description: Laser capture microdissection sample


title: Tumor EP053TT1

description: Laser capture microdissection sample


title: Tumor EP020TT1

description: Laser capture microdissection sample


title: Tumor EP018TT1

description: Laser capture microdissection sample


title: Tumor EP033TT1

description: Laser capture microdissection sample


title: Tumor EP029TT1

description: Laser capture microdissection sample


title: Tumor EP030TT1

description: Laser capture microdissection sample


title: Tumor EP048TT1

description: Laser capture microdissection sample


title: Tumor EP011TT1

description: Laser capture microdissection sample


title: Tumor MM098TT1

description: Laser capture microdissection sample


title: Tumor EP019TT1

description: Laser capture microdissection sample


title: Tumor EP023TT1

description: Laser capture microdissection sample


title: Tumor EP021TT1

description: Laser capture microdissection sample


title: Tumor EP026TT1

description: Laser capture microdissection sample


title: Tumor EP035TT1

description: Laser capture microdissection sample


title: Tumor EP017TT1

description: Laser capture microdissection sample


title: Tumor EP008TT1

description: Laser capture microdissection sample


title: Tumor EP009TT1

description: Laser capture microdissection sample


title: Tumor EP012TT1

description: Laser capture microdissection sample


title: Tumor DC088TT1

description: Laser capture microdissection sample


title: Tumor EP013TT1

description: Laser capture microdissection sample


title: Tumor EP007TT1

description: Laser capture microdissection sample


title: Tumor DC089TT1

description: Laser capture microdissection sample


title: Tumor EP003TT1

description: Laser capture microdissection sample


title: Tumor EP005TT1

description: Laser capture microdissection sample


title: Tumor DC091TT1

description: Laser capture microdissection sample


title: Tumor DC086TT1

description: Laser capture microdissection sample


title: Tumor DC070TT1

description: Laser capture microdissection sample


title: Tumor DC075TT1

description: Laser capture microdissection sample


title: Tumor DC059TT1

description: Laser capture microdissection sample


title: Tumor DC085TT1

description: Laser capture microdissection sample


title: Tumor DC084TT1

description: Laser capture microdissection sample


title: Tumor DC080TT1

description: Laser capture microdissection sample


title: Tumor DC063TT1

description: Laser capture microdissection sample


title: Tumor DC060TT1

description: Laser capture microdissection sample


title: Tumor DC067TT1

description: Laser capture microdissection sample


title: Tumor DC074TT1

description: Laser capture microdissection sample


title: Tumor DC081TT1

description: Laser capture microdissection sample


title: Tumor DC062TT1

description: Laser capture microdissection sample


title: Tumor DC065TT1

description: Laser capture microdissection sample


title: Tumor DC083TT1

description: Laser capture microdissection sample


title: Tumor DC069TT1

description: Laser capture microdissection sample


title: Tumor DC055TT1

description: Laser capture microdissection sample


title: Tumor DC058TT1

description: Laser capture microdissection sample


title: Tumor DC076TT1

description: Laser capture microdissection sample


title: Tumor DC071TT1

description: Laser capture microdissection sample


title: Tumor DC057TT1

description: Laser capture microdissection sample


title: Tumor DC064TT1

description: Laser capture microdissection sample


title: Tumor DC054TT1

description: Laser capture microdissection sample


title: Tumor DC050TT1

description: Laser capture microdissection sample


title: Tumor EP001TT1

description: Laser capture microdissection sample


title: wild-type cochlea at E15, biological rep 1

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

country: Spain

institute: CSIC

description: whole cochlea

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the 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

organism: Mus musculus

source_name: wild-type E15 cochlea

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

growth_protocol: Cochleas dissected from E15 mouse embryos

extract_protocol: N-myc mutant embryos were distinguished from wild-type embryos by PCR genotyping. Total RNA was extracted from cochlear tissue using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). cDNA synthesis and amplification was performed using the WT Expression Kit (Ambion).

treatment_protocol: not applicable

value: 129/Sv and CD-1

tag: age


title: Tumor DC051TT1

description: Laser capture microdissection sample


title: Tumor DC053TT1

description: Laser capture microdissection sample


title: Tumor DC048TT1

description: Laser capture microdissection sample


title: Tumor DC045TT1

description: Laser capture microdissection sample


title: Tumor DC042TT1

description: Laser capture microdissection sample


title: N-myc ko cochlea at E15, biological rep 2

description: whole cochlea

source_name: N-myc ko E15 cochlea


title: Tumor DC049TT1

description: Laser capture microdissection sample


title: Tumor DC040TT1

description: Laser capture microdissection sample


title: Ebf2(GFP)-:Pdgfra+, replicate 3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression from Ebf2(GFP)-:Pdgfra+ cells

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray signals were RMA-normalized, and differential gene expression anlaysis was performed using 'limma' package.

source_name: E14.5 embryonic fibroblasts

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

growth_protocol: E14.5 embryos harvested from Ebf2(GFP) mice housed at 20°C with a 12-hour light/12-hour dark cycle..

extract_protocol: Total RNA was extracted from freshly sorted cells using the TRIzol method (Invitrogen) combined with QIAGEN RNeasy Micro Column.

treatment_protocol: Embryos were digested in 6.1 mg ml-1 collagenase and 2.4 mg ml-1 dispase in DMEM for 40 min at 37 °C in a shaking water bath.Digested tissue was successively filtered through 100 µm and 40 µm cell strainers. Cells were then suspended in DMEM with 5% FBS, and stained with antibodies for 30 min at 4 °C in the dark. Stained cells were sorted with BD FACS Aria.

value: embryo, dorsal body wall

tag: developmental stage


title: N-myc ko cochlea at E15, biological rep 1

description: whole cochlea


title: Tumor DC036TT1

description: Laser capture microdissection sample


title: Tumor DC047TT1

description: Laser capture microdissection sample


title: wild-type cochlea at E15, biological rep 2

description: whole cochlea


title: Ebf2(GFP)+:Pdgfra+, replicate 3

description: Gene expression from Ebf2(GFP)+:Pdgfra+ cells


title: Tumor DC039TT1

description: Laser capture microdissection sample


title: Tumor DC037TT1

description: Laser capture microdissection sample


title: Tumor DC035TT1

description: Laser capture microdissection sample


title: Ebf2(GFP)+:Pdgfra+, replicate 1


title: Tumor MM046TT1

description: Laser capture microdissection sample


title: Ebf2(GFP)+:Pdgfra+, replicate 2


title: N7

city: Randwick

first: Max

last: Yan

state: NSW

address: Prince of Wales Hospital

department: Anatomical Pathology

country: Australia

institute: SEALS

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip U1536-16 according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: The BeadChips were scanned with the Illumina iScan Reader. Data were imported into GenomeStudio (Illumina), from which raw data with background subtraction were exported to PARTEK Genomics Suite (St. Louis, Missouri, USA) for further analysis. Probes with a maximum intensity value of less than 150 units across all samples were excluded. Of the 1145 probes present on the array, 1037 were used for subsequent analyses. Raw probe intensities were shifted, such that the minimum probe intensity for each sample was equal to 1. All values were transformed by taking logs (base 2), followed by quantile normalisation.

source_name: FFPE breast cancer

label_protocol: Biotinylated cDNA were prepared from 0.2-1ug total RNA using the high-throughput Gene expression profiling, the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: For primary tumours and normal breast tissue, 10μm thick sections were cut from FFPE tissue blocks. The sections were dewaxed in xylene, placed through 100% alcohol and allowed to dry. The samples were needle microdissected to ensure the proportion of tumour (or normal epithelium) was greater than 80%, prior to placement into lysis buffer (Agencourt Formapure kit, Beckman Coulter, Beverly, MA, USA). Tissue was digested as per kit protocol (incubate at 70oC for 1 hr, then add 20 µl of Proteinase K and incubate at 55oC for 1hr). Total RNA was extracted via a standard TRIZOL(Sigma)/chloroform protocol. For cell lines, total RNA was extracted using the total RNA protocol from the mirVana miRNA Isolation Kit (Ambion, TX, USA). All samples underwent DNase treatment with the Ambion DNA-free kit (Ambion, TX, USA).

value: FFPE breast cancer

tag: breast cancer subtype

value: Normal


title: L9

value: Luminal


title: Control 1 e

source_name: Breast cancer cell line

value: Breast cancer cell line

value: Luminal Cell Line


title: Tumor DC033TT1

description: Laser capture microdissection sample

value: Tumor


title: Tumor DC038TT1

description: Laser capture microdissection sample

value: Mammary Gland Cell from Tumor


title: CL-b

tag: cell line


title: S9

value: Sporadic basal


title: Ebf2(GFP)-:Pdgfra+, replicate 2


title: B7

value: BRCA1 basal


title: S8


title: L7


title: Ebf2(GFP)-:Pdgfra+, replicate 1


title: Tumor DC031TT1

description: Laser capture microdissection sample


title: N6


title: B6


title: S6


title: S7


title: S5


title: L6


title: B3


title: Tumor DC027TT1

description: Laser capture microdissection sample


title: Tumor DC022TT1

description: Laser capture microdissection sample


title: Tumor DC023TT1

description: Laser capture microdissection sample


title: Tumor DC019TT1

description: Laser capture microdissection sample


title: Tumor DC024TT1

description: Laser capture microdissection sample


title: Tumor DC012TT1

description: Laser capture microdissection sample


title: Tumor DC018TT1

description: Laser capture microdissection sample


title: Tumor DC013TT1

description: Laser capture microdissection sample


title: Control 1 d


title: N3


title: Tumor DC016TT1

description: Laser capture microdissection sample


title: N5


title: Tumor DC008TT1

description: Laser capture microdissection sample


title: Tumor DC010TT1

description: Laser capture microdissection sample


title: Control 2 b


title: B2


title: L5


title: N4


title: L2


title: S2


title: Tumor DC015TT1

description: Laser capture microdissection sample


title: Tumor DC014TT1

description: Laser capture microdissection sample


title: CB-c

value: Basal Cell Line


title: L18


title: Tumor DC017TT1

description: Laser capture microdissection sample


title: Tumor DC007TT1

description: Laser capture microdissection sample


title: Tumor DC005TT1

description: Laser capture microdissection sample


title: Tumor DC006TT1

description: Laser capture microdissection sample


title: Tumor DC002TT1

description: Laser capture microdissection sample


title: Tumor DC001TT1

description: Laser capture microdissection sample


title: S18


title: Tumor DC003TT1

description: Laser capture microdissection sample


title: Tumor 1M057TT1

description: Laser capture microdissection sample


title: Tumor 1M056TT1

description: Laser capture microdissection sample


title: Tumor 1M058TT1

description: Laser capture microdissection sample


title: Tumor DC004TT1

description: Laser capture microdissection sample


title: Tumor 1M055TT1

description: Laser capture microdissection sample


title: S17


title: Control 1 c


title: Tumor 1M053TT1

description: Laser capture microdissection sample


title: B14


title: Tumor 1M051TT1

description: Laser capture microdissection sample


title: L17


title: N2


title: PDAC_3

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: The data were analyzed using Bioconductor and package Affy, using the JustRMA() function with default setting (quantile normalization and RMA background correction).

source_name: PDAC, sample 3

label_protocol: Total mRNA was RNase H reduced and labelled with the SuperScript One-Cycle cDNA Kit following manufacturer's instructions (Invitrogen).

extract_protocol: Chirgwin's extraction of total RNA (Chirgwin JM et al., 1979) performed on fresh tissues.

treatment_protocol: No treatment.

value: pancreatic ductal adenocarcinoma tumor

tag: genotype

value: Pdx1-Cre; Ink4a/Arffl/fl; LSL-KrasG12D

value: Male

value: 7 weeks-old


title: PDAC_2

source_name: PDAC, sample 2

value: 8.5 weeks-old


title: B13


title: Control_pancreas_3

source_name: Control pancreas, sample 3

value: pancreas

value: Ink4a/Arffl/fl; LSL-KrasG12D

value: 9 weeks-old


title: S15

value: FFPE breast cancer


title: N13

value: Normal


title: Control_pancreas_2

source_name: Control pancreas, sample 2


title: PDAC_1

source_name: PDAC, sample 1

value: 10 weeks-old


title: Tumor 1M050TT1

description: Laser capture microdissection sample


title: Tumor 1M047TT1

description: Laser capture microdissection sample


title: Tumor 1M052TT1

description: Laser capture microdissection sample


title: L3

value: Luminal


title: Control_pancreas_1

source_name: Control pancreas, sample 1


title: HGF at day 14, biological rep1

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Gene expression data from Human Gingival Fiabroblast transfected with empty vector

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: The statistical analyses were performed with R 2.11.0. All samples were normalized and summarized by Robust Multiarray Average (RMA). Times series analysis was carried out using bioconductor timecourse package. Differential expression analysis between HGF and HGF/CEMP1 cells was performed using LIMMA. The Benjamini and Hochberg multiple hypothesis testing correction procedure was applied to control the false discovery rate (FDR). Data were filtered to include only genes that had a 2-fold-change difference between the groups and an adjusted p value of 0.001

source_name: Human gingival fibroblast transfected with empty vector day 14

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

growth_protocol: All cell cultures were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) in a 37 C humidified incubator containing 5% CO2

extract_protocol: RNA was isolated from human gingival fibroblast (HGF/CEMP1) overexpressing CEMP1 and controls (HGF) using RNeasy Mini Kit according to the manufacturer´s directions

treatment_protocol: The coding region of CEMP1 (GenBank Accession No. NM_001048212) was subcloned into the pENTR/SD/D vector (Invitrogen, Carlsbad, CA). The resultant pENTR/SD/D-CEMP1 cDNA construct was ligated into a pcDNA40 (+) vector (CEMP1-pcDNA40 (+)) with a 6×His tag-COOH terminal (Invitrogen, Carlsbad, CA). The plasmid, pcDNA40-CEMP1, was transfected into HGF cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA). Control HGF cells were transfected with pcDNA40 (+) vector. Stably expressing cells were selected with of 600 μg/mL of G418 (Sigma Chemical Co., St. Louis, MO) up to eight weeks.

value: Human gingival fibroblasts

tag: transfection

value: Empty vector


title: Tumor 1M046TT1

description: Laser capture microdissection sample

source_name: Mammary Gland Cell

value: Tumor

tag: cell type

value: Mammary Gland Cell from Tumor


title: Tumor 1M044TT1

description: Laser capture microdissection sample


title: Tumor 1M048TT1

description: Laser capture microdissection sample


title: HGF at day 14, biological rep3


title: B12

value: BRCA1 basal


title: HGF at day 14, biological rep2


title: Tumor 1M043TT1

description: Laser capture microdissection sample


title: S14

value: Sporadic basal


title: Tumor 1M045TT1

description: Laser capture microdissection sample


title: L15


title: S13


title: B11


title: HGF at day 7, biological rep2

source_name: Human gingival fibroblast transfected with empty vector day 7


title: Tumor 1M040TT1

description: Laser capture microdissection sample


title: HGF at day 7, biological rep1


title: Tumor 1M041TT1

description: Laser capture microdissection sample


title: HGF at day 3, biological rep1

source_name: Human gingival fibroblast transfected with empty vector day 3


title: Tumor 1M042TT1

description: Laser capture microdissection sample


title: HGF at day 3, biological rep3


title: Tumor 1M039TT1

description: Laser capture microdissection sample


title: Tumor 1M038TT1

description: Laser capture microdissection sample


title: Control 1 b

value: Breast cancer cell line

value: Luminal Cell Line


title: HGF at day 7, biological rep3


title: HGF/CEMP1 at day 14, biological rep3

description: Gene expression data from Human Gingival Fiabroblast transfected with CEMP1

source_name: Human gingival fibroblasts transfected with CEMP1 day 14

value: CEMP1 construct


title: L13


title: CL-a


title: N12


title: Tumor 1M037TT1

description: Laser capture microdissection sample


title: L12


title: Control 2 a


title: HGF at day 3, biological rep2


title: HGF/CEMP1 at day 14, biological rep2


title: Tumor 1M033TT1

description: Laser capture microdissection sample


title: Tumor 1M036TT1

description: Laser capture microdissection sample


title: HGF/CEMP1 at day 14, biological rep1


title: Tumor 1M034TT1

description: Laser capture microdissection sample


title: Tumor 1M035TT1

description: Laser capture microdissection sample


title: Tumor 1M031TT1

description: Laser capture microdissection sample


title: N9


title: S16


title: L8


title: N8


title: HGF/CEMP1 at day 7, biological rep1

source_name: Human gingival fibroblasts transfected with CEMP1 day 7


title: L16


title: HGF/CEMP1 at day 7, biological rep3


title: B9


title: HGF/CEMP1 at day 3, biological rep3

source_name: Human gingival fibroblasts transfected with CEMP1 day 3


title: HGF/CEMP1 at day 7, biological rep2


title: Tumor 1M029TT1

description: Laser capture microdissection sample


title: Tumor 1M027TT1

description: Laser capture microdissection sample


title: Tumor 1M030TT1

description: Laser capture microdissection sample


title: HGF/CEMP1 at day 3, biological rep2


title: N10


title: S11


title: L14


title: HGF/CEMP1 at day 3, biological rep1


title: Tumor 1M026TT1

description: Laser capture microdissection sample


title: Tumor 1M022TT1

description: Laser capture microdissection sample


title: B8


title: S12


title: N11


title: L11


title: Tumor 1M021TT1

description: Laser capture microdissection sample


title: Interference_2_3

city: Chongqing

first: Jun

last: Rao

address: No 183, Xinqiao street, Shapingba

department: Medical center of hematology

country: China

institute: Xinqiao hospital

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (Scan resolution=5μm, PMT 100%，10%.) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: human colorectal cancer cell_knock down

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)

growth_protocol: cells were cultured 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were infected with concentrated eGFP-sh-SEMA3F lentivirus and empty control lentivirus vectors. Cells with stable integration of Sh-SEMA3F were selected and enriched by flow cytometry (BD FACSAria II) to obtain eGFP positive cells.

value: colorectal cancer cell line

tag: infected with

value: eGFP-Sh-SEMA3F lentivirus


title: Tumor 1M020TT1

description: Laser capture microdissection sample


title: Interference_2_1


title: Tumor 1M019TT1

description: Laser capture microdissection sample


title: Interference_2_2


title: Ctrl_1_3

source_name: human colorectal cancer cell_control

value: empty control lentivirus


title: Ctrl_1_1


title: Ctrl_1_2


title: Tumor 1M015TT1

description: Laser capture microdissection sample


title: Tumor 1M016TT1

description: Laser capture microdissection sample


title: Tumor 1M017TT1

description: Laser capture microdissection sample


title: Tumor 1M018TT1

description: Laser capture microdissection sample


title: CB-a

value: Basal Cell Line


title: S10

source_name: FFPE breast cancer

value: FFPE breast cancer


title: CB-b

source_name: Breast cancer cell line


title: L10


title: N1

value: Normal


title: Tumor 1M013TT1

description: Laser capture microdissection sample


title: L1


title: S1


title: B1


title: Control 1 a


title: Tumor 1M008TT1

description: Laser capture microdissection sample


title: Tumor 1M009TT1

description: Laser capture microdissection sample


title: Tumor 1M007TT1

description: Laser capture microdissection sample


title: Tumor 1M006TT1

description: Laser capture microdissection sample


title: Tumor 1M012TT1

description: Laser capture microdissection sample


title: Tumor 1M004TT1

description: Laser capture microdissection sample


title: control2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
uninfected HIBCPP control cells; replicate 2
HIBCPP-untreated #2

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of HG-U133_Plus_2 -type from Affymetrix. A Custom CDF Version 13 with unigene based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: untreated HIBCPP cells

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

growth_protocol: HIBCPP cells were cultured in DMEM/F-12 (Ham) 1x with 4 mM L-Glutamine and 15 mM HEPES supplemented with 5 µg ml-1 insulin, 100 U ml-1 penicillin and 100 µg ml-1 streptomycin as well as 15% heat inactivated fetal calf serum (FCS). For inverted cell culture insert based experiments 0.7 * 105 cells were seeded on filter inserts (pore diameter 3.0 µm, pore density 2.0 * 106 pores per cm2, growth area 0.33 cm2, from either Millipore, Schwalbach, Germany or Greiner Bio-one, Frickenhausen, Germany) that were flipped over and placed in a medium flooded 12-well plate.

extract_protocol: Following exposure to bacteria, cells were washed twice with PBS to exclude bacteria. Total RNA from HIBCPP cells was extracted using the QIAGEN RNeasy® Mini or Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. During RNA purification an on-column DNAse digestion (RNase-Free DNase Set, Qiagen, Hilden, Germany) was performed to avoid DNA carryover. RNA purity was evaluated by spectrophotometer (ND1000, Peqlab Biotechnoloy, Erlangen, Germany) and RNA quality of the microarray samples was additionally assessed using the Agilent RNA 6000 Nano Kit according to the manufacturer’s instructions and the Agilent Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany). Samples with RNA integrity numbers (RIN) higher than 9.8 were used for microarray analysis.

treatment_protocol: Cells were seeded on inverted cell culture inserts and transferred to phenol red free DMEM/F-12 with 4 mM L-Glutamine and 15 mM HEPES supplemented with 5 µg ml-1 insulin and 1% fetal calf serum when TEER values reached 60 Ω * cm2.  Infection from the basolateral side (mimicking the blood facing side in vivo) was carried out the next day when TEER values ranged around 500 Ω * cm2. Using the inverted cell culture insert system infection from the upper compartment simulates the pathophysiological situation in vivo, when pathogens invade the CSF from the blood. HIBCPP cells were infected with either strain MC58, MC58siaD- or α14 at a multiplicity of infection (MOI) of 10 at 37°C and 5% CO2 atmosphere for the indicated periods of time with antibiotical killing of the bacteria after 4 h and prolonged infection up to 24 h.

value: Human malignant choroid plexus papilloma (HIBCPP) cells

value: none (control)

tag: pathology

value: control


title: Tumor 1M002TT1

description: Laser capture microdissection sample


title: Tumor 1M005TT1

description: Laser capture microdissection sample


title: control3

description:
uninfected HIBCPP control cells; replicate 3
HIBCPP-untreated #3


title: NSC

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: A CDF mouse4302cdf was used to process the CLE files. The data were analyzed with Bioconductor using the MAS5 normalization method.

source_name: Embryonic stem cells

growth_protocol: Primary-derived neural stem cells and established iNSCs were cultured in N2 medium (Okabe et al., 1996) [DMEM/F-12 medium containing insulin (5 mg/ml) (Sigma), transferrin (100 mg/ml) (Sigma), sodium selenite (30 nM) (Sigma), progesterone (20 nM) (Sigma), putrescine (100 nM) (Sigma), and penicillin and streptomycin (100 mg/ml) (Life Technologies)] supplemented with 20 ng/ml epidermal growth factor (EGF) (R & D systems), 20 ng/ml basic fibroblast growth factor (bFGF) (Sigma), and laminin (1 mg/ml) (Life Technologies).  NSC medium was replenished every 24-48 hours, and cells were passaged every 2-3 days.

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

value: primary-derived neural stem cells (NSCs)


title: wt3

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis disease isolate strain MC58; replicate 3
HIBCPP + MC58 #3

source_name: HIBCPP cells infected for 4 h with strain MC58

value: MC58 strain for 4h

tag: capsule phenotype

value: capsulated

value: path


title: bac_control3

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis carrier isolate strain α14; replicate 3
HIBCPP + a14 #3

source_name: HIBCPP cells infected for 4 h with strain α14

value: α14 strain for 4h

value: non-capsulated mutant

value: apatho


title: bac_control2

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis carrier isolate strain α14; replicate 2
HIBCPP + a14 #2


title: HFCore (HCFD-fed HCV Core transgenic mouse)

city: Los Angeles

first: Keigo

last: Machida

state: CA

address: 2011 Zonal Ave., HMR503C

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Labeling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HCFD-fed HCV Core transgenic mouse

growth_protocol: No culture

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

treatment_protocol: Liver tissues were collected from mice. The procedure of cell isolation from liver tissues was performed as previously described with some modifications. Liver tissues were immediately frozen and saved in -80 degree deep freezer space.

value: Liver

value: HCV Core

tag: passages

value: Passage 6


title: iNSC_13F

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

value: induced neural stem cells (iNSCs) with 13 factors


title: Tumor 1M003TT1

description: Laser capture microdissection sample

tag: tumor/nontumor

value: Tumor

value: Mammary Gland Cell from Tumor


title: mut3

description:
HIBCPP cells infected basolaterally for 4 h with non-encapsulated mutant of Neisseria meningitidis disease isolate strain MC58 (strain MC58siaD-); replicate 3
HIBCPP + MC58siaD- #3

source_name: HIBCPP cells infected for 4 h with strain MC58siaD-

value: MC58siaD- strain for 4h


title: MEF

label_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

value: mouse embryonic fibroblasts


title: Wild type [bo12-8]

city: Clayton

first: Ian

last: Smyth

state: Victoria

address: Wellington Rd

department: Department of Biochemistry & Molecular Biology, Department of Anatomy & Developmental Biology

institute: Monash University

description: Biological Replicate 3

hyb_protocol: A total of 1.5microgram of labelled cRNA was prepared at 0.05microgram/microlitre in GEX-HYB hybridisation buffer and 30microlitres loaded into each array on a Sentrix MouseWG6v2 Beadchip. Hybridisation was performed at 58 degrees celsius for 16 hours in a rocking platform oven. The chip was then washed as per Illumina protocol and coupled with Cy3.

scan_protocol: The chip was then washed as per Illumina protocol and coupled with Cy3. Scanning was performed with Illumina Bead Array Reader.

data_processing: The scanner operating software, BeadStudio coverted signals on the array into a txt file for analysis with GeneSpring GX

source_name: Wild type

label_protocol: 500 nanogram of total RNA was labelled using Illumina Total Prep RNA amplification kit (IL1791) and quality assessed using the Agilent Bioanalyser 2100 nanochip protocol.

extract_protocol: Total RNA from epidermal peels was isolated with RNAqueous (Ambion) according to manufacturer's protocol. RNA quality was assessed using the Agilent Bioanalyser 2100 nanochip protocol.

treatment_protocol: The epidermis of E17.5 embryos was peeled from the dermis following disection and 5mM EDTA treatment in PBS for 1 hr at 37 degrees Celsius.

value: Embryonic back skin epidermis


title: Harlequin Ichthyosis Mutant [bo12-4]

description: Biological Replicate 3

source_name: Harlequin Ichthyosis Mutant


title: HFNS5A (HCFD-fed HCV Ns5a transgenic mouse)

source_name: HCFD-fed HCV Ns5a transgenic mouse

value: HCV Ns5a


title: iNSC_14F

value: induced neural stem cells (iNSCs) with 14 factors


title: wt2

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis disease isolate strain MC58; replicate 2
HIBCPP + MC58 #2

value: Human malignant choroid plexus papilloma (HIBCPP) cells

value: MC58 strain for 4h


title: Harlequin Ichthyosis Mutant [bo20-7]

description: Biological Replicate 2


title: ALNS5A (Alcohol-fed HCV Ns5a transgenic mouse)

source_name: Alcohol-fed HCV Ns5a transgenic mouse


title: HFWT (HCFD-fed wild type mouse)

source_name: HCFD-fed wild type mouse

value: Wild type


title: control1

description:
uninfected HIBCPP control cells; replicate 1
HIBCPP-untreated #1

value: none (control)

value: control


title: ALCore (Alcohol-fed HCV Core transgenic mouse)

source_name: Alcohol-fed HCV Core transgenic mouse


title: Tumor 1M010TT1

description: Laser capture microdissection sample

source_name: Mammary Gland Cell

tag: scan date (yymmdd)


title: prostate_12hr_after TmT_TRAMP mice

city: New Brunswick

first: Tony

last: Kong

state: NJ

address: 160 Frelinghuysen Road

department: Pharmaceutical Science

institute: Rutgers University

description: Gene expression  in the prostate 12h after 600 mg/kg gamma-TmT treatment

hyb_protocol: Labeled RNA was hybridized to the arrays overnight at 65°C on a rotator.

scan_protocol: Arrays were scanned suing Agilent technologies Scanner G2505C according to manufacturer's recommendations. Features were extracted using Agilent's feature exraction software 10.2.1.3.

data_processing: Spot values are dark-offset substracted, thresholded, and filtered to remove bad spots. Data were normalized by the quantile normalization method using the R package PrepreocesCore. Differential gene expression was identified using R.

source_name: prostate, 12hr after TmT, TRAMP mice

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit. One microgramRNA were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol: In groups 1 and 2, C57BL/6 mice were orally administered olive oil and 600 mg/kg γ-TmT, respectively. In groups 3 and 4, TRAMP mice were orally administered olive oil and 600 mg/kg γ-TmT, respectively. Three mice were used in each experimental group. The mice were given an AIN-76A diet from one week prior to the treatment until the day before the experiment, when they were fasted overnight before oral gavage. The mice were euthanized with CO2 12 hours after dosing, and their prostates were collected and snap-frozen in liquid nitrogen.

tag: strain/genotype

value: TRAMP

value: prostate

value: male


title: mut2

description:
HIBCPP cells infected basolaterally for 4 h with non-encapsulated mutant of Neisseria meningitidis disease isolate strain MC58 (strain MC58siaD-); replicate 2
HIBCPP + MC58siaD- #2

value: non-capsulated mutant

value: path


title: prostate_12hr_after olive oil_TRAMP mice

description: Gene expression  in the prostate 12h after olive oil

source_name: prostate, 12hr after olive oil, TRAMP mice

tag: gender


title: Wild type [bo20-4]

description: Biological Replicate 2

tag: tissue

tag: strain


title: bac_control1

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis carrier isolate strain α14; replicate 1
HIBCPP + a14 #1

value: α14 strain for 4h

value: apatho


title: ALWT (Alcohol-fed wild type mouse)

source_name: Alcohol-fed wild type mouse

value: Liver

value: Passage 6


title: mut1

description:
HIBCPP cells infected basolaterally for 4 h with non-encapsulated mutant of Neisseria meningitidis disease isolate strain MC58 (strain MC58siaD-); replicate 1
HIBCPP + MC58siaD- #1

value: MC58siaD- strain for 4h


title: wt1

description:
HIBCPP cells infected basolaterally for 4 h with Neisseria meningitidis disease isolate strain MC58; replicate 1
HIBCPP + MC58 #1

value: capsulated


title: Tumour from mouse p110-416

status: Public on Sep 15 2014

city: Montreal

first: Alain

last: Nepveu

state: Qc

address: 1160 Pine Avenue West

department: Goodman Cancer Centre

country: Canada

institute: McGill University

description: RNA extracted from epithelial tumour cells is hybridized in dye swaps with a common reference used for normalization between experimental samples

hyb_protocol: Labeled aRNA was hybridized to Agilent's Whole Mouse Genome Microarray (G4122F).

scan_protocol: scanned on an Agilent 5mm scanner model G2505B according to the manufacturer's instructions. Images were quantified using Agilent Feature Extraction Software

data_processing: Data was processed in R using the Limma package

molecule: cytoplasmic RNA

source_name: Microdissected epithelial tumour cells

label_protocol: RNA isolated from microdissected tissue was amplified using the Arcturus RiboAmp HS PLUS RNA amplification kit according to the manufacturer's instructions for 2 rounds of amplification. Amplified mRNA (aRNA) was labeled using the Arcturus Turbo Labeling Cy5 and Cy3 kits using slightly modified instructions: The labeling reaction was carried out using 5mg of aRNA in a 20ml volume instead of 50ml to increase the dye incorporation rate.

extract_protocol: Tumours were embedded in Tissue Freezing Medium and flash frozen in liquid nitrogen. 10mm slices of tissue were prepared in a Microm HM505E Cryostat at ~-30°C on positively charged slides. Epithelial cells were then isolated by IR (InfraRed) pulse on an Arcturus XTLCM instrument within 30-45 minutes of H&E staining.

tag: transgene

value: Microdissected epithelial tumour cells

tag: histological tumour type

value: Solid Carcinoma

value: FVB

source_name: Stratagene universal mouse reference (Agilent catalog # 750600)

extract_protocol:
preparation: 4 batches of 500 ng of RNA was amplified for 2 rounds using the same protocol as tumour samples,
storage and use: amplified reference batches were pooled, then aliquoted and stored at -80oC for hybridization against experimental samples.

tag: reference

value: universal reference


title: prostate_12hr_after olive oil_BL6 mice

source_name: prostate, 12hr after olive oil, BL6 mice

tag: age


title: Harlequin Ichthyosis Mutant [bo20-3]

description: Biological Replicate 1

value: Embryonic back skin epidermis


title: prostate_12hr_after TmT_BL6 mice

source_name: prostate, 12hr after TmT, BL6 mice


title: Tumour from mouse p110-374

value: Adenomyoepithelioma


title: Tumour from mouse p110-225


title: Tumour from mouse p110-143


title: Tumour from mouse p110-360


title: Wild type [bo20-2]

description: Biological Replicate 1


title: Tumour from mouse p75-216

value: Adenocarcinoma


title: Tumour from mouse p75-129


title: Tumour from mouse p110-314


title: Tumour from mouse p75-534


title: Tumour from mouse p75-101

value: Adenosquamous Carcinoma


title: Tumour from mouse p75-150


title: Tumour from mouse p110-98

value: Adenoma


title: Tumour from mouse p75-90


title: Tumour from mouse p110-121


title: Tumour from mouse p75-80


title: Tumour from mouse p75-94


title: Tumour from mouse p75-47


title: Wild type at week 15, replicate 6

city: Strasbourg

first: Alexandre

last: Henriques

address: 11 rue Humann

institute: University of Strasbourg

description: Gene expression of motor neuron from WT mice, control of SOD1 mice at week 15

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Expression console software was used to normalize arrays with the gcrma algorithm. The database was filtered with intensity and standard deviation. Analyses were performed using BRB-ArrayTools.

source_name: Motor neuron from WT mice, control of SOD1 mice at week 15

growth_protocol: Mice were housed under in standard conditions and fed ad libitum.

treatment_protocol: After anesthesia, and perfusion with ice-cold HBSS, spinal cords have been dissected on ice, snap frozen for cryosection procedures. Lumbar motor neurons were dissected by laser microdissection with moving laser beam.

value: Isolated lumbar motor neurons

value: 15 weeks


title: SOD1 mice treated with GCSF, at week 15, replicate 7

description: Gene expression of motor neuron from SOD1 mice, treated with G-CSF, at symptomatic disease stage

source_name: Motor neuron from SOD1 mice, treated with G-CSF, at symptomatic disease stage

value: B6.Cg-Tg(SOD1-G93A)1Gur/J strain


title: Wild type at week 15, replicate 7


title: SOD1 mice treated with GCSF, at week 15, replicate 6


title: Wild type at week 15, replicate 4


title: Wild type at week 15, replicate 2


title: SOD1 mice treated with GCSF, at week 15, replicate 1


title: Wild type at week 15, replicate 1


title: Wild type at week 15, replicate 3


title: Wild type at week 15, replicate 5


title: SOD1 mice treated with GCSF, at week 15, replicate 4


title: SOD1 mice at week 15, replicate 2

description: Gene expression of motor neuron from SOD1 mice, terated with a placebo, at symptomatic disease stage

source_name: Motor neuron from SOD1 mice, treated with a placebo, at symptomatic disease stage


title: SOD1 mice treated with GCSF, at week 15, replicate 5


title: SOD1 mice at week 15, replicate 5


title: SOD1 mice at week 15, replicate 6


title: SOD1 mice at week 15, replicate 1


title: SOD1 mice at week 15, replicate 7


title: SOD1 mice at week 15, replicate 3


title: Wild type at week 11, replicate 6

description: Gene expression of motor neuron from WT mice, control of SOD1 mice at week 11

source_name: Motor neuron from WT mice, control of SOD1 mice at week 11

value: 11 weeks


title: SOD1 mice at week 15, replicate 4


title: SOD1 mice treated with GCSF, at week 15, replicate 3


title: LIM_4

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description: LM biological replicate 4 of 4.

hyb_protocol: Hybridization was performed according to Agilent's instructions miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Version 2.4, September 2011.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner G2505C (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.10 (Agilent Technologies). In analysis grid 049625_D_F_20130521 was used.

data_processing: Raw data were exported to GeneSpring 12.0 (Agilent, USA). Agilent.miRNA.49625 technology was used during analysis. To minimize the biological variability across arrays, raw data were 1.0 thresholded, log2 transformed and 75 percentile shifted with baseline transformation (mean of all samples). Then all entities were filtered by flags (detected, non-detected), and statistically analyzed using unpaired t-test with Benjamini-Hohberg FDR multiple testing corrections (p≤0.05).

organism: Bos taurus

source_name: quarter of mammary gland

label_protocol: Total RNA from each sample was amplified, labelled, and hybridized according to Agilent's instructions miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Version 2.4, September 2011. 100 ng of total RNA was labelled with Cyanine 3-pCp

extract_protocol: Mammary tissue was obtained at slaughterhouse from 2 years-old non-pregnant heifers (four Holstein–Friesian and four Limousin) free of clinical signs of mastitis. Udders were removed and mammary tissue was collected, fixed in RNAlater solution (Qiagen, USA) and stored at -80oC until further analysis. The total RNA containing miRNA from the samples was isolated using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol. Total RNA quantity and purity were assessed using NanoDrop (NanoDrop Technologies, USA), and RNA integrity was verified using an Agilent 2100 Bioanalyser.

value: heifer

value: 20 months

tag: breed

value: Limousine (LM)

tag: health status

value: healthy


title: LIM_3

description: LM biological replicate 3 of 4.


title: LIM_1

description: LM biological replicate 1 of 4.


title: LIM_2

description: LM biological replicate 2 of 4.


title: NG11A_055_ca

first: Brent

middle: L

last: Fogel

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: blood

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

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

tag: diagnosis

value: carrier

tag: disease

tag: definite analysis

value: definite


title: Wild type at week 11, replicate 5


title: NG10A_051_af

value: affected

value: presumed


title: NG11A_057_af


title: NG11A_056_ca


title: NG10A_052_ca


title: HF_4

description: HF biological replicate 4 of 4.

value: Holstein-Freisian (HF)


title: NG10A_030_ca


title: NG10A_050_ca


title: HF_3

description: HF biological replicate 3 of 4.


title: NG10A_076_ca


title: Wild type at week 11, replicate 4


title: Wild type at week 11, replicate 3


title: NG11A_063_af


title: NG10A_075_ca


title: NG10A_029_ca


title: Wild type at week 11, replicate 2


title: NG10A_074_ca


title: HF_2

description: HF biological replicate 2 of 4.


title: Wild type at week 11, replicate 1


title: NG10A_077_ca


title: SOD1 mice at week 11, replicate 8

description: Gene expression of motor neuron from SOD1 mice before disease onset

source_name: Motor neuron from SOD1 mice before disease onset


title: HF_1

description: HF biological replicate 1 of 4.


title: NG10A_073_af


title: NG08A_008_af


title: ZA16_30_af


title: NG09A_068_ca


title: SOD1 mice at week 11, replicate 6


title: SOD1 mice at week 11, replicate 7


title: SOD1 mice at week 11, replicate 5


title: NG09A_021_af


title: NG10A_022_ca


title: NG09A_040_af


title: CL_3_af


title: SOD1 mice at week 11, replicate 4


title: HFK treated with Y-27632

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit with Affymetrix Fluidics Station 450 and Hybridization Oven 450.

scan_protocol: GeneChip Scanner 3000 7-G Plus, GCOS v1.4

data_processing: Processing done in R/Bioconductor, GC-RMA was used for normalization

source_name: HFK Human foreskin keratinocytes grown in F medium with ROCK inhibitor Y-27632 treatment

label_protocol: Biotin labeling using 3' IVT Express kit and manufacturer-recommended protocol

extract_protocol: Qiagen RNeasy Miniprep and Trizol

tag: cell type

value: HFK (Human foreskin keratinocytes)

tag: treatment


title: HFK in conditioned medium and treated with Y-27632

source_name: HFK Human foreskin keratinocytes grown in conditioned medium collected from irridiated fibroblasts and treated with ROCK inhibitor Y-27632

value: Y-27632 and J2 cells


title: HFK in conditioned medium

source_name: HFK Human foreskin keratinocytes grown in conditioned medium collected from irridiated fibroblasts

value: J2 cells only


title: CT_6_af


title: SOD1 mice at week 11, replicate 3


title: SS_5_ca


title: CF_7_ca


title: MN_1_af


title: SOD1 mice at week 11, replicate 2


title: SOD1 mice at week 11, replicate 1


title: NG09A_067_af


title: NG09A_066_af


title: NG08A_018_ca


title: CM_4_af


title: NG09A_074_ca


title: MR_2_ca


title: NG09A_065_af


title: Non-exposed cells, sample 3, 2 days

city: Madison

first: Jacob

last: Scherf

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

description: GCRMA expression value derived from Affymetrix Expression Console software

hyb_protocol: After cDNA fragmentation, 10 µg of each sample was hybridized to an individual Affymetrix HG U133 Plus 2.0 gene chip according to the methods described in the Affymetrix “Genechip Expression Analysis Technical Manual with Specific Protocols for Using the GeneChip Hybridization, Wash, and Stain Kit” manual.  Samples were hybridized for 16 h at 45 °C in an Affymetrix Hybridization Oven 640.

scan_protocol: Post-processing was conducted using an Affymetrix GeneChip Fluidics Station 450 following HG U133 Plus 2.0-specific protocols provided by Affymetrix, and each GeneChip was scanned using an Affymetrix GC3000 G7 scanner.

data_processing: Data was extracted from the scanned images using the Affymetrix Expression Console v 1.2.0.20 software.  Gene enrichment was conducted on all samples using GeneSpring 12.6 (Agilent) software.  Robust Multi-array Analysis with correction for oligo GC content (GCRMA) was used for summarization with quantile normalization, and background reduction was performed on all samples by filtering for present probes as called by the MAS 5.0 algorithm.

source_name: iCell Neurons (hipsc neurons)

label_protocol: After quantification (NanoDrop 2000) and determination of sample integrity (Agilent 2100 Bioanalyzer, RNA 6000 Pico chip), 400 ng of each sample was labeled with an Ambion MessageAmp Premier IVT kit as per manufacturer instructions

growth_protocol: Cells were plated according to manufacturer's instructions (Cellular Dynamics International, Madison, WI).  Approximately 650,000 live cells were plated per well in a 6-well plate (Techno Plastic Products [TPP]) treated with 0.01% poly-L-ornithine (PLO) (Sigma) and coated with 8.3 µg / ml Matrigel (Biosciences).  Cells were maintained in media supplied by CDI in a 37 °C, 5% CO2 incubator.

extract_protocol: Total RNA was isolated from exposed and non-exposed iCell neurons at 2 d and 14 d post-initial exposure using an RNeasy mini kit (Qiagen) and adding β-mercaptoethanol (βME) to the lysis buffer as recommended by the manufacturer’s instructions.  DNA was removed during isolation using an RNeasy RNase-free DNase kit (Qiagen).  Samples were stored at -20 °C after isolation.

treatment_protocol: Cells were exposed to 10 pM of BoNT/A or BoNT/A ad suspended in 3 ml of neuronal maintenance medium and incubated for 48 h.  All cells were gently washed twice with 5 ml of fresh media to remove all extracellular toxin, and either RNA was harvested as described below (for 2 d post exposure) or the cells were maintained for another 12 d before harvesting RNA (for 14 d post exposure).  All experiments were performed in triplicate.  Non-exposed control samples were concurrently grown with exposed cells and harvested at the same time.

value: hipsc-derived neurons

tag: exposure

value: Non-exposed

tag: time post-exposure

value: 2 days


title: SOD1 mice treated with GCSF, at week 15, replicate 2

value: Isolated lumbar motor neurons

tag: strain/genotype

value: B6.Cg-Tg(SOD1-G93A)1Gur/J strain

value: 15 weeks


title: Non-exposed cells, sample 3, 2 weeks

value: 2 weeks


title: WT_66B_af

description: replicate B

source_name: fibroblasts

tag: transfection

value: WT


title: Liver_HCV_0802-0036

city: Izunokuni

first: Shunsuke

last: Sato

state: Shizuoka

address: 1129 Nagaoka

department: Department of Internal Medicine

country: Japan

institute: Juntendo University Shizuoka Hospital

description: chronic hepatitis C

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.1

source_name: Liver tissue

label_protocol: Agilent one-color Quick Amp Labeling Kit labeling protocol

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and evaluated by the Agilent 2100 Bioanalyzer (Agilent Technologies). Only high quality RNA with RNA integrity numbers greater than 7.0 was used for experiments

treatment_protocol: We performed percutaneous liver biopsy for diagnosis and they were not conducted by anti-viral treatment until biopsy.

tag: disease state

value: chronic hepatitis C

tag: tissue

value: Liver biopsy specimens

tag: gender

value: male

tag: afp(ng/ml)


title: HFK

source_name: HFK Human foreskin keratinocytes grown in F medium

value: Medium only


title: T5927G_66A_af

description: replicate A

value: affected


title: Non-exposed cells, sample 2, 2 weeks


title: NG09A_075_ca

value: carrier

value: definite


title: Liver_HCV_0802-0187

description: chronic hepatitis C


title: G6407A_68A_ca

description: replicate A


title: Non-exposed cells, sample 2, 2 days


title: T5927G_68B_ca

description: replicate B


title: Liver_HCV_0802-0037

description: chronic hepatitis C

value: female


title: T5927G_66B_af

description: replicate B


title: Liver_HCV_0802-0098

description: chronic hepatitis C


title: WT_68B_ca

description: replicate B


title: 25b_66B_af

description: replicate B


title: G6407A_68B_ca

description: replicate B


title: Liver_HCV_0802-0017

description: chronic hepatitis C


title: Liver_HCV_0709-0030

description: chronic hepatitis C


title: 25b_68A_ca

description: replicate A


title: WT_68A_ca

description: replicate A


title: BoNT/A ad exposed cells, sample 3, 2 days

value: BoNT/A ad


title: Non-exposed cells, sample 1, 2 days

value: hipsc-derived neurons


title: Liver_HCV_0801-0052

description: chronic hepatitis C


title: 25b_68B_ca

description: replicate B


title: Liver_HCV_0709-0029

description: chronic hepatitis C


title: WT_66A_af

description: replicate A


title: 25b_66A_af

description: replicate A


title: Liver_HCV_0709-0028

description: chronic hepatitis C


title: G6407A_66A_af

description: replicate A


title: BoNT/A ad exposed cells, sample 3, 2 weeks


title: G6407A_66B_af

description: replicate B


title: Liver_HCV_0709-0022

description: chronic hepatitis C


title: Non-exposed cells, sample 1, 2 weeks

value: Non-exposed


title: BoNT/A ad exposed cells, sample 2, 2 days

value: 2 days


title: BLF_66_2_af

description: replicate 2


title: BoNT/A ad exposed cells, sample 2, 2 weeks


title: KO_30_C

description: cerebellum

source_name: cerebellum

tag: region

value: cerebellum

tag: genotype/variation

value: Setx knockout


title: BLF_68_2_ca

description: replicate 2


title: Liver_HCV_0709-0019

description: chronic hepatitis C


title: BLF_68_1_ca

description: replicate 1


title: Liver_HCV_0708-0048

description: chronic hepatitis C


title: T5927G_68A_ca

description: replicate A


title: BoNT/A ad exposed cells, sample 1, 2 days


title: BoNT/A ad exposed cells, sample 1, 2 weeks


title: BLF_66_1_af

description: replicate 1


title: BoNT/A1 exposed cells, sample 3, 2 days


title: Liver_HCV_0708-0027

description: chronic hepatitis C


title: KO_30_B

description: brain

source_name: brain

value: brain


title: KO_00_B

description: brain


title: Liver_HCV_0709-0017

description: chronic hepatitis C


title: BoNT/A1 exposed cells, sample 3, 2 weeks

value: 2 weeks


title: KO_00_C

description: cerebellum


title: Liver_HCV_0707-0058

description: chronic hepatitis C


title: WT_10_B

description: brain

value: WT


title: BoNT/A1 exposed cells, sample 2, 2 days


title: WT_11_B

description: brain


title: BoNT/A1 exposed cells, sample 2, 2 weeks


title: WT_11_C

description: cerebellum


title: Liver_HCV_0708-0026

description: chronic hepatitis C

value: chronic hepatitis C


title: WT_10_C

description: cerebellum


title: Liver_HCV_0705-0003

description: chronic hepatitis C

value: Liver biopsy specimens


title: Un sucrose

city: Notredame

first: prachi

last: singh

state: indiana

address: 130 Galvin

department: biological sciences

institute: university of notredame

description: Total RNA from exosomes released from uninfected RAW264.7 macrophages following exosome purification by sucrose gradient

hyb_protocol: Hybridization was performed according to Nimblegen protocols

scan_protocol: Scanning was performed according to Nimblegen protocol

data_processing: The raw data was subject to RMA using Nimblescan, quantile normalization

organism: Mycobacterium tuberculosis H37Rv

source_name: Exosomal RNA from uninfected macrophages and exosomes purified by sucrose gradient

label_protocol: Labeling was performed using standard labeling procedures from Nimblegen and following manufacture's instructions

growth_protocol: Murine RAW264.7 macrophages were cultured in complete DMEM media at 37 degrees in a CO2 incubator; Mycobacteria was cultured in 7H9 broth with OADC at 37 degrees incubator shaker

extract_protocol: Total RNA was isolated using MirVana kit (Ambion) and treated with DNAse1 (Invitrogen)

treatment_protocol: Macrophages were infected with opsonized bacteria so as to achieve 80% infectivity of cells as determined by an uptake assay

tag: sample type

value: Exosomes

tag: infection

value: purification by sucrose gradient


title: Liver_HCV_0702-0035

description: chronic hepatitis C

value: male


title: Liver_HCV_0706-0009

description: chronic hepatitis C


title: Liver_HCV_0702-0057

description: chronic hepatitis C


title: Rv exoquick

description: Total RNA from exosomes released from M.tb infected RAW264.7 macrophages following exosome purification by exoquick

source_name: Exosomal RNA from M.tb infected macrophages and exosomes purified by exoquick

value: M.tb infected

value: purification by exoquick


title: Liver_HCV_0703-0010

description: chronic hepatitis C


title: Liver_HCV_0702-0058

description: chronic hepatitis C


title: Rv sucrose

description: Total RNA from exosomes released from M.tb infected RAW264.7 macrophages following exosome purification by sucrose gradient

source_name: Exosomal RNA from M.tb infected macrophages and exosomes purified by sucrose gradient


title: BoNT/A1 exposed cells, sample 1, 2 days