title: NPC

city: Shanghai

last: Cheng

address: Yueyang Road 320

institute: New Building #1003, SIBCB

description: Gene expression of primary cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 mouse GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: NPC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

value: brain-derived NPC  (control NPC)


title: subcuaneous WAT, technical rep2

status: Public on Apr 27 2015

type: RNA

city: Mohali

first: Mahendra

last: Bishnoi

state: Punjab

address: C-127, Industrial Area, SAS Nagar, Phase 8

department: Nutrition Science and Technology

country: India

institute: National Agri-Food Biotechnology Institute

description:
LACA (Laboratory Animal Centre A-strain) mice
Gene expression data from subcutaneous white adipose tissue

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on gene chip (mouse 430.2.0 Affymetrix array). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: The data were analyzed with GeneSpring GX 12.1 using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Murine  white adipose tissue (subcutaneous region)

label_protocol: Biotinylated aRNA were prepared as per the protocol and guidelines provided by Affymetrix, Inc. (Santa Clara, CA).

growth_protocol: The mice were fed standard chow (70% carbohydrate, 10% Fat) until sacrifice at the described weight range (25 ± 3g).

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

treatment_protocol: There was no treatment administed to the animals. Tissue samples analyzed are from control animals.

tag: tissue

value: White adipose tissue (subcutaneous region)

tag: gender

value: Male


title: rarb_24_rep2

type: genomic

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

country: USA

institute: Stowers Institute

hyb_protocol: Arrays were hybridized with a mixture of 4µg Cy3 labeled DNA and 4µg Cy5 labeled DNA probes. Hybridizations were performed at 650C for 24 hours under standard conditions (45 mg/mL Human Cot-1 DNA, 1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent ChIP wash buffer 1, at room temperature and then Agilent ChIP wash buffer 2, at 31C,  prior to scanning.

scan_protocol: Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C). For image analysis Agilent Feature Extraction software (Version 10.5.1.1) was used.

data_processing: Agilent tiling arrays were hybridized in a two-color configuration and data was read into R (2.11.1). Data was analyzed using the limma (3.4.3) package. Data was normalized within arrays using loess normalization.

molecule: genomic DNA

source_name: rarb chIP, KH2 cells, 24 hrs RA

label_protocol: Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).

extract_protocol: 37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).

value: Mouse Embryonic Stem Cells (KH2)

tag: timepoint

value: 24 hrs after RA

tag: chip antibody

value: rarb

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog

tag: sample type

value: input

tag: cell type

value: KH2 cells


title: subcuaneous WAT, biological rep4


title: ciNPC p13-1

first: Lin

country: China

description: Gene expression of primary cells

source_name: ciNPC p13-1

value: chemical-induced NPC (ciNPC)

tag: passage


title: rarg_un_rep1

source_name: rarg chIP, KH2 cells, uninduced

value: uninduced

value: rarg


title: rarg_24_rep2

source_name: rarg chIP, KH2 cells, 24 hrs RA


title: rara_un_rep2

source_name: rara chIP, KH2 cells, uninduced

value: rara


title: ciNPC p13-2

description: Gene expression of primary cells

source_name: ciNPC p13-2


title: rarb_un_rep1

source_name: rarb chIP, KH2 cells, uninduced


title: rara_24_rep1

source_name: rara chIP, KH2 cells, 24 hrs RA


title: rarg_24_rep1


title: pol2_36

source_name: pol2 chIP, KH2 cells, 36 hrs RA

value: 36 hrs after RA

value: Santa Cruz Biotechnology, Inc.


title: rarb_24_rep1


title: rarb_un_rep2


title: pol2_un

source_name: pol2 chIP, KH2 cells, uninduced


title: pol2_24

source_name: pol2 chIP, KH2 cells, 24 hrs RA


title: pol2_4

source_name: pol2 chIP, KH2 cells, 4 hrs RA

value: 8 hrs after RA

value: 4 hrs after RA


title: MEF

description: Gene expression of primary cells

source_name: MEF

value: MEF


title: pol2_8

source_name: pol2 chIP, KH2 cells, 8 hrs RA


title: ciNPC p5

description: Gene expression of primary cells

source_name: ciNPC p5


title: h3k27me3_36

source_name: h3k27me3 chIP, KH2 cells, 36 hrs RA

source_name: input, KH2 cells, 36 hrs RA


title: kh2_8hrs_rep3

hyb_protocol: Labeled aRNA was quantified on the NanoDrop ND-1000 and a 1.5µg mass of cy3 labeled aRNA was hybridized to custom Agilent 2x105K HOX tiling arrays.  Hybridizations were performed at 65 degrees C for 17 hours under standard conditions (1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent GE wash buffer 1, at room temperature and with Agilent GE wash buffer 2, at 31oC, prior to scanning.

scan_protocol: Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C).   Hybridization, array washing, scanning and probe information extraction with Agilent’s Feature Extraction Software (Version 10.5.1.1) were all performed according to Agilent’s One-Color Microarray-Based Gene Expression Analysis Protocol, Version 6.0, December 2009 (Low Input Quick Amp Labeling).

data_processing: Agilent tiling arrays were hybridized in a single-color configuration and data was read into R. Agilent gMeanSignal was used as the measurement (mean green signal for each spot). Data was analyzed using the limma package. Data was normalized between arrays using scale normalization. Replicates were averaged and bedgraph files were created and visualized using IGV and UCSC genome browser.

source_name: KH2 cells, 8 hrs RA

label_protocol: Amplified mRNA, referred to as aRNA, was quantified on a NanoDrop ND-1000 and a mass of 2ug was labeled with cy3 dye using Kreatech’s ULS Fluorescent Labeling Kit, part number EA-023.

growth_protocol: KH2 cells at Passage 12 were cultured on gamma irradiated feeder cells with DMEM containg 15% fetal bovine serum, NAA and β-mercaptoethanol.

extract_protocol: RNA isolation was performed using Trizol and later purified by RNA Easy Kit (Quiagen). Total RNA in the amount of 1ug was amplified according to Ambion’s Message Amp II aRNA Amplification Kit, part number AM1751.  Positive control RNA from Agilent’s One Color RNA Spike-In Kit, part number 5188-5282, was used to monitor sample amplification and labeling as well as array hybridization.

treatment_protocol: ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time.  Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.

value: 8hrs after RA


title: h3k27me3_un_rep2

source_name: h3k27me3 chIP, KH2 cells, uninduced

source_name: input, KH2 cells, uninduced


title: atypicalMBC_5

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent-039494 8x60k human gene expression microarrays as per manufacturer instructions.

scan_protocol: Arrays were scanned on an Agilent scanner at 3 um resolution as 20-bit TIFF images.

data_processing: Features were extracted using Agilent Feature Extraction software. Non-background-subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.

organism: Homo sapiens

source_name: Atypical memory B cells from patient 5

label_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

growth_protocol: PBMCs were isolated from Ugandan children over Ficoll-Histopaque and cryopreserved in liquid nitrogen.

extract_protocol: RNA was isolated with the RNAqueous Micro kit (Life Technologies). Isolated RNA was amplified using the Aminoallyl MessageAmp II kit (Life Technologies).

treatment_protocol: PBMCs were thawed and immediately stained for FACS isolation of memory B cell subsets.

value: atypical memory B cells

tag: patient id


title: h3k4me3_36

source_name: h3k4me3 chIP, KH2 cells, 36 hrs RA

value: Mouse Embryonic Stem Cells (KH2)


title: classicalMBC_6

source_name: Classical memory B cells from patient 6

value: classical memory B cells


title: h3k4me3_8

source_name: h3k4me3 chIP, KH2 cells, 8 hrs RA

source_name: input, KH2 cells, 8 hrs RA


title: atypicalMBC_6

source_name: Atypical memory B cells from patient 6


title: classicalMBC_5

source_name: Classical memory B cells from patient 5


title: classicalMBC_4

source_name: Classical memory B cells from patient 4


title: classicalMBC_2

source_name: Classical memory B cells from patient 2


title: atypicalMBC_1

source_name: Atypical memory B cells from patient 1


title: atypicalMBC_2

source_name: Atypical memory B cells from patient 2


title: atypicalMBC_4

source_name: Atypical memory B cells from patient 4


title: h3k27me3_un_rep1


title: classicalMBC_3

source_name: Classical memory B cells from patient 3


title: h3k4me3_un_rep1

source_name: h3k4me3 chIP, KH2 cells, uninduced


title: classicalMBC_1

source_name: Classical memory B cells from patient 1


title: h3k4me3_24_rep1

source_name: h3k4me3 chIP, KH2 cells, 24 hrs RA

value: 24 hrs after RA

source_name: input, KH2 cells, 24 hrs RA


title: Sample 2 PRA

city: Urbana

first: Milan

middle: K

last: Bagchi

state: IL

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

description:
Human endometrial stromal cell, decidualization, PGR
PRA expressing, 6h differentiation

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to a Human Genome HG-U133 A2.0 Array .  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing:
To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix Expression Console with default analysis settings.

source_name: Human endometrial stromal cell sample 2 expressing flag-PRA

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: growth in 5%FBS containing DMEM:F12 medium

extract_protocol: Total RNA was performed using TRIzol® according to the manufacturer's instructions. Total RNA was cleaned up using RNeasy Mini Kit (Qiagen)  following manufacturer's instructions

treatment_protocol: treatment in 2% charcoal stripped serum sontaining DMEM:F12 medium, 48h siRNA transfection, 24h adenovirus transduction, 6h differentiation cocktail treatment composed of E, P and cAMP

value: endometrial stromal cell

tag: treatment

value: PGR kd + PRA expression


title: h3k27me3_24_rep1

source_name: h3k27me3 chIP, KH2 cells, 24 hrs RA

value: Abcam

value: input

value: KH2 cells


title: h3k4me3_24_rep2


title: h3k27me3_4

source_name: h3k27me3 chIP, KH2 cells, 4 hrs RA

source_name: input, KH2 cells, 4 hrs RA


title: atypicalMBC_3

source_name: Atypical memory B cells from patient 3


title: Sample 2 PRB

description:
Human endometrial stromal cell, decidualization, PGR
PRB expressing, 6h differentiation

source_name: Human endometrial stromal cell sample 2 expressing flag-PRB

value: PGR kd + PRB expression


title: h3k27me3_24_rep2


title: h3k4me3_4

source_name: h3k4me3 chIP, KH2 cells, 4 hrs RA


title: h3k4me3_un_rep2

value: uninduced

source_name: input, KH2 cells, uninduced


title: h3k27me3_8

source_name: h3k27me3 chIP, KH2 cells, 8 hrs RA

source_name: input, KH2 cells, 8 hrs RA


title: Sample 2 siPGR

description:
Human endometrial stromal cell, decidualization, PGR
PGR knock down, 6h differentiation

source_name: Human endometrial stromal cell sample 2 endogenous PGR knockdown

value: PGR kd


title: D16 #1

city: New Orleans

first: Frank

middle: E

last: Jones

state: LA

address: 6400 Freret Street, 2000 Percival Stern Hall

department: Cell and Molecular Biology

institute: Tulane University

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

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

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

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: Growth in complete DMEM with 10% FBS

extract_protocol: miRvana Kit

treatment_protocol: No treatments

tag: cell line

value: breast tumor


title: pcdna #2


title: pcdna #1


title: Sample 1 siPGR

source_name: Human endometrial stromal cell sample 1 endogenous PGR knockdown


title: Sample 2 PRA and PRB

description:
Human endometrial stromal cell, decidualization, PGR
PRA and PRB expressing, 6h differentiation

source_name: Human endometrial stromal cell sample 2 expressing flag-PRA and flag-PRB

value: PGR kd + PRA and PRB expression


title: Sample 1 PRA and PRB

source_name: Human endometrial stromal cell sample 1 expressing flag-PRA and flag-PRB


title: Sample 1 PRB

source_name: Human endometrial stromal cell sample 1 expressing flag-PRB


title: Sample 2 siCtrl

description:
Human endometrial stromal cell, decidualization, PGR
Control 6h differentiation

source_name: Human endometrial stromal cell sample 2 expressing endogenous PGR

value: control


title: 252800517462-3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: MEF VDAC ko Nx1

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis within in Limma package in R / Bioconductor.

source_name: MEF VDAC ko Nx1

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: Mouse embryonic fibroblasts (MEFs) derived from VDAC1-deficient mice as described in: (i) Wu et al., Biochim Biophys Acta. 1999 Oct 13;1452(1):68-78 and (ii) Weeber et al. J Biol Chem. 2002 May 24;277(21):18891-7.

extract_protocol: Qiagen - miRNeasy

value: Embryonic fibroblasts (MEFs)

tag: genotype

value: VDAC knockout

tag: oxygen status

value: normoxic

tag: amount in (µg)

tag: rin number


title: 252800517462-5

description: MEF VDAC ko Hx2

source_name: MEF VDAC ko Hx2

value: hypoxic


title: Sample 1 siCtrl

source_name: Human endometrial stromal cell sample 1 expressing endogenous PGR


title: Sample 1 PRA

source_name: Human endometrial stromal cell sample 1 expressing flag-PRA


title: Root 5 hrs-1

status: Public on Apr 26 2015

city: Dallas

first: Paul

middle: J

last: Rushton

state: Texas

address: 17360 Coit Road

institute: Texas A&M AgriLife Research & Extension Center

hyb_protocol: NimbleGen expression array hybridization using NimbleGen Hybridization Kit.

scan_protocol: NimbleGen MS-200 scanner with auto-gain - 2um scan

data_processing:
NimbleScan v. 2.6
NimbleScan software normalizes expression data using quantile normalization  as described by Bolstad, et al. (Bioinformatics 2003; 19:185).  Gene calls are generated using the Robust Multichip Average (RMA) algorithm  as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).  The *_532_norm_RMA.pair files do not have filtering. They have all 137,503  rows of probes (many of which are duplicates in this design). This  corresponds to the number of records in the .ndf file. On the other hand,  the *_532_RMA.calls files have 52,181 rows where duplicates have been combined (averaged).

organism: Glycine max

source_name: Root 5 hrs

label_protocol: total RNA was amplified using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Ref. 11917-020).  Amplified product was labeled using NimbleGen DNA Labeling Kit.

growth_protocol: Soybean W-82 seeds were grown in hydrophonics using 0.5x Hoaglonad solution, ph5.8 in a growth chamber with a 16hrs/8hrs day/night cycle at 25°C and 50% relative humidity.

extract_protocol: Total RNA was isloated for both tissues using Qiagen RNAeasy Midi Kit.

treatment_protocol: After 30days, plants were subjected to water stress by removing them without touching th eplants. Leaves and Roots were harvested by flash freezing in liquid nitrogen. Nine plants were utlized for each time point( three replicates per time-point and three plants per replicate.)

tag: cultivar/genotype

value: William -82

tag: age

value: 30 days

tag: dehydated for

value: 5 hrs

value: roots


title: Root 2 hrs-3

source_name: Root 2 hrs

value: 2 hrs

tag: tissue


title: 252800517462-7

description: MEF VDAC ko Nx2

source_name: MEF VDAC ko Nx2


title: Root 3 hrs-3

source_name: Root 3 hrs

value: 3 hrs


title: 252800517462-2

description: MEF WT Hx1

source_name: MEF WT Hx1

value: wildtype


title: 252800517462-6

description: MEF WT  Hx2

source_name: MEF WT  Hx2


title: Root 30min-3

source_name: Root 30min


title: 252800517462-4

description: MEF WT Nx1

source_name: MEF WT Nx1


title: Root 3 hrs-2


title: 252800517462-1

description: MEF VDAC ko Hx1

source_name: MEF VDAC ko Hx1


title: Root 30min-1


title: Root 0min-3

source_name: Root 0min


title: Root 2 hrs-2


title: Root 30min-2


title: Root 3 hrs-1


title: Root 1 hr-1

source_name: Root 1 hr

value: 1 hr


title: Root 2 hrs-1


title: Root 0min-2


title: Root 0min-1


title: Root 1 hr-3


title: MaSCs-1

city: chong qing

first: ming

middle: zhong

last: feng

address: Shapingba District Street Bridge

institute: Xinqiao Hospital

description: We compared miRNA profiles between BCSCs and MaSCs, and obtained 12 differential miRNAs. Among them, 8 miRNAs were upregulated in BCSCs and 4 miRNAs downregulated in BCSCs

hyb_protocol: After separation amplification and fluorescent labeling of small molecules of RNA, hybridization was conducted at 42°C overnight.

scan_protocol: Arrays were scanned with a LuxScan 10K-A laser confocal scanner, and the images obtained were then analyzed using LuxScan 3.0 software (both from CapitalBio).

data_processing: For all samples, after average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out if the expression signal was <800. Signals were normalized using the median center tool for genes in the Cluster 3.0 software before performing the unsupervised clustering with complete linkage and uncentered Pearson correlation to reveal the underlying structure of the miRNA expression . Differentially expressed miRNAs were identified by significance analysis of microarrays .

label: 5'-phosphate-cytidyl-uridyl-cy3-3' with 2 units T4 RNA ligase

source_name: Mammary epithelial cells

label_protocol: The amplified RNA was labeled with 5 '-phosphate-cytidyl-uridyl-cy3-3 ' with 2 units T4 RNA ligase according to Thomson’protocol.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen), and the low-molecular-weight RNA was isolated using a PEG solution precipitation method.

value: mammary epithelial stem cells (MaSCs)


title: MaSCs-2


title: BCSCs-2

description: There were 19 miRNAs with an expression level that was four times higher in BCSCs than in MCF-7 cells,there were six miRNAs with an expression level that was four times lower in BCSCs than in MCF-7 cells.And we compared miRNA profiles between BCSCs and MaSCs, and obtained 12 differential miRNAs. Among them, 8 miRNAs were upregulated in BCSCs and 4 miRNAs downregulated in BCSCs

source_name: Breast cancer cells

value: breast cancer stem cells (BCSCs)


title: Leaf 5 hrs-3

source_name: Leaf 5 hrs

value: leaves


title: Leaf 3 hrs-2

source_name: Leaf 3 hrs


title: Leaf 5 hrs-2


title: BCSCs-1


title: Leaf 3 hrs-3


title: Leaf 1 hr-2

source_name: Leaf 1 hr


title: Leaf 0min-1

source_name: Leaf 0min


title: Leaf 30min-2

source_name: Leaf 30min


title: Leaf 2 hrs-2

source_name: Leaf 2 hrs


title: Leaf 2 hrs-3


title: Leaf 5 hrs-1


title: Leaf 30min-3


title: Leaf 2 hrs-1


title: Leaf 1 hr-3


title: Leaf 0min-2


title: THP-1 1,25D 24h rep1

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
replicate 1
1710

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package

source_name: THP-1 cells 1,25D 24h rep1

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

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Total RNA was extracted with Mini RNA Isolation II kit (Zymo Research). Quality control, including verification of the absence of genomic DNA, was performed with Biorad Experion.

treatment_protocol: Prior to mRNA extraction, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for indicated time(s) with vehicle (ethanol, finally 0.1%) or 100 nM 1α,25(OH)2D3 (Sigma-Aldrich)

tag: origin

value: monocytic leucemia


title: Leaf 0min-3


title: D16 #3

value: breast tumor


title: THP-1 1,25D 24h rep3

description:
replicate 3
1712

source_name: THP-1 cells 1,25D 24h rep3


title: THP-1 vehicle 24h rep3

description:
replicate 3
1706

source_name: THP-1 cells vehicle 24h rep3

value: vehicle


title: THP-1 1,25D 24h rep2

description:
replicate 2
1711

source_name: THP-1 cells 1,25D 24h rep2


title: Leaf 3 hrs-1


title: Leaf 1 hr-1


title: Root 5 hrs-3

source_name: Root 5 hrs


title: MCF-7-1

description: There were 19 miRNAs with an expression level that was four times higher in BCSCs than in MCF-7 cells,there were six miRNAs with an expression level that was four times lower in BCSCs than in MCF-7 cells.

value: Breast cancer cells


title: THP-1 vehicle 24h rep1

description:
replicate 1
1704

source_name: THP-1 cells vehicle 24h rep1


title: Leaf 30min-1


title: LR-MSCs, biological rep2

status: Public on Apr 25 2015

last: Tong

address: 180 Fenglin Road

department: Department of Pulmonary Medicine

institute: Zhongshan Hospital, Fudan University

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

organism: Rattus norvegicus

source_name: lung-resident mesenchymal stem cells

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

growth_protocol: The cells were maintained in medium consisting of DMEM/F12 supplemented with 10% fetal bovine serum, 2mmol/l L-glutamine, 100 U/ml penicillin/streptomycin, and 2.5 ug/ml amphotericin B and incubated at 37°C in 5% CO2 / 95% air.

extract_protocol: All samples were prepared using Trizol. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: passage 5

value: mesenchymal stem cells

value: wild type

value: lung


title: THP-1 vehicle 24h rep2

description:
replicate 2
1705

source_name: THP-1 cells vehicle 24h rep2


title: LR-MSCs, biological rep1


title: BM-MSCs, biological rep2

source_name: bone marrow-derived mesenchymal stem cells

value: bone marrow


title: BM-MSCs, biological rep1


title: (M)-K676-HER2 60h

city: Barcelona

first: Kim

last: Pedersen

address: Psg. Vall d'Hebron 119-129

country: Spain

institute: Vall d'Hebron Institute of Oncology (V.H.I.O.)

description: SAMPLE 48

hyb_protocol: Approximately 15μg of fragmented and labeled cRNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven 650

scan_protocol: Arrays were scanned in the Scanner 3000 7G

data_processing: The data files were analyzed in the program ArrayAssist 5.5.1 (Stratagene) with probe levels normalized by the RMA algorithm

label_protocol: One-cycle amplification target labeling protocol

growth_protocol: 37°C and 5% CO2 in DMEM/F-12 (1:1)(Gibco) containing 10% FBS (Gibco), 4mM L-Glutamine (PAA Laboratories), 0.2mg/ml G418 (Gibco) and 1µg/ml doxycycline (Sigma)

extract_protocol: Qiagen Rneasy kit (integrity of the total RNA samples was validated in an Agilent BioAnalyzer Nanochip)

treatment_protocol: 15 or 60 hours +/- 1µg/ml doxycycline in medium

value: MCF7 tet/off clone

tag: protein expressed

tag: time point

value: 60 hours


title: M687-HER2 +dox 60h

description: SAMPLE 49


title: M687-HER2 60h

description: SAMPLE 50


title: (M)-K676-HER2 +dox 60h

description: SAMPLE 47


title: 3100196

city: Morgantown

first: Taura

middle: L.

last: Barr

state: WV

address: One Medical Center Drive, BMRB Rm 119

department: School of Nursing

institute: West Virginia University

description: SAMPLE 64_Patient 23 Follow-Up

hyb_protocol: Illumina Whole genome gene expression direct hybridization assay

scan_protocol: Illumina Bead Station 500x, scanning conducted using standard protocol

data_processing:
Raw intensity values were saved in Illumina's Bead Studio program manager and then downloaded into GeneSpring Agilent GX v10, RMA normalization collated the probe data (background correction; quantile normalization; summarization)
Matrix normalized is the RMA normalized data for each probe; non-normalized is the raw signal intensity for each probe.

label: Biotin

source_name: Human Peripheral Blood

label_protocol: Biotinylated, amplified RNA was generated from the Illumina TotalPrep amplification kit (Applied Biosystems)

extract_protocol: Total mRNA was extracted from the Paxgene Blood RNA tubes using the Paxgene Blood RNA Kit, PreAnalytiX Qagen

value: Human Peripheral Blood

value: PBMC

tag: patient number

value: Patient 23

tag: gender

value: Male

tag: ethnicity

value: Caucasian

tag: disease state

value: Ischemic Stroke

tag: time

value: Follow-Up


title: 3100138

description: SAMPLE 65_Patient 15 Baseline

tag: cell type

value: Patient 15

value: Baseline


title: 3100037

description: SAMPLE 66_Patient 26 Follow-Up

value: Patient 26


title: (M)-A648-HER2 +dox 60h rep1

description: SAMPLE 43

tag: cell line


title: 3100136

description: SAMPLE 67_Patient 11 Follow-Up

value: Patient 11


title: (M)-A648-HER2 60h rep1

description: SAMPLE 44


title: M611-HER2 +dox 60h rep2 clone B

description: SAMPLE 41


title: 3100065

description: SAMPLE 63_Patient 5 Follow-Up

value: Patient 5


title: 3100133

description: SAMPLE 62_Patient 13 Follow-Up

value: Patient 13


title: (M)-A648-HER2 60h rep2

description: SAMPLE 46


title: 3100069

description: SAMPLE 61_Patient 7 Follow-Up

value: Patient 7


title: 3100115

description: SAMPLE 60_Patient 15 Follow-Up


title: 3100192

description: SAMPLE 59_Patient 34 Follow-Up

value: Patient 34


title: BM-MSCs, biological rep3

tag: passage

value: passage 5

value: mesenchymal stem cells

tag: genotype

value: wild type

value: bone marrow


title: M611 -HER2 60h rep1 clone B

description: SAMPLE 40

value: MCF7 tet/off clone

value: 60 hours


title: M611-HER2 60h rep2 clone B

description: SAMPLE 42


title: M611-HER2 +dox 60h rep1 clone B

description: SAMPLE 39


title: 3100067

description: SAMPLE 57_Patient 17 Follow-Up

value: Human Peripheral Blood

value: PBMC

value: Patient 17

value: Female

value: Caucasian


title: Full length HER2 60h rep2

description: SAMPLE 38


title: 3100020

description: SAMPLE 68_Patient 1 Follow-Up

value: Patient 1

value: Male

value: Ischemic Stroke

value: Follow-Up


title: Root 5 hrs-2

value: William -82

value: 30 days

value: 5 hrs

value: roots


title: 3100063

description: SAMPLE 56_Patient 30 Follow-Up

value: Patient 30


title: Empty vector 60h

description: SAMPLE 34

source_name: #71, neg ctrl


title: Full length HER2 60h rep1

description: SAMPLE 36


title: 3100053

description: SAMPLE 58_Patient 10 Follow-Up

value: Patient 10


title: Empty vector +dox 60h

description: SAMPLE 33

value: MCF7 tet/off clone


title: Full length HER2 +dox 60h rep2

description: SAMPLE 37

value: 60 hours


title: 3100024

description: SAMPLE 54_Patient 29 Follow-Up

value: Human Peripheral Blood

value: Patient 29


title: 3100072

description: SAMPLE 51_Patient 6 Follow-Up

value: PBMC

value: Patient 6


title: Lung cancer cells_H2AX knockdown_rep3

city: Beijing

first: Chengrong

last: Lu

address: Fucheng road 30

department: Aviation Medicine Research lab

institute: General Hospital of Air Force

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software 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: Lung cancer cells_P1 treated with VP 16

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: A549 stable cells (C and P1) were seeded in 10 cm dishes and cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) until they reached 80% confluence.

treatment_protocol: The cells (C and P1) were then treated with VP16 (100M) for 48 h after serum starvation overnight

value: lung cancer cell line

tag: genotype/variation

value: H2AX knockdown (P1)

tag: treated with

value: 100M VP16 for 48 h


title: 3100015

description: SAMPLE 52_Patient 18 Follow-Up

tag: age

value: Patient 18

value: Female

value: Caucasian

value: Ischemic Stroke


title: 3100139

description: SAMPLE 53_Patient 12 Follow-Up

value: Patient 12

value: Follow-Up


title: 3100028

description: SAMPLE 49_Patient 19 Follow-Up

value: Patient 19


title: Full length HER2 +dox 60h rep1

description: SAMPLE 35


title: (M)-A648-HER2 +dox 60h rep2

description: SAMPLE 45


title: M611-HER2 kinase dead 15h rep2

description: SAMPLE 32

value: M611-CTF (KD)

value: 15 hours


title: 3100144

description: SAMPLE 50_Patient 33 Follow-Up

value: Patient 33


title: 3100018

description: SAMPLE 48_Patient 3 Follow-Up

value: Human Peripheral Blood

value: Patient 3


title: Root 1 hr-2

source_name: Root 1 hr

tag: cultivar/genotype

value: William -82

value: 30 days

tag: dehydated for

value: 1 hr

value: roots


title: Lung cancer cells_H2AX knockdown_rep1

value: lung cancer cell line

value: H2AX knockdown (P1)

value: 100M VP16 for 48 h


title: M611-HER2 kinase dead +dox 15h rep2

description: SAMPLE 31

value: MCF7 tet/off clone


title: 3100029

description: SAMPLE 55_Patient 28 Follow-Up

tag: tissue

value: PBMC

value: Patient 28

value: Female

value: Caucasian

value: Ischemic Stroke


title: LR-MSCs, biological rep3

value: passage 5

value: mesenchymal stem cells

value: wild type

value: lung


title: 3100198

description: SAMPLE 47_Patient 24 Follow-Up

value: Human Peripheral Blood

value: Patient 24

value: Follow-Up


title: Lung cancer cells_H2AX knockdown_rep2


title: MCF-7-2

source_name: Breast cancer cells

value: Breast cancer cells


title: Lung cancer cells_control_rep3

source_name: Lung cancer cells_control treated with VP 16

value: lung cancer cell line

value: control


title: 3100075

description: SAMPLE 46_Patient 9 Follow-Up

value: Patient 9


title: 3100056

description: SAMPLE 45_Patient 2 Follow-Up

value: Patient 2


title: M611-HER2 kinase dead 15h rep1

description: SAMPLE 30

value: MCF7 tet/off clone

tag: protein expressed

value: M611-CTF (KD)

value: 15 hours


title: M687-HER2 15h rep2

description: SAMPLE 28

tag: time point


title: M611-HER2 kinase dead +dox 15h rep1

description: SAMPLE 29


title: 3100064

description: SAMPLE 43_Patient 8 Follow-Up

value: PBMC

tag: patient number

value: Patient 8

value: Female

value: Caucasian


title: Lung cancer cells_control_rep1

value: 100M VP16 for 48 h


title: M687-HER2 +dox 15h rep1

description: SAMPLE 25


title: 3100206

description: SAMPLE 44_Patient 32 Follow-Up

value: Patient 32

tag: gender

value: Ischemic Stroke


title: 3100194

description: SAMPLE 41_Patient 16 Follow-Up

value: Human Peripheral Blood

value: Patient 16

tag: ethnicity


title: M687-HER2 15h rep1

description: SAMPLE 26


title: M687-HER2 +dox 15h rep2

description: SAMPLE 27


title: 3100021

description: SAMPLE 34_Patient 17 Baseline

value: Patient 17

tag: disease state

value: Baseline


title: Lung cancer cells_control_rep2

value: lung cancer cell line

value: control


title: 3100027

description: SAMPLE 42_Patient 20 Follow-Up

value: Patient 20

tag: time

value: Follow-Up


title: 3100152

description: SAMPLE 36_Patient 22 Follow-Up

tag: cell type

value: Patient 22

value: Male


title: 3100084

description: SAMPLE 33_Patient 30 Baseline

value: PBMC

value: Patient 30


title: 3100122

description: SAMPLE 38_Patient 14 Follow-Up

value: Patient 14

value: Female


title: 3100044

description: SAMPLE 32_Patient 28 Baseline

value: Patient 28

value: Caucasian


title: 3100054

description: SAMPLE 39_Patient 27 Follow-Up

value: Patient 27

value: Ischemic Stroke


title: 3100055

description: SAMPLE 40_Patient 25 Follow-Up

value: Human Peripheral Blood

value: Patient 25


title: 3100140

description: SAMPLE 35_Patient 31 Follow-Up

value: Patient 31


title: (M)-K676-HER2 15h rep2

description: SAMPLE 24

tag: cell line

value: MCF7 tet/off clone

value: 15 hours


title: SkeletalMuscle_T2D [EP22]

city: Melbourne

first: Celine

last: Latouche

state: VIC

address: 75 Commercial Road

country: Australia

institute: Baker IDI Heart and Diabetes Institute

description:
microRNA expression in patients with Type 2 Diabetes
EP22

hyb_protocol: Hybridization of labeled miRNA to 8x60K Human miRNA microarray slides (based on miRBase release 16.0) was for 20 hours at 55ºC on a rotator at 20 rpm.

scan_protocol: The slides were then washed and scanned with an Agilent microarray scanner.

data_processing: Extracted data were analyzed with GeneSpring GX7.3 expression analysis software (Agilent Technologies).

source_name: vastus lateralis_T2Diabetics

label_protocol: Cy3-labeled RNA was generated using the Agilent’s miRNA Complete Labeling and Hyb Kit with a sample input of 100 ng of total RNA.

extract_protocol: Total RNA (including microRNAs) was extracted from frozen tissues using the TRIZOL reagent (Invitrogen) following the manufacturer’s recommended protocol. Concentration and purity of the total RNAs were assessed by spectrophotometer (Nanodrop 1000, Nanodrop Technologies, Wilmington, DE, USA) and RNA integrity was verified using an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: Human: Healthy vs Pre-diabetics vs Type 2 diabetics;

tag: subject status

value: type 2 diabetes (T2D)

value: male

value: skeletal muscle (vastus lateralis)


title: 3100119

description: SAMPLE 37_Patient 21 Follow-Up

value: Patient 21

value: Male

value: Follow-Up


title: SkeletalMuscle_PD [EP23]

description:
microRNA expression in patients with pre-diabetes
EP23

source_name: vastus lateralis_prediabetics

value: pre-diabetics


title: SkeletalMuscle_T2D [EP20]

description:
microRNA expression in patients with Type 2 Diabetes
EP20


title: 3100047

description: SAMPLE 31_Patient 29 Baseline

value: PBMC

value: Patient 29

value: Female

value: Baseline


title: (M)-K676-HER2 15h rep1

description: SAMPLE 22


title: SkeletalMuscle_PD [EP18]

description:
microRNA expression in patients with pre-diabetes
EP18


title: 3100035

description: SAMPLE 29_Patient 18 Baseline

value: Patient 18

value: Caucasian

value: Ischemic Stroke


title: SkeletalMuscle_H [EP15]

description:
microRNA expression in skeletal muscle of healthy human
EP15

source_name: vastus lateralis_healthy

value: healthy


title: 3100126

description: SAMPLE 30_Patient 12 Baseline

value: Human Peripheral Blood

value: Patient 12


title: SkeletalMuscle_T2D [EP11]

description:
microRNA expression in patients with Type 2 Diabetes
EP11

value: type 2 diabetes (T2D)


title: (M)-A648-HER2 15h rep2

description: SAMPLE 20

value: MCF7 tet/off clone

value: 15 hours


title: SkeletalMuscle_H [EP12]

description:
microRNA expression in skeletal muscle of healthy human
EP12

value: male

value: skeletal muscle (vastus lateralis)


title: 3100061

description: SAMPLE 28_Patient 6 Baseline

value: Patient 6


title: SkeletalMuscle_H [EP10]

description:
microRNA expression in skeletal muscle of healthy human
EP10


title: 3100036

description: SAMPLE 25_Patient 19 Baseline

value: Patient 19


title: (M)-A648-HER2 +dox 15h rep2

description: SAMPLE 19


title: (M)-K676-HER2 +dox 15h rep2

description: SAMPLE 23


title: SkeletalMuscle_H [EP09]

description:
microRNA expression in skeletal muscle of healthy human
EP09


title: 3100077

description: SAMPLE 23_Patient 9 Baseline

value: PBMC

value: Patient 9


title: (M)-A648-HER2 15h rep1

description: SAMPLE 18


title: (M)-A648-HER2 +dox 15h rep1

description: SAMPLE 17


title: M611-HER2 15h rep2 clone B

description: SAMPLE 16


title: 3100034

description: SAMPLE 21_Patient 25 Baseline

value: Patient 25

value: Female


title: 3100193

description: SAMPLE 22_Patient 16 Baseline

value: Patient 16

value: Baseline


title: 3100121

description: SAMPLE 27_Patient 33 Baseline

value: Patient 33

value: Caucasian

value: Ischemic Stroke


title: SkeletalMuscle_H [EP08]

description:
microRNA expression in skeletal muscle of healthy human
EP08

value: healthy


title: SkeletalMuscle_T2D [EP13]

description:
microRNA expression in patients with Type 2 Diabetes
EP13

value: type 2 diabetes (T2D)


title: M611-HER2 +dox 15h rep2 clone B

description: SAMPLE 15

value: MCF7 tet/off clone


title: 3100050

description: SAMPLE 26_Patient 3 Baseline

value: Human Peripheral Blood

value: Patient 3


title: SkeletalMuscle_T2D [EP07]

description:
microRNA expression in patients with Type 2 Diabetes
EP07

value: male

value: skeletal muscle (vastus lateralis)


title: SkeletalMuscle_T2D [EP06]

description:
microRNA expression in patients with Type 2 Diabetes
EP06


title: 3100042

description: SAMPLE 20_Patient 27 Baseline

value: Patient 27


title: 3100197

description: SAMPLE 24_Patient 24 Baseline

value: PBMC

value: Patient 24


title: SkeletalMuscle_PD [EP17]

description:
microRNA expression in patients with pre-diabetes
EP17

value: pre-diabetics


title: 3100048

description: SAMPLE 18_Patient 2 Baseline

value: Patient 2

value: Female


title: SkeletalMuscle_PD [EP16]

description:
microRNA expression in patients with pre-diabetes
EP16


title: 3100118

description: SAMPLE 17_Patient 32 Baseline

value: Patient 32

value: Baseline


title: 3100137

description: SAMPLE 19_Patient 14 Baseline

value: Patient 14

value: Caucasian


title: SkeletalMuscle_PD [EP05]

description:
microRNA expression in patients with pre-diabetes
EP05


title: M611-HER2 +dox 15h rep1 clone B

description: SAMPLE 13

value: 15 hours


title: 3100076

description: SAMPLE 16_Patient 8 Baseline

value: Patient 8

value: Ischemic Stroke


title: M611-HER2 +dox 15h rep2 clone A

description: SAMPLE 11

value: MCF7 tet/off clone


title: M611-HER2 15h rep2 clone A

description: SAMPLE 12


title: M611 -HER2 15h rep1 clone B

description: SAMPLE 14


title: M611-HER2 15h rep1 clone A

description: SAMPLE 10


title: 3100066

description: SAMPLE 15_Patient 20 Baseline

value: Human Peripheral Blood

value: Patient 20


title: Full length HER2 15h rep2

description: SAMPLE 8


title: 3100114

description: SAMPLE 14_Patient 21 Baseline

value: Patient 21

value: Male


title: Mouse_sham_24h_rep4

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description: Gene expression in mouse ventricles after 24 hours sham operation

hyb_protocol: cDNA obtained were purified with RNeasy Minikit (Qiagen) and hybridized with Gene expression Hybridization kit (Agilent)

scan_protocol: Microarrays were scanned by Agilent G2505C scanner with the standard protocol of the manufacturer.

data_processing: Data pre-processing was performed using Limma (Smyth 2005) and vsn (Huber et al. 2002) packages rooted in the statistical computing environment R. The “bad spots”, i.e. signals were not well above the background, were removed. Normalization between arrays was performed with Agilent Spike-in probes.

source_name: ventricles, sham, 24h, replicate 4

label_protocol: 200 ng of total RNA of each sample was labeled and amplified with Low input Quick Amp labeling kit.

extract_protocol: Total RNA was extracted using miRvana isolation kit (Life technologies). A DNase (Qiagen) was used to digest potential genomic DNA contamination. The RNA quantity was measured by Nanodrop (Nanodrop, Nanodrop products, Wilmington, USA) and the RNA integrity was assessed by bioanalyzer (RNA 6000 Nano kit, Agilent technologies, Santa-Clara, USA).

value: Ventricles of the heart

tag: treatment

value: sham

value: male

tag: genetic background


title: 3100157

description: SAMPLE 13_Patient 22 Baseline

value: PBMC

value: Patient 22


title: Full length HER2 +dox 15h rep1

description: SAMPLE 5


title: Full length HER2 15h rep1

description: SAMPLE 6


title: Control for group A, biological rep1

first: Lalita

last: Wattanachanya

address: 1700 Owens St.

institute: San Francisco VA Medical Center

description: Calvarial OBs from 1 week-old mice

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

source_name: wild type osteoblasts

label_protocol: NuGEN FFPE WTA System, NuGEN Exon Module, and NuGEN Encore Biotin Module

growth_protocol: We utilized green fluorescent protein (GFP)-based reporters to identify Rs1 expressing cells for investigating OB transcriptome analysis. We co-expressed a histone-GFP marker in OBs in vivo either alone (abbreviated Col1(2.3)/GFP) or together with Rs1 in triple transgenic mice (abbreviated Col1(2.3)/GFP/Rs1). This was accomplished by generating mice harboring a TetO-histone-GFP gene together with a TetO-Rs1 gene. Double transgenic mice were then crossed with mice homozygous for the 2.3 Col1-tTA genes to examine the skeletal effects of Gs signaling in mature OBs. Both transgenes driven by TetO were expressed in OBs only when the 2.3 Col1-tTA transgene was present.

extract_protocol: Total RNA extraction was performed using Arcturus PicoPure RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Calvariae with OB-specific expression of histone-GFP either alone or together with Rs1 under control of the 2.3kb-Col I promoter were isolated from one-week-old transgenic mice, pooled and divided into 3 groups according to their genotype (Col1(2.3) and Col1(2.3)/Rs1; Col1(2.3)/GFP; or Col1(2.3)/GFP/Rs1). After removal of the calvarial sutures, calvarial tissues were subjected to four sequential, 30-minute long digestions in an enzymatic mixture (1.5U/ml collagenase P, 0.05% trypsin and 0.25 mM EDTA in PBS) at 37°C. Cell fractions 2-4 were collected, pooled and resuspended in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and centrifuges. Then, cells were resuspended in 0.5-1 ml of 2% FCS in PBS and filtered through a 70-µm cell strainer. Individual cell populations were sorted based on GFP expression utilizing a fluorescent activated cell sorting with a 100-µm nozzle at the Cell Sorting Core at the San Francisco VA Medical Center. Cells from GFP non-expressing mice (Col1(2.3) plus Col1(2.3)/Rs1) were used as controls to preset the sorting gate. Sorted cells were collected into 30% FCS in DMEM. A fraction of the sorted cell population (5x103) was used for FACS reanalysis using the same gating strategy used in the sorted procedure to assure the maximum purity. Cell suspensions were kept cold during the entire sorting process to minimize changes in gene expression.

value: osteoblasts

tag: strain

value: FVB/N


title: 3100031

description: SAMPLE 12_Patient 1 Baseline

tag: age

value: Patient 1

value: Baseline


title: Mouse_ligation_24h_rep4

description: Gene expression in mouse ventricles after 24 hours  anterior interventricular artery ligation

source_name: ventricles,  anterior interventricular artery ligation, 24h, replicate 4


title: 3100113

description: SAMPLE 11_Patient 11 Baseline

value: Patient 11

value: Caucasian


title: Col1(2.3).GFP.Rs1 mice, biological rep3

description: Calvarial OBs from 1 week-old mice

source_name: Rs1 expressing osteoblasts


title: Full length HER2 +dox 15h rep2

description: SAMPLE 7

value: 15 hours


title: Control for group A, biological rep2

description: Calvarial OBs from 1 week-old mice


title: Mouse_ligation_24h_rep3

source_name: ventricles,  anterior interventricular artery ligation, 24h, replicate 3


title: 3100039

description: SAMPLE 10_Patient 26 Baseline

value: Patient 26

value: Ischemic Stroke


title: Empty vector 15h rep2

description: SAMPLE 4

value: MCF7 tet/off clone


title: Mouse_sham_24h_rep3

source_name: ventricles, sham, 24h, replicate 3


title: Col1(2.3).GFP.Rs1 mice, biological rep2

description: Calvarial OBs from 1 week-old mice


title: 3100112

description: SAMPLE 9_Patient 31 Baseline

value: Human Peripheral Blood

value: Patient 31


title: Empty vector 15h rep1

description: SAMPLE 2


title: 3100195

description: SAMPLE 7_Patient 23 Baseline

value: Patient 23

value: Male


title: Empty vector +dox 15h rep2

description: SAMPLE 3


title: Mouse_ligation_24h_rep2

source_name: ventricles,  anterior interventricular artery ligation, 24h, replicate 2

value: Ventricles of the heart

value: male


title: SkeletalMuscle_C [A75]

description:
A75
microRNA expression in adult offspring from control dams

hyb_protocol: Hybridization of labeled miRNA to 8x15K Rat miRNA microarray slides (based on miRBase release 16.0) was for 20 hours at 55ºC on a rotator at 20 rpm.

treatment_protocol: Rats: offspring from control dams vs offspring from dams fed a high fat diet during pregnancy and lactation

tag: strain background

value: Sprague-Dawley

tag: diet during pregnancy/lactation

value: control

tag: offspring gender

tag: offspring age

value: 1 year

value: skeletal muscle (soleus)


title: Mouse_sham_24h_rep2

source_name: ventricles, sham, 24h, replicate 2

tag: tissue

value: sham


title: Mouse_sham_24h_rep1

source_name: ventricles, sham, 24h, replicate 1


title: Empty vector +dox 15h rep1

description: SAMPLE 1

source_name: #71, neg ctrl

tag: protein expressed

tag: time point


title: SkeletalMuscle_C [A89]

description:
A89
microRNA expression in adult offspring from control dams


title: Mouse_ligation_24h_rep1

source_name: ventricles, anterior interventricular artery ligation, 24h, replicate 1

tag: gender


title: 3100058

description: SAMPLE 8_Patient 4 Baseline

source_name: Human Peripheral Blood

value: PBMC

tag: patient number

value: Patient 4

tag: ethnicity

tag: disease state

value: Baseline


title: SkeletalMuscle_HF [H20]

description:
H20
microRNA expression in adult offspring from high fat-fed dams

value: high fat


title: Col1(2.3).GFP.Rs1 mice, biological rep1

description: Calvarial OBs from 1 week-old mice

tag: cell type

value: osteoblasts

value: FVB/N


title: SkeletalMuscle_HF [A37]

description:
A37
microRNA expression in adult offspring from high fat-fed dams


title: 3100135

description: SAMPLE 6_Patient 13 Baseline

value: Human Peripheral Blood

value: Patient 13

value: Caucasian

value: Ischemic Stroke

tag: time


title: SC5

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

description: Gene expression of S. suis grown in working culture

hyb_protocol: After fragmentation, microarray slides were hybridized with 600ng Cy3-labeled cRNA. Hybridization was performed at 65ºC for 17 h with rotation at 10 rpm.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0.

organism: Streptococcus suis

source_name: S. suis grown in working cultures, replicate 4

label_protocol: Total RNA was  were amplified and labeled with Cy3-CTP. Labeled cRNA was purified using the RNeasy mini kit (Qiagen).

growth_protocol: Working cultures were prepared by inoculating 10 ul of an overnight culture into 40 ml of fresh medium which was incubated for 6 h at 37 ºC.

extract_protocol: Total RNA was isolated using an SV total RNA isolation system (Promega), according to the manufacturer’s recommended protocol.

treatment_protocol: S. suis were injected into the air pouches. Bacterial cells were collected at 6 h post infection.

tag: serotype

value: serotype 2


title: 6wk_wt_1

city: Yokohama

first: Hisahiro

last: Yoshida

address: Tsurumi, 1-7-22

department: IMS

country: Japan

institute: RIKEN Institute

description:
Gene expression data from whole ears tissue from 6 weeks mouse
RMSKXX008001

hyb_protocol: Microarray analysis was performed using GeneChip mouse genome 430_2.0 array (Affymetrix).

scan_protocol: The CEL file stores the results of the intensity calculation on the pixel values generated by the GCOS software (Affymetrix, Inc.).

data_processing:
The .txt.gz and .norm.txt.gz files store the raw and normalized values of the signal intensity of probe sets on the microarray, respectively, calculated with MAS5 algorithm.
The data were further analyzed by using packages in R and Bioconductor. Per chip normalization of datasets was performed by GCRMA package. An average intensity of two independent of duplicate for each week-wise (second-, fourth-, sixth-week) and mixture dataset was adopted in differential gene expression analysis. The differential genes were identified based on the following criteria: (i) twofold changes between wild-type and Spade (ii) false discovery rate (FDR) calculated by RankProd package with permutation number 1000 (49) for week-wise (FDR<0.05) and mixture (FDR<0.001) datasets

source_name: Mouse ears 6weeks old wild type #1

label_protocol: not provided

extract_protocol: RNA from ear tissue was isolated using an RNeasy Fibrous Tissue Kit (Qiagen).

value: whole ear tissue

tag: genotype

value: wild type

value: 6 weeks


title: 4wk_mutant_2

description:
Gene expression data from whole ears tissue from 4 weeks mouse
RMSKXX003001

source_name: Mouse ears 4weeks old Spade/Spade mutant #2

value: Spade/Spade

value: 4 weeks


title: 3100038

description: SAMPLE 5_Patient 4 Follow-Up

value: Male

value: Follow-Up


title: SkeletalMuscle_HF [C25]

description:
C25
microRNA expression in adult offspring from high fat-fed dams

value: Sprague-Dawley

value: male

value: 1 year

value: skeletal muscle (soleus)


title: SC3

source_name: S. suis grown in working cultures, replicate 3

tag: strain


title: SkeletalMuscle_C [H10]

description:
H10
microRNA expression in adult offspring from control dams

value: control


title: 3100068

description: SAMPLE 3_Patient 7 Baseline

tag: age

value: Human Peripheral Blood

value: PBMC

value: Patient 7

value: Baseline


title: 3100060

description: SAMPLE 4_Patient 5 Baseline

value: Patient 5

value: Caucasian

value: Ischemic Stroke


title: SkeletalMuscle_HF [H1]

description:
H1
microRNA expression in adult offspring from high fat-fed dams

tag: strain background

value: high fat


title: 4wk_wt_1

description:
Gene expression data from whole ears tissue from 4 weeks mouse
RMSKXX004001

source_name: Mouse ears 4weeks old wild type #1

value: whole ear tissue

value: wild type


title: 3100191

description: SAMPLE 2_Patient 34 Baseline

value: Patient 34

value: Male


title: SkeletalMuscle_HF [H3]

description:
H3
microRNA expression in adult offspring from high fat-fed dams

value: Sprague-Dawley

tag: diet during pregnancy/lactation


title: SC2

source_name: S. suis grown in working cultures, replicate 2

value: serotype 2


title: SC1

source_name: S. suis grown in working cultures, replicate 1


title: SkeletalMuscle_C [A110]

description:
A110
microRNA expression in adult offspring from control dams

tag: offspring gender

value: male

value: 1 year


title: 4wk_mutant_1

description:
Gene expression data from whole ears tissue from 4 weeks mouse
RMSKXX002001

source_name: Mouse ears 4weeks old Spade/Spade mutant #1

value: Spade/Spade

value: 4 weeks


title: SkeletalMuscle_C [C60]

description:
C60
microRNA expression in adult offspring from control dams

value: control

tag: offspring age

value: skeletal muscle (soleus)


title: 6h42

description: Gene expression of S. suis after 6 h in the air pouch

source_name: S. suis collected from the air pouches, replicate 3


title: 6wk_mutant_3

description:
Gene expression data from whole ears tissue from 6 weeks mouse
RMSKXX019001

source_name: Mouse ears 6weeks old Spade/Spade mutant #3

tag: tissue

value: 6 weeks


title: 3100083

description: SAMPLE 1_Patient 10 Baseline

value: Human Peripheral Blood

value: PBMC

value: Patient 10

value: Baseline


title: 2wk_mutant_2

description:
Gene expression data from whole ears tissue from 2 weeks mouse
RMSKXX026001

source_name: Mouse ears 2weeks old Spade/Spade mutant #2

value: whole ear tissue

value: 2 weeks


title: 6h74

source_name: S. suis collected from the air pouches, replicate 4


title: SkeletalMuscle_HF [C51]

description:
C51
microRNA expression in adult offspring from high fat-fed dams

value: high fat


title: 4wk_wt_3

description:
Gene expression data from whole ears tissue from 4 weeks mouse
RMSKXX017001

source_name: Mouse ears 4weeks old wild type #3

value: wild type


title: 6wk_wt_3

description:
Gene expression data from whole ears tissue from 6 weeks mouse
RMSKXX018001

source_name: Mouse ears 6weeks old wild type #3


title: 2wk_wt_2

description:
Gene expression data from whole ears tissue from 2 weeks mouse
RMSKXX024001

source_name: Mouse ears 2weeks old wild type #2


title: 6h23

source_name: S. suis collected from the air pouches, replicate 2


title: 6h11

source_name: S. suis collected from the air pouches, replicate 1


title: SkeletalMuscle_C [C73]

description:
C73
microRNA expression in adult offspring from control dams

value: Sprague-Dawley


title: (M)-K676-HER2 +dox 15h rep1

description: SAMPLE 21

tag: cell line

value: MCF7 tet/off clone

tag: protein expressed

value: 15 hours


title: 2wk_wt_1

description:
Gene expression data from whole ears tissue from 2 weeks mouse
RMSKXX023001

source_name: Mouse ears 2weeks old wild type #1


title: 6wk_mutant_4

description:
Gene expression data from whole ears tissue from 6 weeks mouse
RMSKXX020001

source_name: Mouse ears 6weeks old Spade/Spade mutant #4


title: Mature dendritic_cells_non_infected_rep3

status: Public on Apr 24 2015

city: Madrid

first: Esther

last: Calonge

address: Ctra Pozuelo-Majadahonda Km 2

department: Centro Nacional Microbiologia

institute: Instituto Salud Carlos III

description: Gene expression aftyer 72h of culture

hyb_protocol: 1.65 ug of Cy3-labeled aRNA were hybridized for 17 hours at 65ºC in a Agilent hybridization oven (G2545A, Agilent Technologies) set to 10 rpm in a final concentration of 1x GEx Hybridization Buffer HI-RPM (Agilent Technologies). Arrays were washed and dried out using a centrifuge according to manufacturer's instructions.

scan_protocol: Arrays were scanned at 5μm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

data_processing:
Images provided by the scanner were analyzed using Feature Extraction software v10.7 (Agilent Technologies).
Notes : Entity List : Filtered on Flags [Detected, Not Detected]
Entities where atleast 1 out of 1  conditions have CV >= 1.0 percent

source_name: Mature dendritic cells, non infected, 72h, rep3

label_protocol: Cyanine-3 (Cy3) labeled anti-sense (aRNA) was prepared from 1.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Dendritic cells were diferentiated from monocyte cells extracted from peripheral blood from healthy donnors and treated with 20 ng/mL of  IL-4 and GM-CSF during 7 days and growth with RPMI 1640 medium supplemented with 10% heat-inactivated fetal. Mature dendritic cells were differentiated with 20 ng/mL of LPS during 24h. The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using  RNeasy Purification kit  (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes on-column DNase digestion.

treatment_protocol: Inmature and mature dendritic cells were infected with pseudotype HIV-1 (VSV-ΔenvGFP-200 ng of CA-p24) with or without Vpx for 72 h at 37ºC replacing the medium at 24h.

value: Monocyte dendritic cells

tag: treatment

value: Gene expression aftyer 72h of culture


title: Mature dendritic_cells_infected_DRT_HIV1_rep3

description: Gene expression after 72h of Defective RT- HIV1 infection

source_name: Mature dendritic cells, DRT-HIV1 infected, 72h, rep3

value: 72h of Defective RT- HIV1 infection


title: Mature dendritic_cells_infected_DRT_HIV1_rep2

source_name: Mature dendritic cells, DRT-HIV1 infected, 72h, rep2


title: Control for group A, biological rep3

description: Calvarial OBs from 1 week-old mice

source_name: wild type osteoblasts

value: osteoblasts

value: FVB/N


title: Mature dendritic_cells_infected_DRT_HIV1_rep1

source_name: Mature dendritic cells, DRT-HIV1 infected, 72h, rep1


title: Mature dendritic_cells_infected_HIV1+Vpx_rep2

description: Gene expression after 72h of HIV1+Vpx infection

source_name: Mature dendritic cells,HIV1+Vpx infected, 72h, rep2

value: 72h of HIV1+Vpx infection


title: 2wk_mutant_3

description:
Gene expression data from whole ears tissue from 2 weeks mouse
RMSKXX027001

source_name: Mouse ears 2weeks old Spade/Spade mutant #3

value: Spade/Spade


title: Immature dendritic_cells_infected_DRT_HIV1_rep3

source_name: Immature dendritic cells, DRT-HIV1 infected, 72h, rep3


title: Immature dendritic_cells_infected_DRT_HIV1_rep1

source_name: Immature dendritic cells, DRT-HIV1 infected, 72h, rep1


title: Immature dendritic_cells_infected_HIV1+Vpx_rep2

source_name: Immature dendritic cells,HIV1+Vpx infected, 72h, rep2


title: Mature dendritic_cells_infected_HIV1+Vpx_rep3

source_name: Mature dendritic cells,HIV1+Vpx infected, 72h, rep3


title: Mature dendritic_cells_non_infected_rep1

description: Gene expression aftyer 72h of culture

source_name: Mature dendritic cells, non infected, 72h, rep1


title: Immature dendritic_cells_infected_DRT_HIV1_rep2

source_name: Immature dendritic cells, DRT-HIV1 infected, 72h, rep2


title: j6_K_A_38

city: Marseille

first: Marc

last: DALOD

address: Parc scientifique de Luminy, Case 906

department: Dendritic cells and antiviral defense

institute: Center of Immunology of Marseille Luminy (CIML)

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 16 hr at 45°C on Mouse Gene 1.0 ST (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with the EukGE_WS2v5 protocol.

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

data_processing: The data were RMA normalized in R and Bioconductor, using the limma package.

source_name: Ly49H+/+MyD88+/+, MCMV d6, replicate 2

label_protocol: 200 ng of RNA from each sample was used to synthesize biotinylated probes, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted from a small piece of spleen with the Qiagen micro RNAeasy PLUS kit, according to the manufacturer protocol.

treatment_protocol: Mice were infected intraperitoneally with salivary gland-murine cytomegalovirus strain v70 (2,5x10e3 pfu/mouse). Spleens were harvested at d0, d1.5, d2, d3 or d6 post-infection.

tag: tissue type

value: Total spleen

tag: infection

value: murine cytomegalovirus


title: Immature dendritic_cells_non_infected_rep1

description: Gene expression after 72h of culture

source_name: Immature dendritic cells, non infected, 72h, rep1

value: 72h of culture


title: Immature dendritic_cells_non_infected_rep3

description: Gene expression after 72h of culture

source_name: Immature dendritic cells, non infected, 72h, rep3


title: j6_K_B_23

source_name: Ly49H+/+MyD88+/+, MCMV d6, replicate 3


title: Immature dendritic_cells_non_infected_rep2

description: Gene expression after 72h of culture

source_name: Immature dendritic cells, non infected, 72h, rep2


title: Immature dendritic_cells_infected_HIV1+Vpx_rep3

source_name: Immature dendritic cells,HIV1+Vpx infected, 72h, rep3


title: Mature dendritic_cells_infected_HIV1+Vpx_rep1

source_name: Mature dendritic cells,HIV1+Vpx infected, 72h, rep1


title: Immature dendritic_cells_infected_HIV1+Vpx_rep1

source_name: Immature dendritic cells,HIV1+Vpx infected, 72h, rep1


title: j6_KM_B_24

source_name: Ly49H+/+MyD88-/-, MCMV d6, replicate 3


title: j6_KM_A_39

source_name: Ly49H+/+MyD88-/-, MCMV d6, replicate 1


title: M611-HER2 +dox 15h rep1 clone A

description: SAMPLE 9

tag: time point


title: j6_K_A_37

source_name: Ly49H+/+MyD88+/+, MCMV d6, replicate 1


title: j6_B_B_21

source_name: Ly49H-/-MyD88+/+, MCMV d6, replicate 3


title: j6_BM_B_22

source_name: Ly49H-/-MyD88-/-, MCMV d6, replicate 3


title: j6_KM_A_40

source_name: Ly49H+/+MyD88-/-, MCMV d6, replicate 2


title: j6_B_A_34

source_name: Ly49H-/-MyD88+/+, MCMV d6, replicate 2


title: t4hr_-I_1

first: Nicole

middle: Janell

last: De Nisco

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UTSW Medical Center

description: Experimental gene expression in culture grown for 4 hours without supplemental IPTG (CtrA depletion)

hyb_protocol: 300 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microliters containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Upon completion of the fragmentation reaction, 25 microliters of 2x Agilent blocking agent was added and mixed by repeated pipetting. The sample was then centrifuged and 40 microliters was then added to the well. Samples were hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were then washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Single channel expression normalization of microarray data was done by using the limma package in R. Briefly, signals were background corrected by fitting a convolution model of normal and exponential distributions to the foreground intensities using the background intensities as a covariate. The expected signal given the observed foreground becomes the corrected intensity. Background corrected values were then quantile normalized for between-array accuracy. For each time point, biological replicate samples were averaged to generate log2 expression values for each gene.

organism: Sinorhizobium meliloti 1021

source_name: log phase S. meliloti 1021 post culture split after 4 hours without IPTG (depletion)

label_protocol: A total of 600ng of RNA was used for cDNA synthesis (Ambion MessageAmp II-Bacterial kit) and cDNA labeling with the Cy3 fluorophores was carried out using the Ambion Amino Allyl MessageAmp II cRNA Amplification kit.

growth_protocol: Cells were cultured at 30 degrees Celsius in LBMC media with 1mM supplemted IPTG as well as 200uM Neomycin on a standing shaker until the culture reached mid log phase, OD = 0.6-0.7.

extract_protocol: At each time point isolated culture was treated with RNAprotect Bacterial Reagent and frozen at -80. RNA was extracted from all samples using the RNAeasy Plus RNA extraction kit (Qiagen)

treatment_protocol: Mid log phase cultures were split into two separate cultures, washed with PBS 2 times and then resuspended in A. LBMC media with 1mM IPTG or B. LBMC media without IPTG. 10mL samples were taken from both cultures 1, 2, 4, and 6 hours after the split.

tag: growth phase

value: log phase


title: t6hr_+I_1

description: Control gene expression in split culture with 1mM IPTG 6 hour after split

source_name: log phase S. meliloti 1021 post culture split after 6hrs growth in 1mM IPTG (internal control)

value: split culture with 1mM IPTG 6 hours after split


title: t4hr_-I_3

value: culture grown for 4 hours without supplemental IPTG (CtrA depletion)


title: t6hr_-I_1

description: Experimental gene expression in culture grown for 6 hours without supplemental IPTG (CtrA depletion)

source_name: log phase S. meliloti 1021 post culture split after 6 hour without IPTG (depletion)


title: t4hr_-I_2


title: j6_B_A_33

source_name: Ly49H-/-MyD88+/+, MCMV d6, replicate 1


title: j3_KM_B_16

source_name: Ly49H+/+MyD88-/-, MCMV d3, replicate 3


title: t4hr_+I_3

description: Control gene expression in split culture with 1mM IPTG 4 hours after split

source_name: log phase S. meliloti 1021 post culture split after 4hrs growth in 1mM IPTG (internal control)


title: j3_K_A_31

source_name: Ly49H+/+MyD88+/+, MCMV d3, replicate 2


title: j6_BM_A_35

source_name: Ly49H-/-MyD88-/-, MCMV d6, replicate 1


title: j3_K_A_15

source_name: Ly49H+/+MyD88+/+, MCMV d3, replicate 1


title: t4hr_+I_1

value: split culture with 1mM IPTG 4 hours after split


title: t4hr_+I_2


title: t2hr_-I_2

description: Experimental gene expression in culture grown for 2 hours without supplemental IPTG (CtrA depletion)

source_name: log phase S. meliloti 1021 post culture split after 2 hours without IPTG (depletion)


title: j3_K_B_13

source_name: Ly49H+/+MyD88+/+, MCMV d3, replicate 3


title: j6_BM_A_36

source_name: Ly49H-/-MyD88-/-, MCMV d6, replicate 2


title: t2hr_-I_3

value: culture grown for 2 hours without supplemental IPTG (CtrA depletion)


title: j3_KM_B_14

source_name: Ly49H+/+MyD88-/-, MCMV d3, replicate 1


title: j3_B_A_29

source_name: Ly49H-/-MyD88+/+, MCMV d3, replicate 2


title: j3_B_B_11

source_name: Ly49H-/-MyD88+/+, MCMV d3, replicate 3


title: j3_KM_B_15

source_name: Ly49H+/+MyD88-/-, MCMV d3, replicate 2


title: j3_BM_A_32

source_name: Ly49H-/-MyD88-/-, MCMV d3, replicate 4


title: t2hr_+I_3

description: Control gene expression in split culture with 1mM IPTG 2 hours after split

source_name: log phase S. meliloti 1021 post culture split after 2hrs growth in 1mM IPTG (internal control)


title: j3_BM_B_12

source_name: Ly49H-/-MyD88-/-, MCMV d3, replicate 5


title: j3_BM_A_30

source_name: Ly49H-/-MyD88-/-, MCMV d3, replicate 3


title: t2hr_+I_2

value: split culture with 1mM IPTG 2 hours after split


title: t2hr_+I_1


title: t2hr_-I_1


title: j3_BM_A_16

source_name: Ly49H-/-MyD88-/-, MCMV d3, replicate 2


title: t1hr_-I_3

description: Experimental gene expression in culture grown for 1 hour without supplemental IPTG (CtrA depletion)

source_name: log phase S. meliloti 1021 post culture split after 1 hour without IPTG (depletion)


title: j3_BM_A_14

source_name: Ly49H-/-MyD88-/-, MCMV d3, replicate 1


title: t1hr_-I_2

value: culture grown for 1 hour without supplemental IPTG (CtrA depletion)


title: j2_K_A_27

source_name: Ly49H+/+MyD88+/+, MCMV d2, replicate 2


title: t1hr_+I_1

description: Control gene expression in split culture with 1mM IPTG 1 hour after split

source_name: log phase S. meliloti 1021 post culture split after 1hr growth in 1mM IPTG (internal control)


title: t1hr_+I_2

value: split culture with 1mM IPTG 1 hour after split


title: t1hr_-I_1


title: j2_K_A_11

source_name: Ly49H+/+MyD88+/+, MCMV d2, replicate 1


title: t0_4

description: Control gene expression in untreated cells

source_name: log phase S. meliloti 1021 bacteria pre-culture split

value: untreated cells


title: t0_2


title: j2_B_A_25

source_name: Ly49H-/-MyD88+/+, MCMV d2, replicate 2


title: Pineapple_21day_8

city: BARI

first: pasquale

last: filannino

address: Via Amendola, 165/A

department: Dipartimento di Scienze del Suolo

country: Italy

institute: Università degli Studi di Bari “Aldo Moro”

description: Gene expression data from Pineapple juice at growth condition 24 hours at 30°C + 21 days at 4°C

hyb_protocol: 2000ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Custom Lactobacillus Gene Expression  8x15k Array (AMADID: 067475). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters. 'gMedianSignal' column was taken as foreground intensity and 'gBGMedianSignal' column was taken as background intensity. Data was background corrected and Quantile normalized using the functions present in 'limma' package of R. If a gene has more than one probe, average intensity value of all the probes was taken to represent the gene

organism: Lactiplantibacillus plantarum

source_name: Pineapple juice, 24 hours at 30°C + 21 days at 4°C

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using WT primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized 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 using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality was assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74106)  as per the manufacturer’s instructions.


title: j2_KM_A_28

source_name: Ly49H+/+MyD88-/-, MCMV d2, replicate 2


title: t0_3


title: j3_B_A_13

source_name: Ly49H-/-MyD88+/+, MCMV d3, replicate 1


title: Pineapple_late_exp_4

description: Gene expression data from Pineapple juice at growth condition 24 hours at 30⁰C, replicate 1

source_name: Pineapple juice, late exponential phase of growth, 30⁰C


title: Carrot_21day_7

description: Gene expression data from Carrot juice at growth condition 24 hours at 30°C + 21 days at 4°C

source_name: Carrot juice, 24 hours at 30°C + 21 days at 4°C


title: j2_BM_B_19

source_name: Ly49H-/-MyD88-/-, MCMV d2, replicate 3


title: j2_B_B_17

source_name: Ly49H-/-MyD88+/+, MCMV d2, replicate 3


title: t1hr_+I_3


title: Pineapple_late_exp_5

description: Gene expression data from Pineapple juice at growth condition 24 hours at 30⁰C, replicate 2


title: MRSBroth_21day_6

description: Gene expression data from MRSBroth at growth condition 24 hours at 30°C + 21 days at 4°C

source_name: MRSBroth, 24 hours at 30°C + 21 days at 4°C


title: j2_KM_A_12

source_name: Ly49H+/+MyD88-/-, MCMV d2, replicate 1


title: t0_1


title: j2_BM_A_10

source_name: Ly49H-/-MyD88-/-, MCMV d2, replicate 2


title: MRSBroth_late_exp_1

description: Gene expression data from MRSBroth at growth condition 24 hours at 30⁰C

source_name: MRSBroth, late exponential phase of growth, 30⁰C


title: Carrot_late_exp_2

description: Gene expression data from Carrot juice at growth condition 24 hours at 30⁰C, replicate 1

source_name: Carrot juice, late exponential phase of growth, 30⁰C


title: Carrot_late_exp_3

description: Gene expression data from Carrot juice at growth condition 24 hours at 30⁰C, replicate 2


title: j2_B_A_9

source_name: Ly49H-/-MyD88+/+, MCMV d2, replicate 1


title: j2_BM_A_26

source_name: Ly49H-/-MyD88-/-, MCMV d2, replicate 1


title: j1.5_K_B_7

source_name: Ly49H+/+MyD88+/+, MCMV d1.5, replicate 3


title: j1.5_K_A_23

source_name: Ly49H+/+MyD88+/+, MCMV d1.5, replicate 2


title: hep_sample_14

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

country: Germany

institute: University of Regensburg

description: Gene expression of Hep3B cell culture after treatment with conditioned medium

hyb_protocol: 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 1.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Raw intensity values from CEL files were normalized with the Bioconductor package VSN. Probes were summarized using median polish and an alternative CDF based on ensembl genes provided by BrainArray, University of Michigan (version 12.1.0).

source_name: HCC cell culture treated with conditioned medium from patient 14

label_protocol: The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual.

growth_protocol: The human HCC cell lines Hep3B (American Type Culture Collection (ATCC) number HB-8064) was cultured as described (Amann et al, 2009, Cancer Science). Primary human hepatic stellate cells (HSCs) were isolated from 15 different human donors as described in (Amann et al, 2009, Cancer Science). The isolation procedure and cell culture on uncoated tissue culture dishes led to the activation of HSCs. For collection of conditioned medium (CM) HSCs were seeded into T75 flasks (2 × 10^6 cells). One day after seeding cells were washed twice with serum-free DMEM, and then incubated for another 24 h with serum-free DMEM (15 mL/T75). CM was clarified by centrifugation at 6,000 g to remove cell debris, sterile filtered (0.45 μm pore size membrane filter), and stored in aliquots at −80 °C until use. Serum-free DMEM incubated for 24 h in cell culture flasks without cells served as the control.

extract_protocol: Isolation of total cellular RNA from cultured cells and tissues and reverse transcription were performed as described in Amann et al., 2009, Cancer Science.

treatment_protocol: For stimulation of HCC cells with HSC conditioned media, HCC cells were seeded into T25 flask (10^6 cells). One day after seeding, cells were washed with serum-free DMEM, and then incubated for another 12 h with serum-free DMEM. Subsequently, the medium was changed and cells were incubated with 3 mL of HSC-CM or control medium (serum-free DMEM) for 4h.

tag: cell type

value: HCC cell line Hep3B


title: hep_sample_15

source_name: HCC cell culture treated with conditioned medium from patient 15


title: hep_sample_13

source_name: HCC cell culture treated with conditioned medium from patient 13


title: j1.5_K_A_7

source_name: Ly49H+/+MyD88+/+, MCMV d1.5, replicate 1


title: hep_sample_9

source_name: HCC cell culture treated with conditioned medium from patient 9


title: Mature dendritic_cells_non_infected_rep2

description: Gene expression aftyer 72h of culture

source_name: Mature dendritic cells, non infected, 72h, rep2

value: Monocyte dendritic cells

value: Gene expression aftyer 72h of culture


title: j1.5_KM_B_8

source_name: Ly49H+/+MyD88-/-, MCMV d1.5, replicate 1


title: hep_sample_10

source_name: HCC cell culture treated with conditioned medium from patient 10


title: j1.5_B_A_21

source_name: Ly49H-/-MyD88+/+, MCMV d1.5, replicate 2


title: j1.5_KM_B_9

source_name: Ly49H+/+MyD88-/-, MCMV d1.5, replicate 2


title: j1.5_KM_B_10

source_name: Ly49H+/+MyD88-/-, MCMV d1.5, replicate 3


title: hep_sample_12

source_name: HCC cell culture treated with conditioned medium from patient 12


title: hep_sample_7

source_name: HCC cell culture treated with conditioned medium from patient 7


title: j1.5_B_A_5

source_name: Ly49H-/-MyD88+/+, MCMV d1.5, replicate 1


title: j1.5_B_B_5

source_name: Ly49H-/-MyD88+/+, MCMV d1.5, replicate 3


title: hep_sample_11

source_name: HCC cell culture treated with conditioned medium from patient 11


title: Foxo 1,3,4 muscle specific knock-out, fed

city: Padova

first: Marco

last: Sandri

address: Viale Colombo 3

department: Department of Biomedical Science

institute: University of Padova

hyb_protocol: Standard Afymetrix Procedure

scan_protocol: Standard Afymetrix Procedure

data_processing: Data was summarized using the MAS 5.0 algorithm in Affymetrix Expression Console.

source_name: gastrocnemius muscle of fed ko mice

label_protocol: Standard Afymetrix Procedure

growth_protocol: animals were kept on standard 12h dark, 12 h light cycles, food an water was given ad libitum except for the starvation experiments

extract_protocol: Muscles were frozen in liquid nitrogen, disrupted using mortar and pescle and RNA was extracted using the standard Trizol method. RNA quality was monitored by UV absorption and Agilent Bioanalyzer.

treatment_protocol: animals were starved 24 hours with water ad libitum, control animals had both food and water ad libitum

tag: genotype/variation

value: knocked-out FoxO 1,3,4

value: cross of C57BL/6N and FVBN

tag: gender

value: male


title: hep_sample_8

source_name: HCC cell culture treated with conditioned medium from patient 8


title: hep_sample_2

source_name: HCC cell culture treated with conditioned medium from patient 2


title: hep_sample_3

source_name: HCC cell culture treated with conditioned medium from patient 3


title: j1.5_BM_B_6

source_name: Ly49H-/-MyD88-/-, MCMV d1.5, replicate 5

value: Total spleen

tag: strain

value: murine cytomegalovirus


title: wild type, starved

source_name: gastrocnemius muscle of starved wt mice

value: wild type


title: hep_sample_5

source_name: HCC cell culture treated with conditioned medium from patient 5


title: j1.5_BM_A_8

source_name: Ly49H-/-MyD88-/-, MCMV d1.5, replicate 2


title: hep_sample_6

source_name: HCC cell culture treated with conditioned medium from patient 6


title: j1.5_BM_A_22

source_name: Ly49H-/-MyD88-/-, MCMV d1.5, replicate 3


title: j1.5_BM_A_24

source_name: Ly49H-/-MyD88-/-, MCMV d1.5, replicate 4


title: Foxo 1,3,4 muscle specific knock-out, starved

source_name: gastrocnemius muscle of starved ko mice


title: j1.5_BM_A_6

source_name: Ly49H-/-MyD88-/-, MCMV d1.5, replicate 1


title: HSC_sample_15

description: Gene expression of hepatic stellate cells (HSC)

source_name: HSC cells from patient 15

value: Primary human hepatic stellate cells (HSCs)


title: j0_K_B_3

source_name: Ly49H+/+MyD88+/+, steady-state, replicate 3


title: HSC_sample_10

source_name: HSC cells from patient 10


title: hep_sample_1

source_name: HCC cell culture treated with conditioned medium from patient 1


title: j0_KM_A_20

source_name: Ly49H+/+MyD88-/-, steady-state, replicate 2


title: wild type, fed

source_name: gastrocnemius muscle of fed wt mice


title: j0_KM_A_4

source_name: Ly49H+/+MyD88-/-, steady-state, replicate 1


title: HSC_sample_13

source_name: HSC cells from patient 13


title: j0_K_A_3

source_name: Ly49H+/+MyD88+/+, steady-state, replicate 1


title: HSC_sample_8

source_name: HSC cells from patient 8


title: j0_B_A_17

source_name: Ly49H-/-MyD88+/+, steady-state, replicate 2


title: hep_sample_4

source_name: HCC cell culture treated with conditioned medium from patient 4


title: HSC_sample_9

source_name: HSC cells from patient 9


title: HSC_sample_7

source_name: HSC cells from patient 7


title: j0_B_A_1

source_name: Ly49H-/-MyD88+/+, steady-state, replicate 1


title: HSC_sample_5

source_name: HSC cells from patient 5


title: j0_K_A_19

source_name: Ly49H+/+MyD88+/+, steady-state, replicate 2


title: j0_BM_A_18

source_name: Ly49H-/-MyD88-/-, steady-state, replicate 2


title: j0_BM_A_2

source_name: Ly49H-/-MyD88-/-, steady-state, replicate 1


title: HSC_sample_3

source_name: HSC cells from patient 3


title: j0_KM_B_4

source_name: Ly49H+/+MyD88-/-, steady-state, replicate 3


title: HSC_sample_11

source_name: HSC cells from patient 11


title: j0_BM_B_2

source_name: Ly49H-/-MyD88-/-, steady-state, replicate 3


title: j0_B_B_1

source_name: Ly49H-/-MyD88+/+, steady-state, replicate 3


title: HSC_sample_14

source_name: HSC cells from patient 14


title: HSC_sample_12

source_name: HSC cells from patient 12


title: HSC_sample_6

source_name: HSC cells from patient 6


title: HSC_sample_2

source_name: HSC cells from patient 2


title: pTH9958_HK_8mer_8776

status: Public on Apr 23 2015

type: protein

city: Toronto

first: Kamesh

last: Narasimhan

state: Ontario

address: 160 college Street

country: Canada

institute: Donnelly Centre for Cellular and Biomolecular Research

hyb_protocol: After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. The VALUE column contains the median intensity for the 8mer sequence.  Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.   Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: ztf-6, HK design

label_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as AscI–SbfI fragments into pTH6838, a modified T7-driven GST expression vector.

tag: dbd source organism

value: Caenorhabditis elegans

tag: dbd

tag: platform_id_id design

value: HK


title: pTH9930_ME_8mer_8537

source_name: lin-29, ME design

value: ME


title: pTH9958_ME_8mer_8792

source_name: ztf-6, ME design


title: pTH9934_HK_8mer_8675

source_name: Y53H1A.2, HK design


title: pTH9951_ME_8mer_8943

source_name: mex-6, ME design

value: zf-CCCH


title: pTH9974_HK_8mer_8778

source_name: hlh-16, HK design

value: HLH


title: pTH9930_HK_8mer_8674

source_name: lin-29, HK design


title: pTH9969_HK_8mer_8777

source_name: pag-3, HK design


title: pTH9951_HK_8mer_8959

source_name: mex-6, HK design


title: pTH9957_ME_8mer_8791

source_name: fkh-9, ME design


title: pTH9969_ME_8mer_8793

source_name: pag-3, ME design


title: pTH9957_HK_8mer_8775

source_name: fkh-9, HK design


title: pTH9928_ME_8mer_8547

source_name: jun-1, ME design


title: pTH9934_ME_8mer_8625

source_name: Y53H1A.2, ME design


title: hep_ctrl_4

description: Gene expression of Hep3B cell culture

source_name: unconditioned HCC cell culture, biological replicate 4


title: hep_ctrl_2

description: Gene expression of Hep3B cell culture

source_name: unconditioned HCC cell culture, biological replicate 2


title: hep_ctrl_1

description: Gene expression of Hep3B cell culture

source_name: unconditioned HCC cell culture, biological replicate 1


title: HSC_sample_1

source_name: HSC cells from patient 1


title: hep_ctrl_3

description: Gene expression of Hep3B cell culture

source_name: unconditioned HCC cell culture, biological replicate 3


title: pTH9974_ME_8mer_8794

source_name: hlh-16, ME design


title: pTH9925_HK_8mer_8672

source_name: ztf-11, HK design


title: pTH9924_HK_8mer_8705

source_name: nhr-46, HK design


title: 14530-1050594-F621

city: Madison

first: Karen

middle: Dyer

last: Montgomery

state: WI

address: 504 S Rosa Rd, Ste 101

department: Cytogenetics

institute: WiCell

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - 5.1 Microarray Hybridization, 5.2 Wash Preparation, 5.3 Microarray Washing

scan_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - 5.4 Microarray Scanning using Agilent C Scanner

data_processing: Data normalized by polynomial data fit performed with Agilent Feature Extraction v12.0.0.7. Data Analyzed with Agilent Genomic Workbench v7.0 - Aberration Algorithm: ADM-2, Threshold: 6.0, Fuzzy Zero: ON, GC Correction: ON, Window Size: 2Kb, Centralization: OFF, Diploid Peak Centralization: ON, Manually Reassign Peaks: OFF, Combine Replicates: ON.

source_name: Tail tip

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - 3. Sample Preparation, 4. Sample Labeling

extract_protocol: DNA was extracted from tail tip biopsies using standard phenol/chloroform extraction.

value: Female

tag: ctr#


title: 14529-1050592-F618


title: pTH9925_ME_8mer_8620

source_name: ztf-11, ME design


title: 14528-1050590-M617

value: Male


title: pTH9928_HK_8mer_8707

source_name: jun-1, HK design


title: pTH9923_ME_8mer_8716

source_name: C07E3.6, ME design

value: Homeobox


title: pTH9913_ME_8mer_8714

source_name: skn-1, ME design


title: pTH9916_ME_8mer_8615

source_name: W08E12.1, ME design


title: pTH9911_HK_8mer_8670

source_name: atf-5, HK design


title: pTH9924_ME_8mer_8717

source_name: nhr-46, ME design


title: pTH9911_ME_8mer_8595

source_name: atf-5, ME design


title: pTH9915_HK_8mer_8671

source_name: zip-3, HK design


title: pTH9907_ME_8mer_8542

source_name: nhr-34, ME design


title: pTH9907_HK_8mer_8669

source_name: nhr-34, HK design


title: pTH9900_HK_8mer_8697

source_name: C46E10.8, HK design


title: pTH9901_HK_8mer_8698

source_name: D1005.3, HK design


title: pTH9900_ME_8mer_8713

source_name: C46E10.8, ME design


title: pTH9913_HK_8mer_8699

source_name: skn-1, HK design


title: pTH9885_ME_8mer_8592

source_name: ceh-18, ME design

value: Pou,Homeobox


title: pTH9916_HK_8mer_8701

source_name: W08E12.1, HK design


title: pTH9923_HK_8mer_8704

source_name: C07E3.6, HK design


title: pTH9884_ME_8mer_8591

source_name: tbx-39, ME design

value: T-box


title: pTH9901_ME_8mer_8536

source_name: D1005.3, ME design


title: pTH9915_ME_8mer_8614

source_name: zip-3, ME design


title: 14527-1050588-M615

source_name: Tail tip


title: pTH9884_HK_8mer_8665

source_name: tbx-39, HK design


title: pTH9880_ME_8mer_8587

source_name: end-1, ME design

value: GATA


title: HSC_sample_4

source_name: HSC cells from patient 4


title: pTH9880_HK_8mer_8664

source_name: end-1, HK design


title: pTH9885_HK_8mer_8693

source_name: ceh-18, HK design


title: pTH9879_HK_8mer_8663

source_name: C27D6.4, HK design


title: pTH9877_ME_8mer_8584

source_name: elt-7, ME design


title: pTH9877_HK_8mer_8662

source_name: elt-7, HK design


title: pTH9709_ME_8mer_8581

source_name: die-1, ME design


title: pTH9478_ME_8mer_7224

source_name: ceh-23, ME design


title: pTH9354_ME_8mer_7887

source_name: ZC328.2, ME design


title: pTH9709_HK_8mer_8661

source_name: die-1, HK design


title: pTH9322_ME_8mer_10589

source_name: nhr-1, ME design


title: pTH9354_HK_8mer_7902

source_name: ZC328.2, HK design


title: pTH9326_HK_8mer_8684

source_name: nhr-122, HK design


title: pTH9323_ME_8mer_7882

source_name: odr-7, ME design


title: pTH9323_HK_8mer_7909

source_name: odr-7, HK design


title: pTH9462_HK_8mer_10758

source_name: tbx-38, HK design


title: pTH9355_HK_8mer_7903

source_name: ZK337.2, HK design


title: pTH9394_ME_8mer_7889

source_name: sptf-3, ME design


title: pTH9462_ME_8mer_10774

source_name: tbx-38, ME design


title: pTH9879_ME_8mer_8586

source_name: C27D6.4, ME design


title: pTH9711_ME_8mer_8368

source_name: atf-2, ME design


title: pTH9355_ME_8mer_8056

source_name: ZK337.2, ME design


title: pTH9708_HK_8mer_8351

source_name: ceh-34, HK design


title: pTH9394_HK_8mer_7904

source_name: sptf-3, HK design


title: pTH9391_ME_8mer_8652

source_name: Y51H4A.4, ME design


title: pTH9391_HK_8mer_8686

source_name: Y51H4A.4, HK design


title: pTH9708_ME_8mer_8367

source_name: ceh-34, ME design


title: pTH9711_HK_8mer_8352

source_name: atf-2, HK design


title: pTH9326_ME_8mer_8526

source_name: nhr-122, ME design


title: pTH9322_HK_8mer_10605

source_name: nhr-1, HK design


title: pTH9317_HK_8mer_7901

source_name: egrh-1, HK design


title: pTH9353_ME_8mer_8528

source_name: ceh-51, ME design


title: pTH9353_HK_8mer_8349

source_name: ceh-51, HK design


title: pTH9478_HK_8mer_7276

source_name: ceh-23, HK design


title: pTH9314_ME_8mer_8651

source_name: atf-7, ME design


title: pTH9314_HK_8mer_8606

source_name: atf-7, HK design


title: pTH9306_ME_8mer_8525

source_name: lsl-1, ME design


title: pTH9177_HK_8mer_10607

source_name: F10B5.3, HK design


title: pTH9174_ME_8mer_7596

source_name: nhr-70, ME design


title: pTH9177_ME_8mer_10591

source_name: F10B5.3, ME design


title: pTH9174_HK_8mer_7908

source_name: nhr-70, HK design


title: pTH9163_ME_8mer_7609

source_name: nhr-3, ME design


title: pTH9165_ME_8mer_8054

source_name: ztf-27, ME design


title: pTH9173_ME_8mer_8022

source_name: efl-2, ME design


title: pTH9164_ME_8mer_10772

source_name: ceh-26, ME design


title: pTH9165_HK_8mer_7899

source_name: ztf-27, HK design


title: pTH9164_HK_8mer_10756

source_name: ceh-26, HK design


title: pTH9158_ME_8mer_7874

source_name: ces-1, ME design


title: pTH9155_HK_8mer_7898

source_name: lin-48, HK design


title: pTH9150_HK_8mer_8556

source_name: odd-2, HK design


title: pTH9150_ME_8mer_8648

source_name: odd-2, ME design


title: pTH9158_HK_8mer_8093

source_name: ces-1, HK design


title: pTH9159_HK_8mer_8682

source_name: atf-6, HK design


title: pTH9159_ME_8mer_8523

source_name: atf-6, ME design


title: pTH9149_ME_8mer_7871

source_name: ham-2, ME design


title: pTH9149_HK_8mer_7897

source_name: ham-2, HK design


title: pTH9163_HK_8mer_8683

source_name: nhr-3, HK design


title: pTH9142_HK_8mer_8552

source_name: C34D1.1, HK design

value: DM


title: pTH9306_HK_8mer_8575

source_name: lsl-1, HK design


title: pTH9137_ME_8mer_7603

source_name: nhr-65, ME design