title: Patient Male M180 Post-vaccine

description: Sample name: M180B


title: BX_M3_P28131

status: Public on Jul 20 2016

type: RNA

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

country: USA

institute: Mount Sinai School of Medicine

description: 3month kidney biopsy post transplant

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console and Batch effects from different labeling protocols were adjusted using the ComBat R package (Johnson WE)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 3 month kidney biopsy post transplant

label_protocol:
pico
ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation PICO amplification kit (NuGen, San Carlos, CA) was applied.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from percutaneous allograft biopsy samples obtained at 3 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: not applicable

tag: m12 cadi

tag: tissue type

value: percutaneous allograft biopsy


title: BX_M3_P27306

description: 3month kidney biopsy post transplant

label_protocol:
encor
ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation PICO amplification kit (NuGen, San Carlos, CA) was applied.

tag: m3 cadi


title: Patient Female M182 Pre-vaccine

city: Edinburgh

first: Paul

last: Dickinson

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

country: United Kingdom

institute: University of Edinburgh

description: Sample name: M182A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor.  Array probe features that had a present count in one or more samples were retained.

source_name: peripheral blood

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

extract_protocol: RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: peripheral blood

tag: Sex

value: Female

tag: age

value: 9 months

tag: vaccine group

value: Measles vaccine + DTP vaccine

tag: vaccine challenge

value: Pre-vaccine


title: BX_M3_P26747

description: 3month kidney biopsy post transplant


title: Patient Male M181 Pre-vaccine

description: Sample name: M181A

value: Male

value: Measles vaccine


title: Patient Female M174 Post-vaccine

description: Sample name: M174B

value: 10 months

value: Post-vaccine


title: Patient Male M183 Pre-vaccine

description: Sample name: M183A


title: Patient Female M176 Pre-vaccine

description: Sample name: M176A

value: DTP vaccine


title: BX_M3_P25395

description: 3month kidney biopsy post transplant


title: BX_M3_P26608

description: 3month kidney biopsy post transplant


title: Patient Female M176 Post-vaccine

description: Sample name: M176B


title: Patient Female M174 Pre-vaccine

description: Sample name: M174A


title: BX_M3_P26166

description: 3month kidney biopsy post transplant


title: BX_M3_P24557

description: 3month kidney biopsy post transplant


title: Patient Male M173 Pre-vaccine

description: Sample name: M173A


title: BX_M3_P24467

description: 3month kidney biopsy post transplant


title: Patient Female M172 Pre-vaccine

description: Sample name: M172A


title: Patient Male M168 Post-vaccine

description: Sample name: M168B


title: Patient Male M168 Pre-vaccine

description: Sample name: M168A


title: Patient Male M169 Pre-vaccine

description: Sample name: M169A


title: Patient Female M172 Post-vaccine

description: Sample name: M172B


title: Patient Male M173 Post-vaccine

description: Sample name: M173B


title: BX_M3_P24369

description: 3month kidney biopsy post transplant


title: BX_M3_P22255

description: 3month kidney biopsy post transplant


title: Patient Male M163 Pre-vaccine

description: Sample name: M163A


title: Patient Male M163 Post-vaccine

description: Sample name: M163B


title: Patient Female M167 Pre-vaccine

description: Sample name: M167A


title: Patient Female M167 Post-vaccine

description: Sample name: M167B


title: BX_M3_P21359

description: 3month kidney biopsy post transplant


title: BX_M3_P21504

description: 3month kidney biopsy post transplant


title: BX_M3_P21037

description: 3month kidney biopsy post transplant


title: Patient Female M161 Post-vaccine

description: Sample name: M161B


title: BX_M3_P20212

description: 3month kidney biopsy post transplant


title: Patient Female M162 Post-vaccine

description: Sample name: M162B


title: BX_M3_P20325

description: 3month kidney biopsy post transplant


title: Patient Male M158 Pre-vaccine

description: Sample name: M158A


title: Patient Male M156 Pre-vaccine

description: Sample name: M156A


title: Patient Male M156 Post-vaccine

description: Sample name: M156B


title: Patient Male M157 Post-vaccine

description: Sample name: M157B


title: Patient Female M159 Post-vaccine

description: Sample name: M159B


title: Patient Female M162 Pre-vaccine

description: Sample name: M162A


title: Patient Male M157 Pre-vaccine

description: Sample name: M157A


title: BX_M3_P19769

description: 3month kidney biopsy post transplant


title: Patient Female M151 Pre-vaccine

description: Sample name: M151A


title: BX_M3_P20066

description: 3month kidney biopsy post transplant


title: BX_M3_P19338

description: 3month kidney biopsy post transplant


title: Patient Female M147 Post-vaccine

description: Sample name: M147B


title: Patient Female M147 Pre-vaccine

description: Sample name: M147A


title: Patient Male M143 Post-vaccine

description: Sample name: M143B


title: Patient Male M143 Pre-vaccine

description: Sample name: M143A


title: Patient Female M159 Pre-vaccine

description: Sample name: M159A


title: Patient Female M161 Pre-vaccine

description: Sample name: M161A


title: Patient Male M158 Post-vaccine

description: Sample name: M158B


title: Patient Female M151 Post-vaccine

description: Sample name: M151B


title: BX_M3_P18463

description: 3month kidney biopsy post transplant


title: BX_M3_P19210

description: 3month kidney biopsy post transplant


title: Patient Male M140 Post-vaccine

description: Sample name: M140B


title: BX_M3_P18399

description: 3month kidney biopsy post transplant


title: Patient Male M139 Post-vaccine

description: Sample name: M139B


title: Patient Female M136 Post-vaccine

description: Sample name: M136B


title: Patient Male M140 Pre-vaccine

description: Sample name: M140A


title: Patient Male M138 Post-vaccine

description: Sample name: M138B


title: Patient Male M139 Pre-vaccine

description: Sample name: M139A


title: BX_M3_P18673

description: 3month kidney biopsy post transplant


title: BX_M3_P17767

description: 3month kidney biopsy post transplant


title: BX_M3_P16756

description: 3month kidney biopsy post transplant


title: BX_M3_P16865

description: 3month kidney biopsy post transplant


title: Patient Female M136 Pre-vaccine

description: Sample name: M136A


title: BX_M3_P15531

description: 3month kidney biopsy post transplant


title: Patient Male M138 Pre-vaccine

description: Sample name: M138A


title: BX_M3_P16220

description: 3month kidney biopsy post transplant


title: Patient Female M123 Pre-vaccine

description: Sample name: M123A


title: Patient Female M126 Pre-vaccine

description: Sample name: M126A


title: Patient Male M130 Post-vaccine

description: Sample name: M130B


title: Patient Male M120 Pre-vaccine

description: Sample name: M120A


title: Patient Female M134 Post-vaccine

description: Sample name: M134B


title: BX_M3_P15761

description: 3month kidney biopsy post transplant


title: Patient Female M134 Pre-vaccine

description: Sample name: M134A


title: Patient Male M130 Pre-vaccine

description: Sample name: M130A


title: BX_M3_P16573

description: 3month kidney biopsy post transplant


title: Patient Male M120 Post-vaccine

description: Sample name: M120B


title: Patient Female M123 Post-vaccine

description: Sample name: M123B


title: Patient Female M126 Post-vaccine

description: Sample name: M126B


title: BX_M3_P14307

description: 3month kidney biopsy post transplant


title: Patient Female M115 Post-vaccine

description: Sample name: M115B


title: BX_M3_P14190

description: 3month kidney biopsy post transplant


title: BX_M3_P14212

description: 3month kidney biopsy post transplant


title: BX_M3_P14912

description: 3month kidney biopsy post transplant


title: Patient Male M116 Post-vaccine

description: Sample name: M116B


title: Patient Male M112 Pre-vaccine

description: Sample name: M112A


title: BX_M3_P14221

description: 3month kidney biopsy post transplant


title: BX_M3_P14029

description: 3month kidney biopsy post transplant


title: BX_M3_P15197

description: 3month kidney biopsy post transplant


title: Patient Male M114 Pre-vaccine

description: Sample name: M114A


title: Patient Male M111 Pre-vaccine

description: Sample name: M111A


title: Patient Male M111 Post-vaccine

description: Sample name: M111B


title: BX_M3_P15063

description: 3month kidney biopsy post transplant


title: BX_M3_P12886

description: 3month kidney biopsy post transplant


title: Patient Female M119 Post-vaccine

description: Sample name: M119B


title: Patient Female M119 Pre-vaccine

description: Sample name: M119A


title: Patient Male M104 Pre-vaccine

description: Sample name: M104A


title: Patient Female M115 Pre-vaccine

description: Sample name: M115A


title: Patient Male M101 Post-vaccine

description: Sample name: M101B


title: Patient Male M101 Pre-vaccine

description: Sample name: M101A


title: Patient Female M099 Pre-vaccine

description: Sample name: M099A


title: Patient Male M116 Pre-vaccine

description: Sample name: M116A


title: Patient Male M104 Post-vaccine

description: Sample name: M104B


title: Patient Female M099 Post-vaccine

description: Sample name: M099B


title: Patient Male M112 Post-vaccine

description: Sample name: M112B


title: Patient Female M095 Pre-vaccine

description: Sample name: M095A


title: Patient Female M095 Post-vaccine

description: Sample name: M095B


title: Patient Male M114 Post-vaccine

description: Sample name: M114B


title: BX_M3_P12666

description: 3month kidney biopsy post transplant


title: BX_M3_P12773

description: 3month kidney biopsy post transplant


title: BX_M3_P12758

description: 3month kidney biopsy post transplant


title: Patient Male M094 Pre-vaccine

description: Sample name: M094A


title: Patient Male M093 Pre-vaccine

description: Sample name: M093A


title: Patient Male M090 Post-vaccine

description: Sample name: M090B


title: BX_M3_P12598

description: 3month kidney biopsy post transplant


title: Patient Female M091 Post-vaccine

description: Sample name: M091B


title: BX_M3_P9246

description: 3month kidney biopsy post transplant


title: BX_M3_P7879

description: 3month kidney biopsy post transplant


title: BX_M3_P7720

description: 3month kidney biopsy post transplant


title: Patient Female M089 Post-vaccine

description: Sample name: M089B


title: Patient Male M094 Post-vaccine

description: Sample name: M094B


title: BX_M3_P7764

description: 3month kidney biopsy post transplant


title: BX_M3_P12351

description: 3month kidney biopsy post transplant


title: 2 month old lateral ventricle choroid plexus, biological replicate 1

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

description: Gene expression data from whole choroid plexus tissue (2 month old mouse)

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on Mouse430_2 Arrays. 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: Probe-level intensity measurements were background-corrected, normalized and summarized by the robust multi-array analysis (RMA) method using GeneSpring GX11 software (Agilent).

label: Biotin

organism: Mus musculus

source_name: Whole lateral ventricle choroid plexus (Two month old mouse)

label_protocol: Standard Affymetrix protocol

extract_protocol: Extraction of total RNA was performed using the miRNeasy kit according to the manufacturer's instructions and cDNA synthesized with Nugen Pico amplification kit.

tag: strain

value: male

value: Whole lateral ventricle choroid plexus

value: Two months old


title: 2 month old lateral ventricle choroid plexus, biological replicate 2


title: Patient Male M093 Post-vaccine

description: Sample name: M093B


title: Patient Male M084 Post-vaccine

description: Sample name: M084B


title: Patient Female M091 Pre-vaccine

description: Sample name: M091A


title: Patient Female M089 Pre-vaccine

description: Sample name: M089A


title: Patient Male M088 Pre-vaccine

description: Sample name: M088A


title: 18 month old lateral ventricle choroid plexus, biological replicate 3

description: Gene expression data from whole choroid plexus tissue (18 month old mouse)

source_name: Whole lateral ventricle choroid plexus (Eighteen month old mouse)

value: Eighteen months old


title: 18 month old lateral ventricle choroid plexus, biological replicate 2


title: Patient Male M090 Pre-vaccine

description: Sample name: M090A


title: Patient Male M084 Pre-vaccine

description: Sample name: M084A


title: Patient Female M092 Post-vaccine

description: Sample name: M092B


title: Patient Male M088 Post-vaccine

description: Sample name: M088B


title: 18 month old lateral ventricle choroid plexus, biological replicate 1


title: BX_M3_P7714

description: 3month kidney biopsy post transplant


title: Patient Male M083 Post-vaccine

description: Sample name: M083B


title: Jejunum_67_DON

city: Toulouse

first: Alix

last: Pierron

address: 180 chemin de Tournefeuille

country: France

institute: INRA

description: Sample name: 13_67_d

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Porcine GE microarray (8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 19 out of 20 microarrays or with a weight of 1 in all 4 microarrays from at least one experimental group. At this step, 34776 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 34775 rows each corresponding to a unique ProbeName.

organism: Sus scrofa domesticus

source_name: Jejunal explant

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: Four crossbreed weaning piglets at 5 weeks of age were housed in standard environmental conditions and fed control diets

extract_protocol: Total RNA from jejunal explants was extracted using EXTRACT-ALL® reagent (Eurobio, Les Ulis, France) following the manufacturer’s manual and lysing matrix D tubes (MP Biomedicals, Illkirch, France) with FastPrep.

treatment_protocol: After 1 week, acclimatized animals were slaughtered and organs were harvested. Explants were initially incubated for 30 minutes in culture medium. The medium was then removed and replaced with a contaminated medium. Indeed, explants were exposed to 10 µM of DON or other mycotoxins/molecules (3-epi DON, DON3G  and DOM-1) for 4 hours. For control, explants were incubated on the same conditions in presence of dimethyl sulfoxide (DMSO).

tag: animal

tag: developmental stage

value: piglet

value: Jejunal explant

tag: treatment

value: DON


title: BX_M3_P7709

description: 3month kidney biopsy post transplant

value: percutaneous allograft biopsy


title: 2 month old lateral ventricle choroid plexus, biological replicate 3


title: BX_M3_P7449

description: 3month kidney biopsy post transplant


title: Patient Male M076 Post-vaccine

description: Sample name: M076B

value: peripheral blood


title: Patient Female M081 Post-vaccine

description: Sample name: M081B

value: Female


title: Jejunum_67_3EpiDON

description: Sample name: 13_67_3e


title: Patient Female M079 Post-vaccine

description: Sample name: M079B


title: Patient Male M083 Pre-vaccine

description: Sample name: M083A

value: 9 months


title: Patient Male M076 Pre-vaccine

description: Sample name: M076A

value: Measles vaccine + DTP vaccine

value: Pre-vaccine


title: Jejunum_70_DOM1

description: Sample name: 13_70_dm


title: BX_M3_P6650

description: 3month kidney biopsy post transplant


title: BX_M3_P7160

description: 3month kidney biopsy post transplant


title: Jejunum_68_DON

description: Sample name: 13_68_d


title: Patient Male M074 Pre-vaccine

description: Sample name: M074A

value: Male


title: BX_M3_P7165

description: 3month kidney biopsy post transplant


title: Jejunum_70_3Gluc

description: Sample name: 13_70_3g


title: Jejunum_68_CTRL

description: Sample name: 13_68_c

value: CTRL


title: Jejunum_69_DOM1

description: Sample name: 13_69_dm


title: Patient Female M073 Post-vaccine

description: Sample name: M073B

value: 10 months

value: Post-vaccine


title: Patient Male M070 Post-vaccine

description: Sample name: M070B

value: DTP vaccine


title: Patient Male M071 Post-vaccine

description: Sample name: M071B

value: Measles vaccine


title: BX_M3_P7148

description: 3month kidney biopsy post transplant


title: Patient Male M071 Pre-vaccine

description: Sample name: M071A


title: Patient Male M070 Pre-vaccine

description: Sample name: M070A


title: Patient Female M073 Pre-vaccine

description: Sample name: M073A


title: BX_M3_P6648

description: 3month kidney biopsy post transplant


title: BX_M3_P6647

description: 3month kidney biopsy post transplant


title: Jejunum_69_CTRL

description: Sample name: 13_69_c


title: Patient Male M074 Post-vaccine

description: Sample name: M074B


title: Patient Male M069 Post-vaccine

description: Sample name: M069B


title: Patient Male M069 Pre-vaccine

description: Sample name: M069A


title: Patient Female M068 Pre-vaccine

description: Sample name: M068A


title: Patient Female M068 Post-vaccine

description: Sample name: M068B


title: BX_M3_P6646

description: 3month kidney biopsy post transplant


title: Jejunum_69_3Gluc

description: Sample name: 13_69_3g


title: Patient Male M067 Post-vaccine

description: Sample name: M067B


title: BX_M3_P6644

description: 3month kidney biopsy post transplant


title: Jejunum_70_3EpiDON

description: Sample name: 13_70_3e


title: Jejunum_70_DON

description: Sample name: 13_70_d


title: Patient Female M066 Pre-vaccine

description: Sample name: M066A


title: Patient Female M066 Post-vaccine

description: Sample name: M066B


title: Patient Male M067 Pre-vaccine

description: Sample name: M067A


title: Patient Female M065 Post-vaccine

description: Sample name: M065B


title: BX_M3_P6643

description: 3month kidney biopsy post transplant


title: Jejunum_67_3Gluc

description: Sample name: 13_67_3g


title: Patient Female M065 Pre-vaccine

description: Sample name: M065A


title: Patient Male M064 Post-vaccine

description: Sample name: M064B


title: Jejunum_67_DOM1

description: Sample name: 13_67_dm


title: Patient Male M063 Post-vaccine

description: Sample name: M063B


title: BX_M3_P6637

description: 3month kidney biopsy post transplant


title: Patient Male M064 Pre-vaccine

description: Sample name: M064A


title: Patient Female M062 Pre-vaccine

description: Sample name: M062A


title: Jejunum_67_CTRL

description: Sample name: 13_67_c


title: Jejunum_69_3EpiDON

description: Sample name: 13_69_3e


title: BX_M3_P6642

description: 3month kidney biopsy post transplant


title: Patient Male M063 Pre-vaccine

description: Sample name: M063A


title: BX_M3_P6634

description: 3month kidney biopsy post transplant


title: BX_M3_P6633

description: 3month kidney biopsy post transplant


title: Jejunum_68_DOM1

description: Sample name: 13_68_dm


title: Jejunum_68_3Gluc

description: Sample name: 13_68_3g


title: Jejunum_68_3EpiDON

description: Sample name: 13_68_3e


title: Patient Female M055 Post-vaccine

description: Sample name: M055B


title: Patient Male M060 Post-vaccine

description: Sample name: M060B


title: BX_M3_P6609

description: 3month kidney biopsy post transplant


title: BX_M3_P6606

description: 3month kidney biopsy post transplant


title: Patient Male M060 Pre-vaccine

description: Sample name: M060A


title: Patient Female M061 Post-vaccine

description: Sample name: M061B


title: Patient Female M055 Pre-vaccine

description: Sample name: M055A


title: norm 3

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: SAMPLE 12

hyb_protocol: Hybridization was performed according to 4x2k CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 1,0 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: The data were normalised using quantile normalisation in R.

source_name: peripheral blood mononuclear cells

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: Mononuclear cells were extracted shortly after bone marrow or blood samples collection. Cells were obtained by a density gradient centrifugation method using DiacollTM  (Ficoll-1077) (Dia-M, Russia).  2-3 ml of bone marrow or blood was dissolved in PBS up to 10 ml. Cell suspension was layered on 2.5 ml of Diacoll in 15 ml centrifuge tube and centrifuged at 400 RCF for 40 min. Buffy coat was removed and dissolved in PBS up to 14 ml followed by centrifugation at 800 RCF for 10 min.  PBS wash procedure was performed twice. Pellet was dissolved in 0,5-1 ml of  RNALater solution (Thermo Fisher Scientific). Cells were counted by Scepter™ 2.0 Handheld Automated Cell Counter (Merck Millipore),  aliquoted and stored at -20°C till RNA extraction and microarray hybridization. For RNA extraction cell suspensions with RNALater were centrifuged at 3000 RCF for 5 min. Pellets were dissolved in TRI Reagent (MRC), Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction. RNA was quantified using Nanodrop (Thermo Fisher Scientific).

tag: age (years)

value: unknown


title: Patient Male M054 Post-vaccine

description: Sample name: M054B


title: BX_M3_P6604

description: 3month kidney biopsy post transplant


title: Jejunum_70_CTRL

description: Sample name: 13_70_c


title: Patient Male M054 Pre-vaccine

description: Sample name: M054A


title: Jejunum_69_DON

description: Sample name: 13_69_d


title: Patient Male M047 Post-vaccine

description: Sample name: M047B


title: Patient Male M053 Post-vaccine

description: Sample name: M053B


title: norm 1

description: SAMPLE 10


title: BX_M3_P6526

description: 3month kidney biopsy post transplant


title: Patient Female M045 Post-vaccine

description: Sample name: M045B


title: Patient Male M047 Pre-vaccine

description: Sample name: M047A


title: 41

description: SAMPLE 9

source_name: mononuclear cells derived from pediatric patients with acute myeloid leucosis


title: 38

description: SAMPLE 8


title: 11

description: SAMPLE 7

source_name: mononuclear cells derived from pediatric patients with acute lymphoid leucosis


title: 9

description: SAMPLE 5


title: BX_M3_P6219

description: 3month kidney biopsy post transplant


title: BX_M3_P5647

description: 3month kidney biopsy post transplant


title: Patient Male M053 Pre-vaccine

description: Sample name: M053A


title: Patient Female M036 Pre-vaccine

description: Sample name: M036A


title: 10

description: SAMPLE 6


title: BX_M3_P3600

description: 3month kidney biopsy post transplant


title: Patient Female M044 Pre-vaccine

description: Sample name: M044A


title: Patient Female M044 Post-vaccine

description: Sample name: M044B


title: Patient Female M024 Pre-vaccine

description: Sample name: M024A


title: Patient Female M028 Pre-vaccine

description: Sample name: M028A


title: Patient Female M036 Post-vaccine

description: Sample name: M036B


title: BX_M3_P5947

description: 3month kidney biopsy post transplant


title: Patient Male M033 Post-vaccine

description: Sample name: M033B


title: norm 2

description: SAMPLE 11


title: BX_M3_P4291

description: 3month kidney biopsy post transplant


title: 6

description: SAMPLE 3


title: BX_M3_P3957

description: 3month kidney biopsy post transplant


title: 8

description: SAMPLE 4


title: BX_M3_P6649

description: 3month kidney biopsy post transplant


title: Patient Female M022 Pre-vaccine

description: Sample name: M022A


title: Patient Female M024 Post-vaccine

description: Sample name: M024B


title: Patient Male M008 Pre-vaccine

description: Sample name: M008A


title: 5

description: SAMPLE 2


title: Patient Male M019 Pre-vaccine

description: Sample name: M019A


title: 4

description: SAMPLE 1


title: Patient Male M008 Post-vaccine

description: Sample name: M008B


title: Patient Male M007 Pre-vaccine

description: Sample name: M007A


title: Patient Male M019 Post-vaccine

description: Sample name: M019B


title: Patient Male M007 Post-vaccine

description: Sample name: M007B


title: Patient Male M033 Pre-vaccine

description: Sample name: M033A


title: 12

description: SAMPLE 4

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

extract_protocol: Mononuclear cells were extracted shortly after bone marrow samples collection. Cells were obtained by a density gradient centrifugation method using DiacollTM  (Ficoll-1077) (Dia-M, Russia).  2-3 ml of bone marrow was dissolved in PBS up to 10 ml. Cell suspension was layered on 2.5 ml of Diacoll in 15 ml centrifuge tube and centrifuged at 400 RCF for 40 min. Buffy coat was removed and dissolved in PBS up to 14 ml followed by centrifugation at 800 RCF for 10 min.  PBS wash procedure was performed twice. Pellet was dissolved in 0,5-1 ml of  RNALater solution (Thermo Fisher Scientific). Cells were counted by Scepter™ 2.0 Handheld Automated Cell Counter (Merck Millipore),  aliquoted and stored at -20°C till RNA extraction and microarray hybridization. For RNA extraction cell suspensions with RNALater were centrifuged at 3000 RCF for 5 min. Pellets were dissolved in TRI Reagent (MRC), Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction. RNA was quantified using Nanodrop (Thermo Fisher Scientific).


title: 13

description: SAMPLE 5


title: wool-bearing skin-rep3

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

country: China

institute: Qingdao Institute of Animal Science and Veterinary Medicine

description: Gene expression at 12 month body side skin

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2505B, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.0 software package (Agilent Technologies). After Quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.0).

organism: Ovis aries

source_name: skin,12 month body side

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: These three sheep were reared normally in pens.

extract_protocol: All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA extraction. TRIzol (Invitrogen) was used for total RNA extractions according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000. Its OD260/OD280 ratio was confirmed to be higher than 1.8. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were sent to Kangchen Biotechnology Limited Company (Shanghai, China) for hybridization to the Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

treatment_protocol: All animals were treated in accordance with the animal protocols deﬁned by national and local animal welfare bodies, and all animal work was approved by the Shandong Province Biological Studies Animal Care and Use Committee. One ram and two ewes of 12-month-old Aohan fine wool sheep were used in the microarray study. These animals were half sibs (sharing the same father). In August 2010, two areas of full-thickness skin were sampled from the same animal under local anaesthesia: body side skin (wool bearing) and groin skin (non-wool bearing) for microarray and proteomic experiments. The area of each sample was about 1 cm2.

tag: breed

value: Aohan

value: skin

value: 12 month

tag: body location

value: body side (wool bearing)

tag: gender

value: female


title: 2

description: SAMPLE 1


title: 7

description: SAMPLE 3


title: 3

description: SAMPLE 2


title: wool-bearing skin-rep1

value: male


title: non-wool bearing skin-rep3

description: Gene expression at 12 month groin skin

source_name: skin,12 month groin

value: groin (non-wool bearing)


title: non-wool bearing skin-rep1

description: Gene expression at 12 month groin skin


title: wool-bearing skin-rep2


title: Patient Female M002 Post-vaccine

description: Sample name: M002B

value: peripheral blood

value: Female


title: non-wool bearing skin-rep2

description: Gene expression at 12 month groin skin


title: OR_1

status: Public on Jul 19 2016

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Larvae harvest at 3rd instar stage

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Hi-RPM Gene Expression Hybridization Kit,) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours. After hybridization, slides were washed sequentially by Gene Expression Wash Buffer Kit .

scan_protocol: Scanned on an Agilent G2565CA scanner(US9230696). one color scan setting for4x44 array slides (Scan Area 61x21.6mm, Scan resolution 5um,  Green PMT is set to 100% and XDR at 0.1).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 10.5.1.1. Using the protocol GE1_105_Dec08 to obtain background subtracted and spatially detrended Processed Signal intensities.
Raw data were normalized with percentile at 75th, and took log2 using Agilent GeneSpring 12.1.

label: Alexa 555

organism: Drosophila melanogaster

source_name: Wild type

label_protocol: cDNA prepared from 10μg of total RNA were labeled with Alexa 555 using Invitrogen SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol.

growth_protocol: Fly grew at 25 degree C, harvest at 3rd instar stage

extract_protocol: After DNaseI treatment, RNA were purification by RNeasy kit (Qiagene)

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

value: whole larvae

tag: Stage

value: 3rd instar stage

tag: genotype/variation

value: wild type


title: OR_3

description: Larvae harvest at 3rd instar stage


title: GAF mutant_1

description: Larvae harvest at 3rd instar stage

source_name: GAF mutant

value: GAF mutant


title: GAF mutant_3

description: Larvae harvest at 3rd instar stage


title: OR_2

description: Larvae harvest at 3rd instar stage


title: GAF mutant_2

description: Larvae harvest at 3rd instar stage


title: Patient Female M002 Pre-vaccine

description: Sample name: M002A

value: 9 months

value: Pre-vaccine


title: hMSC_T7_bmp+tgf_rep1

city: Nijmegen

first: Everardus

middle: J

last: van Zoelen

address: Heyendaalseweg 135

department: Faculty of Science

country: Netherlands

institute: Radboud University Nijmegen

description: Gene Expression data from hMSCs differentiated for 168 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta

hyb_protocol: The Eukaryotic Target Hybridization protocol from Affymetrix was followed (GeneChip Expression Analysis Technical Manual - P/N 702232 Rev. 3). Briefly, the fragmented target was hybridized to the probe array GeneChip Human Genome U133 Plus 2.0 during a 16-hour incubation. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450, following the FS450_0005 fluidics protocol (GeneChip Expression Wash, Stain and Scan User Manual, P/N 702731).

scan_protocol: The HG-U133_Plus_2 arrays were scanned using the M10 (GCS3000 high resolution scanner); program-nameFAffymetrix Genechip Command Console (program-id3.2.0.1515); program-nameAGCCScanCom.exe (program-id3.2.1.1515)

data_processing: The R/Bioconductor package affy (version 1.46.1) was used for probe set summarization and normalization by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization). Annotation was conducted using annotate (version 1.46.1) and hgu133plus2.db (version 3.1.3).

source_name: hMSC, treated with BMP2+TGFB, 7 days differentiation

label_protocol: All samples were processed according to the standard Affymetrix Eukaryotic Target Preparation protocol (GeneChip Expression Analysis Technical Manual - P/N 702232 Rev. 3). Briefly: Double-stranded cDNA was synthesized from 5ug total RNA, followed by an in vitro transcription (IVT) reaction to produce biotin-labeled cRNA from the cDNA. The cRNA was fragmented before hybridization.

growth_protocol: hMSCs (Lonza) were plated at 4.0 x 10^4 cells/cm2 and grown overnight in serum-containing medium.

extract_protocol: RNA was extracted from the cells using TRIzol according to the manufacturer's protocol (Invitrogen), followed by column purification using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Cells were subsequently incubated for 1; 2; 3 or 7 days in differentiation medium with the above added components. Untreated cells (day 0) were used as control.

tag: cell type

value: hMSC

tag: time


title: hMSC_T7_bmp+tgf_rep2


title: hMSC_T7_bmp+tgf+ibmx_rep3

description: Gene Expression data from hMSCs differentiated for 168 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+TGFB+IBMX, 7 days differentiation


title: hMSC_T3_bmp+tgf+ibmx_rep1

description: Gene Expression data from hMSCs differentiated for 72 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+TGFB+IBMX, 3 days differentiation


title: hMsc_T7_bmp_rep3

description: Gene Expression data from hMSCs differentiated for 168 hours in the presence of Bone Morphogenetic Protein 2

source_name: hMSC, treated with BMP2, 7 days differentiation


title: hMSC_T7_bmp+ibmx_rep3

description: Gene Expression data from hMSCs differentiated for 168 hours in the presence of Bone Morphogenetic Protein 2 and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+IBMX, 7 days differentiation


title: hMSC_T7_bmp+tgf+ibmx_rep2


title: hMSC_T7_bmp+ibmx_rep1


title: hMSC_T3_bmp+tgf+ibmx_rep3


title: hMSC_T3_bmp+ibmx_rep2

description: Gene Expression data from hMSCs differentiated for 72 hours in the presence of Bone Morphogenetic Protein 2 and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+IBMX, 3 days differentiation


title: hMsc_T7_bmp_rep1


title: hMSC_T3_bmp+tgf_rep1

description: Gene Expression data from hMSCs differentiated for 72 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta

source_name: hMSC, treated with BMP2+TGFB, 3 days differentiation


title: hMSC_T3_bmp+tgf_rep2


title: hMsc_T3_bmp_rep3

description: Gene Expression data from hMSCs differentiated for 72 hours in the presence of Bone Morphogenetic Protein 2

source_name: hMSC, treated with BMP2, 3 days differentiation


title: hMsc_T3_bmp_rep2


title: hMSC_T3_bmp+ibmx_rep3


title: hMSC_T7_bmp+tgf+ibmx_rep1


title: hMsc_T7_bmp_rep2


title: hMSC_T7_bmp+ibmx_rep2


title: hMSC_T7_bmp+tgf_rep3


title: hMSC_T3_bmp+ibmx_rep1


title: hMSC_T3_bmp+tgf_rep3


title: hMSC_T3_bmp+tgf+ibmx_rep2


title: hMSC_T2_bmp+tgf+ibmx_rep3

description: Gene Expression data from hMSCs differentiated for 48 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+TGFB+IBMX, 2 days differentiation


title: hMSC_T2_bmp+ibmx_rep3

description: Gene Expression data from hMSCs differentiated for 48 hours in the presence of Bone Morphogenetic Protein 2 and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+IBMX, 2 days differentiation


title: hMSC_T2_bmp+ibmx_rep2


title: hMSC_T2_bmp+tgf+ibmx_rep2


title: hMSC_T2_bmp+tgf+ibmx_rep1


title: hMSC_T2_bmp+ibmx_rep1


title: hMSC_T2_bmp+tgf_rep2

description: Gene Expression data from hMSCs differentiated for 48 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta

source_name: hMSC, treated with BMP2+TGFB, 2 days differentiation


title: hMSC_T2_bmp+tgf_rep3


title: hMsc_T2_bmp_rep3

description: Gene Expression data from hMSCs differentiated for 48 hours in the presence of Bone Morphogenetic Protein 2

source_name: hMSC, treated with BMP2, 2 days differentiation


title: hMsc_T1_bmp_rep2

description: Gene Expression data from hMSCs differentiated for 24 hours in the presence of Bone Morphogenetic Protein 2

source_name: hMSC, treated with BMP2, 1 day differentiation


title: hMsc_T2_bmp_rep1


title: hMsc_T2_bmp_rep2


title: hMSC_T1_bmp+tgf+ibmx_rep3

description: Gene Expression data from hMSCs differentiated for 24 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+TGFB+IBMX, 1 day differentiation


title: hMSC_T1_bmp+ibmx_rep1

description: Gene Expression data from hMSCs differentiated for 24 hours in the presence of Bone Morphogenetic Protein 2 and 3-isobutyl-1-methylxanthine

source_name: hMSC, treated with BMP2+IBMX, 1 day differentiation


title: hMSC_T1_bmp+ibmx_rep2


title: hMSC_T1_bmp+tgf_rep1

description: Gene Expression data from hMSCs differentiated for 24 hours in the presence of Bone Morphogenetic Protein 2 and Transforming Growth Factor Beta

source_name: hMSC, treated with BMP2+TGFB, 1 day differentiation


title: hMSC_T2_bmp+tgf_rep1


title: hMsc_T1_bmp_rep1


title: hMsc_T1_bmp_rep3


title: hMSC_T0_Ctrl_rep5

description: Gene Expression data from undifferentiated hMSCs (without any treatment)

source_name: human Mesenchymal Stem Cells (hMSC), no treatment (control), undifferentiated (time 0)


title: hMSC_T1_bmp+tgf_rep3


title: hMSC_T1_bmp+tgf+ibmx_rep2


title: hMSC_T1_bmp+tgf+ibmx_rep1


title: hMSC_T0_Ctrl_rep6


title: MLL-NRIP3 RictorΔ/Δ-2

city: Wuhan

first: Yang

last: Yang

address: #1095,Jiefang Avenae

institute: Tongji Hospital

hyb_protocol: Following fragmentation, 12.5 μg of fragmented cRNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: leukemia cells from Rictor Deletion MLL-NRIP3 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The percentage of CD45.2+ cells in the PB of the recipient mice was determined every 5 days from day 15 after the transplantation. When the proportion of CD45.2+> 50% of the PB WBCs (1st BMT), The K+G- BM cells were sorted using flow cytometry for subsequent microarray analysis.

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

treatment_protocol: Mice K+G- BM leukemia cells were rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: host tissue

value: K+G–  BM leukemia cells

tag: cell genotype

value: Rictor deletion

tag: leukemia mouse model


title: hMSC_T1_bmp+ibmx_rep3


title: MLL-NRIP3 Control-3

source_name: leukemia cells from Rictor wild-type MLL-NRIP3 mice

value: Rictor wild type


title: MLL-NRIP3 RictorΔ/Δ-3


title: MLL-NRIP3 RictorΔ/Δ-1


title: hMSC_T0_Ctrl_rep4


title: hMSC_T0_Ctrl_rep2


title: MLL-AF9 Control-2

source_name: leukemia cells from Rictor wild-type MLL-AF9 mice


title: MLL-AF9 RictorΔ/Δ-2

source_name: leukemia cells from Rictor Deletion MLL-AF9 mice


title: MLL-AF9 Control-1


title: hMSC_T0_Ctrl_rep1


title: MLL-NRIP3 Control-1


title: MLL-NRIP3 Control-2


title: MLL-AF9 RictorΔ/Δ-1


title: hMSC_T0_Ctrl_rep3


title: Patient_CODE11 - T1

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

country: Italy

institute: IRCCS Ospedale Oncologico di Bari

description:
replicate 1
5920789004  K

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <700 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

source_name: PBMCs

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the QIAzol® Lysis Reagent, according to the manufacturer’s instructions. Quality control was performed with Biorad Experion.

tag: age

tag: tissue

value: PBMCs


title: hMSC_T1_bmp+tgf_rep2


title: Patient_CODE9 - T1

description:
replicate 1
5920789004  D


title: Patient_CODE4 - T1

description:
replicate 1
5920789004  G


title: Patient_CODE10 - T1

description:
replicate 1
5920789004  F


title: Patient_CODE5 - T1

description:
replicate 1
5920789010  J


title: Patient_CODE7 - T1

description:
replicate 1
5920789004  B


title: Patient_CODE6 - T1

description:
replicate 1
5920789004  A


title: Patient_CODE12 - T1

description:
replicate 1
5920789004  H


title: Patient_CODE8 - T1

description:
replicate 1
5920789010  I


title: MLL-AF9 RictorΔ/Δ-3


title: MLL-AF9 Control-3


title: Patient_CODE3 - T1

description:
replicate 1
5920789004  E


title: Patient_CODE12 - T0

description:
replicate 1
5920789011  K


title: Patient_CODE1 - T1

description:
replicate 1
5920789010  G


title: Patient_CODE11 - T0

description:
replicate 1
5920789012  K


title: Patient_CODE10 - T0

description:
replicate 1
5920789012  H


title: Patient_CODE7 - T0

description:
replicate 1
5920789012  C


title: Patient_CODE9 - T0

description:
replicate 1
5920789012  F


title: Patient_CODE6 - T0

description:
replicate 1
5920789012  B


title: MS Patient_CODE19 - T1

description: replicate 1

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <120 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

tag: time point


title: MS Patient_CODE20 - T1

description: replicate 1


title: MS Patient_CODE13 - T1

description: replicate 1


title: MS Patient_CODE21 - T1

description: replicate 1


title: MS Patient_CODE24 - T1

description: replicate 1


title: MS Patient_CODE22 - T1

description: replicate 1


title: MS Patient_CODE21 - T0

description: replicate 1


title: MS Patient_CODE22 - T0

description: replicate 1


title: MS Patient_CODE24 - T0

description: replicate 1


title: Patient_CODE4 - T0

description:
replicate 1
5920789010  E


title: MS Patient_CODE23 - T0

description: replicate 1


title: Patient_CODE5 - T0

description:
replicate 1
5920789010  F


title: MS Patient_CODE14 - T1

description: replicate 1


title: MS Patient_CODE18 - T1

description: replicate 1


title: MS Patient_CODE17 - T1

description: replicate 1


title: MS Patient_CODE19 - T0

description: replicate 1


title: MS Patient_CODE16 - T1

description: replicate 1


title: hMsc_T3_bmp_rep1


title: MS Patient_CODE18 - T0

description: replicate 1


title: Patient_CODE3 - T0

description:
replicate 1
5920789010  C


title: MS Patient_CODE15 - T1

description: replicate 1


title: MS Patient_CODE23 - T1

description: replicate 1


title: MS Patient_CODE20 - T0

description: replicate 1


title: MS Patient_CODE17 - T0

description: replicate 1


title: MS Patient_CODE15 - T0

description: replicate 1


title: MS Patient_CODE16 - T0

description: replicate 1


title: Patient_CODE8 - T0

description:
replicate 1
5920789012  E


title: Patient_CODE1 - T0

description:
replicate 1
5920789010  A


title: MS Patient_CODE13 - T0

description: replicate 1


title: Patient_CODE2 - T0

description:
replicate 1
5920789010  B


title: Patient_CODE5 - T1

description:
replicate 1
6062739184 J


title: Patient_CODE10 - T1

description:
replicate 1
9252621034 L


title: Patient_CODE12 - T1

description:
replicate 1
5753677035 J


title: Patient_CODE9 - T1

description:
replicate 1
9252621034 H


title: MS Patient_CODE14 - T0

description: replicate 1


title: Patient_CODE7 - T1

description:
replicate 1
9234921141 F


title: Patient_CODE2 - T1

description:
replicate 1
9031313030 D


title: Patient_CODE11 - T1

description:
replicate 1
9234921141 G


title: Patient_CODE3 - T1

description:
replicate 1
9234921127 A


title: Patient_CODE1 - T1

description:
replicate 1
9031313030 B


title: Patient_CODE12 - T0

description:
replicate 1
9031313041 C


title: Patient_CODE10 - T0

description:
replicate 1
9252621034 K


title: Patient_CODE9 - T0

description:
replicate 1
9252621034 G


title: Patient_CODE6 - T1

description:
replicate 1
5753677035 K


title: Patient_CODE8 - T1

description:
replicate 1
5753677035 H


title: Patient_CODE7 - T0

description:
replicate 1
9234921141 D


title: Patient_CODE5 - T0

description:
replicate 1
6062739174 J


title: Patient_CODE8 - T0

description:
replicate 1
9234921141 E


title: Patient_CODE6 - T0

description:
replicate 1
6062739174 L


title: Patient_CODE4 - T1

description:
replicate 1
6062739184 E


title: NBS-NPCs36

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

description: gene expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: NPCs differentiated from human derived iPSCs from fibroblasts of an healthy individual

label_protocol: Affymetrix protocol, 11 µg cRNA

growth_protocol: as described in the article, iPSCs were grown under low oxygen conditions on matrigel with mTser and MEF feeder cells, differentiation was done according to Kim et al. direct differentiation protocol 2010

extract_protocol: 200 ng total RNA, Affymetrix protocol

treatment_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit (5 PRIME)

tag: material

value: Cell line

value: Male

value: Neural progenitor cells (NPCs)


title: Patient_CODE4 - T0

description:
replicate 1
6062739174 E


title: Patient_CODE2 - T0

description:
replicate 1
6062739174 B


title: Patient_CODE11 - T0

description:
replicate 1
9031313041 A


title: NBS-NPCs34

description: gene expression


title: Patient_CODE1 - T0

description:
replicate 1
9031313030 A


title: Patient_CODE3 - T0

description:
replicate 1
6062739174 D


title: NBS-iPS34

description: gene expression

source_name: Human derived iPSCs from fibroblasts of an NBS patient

value: Human derived induced pluripotent stem cells (iPSCs)


title: NBS-iPS36

description: gene expression


title: AE_Low_rep2

city: Cincinnati

first: Kevin

middle: A

last: Link

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Labeled probes were hybridized to GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

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

data_processing: CHP files were generated and normalized using Affymetrix Expression Console Software via RMA. Further analysis was performed with Qlucore Omics Explorer software.

source_name: AE low bone marrow

label_protocol: For each sample, the Ambion® WT Expression Kit (Life Technologies) synthesizes cDNA target from 300 nanograms of total RNA.Then the GeneChip® WT Terminal Labeling Kit (Affymetrix) is used to both chemically fragment and biotin-label the cDNA target.

growth_protocol: Cells were cultured in StemSpan media with 50ng/ml rat recombinant SCF, 10ng/ml human IL-6, and 10ng/ml murine IL-3. After overnight stimulation, cells were collected and transduced with two rounds of retrovirus (MIG-AE9a). Post transduction, cells were collected, counted and transplanted into lethally irradiated BoyJ recipient mice. Cells were expanded two to three weeks in vivo, mice were sacrificed, and bone marrow (BM) harvested.

extract_protocol: RNA was isolated via the Qiagen Rneasy RNA isolation kit per manufacturer instructions

treatment_protocol: c-Kit+ cells were sorted (BD FACS Aria) for 30% low and 30% high GFP-expressing populations.

tag: strain

value: bone marrow

tag: cell marker

value: c-Kit+

tag: expression status

value: AE low


title: AE_High_rep2

source_name: AE high bone marrow

value: AE high


title: AE_High_rep1


title: WT-NPCs B

description: gene expression


title: MIG-_ctrl_rep1

description: control

source_name: Control bone marrow

value: control


title: WT-NPCs A

description: gene expression


title: MIG-_ctrl_rep2

description: control


title: MIG+_ctrl_rep1

description: control


title: AE9a_High_rep6

source_name: AE9a high bone marrow

value: AE9a high


title: AE9a_Low_rep5

source_name: AE9a low bone marrow

value: AE9a low


title: MIG-_ctrl_rep3

description: control


title: AE_Low_rep1


title: AE9a_Low_rep6


title: Hp+CLA

city: Jinan

first: Yundong

last: Sun

address: Wenhua xi road NO.44

department: Medicine

institute: Shandong university

description: H.pylori+CLA

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (8x15K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing:
1. Raw gene data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity genes were filtered (Genes that at least 2 out of 2 samples have flags in Present orMarginal were chosen for further analysis).
2. Quality assessment of gene data after filtering: Contains Box Plot and Scatter Plot for genes after filtering.
3. Differentially expressed genes screening: Contains differentially expressed genes between the two samples that passed Fold Change filtering (Fold Change >= 1.5).
4. Heat map and hierarchical clustering: Hierarchical clustering of All Targets Value.
5. Pathway analysis: Pathway analysis of the differentially expressed genes.

organism: Helicobacter pylori 26695

source_name: H.pylori with CLA treatment

label_protocol: 1 μg of total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

growth_protocol: H. pylori26695 was cultured by liquid media consisted of Brucella broth containing 10% fetal bovine serum for incubation in a microaerobic environment at 37°C on a shaker set at 120 rpm.

extract_protocol: Total RNA was extracted from H.pylori without CLA treatment and H.pylori treated with 0.25μg/ml Clarithromycin with use of TRIzol reagent (Invitrogen, USA)

treatment_protocol: 10 mL aliquots of liquid overnight-cultured H. pylori 26695 was treated with 0.25μg/ml Clarithromycin for 20 minutes.

tag: stress

value: CLA


title: Patient_CODE2 - T1

description:
replicate 1
5920789010  H


title: AE9a_Low_rep4


title: AE9a_High_rep4


title: Hp-CLA

description: H.pylori-CLA

source_name: H.pylori without CLA treatment

value: Control


title: AE9a_Low_rep3


title: young adult 24h GO exposure_rep1.

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description: Gene expression data from Caenorhabditis elegans young adults

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.

data_processing: Image data were extracted through Affymetrix GCOS software. Data were subjected to normalization, background correction and data summarization using Affymetrix Expression Console software, using the standard Robust Multi-array Average (RMA) algorithm.

organism: Caenorhabditis elegans

source_name: mRNA isolated from wildtype young adult

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. 300 ng total RNA from each sample amplified double strated cDNA were labeled with biotin-labeling (Ambion® WT Expression kit)

growth_protocol: C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli and young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce agesynchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.

extract_protocol: The total RNA prepared from the exposed and control worms according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentration of GO and rGO was prepared in k-media (0.032 M KCl and 0.051M NaCl; 28). For toxicity tests, worms were incubated at 20 °C for 24 hr without a food source and then subjected to each type of analysis.

value: wildtype

value: hemaphrodite

value: young adult


title: AE9a_Low_rep1


title: AE9a_High_rep5


title: AE9a_High_rep3


title: AE9a_High_rep1


title: young adult 24h rGO exposure_rep1.


title: young adult Control


title: AE9a_High_rep2


title: AE9a_Low_rep2


title: Bacillus subtilis_Temp_High_rep4

status: Public on Jul 18 2016

city: Nanjing

first: weiying

last: wang

address: 1 Wenyuan Road

department: College of Life Sciences

institute: Nanjing Normal University

description:
BS_A4
gene experssion response to High temperature

hyb_protocol: not provided

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 (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.

organism: Bacillus subtilis

source_name: Bacillus subtilis, High temperature fermentation,replicate 4

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: A wort agar medium including a quarter of  beef extract peptone was used to Bacillus subtilis fermentation for 48 hours. The seed of B.subtilis was prepared in the Luria-Bertani medium at 37℃ overnight.

extract_protocol: A modified CTAB method was used for total RNA extraction. The ingredient of the CTAB extraction liquid including 2% CTAB, 30mmol/L EDTA, 2mol/L NaCl, 100mmol/L Tris-HCl, pH 8.0，0.05% spermidine. adding the reagents  in a clean RNase-free 1.5 ml centrifugal tube (including 600 L CTAB extraction liquid, 12 µL 2% PVP, 12 ul mercaptoethanol and final concentration of 1.5 mg/ml of proteinase K, 42 ℃ incubation for 10 minutes.Then transferred it to the sample tube and added 100 ul lysozyme (1 mg/ml), vortex oscillation, 42 ℃ incubation 90min ( vortexing several times during the time).For cell lysis nucleic acid substances released after the separation and purification of RNA as follows: in the previous step sample tube with equal volume of chloroform, isoamyl alcohol, vortex, 13000 rpm, 4 ℃ centrifuge for 15 min.Transfered the upper water phase to a new tube, repeating the above steps.Add precooling the solution (volume of 4 m LiCl and 1/2 volume of anhydrous ethanol) to the previous upper water. Precipitating the nucleic acid on ice for 3 hours. the pellets was ultraclean using  600 ul - 800 ul 2M LiCl and 75% ethanol.Obtaining total RNA.by add approprate amount DEPC water dissolved the pellets .

treatment_protocol: The sample of BS_A1, BS_A2, BS_A3, BS_A4 were cultuered according to the workflow below: culturing at 37℃ for 12 hours, then taking it into 46℃ for 12 hours. It continued to culturing at 55℃ for 24 hours in the final step. The sample of BS_B1,BS_B2,BS_B3,BS_B4 were cultured at 37℃ in the whole 48 hours.

tag: culture time


title: Bacillus subtilis_Temp_normal_rep1

description:
BS_B1
gene experssion at a normal temperature

source_name: Bacillus subtilis, normaltemperature fermentation,replicate 1


title: Bacillus subtilis_Temp_normal_rep2

description:
BS_B2
gene experssion at a normal temperature

source_name: Bacillus subtilis, normaltemperature fermentation,replicate 2


title: Bacillus subtilis_Temp_normal_rep4

description:
BS_B4
gene experssion at a normal temperature

source_name: Bacillus subtilis, normaltemperature fermentation,replicate 4


title: Bacillus subtilis_Temp_High_rep3

description:
BS_A3
gene experssion response to High temperature

source_name: Bacillus subtilis, High temperature fermentation,replicate 3


title: Bacillus subtilis_Temp_High_rep2

description:
BS_A2
gene experssion response to High temperature

source_name: Bacillus subtilis, High temperature fermentation,replicate 2


title: Bacillus subtilis_Temp_normal_rep3

description:
BS_B3
gene experssion at a normal temperature

source_name: Bacillus subtilis, normaltemperature fermentation,replicate 3


title: Subject 20: Healthy control

city: Toronto

first: Claudia

last: dos Santos

state: Ontario

address: 30 Bond St.

department: Intensive Care

country: Canada

institute: St. Michael's Hospital

data_processing: The data were normalised using NormExp Background Correction and Normalization Using Control Probes (neqc function) in the limma package in R.  The data was then output as residual values from a linear mixed model (using lme4 package in R) used to correct the normalized gene expression for age and sex effects (fixed effects) with random intercept terms to account for correlation among samples from the same patient and for potential differences in age- or sex-related expression effects between ICUAW and controls.

source_name: Vastus lateralis muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep-96 kit for Illumina arrays

extract_protocol: RNA was extracted using TrIzol reagent and purified using RNeasy per manufacturer specifications. RNA quality was ensured using Agilent Bioanalyzer

tag: Sex

value: F


title: Bacillus subtilis_Temp_High_rep1

description:
BS_A1
gene experssion response to High temperature

source_name: Bacillus subtilis, High temperature fermentation,replicate 1


title: Subject 15: Healthy control


title: Subject 18: Healthy control

value: M


title: Subject 11: Day 7 post-ICU


title: Subject 22: Healthy control


title: Subject 13: Day 7 post-ICU


title: Subject 9: ICUAW Day 7 post-ICU


title: Subject 8: ICUAW Day 7 post-ICU


title: Subject 16: Healthy control


title: Subject 14: Day 7 post-ICU


title: Subject 7: ICUAW Month 6 post-ICU


title: Subject 10: ICUAW Month 6 post-ICU


title: Subject 10: ICUAW Day 7 post-ICU


title: Subject 8: ICUAW Month 6 post-ICU


title: Subject 12: Day 7 post-ICU


title: Subject 9: ICUAW Month 6 post-ICU


title: Subject 7: ICUAW Day 7 post-ICU


title: Subject 21: Healthy control


title: Subject 19: Healthy control


title: Subject 17: Healthy control


title: Ses 2_TR_2

city: Gurgaon

first: Saif

last: Hameed

state: Haryana

address: Amity Education Valley

country: India

institute: Amity University Haryana

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

hyb_protocol: 1000ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Candida albicans_8x15K (AMADID: 026377). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method. Gene based analysis was performed.

organism: Candida albicans

source_name: Ses treated Candida cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: All Candida strains were grown at 30°C

extract_protocol: RNA extraction was perforemd by using combination of Trizol and Qiagen RNeasy mini kit with Dnase treatment (Cat # 74106).

treatment_protocol: The SC5314 strain of Candida cells were treated with 4mM Sesamol till OD600 1 and freezed with liquid nitrogen and stored at -80°C until used.

tag: treatment

value: Ses treated


title: Ses 2_TR_1


title: Control 2_TR_2

source_name: Untreated Candida cells

value: Untreated


title: Ses 1_BR


title: Subject 6: ICUAW Month 6 post-ICU


title: Subject 2: ICUAW Month 6 post-ICU


title: Control 2_TR_1


title: Subject 1: ICUAW Day 7 post-ICU


title: Subject 5: ICUAW Month 6 post-ICU


title: Subject 5: ICUAW Day 7 post-ICU


title: Subject 1: ICUAW Month 6 post-ICU


title: siPIAS1_R1881_16h_rep3

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing: The data was analyzed using the Bioconductor associated packages (lumi, limma). Data were preprocessed (bgAdjust), variance stabilizing transformed (VST) and robust spline normalized (RSN) with lumi package and analyzed using LIMMA to identify statistically significant genes.

source_name: MDA-MB453_siPIAS1_R1881-treated_16 h

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

growth_protocol: The cells were grown in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin and 25 ug/ml streptomycin.

extract_protocol: Total RNA was extracted with TriPure isolation reagent (Roche Diagnostics GmbH, Mannheim, Germany), Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: The cells were seeded onto 6-well plates and growth 72h in 5% stripped FBS in DMEM before treating 16h with 10 nM R1881 or vehicle (ethanol).

tag: cell line

value: MDA-MB453 breast cancer cell line

tag: transfected with

value: PIAS1 siRNA

tag: treated with

value: 10 nM R1881 for 16hrs


title: siPIAS1_EtOH_16h_rep2

source_name: MDA-MB453_siPIAS1_vehicle-treated_16 h

value: ethanol (vehicle) for 16hrs


title: Subject 4: ICUAW Month 6 post-ICU


title: Subject 6: ICUAW Day 7 post-ICU


title: siPIAS1_EtOH_16h_rep3


title: siPIAS1_EtOH_16h_rep1


title: Subject 3: ICUAW Month 6 post-ICU


title: siPIAS1_R1881_16h_rep1


title: Subject 2: ICUAW Day 7 pos- ICU


title: siPIAS1_R1881_16h_rep2


title: siNON_R1881_16h_rep3

source_name: MDA-MB453_siNON_R1881-treated_16 h

value: control siRNA (siNON, Non-targeting pool)


title: siNON_EtOH_16h_rep2

source_name: MDA-MB453_siNON_vehicle-treated_16 h


title: siNON_R1881_16h_rep1


title: siNON_EtOH_16h_rep1


title: 6_12

type: genomic

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Standard Illumina protocol.

scan_protocol: Illumina iScan as per array manufacturer's instruction.

data_processing: minfi 1.12.0 in R using SWAN normalisation.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: FFPE Primary OGSCC Tumour

label_protocol: Standard Illumina protocol.

extract_protocol: 2mm core punch from FFPE tissue blocks were deparaffinized and treated with proteinase K over 3 days at 56C. Genomic DNA was extracted using QIAamp DNA Blood Mini Kit.

value: oral tongue squamous cell carcinoma (OTSCC)

tag: gender

value: f

tag: 45 and over years

value: yes

tag: ostime (days)

tag: dsstime (days)

tag: pfstime (days)


title: siNON_EtOH_16h_rep3


title: siNON_R1881_16h_rep2


title: Subject 4: ICUAW Day 7 post-ICU

tag: age


title: CESCs cultured under hypoxia [alt-splice]

city: Chongqing

first: Yuan

last: Yao

address: 83 Xinqiao Street, District of Shapingba

institute: Xinqiao Hospital, Third Military Medical University

description:
140411-131411B_3_(HTA-2_0).CEL
Gene expression data from osteogenic differentiated CESCs under hypoxia

hyb_protocol: After fragmentation, 5 ug cDNA were hybridized for 16hr at 45C in 60rpm of spanning on Human Transcriptome Array 2.0. The microarray was washed and stained using Affymetrix GeneChip Command Console (AGCC) software

scan_protocol: The microarray was scanned using AGCC software.

data_processing: We used Expression Console software to pre-treat .CEL files through Robust Multichip Analysis (RMA) algorithm (3), including background correction, probeset signal integration, quantile normalization. After pretreatment, the obtained chp files were analyzed by Transcriptome Analysis Console software to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs).

source_name: CESCs cultured under hypoxia for 21 days

label_protocol: Fragmented single-stranded DNA was labeled using DNA labeling reagent according to standard Affymetrix protocol.

growth_protocol: CESCs were isolated from the human cartilage endplate and cultured at 37C and 5% CO2 condition. The cells within 3 passages were used in this study.

treatment_protocol: CESCs were cultured for 21 days under hypoxia and normoxia respectively.

tag: cell

value: Cartilage endplate-derived stem cells (CESCs)


title: 6_18

tag: tissue

value: m


title: 6_7


title: 6_15


title: CESCs cultured under normoxia [alt-splice]

description:
140411-131411B_4_(HTA-2_0).CEL
Gene expression data from osteogenic differentiated CESCs under normoxia

source_name: CESCs cultured under normoxia for 21 days


title: 6_6


title: 6_5


title: 6_9


title: 6_14


title: 6_10


title: Subject 3: ICUAW Day7 post-ICU

hyb_protocol: Standard Illumina hybridization protocol


title: 6_4


title: 6_16


title: 6_8


title: 6_2


title: 6_3

value: no


title: 5_8


title: 6_19


title: 4_32


title: 6_11


title: 6_1


title: 5_11


title: 5_7


title: 4_34


title: 5_5


title: 5_3


title: 6_13


title: 4_35


title: 5_4


title: 4_27


title: 4_28


title: 4_31


title: CESCs cultured under normoxia [gene]


title: 4_20


title: 4_23


title: CESCs cultured under hypoxia [gene]


title: 4_25


title: 4_21


title: CD11c+ macrophage cells wild-type replicate 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.

source_name: CD11c+ macrophage cells from WT mouse

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Mouse lungs were finely minced with a surgical blade and digested in Neurobasal medium (Gibco) containing 1 mg/ml DNaseI (Worthington), 2.5 mg/ml Collagenase P (Roche), 2.5 mg/ml Collagenase/Dispase (Roche), and 1x B27 and N2 supplements (Gibco) at 37C for 30 min. The digest was dissociated though a 1 ml pipette tip and passed through a 70 µM nylon mesh to obtain a single cell suspension. Alveolar CD11c+ macrophage populations were sorted by flow cytometry using anti-CD11b (M1/70), anti-CD11c (HL3), and anti-F4/80 (BM8) antibodies (BioLegend) where all cells were gated on autofluorescence in the FITC channel.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer's protocol.

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: alveolar CD11c+ macrophage cells


title: CD11c+ macrophage cells β6 integrin knockout replicate 2

source_name: CD11c+ macrophage cells from β6 integrin knockout mouse

value: beta-6 integrin KO


title: CD11c+ macrophage cells wild-type replicate 1


title: CD11c+ macrophage cells β6 integrin knockout replicate 1


title: 4_26


title: 4_22


title: 4_17


title: 4_13


title: P5 Back 3

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

hyb_protocol: Purified RNA hybridized to Affymetrix MG430.2A arrays by the Cancer Research UK Patterson Institute Affymetrix Genechip Microarray Service.

scan_protocol: Array images were produced by the Affymetrix PICR 3000 scanner.

data_processing: Data analysed as Cell files using Genespring-13X (Agilent Technologies). RMA normalization was used and the bottom twentieth-percentile of genes (i.e., the 20% of genes with the lowest expression levels) were excluded from subsequent analysis.

source_name: Mouse back skin 5 days after birth

label_protocol: standard label protocol

extract_protocol: To generate back and tail dermis microarray from P1 mouse (C57Bl6/CBA F1), tail skin was incubated in 5mM EDTA/PBS solution at 37°C, 1h, whereas back skin was incubated in dispase-trypsin solution at 37°C, 1h. Tail and back skin dermis were separated from the epidermis with forceps, washed once in PBS and digested as described above. Single-cell suspensions were washed 3x in PBS, before cells were lysed in Trizol (Invitrogen) and RNA was purified using Qiagen RNeasy columns. RNA was extracted from triplicate mice. cDNA was amplified from

tag: strain

value: C57Bl6/CBA F1

value: back skin

tag: time point

value: 5 days after birth


title: P5 Back 1


title: P5 Back 2


title: 4_16


title: 4_8


title: 4_9


title: 4_2


title: 4_11


title: 4_10


title: P5 Tail 4

source_name: Mouse tail skin 5 days after birth

value: tail skin


title: 4_3


title: 4_14


title: P5 Tail 3


title: 4_7


title: 4_4


title: 4_18


title: P1 Back 6

source_name: Mouse back skin 1 day after birth

value: 1 day after birth


title: 3_3


title: 4_1


title: P1 Back 5


title: P1 Tail 6

source_name: Mouse tail skin 1 day after birth


title: P1 Back 1


title: P1 Tail 5


title: 2_15


title: 2_19


title: 2_16


title: 4_24


title: P5 Tail 2


title: P1 Tail 4


title: KO5

city: Lausanne

first: Tamara

last: Seredenin

address: AI2135 Station 15 EPFL

country: Switzerland

institute: EPFL

description: Biotinylated cRNAs were prepared from 300ng of total RNA using the GeneChip® 3’ IVT Express Kit (Affymetrix) following the instructions of the manufacturer.

hyb_protocol: cRNA (15 ug) was hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) at  45°C for 17 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Microarray quality control was performed using the software package provided on RACE (http://race.unil.ch). Chips with a median normalized unscaled standard error  > 1.05 were excluded. Affymetrix annotations (version 30) were used for probeset-to-gene assignments. T-test was performed to assess the differences in gene expression between groups for each genotype.

source_name: cortex

growth_protocol: Crtc1KO mice and WT littermates were generated and genotyped as described in (Breuillaud L, Halfon O, Magistretti PJ, Pralong FP, Cardinaux JR (2009): Mouse fertility is not dependent on the CREB coactivator Crtc1. Nat Med 15:989-990). Mice were housed under a 12-hour light-dark cycle with ad libitum access to water and standard rodent chow diet. All animal experiments were conducted in accordance with the Swiss Federal Veterinary Office’s guidelines and were approved by the Cantonal Veterinary Service.

extract_protocol: Total RNA was extracted with the mini-RNA kit accordingly to manufacturer instructions (Qiagen).

value: female

value: cortex

tag: developmental stage

value: adult, 2 months


title: 3_5

value: oral tongue squamous cell carcinoma (OTSCC)


title: KO4

label_protocol: Biotinylated cRNAs were prepared from 300ng of total RNA using the GeneChip® 3’ IVT Express Kit (Affymetrix) following the instructions of the manufacturer.


title: KO1


title: 4_12


title: 2_12


title: 2_8

value: f


title: KO2


title: 2_9

value: yes


title: WT3

value: wild type


title: WT5


title: WT4


title: U3A_UI_IFN-γ_mean

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

institute: CNRS

description: Gene expression after 6h  IFN-γ stimulation

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 27 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the R software (version 2.15). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: U3A infected left uninfected and IFN-γ stimulated, mean of replicate 1,2 and 3

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: T. gondii strains were maintained in vitro by serial passage on monolayers of HFFs. HFFs primary cells, 2fTGH(STAT1+/+) and U3A (STAT1-/-) cell lines were cultured in DMEM supplemented with 10% heat inactivated FBS (Invitrogen), 10 mM Hepes buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Host cells were left uninfected or infected for 24 hours with Toxoplasma and stimulated with 100 U/ml IFN-γ for 6 hour or left unstimulated.

tag: cell line

tag: host cell type

value: epithelial cell STAT1-/-


title: KO3


title: WT2


title: 2_1

value: m


title: 2_11


title: WT1


title: 19


title: 2_4


title: 2_3

value: no


title: Vascular endothelial cells si-Mix (si-Gata2, si-Fli1, si-Sox7, and si-Sox18)

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

country: Japan

institute: The University of Tokyo

description:
Gene expression data of endothelial cells under si-RNA transfection
si-Mix

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: si-Mix

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Induction of differentiation was carried out using differentiation medium (DM; alpha minimal essential medium [MEM; Gibco] supplemented with 10 % fetal calf serum [Japan Bioserum Co Ltd] and 5 × 10-5 M 2-mercaptoethanol [Gibco]) as previously described (yamamizu 2009 blood). In brief, undifferentiated ES cells were cultured without leukemia inhibitory factor on collagen-coated dishes (Becton Dickson) at cell density 0.75 to 1 × 103 cells/cm2 for 96 hours. Then, cells were harvested and purified by magnetic cell sorting (MACS) with anti-Flk1 antibody. Purified Flk positive cells were seeded onto collagen-coated dishes at cell density 0.75 to 1 × 104 cells/cm2 in DM. Under this condition, Flk positive cells differentiated to ECs with VEGF in contrast to SMCs without VEGF.

extract_protocol: Total RNA was collected with RNeasy Micro kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Cells were incubated with a mixture of 100 nM siRNA and Lipofectamine RNAiMax (Invitrogen).

value: ES cells

tag: condition

value: si-Mix


title: 15

tag: gender


title: U3A_WT_IFN-γ_mean

source_name: U3A infected with 76K WT and IFN-γ stimulated, mean of replicate 1,2 and 3

tag: tg type strain

value: Type II


title: U3A_KO_IFN-γ_mean

source_name: U3A infected with 76K_TgIST KO and IFN-γ stimulated, mean of replicate 1,2 and 3


title: HFF_WT_IFN-γ_mean

source_name: HFF infected with 76K WT and IFN-γ stimulated, mean of replicate 1,2 and 3

value: HFF

value: human foreskin fibroblast


title: Vascular endothelial cells si-Sox18

description:
Gene expression data of endothelial cells under si-RNA transfection
si-Sox18


title: Vascular endothelial cells si-control*4

description:
Gene expression data of endothelial cells under si-RNA transfection
si-control*4


title: 16

tag: 45 and over years

tag: ostime (days)


title: HFF_UI_IFN-γ_mean

source_name: HFF infected left uninfected and IFN-γ stimulated, mean of replicate 1,2 and 3


title: 10

tag: dsstime (days)

tag: pfstime (days)


title: Vascular endothelial cells si-Sox7

description:
Gene expression data of endothelial cells under si-RNA transfection
si-Sox7


title: HFF_KO_IFN-γ_mean

source_name: HFF infected with 76K_TgIST KO and IFN-γ stimulated, mean of replicate 1,2 and 3


title: Vascular endothelial cells si-Fli1

description:
Gene expression data of endothelial cells under si-RNA transfection
si-Fli1


title: 2fTGH_UI_IFN-γ_mean

source_name: 2fTGH infected left uninfected and IFN-γ stimulated, mean of replicate 1,2 and 3

value: epithelial cell STAT1+/+


title: 12

source_name: FFPE Primary OGSCC Tumour


title: Fetal Liver Fasted 48hr, Total RNA, biological rep 3

city: Providence

first: Joan

middle: M

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

description:
IUGR Total 3
Fetal rat liver transcriptome, dam fasted 48 hr.
Biological replicate 3 (IUGR).

hyb_protocol: After fragmentation, 2.475ug cDNA was hybridized for 17 h at 45 C, 60rpm, on a GeneChip Rat Gene 1.0ST Array. Then, washing and staining were done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/ Hyb kit.

scan_protocol: The arrays were scanned with an Affymetrix 3000 7G scanner using manufacturer's instructions.

data_processing: Identification of differentially expressed genes was done in GenePattern (Broad Institute) (Reich M, et al. GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501) using the Expression File Creator module. RMA algorithm.

organism: Rattus norvegicus

source_name: fetal liver total RNA from dam fasted 48 hr

label_protocol: Samples (100ng total RNA) were reversed transcribed, turned into ds DNA, IVT transcribed and amplified using the Ambion WT expression kit. The WT labeling kit (Cat#900670) was used to fragment the ssDNA and end label it with a biotinylated nucleotide.

extract_protocol: RNA was extracted from pooled polysome preparations by acid-phenol:chloroform extraction followed by precipitation in ethanol plus ammonium acetate. Total RNA was isolated from frozen liver by homogenization in guanidine thiocyanate followed by cesium chloride density centrifugation. RNA was further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: For control livers, pregnant dams (n=3) were fed ad libitum until day E19 of gestation. Fetuses were delivered by C-section, and livers were removed and immediately placed in liquid nitrogen. IUGR livers were collected in the same way from pregnant dams (n=3) that were fasted for 48 hr before C-section.

value: Sprague Dawley

tag: age

value: fetal E19

value: liver

tag: treatment

value: dam fasted 48 hr (IUGR)

tag: rna fraction

value: total


title: 4_6

tag: tissue

value: oral tongue squamous cell carcinoma (OTSCC)


title: Vascular endothelial cells si-Gata2

description:
Gene expression data of endothelial cells under si-RNA transfection
si-Gata2

tag: cell type


title: 14

value: yes


title: Fetal Liver Fasted 48hr, Total RNA, biological rep 1

description:
IUGR Total 1
Fetal rat liver transcriptome, dam fasted 48 hr.
Biological replicate 1 (IUGR).

tag: strain/background


title: Vascular endothelial cells si-control

description:
Gene expression data of endothelial cells under si-RNA transfection
si-control

source_name: si-control

value: si-control


title: 2fTGH_WT_IFN-γ_mean

source_name: 2fTGH infected with 76K WT and IFN-γ stimulated, mean of replicate 1,2 and 3


title: Fetal Liver Fasted 48hr, Total RNA, biological rep 2

description:
IUGR Total 2
Fetal rat liver transcriptome, dam fasted 48 hr.
Biological replicate 2 (IUGR).


title: 8

value: f


title: 2fTGH_KO_IFN-γ_mean

source_name: 2fTGH infected with 76K_TgIST KO and IFN-γ stimulated, mean of replicate 1,2 and 3


title: Fetal Liver Fasted 48hr, Polysome RNA, biological rep 3

description:
IUGR Poly 3
mRNA
Gene expression data from fetal liver polysome RNA, dam fasted 48 hr.
Biological replicate 3 (IUGR).

source_name: fetal liver polysome RNA from dam fasted 48 hr

value: polysome


title: 5

value: m


title: 3_8


title: Fetal Liver Fasted 48hr, Polysome RNA, biological rep 2

description:
IUGR Poly 2
mRNA
Gene expression data from fetal liver polysome RNA, dam fasted 48 hr.
Biological replicate 2 (IUGR).


title: 48 hours without VEGF stimuli

description:
Gene expression data during smooth muscle cells differentiation
48h VEGF (-)

source_name: 48h control

value: ES cells

value: control for 48h


title: 13


title: 17


title: 6

value: no


title: 11


title: 12 hours without VEGF stimuli

description:
Gene expression data during smooth muscle cells differentiation
12h VEGF (-)

source_name: 12h control

value: control for 12h


title: Fetal Liver Fasted 48hr, Polysome RNA, biological rep 1

description:
IUGR Poly 1
mRNA
Gene expression data from fetal liver polysome RNA, dam fasted 48 hr.
Biological replicate 1 (IUGR).


title: 4


title: 2


title: 1


title: 24 hours without VEGF stimuli

description:
Gene expression data during smooth muscle cells differentiation
24h VEGF (-)

source_name: 24h control

value: control for 24h


title: 24 hours after VEGF stimuli

description:
Gene expression data during endothelial cells differentiation
24h VEGF (+)

source_name: 24h VEGF

value: VEGF treatment for 24h


title: Fetal Liver Total RNA, biological rep 2

description:
Control Total 2
Fetal rat liver transcriptome.
Biological replicate 2 (control).

source_name: fetal liver total RNA from dam fed ad libitum

value: Sprague Dawley

value: dam fed ad libitum (control)


title: 3


title: 6 hours without VEGF stimuli

description:
Gene expression data during smooth muscle cells differentiation
6h VEGF (-)

source_name: 6h control

value: control for 6h


title: 48 hours after VEGF stimuli

description:
Gene expression data during endothelial cells differentiation
48h VEGF (+)

source_name: 48h VEGF

value: VEGF treatment for 48h


title: Fetal Liver Total RNA, biological rep 1

description:
Control Total 1
Fetal rat liver transcriptome.
Biological replicate 1 (control).

value: fetal E19

value: liver

value: total


title: Fetal Liver Polysome RNA, biological rep 3

description:
Control Poly 3
mRNA
Gene expression data from fetal liver polysome RNA.
Biological replicate 3 (control).

source_name: fetal liver polysome RNA from dam fed ad libitum


title: Fetal Liver Polysome RNA, biological rep 2

description:
Control Poly 2
mRNA
Gene expression data from fetal liver polysome RNA.
Biological replicate 2 (control).


title: Mouse embryonic stem cells

description:
Gene expression data of ES cells
ES cells

source_name: ES cells

value: ES


title: siSTAiR18-Ex1 set4

status: Public on Jul 17 2016

city: Leipzig

first: Stefanie

last: Binder

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarray SurePrint G3 8x60k v2 (G4851B) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 3, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: INA-6, siRNA to STAiR18, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1µg total RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) 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: INA-6 multiple myeloma cells were grown in RPMI1640 medium supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO2 in an H2O-saturated atmosphere. 1ng IL-6 was additionally added per ml medium.

extract_protocol: Cells were harvested, washed with PBS and total RNA isolation was performed using TRIzol (LIFE Technologies, Carlsbad, USA), following the standard protocol. Total RNA was DNase-digested using the TURBO-DNA-free Kit (LIFE Technologies) as recommended by the manufacturer. Determination of the RNA quality and concentration occurred by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit (LIFE Technologies).

treatment_protocol: 5x10^6 INA-6 cells were washed in PBS and the cell pellet was resuspended in 100µl transfection buffer together with 20pmol/ml siRNA: either a negative control siRNA with medium GC content, an siRNA targeting the STAT3 mRNA in exon 9 or an siRNA targeting the STAiR18 [LINC00152/LOC541471] RNA in exon 1. Transfection occurred by electroporation and cells were then transferred to 10ml RPMI1640 cell culture medium supplemented with 10% FCS, 1% penicillin/streptomycin and 1ng/ml IL-6, followed by a 40h cultivation at 37°C and 5% CO2 in an H2O-saturated atmosphere.

value: multiple myeloma

tag: sirna


title: 6 hours after VEGF stimuli

description:
Gene expression data during endothelial cells differentiation
6h VEGF (+)

source_name: 6h VEGF

value: VEGF treatment for 6h


title: 12 hours after VEGF stimuli

description:
Gene expression data during endothelial cells differentiation
12h VEGF (+)

source_name: 12h VEGF

value: VEGF treatment for 12h


title: siSTAT3 set4

source_name: INA-6, siRNA to STAT3, replicate 4


title: 9

source_name: FFPE Primary OGSCC Tumour

value: oral tongue squamous cell carcinoma (OTSCC)

value: m

value: yes


title: Fetal Liver Polysome RNA, biological rep 1

country: USA

description:
Control Poly 1
mRNA
Gene expression data from fetal liver polysome RNA.
Biological replicate 1 (control).

value: polysome


title: siSTAiR18-Ex1 set3

source_name: INA-6, siRNA to STAiR18, replicate 3


title: siSTAT3 set1

source_name: INA-6, siRNA to STAT3, replicate 1


title: siSTAiR18-Ex1 set1

source_name: INA-6, siRNA to STAiR18, replicate 1


title: siSTAT3 set3

source_name: INA-6, siRNA to STAT3, replicate 3


title: siSTAiR18-Ex1 set2

source_name: INA-6, siRNA to STAiR18, replicate 2


title: control set3

source_name: INA-6, negative control siRNA, replicate 3

value: negative control


title: control set1

source_name: INA-6, negative control siRNA, replicate 1


title: siSTAT3 set2

source_name: INA-6, siRNA to STAT3, replicate 2


title: control set4

source_name: INA-6, negative control siRNA, replicate 4


title: control set2

source_name: INA-6, negative control siRNA, replicate 2


title: Flk-sorted mesoderm cells

description:
Gene expression data of flk positive mesoderm cells
Flk mesoderm cells

source_name: Flk

value: ES cells

value: Flk sorted mesoderm