title: COLO829_shSCR_PLX4032_A

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive

institute: Stanford University

hyb_protocol: Standard hybridization protocol for Affymetrix arrays was processed by the Stanford PAN facility

scan_protocol: Standard scanning protocol for Affymetrix arrays was processed by the Stanford PAN facility

data_processing: Array data was RMA normalized and differential expression was evaluated with statistical analysis of microarrays (SAM) with an FDR < 0.05 and fold change >= 2

source_name: COLO829 cells with shScrambled knockdown and PLX4032 treatment

label_protocol: Standard labeling protocol for Affymetrix arrays was processed by the Stanford PAN facility

growth_protocol: COLO829 cells were grown in RPMI 1640 medium with 10% FBS and Pen/Strep

extract_protocol: Rneasy Plus kit following manufacturers instructions

treatment_protocol: Cell populations were infected with pGIPZ shMITF vector or scrambled control and then selected with puromycin for 2 days. Cells were then subjected to 1uM PLX4032 or DMSO control for 24hr and RNA was then harvested.

tag: cell line

value: COLO829 melanoma cell line

value: control

tag: agent

value: BRAF inhibitor PLX4032 (Vemurafenib)


title: Sensitized Mouse 328

status: Public on Jan 14 2014

type: RNA

city: New York

first: Dennis

last: Lazarev

state: NY

address: 1212 Amsterdam Av

department: Biological Sciences

country: USA

institute: Columbia University

hyb_protocol: Hybridization of labeled DNA to the Beadchip and washing and scanning were performed according to the Illumina BeadStation 500x manual.

data_processing: Since it was a custom array- i.e. aimed at splice junctions, the analysis was run through the custom workflow, where signal levels of  junctions were measured.  The measurements of each junction signal was   averaged over a group of samples- either healthy mice or allergen-  sensitized mice.  Each junction was, by array design, paired wit  another junction, also represented on the array, that would result  from alternative splicing event. These measurements produced four data   points for each tested event: average signal intensity for each   junction in a pair, in control and in sensitized group.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: spleen from Aspergillus fumigatus sensitive mice

label_protocol: Illumina protocol

extract_protocol: Trizol

tag: strain

value: BALB/c

tag: gender

value: female and male

tag: age

value: 6 wks

tag: tissue

value: spleen


title: Sensitized Mouse 327

scan_protocol: Hybridization of labeled DNA to the Beadchip and washing and scanning were performed according to the Illumina BeadStation 500x manual.


title: Sensitized Mouse 633


title: Sensitized Mouse 634


title: 1M_WildType_Control 3

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

hyb_protocol: follow Agilent's two-color expression array hybridization protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: GeneSpring version11 was used to filter, normalize, and calculate the signal intensities.

source_name: liver RNA

label_protocol: Invitrogen SuperScript indirect cDNA labeling system

growth_protocol: Mice were 6-8 weeks old when the treatment started

extract_protocol: Total RNA extracted using Trizol followed by RNeasy Midi kit

treatment_protocol: Alcohol-treated mice were fed ad libitum a liquid diet containing 4% ethanol. Control animals were fed an isocaloric diet supplemented with maltose dextran

value: liver

tag: treatment

tag: time

value: Control

tag: genotype

value: Wild Type


title: COLO829_shSCR_PLX4032_B

organism: Homo sapiens

tag: genotype/variation


title: 1M_WildType_Control 2


title: 1M_PPARa-null_Alcohol 1

value: Alcohol

value: PPARa-null


title: COLO829_shMITF_DMSO_B

source_name: COLO829 cells with shMITF knockdown and DMSO treatment

value: MITF knockdown


title: COLO829_shMITF_PLX4032_A

source_name: COLO829 cells with shMITF knockdown and PLX4032 treatment


title: COLO829_shMITF_PLX4032_B


title: Sensitized Mouse 326


title: COLO829_shSCR_DMSO_B

source_name: COLO829 cells with shScrambled knockdown and DMSO treatment


title: Sensitized Mouse 329


title: CF 5F SB Rep 3

city: Philadelphia

first: John

last: Gearhart

state: PA

address: 3400 Civic Center Blvd, Building 421, 9-121 Smilow Center for Translational Research

department: Dept of Cell and Developmental Biology, Institute for Regenerative Medicine

institute: University of Pennsylvania

description:
CF 5TF treatment SB
Gene expression data from SB treated CFs that received 5TF treatment

hyb_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

data_processing: Initial data analysis was performed using Affymetrix Microarray Suite 5.0 and further analyzed using PartekGS software.

source_name: CFs treated with 5F in the presence of 5 uM SB

growth_protocol: MEFs were grown in DMEM with 10% fetal bovine serum and 1X Glutamax.

extract_protocol: Cells were collected in Trizol at Day 3 post-transduction.  Non-transduced MEFs were cultured and collected at Day 3.  Samples were collected in triplicate from independent biological replicates and total RNA was prepared by the University of Pennsylvania Molecular Profiling Facility.

treatment_protocol: MEFs were plated into poly-L-lysine-coated 6 well dishes at 75,000 cells/well on Day -2, with 500 μL (≥ 2.5x105 IFU) each of rtTA lentivirus (FUdeltaGW-rtTA, Addgene plasmid 19780) and TroponinT-GCaMP-Zeo reporter lentivirus per well with 2 mL MEF medium. The following day (Day -1), culture medium was replaced with 2 mL fresh MEF medium with the molecules or DMSO vehicle and cells were transduced with 500 μL (≥ 2.5x105 IFU) of each tetO-transcription factor lentivirus. The next day (Day 0), medium was switched to 3 mL/well Reprogramming Medium consisting of AGM (Lonza CC-3186) without EGF, supplemented with 2 μg/mL doxycycline (Sigma).

tag: cell type

value: cardiac fibroblast

value: 5F in the presence of 5 uM SB


title: Sensitized Mouse 270


title: COLO829_shSCR_DMSO_A


title: COLO829_shMITF_DMSO_A


title: CF 5F TGFb Rep 3

description:
CF 5TF treatment TGFb
Gene expression data from TGFb treated CFs that received 5TF treatment

scan_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility

source_name: CFs treated with 5F in the presence of TGFb

value: 5F in the presence of TGFb


title: 1M_WildType_Control 1


title: Probiotic Combination treatment

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

description:
Control rep 5, Control rep 1, PC rep 4, PC rep 2
PC rep 5,PC rep 1,Control rep 4,Control rep 2

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the Immune Array chips in an ArrayBooster (Advalytix, Beckman Coulter, Germany).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with QuantArray software (Perkin Elmer).

data_processing: Statistical analyses were done with R software (v. 2.13.0) and the Limma package from Bioconductor. Normalization within slide was obtained by LOWESS correction and between slides normalization was done with Aquantile method.

label: Cy5, Cy3

source_name: Colonic adenocarcinoma cells

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Burlington, ON, Canada) following manufacturer's protocol and with PhaseLock tubes (5 Prime, Gaithersburg, MD) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, Germantown, MD). Quality was assessed by Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). RIN over 9.0 were considered good quality RNA for reverse transcription.

treatment_protocol: HT-29 cells were incubated for 3 h with poly(I·C) or probiotic combination (PC) alone or PC in combination with poly(I·C) at 10 µg/ml.

value: Colonic adenocarcinoma cells

value: 3 h with probiotic combination (PC) at at 10 µg/ml

label: Cy3, Cy5

value: unchallenged


title: Probiotic Combination with Poly IC treatment

description:
Control rep B5, PC-IC rep B8, PC-IC rep B6, Control rep B3
PC-IC rep B5,Control rep B8,Control rep B6,PC-IC rep B3

value: 3 h with PC in combination with poly(I·C) at 10 µg/ml


title: Control Mouse 371

source_name: spleen from control mice

value: BALB/c


title: CF 5F SB Rep 1

label_protocol: The labeling, hybridization, and scanning procedures were performed by the University of Pennsylvania Molecular Profiling facility


title: Control Mouse 370

value: female and male


title: Control Mouse 337

value: 6 wks


title: Poly IC only treatment

description:
Control rep 1, Poly IC rep 4, Control rep 5, Poly IC rep 2
Poly IC rep 1,Control rep 4,Poly IC rep 5, Control rep 2

value: 3 h with poly(I·C) at 10 µg/ml


title: Control Mouse 338

value: spleen


title: Control Mouse 336


title: CF 5F TGFb Rep 2


title: Control Mouse 324


title: CF 5F TGFb Rep 1


title: CF 5F SB Rep 2


title: CF 5F DMSO Rep 1

description:
CF 5TF treatment DMSO
Gene expression data from DMSO treated CFs that received 5TF treatment

source_name: CFs treated with 5F in the presence of DMSO

value: 5F in the presence of DMSO


title: aorta-6m-rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60k Microarrays for 17 h at 65 °C

scan_protocol: Samples were scanned as described in the manufacturers protocol. Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies).

data_processing: Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability (Bolstad et al., 2003). Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: aorta, 6 months

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on six replicates of each experimental condition (adult and old mice) according to the manufacturers protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

extract_protocol: The descending aorta was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C. Extraction of total RNA from the tissue was followed with Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA from 6 individual mice of each group was treated with DNase I to remove residual genomic DNA. Total RNA preparations were checked for RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples showed common high quality RNA Integrity Numbers (RIN 9.0-9.6) and RNA was quantified by photometric Nanodrop measurement.

treatment_protocol: Male C57BL/6 mice were obtained from Janvier (Saint Berthevin, France) and kept one week in the local animal house for acclimatization. Mice were aged 6 months and 20 months and water and standard rodent chow were fed ad libitum.

value: aorta

value: male

value: 6 months


title: CF 5F DMSO Rep 3


title: aorta-6m-rep5


title: 1120 - mAdbID:98343

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 98343

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample RNA Extraction Protocol
Other: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

value: female

value: lymph node

tag: disease state

value: Lymphoma

tag: individual

tag: clinical info

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL

value: Follow up status:Dead

value: Follow up years:3.67

value: ECOG performance status:1

value: LDH ratio:4.03

value: Number of extranodal sites:1


title: aorta-6m-rep3


title: aorta-6m-rep6


title: LH022 (replica 3)

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

institute: Concordia University

description: ste18 ectopic expressing Gβ with pheromone vs WT without pheromone  (replica 3)

hyb_protocol: Microarray slides were hybridized with labeled cDNAs overnight at 42°C DIG easy Hyb solution (Roche) containing 0.5 ug/ul of Bakers tRNA and 0.5 ug/ul of salmon sperm DNA. The slides were washed twice with 1X SSC/0.1% SDS and 3 times with 0.1X SSC and spin dry.

scan_protocol: The scanning was done using GenePix4000B microarray scanner

data_processing: The images were quantified in GenePix Pro 4.1 software and final Lowess normalization and inspection of the data was done with Microsoft Excel 2013 and MultiExperiment Viewer.

molecule: polyA RNA

organism: Candida albicans

source_name: ste18+CAG1 opaque cells with pheromone (SD-medida RT)

label_protocol: Indirect cDNA labeling with amino-allyl Dutp

growth_protocol: Overnight opaque form cultures grown in SD complete media were diluted to OD600nm = 0.01 in SD complete and grown until OD600nm = 0.8~1.0 at RT

extract_protocol: Hot phenol method for total RNA extraction of Candida albicans opaque cells; polyA Spin mRNA Isolation Kit from Biolabs for mRNA isolation

treatment_protocol: Cell treatments with mating pheromone(10μg/ml α factor) were done when cells are in log phase(OD600nm=0.5)

source_name: ste18+CAG1 opaque cells without pheromone (SD-medida RT)


title: aorta-6m-rep4


title: MEF 5F SB Rep 3

description:
MEF 5TF treatment SB
Gene expression data from SB treated MEFs that received 5TF treatment

source_name: MEFs treated with 5F in the presence of 0.5 uM SB

value: embryonic fibroblast

value: 5F in the presence of 0.5 uM SB


title: aorta-6m-rep1


title: Control Mouse 323

value: BALB/c

value: female and male

value: 6 wks

value: spleen


title: 1865 - mAdbID:92574

description: mAdb experiment ID: 92574

value: Follow up years:1.17

value: LDH ratio:4.6


title: CF 5F DMSO Rep 2

value: cardiac fibroblast

value: 5F in the presence of DMSO


title: HPK-18E2 rep4

city: Khantharawichai

first: Nuchsupha

last: Sunthamala

state: Mahasarakham

address: Department of Biology, Faculty of Science, Mahasarakham University

department: Biology

country: Thailand

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data files were quantified in GenomeStudio Version 2011.1 (Illumina). The data were qunatile normalized and compared fluorescence level with GFP control to obtain the fold-change expression.

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

growth_protocol: The human primary neonatal foreskin keratinocytes (HPK) (Lonza, Basel, Switzerland) were cultured in supplemented CnT-57 medium (CELLnTEC, Bern, Switzerland). All cells used were tested and found free of mycoplasma.

extract_protocol: Total RNA were isolated using RNeasy mini kit (QIAGEN, Singapore) followed by RNeasy mini protocol.

treatment_protocol: Keratinocytes were allowed to attach on plate surface for 24 h and transduced with recombinant adenoviruses containing GFP, GFP-HPV16E2 or GFP-HPV18E2 at MOI 50. The transduced cells were collected by scraping for RNA extraction after transduction 48 h.

tag: transduced with

value: recombinant adenoviruses containing GFP-HPV18E at MOI 50


title: 1862 - mAdbID:92577

description: mAdb experiment ID: 92577

value: male

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL

value: Follow up status:Alive

value: Follow up years:1.12


title: LH022 (replica 2)

description: ste18 ectopic expressing Gβ with pheromone vs WT without pheromone  (replica 2)


title: 1866 - mAdbID:92573

description: mAdb experiment ID: 92573

value: Follow up status:Dead

value: Follow up years:0.92

value: LDH ratio:1.82


title: MEF 5F SB Rep 2

value: embryonic fibroblast

value: 5F in the presence of 0.5 uM SB


title: Control Mouse 322

value: BALB/c

value: female and male

value: 6 wks

value: spleen


title: MEF 5F SB Rep 1


title: HPK-18E2 rep2

institute: Faculty of Science, Mahasarakham University

value: human primary neonatal foreskin keratinocytes (HPK)

value: recombinant adenoviruses containing GFP-HPV18E at MOI 50


title: LH022 (replica 1)

description: ste18 ectopic expressing Gβ with pheromone vs WT without pheromone  (replica 1)


title: 1208 - mAdbID:87747

description: mAdb experiment ID: 87747

value: female

value: lymph node

value: Follow up years:2.37

value: ECOG performance status:1

value: LDH ratio:2.37


title: HPK-18E2 rep1


title: Control Mouse 321


title: MEF 5F TGFb Rep 3

description:
MEF 5TF treatment TGFb
Gene expression data from TGFb treated MEFs that received 5TF treatment

source_name: MEFs treated with 5F in the presence of TGFb

value: 5F in the presence of TGFb


title: LH021 (replica 2)

description: ste18 ectopic expressing Gα with pheromone vs WT without pheromone  (replica 2)

source_name: ste18+STE4 opaque cells with pheromone (SD-medida RT)

source_name: ste18+STE4 opaque cells without pheromone (SD-medida RT)


title: HPK-18E2 rep3


title: HPK-16E2 rep4

value: recombinant adenoviruses containing GFP-HPV16E2 at MOI 50


title: LH021 (replica 1)

description: ste18 ectopic expressing Gα with pheromone vs WT without pheromone  (replica 1)


title: LH003 (replica 3)

description: ste18 with pheromone vs WT without pheromone  (replica 3)

source_name: ste18 opaque cells with pheromone (SD-medida RT)

source_name: ste18 opaque cells without pheromone (SD-medida RT)


title: LH003 (replica 2)

description: ste18 with pheromone vs WT without pheromone  (replica 2)


title: MEF 5F TGFb Rep 2


title: MEF 5F DMSO Rep 3

description:
MEF 5TF treatment DMSO
Gene expression data from DMSO treated MEFs that received 5TF treatment

source_name: MEFs treated with 5F in the presence of DMSO

value: 5F in the presence of DMSO


title: LH021 (replica 3)

description: ste18 ectopic expressing Gα with pheromone vs WT without pheromone  (replica 3)


title: LH003 (replica 1)

description: ste18 with pheromone vs WT without pheromone  (replica 1)


title: MEF 5F TGFb Rep 1


title: HPK-16E2 rep1


title: Col leaves at 120h LT, biological rep3

city: East Lansing

first: Dean

last: DellaPenna

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: gene expression data for Col after 120h LT treatment, when soluble sugar accumulation is significantly different between genotypes.

hyb_protocol: Total RNA was converted into cDNA, which was in turn used to synthesize biotinylated cRNA. The cRNA was fragmented into smaller pieces and then was hybridized to the GeneChips. After hybridization, the chips were automatically washed and stained with streptavidin phycoerythrin using a fluidics station.

scan_protocol: The chips were scanned by the GeneArray scanner at 570 nm emission and 488 nm excitation.

data_processing: Raw chip data were analyzed with R/Bioconductor. Only perfect match (PM) intensities were used. RMA function as implemented in the affy package was used for background adjustment, normalization and summarization.

organism: Arabidopsis thaliana

source_name: 4 week old Col leaves after 120h LT treatment

label_protocol: Labeling of RNA were conducted using standard Affymetrix protocols by the Michigan State University DNA Microarray Facility.

growth_protocol: Seed were stratified for 4 to 7 days (4°C), planted in an equal mixture of vermiculite, perlite, and soil with 1 × Hoagland solution, and grown under permissive conditions: 12 hour, 120 μmol photon m-2 s-1 light at 22°C/12 hour darkness at 18°C and 70% relative humidity. Plants were watered every other day and with a half strength Hoagland solution once a week.

extract_protocol: Total RNA was extracted using the RNAqueous RNA extraction kit and the Plant RNA Isolation Aid (Ambion) according to the manufacturer’s instructions.

treatment_protocol: For LT treatments, 4-week-old plants were transferred at the beginning of the light cycle to 12 hour, 120 μmol photon m-2 s-1 light/12 hour darkness at 7°C.

value: 9-11th adult leaves

value: Col

tag: lt treatment time


title: MEF 5F DMSO Rep 2

value: embryonic fibroblast


title: HPK-GFP Control rep4

source_name: HPK-GFP Control

value: recombinant adenoviruses containing GFP at MOI 50


title: vte2 leaves at 120h LT, biological rep3

description: gene expression data for vte2 after 120h LT treatment, when soluble sugar accumulation is significantly different between genotypes.

source_name: 4 week old vte2 leaves after 120h LT treatment


title: HPK-16E2 rep3


title: 3294 (replica 3)

description: WT with pheromone vs WT without pheromone  (replica 3)

source_name: WT opaque cells with pheromone (SD-media RT)

source_name: WT opaque cells without pheromone (SD-media RT)


title: HPK-GFP Control rep3


title: vte2 leaves at 120h LT, biological rep1


title: MEF 5F DMSO Rep 1


title: MEF 0F SB Rep 3

description:
MEF No TF treatment SB
Gene expression data from SB treated MEFs that did not receive any transcription factor treatment

source_name: MEFs treated with empty vector in the presence of 0.5 uM SB


title: 3294 (replica 2)

description: WT with pheromone vs WT without pheromone  (replica 2)


title: MEF 0F SB Rep 2

value: empty vector in the presence of 0.5 uM SB


title: HPK-GFP Control rep2


title: Col leaves at 120h LT, biological rep2


title: vte2 leaves at 48h LT, biological rep3

description: gene expression data for vte2 after 48h LT treatment, when soluble sugar accumulation is similar between genotypes.

source_name: 4 week old vte2 leaves after 48h LT treatment


title: vte2 leaves at 120h LT, biological rep2


title: HPK-16E2 rep2


title: MEF 0F SB Rep 1


title: HPK-GFP Control rep1


title: MEF 0F TGFb Rep 3

description:
MEF No TF treatment TGFb
Gene expression data from TGFb treated MEFs that did not receive any transcription factor treatment

source_name: MEFs treated with empty vector in the presence of TGFb

value: empty vector in the presence of TGFb


title: vte2 leaves at 48h LT, biological rep2


title: 3294 (replica 1)

description: WT with pheromone vs WT without pheromone  (replica 1)


title: vte2 leaves at 48h LT, biological rep1


title: MEF 0F TGFb Rep 2


title: Normal_Control_97d_rat10

city: Madison

first: Amy

last: Irving

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9.5 for background subtraction - localbackground and normalization Linear LOWESS. Agilent Feature Extraction .txt files were directly used to generate fold-change data Pirc Fold Changes.xls by Partek.

organism: Rattus norvegicus

source_name: colon

label_protocol: Total RNA was amplified and labeled according to manufacturer instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark.

extract_protocol: Qiagen Qiashredder columns followed by Qiagen Allprep DNA/RNA Extraction Kit with optional on-the-column Dnase treatment

treatment_protocol: Indicated animals given 4% DSS (500,000 MW) in drinking water from 40-47 and 54-61 days of age.  Sacrificed and dissected at 97 days, samples homogenized in RLTplus and stored at -80C

value: Apc-Pirc/+

value: 97 days

value: normal tissue

value: Control

source_name: Colonic tissue reference.

value: Apc wild type

value: Range

value: normal colon


title: Col leaves at 48h LT, biological rep3

description: gene expression data for Col after 48h LT treatment, when soluble sugar accumulation is similar between genotypes.

source_name: 4 week old Col leaves after 48h LT treatment


title: MEF 0F DMSO Rep 3

description:
MEF No TF treatment DMSO
Gene expression data from DMSO treated MEFs that did not receive any transcription factor treatment

source_name: MEFs treated with empty vector in the presence of DMSO

value: empty vector in the presence of DMSO


title: MEF 0F TGFb Rep 1


title: genomic DNA from normal human endometrial epithelium_G622

type: genomic

city: Zerifin

first: Ella

last: Evron

address: Oncology Department

department: Oncology

country: Israel

institute: Asaf Harofeh Medical Center Affiliated with Tel Aviv University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2: Unmethylated and methylated signal intensities are included in the 'non_normalized.txt'.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: surgical specimen of normal endometrium epithelial layer

label_protocol: Standard Illumina protocol

extract_protocol: Fresh surgical samples were removed by the pathologists. Oranoids were prepared from breast tissues. WBC were purified from whole blood. Genomic DNA was extracted usind standard phenol-chloroform-ethanol precipitation method. Sodium Bi-Sulfite treatment used EZ-methylation kit (Zymo Research).

treatment_protocol: Breast organoids were purified as in Bloushtain-Qimron et el., Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):14076-8

tag: subject id

value: individual 16

value: female

value: normal/healthy

tag: tissue type

value: normal endometrial epithelium

tag: tissue info

value: normal tissue from uterine myoma surgery


title: MEF 0F DMSO Rep 2

value: embryonic fibroblast


title: advanced CaP_P408

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: miRNA expression in the advanced CaP 408

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression Blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s Human miRNA Microarray (60K, Release 16.0) and hybridized at 55 °C for 20 h with 20 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner.

data_processing:
Feature Extraction software (version 10.10.1.1) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. Background intensity and feature nonuniform outliers were removed by standard procedures. Data visualization and analysis were performed with GeneSpring GX (version 7.3) software (Agilent Technologies). Signal cut-off measurements were less than 0.01, and normalized to 75th percentile of signal intensity to standardize each chip for cross-array comparison. Differentially expressed miRNAs were identified using a Student’s two-sample t-test with p values cut off by 0.05 and fold change more than 2.0. One-way ANOVO was used to analyze the correlation between the expression levels of miRNAs and clinic-pathological features of the patients.
The normalized ratios were calculated by dividing the average of CaP channel intensity (localized CaPs or advanced CaPs) by the average of normalized control channel intensity (BPH).

source_name: Human urine

label_protocol: 400 ng of total RNA was labeled with cyanine 3-pCp using the Agilent miRNA Complete Labeling kit and hybridized to the array according to the manufacturer’s protocol.

growth_protocol: 19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH) were selected.

extract_protocol: Total RNA was extracted using RecoverAllTM Total Nucleic Acid Isolation kit (Life Technologies, Carlsbad, CA) according to the protocol of the manufacturer. RNA quantity and integrity were examined by RNA 6000 Pico Chip Kit (Agilent Technologies, Santa Clara, CA) on Agilent 2100 Bioanalyzer.

treatment_protocol: A total 14 urines from patients with CaP (7 localized and 7 advanced stage) and 5 of BPH controls were used for miRNA array analysis.

tag: disease

value: advanced CaP


title: advanced CaP_P370

description: miRNA expression in the advanced CaP 370


title: genomic DNA from normal human endometrial epithelium_G724

source_name: surgical specimen of normal lung epithelial layer in distance to tumor removal

value: individual 18

tag: gender

value: normal lung epithelium

value: normal tissue from lung cancer patient, distal to tumor


title: genomic DNA from normal human lung epithelium_G723

value: individual 17


title: vte2 leaves at 0h LT, biological rep2

description: gene expression data for vte2 before LT treatment, when genotypes are indistinguishable

source_name: 4 week old vte2 leaves before LT treatment

value: 9-11th adult leaves


title: Normal_DSS_97d_rat9

tag: strain

value: Apc-Pirc/+

tag: age

value: 97 days

value: normal tissue

value: DSS


title: Tumor_Control_97d_rat8

tag: tissue

value: colonic tumor

tag: treatment

value: Control

value: Apc wild type

value: Range

value: normal colon


title: vte2 leaves at 0h LT, biological rep3

tag: genotype


title: Tumor_Control_97d_rat10


title: Normal_Control_97d_rat8


title: Normal_DSS_97d_rat7


title: Col leaves at 48h LT, biological rep1

value: Col


title: vte2 leaves at 0h LT, biological rep1


title: genomic DNA from normal human endometrial epithelium_G621

value: individual 15

value: female

value: normal/healthy

value: normal endometrial epithelium

value: normal tissue from uterine myoma surgery


title: genomic DNA from normal human colon epithelium_G520

source_name: surgical specimen of normal colon epithelial layer in distance to polip removal

value: individual 14

value: normal colon epithelium

value: normal tissue from colon cancer patient distal to tumor


title: Tumor_DSS_97d_rat9

value: Apc-Pirc/+

value: 97 days


title: MEF 0F DMSO Rep 1

value: embryonic fibroblast

value: empty vector in the presence of DMSO


title: Tumor_DSS_97d_rat7

value: colonic tumor

value: DSS


title: Col leaves at 0h LT, biological rep3

description: gene expression data for Col before LT treatment, when genotypes are indistinguishable

source_name: 4 week old Col leaves before LT treatment

value: 9-11th adult leaves


title: Col leaves at 48h LT, biological rep2


title: genomic DNA from normal human colon epithelium_G518

value: individual 12


title: genomic DNA from normal human colon epithelium_G519

value: individual 13


title: Col leaves at 0h LT, biological rep2

value: Col


title: advanced CaP_P320

description: miRNA expression in the advanced CaP 320

value: advanced CaP


title: Normal2_Control_97d_rat2

value: normal tissue

value: Control

value: Apc wild type

value: Range

value: normal colon


title: advanced CaP_P362

description: miRNA expression in the advanced CaP 362


title: advanced CaP_P235

description: miRNA expression in the advanced CaP 235


title: advanced CaP_P209

description: miRNA expression in the advanced CaP 209


title: localized CaP_P418

description: miRNA expression in the localized CaP 418

value: localized CaP


title: Col leaves at 0h LT, biological rep1


title: localized CaP_P748

description: miRNA expression in the localized CaP 748


title: Tumor_Control_97d_rat2

value: Apc-Pirc/+


title: Normal2_DSS_97d_rat6

value: 97 days


title: genomic DNA from human sperm treated with SssI CpG methylase_rep2_CM-POS2

source_name: Human sperm treated with CpG methylase SssI

value: normal/healthy

value: sperm-SssI treated

value: HSD from healthy donor


title: localized CaP_P409

description: miRNA expression in the localized CaP 409


title: genomic DNA from white blood cells_G416

source_name: WBC of normal healthy female individual

value: individual 10

value: female

value: white blood cells

value: WBC from healthy donor


title: Tumor2_DSS_97d_rat6

value: colonic tumor

value: DSS


title: Normal2_Control_97d_rat3

value: normal tissue


title: genomic DNA from human sperm_rep2_CU-NEG2

source_name: Human sperm

value: sperm


title: advanced CaP_P232

description: miRNA expression in the advanced CaP 232

value: advanced CaP


title: High avidity T cells 3

city: Baltimore

first: Elizabeth

middle: M

last: Jaffee

address: 1850 Orleans street

institute: Johns Hopkins School of Medicine

description: RNA from high avidity T cells taken out of treated neu-N mice

hyb_protocol: Labeled single-stranded DNA (5.5 μg) was combined with hybridization and spike controls and hybridized with a pre-equilibrated Affymetrix chip.

scan_protocol: Following hybridization, arrays were washed and stained with a streptavidin phycoerythrin conjugate using an automated GeneChip® Fluidics Station 450. They were then scanned with a GeneChip® Scanner 3000 using a 570-nm excitation wavelength laser.

data_processing:
Raw CEL file data were extracted and RMA normalized with the Partek Genomics Suite platform (Partec Inc. St Louis MO USA).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na31.mm9.probeset_extended.mps

label: Biotin

source_name: High avidity T cells from tumor draining nodes

label_protocol: cDNA was generated using Invitrogens cDNA Synthesis Kit and amplified with NuGen's amplification system according to the manufacturers instructions.

growth_protocol: CD8+ T cells were isolated from tumor-draining lymph nodes from treated neu-N mice three days after they were adoptively transferred in.

extract_protocol: RNA was extracted from T cells sorted from neu-N mice using the Qiagen RNeasy Mini Kit.

treatment_protocol: Neu-N mice were given tumor one week before being treated with 100mg/kg Cy, one day later mice were vaccinated with 3x10^6 3T3neuGM cells.  One day following vaccination high or low avidity T cells were adoptively transferred into neu-N mice.

value: T cells

tag: avidity

value: High avidity


title: Normal_DSS_97d_rat6

value: Apc wild type

value: Range

value: normal colon


title: Low avidity T cells 3

description: RNA from low avidity T cells taken out of treated neu-N mice

source_name: Low avidity T cells from tumor draining nodes

tag: cell type

value: Low avidity


title: Tumor_DSS_97d_rat6

value: Apc-Pirc/+

value: 97 days


title: Tumor_Control_97d_rat3

value: Control


title: localized CaP_P396

description: miRNA expression in the localized CaP 396

value: localized CaP


title: Low avidity T cells 4


title: genomic DNA from white blood cells_G415

value: individual 9

value: female

tag: disease state

value: normal/healthy

value: white blood cells


title: genomic DNA from white blood cells_G306

source_name: WBC isolated from BRCA1mut carrier healthy individual

value: individual 6

value: healthy BRCA1 mutation carrier/brca1 mutation 185 del g


title: Low avidity T cells 1


title: High avidity T cells 2


title: Low avidity T cells 2


title: High avidity T cells 1


title: genomic DNA from white blood cells_G307

source_name: WBC isolated from BRCA1mut carrier breast cancer patient, 2 years after treatments, no evidence of disease

value: individual 7

value: breast cancer patient/brca1 mutation 185 del g


title: localized CaP_P306

description: miRNA expression in the localized CaP 306


title: localized CaP_P231

description: miRNA expression in the localized CaP 231


title: BPH-768

description: miRNA expression in the benign prostatic hyperplasia 768

value: BPH


title: Tumor_DSS_97d_rat5

source_name: colon

value: colonic tumor

value: DSS

value: Apc wild type


title: Normal_DSS_97d_rat5

value: normal tissue

source_name: Colonic tissue reference.

value: Range

value: normal colon


title: localized CaP_P222

description: miRNA expression in the localized CaP 222


title: BPH-767

description: miRNA expression in the benign prostatic hyperplasia 767


title: Normal_Control_97d_rat4

value: Apc-Pirc/+

value: 97 days

value: Control


title: genomic DNA from normal breast epithelium_G206

source_name: organoids from BRCA1mut carrier healthy individual

value: female

value: normal brca1 mutation 185 del g

value: breast epithelium

value: preventive bi-lateral mastectomy organoids (right plus left)


title: Tumor_Control_97d_rat4


title: BPH-746

description: miRNA expression in the benign prostatic hyperplasia 746


title: BMDM_0.1ng_4hr_2nd

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
7604659025_H
Primary cultured BMDM cells.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ.

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset. After filtering probes, quantile normalization was applied across all arrays. ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences. A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywise error rate (FWER) using Benjamini-Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.

source_name: BMDM cells, low LPS

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Bone-marrow-derived macrophages (BMDMs) were differentiated from bone marrow precursors with M-CSF by standard protocols.

extract_protocol: RNA was purified by Qiagen RNeasy kit.

treatment_protocol: BMDM cells were preincubated in Hanks' balanced salt solution containing 2% FBS (v/v) at 37°C and 5% CO2 for at least 2 hours before the application of LPS (Alexis Biochemicals; Salmonella minnesota R595 TLRgrade, ALX-581-008-L002).

tag: strain/background

value: bone-marrow-derived macrophages


title: genomic DNA from normal breast epithelium_G205L

source_name: organoids from BRCA1mut breast cancer patient

value: individual 5

value: bi-lateral mastectomy post treatment left breast (healthy)


title: genomic DNA from normal breast epithelium_G104

source_name: organoids from reduction mammoplast healthy individual

value: individual 4

value: normal/healthy

value: breast tissue from reduction mammoplast healthy donor


title: BMDM_Zero_4hr_2nd

description:
7604659025_G
Primary cultured BMDM cells.

source_name: BMDM cells, zero LPS

value: zero


title: Normal_Control_97d_rat3

value: normal tissue

value: Apc wild type


title: BMDM_Zero_4hr_1st

description:
7604659008_E
Primary cultured BMDM cells.


title: BMDM_0.1ng_4hr_1st

description:
7604659008_F
Primary cultured BMDM cells.


title: Normal_Control_97d_rat2

value: Range

value: normal colon


title: ST-cycle mice MeDIP

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

scan_protocol: Arrays were scanned on NimbleGen MS 200 Microarray Scanner

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan MeDIP-ChIP data extraction.
The processed data include the methylation estimate file for the NT-cycle mice, methylation estimate file for the ST-cycle mice, the methylation estimate  difference file between the NT and ST-cycle mice.

source_name: Input DNA from SCN of mice entrained to ST-cycle

label_protocol: For genome-wide methylation analysis, we used 10 ng of input DNA and immunoprecipitated DNA for library preparation and DNA amplification using GenomPlex® complete whole genome amplification WGA2 (Sigma). For labeling, we used 1 ug of DNA (IP and input) with Cy5 and Cy3 respectively using the dual-color labeling kit (Roche). Labeled DNA was used for hybridization to the Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays (Nimblegen). Hybridization and washing were carried out according the manufacturer’s instructions.

extract_protocol: Isolation of DNA from SCN and MeDIP-array: For methyl-DNA immunoprecipitation (MeDIP), we adapted the protocol developed by Weber and colleagues6 . First we exposed 2 groups of 3-week-old mice to ST and NT cycles (n = 25 mice per group).  After six weeks we recorded wheel-running behavior in constant darkness for one week and then we isolated brains and sliced with a vibratome. Brain slices (70 um) were stained with cresyl-violet to identify SCN tissue. Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation. After RNase treatment, intact genomic DNA was sonicated to generate small fragments (average 500 bp), using a Covaris sonicator (BioRuptor). Sonicated DNA was denatured for 10 min at 95° C. For immunoprecipitation, we used 1.5 ug denatured DNA with 2 ug monoclonal antibody against 5-methylcytidine (BI-MECY-0100) (Eurogentec) for 3h at 4° C. The mixture (DNA plus antibody) was incubated with 30 ul of protein A-sepharose during 2h at 4° C. After washing, beads were resuspended in 250 ul elution buffer and incubated 3h at 55° C on a rotating wheel. The immunoprecipitated DNA was then submitted to phenol/chloroform extraction and ethanol precipitation.

value: wild type mice

value: SCN (Suprachiasmatic nucleus)

tag: chip antibody

value: Input non_immunoprecipitated

source_name: DNA immunoprecipitated with monoclonal antibody against 5-methylcytidine

treatment_protocol: we isolated brains and sliced with a vibratome. Brain slices (70 mm) were stained with cresyl-violet to identify SCN tissue. Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation. After RNase treatment, intact genomic DNA was sonicated to generate small fragments (average 500 bp), using a Covaris sonicator (BioRuptor).

value: wild type

value: SCN (suprachiasmatic nucleus)


title: genomic DNA from normal breast epithelium_G205R

source_name: organoids from BRCA1mut breast cancer patient bi-lateral mastectomy post treatment right breast (after lumpectomy)

value: female

value: normal brca1 mutation 185 del g

value: breast epithelium


title: genomic DNA from normal breast epithelium_G101

value: individual 1


title: genomic DNA from normal breast epithelium_G103

value: individual 3


title: BMDM_10ng_4hr_2nd

description:
7604659006_A
Primary cultured BMDM cells.

source_name: BMDM cells, high LPS

value: bone-marrow-derived macrophages


title: Normal_DSS_97d_rat1

value: Apc-Pirc/+

value: 97 days

value: DSS


title: genomic DNA from human sperm treated with SssI CpG methylase_rep1_CM-POS

source_name: Human sperm treated with CpG methylase SssI

value: normal/healthy

value: sperm-SssI treated

value: HSD from healthy donor


title: BMDM_10ng_4hr_1st

description:
7604659008_G
Primary cultured BMDM cells.


title: NT-cycle mice MeDIP

hyb_protocol: Labeled DNA was used for hybridization to the Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays (Nimblegen). Hybridization and washing were carried out according the manufacturer’s instructions.

source_name: Input DNA from SCN of mice entrained to NT-cycle

treatment_protocol: Genomic DNA was extracted from SCN slices by overnight Proteinase K digestion, followed by phenol-chloroform and ethanol precipitation

value: wild type mice

value: monoclonal antibody against 5-methylcytidine


title: Col leaves at 120h LT, biological rep1

description: gene expression data for Col after 120h LT treatment, when soluble sugar accumulation is significantly different between genotypes.

source_name: 4 week old Col leaves after 120h LT treatment

value: 9-11th adult leaves

value: Col


title: Tumor_DSS_97d_rat1

value: colonic tumor

value: Apc wild type

value: Range

value: normal colon


title: BPH-714

description: miRNA expression in the benign prostatic hyperplasia 714

source_name: Human urine

value: BPH


title: TSA treatment replicate #2

status: Public on Jan 13 2014

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

description:
TSA_2
technical replicate

hyb_protocol: Hybridization was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

scan_protocol: Scanned on an Agilent High Resolution Model B scanner that has been upgraded to Model C.

data_processing:
Images were quantified using Agilent Feature Extraction software.
The normexp background correction and loess normalization procedures were applied to the probe-level data using the limma R package.  Normalized log2 ratios (test/reference) were then computed.

source_name: [test] H522 cells treated with TSA

label_protocol: Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

growth_protocol: H522 cells were maintained in RPMI1640 plus 10% fetal bovine serum.

extract_protocol: Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

treatment_protocol: H522 cells were either infected with adenovirus-GFP or adenovirus GFP-BRG1 (m.o.i.=20) or treated with 5µM 5-dAzaC or 100nM TSA for 48 hours.

tag: cell line

value: NCI-H522 NSCLC cells

value: TSA

source_name: [reference] H522 untreated

value: untreated


title: BPH-707

description: miRNA expression in the benign prostatic hyperplasia 707


title: HRT-18_vs_Caco-2_rep3

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

description: Biological replicate 3, cells harvested at approx. 80% confluence

hyb_protocol: Before applying the samples, slides were placed in a Tecan HS400 hybridization station, washed with 0.2% SDS (23°C, 1 min wash time), incubated in prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) at 39°C for 20 min, and washed with Wash Buffer A (2xSSC, 0.2%SDS, 39°C, 1 min wash time). Cy5/Cy3 labelled microRNAs were mixed with 2x Hybridization buffer (Exiqon, Catalog number 208022) and hybridized on the slides for 16 h at 56°C (with medium agitation). Afterwards, slides were washed two times with Wash Buffer A (1 min wash time, 1 min soak time), then two times with Wash Buffer B (1xSSC, 23°C, 1 min wash time, 1 min soak time), then two times with Wash Buffer C (0.2xSSC, 23°C, 1 min wash time, 1 min soak time), and finally once with Wash Buffer C (23°C, 30 sec wash time). Subsequently, slides were dried (Nitrogen stream, 30°C).

scan_protocol: Arrays scanned using an Axon instruments GenePix 4000B scanner and GenePix Pro 4.1 software.

data_processing: GenePix Pro 4.1 was used to filter out low intensity, saturated and inhomogenous spots. Further, the raw data was background corrected, normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026), and then exported as text-file containing log2 transformed ratios of gene expression.

source_name: HRT-18 colorectal cancer cell line

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 1 µg total RNA in 4 µL RNase-free H2O were prepared. Labeling of aliquots with Cy5/Cy3 dyes was performed using the miRCURY  LNA™ microRNA Array Hi-Power Labeling kit (Exiqon, Catalog number 208035) according to the manual provided by the manufacturer.

growth_protocol: Caco-2 was grown in MEM with Earle's salts (PAA Laboratories) supplemented with 2 mmol/L of L-glutamine, 1.5 g/L of sodium bicarbonate, 0.1 mmol/L of nonessential amino acids, 50 units/mL of penicillin, 50 μg/mL of streptomycin, and 10% FCS (PAA Laboratories). HRT-18 cells were maintained in RPMI 1640 (GIBCO) containing 2 mmol/L of L-glutamine, 50 units/mL of penicillin, 50 μg/mL of streptomycin, and 10% FCS (v/v).

extract_protocol: Cells were harvested with TRIzol reagent (lifetechnologies, Catalog number 15596-026) and total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: Cells were grown in the respective proliferation medium until approx. 80% confluence was reached.

tag: phenotype

value: poorly differentiated; doubling time 20 hrs

source_name: Caco-2 colorectal cancer cell line

value: highly differentiated; doubling time 80 hrs


title: HRT-18_vs_Caco-2_rep2

description: Biological replicate 2, cells harvested at approx. 80% confluence


title: TSA treatment replicate #3

description:
TSA_3
technical replicate


title: TSA treatment replicate #1

description:
TSA_1
technical replicate


title: TSA treatment replicate #4

description:
TSA_4
technical replicate


title: Adenovirus-GFP replicate #3

description:
GFP-3
technical replicate

source_name: [test] H522 cells infected with Adenonvirus-GFP

value: Adenonvirus-GFP


title: Adenovirus-GFP replicate #4

description:
GFP-4
technical replicate


title: Adenovirus-GFP replicate #1

description:
GFP-1
technical replicate


title: Adenovirus-GFP replicate #2

description:
GFP-2
technical replicate


title: HRT-18_vs_Caco-2_rep1

description: Biological replicate 1, cells harvested at approx. 80% confluence


title: genomic DNA from human sperm_rep1_CU-NEG

source_name: Human sperm

value: normal/healthy

value: sperm


title: Mouse RSK2 mutant mandibular molar [ABH_15A]

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.3.1.187 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Mouse RSK2 mutant mandibular molar

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Pregnant female mice (C57Bl6 genetic background) were euthanized at 14.5 days of gestation (E14.5), embryos were collected and tooth samples (lower incisors, mandibular and maxillary first molars) were microdissected.

extract_protocol: Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from pools of 4 tooth germs to obtain enough RNA for subsequent microarray hybridization.

tag: background strain

value: Rsk2 knockout


title: DMSO treatment replicate #3

description:
DMSO_3
technical replicate

source_name: [test] H522 cells treated with DMSO

value: DMSO


title: DMSO treatment replicate #4

description:
DMSO_4
technical replicate


title: DMSO treatment replicate #1

description:
DMSO_1
technical replicate


title: Adenovirus-BRG1 replicate #3

description:
BRG1_3
technical replicate

source_name: [test] H522 cells infected with Adenovirus-BRG1


title: Mouse RSK2 mutant mandibular molar [AZN_MolairesMutant4]


title: Mouse RSK2 mutant mandibular molar [ABH_16A]


title: Mouse RSK2 mutant mandibular molar [AZN_MolairesMutant1]


title: Adenovirus-BRG1 replicate #4

description:
BRG1_4
technical replicate


title: Mouse RSK2 mutant mandibular molar [ABH_26A]


title: Adenovirus-BRG1 replicate #2

description:
BRG1_2
technical replicate


title: Mouse RSK2 mutant mandibular molar [ABH_14A]


title: Mouse RSK2 mutant mandibular molar [AZN_MolairesMutant]


title: DMSO treatment replicate #2

description:
DMSO_2
technical replicate


title: Mouse RSK2 mutant mandibular molar [AZN_MolairesMutant3]


title: Adenovirus-BRG1 replicate #1

description:
BRG1_1
technical replicate


title: genomic DNA from white blood cells_G417

source_name: WBC of normal healthy female individual

tag: subject id

value: individual 11

value: female

tag: tissue type

value: white blood cells

value: WBC from healthy donor


title: 5dAzaC treatment replicate #4

description:
5AzaC_4
technical replicate

source_name: [test] H522 cells treated with 5dAzaC


title: Mouse WT mandibular molar [AZN_MolairesWT]

source_name: Mouse WT mandibular molar

value: wildtype


title: 5dAzaC treatment replicate #3

description:
5AzaC_3
technical replicate


title: 5dAzaC treatment replicate #1

description:
5AzaC_1
technical replicate


title: 5dAzaC treatment replicate #2

description:
5AzaC_2
technical replicate


title: Mouse WT mandibular molar [AZN_MolairesWT1]


title: Mouse WT mandibular molar [AZN_MolairesWT3]


title: Mouse WT mandibular molar [AZN_MolairesWT2]


title: Mouse WT mandibular molar [ABH_25A]


title: Blood LPS 2 hr rep 3

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: 2 hours after LPS treatment

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

scan_protocol: Labeled targets were hybridized to Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Array GeneChip™ microarrays for 16 hours at 45° C. The arrays were washed and scanned according to Affymetrix standard protocols

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0/GCOS 1.4 ) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: mouse leukocytes

label_protocol: 1-2 μg of total RNA was used to make single-stranded antisense cDNA using the NuGEN Technologies (San Carlo, CA) Ovation™ Biotin System in accordance with the manufacturer’s directions.

extract_protocol: Total RNA was isolated using the manufacturer’s recommended protocol for RNeasy (Qiagen, Valencia, CA).

value: LPS treated

tag: genetic background

value: leukocytes

tag: time

value: 2 hours


title: Blood LPS 2 hr rep 2

description: 2 hours after LPS treatment


title: Mouse WT mandibular molar [ABH_13A]


title: PGC-1a-/-bf/f/MerCre rep5

city: Orlando

first: Ola

last: Martin

state: FL

address: 6400 Sanger Rd

institute: Sanford-Burnham Medical Research Institute

description: 3 months of age (collected 1 m after tamoxifen injection)

hyb_protocol: Following the labeling of sscDNA, 2.5 microgram of sscDNA was used to prepare hybridization cocktail. The cocktail was immediately added to the Affymetrix WT GENE 1.0 ST chip and hybridized using GeneChip Hybridization oven 645 for 17hrs at 45C.

scan_protocol: The arrays were washed and stained using Fluidics protocol FS450_0007 on GeneChip Fluidics Station 450. Following wash and stain the GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed using RMA algorithm using the Expression Console software Version 1.1 default settings.

source_name: Cardiac biventricle of Tamoxifen injected PGC-1a-/-bf/f/MerCre mouse

label_protocol: sscDNA were prepared from 450ng of total RNA using the Ambion’s WT expression kit protocol, followed by fragmentation and labeling using the WT Terminal label kit according to the protocol provided by affymetrix. The Affymetrix proprietary DNA labeling reagent covalently linked to biotin was used to label the sscDNA

extract_protocol: RNAzol B -followed manufacturers protocol

treatment_protocol: At 2 months of age, mice were injected on two sequential days with 50mg/kg/day of Tamoxifen (10mg/ml) dissolved in sunflower seed oil to induce the Cre recombinase. Vehicle injected control mice were injected with sunflower seed oil alone at the same timepoints.

value: cardiac biventricle

tag: genotype/variation

value: PGC-1a KO/PGC-1b KO


title: PGC-1a-/-bf/f/MerCre rep4


title: Mouse WT mandibular molar [ABH_11A]


title: Blood LPS 1 day rep 1

description: 1 day after LPS treatment

value: 1 day


title: PGC-1a-/-bf/f/MerCre rep1


title: Blood LPS 2 hr rep 1

description: 2 hours after LPS treatment


title: Blood LPS 1 day rep 4

description: 1 day after LPS treatment


title: Blood LPS 1 day rep 2

description: 1 day after LPS treatment


title: Blood LPS 2 hr rep 4

description: 2 hours after LPS treatment


title: Blood Sham 2 hr rep 4

description: 2 hours after sham LPS

value: Sham


title: Mouse WT mandibular molar [ABH_12A]


title: PGC-1a-/-bf/f/MerCre rep2


title: PGC-1a-/- rep5

description: 3 months of age (collected 1 m after control vehicle injection)

source_name: Cardiac biventricle of vehicle injected PGC-1a-/-bf/f/MerCre mouse (control)

value: PGC-1a KO (PGC-1b expression is unaffected)


title: genomic DNA from white blood cells_G308

source_name: WBC isolated from BRCA1mut carrier breast cancer patient, before neoadjuvant treatments

value: individual 8

tag: gender

value: breast cancer patientl/brca1 mutation 185 del g

tag: tissue info


title: PGC-1a-/- rep3

tag: tissue


title: Blood LPS 1 day rep 3

description: 1 day after LPS treatment

tag: treatment


title: Blood Sham 2 hr rep 3

description: 2 hours after sham LPS


title: Blood Sham 1 Day rep 4

description: 1 day after sham LPS


title: PGC-1a-/- rep4


title: PGC-1a-/- rep2


title: PGC-1a-/-bf/f/MerCre rep3


title: Blood Sham 2 hr rep 2

description: 2 hours after sham LPS


title: Blood Sham 2 hr rep 1

description: 2 hours after sham LPS


title: Blood Sham 1 Day rep 3

description: 1 day after sham LPS


title: PGC-1a-/- rep1


title: Blood Sham 1 Day rep 1

description: 1 day after sham LPS


title: mammary tumour-untreated-rep2

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp.

source_name: MTB x Elf5–IRES–EGFP mouse, untreated

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: Elf5+ MTB+ transgenic mice were generated as described previously, Oakes et al, Genes Dev 22, 581-586 (2008). PyMT transgenic mice were previously described (Guy et al. Mol. Cell. Biol. 12: 954-961. 1992)

extract_protocol: Tumours were disgregated into single cells. Lin and Iodidium propide negative population was sorted acording to eGFP expression in a FACS Vantage SE™ DiVa Cell Sorter (BD Biosciences). Positive and negative GFP populations were snap-frozen in liquid nitrogen. Total RNA was extracted with the RNeasy Minikit (Qiagen) and DNase-treated with the DNase kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Elf5+ MTB+ PyMT transgenic mice were given 700 mg/kg Dox containing food for a period of 1 wk.

tag: genotype

value: MTB x Elf5–IRES–EGFP mouse

tag: inducible vector

value: vehicle


title: mammary tumour-dox treated-rep1

source_name: MTB x Elf5–IRES–EGFP mouse, dox-treated

value: doxycycline


title: mammary tumour-dox treated-rep3


title: WH291 at 28DAA, biological rep 2

city: Mohali

first: JOY

middle: K

last: ROY

state: Punjab

address: C-127, Industrial Area, Phase 8

department: Agri-Biotech

country: India

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 45˚C on GeneChip®Wheat Genome Array using Affymetrix GeneChip® Hybridization Oven 640 . GeneChips were washed and stained by running fluidic script EukGE-WS2v5-450 on an Affymetrix GeneChip® Fluidics Station 450

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

data_processing: The normalization of the signal intensities of the probe sets was carried out using the Robust Multi-array normalization algorithm (RMA) implemented in GeneSpring’s Multi-omic analysis (version 11.5.1, build-138755) software (Agilent Technologies, Santa Clara, USA)

organism: Triticum aestivum

source_name: WH291-28 days after anthesis (late stage)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Affymetrix GeneChip® expression analysis manual.

growth_protocol: Plants were grown in three replication at the research farm of National Agri-Food Biotechnology Institute (NABI) Mohali, India during 2010-11. The main individual spikes of the three biological replications of each of the four varieties were tagged at first day of anthesis. The tagged spikes were harvested at three main seed developmental stages i.e. 7, 14, and 28 DAA, immediately frozen in liquid nitrogen, and stored at -80˚C for RNA extraction.

extract_protocol: Surface sterlized seeds were used for total RNA extraction using Trizol reagent (Invitrogen, USA)  and further purified by using RNeasy mini columns (Qiagen, Germany) according to the manufacturer manual.

tag: genotype/cultivar

value: Indian bread wheat variety, WH291

tag: processing quality group

value: poor chapatti making varieties

tag: seed developmental stage

value: 28 days after anthesis (late stage)

value: developing seed


title: WH291 at 28DAA, biological rep 1

institute: National Agri-Food Biotechnology Institute (NABI)


title: WH291 at 28DAA, biological rep 3


title: mammary tumour-untreated-rep1


title: mammary tumour-dox treated-rep2


title: mammary tumour-untreated-rep3


title: Blood Sham 1 Day rep 2

description: 1 day after sham LPS

tag: cell type


title: WH291 at 14DAA, biological rep 3

source_name: WH291-14 days after anthesis (mid stage)

value: 14 days after anthesis (mid stage)


title: WH291 at 14DAA, biological rep 1


title: Rat Normal Kidney Replicate 2

city: Higashi-ku, Fukuoka

first: Minako

last: Yoshihara

state: Fukuoka

address: 3-1-1 Maidashi

department: Division of Bioinformatics

country: Japan

institute: Medical institute of Bioregulation, Kyushu University

description:
rat-normal-rep2
Biological replicate 2 of 2. Control rat kidney, untreated.

hyb_protocol: The mixed sample were applied to the Rat Genome CGH Microarray Kit 244A (Agilent Technologies) according to the instruction supplied by the manufacturer.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2505B (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for LOWESS normalization.

source_name: 8-oxoG IP DNA

label_protocol: The test and the reference samples (800 ng DNA per sample) were labeled with Cy5 and Cy3, respectively, by using the standard protocol of Agilent DNA Labeling Kit (Agilent Technologies).

growth_protocol: Male Wister rats (specific pathogen-free; SPF), obtained from Japan SLC, Inc. (Shizuoka, Japan), were maintained in a SPF environment.

extract_protocol: Genomic DNA was extracted by the NaI method (Wako, Osaka, Japan) under argon gas saturated condition with 0.1 mM Desferal to prevent further DNA oxidation.

treatment_protocol: Normal condition

tag: strain

value: Wister rat

value: male

tag: age

value: 5 weeks

value: kidney

tag: ip antibody

value: 8-oxoG antibody (N45.1)

tag: ip antibody vendor

value: Japan Institute for the Control of Aging (JaICA), Nikken SEIL Co., Ltd.

tag: ip antibody code

tag: ip antibody ref.

source_name: Input DNA

value: none, input DNA


title: Rat Normal Kidney Replicate 1

description:
rat-normal-rep1
Biological replicate 1 of 2. Control rat kidney, untreated.

source_name: 8-oxoG IP DNA from


title: N3

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with JMP/Genomics after dropping probes with detection p-value greater than 0.1 in all arrays.

source_name: whole spleen, mock infection

label_protocol: Biotinylated cRNA were prepared with the AB TotalPrep kit for Illumina arrays.

growth_protocol: Inbred female C57BL/6 mice, aged 6-8 weeks old, were purchased from Charles River Laboratories International, Inc. (Frederick, Maryland, USA), Jackson Laboratory (Bar Harbor, Maine, USA), or were obtained from the NIAID/Taconic repository.

extract_protocol: Four days after parasite injection, spleens from infected or uninfected mice were removed and preserved in RNA Later solution (Qiagen, Valencia, California, USA). RNA was isolated using an RNeasy mini kit following the manufacturer's protocol (Qiagen).

treatment_protocol: Freshly thawed parasites were injected into naïve C57BL/6 mice to initiate infection. An inoculum containing 1x10^6 infected red blood cells (iRBCs) suspended in 100 µl phosphate buffer saline (PBS), pH 7.4, from the donor mice was injected intravenously into experimental mice. Naïve mice receiving an equivalent number of uninfected RBCs served as a negative control group.

tag: strain/background

tag: genotype/variation

value: WT

value: female

value: whole spleen

tag: p. yoeli infection strain (control=n)

value: N

tag: experiment


title: WH291 at 7DAA, biological rep 2

source_name: WH291-7 days after anthesis (early stage)

value: 7 days after anthesis (early stage)

tag: tissue


title: WH291 at 14DAA, biological rep 2

value: Indian bread wheat variety, WH291


title: WH291 at 7DAA, biological rep 3

value: poor chapatti making varieties


title: N67#3

source_name: whole spleen, P. yoeli N67 infection

tag: gender


title: N67C#3

source_name: whole spleen, P. yoeli N67C infection


title: Sonalika at 28DAA, biological rep 3

source_name: Sonalika-28 days after anthesis (late stage)

value: Indian bread wheat variety, Sonalika

value: 28 days after anthesis (late stage)


title: Sonalika at 7DAA, biological rep 3

source_name: Sonalika-7 days after anthesis (early stage)

value: developing seed


title: Sonalika at 28DAA, biological rep 2


title: Sonalika at 14DAA, biological rep 3

source_name: Sonalika-14 days after anthesis (mid stage)

value: 14 days after anthesis (mid stage)


title: Sonalika at 28DAA, biological rep 1


title: N2

description:
7604659027_C
Technical replicate.


title: Sonalika at 14DAA, biological rep 1


title: Sonalika at 14DAA, biological rep 2


title: N5


title: Sonalika at 7DAA, biological rep 2


title: Lok1 at 28DAA, biological rep 3

source_name: Lok1-28 days after anthesis (late stage)

value: Indian bread wheat variety, Lok1

value: good chapatti making varieties


title: Lok1 at 14DAA, biological rep 3

source_name: Lok1-14 days after anthesis (mid stage)


title: Sonalika at 7DAA, biological rep 1


title: WH291 at 7DAA, biological rep 1


title: Lok1 at 28DAA, biological rep 2


title: N67C#7

description:
7604659023_D
Repeat failed sample.


title: N67#6


title: N67#5


title: N67C#5


title: N4


title: Lok1 at 28DAA, biological rep 1


title: Lok1 at 7DAA, biological rep 3

source_name: Lok1-7 days after anthesis (early stage)


title: Lok1 at 14DAA, biological rep 2


title: C306 at 28DAA, biological rep 3

source_name: C306-28 days after anthesis (late stage)

value: Indian bread wheat variety, C306


title: Lok1 at 7DAA, biological rep 2


title: C306 at 28DAA, biological rep 2


title: N67#4


title: Lok1 at 14DAA, biological rep 1


title: Lok1 at 7DAA, biological rep 1


title: C306 at 14DAA, biological rep 3

source_name: C306-14 days after anthesis (mid stage)


title: C306 at 14DAA, biological rep 2


title: N1.2


title: N67C#4


title: N67C#2


title: C306 at 28DAA, biological rep 1


title: N67C#1


title: 48h Right Carotid Artery Endothelium 5

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

source_name: RCA endothelium post partial ligation 48h

label_protocol: Illumina-prescribed standard Labeling protocol was followed

growth_protocol: Utilized 6- to 8-week-old C57Bl6 male mice

extract_protocol: microRNA was extracted using Qiazol based miREasy Kit

treatment_protocol: 48 hours post partial ligation surgery, the carotid intima were flushed with qiazol

value: 6- to 8-week-old

value: male

value: Right carotid

tag: timepoint


title: 48h Right Carotid Artery Endothelium 4


title: 48h Right Carotid Artery Endothelium 6


title: N67#2

city: Bethesda

value: WT


title: N67#1

value: female


title: C306 at 14DAA, biological rep 1

tag: genotype/cultivar


title: C306 at 7DAA, biological rep 3

source_name: C306-7 days after anthesis (early stage)

tag: processing quality group


title: 48h Right Carotid Artery Endothelium 3


title: C306 at 7DAA, biological rep 1

tag: seed developmental stage


title: C306 at 7DAA, biological rep 2


title: 48h Right Carotid Artery Endothelium 2


title: 48h Right Carotid Artery Endothelium 1


title: 48h Left Carotid Artery Endothelium 5

source_name: LCA endothelium post partial ligation 48h

value: Left carotid


title: 48h Left Carotid Artery Endothelium 6


title: hES-S6-1-processed

first: Sinisa

last: Hrvatin

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

description: Processed sample was fixed with 4% parafromaldehyde, permabilized, antibody stained and mock sorted to collect all cells. RNA was extracted using a modified RecoverAll Total Nucleic Acid Isolation kit (Ambion). See MARIS: Method for Analyzing RNA following Intracellular Sorting manuscript for details

hyb_protocol: 750 ng cRNA per sample was then hybridized to Human HT-12 Expression BeadChips (Illumina) using the Whole- Genome Expression Direct Hybridization kit (Illumina)

scan_protocol: Illumina Beadstation 500

data_processing: GenomeStudio (Illumina, V2011.1). Raw data were adjusted by background subtraction and rank-invariant normalization. Before calculating fold change, an offset of 20 was added to all probe set means to eliminate negative signals. The p- values for differences between mean signals were calculated in GenomeStudio by t-test and corrected for multiple hypotheses testing by the Benjamini-Hochberg method in combination with the Illumina custom false discovery rate (FDR) model.

source_name: H1 human embryonic stem cells differentiation 1

label_protocol: Using the Illumina TotalPrep RNA Amplification kit (Ambion), double-stranded cDNA was generated following reverse transcription from 100 ng of total RNA. In vitro transcription overnight with biotin-labeled nucleotides created amplified mRNA (cRNA), which was concentrated by vacuum centrifugation at 30°

growth_protocol: Human embryonic stem cells were grown on matrigel using mTeSR media

treatment_protocol: Human embryonic stem cells were differentiated to insulin-expressing cells using a stepwise protocol described in the manuscript: MARIS: Method for Analyzing RNA following Intracellular Sorting

tag: cell type

value: human embryonic stem cells differentiated to stage 6 containing insulin-expressing cells

tag: cell line


title: hES-S6-3-live

description: RNA from Live sample was extracted using the RNAeasy protocol.

source_name: HUES8 human embryonic stem cells differentiation 3


title: hES-S6-2-live

source_name: H1 human embryonic stem cells differentiation 2

extract_protocol: RNA from Live sample was extracted using the RNAeasy protocol.


title: 48h Left Carotid Artery Endothelium 4

hyb_protocol: Standard Illumina hybridization protocol

tag: age

tag: strain


title: 48h Left Carotid Artery Endothelium 3


title: 48h Left Carotid Artery Endothelium 2


title: hES-S6-3-processed

extract_protocol: Processed sample was fixed with 4% parafromaldehyde, permabilized, antibody stained and mock sorted to collect all cells. RNA was extracted using a modified RecoverAll Total Nucleic Acid Isolation kit (Ambion). See MARIS: Method for Analyzing RNA following Intracellular Sorting manuscript for details


title: hES-S6-2-processed


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hHypoxia+20'Reoxy_Rep1

city: Riverside

first: Reed

middle: S

last: Sorenson

state: CA

address: 4126 Genomics Bldg

department: Botany and Plant Science

institute: University of California, Riverside

description:
7 day old whole seedlings grown on MS + 1% Suc in long day (16h L: 8h D ) at 22C, in 125 uE m-2 s-1
UBP1C IP RNA

hyb_protocol: Standard affy Workstation protocols

scan_protocol: Standard affy Workstation protocols

data_processing:
Microarray features of the above data sets were background corrected, normalized, and probe set intensities were summarized using the affy (22) and limma (linear models for microarray data) (23) packages. Present, marginal, absent (PMA) calls were made using the Wilcoxon signed rank-based gene expression presence/absence detection algorithm as implemented by MAS5. The “expresso” function calculated expression values using rma background adjustment, constant normalization for microarray scaling, and median polish method for probe set summarization of perfect match only features, specified as PMonly.
Bioconductor affy and limma package expresso funcion, rma background adjustment, constant normalization, median polish method for probe set summarization of  perfect macth only features specified as PMonly

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h hypoxia +20' reoxy, Rep1

label_protocol: For microarray analysis, 150 ng total and 15 ng UBP1C IP RNA were used to synthesize biotinylated, amplified RNA (aRNA) via 15 rounds of in vitro transcription using the 3' IVT Express Kit (Affymetrix, Santa Clara, CA). aRNA was fragmented and probed using the Arabidopsis ATH1 Genome Array (Lot 4160460; Affymetrix). Hybridizations were performed with 15 µg fragmented aRNA at 45oC for 16 h on a rotating platform.

extract_protocol: two aliquots of approximately 100 mg frozen ground powder tissue were thawed in 1.5 mL ice cold RNP extraction buffer modified from Oeffinger et al. (17) for plant extracts (200 mM Tris [pH 9.0], 110 mM potassium acetate, 0.5% (v/v) Triton-X100, 0.1% (v/v) Tween-20, 1.5% (v/v) protease inhibitor cocktail for plant cell and tissues extracts (Sigma P9599, St. Louis, MO), 5 mM dithiothrietol, 0.1% (v/v) RNaseOUT (Invitrogen, Carlsbad, CA)). The sample tube was briefly vortexed and the extract filtered through two layers of sterilized Miracloth (EMD Millipore, Billerica, MA) into a clean 1.5 mL microfuge tube. The filtrate was centrifuged in a swinging bucket clinical centrifuge at approximately 1500g for 2 min at 4oC.The supernatant (S-1.5K) was removed and a sample aliquoted for RNA extraction (100 µL per replicate sample). The remaining S-1.5K was transferred to a 1.5 mL microfuge tube containing antibody-conjugated beads for the IP. Protein G-conjugated paramagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA) were prepared according to the manufacturer’s directions. Briefly, for each 100 mg of tissue processed, 100 µL of resuspended Dynabeads were magnetically separated from the storage solution and resuspended in 400 µL α-FLAG M2 monoclonal antibody (Sigma F1804) in phosphate buffered saline Tween (PBST; 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate dibasic, 2 mM sodium phosphate monobasic [pH 7.4], 0.02% (v/v) Tween-20). The final FLAG M2 monoclonal antibody concentration was 25 ng µL-1 α-FLAG M2, The bead antibody mixture was incubated for 1 h on a rocker at 20-23oC. Following antibody conjugation to the beads, excess antibody was removed by magnetic separation and washing. IP of FLAG-UBP1C-containing complexes was accomplished by rocking the S-1.5K-Dynabead slurry at 4 oC for 1.5 h. Following incubation, the Dynabeads were magnetically separated, 30 µL supernatant was saved as the unbound fraction, and the beads were washed with 0.75 mL RNP extraction buffer for 5 min with rocking at 4oC and magnetically collected. Bead washing steps were repeated five more times. FLAG-UBP1C was eluted in 100 µL RNP extraction buffer plus 400 ng µL-1 3X Flag® Peptide (Sigma F4799) at 4oC for 30 min with rocking. Eluates of replicate IPs were combined for a total of 200 µL. 180 µL was used for RNA extraction.

treatment_protocol: Control light plants were maintained in light. Control dark plants were transferred to near darkness (<0.05 µE m-1 s-1) for 2 h in a humidified 13.5 L Plexiglas chamber open to ambient air (dark control, D). For hypoxia treatment (H), plants were placed under the same low light and deprived of oxygen for 2 h by sealing the chamber and continuously flushing it with humidified 99.99% Ar(g) at a rate of 50 mL s-1 for 2 h at 20oC. For 2 h hypoxia followed by 20 min reoxygenation (R), reoxygenation was facilitated by removing the top of the chamber and fanning with a rigid plastic fan (~25 x 40 cm) immediately and again after 10 min for 1 minute. All seedlings were harvested rapidly into N2(l), ground to a powder and stored at -80oC.

tag: sample type

value: UBP1C IP RNA

value: seedling

tag: treatment

value: 2 h hypoxia +20' reoxy

tag: genotype

value: ubp1c-1 35S:FLAG-UBP1C

tag: antibody

value: FLAG


title: 48h Left Carotid Artery Endothelium 1


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hHypoxia+20'Reoxy_Rep2

description:
7 day old whole seedlings grown on MS + 1% Suc in long day (16h L: 8h D ) at 22C, in 125 uE m-2 s-1
Total RNA

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h hypoxia +20' reoxy, Rep2

value: Total RNA


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hHypoxia+20'Reoxy_Rep2

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h hypoxia +20' reoxy, Rep2

growth_protocol: 7 day old whole seedlings grown on MS + 1% Suc in long day (16h L: 8h D ) at 22C, in 125 uE m-2 s-1


title: 12h Right Carotid Artery Endothelium 6

source_name: RCA endothelium post partial ligation 12h

treatment_protocol: 12 hours post partial ligation surgery, the carotid intima were flushed with qiazol


title: 12h Right Carotid Artery Endothelium 5


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hHypoxia+20'Reoxy_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h hypoxia +20' reoxy, Rep1


title: hES-S6-1-live


title: 12h Right Carotid Artery Endothelium 4


title: 12h Right Carotid Artery Endothelium 3


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hLight_Rep2

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h light, Rep2

value: 2 h light


title: 12h Right Carotid Artery Endothelium 2


title: 12h Right Carotid Artery Endothelium 1


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hLight_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h light, Rep1


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hLight_Rep2

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h light, Rep2


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hLight_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h light, Rep1


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hHypoxia_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h hypoxia, Rep1

value: 2 h hypoxia


title: 12h Left Carotid Artery Endothelium 6

source_name: LCA endothelium post partial ligation 12h


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hMockDark_Rep2

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h mock dark, Rep2

value: 2 h mock dark


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hMockDark_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h mock dark, Rep1


title: 12h Left Carotid Artery Endothelium 5


title: 12h Left Carotid Artery Endothelium 4


title: 12h Left Carotid Artery Endothelium 2


title: 12h Left Carotid Artery Endothelium 3


title: 12h Left Carotid Artery Endothelium 1


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hHypoxia_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h hypoxia, Rep1


title: 11-S-11311-E

city: Washington

first: Jeffrey

last: Bethony

state: DC

address: 2300 Eye St. NW.

department: Microbiology, Immunology, and Tropical Medicine

institute: George Washington University

hyb_protocol: Labeled total RNA samples were dried completely by using speed-vac, and then hybrized with probes on array slides, accorkding to the manufacture. The hybridization lasted for 20 hours inside 55'C hybridization oven (Agilent). After hybridization, arrays were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature, and then wahsed with Wash Buffer 2 (Agilent) at 37'C. The washed array were dried and processed to scanning step immediately.

scan_protocol: Slides was scanned immediated after washing step on Agilent G2565CA Microarray Scanner System. (Scan Area is 61x21.6 mm; Scan resolution is 3um; Color channel is Green; Green PMT is 100%)

data_processing: The feature intensities were transferred to digital data and Log2 transformed by using Feature Extraction (V.10.7) software on default setting. (Protocol is miRNA_107_Sep09, Grid is 031181_D_F_20111226). For data analysis, inter-sample variance was normalized by using quantile normalization strategies on GeneSpringGX 12.0.

source_name: Control_FFPE tissue

label_protocol: 250ng Total RNA from each FFPE case was labeled with Cyanine 3-pCp by using Agilent miRNA labeling kits according to the manufacturer's instructions. Labeled samples were desalted by using MicroBioSpin 6 Columns (Bio-Rad).

extract_protocol: Total RNA was isolated from FFPE sections using the miRNeasy FFPE kit (Qiagen) according to manufacturer’s protocol. Briefly, 320 µL Deparaffinization Solution (Qiagen) was added followed by brief vortexing, centrifugation and incubation. Buffer PKD was added, samples centrifuged and proteinase K added. Digestion was performed at 56◦C for 15 minutes and 80◦C for 15 minutes in order to partially reverse formaldehyde modification. The lower phase was removed and DNase digestion performed at room temperature for 15 minutes. 500 µL RBC buffer was then added, followed by 100% Ethanol (Acros Chemical) and transferred to the RNeasy MiniElute column. The column was washed twice with RPE, followed by drying and then eluted with 30 µL RNase-free water

treatment_protocol: Formalin Fixed Paraffin Embedded (FFPE) biopsy samples from four cases of histologically proven nasopharyngeal carcinoma.2 x 20 µm slices from each case were prepared for RNA purification.

value: FFPE tissue

value: Control

tag: histology

value: Non-NPC tissue. Undifferentiated


title: 05-S-5264-F


title: 04-S-341E

value: Non-NPC tissue. Differentiated


title: N1.1

source_name: whole spleen, mock infection

tag: strain/background

tag: genotype/variation

value: WT

value: whole spleen

tag: p. yoeli infection strain (control=n)

value: N


title: 08-S-6658C

tag: tissue


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hMockDark_Rep1

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h mock dark, Rep1


title: 12-S-432A

source_name: Tumor_FFPE tissue

value: Tumor

value: Non-keratinizing. Undifferentiated (99% tumor)


title: 04-S-6103A


title: 04-S-341B

value: Non-keratinizing. Differentiated (90% tumor)


title: liver_wt_1409

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

hyb_protocol: Hybridized to Affymetrix® Mouse Genome 430A 2.0 GeneChip Arrays according to manufacturer protocol.

scan_protocol: Scanned according to manufacturer protocol.

data_processing: Analyzed with the ArrayAssist software (Stratagene) to generate GC-RMA absolute expression values (log2 scale).

label_protocol: Biotin-labeled cRNA probes were synthesized according to manufacturer protocol.

extract_protocol: RNA was extracted from adult liver tissue samples of 3 Jag1 conditional/null mutant animals, and 3 littermate wildtype control animals.

value: liver

value: wildtype

tag: litter

value: B

value: 8 weeks


title: 08-S-6658A


title: liver_mut_2076

value: Jag1 conditional/null

value: C

value: 4 weeks


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hMockDark_Rep2

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h mock dark, Rep2

value: UBP1C IP RNA

value: seedling

value: 2 h mock dark

value: ubp1c-1 35S:FLAG-UBP1C

value: FLAG


title: liver_mut_1407


title: liver_mut_1208

value: A

value: 12 weeks


title: liver_wt_1207


title: NAG-1-HF-rep3

city: Research Triangle Park

first: Deepak

last: Mav

address: 2 Davis Drive

institute: Sciome LLC

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: The feature extractor processed signal intensity values were log2 transformed, quantile normalized, the multiple values for same probe were summarized using median polish. The resulting value was batch corrected using Emprical Bayes method from Johnson et al. 2006 (Johnson EW, Rabinovic A, Li C . Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics Advance Access published on April 21, 2006, DOI 10.1093/biostatistics/kxj037).

source_name: NAG-1 transgenic, high fat

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to Agilent's protocol.

extract_protocol: Total RNA in colon epithelium was prepared using AllPrep DNA/RNA Mini Kit (Qiagen).

treatment_protocol: Female h-NAG-1 transgenic mice and wild type C57BL/6J mice at 5 weeks of age were placed on either 10% fat diet (D12450B) or 60% fat diet (D12492, Research Diets, New Brunswick, NJ) for 20 weeks.

value: NAG-1 transgenic

tag: gender

value: female

value: colon epithelium

value: high fat diet

tag: processing batch


title: liver_wt_2077

value: liver

value: wildtype


title: WT-HF-rep1

source_name: Wild type, high fat

value: WT


title: NAG-1-LF-rep2

source_name: NAG-1 transgenic, low fat

value: low fat diet


title: NAG-1-LF-rep3


title: NAG-1-HF-rep2


title: NAG-1-LF-rep1


title: NAG-1-HF-rep1


title: WT-LF-rep2

source_name: Wild type, low fat


title: Patient 150

status: Public on Jan 12 2014

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

institute: INSA

description: This sample is of human frozen breast cancer tumors

hyb_protocol: One µg ds-cDNA was Cy3 labeled using One-Color DNA labeling kit (NimbleGen Roche Diagnostics, Meylan, France). Hybridization on our Roche NimbleGen 4x72K custom microarray, washing slides and scan were performed according to the manufacturer’s protocol (NimbleGen Roche Diagnostics, Meylan, France).

scan_protocol: Scanning was performed on NimbleGen MS 200 scanner, following the standard operating protocol. See www.nimblegen.com. DEVA software v1.2 (NimbleGen Roche Diagnostics, Meylan, France) was used to extract the raw intensity values.

data_processing: All data (.pair files) were RMA background corrected (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), log2-transformed, summarized by a robust mean. Then an housekeeping normalization was done on the experimental data.

source_name: Human frozen breast cancer tumors

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 2 μg of total RNA using SuperScript One cycle kit (Invitrogen Life Technologies, Saint-Aubin, France) with random primers and Oligo(dT) primers, then cleaned with MinElute PCR Purification Kit (Qiagen, Courtaboeuf, France)

growth_protocol: 151 frozen breast cancer tumors from the tumor bank of the Claudius Regaud Institute (ICR Toulouse, France) were selected

extract_protocol: Total RNA was extracted from 12 µm-thickcryostat sections of with Qiazol and RNeasy Lipid Tissue Kit (Qiagen, Courtaboeuf, France). The concentration of total RNA obtained from each tumor sample was determined using a Nanodrop® spectrophotometer (Labtech, Palaiseau, France) and the integrity of the RNA was assessed using a 2100 Bioanalyzer® (Agilent Technologies, Massy, France). The percentage of tumor cells was evaluated on frozen a section stained with hematoxylin-eosin.

tag: tumor bank

tag: individual

tag: disease state

value: invasive breast carcinoma

tag: tumor stage


title: WT-LF-rep1


title: WT-HF-rep3


title: Patient 148

value: Claudius Regaud Institute (ICR Toulouse, France)


title: Patient 149


title: Patient 151


title: Patient 146


title: Patient 145


title: Patient 144


title: Patient 138


title: Patient 147


title: Patient 139


title: Patient 141


title: Patient 135


title: WT-HF-rep2


title: Patient 140


title: Patient 143


title: Patient 136


title: Patient 133


title: Patient 142


title: Patient 134


title: Patient 137


title: Patient 132


title: Patient 130


title: Patient 131


title: Patient 128


title: Patient 127


title: Patient 129


title: Patient 126


title: Patient 125


title: Patient 124


title: Patient 122


title: Patient 120


title: Patient 121


title: Patient 123


title: Patient 119


title: Patient 117


title: Patient 118


title: Patient 116


title: Patient 112


title: Patient 115


title: Patient 110


title: Patient 108


title: Patient 111


title: Patient 109


title: Patient 105


title: Patient 106


title: Patient 100


title: Patient 103


title: Patient 102


title: Patient 104


title: Patient 113


title: Patient 97


title: Patient 96


title: Patient 107


title: Patient 101


title: Patient 98


title: Patient 95


title: Patient 114


title: Patient 92


title: Patient 91


title: Patient 93


title: Patient 99


title: Patient 90


title: Patient 84


title: Patient 86


title: Patient 83


title: Patient 94


title: Patient 79


title: Patient 85


title: Patient 87


title: Patient 89


title: Patient 78


title: Patient 81


title: Patient 88


title: Patient 82


title: Patient 80


title: Patient 74


title: Patient 77


title: Patient 72


title: Patient 75


title: Patient 71


title: Patient 70


title: Patient 66


title: Patient 76


title: Patient 68


title: Patient 73


title: Patient 63


title: Patient 64


title: Patient 67


title: Patient 58


title: Patient 65


title: Patient 69


title: Patient 61


title: Patient 59


title: Patient 57


title: Patient 49


title: Patient 55


title: Patient 54


title: Patient 47


title: Patient 48


title: Patient 53


title: Patient 62


title: Patient 60


title: Patient 56


title: Patient 52


title: Patient 44


title: Patient 50


title: Patient 46


title: Patient 43


title: Patient 42


title: Patient 51


title: Patient 45


title: Patient 41


title: Patient 40


title: Patient 38


title: Patient 35


title: Patient 33


title: Patient 34


title: Patient 29


title: Patient 31


title: Patient 28


title: Patient 25


title: Patient 23


title: Patient 39


title: Patient 37


title: Patient 27


title: Patient 36


title: Patient 32


title: Patient 20


title: Patient 24


title: Patient 30


title: Patient 16


title: Patient 22


title: Patient 19


title: Patient 13


title: Patient 8


title: Patient 17


title: Patient 7


title: Patient 18


title: Patient 26


title: Patient 14


title: Ad.Null 48h versus Ad.p75NTR 48h Replicate 5

status: Public on Jan 11 2014

city: EDINBURGH

first: Andrea

last: Caporali

address: 47 Litlte France Crescent

institute: University of Edinburgh

description: microRNA expression data from HUVEC over-expressing p75

hyb_protocol: 2-color hybridization was performed using miRCURY LNA microRNA Arrays (v.10.0, EXIQON). 2.5ug of each labeled RNA were co-hybridized at 53°C for 16 hours. Hybridization and washing steps were performed on the HS 400 PRO hybridization station (Tecan).

scan_protocol: MicroRNA arrays were scanned using the GenePix 4100A microarray scanner and the GenePix Pro 6.0.1.25 software (Molecular Devices).

data_processing:
The obtained signal intensities were analyzed by using the limma package (Bioconductor 2.5 on R 2.10 ). Background correction (normexp, cutoff=10), within (global LOESS) -and between  (scale method)  array normalization was performed. Differential expression and statistical significance were assessed for each miRNA species across all 4 arrays using linear model fit and empirical Bayes method (lmFit, eBayes), taking into account the dye-swap. Features showing intensities with a signal-to-noise ration (SNR) lower than 3 were considered as bad quality spot. The calling of a miRNA failed if two or more of the four replicates present per miRNA species were bad quality spots and if this occurred on more than 3 arrays.
Log2FC: Normalized log2 ratio (Hy5/Hy3). P value adjusted for False Discovery Rate (Benjamini and Hochberg's method).

source_name: HUVEC infected by adenoviral vector Ad-rad66 (empty vector, also called Null)

label_protocol: 2.5 ug total RNA was labeled with Hy3, Hy5 resepctively according to the manufacturer's protocol (miRCURY LNA microRNA Array Power labeling kit, EXIQON).

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS.

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

treatment_protocol: To obtain p75 over-expressing cells, HUVEC were infected by adenoviral vectors carrying human p75NTR sequence (Ad. p75NTR) or by empty vector (Ad-rad66).

tag: cell line

value: HUVEC

source_name: HUVEC infected by adenoviral vectors carrying human p75NTR (Ad. p75NTR)


title: Ad.p75NTR 48h versus Ad.Null 48h (Replicate 4 dye swap)


title: Patient 12


title: Patient 21


title: Patient 10


title: Ad.Null 48h versus Ad.p75NTR 48h Replicate 2


title: Patient 15


title: Patient 3


title: Patient 4


title: Patient 1


title: Ad.Null 48h versus Ad.p75NTR 48h Replicate 4


title: Patient 11


title: Ad.Null 48h versus Ad.p75NTR 48h Replicate 3


title: Ad.Null 48h versus Ad.p75NTR 48h Replicate 1