title: FB3135_60m_40


title: FB3135_360m_76

status: Public on Aug 03 2015

type: RNA

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

country: USA

institute: HHMI/University of Michigan

description: primary fibroblast, insulin treated for 6 hours

hyb_protocol: cRNA was fragmented in 1X Fragmentation buffer (Ambion).  10 ug of cRNA were hybridized for 16 hours at 45C on GeneChip Human Genome HG-U133A_2 Arrays (GEO Platform GPL571). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: 500ng of total RNA was used for each sample.  cRNA was amplified and biotin-labeled following manufacturer's protocol using MessageAmp™ Premier RNA Amplification Kits (Ambion).

growth_protocol: Primary fibroblasts were cultured at 37°C in 5% CO2 in MEM medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/ml streptomycin, and were passaged every 3 days.

extract_protocol: Total RNA was extracted from cells before or after treatment using RNeasy Micro Kit (QIAGEN).

treatment_protocol: To minimize technical variability, fibroblasts from the 35 individuals were passaged, treated and harvested in one batch for the signaling assays and microarray experiments.  Fibroblasts from 35 individuals were serum starved for 18 hours and treated with 100nM insulin for one hour and 6 hours.  In the ERK inhibition studies, cells from 4 individuals were treated with 10 uM UO126 (Cell Signaling) or DMSO (Sigma-Aldrich) for 1 hour before 100nM insulin or ddH2O (mock treatment) was added, and cells were incubated for another 1 hour or 6 hours before being harvested.

tag: individual id

tag: cell type

value: primary fibroblast

tag: agent

value: insulin

tag: time point (insulin treatment)

value: 6 hour


title: FB3136_0m_5

description: primary fibroblast, serum starved

source_name: primary fibroblast, serum starved

value: no insulin

value: baseline


title: E8.5 WT-3

city: San Francisco

first: Ron

last: Parchem

address: 35 Medical Center Way

institute: UCSF

description:
replicate 3
Sample14

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were preprocessed using Combat and quantile normalized in R (combat was used to normalize for batch effects across microarray plates)

organism: Mus musculus

source_name: mouse embryonic tissue

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

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

tag: strain

tag: developmental stage

tag: genotype

value: WT

tag: plate

tag: tissue

value: anterior neural tissue


title: E8.5 WT-2

description:
replicate 2
Sample13


title: E8.5 WT-1

description:
replicate 1
Sample12


title: pBI121_rep1

city: Santa Fe

first: Jorge

middle: Ignacio

last: Giacomelli

state: Santa Fe

address: Ciudad Universitaria

department: LBV

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

description: control replicate

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Helianthus annuus

source_name: Leaves from V3 stage sunflower

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sunflower plants were grown in a controlled growth chamber under a long-day photoperiod (16-h light and 8-h dark at 25 °C) with an illumination of 130–150 μE m−2 s−1 and 40–65% relative humidity for 2–3 weeks

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen using the Trizol® method (Invitrogen, Argentina). The genomic DNA was eliminated after treatment with Dnase I for 20 min at RT using DNAse I® (Invitrogen, Argentina). RNA concentration was measured using an Implen nanophotometer (Implen GmbH, Munich, Germany). Purity and integrity of total RNA was determined by 260/280 nm ratio and the integrity was checked by electrophoresis in 1% agarose gel and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Sunflower disc from tissue obtained from leaves from V3 sunflower plants were obtained as described in Manavella and Chan, Nature Protocols 2009 (doi:10.1038/nprot.2009.178)

tag: construct

value: pBI121_35S Promoter::GUS

tag: genotype/variation

value: control

value: sunflower leave disc


title: E8.5 KO-3

description:
replicate 3
Sample17

value: miR-302 KO


title: infected.4h.2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: L. major infected BMDM at 4h p.i., biological replicate 2

hyb_protocol: 130µl hybridization mix prepared from biotin-labeled RNAs was hybridized to oligonucleotide arrays for 17h at 48°C. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

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

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: L. major infected BMDM at 4h p.i.

label_protocol: 1µg of total RNA was labeled with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: BMDM from BALB/c mice were generated as previously described (Bringmann et al. 2013; PMID: 23587955), harvested and seeded in suspension culture plates at a cell concentration of 2*10^5*ml^-1 in RPMI-1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 10 mM hepes, 0.05 mM 2-mercaptoethanol, 100 U*ml^-1 penicillin, 50 µg*ml^-1 gentamycin and incubated for 4 h at 37°C.

extract_protocol: Total RNA was isolated with TRIzol (Life Technologies, Darmstadt, Germany) according to the manufacturer’s protocol.

treatment_protocol: BMDM were infected with L. major promastigotes (strain MHOM/IL/81/FE/BNI) at a parasite concentration of 3*10^6*ml^-1.

value: BALB/c

tag: infection

value: Leishmania major infection at 4h


title: uninfected.24h.1

description: uninfected BMDM at 24h p.i., biological replicate 1

source_name: uninfected BMDM at 24h p.i.

value: uninfected 24h


title: FB3134_60m_39

description: primary fibroblast, insulin treated for 1 hour

value: 1 hour


title: E8.0 KO-3

description:
replicate 3
Sample11


title: FB3134_360m_75

source_name: primary fibroblast, insulin treated for 6 hours


title: infected.24h.1

description: L. major infected BMDM at 24h p.i., biological replicate 1

source_name: L. major infected BMDM at 24h p.i.

value: Leishmania major infection at 24h


title: infected.4h.1

description: L. major infected BMDM at 4h p.i., biological replicate 1


title: uninfected.4h.1

description: uninfected BMDM at 4h p.i., biological replicate 1

source_name: uninfected BMDM at 4h p.i.

value: uninfected 4h


title: E8.0 KO-2

description:
replicate 2
Sample10


title: FB3134_0m_3

description: primary fibroblast, serum starved

value: primary fibroblast


title: E8.0 WT-3

description:
replicate 3
Sample08


title: E8.0 WT-1

description:
replicate 1
Sample06

value: whole embryo


title: FB3133_60m_38

source_name: primary fibroblast, insulin treated for 1 hour

value: insulin


title: E8.0 WT-2

description:
replicate 2
Sample07


title: E7.5 KO-3

description:
replicate 3
Sample05


title: FB3132_60m_37


title: E7.5 KO-2

description:
replicate 2
Sample04


title: Bone_Parietal_male_6

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 at the transcript level using the oligo package of Bioconductor

label: Cy3 fluorescent label

source_name: Bone, Paraxial mesoderm, Parietal

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Gene 2.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was isolated from the cells using Roche High Pure miRNA Isolation Kit (Indianapolis, IN) according to the manufacturer’s protocol. RNA was isolated from triplicate wells separately and then combined to have one RNA sample for microarray. The quality and quantity of the sample were assessed using Agilent 2100 Bioanalyzer and NanoDrop 1000 spectrophotometer.

tag: gender

value: male

tag: origin

value: Paraxial mesoderm

tag: group

value: Parietal

value: Bone

tag: source

value: fetal crania


title: FB3133_360m_74

value: 6 hour


title: E7.5 KO-1

description:
replicate 1
Sample03


title: 662

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
mouse 25
SAMPLE 37

data_processing: Genome Studio 5.0

label: Biotin

source_name: kidney

growth_protocol: N/A: adult mouse kidney tissue

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were subjected to Unilateral Ureter Obstruction (UUO)

value: kidney

value: mix C57Bl/6 and Balb/c genetic background

tag: age (days)

value: 26 weeks of age

value: ggt-cre+;Snail flox/flox genotype (loss of Snail in proximal tubular epithelial cells)

tag: phenotype

value: healthy


title: E8.0 KO-1

description:
replicate 1
Sample09

value: miR-302 KO

value: anterior neural tissue


title: Bone_Frontal_male_6

source_name: Bone, Neural crest, Frontal

value: Neural crest

value: Frontal


title: Mesenchyme_Sagittal_male_6

source_name: Mesenchyme, Neural crest, Sagittal

value: Sagittal

value: Mesenchyme


title: FB3132_0m_1

description: primary fibroblast, serum starved

tag: individual id

tag: cell type

value: primary fibroblast

value: no insulin

value: baseline


title: Mesenchyme_Sagittal_male_5

value: male


title: FB3133_0m_2

description: primary fibroblast, serum starved

tag: agent

tag: time point (insulin treatment)


title: FB3132_360m_73

value: insulin


title: E7.5 WT-1

description:
replicate 1
Sample01

tag: strain

tag: developmental stage

value: WT

value: whole embryo


title: E7.5 WT-2

description:
replicate 2
Sample02

tag: genotype

tag: plate


title: 616

description:
mouse 23
SAMPLE 35

tag: tissue

value: kidney

value: mix C57Bl/6 and Balb/c genetic background


title: Bone_Parietal_male_5

value: Paraxial mesoderm

value: Parietal

value: Bone

value: fetal crania


title: Mesenchyme_Metopic_male_6

source_name: Mesenchyme, Neural crest, Metopic

value: Neural crest

value: Metopic


title: 617

description:
mouse 24
SAMPLE 36

value: 26 weeks of age

value: ggt-cre+;Snail flox/flox genotype (loss of Snail in proximal tubular epithelial cells)

value: healthy


title: R314

description:
mouse 22
SAMPLE 34

value: mix C57Bl/6 and sv129 genetic background

value: ggt-cre+;Twist flox/flox genotype (loss of Twist1 in proximal tubular epithelial cells)


title: R313

description:
mouse 21
SAMPLE 33


title: S401

description:
mouse 18
SAMPLE 30

value: 10 weeks of age

value: ggt-cre-;WT genotype (Wildtype)


title: Bone_Parietal_male_4

value: male


title: E8.5 KO-1

description:
replicate 1
Sample15

value: miR-302 KO

value: anterior neural tissue


title: S403

description:
mouse 19
SAMPLE 31

value: kidney


title: Mesenchyme_Sagittal_male_4

value: Sagittal

value: Mesenchyme


title: R252

description:
mouse 20
SAMPLE 32


title: 598E

description:
mouse 17
SAMPLE 29


title: Esm / Control

city: Garches

first: Arnaud

last: Mansart

address: 104 boulevard Raymond Poincaré

country: France

institute: Université de Versailles

description: data table include data for 4 replicates (merge dye-swap)

hyb_protocol: The hybridization procedure has been done according to the manufacturer (Agilent)

scan_protocol: Fluorescent signals were acquired with a Genepix 4200AL microarray scanner (Axon Instruments) with 5 microns per pixel resolution. The PMT gain for the 635 and 532nm wavelengths were automatically set with control yellow hybridizations (sample hybridized versus itself). The quantification of the signal for each spot was performed with the image analysis GenePix Pro 6.0 software (Axon Instruments).

data_processing: All the data generated by the scan were imported into the statistical data analysis system R. The data were globally normalized using the Lowess regression approach. Data were then converted to relative ratio of fold activation changes. The robustness of the results was ensured by applying the “varmixt” method.

source_name: Esmolol

label_protocol:
labeled cDNA obtained by using the SuperScript Indirect cDNA
Labeling System (Invitrogen)

extract_protocol: total RNA was isolated and purified from a 30mg sample of the heart by using RNeasy kit (Qiagen)

tag: organism part

value: heart

tag: treatment

value: Esmolol by continuous infusion (20 mg/kg/h) via a right jugular central venous catheter

source_name: Control

value: No


title: Mesenchyme_Metopic_male_5

tag: gender

value: Neural crest

value: Metopic

value: fetal crania


title: CLP / CLP+Esm

source_name: CLP

tag: sepsis

value: induced by cecal ligature and perforation (CLP)

source_name: CLP+Esm


title: Bone_Frontal_male_4

tag: origin

tag: group

value: Frontal

value: Bone


title: Bone_Frontal_male_5

tag: source


title: S402

description:
mouse 16
SAMPLE 28

value: mix C57Bl/6 and sv129 genetic background

tag: age (days)

value: 10 weeks of age

value: ggt-cre+;WT genotype (Wildtype)

tag: phenotype

value: healthy


title: Mesenchyme_Sagittal_male_3

value: male


title: Mesenchyme_Metopic_male_4


title: 600E

description:
mouse 15
SAMPLE 27

value: kidney


title: Bone_Frontal_male_3


title: Bone_Parietal_male_3

value: Paraxial mesoderm

value: Parietal


title: 599E

description:
mouse 14
SAMPLE 26


title: Mesenchyme_Sagittal_male_2

value: Sagittal

value: Mesenchyme


title: 481 HK

description:
mouse 11
SAMPLE 23

value: mix C57Bl/6 and Balb/c genetic background

value: ggt-cre+;Snail flox/flox genotype (loss of Snail in proximal tubular epithelial cells)

value: contralateral


title: S600 HK

description:
mouse 13
SAMPLE 25


title: Bone_Parietal_male_2

value: fetal crania


title: Mesenchyme_Metopic_male_3

value: Neural crest

value: Metopic


title: 8821 HK

description:
mourse 10
SAMPLE 22

value: ggt-cre-;Snail flox/flox genotype (Wildtype like)


title: Bone_Parietal_male_1

value: Bone


title: 8822 HK

description:
mouse 12
SAMPLE 24

value: 10 weeks of age


title: Mesenchyme_Metopic_male_2


title: Fibroblast 1 [Fb-44B-P5]

type: genomic

city: Bethesda

first: Thierry

last: Vilboux

state: MD

address: 10 Center drive

department: NHGRI

institute: NIH

description: Original fibroblast 1 used to generate the different iPSC clones

data_processing:
Data was processed using the Genotyping Module of Genomestudio v2011.1 (Illumina).
GenomeStudio v2011.1
SCORE : This is the GenCall Score. It is a quality metric that indicates the reliability of each genotype call. It is used to rank and filter out failed genotypes. It also appears as GC_SCORE.
Theta : Allelic intensity ratio
R : Normalized intensity values
B_Allele_Freq : B allele frequency
Log_R_Ratio: log2(Robserved/Rexpected)

label: biotin and dinitrophenyl

molecule: genomic DNA

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl-labeled

growth_protocol: Cells grown in monolayer on Geltrex in Freedom Media (both life Technologies). Media was exchange every day until cells reached 90% confluence and passaged using Accutase (Life Technologies).

extract_protocol: Genomic DNA was extracted from cell pellets using the Blood & Cell Culture DNA Midi Kit  (Qiagen)  as  per  the  manufacturer’s  instructions.  The  DNA  was  quantified  using  a Qubit Fluorometer (Life Technologies).  Kit (Qiagen) as per the manufacturer’s instructions. The DNA was quantified using a  Qubit Fluorometer (Life Technologies).

tag: Sex

value: Male

tag: original fibroblast id

tag: cell type

value: Fibroblast

tag: passage


title: S439 HK

description:
mouse 7
SAMPLE 19

value: mix C57Bl/6 and sv129 genetic background

value: ggt-cre+;Twist flox/flox genotype (loss of Twist1 in proximal tubular epithelial cells)


title: Mesenchyme_Sagittal_male_1

value: male


title: 475 HK

description:
mouse 8
SAMPLE 20

value: kidney


title: Bone_Frontal_male_2

value: Frontal


title: 687 HK

description:
mouse 6
SAMPLE 18


title: Mesenchyme_Metopic_male_1

value: Mesenchyme


title: Bone_Frontal_male_1


title: 649 HK

description:
mouse 4
SAMPLE 17


title: Fibroblast 2 [Fb-BJ-P8]

description: Original fibroblast 2 used to generate the different iPSC clones


title: iPSC4 Fibroblast2 P20 [28352-P20-Pick]

description: iPSC clone number 4 passage 20 of fibroblast Fb-BJ-P8

source_name: iPSC clone_passage 20 of fibroblast Fb-BJ-P8

value: Induced pluripotent stem cell (iPSC)

value: passage 20

tag: clone id

value: iPSC clone number 4


title: 485 HK

description:
mouse 9
SAMPLE 21

tag: genotype

value: mix C57Bl/6 and Balb/c genetic background

value: contralateral


title: LPS+Esm / LPS

source_name: LPS+Esm

value: heart

tag: strain

value: induced by intraperitoneal injection of LPS

value: Esmolol by continuous infusion (20 mg/kg/h) via a right jugular central venous catheter

source_name: LPS

value: No


title: iPSC4 Fibroblast2 P8 [28357-P8-Pick]

description: iPSC clone number 4 passage 8 of fibroblast Fb-BJ-P8

source_name: iPSC clone_passage 8 of fibroblast Fb-BJ-P8

value: Male

value: passage 8


title: Bone_Frontal_female_6

value: female

value: Neural crest

tag: tissue

value: Bone

value: fetal crania


title: 653 HK

description:
mouse 2
SAMPLE 15

value: kidney

value: mix C57Bl/6 and sv129 genetic background

value: 10 weeks of age

value: ggt-cre-;Twist flox/flox genotype (Wildtype like)


title: Mesenchyme_Sagittal_female_6

value: Sagittal

value: Mesenchyme


title: S600 DK

description:
mouse 13
SAMPLE 13

value: mix C57Bl/6 and Balb/c genetic background

value: ggt-cre+;Snail flox/flox genotype (loss of Snail in proximal tubular epithelial cells)

value: obstructed


title: 646 HK

description:
mouse 1
SAMPLE 14

value: contralateral


title: Mesenchyme_Sagittal_female_5


title: 481 DK

description:
mouse 11
SAMPLE 11


title: Bone_Parietal_female_6

value: Paraxial mesoderm

value: Parietal


title: Bone_Parietal_female_5


title: iPSC5 Fibroblast2 P8 [28352-P8-Pick]

description: iPSC clone number 5 passage 8 of fibroblast Fb-BJ-P8

value: Male

value: Induced pluripotent stem cell (iPSC)

value: passage 8

value: iPSC clone number 5


title: iPSC2 Fibroblast2 P20 [C11421D1-P20-Pool]

description: iPSC clone number 2 passage 20 of fibroblast Fb-BJ-P8

value: passage 20

value: iPSC clone number 2


title: Bone_Parietal_female_4

value: female

value: Bone

value: fetal crania


title: iPSC3 Fibroblast2 P8 [C11421E1-P8-Pool]

description: iPSC clone number 3 passage 8 of fibroblast Fb-BJ-P8

value: iPSC clone number 3


title: 8822 DK

description:
mouse 12
SAMPLE 12

value: kidney

value: 10 weeks of age


title: Mesenchyme_Metopic_female_6

value: Neural crest

value: Metopic

value: Mesenchyme


title: 8821 DK

description:
mourse 10
SAMPLE 10

value: mix C57Bl/6 and Balb/c genetic background

value: ggt-cre-;Snail flox/flox genotype (Wildtype like)

value: obstructed


title: iPSC5 Fibroblast2 P20 [28357-P20-Pick]

description: iPSC clone number 5 passage 20 of fibroblast Fb-BJ-P8

value: Male

value: Induced pluripotent stem cell (iPSC)


title: 485 DK

description:
mouse 9
SAMPLE 9


title: Bone_Frontal_female_5

value: Frontal


title: Mesenchyme_Metopic_female_5


title: S439 DK

description:
mouse 7
SAMPLE 7

value: mix C57Bl/6 and sv129 genetic background

value: ggt-cre+;Twist flox/flox genotype (loss of Twist1 in proximal tubular epithelial cells)


title: 475 DK

description:
mouse 8
SAMPLE 8


title: 687 DK

description:
mouse 6
SAMPLE 6


title: Placenta_GDM_Yes_Sample68

city: Los Angeles

first: Alexandra

last: Binder

state: California

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

description: chart-reported case of gestational diabetes

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing:
Color bias adjustment and quantile normalization was performed on signal intensities, adjustment for probe-type bias was performed on the beta-values using beta-mixture quantile normalization (BMIQ)
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

source_name: Placenta tissue from the maternal (decidual basalis) side near the umbilical cord

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from placenta tissue using the QIAmp DNA Mini Kit (Qiagen) according to manufacturer’s instruction

value: placenta

tag: gestational diabetes

value: Yes


title: 649 DK

description:
mouse 4
SAMPLE 4


title: iPSC3 Fibroblast1 P20 [48740-P20-Pool]

description: iPSC clone number 3 passage 20 of fibroblast Fb-44B-P5

source_name: iPSC clone_passage 20 of fibroblast Fb-44B-P5

value: passage 20


title: 691 HK

description:
mouse 3
SAMPLE 16

value: ggt-cre-;Twist flox/flox genotype (Wildtype like)

value: contralateral


title: iPSC1 Fibroblast2 P8 [28361-P8-Pick]

description: iPSC clone number 1 passage 8 of fibroblast Fb-BJ-P8

value: passage 8

value: iPSC clone number 1


title: 690 DK

description:
mouse 5
SAMPLE 5

value: kidney

value: 10 weeks of age


title: 691 DK

description:
mouse 3
SAMPLE 3


title: iPSC2 Fibroblast2 P8 [C11421D1-P8-Pool]

description: iPSC clone number 2 passage 8 of fibroblast Fb-BJ-P8

value: iPSC clone number 2


title: Mesenchyme_Metopic_female_4

value: female

value: Neural crest

value: Metopic

value: Mesenchyme

value: fetal crania


title: Bone_Parietal_female_3

value: Paraxial mesoderm

value: Parietal

value: Bone


title: Mesenchyme_Sagittal_female_3

value: Sagittal


title: 653 DK

description:
mouse 2
SAMPLE 2

value: mix C57Bl/6 and sv129 genetic background

value: obstructed


title: iPSC2 Fibroblast1 P20 [48712-P20-Pick]

description: iPSC clone number 2 passage 20 of fibroblast Fb-44B-P5

value: Male

value: Induced pluripotent stem cell (iPSC)

value: passage 20


title: Bone_Frontal_female_3

value: Frontal


title: iPSC1 Fibroblast2 P20 [28361-P20-Pick]

description: iPSC clone number 1 passage 20 of fibroblast Fb-BJ-P8

value: iPSC clone number 1


title: 646 DK

description:
mouse 1
SAMPLE 1

value: kidney

value: 10 weeks of age

value: ggt-cre-;Twist flox/flox genotype (Wildtype like)


title: iPSC1 Fibroblast1 P20 [48771-P20-Pick]

description: iPSC clone number 1 passage 20 of fibroblast Fb-44B-P5


title: Mesenchyme_Sagittal_female_2

value: female

value: Neural crest


title: Mesenchyme_Sagittal_female_4

value: Mesenchyme

value: fetal crania


title: non-Tg

city: Tokushima

first: Mitsuru

last: Matsumoto

address: 3-18-15 Kuramoto

department: Division of Molecular Immunology

country: Japan

institute: Institute for Enzyme Research, Tokushima University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat the hybridization cocktails at 99 °C for 2 minutes, then 45 °C for 5 minutes • Transfer 80 μl of cocktail to Mouse Gene 1.0ST Array (Affymetrix). • Hybridize 20 hours at 45° at 60 rpm.

scan_protocol: GeneChips were washed and stained immediately after completion of hybridization. Fluidics Script Protocol is FS450_0007.  GeneChips were scanned using the Scanner 3000 7G (Affymetrix), and CEL files were generated.

data_processing: The scanned images were analyzed with GeneSpring GX 13.0 ( Agilent Technologies).

source_name: cTECs from 5 non-Tg

label_protocol: cDNA synthesis and amplification was performed using Ovation One-Direct System (NuGEN) using 400 pg of purified total RNA . 5.5 ug of cDNA was fragmented and end-labeled with Encore Biotin Module (TaKaRa). Fragmented cDNA was monitored with the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was prepared using an RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions. The quantity and qualty of the RNA was monitored using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: sample type

value: NOD mice at day 7

value: cortical thymic epithelial cells

value: control


title: iPSC3 Fibroblast2 P20 [C11421E1-P20-Pool]

description: iPSC clone number 3 passage 20 of fibroblast Fb-BJ-P8

value: iPSC clone number 3


title: iPSC2 Fibroblast1 P8 [48712-P8-Pick]

description: iPSC clone number 2 passage 8 of fibroblast Fb-44B-P5

source_name: iPSC clone_passage 8 of fibroblast Fb-44B-P5

value: passage 8

value: iPSC clone number 2


title: Mesenchyme_Metopic_female_2

tag: gender

value: Metopic


title: iPSC1 Fibroblast1 P8 [48771-P8-Pick]

description: iPSC clone number 1 passage 8 of fibroblast Fb-44B-P5

value: Male

value: Induced pluripotent stem cell (iPSC)


title: Tg

source_name: cTECs from 7 Tg

value: Aire transgenic


title: Mesenchyme_Metopic_female_3


title: Mesenchyme_Sagittal_female_1

value: Sagittal


title: Bone_Parietal_female_2

source_name: Bone, Paraxial mesoderm, Parietal

value: Paraxial mesoderm

value: Parietal

value: Bone


title: Treated MuSK-/- myotubes_rep2

city: Basel

first: Atilgan

last: Yilmaz

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description: biological replicate 2

hyb_protocol: Approximately 2.5 mg of cDNA was hybridizied over night at 45 0C and 60 rpm to Affymetrix Mouse 1.0 Gene ST(cat # 901168).

scan_protocol: The arrays were washed and stained following Affymetrix standard protocol using GeneChip® Hybridization Wash and Stain Kit (cat # 900720) and subsequently scanned on a Affymterix 3000 7G scanner.

data_processing: Affymetrix Expression console was used to analyze the overall performance and quality of the arrays and Partek Genomics Suite was used to detect differentially expressed genes. To call genes differentially expressed between samples we used false discovery rate (FDR) as selection criteria or unadjusted p-values of 0.05.

source_name: MuSK-null myotubes, BMP4-treated, 8 hours, 25ng/ml

label_protocol: Total RNA was converted to double-stranded cDNA and then in-vitro transcribed overnight using the WT expression kit from Invitrogen (cat # 4411981). After cleanup 10 mg IVT-cRNA was converted to dUTP labeled cDNA and 5.5 mg of the generated single stranded cDNA was enzymatically fragmented followed by TdT mediated biotin end labeling using Affymterix WT terminal labeling kit (cat # 900670). The fragmentation resulted in DNA fragments with a distribution peak at approximately 75 nucleotides and successful fragmentation was demonstrated on the bioanalyzer with RIN scores of 2.6.

growth_protocol: Immortalized myoblast cultures of wild-type mouse H-2Kb-tsA58 and MuSK-/- lines were cultured on gelatin-coated dishes in DMEM supplemented with 20% fetal bovine serum, 2% L-Glutamine, 1% Penicillin-Streptomyocin, 1% Chicken Embryo Extract, 1U interferon-γ under permissive temperature at 33 0C in 8% CO2. Myotubes were obtained by switching the confluent myoblast cultures to a medium with DMEM supplemented with 5% horse serum, 2% L-Glutamine and 1% Penicillin-Streptomyocin at 37 0C in 8% CO2 for 3 days.

extract_protocol: Total RNA was isolated from myoblast and myotube cultures of wild type and MuSK null cells after 8 hours of BMP4 treatment with Trizol (Invitrogen).Total RNA was cleaned up and DNase-treated in Qiagen RNeasy columns. 150-200 ng total RNA of good quality RNA (bioanalyzer RIN scores of >9 ) were used as input material for all arrays.

treatment_protocol: Wild type H-2Kb-tsA58 and MuSK null myoblasts were serum deprived for 4 hours and treated with 25ng/ml BMP4 for 8 hours. 3-days old wild type H-2Kb-tsA58 and MuSK-null myotubes were treated without serum-deprivation with 25ng/ml BMP4 for 8 hours.

tag: differentiation status

value: myotubes

tag: musk expression

tag: bmp4 treatment

value: 25ng/ml, 8 hours


title: Bone_Frontal_female_2

source_name: Bone, Neural crest, Frontal

value: female

tag: origin

value: Neural crest

tag: group

value: Frontal

tag: source

value: fetal crania


title: Bone_Parietal_female_1


title: Treated wild-type myotubes_rep2

description: biological replicate 2

source_name: Wild type H-2Kb-tsA58 myotubes, BMP4-treated, 8 hours, 25ng/ml


title: Treated MuSK-/- myotubes_rep3

description: biological replicate 3


title: Untreated MuSK-/- myotubes_rep1

description: biological replicate 1

source_name: MuSK-null myotubes, untreated


title: Treated MuSK-/- myotubes_rep1

description: biological replicate 1


title: Untreated MuSK-/- myotubes_rep2

description: biological replicate 2


title: Untreated MuSK-/- myotubes_rep3

description: biological replicate 3


title: Treated wild-type myotubes_rep1

description: biological replicate 1


title: Bone_Frontal_female_1


title: iPSC3 Fibroblast1 P8 [48740-P8-Pool]

description: iPSC clone number 3 passage 8 of fibroblast Fb-44B-P5

tag: Sex

value: iPSC clone number 3


title: Mesenchyme_Metopic_female_1

source_name: Mesenchyme, Neural crest, Metopic

value: Mesenchyme


title: Bone_Frontal_female_4


title: Untreated wild-type myotubes_rep1

description: biological replicate 1

source_name: Wild type H-2Kb-tsA58 myotubes, untreated


title: mESCs Pax3-GFP -positive at day6, Chir differentiation, biological rep3

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

institute: IGBMC

description: Gene expression data from differentiated mouse embryonic stem cells (mESCs) for 6 days in serum-free CDL conditions and sorted for Pax3-GFP expression

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Chicken Genome arrays. Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

source_name: mESCs Pax3GFP+, CDL, day6

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Undifferentiated mouse ES cells were cultured on feeders of mitomycin-C inactivated mouse embryonic fibroblasts at 37 °C in 5% CO2, in a maintenance medium composed of DMEM supplemented with 15% fetal bovine serum (Millipore), penicillin, streptomycin, 2 mM l-glutamine, 0.1 mM nonessential amino acids, 0.1% β-mercaptoethanol, 1,500 U/ml LIF and 2i inhibitors. Cells were passaged by trypsinization (Invitrogen). Prior to differentiation, cells were passaged once onto gelatin-coated, feeder-free culture plates.

extract_protocol: Total RNA was extracted from ES cell populations using Trizol (Invitrogen) or with the RNAeasy plus mini-kit (Qiagen).

treatment_protocol: Serum-free differentiation of mouse ES cells toward a Presomitic mesoderm-like fate. ES cells were trypsinized and plated at various densities in gelatin-coated, feeder-free, 6-well plates directly in serum-free N2B27 medium supplemented with 1% Knock-out Serum Replacement (KSR, Gibco), 0.1% bovine serum. albumin (Gibco) and BMP4 at 10 ng/ml (Peprotech) for 2 days. Cells were then changed to a DMEM-based medium, with 15% KSR, supplemented with recombinant 10 ng/ml Rspo3 (Peprotech, R&D Biosystems), 0.5% DMSO (Sigma), and 0.1 μM LDN193189 (Tocris, Miltenyi Biotec/Stemgent) (RDL medium) for 4 d. Alternatively, Rspo3 was replaced with CHIRON99021 (Chir; Tocris, Stemgent) at 1 μM (CDL medium).

tag: time point

value: day 6

tag: cell line

value: ES cell line CK35

tag: marker

tag: treatment

value: Serum-free- CHIRON99021, DMSO, LDN193193


title: Untreated wild-type myotubes_rep3

description: biological replicate 3


title: mESCs Pax3-GFP -positive at day6, Chir differentiation, biological rep1


title: mESCs Pax3-GFP -positive at day6, Rspo3 differentiation, biological rep3

description: Gene expression data from differentiated mouse embryonic stem cells (mESCs) for 6 days in serum-free RDL conditions and sorted for Pax3-GFP expression

source_name: mESCs Pax3GFP+, RDL, day6

value: Serum-free- Rspo3, DMSO, LDN193191


title: Treated MuSK-/- myoblasts_rep3

description: biological replicate 3

source_name: MuSK-null myoblasts, BMP4-treated, 8 hours, 25ng/ml

value: myoblast


title: mESCs Pax3-GFP -positive at day6, Chir differentiation, biological rep2


title: Untreated wild-type myotubes_rep2

description: biological replicate 2


title: Treated wild-type myotubes_rep3

description: biological replicate 3


title: Treated MuSK-/- myoblasts_rep2

description: biological replicate 2


title: Treated MuSK-/- myoblasts_rep1

description: biological replicate 1


title: mESCs Msgn1-repV -positive at day4, Chir differentiation, biological rep3

description: Gene expression data from differentiated mouse embryonic stem cells (mESCs) for 4 days in serum-free CDL conditions and sorted for Msgn1-repV expression

source_name: mESCs Msgn1-repV+, CDL, day4

value: day 4

value: ES cell line E14

value: Serum-free- CHIRON99021, DMSO, LDN193191


title: Untreated MuSK-/- myoblasts_rep2

description: biological replicate 2

source_name: MuSK-null myoblasts, untreated


title: mESCs Msgn1-repV -positive at day4, Rspo3 differentiation, biological rep3

description: Gene expression data from differentiated mouse embryonic stem cells (mESCs) for 4 days in serum-free RDL conditions and sorted for Msgn1-repV expression

source_name: mESCs Msgn1-repV+, RDL, day4

value: Serum-free- Rspo3, DMSO, LDN193189


title: Untreated MuSK-/- myoblasts_rep3

description: biological replicate 3


title: mESCs Msgn1-repV -positive at day4, Chir differentiation, biological rep2


title: Untreated MuSK-/- myoblasts_rep1

description: biological replicate 1


title: Placenta_GDM_Yes_Sample44

source_name: Placenta tissue from the maternal (decidual basalis) side near the umbilical cord

value: placenta

value: Yes


title: mESCs Pax3-GFP -positive at day6, Rspo3 differentiation, biological rep1


title: Treated wild-type myoblasts_rep3

description: biological replicate 3

source_name: Wild type H-2Kb-tsA58 myoblasts, BMP4-treated, 8 hours, 25ng/ml

value: 25ng/ml, 8 hours


title: Treated wild-type myoblasts_rep1

description: biological replicate 1


title: mESCs undifferentiated at day0, biological rep3

description: Gene expression data from undifferentiated mouse embryonic stem cells (mESCs)

source_name: mESCs undifferentiated, day0

value: day 0


title: mESCs Msgn1-repV -positive at day4, Chir differentiation, biological rep1


title: mESCs Msgn1-repV -positive at day4, Rspo3 differentiation, biological rep1


title: Untreated wild-type myoblasts_rep2

description: biological replicate 2

source_name: Wild type H-2Kb-tsA58 myoblasts, untreated


title: Treated wild-type myoblasts_rep2

description: biological replicate 2


title: Untreated wild-type myoblasts_rep1

description: biological replicate 1


title: Untreated wild-type myoblasts_rep3

description: biological replicate 3


title: mESCs undifferentiated at day0, biological rep1


title: mESCs undifferentiated at day0, biological rep2


title: mESCs Pax3-GFP -positive at day6, Rspo3 differentiation, biological rep2


title: Nrdp1-/- CD8+ T cells, treated for 4h

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Gene expression data from Nrdp1 KO CD8+ T cells

hyb_protocol: The hybridization was done at the Shanghai Biotechnology Corporation (Shanghai, China). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat #900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat #00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat #00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: The scanning was done at the Shanghai Biotechnology Corporation (Shanghai, China). Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Nrdp1-/- CD8+ T cells, treated for 4h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’ IVT Express Kit (Cat #901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA at the Shanghai Biotechnology Corporation (Shanghai, China).

extract_protocol: Total RNA was isolated from the entire colon from each mouse using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).

treatment_protocol: Naive CD8+ T cells derived spleens of Nrdp1+/+ and Nrdp1-/- mice  were either untreated or treated with immobilized anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml) Abs for 4h or 8h.

tag: genotype

value: Nrdp1 KO

tag: cell type

value: CD8+ T cell

value: anti-CD28 for 4h


title: Nrdp1+/+ CD8+ T cells, untreated

description: Gene expression data from wild type CD8+ T cells

source_name: Nrdp1+/+ CD8+ T cells, untreated

tag: strain

value: wild type

value: untreated


title: infection.24h2

description: L. major infected BMDM at 24h p.i., biological replicate 2

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized to oligonucleotide arrays for 16h at 45°C. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; signals from probes with a sequence match in the L. major genome (5'-AACATGAACGACCTCGTCTCTGAGT-3', 5'-CGACCTCGTCTCTGAGTACCAGCAG-3', 5'-ATTTGGCTACCTTAAGAGAGTCATA-3', 5'-ATCGAGAATGTGAAGGCCAAGATCC-3', 5'-ATCGAGAATGTGAAGGCCAAGATCC-3', 5'-AACATGAACGACCTCGTCTCTGAGT-3', 5'-CGACCTCGTCTCTGAGTACCAGCAG-3', 5'-CGAGAACGTGAAGGCCAAGATCCAG-3', 5'-ATCGAGAATGTGAAGGCCAAGATCC-3', 5'-CGAGAACGTGAAGGCCAAGATCCAG-3' and 5'-ATCGAGAATGTGAAGGCCAAGATCC-3') were set to missing values to avoid confounding of host expression values due to cross-hybridization with parasite transcripts; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: L. major infected BMDM at 24h p.i.

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturer's protocol.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen, Hilden, Germany) and homogenized by QIAshredder (Qiagen) according to the manufacturer’s protocol.

value: BALB/c

tag: animal

value: bone marrow-derived macrophages (BMDM)

tag: infectious agent

value: Leishmania major


title: Nrdp1-/- CD8+ T cells, treated for 8h

source_name: Nrdp1-/- CD8+ T cells, treated for 8h

value: anti-CD28 for 8h


title: Nrdp1-/- CD8+ T cells, untreated

source_name: Nrdp1-/- CD8+ T cells, untreated


title: mESCs Msgn1-repV -positive at day4, Rspo3 differentiation, biological rep2

value: day 4


title: control.1h2

description: uninfected BMDM at 1h p.i., biological replicate 2

source_name: uninfected BMDM at 1h p.i.


title: control.24h1

description: uninfected BMDM at 24h p.i., biological replicate 1

source_name: uninfected BMDM at 24h p.i.


title: Nrdp1+/+ CD8+ T cells, treated for 8h

source_name: Nrdp1+/+ CD8+ T cells, treated for 8h


title: Placenta_GDM_No_Sample41

description: pregnancy without maternal complications

tag: tissue

tag: gestational diabetes

value: No


title: control.24h2

description: uninfected BMDM at 24h p.i., biological replicate 2


title: Nrdp1+/+ CD8+ T cells, treated for 4h

source_name: Nrdp1+/+ CD8+ T cells, treated for 4h


title: control.1h1

description: uninfected BMDM at 1h p.i., biological replicate 1


title: infection.24h1

description: L. major infected BMDM at 24h p.i., biological replicate 1


title: undifferentiated_rep5

city: Pittsburgh

first: Sandeep

last: Kathju

state: PA

address: 200 Lothrop Str

department: Plastic Surgery

institute: University of Pittsburgh

hyb_protocol: Fifteen micrograms of purified, amplified, biotin labeled cRNA was fragmented and hybridized onto Affymetrix Human Genome HGU133A plus 2.0 arrays following manufacturer's recommendations

scan_protocol: Washing, staining and scanning of arrays was performed on the Affymetrix Fluidics Station 450 and Scanner 3000 immediately after completion of hybridization.

data_processing: Microarray data was processed using the Expression Console (Affymetrix) with signal intensity calculated by Microarray Suite version 5.0 (MAS 5.0).

source_name: undifferentiated Adipose Derived Stem Cells

label_protocol: In vitro transcription was performed using the Ambion Message Amp Premier Enhanced assay protocol (Ambion Inc, Austin, TX) starting with 500 ng of purified total RNA.

growth_protocol: Adipose-derived stem cells (ASCs) were isolated from abdominal subcutaneous adipose tissue. Cells cultured in ASC plating media served as undifferentiated Day 0 controls or grown for 7 or 21 days in Adiposite differentiation media.

extract_protocol: Total RNA from undifferentiated ASCs, and cells subjected to 7 and 21-day differentiated protocols was extracted using the RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells cultured in ASC plating media served as undifferentiated Day 0 controls. The differentiation media was replaced every other day for either 7 days or 21 days.

tag: days differentiated

value: Day 0, undifferentiated

tag: gender

value: female

value: abdominal subcutaneous adipose

value: Adipose tissue-derived stromal stem cells


title: Placenta_GDM_No_Sample34

value: placenta


title: 6 day starvation vs. day 0 replicate 3

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

description:
[channel 1] Mtb ΔmetA methionine starved for 6 days replicate 3
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 3
Biological replicate 3 of 3.

hyb_protocol: Each pair of differentially labeled probes was resuspended in 60 ml of hybridization buffer (500 ml formamide, 250 ml 206 SSC, 5 ml 10% SDS, 245 ml ultrapure water) and hybridized to the microarray slide overnight in a 42C water bath. Slides were then washed in increasingly stringent wash conditions (3 times 5 min 16SSC 0.1% SDS, 3 times 5 min 0.16 SSC 0.1% SDS, 3 times 5 min 0.16 SSC and a final dip in 0.22 mm-filtered MQ water).

scan_protocol: Arrays were scanned in a Genepix 4000A scanner Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Spots quantified with TIGR Spotfinder. The data was then processed in TIGR MIDAS. Two color tiff images of the microarrays were visually inspected for defects and obvious spatial biases. Prior to normalization pin-tip (block) intensity box plots were used to detect slides exhibiting spatial and/or pin biases, with post-normalization intensity box plots and MA plots used to assess the effectiveness of normalization in correcting these biases. RI plots were also used to identify outlier slides and for assessing the effectiveness of the normalization process, and Z-score histograms were used to look for slides with abnormal intensity distributions. Slides that did not pass the quality control process were rejected, and repeat hybridizations were performed. Post normalization (Total Intensity and LOWESS) the in-slide replicate spots were averaged before expression ratios were calculated. The results from 3 biological replicates including two dye swaps were then subjected to a t-test without false discovery correction in TIGR MeV software.

organism: Mycobacterium tuberculosis

source_name: Mtb ΔmetA _6.3

label_protocol: Labeling was performen using protocols SOP# M007 from The Institute of Genomic Research (TIGR)

extract_protocol: Cells were collected by centrifugation and resuspended in 1 ml TRIzol reagent (Life Technologies, Fisher, Grand Island, NY). The suspension was transferred to Fast-Prep Blue Cap tubes and processed 2x for 45 s at speed 6 in a Fast-Prep apparatus (MP Bio, Irvine, CA). After a brief incubation on ice, the debris was spun down and the supernatant (~750 ml) further process with Direct-zol™ RNA MiniPrep (Zymo Research Corporation, Irvine, CA) according to manufacturer’s protocol.

tag: genotype/variation

value: ΔmetA

tag: condition

value: methionine starved

tag: time

value: 6 days

source_name: Mtb ΔmetA _0.3

value: before methionine starvation

value: day 0


title: undifferentiated_rep1

value: differentiated Adipose Derived Stem Cells


title: undifferentiated_rep2


title: infection.1h2

description: L. major infected BMDM at 1h p.i., biological replicate 2

source_name: L. major infected BMDM at 1h p.i.

value: BALB/c


title: 6 day starvation vs. day 0 replicate 1

description:
[channel 1] Mtb ΔmetA methionine starved for 6 days replicate 1
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 1
Biological replicate 1 of 3.

source_name: Mtb ΔmetA _6.1

source_name: Mtb ΔmetA _0.1


title: undifferentiated_rep4


title: 6 day starvation vs. day 0 replicate 2

description:
[channel 1] Mtb ΔmetA day 0 before methionine starvation replicate 2
[channel 2] Mtb ΔmetA methionine starved for 6 days replicate 2
Biological replicate 2 of 3.

source_name: Mtb ΔmetA _0.2

source_name: Mtb ΔmetA _6.2


title: Late exponential vtlR, biological rep 2

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from late exponential phase 2308 cells containing vtlR mutation

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Brucella abortus

source_name: Brucella abortus late exponential phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to late exponential phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching stationary phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

tag: growth phase

value: Late exponential


title: undifferentiated_rep3


title: Late exponential vtlR, biological rep 1


title: 21day_rep4

source_name: 21 day differentiated Adipose Derived Stem Cells

value: 21 day


title: Placenta_GDM_No_Sample30

source_name: Placenta tissue from the maternal (decidual basalis) side near the umbilical cord


title: 2 day starvation vs. day 0 replicate 3

description:
[channel 1] Mtb ΔmetA methionine starved for 2 days
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 3
Biological replicate 3 of 3.

source_name: Mtb ΔmetA _2.3

value: 2 days


title: 4 day starvation vs. day 0 replicate 3

description:
[channel 1] Mtb ΔmetA methionine starved for 4 days replicate 3
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 3
Biological replicate 3 of 3.

source_name: Mtb ΔmetA _4.3

value: 4 days


title: 21day_rep1


title: 21day_rep3


title: Late exponential vtlR, biological rep 3


title: 21day_rep6


title: infection.1h1

description: L. major infected BMDM at 1h p.i., biological replicate 1

value: bone marrow-derived macrophages (BMDM)

value: Leishmania major


title: 4 day starvation vs. day 0 replicate 2

description:
[channel 1] Mtb ΔmetA methionine starved for 4 days replicate 2
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 2
Biological replicate 2 of 3.

source_name: Mtb ΔmetA _4.2


title: 21day_rep2

value: female

value: abdominal subcutaneous adipose


title: Placenta_GDM_Yes_Sample38

description: chart-reported case of gestational diabetes

value: placenta

value: Yes


title: Placenta_GDM_No_Sample26

value: No


title: 7day_rep4

source_name: 7 day differentiated Adipose Derived Stem Cells

value: 7 day


title: Placenta_GDM_Yes_Sample22


title: Placenta_GDM_Yes_Sample20


title: Late exponential 2308, biological rep 2

description: Gene expression data from late exponential phase wildtype 2308 cells

value: Wildtype


title: 4 day starvation vs. day 0 replicate 1

description:
[channel 1] Mtb ΔmetA day 0 before methionine starvation replicate 1
[channel 2] Mtb ΔmetA methionine starved for 4 days replicate 1
Biological replicate 1 of 3.

value: ΔmetA

value: before methionine starvation

value: day 0

source_name: Mtb ΔmetA _4.1

value: methionine starved


title: 2 day starvation vs. day 0 replicate 1

description:
[channel 1] Mtb ΔmetA methionine starved for 2 days
[channel 2] Mtb ΔmetA day 0 before methionine starvation replicate 1
Biological replicate 1 of 3.

source_name: Mtb ΔmetA _2.1


title: 2 day starvation vs. day 0 replicate 2

description:
[channel 1] Mtb ΔmetA day 0 before methionine starvation replicate 2
[channel 2] Mtb ΔmetA methionine starved for 2 days replicate 2
Biological replicate 2 of 3.

source_name: Mtb ΔmetA _2.2


title: 7day_rep3

value: differentiated Adipose Derived Stem Cells


title: Late exponential 2308, biological rep 1

value: Whole cell

value: Late exponential


title: Late exponential 2308, biological rep 3


title: 21day_rep5

value: 21 day


title: Placenta_GDM_No_Sample12

description: pregnancy without maternal complications


title: 7day_rep2


title: 7day_rep1


title: EB HP1bKO, biological replicate 1

status: Public on Aug 02 2015

city: Jerusalem

first: Eran

last: Meshorer

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description:
EB-HP1bKO-1
Gene expression data from 7-day EBs Cbx1 (HP1beta) KO.

hyb_protocol: According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with Autoloader according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

data_processing: Data processing was performed in Gene Expression Console using Robust Multichip Analysis (RMA) probe summarization algorithm. Data was further processed and statistics were generated using Excel. Non-expressing genes were filtered out on a pre-determined set point. Differential expression analysis was performed by carrying out a t-test for differences between the average signal values for each gene.

source_name: EB, Cbx1 (HP1beta) KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (based on Expression Analysis Technical Manual, Affymetrix).

growth_protocol: ESCs were cultured in 5% CO2 at 37°C on gelatin-coated dishes and mitomycin-C treated MEF feeder layer in standard ESC media. For EBs formation, ESCs were cultured in suspension in Petri dishes in standard ESC media without LIF.

extract_protocol: RNA was purified from ESCs and EBs using the RNeasy Mini Kit (Qiagen) supplemented with DNaseI.

treatment_protocol: No treatment.

tag: cell line

value: Cbx1-/- (HP1beta)

value: embryoid bodies (EBs)


title: LNCaP treated with DMSO

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). The Subio Platform and Subio Basic Plug-in (v1.15; Subio Inc., Aichi, Japan) was then used to further calculate the between-sample fold change.

source_name: LNCaP_4h with DMSO

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: Human cells were purchased from the indicated companies: PC-3, DU-145, SAS (RIKEN Bioresource Center), TIG-1 (Japanese Cancer Research Resources Bank), LNCaP (ATCC). TIG-1 and SAS were maintained in 5% CO2 at 35°C in DMEM supplemented with FBS (10%), penicillin (100 U/mL), and streptomycin (100 μg/mL). For PC-3, DU-145 and LNCaP cell culture, DMEM was replaced by RPMI-1640 medium.

extract_protocol: Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA)..

treatment_protocol: About 1.0x103 cells plated in a petri dish (diameter, 3.5 cm) were incubated at 35°C overnight, then with Withaferin A dissolved in DMSO were added into the medium.

value: LNCaP

value: low-grade prostate cancer cells

tag: treated with

value: DMSO for 4hr


title: DU145 treated with WA

source_name: DU145_8h with 4μM WA

value: high-grade prostate cancer cells

value: 2μM Withaferin A (WA) for 8hr


title: PC-3 treated with WA

source_name: PC-3_4h with 2μM WA

value: 2μM Withaferin A (WA) for 4hr


title: LNCaP treated with WA

source_name: LNCaP_4h with 4μM WA


title: EB HP1bKO, biological replicate 2

description:
EB-HP1bKO-2
Gene expression data from 7-day EBs Cbx1 (HP1beta) KO.


title: EB HP1aKO, biological replicate 1

description:
EB-HP1aKO-1
Gene expression data from 7-day EBs Cbx5 (HP1alpha) KO.

source_name: EB, Cbx5 (HP1alpha) KO

value: Cbx5-/- (HP1alpha)


title: EB WT, biological replicate 2

description:
EB-WT-2
Gene expression data from 7-day EBs WT.

source_name: EB, WT

value: WT


title: Donor 5 - 09FC49 - 100% confluence - mAdbID:107362

status: Public on Aug 01 2015

first: Jiaqiang

last: Ren

address: 9000 Rockville Pike

institute: National Institutes of Health

description: mAdb experiment ID: 107362

hyb_protocol: Sample Hybridization Protocol Other: The samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.62 Temperature: 31.76

data_processing:
miRNA Data Processing
Calculation Method: The signal intensities and logRatio were exported into BRRArray Tools, and median-normalized.

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV-infected lymphcytes

label_protocol:
Hy3 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY(TM) LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture's procedure.

extract_protocol:
Trizol RNA Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturer's instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)

source_name: Donor 5 - 09FC49

label_protocol:
Hy5 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY(TM) LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture's procedure.

treatment_protocol: In-vitro treatment: Bone marrow collection and BMSC culture were performed. Passage 2 BMSCs from 7 consenting donors were thawed from a working cell bank and plated at a density of 3 x 103/cm2 in T-75 flasks (Corning Life Sciences, Corning, NY), the cells were cultured to passage 3 with complete culture medium [alpha MEM with 2 mM glutamine (Lonza, Walkersville, MD, USA), supplemented with 20% lot-selected FBS (Hyclone, Thermo Fischer Scientific, Waltham, MA) and 10 ug/ml Gentamicin]. Upon reaching 80% confluence, passage 3 BMSCs were lifted by TryPLE Express (Invitrogen, Life Technologies, Grand Island, NY) and sub-cultured at the same density. When the cells reached 50%, 80% and 100% confluence as determined by microscope observation, they were harvested.

value: Bone Marrow

value: Bone Marrow Stromal Cell (BMSC)

tag: individual


title: TIG-1 treated with WA

source_name: TIG-1_24h with 2μM WA

value: normal human fibroblasts

value: 2μM Withaferin A (WA) for 24hr


title: PC-3 treated with DMSO

source_name: PC-3_4h with DMSO


title: TIG-1 treated with DMSO

source_name: TIG-1_24h with DMSO

value: DMSO for 24hr


title: Donor 5 - 09FC49 - 50% confluence - mAdbID:107360

description: mAdb experiment ID: 107360

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.57 Temperature: 31.67


title: EB HP1aKO, biological replicate 2

description:
EB-HP1aKO-2
Gene expression data from 7-day EBs Cbx5 (HP1alpha) KO.


title: Donor 5 - 09FC49 - 80% confluence - mAdbID:107361

description: mAdb experiment ID: 107361

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.61 Temperature: 31.7


title: ESC HP1bKO, biological replicate 1

description:
ESC-HP1bKO-1
Gene expression data from ESCs Cbx1 (HP1beta) KO.

source_name: ESC, Cbx1 (HP1beta) KO

value: embryonic stem cells (ESCs)


title: ESC HP1aKO, biological replicate 2

description:
ESC-HP1aKO-2
Gene expression data from ESCs Cbx5 (HP1alpha) KO.

source_name: ESC, Cbx5 (HP1alpha) KO


title: Donor 4 - 09FC45 - 100% confluence - mAdbID:107359

description: mAdb experiment ID: 107359

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.56 Temperature: 31.58

source_name: Donor 4 - 09FC45


title: DU145 treated with DMSO

source_name: DU145_8h with DMSO

value: DMSO for 8hr


title: Donor 4 - 09FC45 - 80% confluence - mAdbID:107358

description: mAdb experiment ID: 107358

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.53 Temperature: 31.55


title: ESC WT, biological replicate 2

description:
ESC-WT-2
Gene expression data from WT-control ESCs.

source_name: ESC, WT


title: EB WT, biological replicate 1

description:
EB-WT-1
Gene expression data from 7-day EBs WT.

value: embryoid bodies (EBs)


title: ESC WT, biological replicate 1

description:
ESC-WT-1
Gene expression data from WT-control ESCs.


title: Donor 3 - 09FC44 - 80% confluence - mAdbID:107355

description: mAdb experiment ID: 107355

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.55 Temperature: 31.18

source_name: Donor 3 - 09FC44


title: Donor 4 - 09FC45 - 50% confluence - mAdbID:107357

description: mAdb experiment ID: 107357

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.56 Temperature: 31.45


title: Donor 3 - 09FC44 - 100% confluence - mAdbID:107356

description: mAdb experiment ID: 107356

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.56 Temperature: 31.27


title: Donor 3 - 09FC44 - 50% confluence - mAdbID:107354

description: mAdb experiment ID: 107354

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.53 Temperature: 31.09


title: ESC HP1aKO, biological replicate 1

description:
ESC-HP1aKO-1
Gene expression data from ESCs Cbx5 (HP1alpha) KO.


title: Donor 2 - 09FC43 - 100% confluence - mAdbID:107353

description: mAdb experiment ID: 107353

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.5 Temperature: 30.97

source_name: Donor 2 - 09FC43


title: Donor 2 - 09FC43 - 80% confluence - mAdbID:107352

description: mAdb experiment ID: 107352

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.46 Temperature: 30.69


title: Donor 1 - 09FC37 - 100% confluence - mAdbID:107350

description: mAdb experiment ID: 107350

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.4 Temperature: 30.23

source_name: Donor 1 - 09FC37


title: Donor 2 - 09FC43 - 50% confluence - mAdbID:107351

description: mAdb experiment ID: 107351

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.41 Temperature: 30.45


title: Donor 1 - 09FC37 - 80% confluence - mAdbID:107349

description: mAdb experiment ID: 107349

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.38 Temperature: 30.11


title: Donor 1 - 09FC37 - 50% confluence - mAdbID:107348

description: mAdb experiment ID: 107348

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.19;; 4.31 Temperature: 29.99


title: ESC HP1bKO, biological replicate 2

description:
ESC-HP1bKO-2
Gene expression data from ESCs Cbx1 (HP1beta) KO.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with Autoloader according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

value: Cbx1-/- (HP1beta)


title: Gastrointestinal stromal tumor 46

city: Stockholm

first: Pinar

last: Akcakaya

address: CCK R8:04

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470A) for 18-20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 9.5.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 20% missing values across the samples were included in the further analysis.

source_name: Non-treated GIST tissue

label_protocol: 100 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.Labeled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221)

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manufacturer.

value: Gastrointestinal stromal tumor

tag: treatment

value: Non-treated


title: iodine-biofortified lettuce 3

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate 3 of 3. Cells treated with the extract of iodine-biofortified lettuce

hyb_protocol: According to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified lettuce, Replicate 3

growth_protocol: Cells were cultured in an incubator, under controlled conditions (temperature, 37°C; air, 95%; CO2, 5%), in Eagle's Minimum Essential Medium (Sigma), with fetal bovine serum (FBS) (Gibco) to a final concentration of 20%, according to ATCC procedure.

extract_protocol: Lettuce and carrot were cultivated and fertilizated with KI as described by Kopeć et al. (2015). The iodine concentration was 0.50 mg/100 g dry mass (d.m.) for biofortified lettuce and 0.12 mg/100 g d.m. for control lettuce (Kopeć et al. 2015). 10 g of fresh lettuce was crushed using a homogenizer (CAT type X 120, USA) and next transferred to the Erlenmaier flask with hot water. Lettuce materials were extracted by shaking (Elpan, water bath shaker type 357, Poland) at 100°C for 2 hours, and next the solution was centrifuged (Centrifuge type MPW-340, Poland). Then, a part of the extracts was used for iodine measurement and other parts were stored at -80 °C for cell culture studies.

treatment_protocol: Cells were seeded in 6-well culture plates for 24 h. After that, growing medium was replaced by medium containing the extract from iodine-biofortified lettuce/carrot and the extract from non-fortified lettuce/carrot. In all studies, at least 4 wells were examined per treatment. Experiments were repeated 3 times.

value: Caco-2 (HTB-37, ATCC)

value: Colon

tag: cell type

value: epithelial

tag: gender/age

value: Male/72 years adult

source_name: Colorectal adenocarcinoma


title: oral cancer cell_parental_control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: These are parental cell.

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

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: parental cell

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM;SIGMA,St. Louis, MO, USA) supplemented with 10% fetal calf serum, 100 μg/ml streptomycin, and 100U/ml penicillin in a humidified atmosphere of 95% air and 5% CO2 at 37℃.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

tag: cell

value: tougue cancer cell


title: non-fortified carrots 1

description: Biological replicate 1 of 3. Cells treated with the extract of non-fortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified carrots, Replicate 1

label_protocol: According to the manufacturer's protocol


title: non-ortified carrots 2

description: Biological replicate 2 of 3. Cells treated with the extract of non-fortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified carrots, Replicate 2


title: non-fortified lettuce 2

description: Biological replicate 2 of 3. Cells treated with the extract of non-fortified lettuce

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified lettuce, Replicate 2


title: non-fortified lettuce 3

description: Biological replicate 3 of 3. Cells treated with the extract of non-fortified lettuce

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified lettuce, Replicate 3


title: iodine-biofortified carrots 3

description: Biological replicate 3 of 3. Cells treated with the extract of iodine-biofortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified carrots, Replicate 3


title: oralcancer cell_parental_treated by SDF-1

description: These cells were parental cells treated by SDF-1.

source_name: parental cell treated by SDF-1

treatment_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM;SIGMA,St. Louis, MO, USA) supplemented with 10% fetal calf serum, 100 μg/ml streptomycin, and 100U/ml penicillin in a humidified atmosphere of 95% air and 5% CO2 at 37℃.


title: iodine-biofortified lettuce 1

description: Biological replicate 1 of 3. Cells treated with the extract of iodine-biofortified lettuce

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified lettuce, Replicate 1


title: negative control 1

description: Biological replicate 1 of 3. Control  cells, untreated.

source_name: Caco-2  colorectal adenocarcinoma cells, negative control, Replicate 1


title: Gastrointestinal stromal tumor 44

description: miRNA expression profile


title: Gastrointestinal stromal tumor 45

description: miRNA expression profile


title: iodine-biofortified carrots 1

description: Biological replicate 1 of 3. Cells treated with the extract of iodine-biofortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified carrots, Replicate 1


title: negative control 3

description: Biological replicate 3 of 3. Control  cells, untreated.

source_name: Caco-2  colorectal adenocarcinoma cells, negative control, Replicate 3


title: non-fortified carrots 3

description: Biological replicate 3 of 3. Cells treated with the extract of non-fortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified carrots, Replicate 3


title: iodine-biofortified carrots 2

description: Biological replicate 2 of 3. Cells treated with the extract of iodine-biofortified carrots

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified carrots, Replicate 2


title: KD

city: Kurume

first: Takafumi

last: Yoshida

state: Fukuoka

address: 67, asahi-machi

department: Department of Medicine

institute: Kurume University

description: Gene expression upon treatment with control siRNA

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray SurePrint G3 Human GE Microarray Kit 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: MThe scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Huh7 cells, THADA knockdown

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: The cells were cultured at 37°C in 5% CO2 in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum, penicillin (100 U/l) and streptomycin (100 ug/ml) in the presence of puromycin (500 ng/ml)

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: THADA knockdown


title: negative control 2

description: Biological replicate 2 of 3. Control  cells, untreated.

source_name: Caco-2  colorectal adenocarcinoma cells, negative control, Replicate 2


title: iodine-biofortified lettuce 2

description: Biological replicate 2 of 3. Cells treated with the extract of iodine-biofortified lettuce

source_name: Caco-2  colorectal adenocarcinoma cells, iodine-biofortified lettuce, Replicate 2


title: control

source_name: Huh7 cells, control

value: control


title: Gastrointestinal stromal tumor 42

description: miRNA expression profile

source_name: Non-treated GIST tissue


title: non-fortified lettuce 1

description: Biological replicate 1 of 3. Cells treated with the extract of non-fortified lettuce

source_name: Caco-2  colorectal adenocarcinoma cells, non-fortified lettuce, Replicate 1

source_name: Colorectal adenocarcinoma


title: Gastrointestinal stromal tumor 40

description: miRNA expression profile


title: Gastrointestinal stromal tumor 43

description: miRNA expression profile


title: Gastrointestinal stromal tumor 36

description: miRNA expression profile


title: Gastrointestinal stromal tumor 35

description: miRNA expression profile


title: Gastrointestinal stromal tumor 30

description: miRNA expression profile


title: Gastrointestinal stromal tumor 38

description: miRNA expression profile


title: Gastrointestinal stromal tumor 34

description: miRNA expression profile


title: Gastrointestinal stromal tumor 26

description: miRNA expression profile


title: Gastrointestinal stromal tumor 32

description: miRNA expression profile


title: Gastrointestinal stromal tumor 39

description: miRNA expression profile


title: Gastrointestinal stromal tumor 25b

description: miRNA expression profile


title: GM12878

city: Chicago

first: Erika

last: Moen

state: IL

department: Medicine

institute: University of Chicago

description: lymphoblasoid cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 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

source_name: genomic DNA from cervical smear 1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LCL samples using phenol/choloroform

value: Female

tag: sample type

value: lymphoblasoid cell line

tag: agent

value: DMSO


title: Gastrointestinal stromal tumor 24

description: miRNA expression profile

tag: tissue


title: GM12815 JQ1

description: lymphoblasoid cell line

source_name: genomic DNA from cervical smear 2

value: 250 nM JQ1


title: Gastrointestinal stromal tumor 6b

description: miRNA expression profile


title: GM12878 JQ1

description: lymphoblasoid cell line


title: GM12815

description: lymphoblasoid cell line


title: GM07055 JQ1

description: lymphoblasoid cell line


title: Gastrointestinal stromal tumor (reanalysis) 20

description: miRNA expression profile

source_name: Imatinib-treated GIST tissue

value: Imatinib-treated


title: Gastrointestinal stromal tumor (reanalysis) 19

description: miRNA expression profile


title: Gastrointestinal stromal tumor (reanalysis) 17

description: miRNA expression profile


title: Gastrointestinal stromal tumor (reanalysis) 18

description: miRNA expression profile


title: Gastrointestinal stromal tumor (reanalysis) 16

description: miRNA expression profile


title: GM07055

description: lymphoblasoid cell line


title: Gastrointestinal stromal tumor (reanalysis) 15

description: miRNA expression profile


title: KO_Chow_SkM_trial3

city: Honolulu

first: April

middle: L

last: Darrow

state: HI

address: 651 Ilalo St.

institute: University of Hawaii

description: Gene expression in the skeletal muscle endothelium of galectin-3 knockout mice after 8wks of chow diet

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent),

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk chow diet, trial#3

label_protocol: Amino-allyl modified cRNA was labeled with Cy3 CyDye Post-Labeling Reactive Dye Pack (GE Healthcare, Waukesha, WI) according to the manufacturer’s instructions. Following purification, 1.6 µg of Cy3 dye-labeled cRNA, as measured by NanoDrop 2000c spectrophotometer (Thermo Scientific, Bellerica, MA), were combined and fragmented

extract_protocol: RNA was extracted and purified with RNeasy columns (Qiagen, Valencia, CA) and then amplified using an Ambion® Amino Allyl MessageAmp kit (Life Technologies, Carlsbad, CA) according to the manufacturer’s protocol to produce approximately 100µg of amino-allyl modified cRNA.

treatment_protocol: After 8 weeks on the diet regimen, the aorta (from the arch to the iliac bifurcation) and skeletal muscle (a collective grouping of plantaris, gastrocnemius, and biceps femoris)  tissues from high-fat-fed and chow-fed galectin-3 (-/-) and wild-type mice were excised and collagenolytically digested. Following red blood cell lysis, aorta and muscle cell suspensions were incubated with anti-mouse CD16/32 then with phycoerythrin-conjugated anti-mouse CD45 and anti-mouse CD105 eFluor®450. Approximately 10,000 live CD105+/CD45- cells were sorted on a FACSAria directly into TriZol.

value: Skeletal muscle endothelium

tag: genotype/strain

tag: diet

value: Chow diet


title: Gastrointestinal stromal tumor (reanalysis) 14

description: miRNA expression profile


title: Gastrointestinal stromal tumor (reanalysis) 13

description: miRNA expression profile


title: Gastrointestinal stromal tumor (reanalysis) 12

description: miRNA expression profile


title: WT_Chow_SkM_trial3

description: Gene expression in the skeletal muscle endothelium of wild-type C57BL/6 mice after 8wks of chow diet

source_name: Wild-type skeletal muscle endothelium, 8wk chow diet, trial#3

value: C57BL/6 (wild type)


title: Gastrointestinal stromal tumor (reanalysis) 11

description: miRNA expression profile

value: Gastrointestinal stromal tumor


title: Gastrointestinal stromal tumor (reanalysis) 9-4

description: miRNA expression profile


title: KO_HFD_SkM_trial3

description: Gene expression in the skeletal muscle endothelium of galectin-3 knockout mice after 8wks of high-fat diet

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk high-fat diet, trial#3

value: High-fat diet


title: WT_Chow_SkM_trial2

source_name: Wild-type skeletal muscle endothelium, 8wk chow diet, trial#2


title: KO_HFD_SkM_trial2

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk high-fat diet, trial#2


title: KO_Chow_SkM_trial2

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk chow diet, trial#2


title: WT_HFD_SkM_trial2

description: Gene expression in the skeletal muscle endothelium of wild-type C57BL/6 mice after 8wks of high-fat diet

source_name: Wild-type skeletal muscle endothelium, 8wk high-fat diet, trial#2


title: TCam-2-2w-1

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

description: biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A subset quantile normalization approach developed by N. Touleimat & J. Tost was applied (Touleimat, Tost, 2012, Pubmed ID: 22690668 ). This processing pipeline includes signal correction for the adjustment of the color balance and background level correction as well as the Infinium I/Infinium II shift correction between sample normalization. Technical quality parameters such as hybridization, extension, bisulfite conversion and specificity were evaluated using the ‚Genome Studio’ software. Beta-value signal distributions were inspected by density plots. Data was analysed using ‚Bioconductor R’ (http://www.bioconductor.org). To increase performance in terms of detection and true positive rate of highly methylated and unmethylated CpG-sites, beta-values were transformed to M-values (Du et al., 2010, Pubmed ID: 21118553)

source_name: Seminoma-like cell line

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

growth_protocol:
cultivation protocol: TCam-2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
xenografting protocol: 1x10^7 TCam-2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)

extract_protocol:
Genomic DNA was isolated by phenol / chloroform / isoamylalcohol isolation as published (Nettersheim et al., 2013, Pubmed ID: 24386123). Quality control was performed with Agilent Bioanalyser.
bisulfite convesion: Genomic DNA was bisulfite converted using the EZ DNA methylation kit according to the manual (Zymo Research) and as published (Nettersheim et al., 2013, Pubmed ID: 24386123)

tag: strain

value: CD1 nude mice

tag: age

value: 6 weeks at start of xenografting

value: Seminoma-like


title: Gastrointestinal stromal tumor (reanalysis) 7

description: miRNA expression profile


title: WT_HFD_SkM_trial3

source_name: Wild-type skeletal muscle endothelium, 8wk high-fat diet, trial#3


title: Gastrointestinal stromal tumor (reanalysis) 5

description: miRNA expression profile


title: KO_Chow_SkM_trial1

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk chow diet, trial#1


title: KO_HFD_SkM_trial1

source_name: Galectin-3(-/-) skeletal muscle endothelium, 8 wk high-fat diet, trial#1


title: 2102EP-8w

source_name: Embryonal carcinoma-like cell line

value: Embryonal carcinoma-like


title: Gastrointestinal stromal tumor (reanalysis) 4

description: miRNA expression profile


title: GM12892

description: lymphoblasoid cell line

tag: gender


title: 2102EP-4w


title: TCam-2-4w-1

description: biological replicate 1


title: TCam-2-1w-2

description: biological replicate 2


title: Gastrointestinal stromal tumor (reanalysis) 1

description: miRNA expression profile


title: TCam-2-2w-2

description: biological replicate 2


title: TCam-2-6w-2

description: biological replicate 2


title: WT_HFD_SkM_trial1

source_name: Wild-type skeletal muscle endothelium, 8wk high-fat diet, trial#1


title: KO_Chow_Aorta_trial3

description: Gene expression in the aortic endothelium of galectin-3 knockout mice after 8wks of chow diet

source_name: Galectin-3(-/-) aortic endothelium, 8 wk chow diet, trial#3

value: Aortic endothelium


title: Gastrointestinal stromal tumor (reanalysis) 2

description: miRNA expression profile


title: TCam-2-4w-2

description: biological replicate 2


title: WT_Chow_SkM_trial1

source_name: Wild-type skeletal muscle endothelium, 8wk chow diet, trial#1


title: TCam-2-6w-1

description: biological replicate 1


title: TCam-2 in vitro


title: 2102EP in vitro


title: TCam-2-1w-1

description: biological replicate 1


title: WT_HFD_Aorta_trial2

description: Gene expression in the aortic endothelium of wild-type C57BL/6 mice after 8wks of high-fat diet

source_name: Wild-type aortic endothelium, 8wk high-fat diet, trial#2


title: KO_HFD_Aorta_trial1

description: Gene expression in the aortic endothelium of galectin-3 knockout mice after 8wks of high-fat diet

source_name: Galectin-3(-/-) aortic endothelium, 8 wk high-fat diet, trial#1


title: Muscle_CH_260_rep1_0423

city: Saint-Genès-Champanelle

first: Isabelle

last: Cassar-Malek

institute: Inra

description: Biological replicate 1 of 3

hyb_protocol: After purification (RNeasy Mini Kit, Qiagen), 1650 ng of labeled cRNA were hybridized onto G2519F Bovine GE 4x44K v2 microarray (Agilent) with hybridization buffer (Gene Expression Hybridization Kit, Agilent) according to the manufacturer’s instructions. After 17h of hybridization, slides were washed with the Gene Expression Wash Pack (Agilent).

scan_protocol: Microarrays were scanned with Agilent G2505 scanner.

data_processing: Data were extracted and normalized with Feature Extraction 10.7 software (Agilent) using background and multiplicative detrend (no background subtraction). The mean intensity between the technical replicates was then calculated for each probe.

organism: Bos taurus

source_name: Longissimus thoracis muscle, CH, 260 dpc

label_protocol: 50 ng of total RNA extracted were amplified and fluorescently labelled to produce Cy3 cRNA using the Low Input Quick Amp Labeling one color Kit (Agilent).

extract_protocol: Total RNA extracted using Purelink RNA Mini Kit (Invitrogen) followed by a Dnase treatment (Qiagen).

value: Longissimus thoracis muscle

tag: breed

value: Charolais

tag: developmental stage

value: fetus

tag: gestational stage

tag: animal number

tag: mother number

tag: father name

value: Indiana

value: male


title: WT_Chow_Aorta_trial2

description: Gene expression in the aortic endothelium of wild-type C57BL/6 mice after 8wks of chow diet

source_name: Wild-type aortic endothelium, 8wk chow diet, trial#2


title: Muscle_CH_260_rep2_0424

description: Biological replicate 2 of 3

value: Jourdan


title: WT_HFD_Aorta_trial3

source_name: Wild-type aortic endothelium, 8wk high-fat diet, trial#3


title: WT_Chow_Aorta_trial3

source_name: Wild-type aortic endothelium, 8wk chow diet, trial#3


title: KO_HFD_Aorta_trial2

source_name: Galectin-3(-/-) aortic endothelium, 8 wk high-fat diet, trial#2


title: KO_Chow_Aorta_trial1

source_name: Galectin-3(-/-) aortic endothelium, 8 wk chow diet, trial#1


title: GM12892 JQ1

description: lymphoblasoid cell line

source_name: genomic DNA from cervical smear 2

value: Female

tag: cell line

value: lymphoblasoid cell line

value: 250 nM JQ1


title: WT_HFD_Aorta_trial1

source_name: Wild-type aortic endothelium, 8wk high-fat diet, trial#1

value: C57BL/6 (wild type)


title: Muscle_CH_210_rep1_0416

description: Biological replicate 1 of 3

source_name: Longissimus thoracis muscle, CH, 210 dpc

value: female


title: KO_HFD_Aorta_trial3

source_name: Galectin-3(-/-) aortic endothelium, 8 wk high-fat diet, trial#3

value: High-fat diet


title: Muscle_CH_180_rep1_0408

description: Biological replicate 1 of 3

source_name: Longissimus thoracis muscle, CH, 180 dpc


title: Muscle_CH_260_rep3_0425

description: Biological replicate 3 of 3


title: Muscle_CH_110_rep2_0414

description: Biological replicate 2 of 2

source_name: Longissimus thoracis muscle, CH, 110 dpc


title: Muscle_CH_210_rep3_0418

description: Biological replicate 3 of 3


title: Muscle_CH_180_rep3_0410

description: Biological replicate 3 of 3


title: Muscle_BA_210_rep2_0707

description: Biological replicate 2 of 3

source_name: Longissimus thoracis muscle, BA, 210 dpc

value: Blonde Aquitaine

value: Fallou


title: HuEx_9_ES-4

city: Bethesda

first: Eric

middle: C

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on Affymetrix GeneChip scanner 3000 7G.

data_processing: Probe set summarization and normalization with the core annotated probes was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R package aroma.affymetrix.

source_name: human cell line

label_protocol: Total RNA (100 ng) was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

extract_protocol: Cells were grown in flasks to approximately 70% confluency, detached with trypsin, and then total RNA extracted using Qiagen miRNeasy mini-kit according to manufacturers instructions. Quality of RNA was assessed using an Agilent 2100 Bioanalyzer and all samples were of good quality with RIN# > 8.

tag: type

value: Ewing Sarcoma


title: Muscle_CH_180_rep2_0409

description: Biological replicate 2 of 3


title: HuEx_72_Hs 132.T

value: Spindle Cell Sarcoma


title: Muscle_CH_110_rep1_0413

description: Biological replicate 1 of 2


title: KO_Chow_Aorta_trial2

source_name: Galectin-3(-/-) aortic endothelium, 8 wk chow diet, trial#2

value: Aortic endothelium

value: Chow diet


title: Gastrointestinal stromal tumor (reanalysis) 3

description: miRNA expression profile

source_name: Imatinib-treated GIST tissue

value: Gastrointestinal stromal tumor

tag: treatment

value: Imatinib-treated


title: HuEx_75_Hs 414.T

value: Fibrosarcoma


title: Muscle_BA_260_rep1_0711

description: Biological replicate 1 of 2

source_name: Longissimus thoracis muscle, BA, 260 dpc

value: Longissimus thoracis muscle

value: fetus

value: Oulou


title: HuEx_8_ES-3


title: Muscle_BA_260_rep2_0717

description: Biological replicate 2 of 2


title: Muscle_BA_210_rep1_0706

description: Biological replicate 1 of 3


title: HuEx_71_Hs 729

value: Rhabdosarcoma


title: Muscle_BA_210_rep3_0708

description: Biological replicate 3 of 3

value: male


title: HuEx_7_ES-1


title: HuEx_74_Hs 819.T

value: Chonodrosarcoma


title: HuEx_73_Hs 93.T


title: HuEx_70_Hs 706.T

value: Giant Cell Sarcoma


title: HuEx_69_Rh28 PX11/LPAM


title: HuEx_68_KHOS-312H

value: Osteosarcoma


title: WT_Chow_Aorta_trial1

source_name: Wild-type aortic endothelium, 8wk chow diet, trial#1

value: C57BL/6 (wild type)


title: Muscle_BA_110_rep3_0715

description: Biological replicate 3 of 3

source_name: Longissimus thoracis muscle, BA, 110 dpc

value: Blonde Aquitaine

value: Fallou


title: Muscle_BA_110_rep1_0607

description: Biological replicate 1 of 3


title: Muscle_BA_180_rep1_0608

description: Biological replicate 1 of 2

source_name: Longissimus thoracis muscle, BA, 180 dpc

value: female


title: Muscle_BA_180_rep2_0713

description: Biological replicate 2 of 2


title: Muscle_BA_110_rep2_0714

description: Biological replicate 2 of 3


title: HuEx_66_ES-6

value: Ewing Sarcoma


title: HuEx_65_ES-2


title: HuEx_60_JJ012

value: Chondrosarcoma


title: HuEx_67_KHOS-240S


title: 2102EP-8w

description: Embryonal carcinoma-like cell line

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

source_name: 2102EP in vivo 8w

extract_protocol:
RNA was extracted with Trizol reagent (Sigma-Aldrich) as already published (Nettersheim et al., 2012, Pubmed ID: 22489004), followed by clean-up  treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
TCam-2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
TCam-2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)

value: CD1 nude

value: 6 weeks at start of xenografting


title: HuEx_63_CHLA-258


title: HuEx_62_CHLA-25


title: HuEx_6_COG-E-352


title: HuEx_52_MHM-25

value: Sarcoma


title: Muscle_CH_210_rep2_0417

description: Biological replicate 2 of 3

value: Longissimus thoracis muscle

value: Charolais

value: Indiana


title: HuEx_58_NHOst

source_name: normal human cell

value: Normal human osteoblast


title: TCam-2-6w-1

description:
biological replicate 1
Seminoma-like cell line

source_name: TCam-2 in vivo 6w 1


title: HuEx_59_SkMC

value: Normal human skeletal muscle


title: HuEx_64_CHLA-32


title: 2102EP-4w

description: Embryonal carcinoma-like cell line

source_name: 2102EP in vivo 4w


title: HuEx_57_NHDF

value: Normal human dermal fibroblast


title: HuEx_54_VA-ES-BJ

value: Epitheloid


title: HuEx_55_hMSC

value: Normal human mesenchymal stem cell


title: TCam-2-6w-2

description:
biological replicate 2
Seminoma-like cell line

source_name: TCam-2 in vivo 6w 2


title: HuEx_53_SK-ES-1


title: HuEx_51_KHOS NP

value: Osteosarcoma


title: HuEx_61_CHA-59


title: TCam-2-4w-1

source_name: TCam-2 in vivo 4w 1


title: HuEx_49_A-204

value: Rhabdosarcoma


title: TCam-2-4w-2

source_name: TCam-2 in vivo 4w 2


title: TCam-2-2w-2

source_name: TCam-2 in vivo 2w 2


title: HuEx_48_LS141

value: Dedifferentiated liposarcoma


title: TCam-2-1w-1

source_name: TCam-2 in vivo 1w 1


title: TCam-2-2w-1

source_name: TCam-2 in vivo 2w 1


title: HuEx_5_CHLA-9

source_name: human cell line


title: HuEx_50_ES-4


title: HuEx_46_SYO-1

value: Synovial Sarcoma


title: TCam-2-1w-2

source_name: TCam-2 in vivo 1w 2


title: HuEx_45_SK-UT-1B

value: Leiomyosarcoma


title: TCam-2 in vitro

description: Seminoma-like cell line

source_name: TCam-2 in vitro


title: HuEx_47_DDLS


title: HuEx_56_NHAC-kn

value: Normal human chondrocyte


title: HuEx_32_SW 684

value: Fibrosarcoma


title: HuEx_42_ST8814

value: Malignant peripheral nerve sheath


title: HuEx_40_CHP-100

value: Ewing Sarcoma


title: HuEx_43_Rh28


title: HuEx_44_HSSY-II


title: HuEx_4_CHLA-10


title: HuEx_28_SJCRH30(RMS 13)


title: HuEx_3_ASPS-1

value: Alveolar Soft Part (Vistica)


title: HuEx_22_RD


title: HuEx_34_TC-32


title: HuEx_33_SW 982


title: HuEx_31_SW 1353

value: Chondrosarcoma


title: HuEx_37_Rh18


title: HuEx_39_SK-UT-1


title: HuEx_36_U-2 OS


title: HuEx_41_MPNST


title: HuEx_25_Rh36


title: HuEx_26_Rh41


title: HuEx_29_SJSA-1