title: FaDu Chelidonine EC50

city: Wuerzburg

first: Marianne

last: Schmidt

state: Outside U.S. & Canada

institute: University of Wuerzburg, Dept. of Otorhinolaryngology

description: FaDu_chel ec50

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

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

data_processing: Data were processed with the Affymetrix Expression console

source_name: FaDu treated with EC50 of chelidonine

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

growth_protocol: FaDu cells were cultured in RPMI 1640medium supplemented with 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA of FaDu cell cultures was isolated with the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated for 48 hrs with cell culture medium supplemented with 10µg/ml NSC-631570, EC50 of chelidonine or 10 µM chelidonine, respectively. Controls were incubated with corresponding volume of destilled water or  for 48 hrs.

value: FaDu hypophryngeal cell line

value: head and neck carcinoma


title: heart_ko_control_rep2

status: Public on Nov 30 2017

type: RNA

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: Prior to hybridization the slides were incubated in a prewarmed BSA blocking solution containing 5x SSC, 0.1% SDS, and 0.1 mg/ml BSA at 42°C for 45 to 60 minutes. Subsequently, slides were rinsed twice in 0.1x SSC for 5 minutes and for 30 seconds in double-distilled water, both at room temperature. The slides were then dried in a nitrogen flow. Cy3-labeled cRNA samples (2.5 µg) were dissolved in hybridization buffer (final concentration 50% formamide, 5x SSC, 0.1% SDS). Hybridization was carried out in a humid chamber at 42°C for 16 h. After the hybridization step, unbound cRNA and hybridization buffer were removed by several washing steps (2 times 10 minutes 2x SSC, 0.1% SDS, 5 times 1 minute 0.1x SSC, and 10 seconds 0.01x SSC).

scan_protocol: Fluorescence signals were visualized by a GenePix 4000B laser scanner (Axon). GenePix Pro software (v. 6.0) was used to calculate fluorescence intensities.

data_processing: Data analyses on microarray probe signal intensities were conducted with GeneSpring GX software (v. 11.0.2; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

molecule: total RNA

organism: Mus musculus

source_name: heart, ko, control

label_protocol: Labeled cRNA probes were synthesized from 500 ng of total RNA using the Quick Amp Labeling Kit (one-color; Agilent Technologies) according to the manufacturer’s protocol.

growth_protocol: 5-6 months old wildtype C57BL/6 mice and p27-deficient littermates received drinking water with 0.05% caffeine or water alone for 10 days.

extract_protocol: RNA was isolated from mouse hearts using Trizol according to the manufacturer`s instruction (Invitrogen) and subjected to a second purification step using RNeasy columns (Qiagen). RNA integrity was checked on an Agilent 2100 Bioanalyzer and concentrations were determined by photometric Nanodrop measurement. All samples in this study showed common high quality RNA Integrity Numbers (RIN 9.7-10).

treatment_protocol: Mice were sacrificed, the hearst excised and used for RNA preparation.

tag: tissue

value: heart

tag: strain

tag: genotype

tag: treatment

value: untreated control

tag: age

value: 5-6 months old


title: GPS22086

city: Castanet-Tolosan

first: Nathalie

last: Villa-Vialaneix

address: 24 chemin de Borde-Rouge

department: MIA

country: France

institute: INRA

description: Gene expression in blood 1 h after LPS injection for individual: FR17MAG201313285

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3600 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)./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 manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 INRA Sus scrofa  v1 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) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

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

data_processing: The scanned images were analThe 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 95 out of 118 microarrays or with a weight of 1 in all 24 microarrays from at least one experimental group. At this step, 27838 spots out of 62976 were selected.  The mean signal of the 31 first samples, 32 next, 32 next ones  and 23 last ones were substracted to individuals signals to correct the batch effect of the 4 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R 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 27837 rows each corresponding to a unique ProbeName (provided as data Matrix).yzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) 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 minimal weight of 1 for 32 out of 40 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 44640 spots out of 61626 were selected.  The mean signal of the 24 first samples and 16 last ones were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R 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 44639 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Whole blood, 01 h, individual: FR17MAG201313285

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng 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 using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: To explore individual variation in the biological response to LPS, whole blood from 30 juvenile Large White pigs (8 weeks of age) was collected at 4 time points ( t = 0, +1 h, +4 h, +24 h) for a total of 120 samples. All pigs were females and were raised in two batches. Arrays were designed such that all observations of a single individual were kept on the same array, with two individuals (one from each batch) on one array. This design secured the kinetics of the response for each individual and prevented confounding effects between batch and array. After quality control, all 120 samples were kept for normalization and analyses.

extract_protocol: A total RNA isolation and purification was done according to the manufacturer’s instructions using the Nucleospin RNA Blood kit (Macherey-Nagel, France) followed by DNase treatment. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies,Massy, France) and low-quality RNA preparations were discarded (RIN < 8).

treatment_protocol: Each animal was injected in the neck muscles with LPS (E. coli serotype 055:B5, Sigma-Aldrich, Saint Quentin Fallavier, FR) at a dose of 15 µg/kg body weight.

tag: breed

value: Large White

value: whole blood

tag: agent

value: LPS injection

tag: individual

tag: time point (h)

tag: gender

value: female


title: heart_wt_caffeine_rep3

source_name: heart, wt, caffeine

value: wild type

value: caffeine treated


title: heart_ko_caffeine_rep3

source_name: heart, ko, caffeine


title: heart_wt_control_rep3

source_name: heart, wt, control


title: heart_wt_control_rep1


title: C11m normal whole venous blood sample

type: genomic

city: Gainesville

first: Christopher

middle: Jordan

last: Clukay

state: Florida

department: Anthropology

country: USA

institute: University of Florida

description: normal whole venous blood sample

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneTitan Multi-Channel Instrument.

data_processing:
Data was processed using the Affymetrix Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).
normal whole venous blood sample. Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: venous whole blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was isolated using Qiagen QIAamp DNA Midi Kits (Qiagen, Valencia, CA) according to the manufacturerÍs instructions

tag: Sex

value: Female

value: whole venous blood


title: 170 0

city: SINGAPORE

first: CHEN

last: BAI

state: SINGPAORE

address: 1 CREATE WAY, INNOVATION WAY, 03-09, NUS-HUJ Cellular & Molecular Mechanisms of Inflammation Programme

department: MICROBIOLOGY

country: Singapore

institute: NATIONAL UNIVERSITY OF SINGAPORE

description: D170A 0 min after removal of methionine

hyb_protocol: standard Agilent procotocol

scan_protocol: standard Agilent procotocol

data_processing: standard Agilent procotocol

organism: Saccharomyces cerevisiae

label_protocol: standard Agilent procotocol

extract_protocol: none provided by the submitter

value: D170A 0 min after removal of methionine


title: C13m normal whole venous blood sample

description: normal whole venous blood sample


title: 170 45

description: D170A 45 min after removal of methionine


title: FaDu Chelidonine 10 µM

description: FaDu_chel 10 µM

label: Biotin

source_name: FaDu treated with 10 µM chelidonine

tag: cell type


title: FaDu untreated 1

source_name: FaDu untreated control cells


title: C15m normal whole venous blood sample

description: normal whole venous blood sample


title: FaDu untreated 2


title: C10m normal whole venous blood sample

description: normal whole venous blood sample


title: C12m normal whole venous blood sample

description: normal whole venous blood sample


title: C9m normal whole venous blood sample

description: normal whole venous blood sample


title: heart_wt_control_rep2


title: 170 150

description: D170A 150 min after removal of methionine


title: H 90

description: H 90 min after removal of methionine

value: H 90 min after removal of methionine


title: vec 150

description: empty vector 150 min after removal of methionine

source_name: empty vector


title: vec 0

description: empty vector 0 min after removal of methionine


title: C1m normal whole venous blood sample

description: normal whole venous blood sample


title: vec 45

description: empty vector 45 min after removal of methionine


title: C6m normal whole venous blood sample

description: normal whole venous blood sample


title: H 0

description: H 0 min after removal of methionine

value: H 0 min after removal of methionine


title: WT 150

description: WT 150 min after removal of methionine

value: WT 150 min after removal of methionine


title: 170 90

description: D170A 90 min after removal of methionine


title: C16m normal whole venous blood sample

description: normal whole venous blood sample


title: WT 45

description: WT 45 min after removal of methionine

value: WT 45 min after removal of methionine


title: vec 90

description: empty vector 90 min after removal of methionine


title: C8m normal whole venous blood sample

description: normal whole venous blood sample


title: C3m normal whole venous blood sample

description: normal whole venous blood sample


title: C5m normal whole venous blood sample

description: normal whole venous blood sample


title: WT 0

description: WT 0 min after removal of methionine

value: WT 0 min after removal of methionine


title: H 45

description: H 45 min after removal of methionine

value: H 45 min after removal of methionine


title: WT 90

description: WT 90 min after removal of methionine

value: WT 90 min after removal of methionine


title: C7m normal whole venous blood sample

description: normal whole venous blood sample


title: Differentiated, 7 days, biological replicate 1

status: Public on Nov 29 2017

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

description: Gene expression data from proliferative cells from the peripheral retina, cultured and differentiated for 7 days

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

source_name: Proliferative cells from the peripeheral retina of human eyes

label_protocol: Total RNA (150 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

growth_protocol: Proliferative cells isolated from the adult human peripheral retina

extract_protocol: Total RNA from 6 samples was extracted using TRIzol Reagent according to the manufacturer’s instructions (Life Technologies).

treatment_protocol: The most peripheral part of the retina, which is attached to the vitreous base, was separated from the CE and isolated, rinsed in Leibowitz-15 medium, incubated with 0.25% Trypsin-EDTA 5+5 min, passed through a 70 μm strainer and plated in DMEM/F12 containing 1M/0.8%Hepes buffer, 2% B27 supplement w/o vitamin A, 20ng/ml EGF, 10ng/ml bFGF, 2.5ug/ml Heparin,1% FBS,100U/ml P/S in culture flasks at 37°C in 5% CO2. Cultures were supplemented with bFGF and EGF twice a week and passaged using 0.25% Trypsin-EDTA. Differentiation was induced for 7 days on P2/P3 cells plated at a density of 1000 – 40 000 cells/cm2 on Matrigel Basement Membrane Matrix (50 μl/cm2) in medium consisting of DMEM/F12, 1% N2 supplement, 10uM DAPT, 100U/ml P/S. After 3 days, the medium was changed to DMEM/F12 containing 2% B27 with vitamin A,1% N2 supplement,100U/ml P/S, 3% FBS, 10ng/ml bFGF,  2.5ug/ml Heparin, 3nM Sonic hedgehog, 100uM Taurine. The medium was changed every second day and the cells were harvested from the matrigel using 2 U/ml Dispase II in Mg2+ and Ca2+-free HBSS at 37°C for 2 hrs.

tag: time

value: 7 days


title: C2m normal whole venous blood sample

description: normal whole venous blood sample


title: C4m normal whole venous blood sample

description: normal whole venous blood sample


title: Undifferentiated, biological replicate 2

description: Gene expression data from proliferative cells from the peripheral retina, cultured and undifferentiated

value: Proliferative cells from the peripeheral retina of human eyes

value: 0 days


title: H 150

description: H 150 min after removal of methionine

value: H 150 min after removal of methionine


title: Undifferentiated, biological replicate 3


title: Differentiated, 7 days, biological replicate 3


title: Differentiated, 7 days, biological replicate 2


title: Female liver specific Bcl-6 deficient mouse_rep4

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

description: Gene expression in female knock out mouse liver

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome Microarray v2 8×60k following manufacture's protocol.

scan_protocol: Arrays were scanned using Agilent G2565A Microarray Scanner System.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent Technology) using default parameters.
The raw signal intensities were log2 transformed and normalized by 75 percent tile shift using Gene spring GX software (Agilent Technology).

label_protocol: Cy3 labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. cRNA was quantified with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissues with Trizol reagents following manufacture's protocol. Extracted RNA quality was checked by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole liver

value: 10 to 11 weeks

value: knock out


title: Male liver specific Bcl-6 deficient mouse_rep4

description: Gene expression in male knock out mouse liver

value: Male


title: HUVEC 1h sMCD40L (50ng/ml)

city: Vienn

first: Rainer

last: de Martin

state: Vienna

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University of Vienna

description: Gene expression data from HUVEC stimualted for 1h with sMCD40L (50ng/ml)

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: CEL files were processed using Affymetrix Expression Console Version 1.1 software and the RMA normalization algorithm.

label: biotin (Affymetrix 3` IVT Express Kit)

source_name: HUVEC passage 4

label_protocol: 150ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: HUVEC were maintained in M199 medium (Lonza) supplemented with 20% FCS (Sigma), 2 mM  L-glutamine (Sigma), penicillin (100 units/ml), streptomycin (100 ug/ml), 5 units/ml heparin, and 25   ug/ml ECGS (Promocell),

extract_protocol: Total RNA was isolated using the Qiagen RNA Plus Universal mini Kit. Total RNA concentration was measured using the NanoDrop 2000C spectrophotometer. Samples were then pooled (700ng/replicate). and processed for analysis using the Affymetrix PrimeView Human Gene Expression Arrays according to the manufacturer's instructions

treatment_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) in passage 4 were seeded in 6 well plates, 80.000 cells/cm2. After reaching post-confluency, the cells were stimulated with  w/ 50ng/ml sMCD40L (Enzo Life Sciences) or 10ng/ml TNF (R&D) for 0, 0.5, 1, 2.5, and 6 hours. The experiment was done in triplicates and then pooled.

value: Primary human venous endothelial cells


title: HUVEC 6h sMCD40L (50ng/ml)

description: Gene expression data from HUVEC stimulated for 6h with sMCD40L (50ng/ml)


title: Undifferentiated, biological replicate 1


title: Female wild type mouse_rep4

description: Gene expression in female wild type mouse liver

source_name: Female wild type mouse

value: Female

value: wild type


title: PA224 CD103+ rep2

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Hybridization was performed according to the manufacturer's instruction (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were normalised using the RMA method in R and batch-normalized using the ComBat algorithm through GenePattern

label: Alexa Flour 488, APC, Brilliant Violet 421

source_name: PA224-233/Db CD103+ lung tissue resident CD8 T cells

label_protocol: RNA quality was tested in an Agilent 2100 bioanalyzer using RNA6000 pico kit (Agilent, Santa Clara). RNA samples passing quality control were used for probe synthesis via Affymetrix wt plus kit (Affymetrix, Santa Clara) or NuGen Ovation Pico WTA (NuGen, San Carlos)

growth_protocol: Tissue resident CD8 T cells obtained and used in this protocol were induced by influenza virus infection in mice lung.

extract_protocol: Total RNA was extracted from sorted CD8 T cells using RNeasy micro kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Lung tissue resident CD8 T cells from 9 female B6 mice were sorted and pooled. Previously, influenza A/PR8/8/34 (H1N1)-infected mice were re-challenged with influenza A/HK/X31 (H3N2) virus 35 days after primary infection. Five days post re-challenge, lungs were harvested after in vivo CD8alpha staining was performed. After cell suspension from the collagen-digested lungs was prepared, non-CD8 T cells were removed using mouse CD8+ T Cell Isolation Kit (Miltenyi Biotec, Inc.). The untouched CD8 T cell-enriched fraction was stained with H-2Db Influenza NP366-374 Tetramer, H-2Db Influenza PA224-233 Tetramer, followed by additional staining with anti-CD8beta and anti-CD103 Abs. Then 4-way sorting was performed using a FACsAria IIu (BD Biosciences) to obtain NP366-374/Db CD103+, NP366-374/Db CD103-, PA224-233/Db CD103+ and PA224-233/Db CD103- CD8 T cells. All sorted lung tissue resident CD8 T cells were from CD8alpha- CD8beta+ population in flow cytometry, hence negative for in vivo-CD8 staining but positive in in vitro-CD8 staining.

value: lymphocyte; CD8 T cell

value: 11-15 weeks of age


title: HUVEC 6h TNF (10ng/ml)

description: Gene expression data from HUVEC stimulated for 6h with TNF (10ng/ml)


title: HUVEC 1h TNF (10ng/ml)

description: Gene expression data from HUVEC stimulated for 1h with TNF (10ng/ml)


title: Patient Healthy smoker

city: Kunming

first: Chuntao

last: Li

address: 295, xichang Road, Wuhua district

country: China

institute: The Affiliated First Hospital of Kunming Medical University

description:
2 Male，1 female
lncRNA and mRNA
A total of 3,359 lncRNAs revealed by microarray analysis have been differentially expressed between the two groups, 1,995 lncRNAs identified to be up-regulated in COPD, whereas 1,364 lncRNAs have been down-regulated. Meanwhile，a total of 3,283 mRNAs have been differentially expressed, 2,589 mRNAs identified to be up-regulated in COPD, whereas 694 mRNAs were down-regulated.

hyb_protocol: The labeled cRNAs have been purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) have been measured by NanoDrop ND-1000. 1μg of each labeled cRNA has been fragmented by adding 5μl 10×Blocking Agent and 1μl of 25×Fragmentation Buffer, then heated the mixture at 60℃ for 30 min, finally 25μl 2×GE Hybridization buffer has been added to dilute the labeled cRNA. 50μl of hybridization solution has been dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides have been incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays have been 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) is used to analyze acquired array images. Quantile normalization and subsequent data processing are performed using the GeneSpring GX v12.1 software package (Agilent Technologies).
Differentially expressed of lncRNA and mRNA are defined as at least±2 Fold change between two groups.

source_name: healthy smoker blood sample

label_protocol: Sample labeling and array hybridization have been performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA is purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample has been amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA has been extracted by Trizol(Takara,Invitrogen). RNA quantity and quality have been measured by NanoDrop ND-1000. RNA integrity has been assessed by standard denaturing agarose gel electrophoresis. We use Arraystar Human LncRNA Microarray V3.0 (KangChen, Shanghai ,China) to analysis the lncRNAs and mRNAs. Arraystar Human LncRNA Microarray V3.0 is designed for the global profiling of human lncRNAs and protein-coding transcripts. About 30,586 lncRNAs and 26,109 coding transcripts can be detected by our lncRNA microarray.

value: blood

tag: mean age

value: 65 years

value: mixed


title: PA224 CD103- rep2

label: Alexa Flour 488, APC

source_name: PA224-233/Db CD103- lung tissue resident CD8 T cells


title: Male wild type mouse_rep4

description: Gene expression in male wild type mouse liver

source_name: Male wild type mouse


title: Female wild type mouse_rep3


title: HUVEC 2.5h sMCD40L (50ng/ml)

description: Gene expression data from HUVEC stimulated for 2.5h with sMCD40L (50ng/ml)


title: Patient COPD

source_name: COPD blood sample

value: 71 years


title: NP336 CD103- rep2

label: Alexa Flour 488, PE

source_name: NP366-374/Db CD103- lung tissue resident CD8 T cells


title: NP336 CD103+ rep2

label: Alexa Flour 488, PE, Brilliant Violet 421

source_name: NP366-374/Db CD103+ lung tissue resident CD8 T cells


title: NP336 CD103+ rep1


title: HUVEC 0.5h TNF (10ng/ml)

description: Gene expression data from HUVEC stimulated for 0.5h with TNF (10ng/ml)


title: NP336 CD103- rep1


title: HUVEC 0h

description: Gene expression data from HUVEC left untreated


title: PA224 CD103- rep1


title: PA224 CD103+ rep1


title: HUVEC 2.5h TNF (10ng/ml)

description: Gene expression data from HUVEC stimulated for 2.5h with TNF (10ng/ml)


title: HUVEC 0.5h sMCD40L (50ng/ml)

description: Gene expression data from HUVEC stimulated for 0.5h with sMCD40L (50ng/ml)


title: Male wild type mouse_rep3


title: Male liver specific Bcl-6 deficient mouse_rep3


title: case_114_CRC_Tumor

status: Public on Nov 28 2017

city: L'Hospitalet de Llobregat

first: Estela

last: Damaso

state: Barcelona

address: Av.Gran Via de l'Hospitalet, 199-203

department: Hereditary Cancer Program

country: Spain

institute: Catalan Institute of Oncology (ICO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: HiScan platform (Illumina)

data_processing: GenomeStudio software (Methylation Module)

source_name: Somatic MLH1-hypermethylated control. Genomic DNA from FFPE colorectal cancer

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from FFPE samples was extracted using QIAmp DNA FFPE Tissue Kit (Qiagen) and Deparaffinization Solution (Qiagen) according to the manufacturer's instructions


title: Myxothiazol_12h_1rep

city: Dresden

first: Natalia

last: Pashkovskaia

address: Zellescher Weg 20B

institute: Technische Universität Dresden

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >14.0 pmol Cy3/ug cRNA) was fragmented and hybridized using Gene Expression Hybridization Kit following the manufacturer's recommendations 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); wash buffers contained 0.005% Triton X-102

scan_protocol: Slides were scanned immediately after washing on the Agilent microarray confocal laser scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61 x 21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: P19 cells exposure to 5nM myxothiazol for 12 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in high glucose DMEM medium (with sodium pyruvate with GlutaMAX, with Phenol Red) supplemented with 10% FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared from 5*10^6 cells using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with 5 nM myxothiazol for 12 h

tag: cell line

value: murine pluripotent stem cells

tag: treated with

value: 5 nM myxothiazol for 12 h


title: case_112_CRC_Tumor

source_name: Constitutional MLH1 epimutation carrier. Genomic DNA from FFPE colorectal cancer


title: case_116_Normal_Colon_Mucosa

source_name: Somatic MLH1-hypermethylated control. Genomic DNA from FFPE normal colorectal mucosa


title: case_117_CRC_Tumor

value: Somatic MLH1-hypermethylated control. Genomic DNA from FFPE colorectal cancer


title: case_116_CRC_Tumor


title: case_115_Normal_Colon_Mucosa

value: Somatic MLH1-hypermethylated control. Genomic DNA from FFPE normal colorectal mucosa


title: case_112_Normal_Colon_Mucosa

source_name: Constitutional MLH1 epimutation carrier. Genomic DNA from FFPE normal colorectal mucosa


title: Female liver specific Bcl-6 deficient mouse_rep3

value: whole liver


title: Lckpr-TCL1A+/- T-cells; chronic phase 2

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

description: Lckpr-TCL1A+/- T-cells; ‘chronic phase’

hyb_protocol: Sample preparation: Murine spleens removed post-mortem were mashed through a 100μm cell strainer (BD Biosciences) and lymphoid cells were isolated using density gradient centrifugation. Cells were subsequently enriched for CD8+ lymphocytes using MACS beads (130-049-401,Miltenyi Biotec). RNA was isolated from murine tissues using the mirVana kit (Invitrogen). We hybridized 3 control RNA samples (pooled from CD3+ T-cells enriched from 9 spleens of age- and background-matched wt animals) as well as RNA isolated from CD8+-enriched splenic T-cells of 3 “chronic phase” and of 5 “exponential phase” Lckpr-hTCL1A+/- mouse lymphoma samples on Affymetrix Mouse Gene 1.0 ST Arrays. Definition of stages: “chronic” - 30-70% tumor cells in PB and spleen, average age 12 months; “exponential” - mean PB lymphocyte doubling time (LDT) 12 days (SEM 0.8), >80% tumor cells in PB, >90% in spleen, average animal age 15 months.

scan_protocol: Affymetrix protocol

data_processing: Bioinformatics: Arrays were pre-processed, background-corrected (RMA), quantile-normalized, and separately analyzed (chronic phase vs. ctrl., exponential phase vs. ctrl.) with the „affy“ R-package. Annotation of mouse probe sets and human orthologues was carried out with biomaRt. We did not only overlap Ensembl IDs, but converted MGI gene names and overlapped them with official gene symbols as well.

source_name: TCL1A-induced murine T-cell leukemia (enriched splenic CD8+ T-cells)

label_protocol: Affymetrix protocol

extract_protocol: Lckpr-TCL1A+/- T-cells and those of age-matched C57BL/6 (wild-type) mice were enriched from splenic lymphocytes by MACS® protocols. Stages: ‘chronic phase’ (30-70% tumor cells in PB and spleen, average age 12 months, n=3) and ‘exponential phase’ (mean PB lymphocyte doubling time (LDT) 12 days (SEM 0.8); >80% tumor cells in PB, >90% in spleen, average age 15 months, n=5). Examples for cell populations submitted to GEP (Figs.1c, Supplementary Fig.2g) and used in immunoblots (Supplementary Fig.6e).

value: enriched splenic CD8+ T-cells

tag: Stage

value: early

tag: genotype/strain


title: Lckpr-TCL1A+/- T-cells; chronic phase 3

description: Lckpr-TCL1A+/- T-cells; ‘chronic phase’


title: Lckpr-TCL1A+/- T-cells; exponential phase 4

description: Lckpr-TCL1A+/- T-cells; ‘exponential phase’

value: late


title: Control_rep4

source_name: P19 cells

value: none (untreated control)


title: age-matched C57BL/6 (wild-type) mice 2

description: age-matched C57BL/6 (wild-type) mice

source_name: Purified splenic CD3+ pan-T-cells

value: Purified splenic CD3+ pan-T-cells

value: normal

value: C57BL/6 (wild-type)


title: Lckpr-TCL1A+/- T-cells; exponential phase 5


title: age-matched C57BL/6 (wild-type) mice 3

description: age-matched C57BL/6 (wild-type) mice


title: Lckpr-TCL1A+/- T-cells; exponential phase 1


title: Lckpr-TCL1A+/- T-cells; exponential phase 3


title: Lckpr-TCL1A+/- T-cells; exponential phase 2


title: case_115_CRC_Tumor

tag: tissue

value: Female


title: Myxothiazol_12h_3rep


title: case_109_Normal_Colon_Mucosa

value: Constitutional MLH1 epimutation carrier. Genomic DNA from FFPE normal colorectal mucosa


title: Control_rep3


title: Lckpr-TCL1A+/- T-cells; chronic phase 1

description: Lckpr-TCL1A+/- T-cells; ‘chronic phase’


title: age-matched C57BL/6 (wild-type) mice 1

description: age-matched C57BL/6 (wild-type) mice


title: case_108_CRC_Tumor

value: Constitutional MLH1 epimutation carrier. Genomic DNA from FFPE colorectal cancer


title: Myxothiazol_12h_2rep


title: case_114_Normal_Colon_Mucosa


title: Control_rep1


title: case_105_Normal_Colon_Mucosa

value: Male


title: case_104_CRC_Tumor


title: case_103_CRC_Tumor


title: case_101_Normal_Colon_Mucosa

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE normal colorectal mucosa


title: case_105_CRC_Tumor


title: case_106_CRC_Tumor


title: case_103_Normal_Colon_Mucosa


title: case_81_Normal_Colon_Mucosa

value: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE normal colorectal mucosa


title: case_77_Normal_Colon_Mucosa


title: case_83_CRC_Tumor

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE colorectal cancer


title: case_84_CRC_Tumor

value: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE colorectal cancer


title: case_84_Normal_Colon_Mucosa


title: case_92_CRC_Tumor


title: case_83_Normal_Colon_Mucosa


title: case_77_CRC_Tumor


title: case_85_Normal_Colon_Mucosa


title: case_80_CRC_Tumor


title: case_85_CRC_Tumor


title: case_80_Normal_Colon_Mucosa


title: case_89_CRC_Tumor


title: case_78_Normal_Colon_Mucosa


title: case_78_CRC_Tumor


title: case_81_CRC_Tumor


title: case_68_CRC_Tumor


title: case_69_CRC_Tumor


title: case_71_Normal_Colon_Mucosa


title: case_71_CRC_Tumor


title: case_64_CRC_Tumor


title: case_64_Normal_Colon_Mucosa


title: case_67_CRC_Tumor


title: case_62_CRC_Tumor_2

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE colorectal cancer. Tumor #2


title: 9998712071_B; T-PLL

description:
NA
9998712071_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Bioinformatics: We used the Illumina proprietary software GenomeStudio v1 to background-correct and to initially annotate the probes of the HumanHT-12 v4 Expression BeadChip. We filtered samples and genes by detection p-values and fluorescence intensities for at least 2/3 hits (p<0.05) to reduce false calls. Batch-effects were corrected by the ComBat method which uses an empiric Bayesian model framework. For literature references to bioinformatics methods and algorithms see Supplementary Table2). Since the official Illumina HumanHT-12 v4 Expression BeadChip annotation is outdated, we used the data mining tool biomaRt, version 75 of the Ensembl data base with R, version 3.1.0, and Bioconductor, version 2.10.
T-PLLs (n=70) and normal controls (CD3+ T-cells from 10 healthy donors) were grouped and tested separately for differential expression using the Student’s t-test on log-transformed fluorescence values (normally distributed). Fold-changes (fc) were calculated on the fluorescence values without logarithmic transformation. False discovery rates (FDRs) were calculated using the R package “qvalue”. Hierarchical clustering was carried out using the R package gplots, version 2.15.0 (distance function: euclidean; clustering: complete linkage).

molecule: polyA RNA

label_protocol: Standard Illumina protocol

extract_protocol: GEP of human T-PLL cells. Sample preparation: PBMCs isolated from T-PLL patients (>95% purity of T-cells) and CD3+ T-cells isolated from PB of healthy donors (see paragraph 2 for detailed descriptions on cell purification) were submitted to RNA isolation using the mirVana kit (Invitrogen). GEP analyses were conducted using Illumina HumanHT‑12 v4 BeadChip arrays according to manufacturer’s instructions.

value: T-PLL

tag: sampleID

tag: caseid

value: POS

value: AWD

tag: pfs


title: 9270006131_L; T-PLL

description:
NA
9270006131_L

source_name: PATIENT_ID: P1354_

value: alive in ongoing CR or PR


title: 9998712071_F; T-PLL

description:
NA
9998712071_F

source_name: PATIENT_ID: P1376_


title: 9270006131_J; T-PLL

description:
NA
9270006131_J

value: DOD


title: 9998712071_J; T-PLL

description:
NA
9998712071_J

value: NEG


title: case_62_CRC_Tumor_1

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from FFPE colorectal cancer. Tumor #1


title: 9998712071_A; T-PLL

description:
early
9998712071_A


title: Control_rep2

value: murine pluripotent stem cells


title: case_60_CRC_Tumor


title: case_57_CRC_Tumor


title: 9998712071_C; T-PLL

description:
NA
9998712071_C

source_name: PATIENT_ID: P1367_


title: case_57_Normal_Colon_Mucosa


title: case_56_Normal_Colon_Mucosa


title: case_49_CRC_Tumor


title: case_49_Normal_Colon_Mucosa


title: 9998712071_I; T-PLL

description:
NA
9998712071_I

source_name: PATIENT_ID: P1379_


title: case_50_CRC_Tumor


title: 9998712071_H; T-PLL

description:
late
9998712071_H


title: 9998712071_E; T-PLL

description:
FU
9998712071_E


title: 9998712071_L; T-PLL

description:
late
9998712071_L


title: case_116_Blood

source_name: Somatic MLH1-hypermethylated control. Genomic DNA from blood

extract_protocol: Genomic DNA was extracted and purified from blood samples using Wizard Genomic DNA Purification Kit  (Promega) according to standard instructions.


title: 9270006131_B; T-PLL

description:
replicate
9270006131_B

source_name: PATIENT_ID: P1375_


title: 9998712071_K; T-PLL

description:
NA
9998712071_K


title: 9270006131_K; T-PLL

description:
NA
9270006131_K

value: death; relapse or progression; primary treatment failure


title: 9998712071_G; T-PLL

description:
NA
9998712071_G

source_name: PATIENT_ID: P1377_


title: 9270006131_F; T-PLL

description:
NA
9270006131_F

source_name: PATIENT_ID: P1349_


title: 9998712071_D; T-PLL

description:
early
9998712071_D


title: 9270006130_J; T-PLL

description:
early
9270006130_J


title: 9270006131_H; Sezary_Syndrome

description:
NA
9270006131_H

source_name: PATIENT_ID: P1357_


title: case_115_Blood

value: Somatic MLH1-hypermethylated control. Genomic DNA from blood


title: 9270006130_I; T-PLL

description:
NA
9270006130_I


title: 9270006131_A; T-PLL

description:
NA
9270006131_A


title: 9270006131_C; T-PLL

description:
NA
9270006131_C

source_name: PATIENT_ID: P1381_


title: 9270006131_D; T-PLL

description:
replicate
9270006131_D


title: 9270006130_G; T-PLL

description:
NA
9270006130_G


title: 9270006131_I; T-PLL

description:
NA
9270006131_I

source_name: PATIENT_ID: P1358_


title: 9270006130_K; T-PLL

description:
late
9270006130_K


title: 9270006130_L; T-ALL

description:
NA
9270006130_L

value: T-ALL


title: 9270006131_E; T-PLL

description:
NA
9270006131_E


title: 9270006130_E; Central_memory_T-cells

description:
NA
9270006130_E

source_name: PATIENT_ID: CM_99_NW


title: 9270006131_G; T-PLL

description:
NA
9270006131_G


title: 9270006130_F; T-PLL

description:
NA
9270006130_F


title: 9270006130_H; T-PLL

description:
NA
9270006130_H


title: case_60_Normal_Colon_Mucosa


title: case_111_Blood

source_name: Constitutional MLH1 epimutation carrier. Genomic DNA from blood


title: 9270006130_D; Central_memory_T-cells

description:
NA
9270006130_D

source_name: PATIENT_ID: CM_17_NW


title: case_112_Blood

value: Constitutional MLH1 epimutation carrier. Genomic DNA from blood


title: case_114_Blood

value: Female


title: case_104_Blood


title: case_113_Blood


title: case_102_Blood

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from blood


title: case_101_Blood

value: Mutation-positive Lynch syndrome control. Genomic DNA from blood


title: case_106_Blood


title: case_108_Blood


title: case_110_Blood


title: case_109_Blood


title: case_107_Blood


title: 9270006124_G; pooled_CD3pos_T-cells

description:
NA
9270006124_G

source_name: PATIENT_ID: pan-T_41_NW


title: case_103_Blood


title: case_105_Blood


title: 9270006130_A; Central_memory_T-cells

description:
NA
9270006130_A

source_name: PATIENT_ID: CM_37_NW


title: 9270006124_K; memory_T-cell_pool

description:
NA
9270006124_K

source_name: PATIENT_ID: memory_37_NW


title: 9270006124_H; pooled_CD3pos_T-cells

description:
NA
9270006124_H

source_name: PATIENT_ID: pan-T_15_NW


title: mice retina under 7378K, biological rep2

city: Hangzhou

first: Chen

last: Xie

state: Zhejiang

address: 79 Qingchun Road

department: Department of Ophthalmology

institute: First Affiliated Hospital, College of Medicine, Zhejiang University

description: Gene expression data from mice retina under 7378K LED light environment

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

source_name: mice retina under 7378K LED white light environment for 14 days

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: 10-week-old female mice were raised under different light condition (dark, 2954K LED light and 7378K LED light) at a suitable temperature with food and water for 14 days (light cycle of 12 hours-on / 12 hours-off)

extract_protocol: Mice retinal neurosensory layer was seperated from the retinal pigment epithelial layer. Total RNA was extracted and purified using mirVanaTM PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Different LED lights were installed at the top with illuminance of 1000 lx

value: retinal neurosensory layer

tag: genotype

value: yellow white and soft tissue

tag: age


title: 9270006124_C; T-PLL

description:
NA
9270006124_C

source_name: PATIENT_ID: P1336_


title: 9270006124_J; memory_T-cell_pool

description:
NA
9270006124_J

source_name: PATIENT_ID: memory_34_NW


title: case_97_Blood


title: 9270006130_C; Central_memory_T-cells

description:
NA
9270006130_C

source_name: PATIENT_ID: CM_20_NW


title: 9270006124_B; Sezary_Syndrome

description:
NA
9270006124_B


title: case_100_Blood

value: Male


title: 9270006124_E; T-PLL

description:
NA
9270006124_E


title: case_96_Blood


title: 9270006130_B; Central_memory_T-cells

description:
NA
9270006130_B

source_name: PATIENT_ID: CM_19_NW


title: 9270006122_L; T-PLL

description:
NA
9270006122_L


title: 9270006124_A; T-PLL

description:
NA
9270006124_A

source_name: PATIENT_ID: P1331_


title: 9270006122_K; T-PLL

description:
NA
9270006122_K


title: 9270006124_I; memory_T-cell_pool

description:
NA
9270006124_I

source_name: PATIENT_ID: memory_31_NW


title: 9270006124_L; memory_T-cell_pool

description:
NA
9270006124_L

source_name: PATIENT_ID: memory_19_NW


title: mice retina under 2954K, biological rep2

description: Gene expression data from mice retina under 2954K LED light environment

source_name: mice retina under 2954K LED white light environment for 14 days


title: mice retina under 7378K, biological rep1


title: mice retina under 7378K, biological rep3


title: case_95_Blood


title: case_94_Blood


title: case_92_Blood


title: case_98_Blood


title: 9270006122_J; T-PLL

description:
NA
9270006122_J


title: mice retina under 2954K, biological rep1


title: case_91_Blood


title: case_89_Blood


title: mice retina of  negative control, biological rep3

description: Gene expression data from mice retina under negative control dark environment

source_name: mice retina in normal dark environment for 14 days


title: case_93_Blood


title: case_86_Blood


title: mice retina of  negative control, biological rep1


title: 9270006122_F; Central_memory_T-cells

description:
NA
9270006122_F

source_name: PATIENT_ID: CM_34_NW


title: 9270006124_D; T-PLL

description:
NA
9270006124_D

source_name: PATIENT_ID: P1339_


title: 9270006124_F; T-PLL

description:
replicate
9270006124_F


title: 9270006122_I; T-PLL

description:
NA
9270006122_I


title: case_90_Blood

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from blood


title: case_87_Blood


title: case_82_Blood


title: case_88_Blood


title: 9270006122_A; Naive_T-cells

description:
NA
9270006122_A

source_name: PATIENT_ID: naive_19_NW


title: case_79_Blood


title: 9270006122_B; Naive_T-cells

description:
NA
9270006122_B

source_name: PATIENT_ID: naive_41_NW


title: mice retina of  negative control, biological rep2


title: 9270006122_E; Central_memory_T-cells

description:
NA
9270006122_E

source_name: PATIENT_ID: CM_15_NW


title: 9270006118_L; pooled_CD3pos_T-cells

description:
NA
9270006118_L

source_name: PATIENT_ID: pan-T_39_NW


title: 9270006118_K; pooled_CD3pos_T-cells

description:
NA
9270006118_K

source_name: PATIENT_ID: pan-T_19_NW


title: 9270006122_C; Naive_T-cells

description:
NA
9270006122_C

source_name: PATIENT_ID: naive_32_AS


title: 9270006118_H; pooled_CD3pos_T-cells

description:
NA
9270006118_H

source_name: PATIENT_ID: pan-T_31_NW


title: case_76_Blood


title: case_80_Blood


title: case_83_Blood


title: case_78_Blood


title: case_73_Blood


title: case_77_Blood


title: 9270006118_J; pooled_CD3pos_T-cells

description:
NA
9270006118_J

source_name: PATIENT_ID: pan-T_37_NW


title: case_81_Blood


title: case_84_Blood


title: 9270006118_C; T-PLL

description:
NA
9270006118_C


title: case_75_Blood


title: 9270006118_G; pooled_CD3pos_T-cells

description:
NA
9270006118_G

source_name: PATIENT_ID: 5850_pan-T_2nd


title: 9270006118_I; pooled_CD3pos_T-cells

description:
NA
9270006118_I

source_name: PATIENT_ID: pan-T_34_NW


title: case_74_Blood


title: 9270006118_E; T-PLL

description:
NA
9270006118_E

source_name: PATIENT_ID: P1329_


title: 9270006118_A; T-PLL

description:
replicate
9270006118_A


title: 9270006104_K; T-PLL

description:
NA
9270006104_K

value: DIM


title: 9270006104_L; T-PLL

description:
NA
9270006104_L

value: T-PLL


title: 9270006118_F; T-PLL

description:
NA
9270006118_F

source_name: PATIENT_ID: P1330_

value: POS


title: 9270006104_H; T-PLL

description:
NA
9270006104_H


title: 9270006104_G; T-PLL

description:
NA
9270006104_G


title: 9270006104_J; T-PLL

description:
NA
9270006104_J

value: AWD


title: case_71_Blood


title: 9270006104_F; Naive_T-cells

description:
NA
9270006104_F

source_name: PATIENT_ID: naive_37_NW


title: mice retina under 2954K, biological rep3

source_name: mice retina under 2954K LED white light environment for 14 days


title: case_70_Blood


title: case_69_Blood


title: case_63_Blood


title: 9270006104_I; T-PLL

description:
NA
9270006104_I

value: alive in ongoing CR or PR


title: case_67_Blood


title: case_65_Blood


title: case_66_Blood


title: case_64_Blood


title: case_72_Blood


title: case_62_Blood


title: case_68_Blood


title: 9270006104_D; Naive_T-cells

description:
NA
9270006104_D

source_name: PATIENT_ID: naive_31_NW


title: 9270006104_B; memory_T-cell_pool

description:
NA
9270006104_B

source_name: PATIENT_ID: memory_41_NW


title: 9270006104_E; Naive_T-cells

description:
NA
9270006104_E

source_name: PATIENT_ID: naive_34_NW


title: 9270006104_C; memory_T-cell_pool

description:
NA
9270006104_C

source_name: PATIENT_ID: memory_32_AS


title: 9250945085_K; T-PLL

description:
clone
9250945085_K

value: DOD


title: 9250945085_I; T-PLL

description:
NA
9250945085_I


title: 9270006104_A; memory_T-cell_pool

description:
NA
9270006104_A

source_name: PATIENT_ID: memory_39_NW


title: 9250945085_J; T-PLL

description:
NA
9250945085_J


title: case_56_Blood

source_name: Mutation-positive Lynch syndrome control. Genomic DNA from blood


title: case_60_Blood


title: 9270006122_G; T-PLL

description:
NA
9270006122_G


title: 9250945085_H; T-PLL

description:
NA
9250945085_H

source_name: PATIENT_ID: P1348_

value: NEG


title: case_54_Blood


title: case_61_Blood


title: 9250945085_E; T-PLL

description:
NA
9250945085_E


title: 9250945085_D; T-PLL

description:
NA
9250945085_D


title: case_58_Blood


title: case_57_Blood


title: 9250945085_F; T-PLL

description:
NA
9250945085_F


title: 9250945085_C; T-PLL

description:
NA
9250945085_C


title: 9250945085_B; T-PLL

description:
NA
9250945085_B

source_name: PATIENT_ID: P1264_


title: case_55_Blood


title: case_52_Blood


title: case_50_Blood


title: case_59_Blood


title: 9270006118_B; T-PLL

description:
NA
9270006118_B


title: case_49_Blood


title: case_48_Blood


title: case_99_Blood


title: case_85_Blood


title: case_44_Blood


title: case_43_Blood


title: 5786065151_H; Cardiac effusion

description:
NA
5786065151_H

source_name: PATIENT_ID: P1173_

value: Cardiac effusion


title: 9250945085_G; T-PLL

description:
NA
9250945085_G

value: death; relapse or progression; primary treatment failure


title: Case_39_Blood

source_name: Healthy control. Genomic DNA from blood

value: Healthy control. Genomic DNA from blood


title: case_53_Blood


title: 5786065151_J; T-PLL

description:
late
5786065151_J


title: 5786065151_K; memory_stimulated_T-cells

description:
NA
5786065151_K

source_name: PATIENT_ID: 5856mem-stin


title: case_47_Blood


title: 9250945085_L; T-PLL

description:
clone
9250945085_L


title: 9270006122_D; Naive_T-cells

description:
NA
9270006122_D

source_name: PATIENT_ID: naive_19_AS


title: case_46_Blood


title: 5786065151_D; memory_experienced_T-cells

description:
NA
5786065151_D

source_name: PATIENT_ID: 5852mem-exp


title: 5753714093_L; TH1

description:
NA
5753714093_L

source_name: PATIENT_ID: 5856TH1


title: 5753714093_H; TH1

description:
NA
5753714093_H

source_name: PATIENT_ID: 5850TH1


title: Case_40_Blood


title: 5786065151_L; T-PLL

description:
NA
5786065151_L

source_name: PATIENT_ID: P1231_


title: 9250945085_A; T-PLL

description:
NA
9250945085_A

source_name: PATIENT_ID: P1080_


title: case_42_Blood


title: case_45_Blood


title: Case_35_Blood


title: Case_41_Blood


title: 5786065151_B; memory_experienced_T-cells

description:
NA
5786065151_B

source_name: PATIENT_ID: 5850mem-exp


title: 5786065151_F; memory_experienced_T-cells

description:
NA
5786065151_F

source_name: PATIENT_ID: 5856mem-exp


title: Case_38_Blood


title: Case_36_Blood


title: case_51_Blood


title: Case_34_Blood


title: Case_37_Blood


title: Case_31_Blood


title: 5753714093_D; Central_memory_T-cells

description:
NA
5753714093_D

source_name: PATIENT_ID: 1134CM


title: 5786065151_C; TH2

description:
NA
5786065151_C

source_name: PATIENT_ID: 5852TH2


title: Case_32_Blood


title: 5786065151_E; TH2

description:
NA
5786065151_E

source_name: PATIENT_ID: 5856TH2


title: 5786065151_I; memory_stimulated_T-cells

description:
NA
5786065151_I

source_name: PATIENT_ID: 5852mem-stin


title: 5786065151_A; TH2

description:
NA
5786065151_A

source_name: PATIENT_ID: 5850TH2


title: Trastuzumab3

city: Silver Spring

first: Wen Jin

last: Wu

state: Maryland

address: 10903 New Hemisphere Ave

department: OBP/OPQ/CDER

institute: FDA

description: Trastuzumab treatment

hyb_protocol: Standard Affymetrix Protocol. Microarray experiment and analysis were performed at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK, Bethesda, MD) Genomic core facility.

label: fluorescent dye

source_name: primary human cardiomyocytes

growth_protocol: Normal growth medium for human cardiomyocytes

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

treatment_protocol: Human cardiomyocytes were treated with trastuzumab (50 µg/ml), trastuzumab (50 µg/ml) plus pertuzumab (50 µg/ml) or T-DM1 (10 µg/ml) for 24h.

value: heart


title: 5753714093_G; memory_T-cell_pool

description:
NA
5753714093_G

source_name: PATIENT_ID: 5850mem


title: 5753714093_I; memory_T-cell_pool

description:
NA
5753714093_I

source_name: PATIENT_ID: 5852mem


title: Case_30_Blood

source_name: Healthy control. Genomic DNA from blood


title: 5753714093_F; Central_memory_T-cells

description:
NA
5753714093_F

source_name: PATIENT_ID: 5856CM


title: Trastuzumab2

description: Trastuzumab treatment

scan_protocol: Standard Affymetrix Protocol. Microarray experiment and analysis were performed at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK, Bethesda, MD) Genomic core facility.


title: 5753714093_K; memory_T-cell_pool

description:
NA
5753714093_K

source_name: PATIENT_ID: 5856mem


title: 5753714042_L; pooled_CD3pos_T-cells

description:
NA
5753714042_L

source_name: PATIENT_ID: 5856panT


title: 5753714093_C; Naive_T-cells

description:
NA
5753714093_C

source_name: PATIENT_ID: 5852naive


title: Case_33_Blood


title: Trastuzumab+pertuzumab1

description: Trastuzumab+pertuzumabtreatment

data_processing: Standard Affymetrix Protocol. Microarray experiment and analysis were performed at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK, Bethesda, MD) Genomic core facility.


title: Case_24_Blood


title: 5786065151_G; memory_stimulated_T-cells

description:
NA
5786065151_G

source_name: PATIENT_ID: 5850mem-stin


title: Case_23_Blood


title: Case_29_Blood


title: Case_28_Blood


title: 5753714042_D; T-PLL

description:
NA
5753714042_D

source_name: PATIENT_ID: P1077_


title: 5753714042_G; T-PLL

description:
NA
5753714042_G

source_name: PATIENT_ID: P704_


title: TDM 2

description: TDM1 treatment

label_protocol: Standard Affymetrix Protocol. Microarray experiment and analysis were performed at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK, Bethesda, MD) Genomic core facility.


title: Trastuzumab+pertuzumab2

description: Trastuzumab+pertuzumabtreatment


title: 5753714042_H; T-PLL

description:
early
5753714042_H


title: 5753714093_A; Naive_T-cells

description:
NA
5753714093_A

source_name: PATIENT_ID: 5850naive


title: Case_27_Blood


title: 5753714093_E; Naive_T-cells

description:
NA
5753714093_E

source_name: PATIENT_ID: 5856naive


title: 5753714042_K; T-PLL

description:
NA
5753714042_K


title: Case_20_Blood


title: Case_19_Blood


title: Case_26_Blood


title: 5753714093_B; Central_memory_T-cells

description:
NA
5753714093_B

source_name: PATIENT_ID: 609CM


title: Trastuzumab1

description: Trastuzumab treatment


title: Case_22_Blood


title: 5753714042_I; T-PLL

description:
NA
5753714042_I

source_name: PATIENT_ID: P966_957_


title: TDM 3

description: TDM1 treatment


title: Trastuzumab+pertuzumab3

description: Trastuzumab+pertuzumabtreatment


title: Control 1

description: control, no treatment


title: Case_17_Blood


title: Case_16_Blood


title: 5753714042_A; T-PLL

description:
NA
5753714042_A

source_name: PATIENT_ID: P626_


title: 5753714054_L; T-PLL

description:
NA
5753714054_L

source_name: PATIENT_ID: P598_


title: 5753714042_J; pooled_CD3pos_T-cells

description:
NA
5753714042_J

source_name: PATIENT_ID: 5852panT


title: 5753714042_E; T-PLL

description:
NA
5753714042_E

source_name: PATIENT_ID: P703_


title: TDM 1

description: TDM1 treatment

source_name: primary human cardiomyocytes


title: Case_21_Blood

source_name: Healthy control. Genomic DNA from blood


title: Case_25_Blood


title: Case_18_Blood


title: Control 2

description: control, no treatment


title: 5753714054_J; T-PLL

description:
NA
5753714054_J

source_name: PATIENT_ID: P543_


title: Case_11_Blood


title: Case_15_Blood


title: 5753714054_H; ALCL

description:
NA
5753714054_H

source_name: PATIENT_ID: P528_

value: ALCL


title: 5753714042_B; T-PLL

description:
NA
5753714042_B

source_name: PATIENT_ID: P1023_


title: Case_10_Blood

value: Female


title: Case_14_Blood


title: Control 3

description: control, no treatment


title: Case_12_Blood


title: 5753714042_C; T-PLL

description:
NA
5753714042_C

source_name: PATIENT_ID: P656_


title: Case_13_Blood


title: 5753714054_G; T-PLL

description:
NA
5753714054_G

source_name: PATIENT_ID: P210_


title: Case_4_Blood


title: 5753714054_F; T-PLL

description:
NA
5753714054_F

source_name: PATIENT_ID: P447_438_


title: Case_6_Blood


title: 5753714054_K; HSTL

description:
NA
5753714054_K

value: HSTL


title: Case_8_Blood


title: Case_7_Blood


title: 5753714054_D; CLL

description:
NA
5753714054_D

source_name: PATIENT_ID: P430_

value: CLL


title: Case_5_Blood


title: Case_2_Blood


title: Case_3_Blood


title: 5753714054_E; T-PLL

description:
NA
5753714054_E

source_name: PATIENT_ID: P202_


title: Case_1_Blood


title: The S. flexneri 2a 301 △phoPQ mutant strain at 10 hours rep3

city: shanghai

first: Zhiwei

last: Lin

state: shanghai

address: dongan road 131 , xuhui district, Shanghai

institute: School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University

description: Microarray profile of S. flexneri 2a 301 △phoPQ mutant strain at 10 hours

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Shigella flexneri

source_name: Shigella flexneri 2a 301 △phoPQ mutant strain at 10 hours

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: S. flexneri were grown in Luria–Bertani medium (LB; Oxoid, Basingstoke, UK) at 37°C with shaking for 6 hours or 10 hours.

extract_protocol: total RNAs were extracted using the RNeasyH Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions.

tag: strain

value: deltaphoPQ

tag: time point

value: 10 hours


title: The S. flexneri 2a 301 △phoPQ mutant strain at 10 hours rep1


title: The S. flexneri 2a 301 △phoPQ mutant strain at 10 hours rep2


title: Testis from WT mouse_rep2

city: Shanghai

first: Chunling

last: Shen

address: 197 Ruijin No.2 Road

department: Research Center for Experimental Medicine

institute: Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Gene expression in testis from 6-8 weeks old WT mouse

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

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

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Testis, WT mouse, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: mixed 129Sv/C57BL/6

value: Testis

tag: gender

value: Male

value: 6-8 weeks

tag: genotype/variation

value: WT


title: 5753714054_I; T-PLL

description:
NA
5753714054_I

source_name: PATIENT_ID: P216_295_

tag: cell type

value: T-PLL

value: POS

value: AWD

value: alive in ongoing CR or PR


title: Testis from Prss55KO mouse_rep1

description: Gene expression in testis from 6-8 weeks old Prss55KO mouse

source_name: Testis, Prss55KO mouse, replicate 1


title: Testis from Prss55KO mouse_rep2

source_name: Testis, Prss55KO mouse, replicate 2


title: 5753714054_A; T-PLL

description:
NA
5753714054_A

source_name: PATIENT_ID: P119_

value: DOD

value: death; relapse or progression; primary treatment failure


title: 5753714054_C; Sezary_Syndrome

description:
NA
5753714054_C

source_name: PATIENT_ID: P148_


title: The wildtype S. flexneri 2a 301 strain at 10 hours rep3

description: Microarray profile of S. flexneri 2a 301 strain at 10 hours

source_name: Shigella flexneri 2a 301 strain at 10 hours

value: wild type


title: Testis from WT mouse_rep3

source_name: Testis, WT mouse, replicate 3


title: Testis from WT mouse_rep1

source_name: Testis, WT mouse, replicate 1


title: Testis from Prss55KO mouse_rep3

source_name: Testis, Prss55KO mouse, replicate 3


title: The S. flexneri 2a 301 △phoPQ mutant strain at 6 hours rep1

description: Microarray profile of S. flexneri 2a 301 △phoPQ mutant strain at 6 hours

source_name: Shigella flexneri 2a 301 △phoPQ mutant strain at 6 hours

value: 6 hours


title: The wildtype S. flexneri 2a 301 strain at 10 hours rep1


title: 5753714054_B; T-PLL

description:
NA
5753714054_B

source_name: PATIENT_ID: P271_


title: The wildtype S. flexneri 2a 301 strain at 6 hours rep1

description: Microarray profile of S. flexneri 2a 301 strain at 6 hours

source_name: Shigella flexneri 2a 301 strain at 6 hours


title: The S. flexneri 2a 301 △phoPQ mutant strain at 6 hours rep2

source_name: Shigella flexneri 2a 302 △phoPQ mutant strain at 6 hours


title: The wildtype S. flexneri 2a 301 strain at 6 hours rep2


title: Wild type spleen, biological replicate 1

city: Seoul

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

country: South Korea

institute: Konkuk University

description: miRNA expression microarray analysis

hyb_protocol: Bitin-laboeled samples were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Dx v.2

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: Wild type mouse Spleen

label_protocol: From each sample, 1 μg total RNA was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: The experimental mice were maintained on a congenic C57Bl/6J background and were allowed to eat standard mouse chow (Cargill Agri Purina, Inc., Seongnam-Si, Korea) and drink on an ad libitum basis.

extract_protocol: Total RNA (including miRNAs) was isolated from mouse spleen tissue using the miRNeasy mini kit (Qiagen, Valencia, CA, USA) following the manufacturer's protocol.

treatment_protocol: Rag2 KO group was deficient of Rag2 gene and possessed severe immuno deficiency status.

tag: background strain

tag: mutation status

value: Wild type


title: The wildtype S. flexneri 2a 301 strain at 10 hours rep2


title: The wildtype S. flexneri 2a 301 strain at 6 hours rep3


title: The S. flexneri 2a 301 △phoPQ mutant strain at 6 hours rep3

source_name: Shigella flexneri 2a 303 △phoPQ mutant strain at 6 hours


title: Rag2 KO spleen, biological replicate 1

description: miRNA expression microarray analysis

source_name: Rag2 KO mouse Spleen

value: Rag2 KO


title: Wild type spleen, biological replicate 3

description: miRNA expression microarray analysis


title: Rag2 KO spleen, biological replicate 2

description: miRNA expression microarray analysis


title: NB39nu_DMSO_24hr

city: chuo-ku, Tokyo

first: Makoto

last: Miyazaki

state: State...

address: 5-1-1, Tsukiji

institute: National Cancer Research Center Institute

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the SurePrint G3 Human Microarrays, 8×60K (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array.

label_protocol: 200ng 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(NanoDrop, Wilmington, USA).

growth_protocol: NB39nu cells were cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum, 100 units/ml penicillin and 100 units/ml streptomycin at 37 ℃ in a 5 % CO2 incubator.

extract_protocol: Total RNA was purified using an RNeasy kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: NB39nu cells were treated with 1 microM of Crizotinib ,Alectinib or control DMSO for 24 hour.

value: parental

value: neuroblastoma

tag: agent

value: DMSO

tag: Sex

value: male


title: Case_9_Blood

source_name: Healthy control. Genomic DNA from blood

value: Healthy control. Genomic DNA from blood

value: Female


title: NB39nu_1uM_Alectinib_24hr

value: Alectinib


title: Rag2 KO spleen, biological replicate 3

description: miRNA expression microarray analysis


title: NB39nu_AR_3D_1uM_Alectinib_24hr

tag: culture protocol

value: Alectinib-Resistant cells


title: Wild type spleen, biological replicate 2

description: miRNA expression microarray analysis


title: NB39nu_1uM_Crizotinib_24hr

value: Crizotinib


title: NB39nu_CR_1uM_Crizotinib_24hr

value: Crizotinib-Resistant cells


title: NB39nu_3D_DMSO_24hr


title: NB39nu_3D_1uM_Alectinib_24hr


title: AX -Cy5

status: Public on Nov 25 2017

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: AX -Cy5

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: Mouse Hippocampus AX Cy5

label_protocol: Manual:  Low Input Quick Amp Labeling Kit, Two-Color  (Agilent)

growth_protocol: Male C57BL/6J mice of 11 weeks old (25-30g of body weight) were obtained from SLC (Shizuoka, Japan). The mice were housed individually in standard polycarbonate cages under a controlled room temperature (21-23°C), relative humidity (50%), and a 12-h light-dark cycle (lights on at 07:00 AM).

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: During the first week of acclimatization, mice were fed an MF powder diet (Oriental Yeast, Tokyo, Japan) ad libitum that consisted of 8.5% moisture, 23.3% protein, 5.6% fat, 3.4% fiber, 5.8% ash and 53.4% nitrogen-free extract. Drinking water was also available ad libitum.  AX diets were made by mixing the MF powder with either AX or a placebo powder (AstaREAL-20F based on 2% content of AX derived from Haematococcus pluvialis; Fuji Chemical Industry, Japan) at concentrations of 0.5% (wt:wt). The mice were randomly divided into 4 groups: (1) sedentary with placebo (SE), (2) mild exercise with placebo (ME), (3) sedentary with AX supplementation (AX), and (4) mild exercise with AX supplementation (AX+ME). All experimental procedures were performed in accordance with protocols approved by the University of Tsukuba Animal Experiment Committee guidelines for the Care and Use of Laboratory Animals (NIH publication, 1996).

value: Brain

tag: condition

value: sedentary+astaxanthin


title: BMDC_RFF_rep2

status: Public on Nov 27 2017

city: Tokushima

first: Koji

last: Yasutomo

address: 3-18-15 Kuramoto-cho

department: Graduate school of Biomedical Sciences

institute: Tokushima University

description: gene expression profile in control BMDC

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65ºC 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 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BMDC from RFF

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input 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.

extract_protocol: Total RNAs were isolated with the ReliaprepTM RNA cell miniprep system (Promega) following manufacturer's instruction. Samples are pooled from 4 mice for each treatment. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Bone marrow cells were harvested from femurs and tibias of C57BL/6 mice (8 weeksold , female) and cultured with 20 ng/mL GM-CSF for 6 days.

value: female

value: 8 weeks old

value: BMDC

value: control


title: NB39nu_AR_3D_DMSO_24hr

tag: tissue


title: normal pancreas_1

city: Wynnewood

first: Janet

middle: A

last: Sawicki

state: PA

address: 100 Lancaster Ave.

institute: Lankenau Institute for Medical Research

description:
C group
RMA expression value derived from Expression Console software

hyb_protocol: Affymetrix gene chips MTA 1.0 array was hybridized with fragmented and biotin-labeled target (5 ug) in 220 ul of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization for 16-18 h.

scan_protocol: Chips (MTA1.0) were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Chp files were generated by Gene Level-SST-RMA normalization from Affymetrix cel file by using Expression Console Software 1.4. TC group was compare with C group by using Transcriptome Analysis Console software 3.1.

source_name: mouse pancreas

label_protocol: Fragmented biotin labeled cDNA (from 250 ng of RNA) was synthesized using the Affymetrix GeneChip WT PLUS reagent kit.

growth_protocol: 6 month- old mice were euthanized by cervical dislocation.

extract_protocol: RNA purified from 700 microliters supernatant using Qiagen Total RNA Extraction Protocol. RINe values determined and only those of sufficient quality were used to make cRNAs, from which cDNAs were generated.

treatment_protocol: Immediately following euthanasia, pancreas was injected with RNAlater. Following dissection, pancreas kept in RNAlater on ice until homogenized in 8 ml Qiazol, then 1.5ml lysate centrifuged at 12,000 G for 5 min at 4oC.

value: pancreas

value: 6 months


title: normal pancreas_3


title: experimental pancreas_3

description:
TC group
RMA expression value derived from Expression Console software

value: Pdx1/Cre + Traffic-HuR


title: experimental pancreas_5


title: AX+ME-Cy5

source_name: Mouse Hippocampus AX+ME Cy5

value: mild exercise+astaxanthin


title: experimental pancreas_2


title: normal pancreas_6


title: NB39nu_3D_1uM_Crizotinib_24hr

value: parental

value: neuroblastoma

value: male


title: normal pancreas_2


title: experimental pancreas_6


title: experimental pancreas_1


title: SED-Cy5

source_name: Mouse Hippocampus SED Cy5

value: sedentary


title: NB39nu_CR_3D_1uM_Crizotinib_24hr


title: ME-Cy5

source_name: Mouse Hippocampus ME Cy5

value: mild exercise


title: BMDC_RFF_rep1

description: gene expression profile in control BMDC


title: BMDC_RFF11_rep2

description: gene expression profile in Rbpj-deficient BMDC

source_name: BMDC from RFF11

value: Rbpj-deficient


title: normal pancreas_4


title: ME-Cy3

source_name: Mouse Hippocampus ME Cy3


title: NB39nu_AR_1uM_Alectinib_24hr

value: Alectinib-Resistant cells

value: Alectinib


title: AX -Cy3

description: AX -Cy3

source_name: Mouse Hippocampus AX Cy3

value: Brain

value: sedentary+astaxanthin


title: K1 (GMP from KrasG12D; CD2Cre mice)

city: Tianjin

first: Feifei

last: Liu

address: 94 Weijin Road

department: School of Medicine

institute: Nankai University

description: Gene expression

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

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

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

source_name: granulocyte-macrophage progenitor cells (GMP) from bone marrow

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: Transgenic mice or littermate control were maintained in SPF animal room.

extract_protocol: Bone marrow cells were extracted by standard approach with syring and PBD flushing. GMP cells were labeled with cell surface marker and sorted from FACS Aria III. Total RNA were extracted by Trizol from the sorted cells.

treatment_protocol: Bone marrow cells were extracted from mice with 6-8 weeks old, when krasG12D/+; CD2Cre+ mice had acute myeloid leukemia.

value: leukemic KrasG12D/+; CD2Cre+


title: SED-Cy3

source_name: Mouse Hippocampus SED Cy3


title: AX+ME-Cy3

source_name: Mouse Hippocampus AX+ME Cy3


title: NB39nu_CR_3D_DMSO_24hr

value: Crizotinib-Resistant cells

value: DMSO


title: normal pancreas_5

value: pancreas


title: BMDC_RFF11_rep1

value: female

value: 8 weeks old

value: BMDC


title: W1 (GMP from wild type)

description: Gene expression

value: granulocyte-macrophage progenitor cells (GMP) from bone marrow

value: wild type


title: Chronic gastritis biopsy. Biological replicate 3

status: Public on Nov 23 2017

city: Ciudad de México

first: Yolanda

last: López-Vidal

state: Ciudad de México

address: Avenida Universidad 3000, Universidad Nacional Autónoma de México. C.U. Coyoacán

department: Departamento de Microbiología y Parasitología, Facultad de Medicina

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Patients undergoing routine endoscopic evaluation for chronic abdominal complaints were recruited and biopsy samples were taken for histological and molecular analysis. An expert pathologist performed histological examination, according to Sydney classification. After histological examination, samples classified as gastritis and intestinal metaplasia were selected. Within samples corresponding to gastritis, chronic and follicular gastritis were distinguished.

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Affymetrix Human Gene 1.0 ST by means of GeneChip Hybridization, Wash and Stain Kit (Affymetrix, USA).

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

data_processing:
Raw data were background-corrected using Robust Multiarray Average (RMA) and normalized using Quantile Normalization.
Differential expression was determined using statistical linear models with arbitrary coefficients, contrasts of interest were analyzed using the bioconductor library limma. Correction for multiple hypotheses was applied using false discovery rate (FDR). Genes were selected based on a Fold-change in base 2 log scale within -0.3 ≥ logFCh ≥ 0.3 and statistical significance according to a B-statistic ≥ -1 (which corresponds to an adjusted p-value ≤ 0.05).

source_name: Gastric tissue with chronic gastritis

label_protocol: Target cDNA was prepared according to the WT Expression Sense Target Kit (Ambion, USA). Purified sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, USA).

extract_protocol: Total RNA was extracted using RNAqueous Kit (Ambion, USA) according to the manufacturer’s instructions


title: Chronic gastritis biopsy. Biological replicate 7

value: male


title: Chronic gastritis biopsy. Biological replicate 5


title: Intestinal metaplasia biopsy. Biological replicate 6

source_name: Gastric tissue with intestinal metaplasia


title: Follicular gastritis biosy. Biological replicate 1

source_name: Gastric tissue with follicular gastritis


title: Chronic gastritis biopsy. Biological replicate 6


title: Intestinal metaplasia biopsy. Biological replicate 7


title: Follicular gastritis biosy. Biological replicate 4


title: Intestinal metaplasia biopsy. Biological replicate 1


title: Follicular gastritis biosy. Biological replicate 5


title: Intestinal metaplasia biopsy. Biological replicate 4


title: Follicular gastritis biosy. Biological replicate 6


title: Follicular gastritis biosy. Biological replicate 3


title: Chronic gastritis biopsy. Biological replicate 4


title: Follicular gastritis biosy. Biological replicate 2


title: Follicular gastritis biosy. Biological replicate 7


title: 49PBMC_HF_rep12

city: Rennes

first: Colette

last: DESERT

address: 65 Rue de St Brieuc

institute: Agrocampus INRA UMR1348 PEGASE

description: Gene expression

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom 8 x 60K chicken gene expression microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Mmicroarray scanner  using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Low Input 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: 2 x 12 chickens per line were placed in individual cages and fed two different diets from 21 to 63 d. These two diets were isocaloric (12.54 MJ ME/kg) and isonitrogenous (190 g CP/kg) but exhibited a high-starch and low-fiber low-lipid contents (LF diet) or a low-starch and high-fiber high-lipid contents (HF diet).

extract_protocol: Total RNA was extracted using TRIzol®. The quantity and quality of extracted RNA was evaluated using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 BioAnalyzer.

treatment_protocol: At 63 days of age, the liver, Pectoralis major muscle and abdominal fat were immediately removed and frozen in liquid nitrogen and then stored at -80°C until analyses. Peripheral blood mononucleated cells (PBMC) were  isolated, just after sampling by density gradient centrifugation (Ficoll Histopaque).

value: Peripheral Blood Mononuclear Cells

tag: diet

value: HF


title: Chronic gastritis biopsy. Biological replicate 1


title: Intestinal metaplasia biopsy. Biological replicate 3


title: Chronic gastritis biopsy. Biological replicate 2


title: Intestinal metaplasia biopsy. Biological replicate 2


title: 47PBMC_HF_rep12

description: Gene expression


title: Intestinal metaplasia biopsy. Biological replicate 5


title: 48PBMC_HF_rep11

description: Gene expression


title: experimental pancreas_4

value: Pdx1/Cre + Traffic-HuR

value: 6 months


title: 46PBMC_LF_rep12

description: Gene expression

value: LF


title: 40PBMC_LF_rep10

description: Gene expression


title: 34PBMC_LF_rep9

description: Gene expression


title: 39PBMC_LF_rep10

description: Gene expression


title: 36PBMC_HF_rep8

description: Gene expression


title: 45PBMC_LF_rep12

description: Gene expression


title: 44PBMC_HF_rep10

description: Gene expression


title: 29PBMC_HF_rep7

description: Gene expression


title: 35PBMC_HF_rep9

description: Gene expression


title: 27PBMC_HF_rep7

description: Gene expression


title: 30PBMC_HF_rep8

description: Gene expression


title: 32PBMC_LF_rep8

description: Gene expression


title: 25PBMC_LF_rep7

description: Gene expression


title: 26PBMC_LF_rep7

description: Gene expression


title: 38PBMC_HF_rep10

description: Gene expression


title: 24PBMC_LF_rep6

description: Gene expression


title: 19PBMC_HF_rep5

description: Gene expression


title: 14PBMC_HF_rep4

description: Gene expression


title: 21PBMC_HF_rep5

description: Gene expression


title: 17PBMC_LF_rep5

description: Gene expression


title: 16PBMC_LF_rep4

description: Gene expression


title: 11PBMC_HF_rep3

description: Gene expression


title: 28PBMC_HF_rep6

description: Gene expression


title: 37PBMC_HF_rep9

description: Gene expression


title: 33PBMC_LF_rep9

description: Gene expression


title: 09PBMC_LF_rep3

description: Gene expression


title: 13PBMC_HF_rep3

description: Gene expression


title: 22PBMC_HF_rep6

description: Gene expression


title: 18PBMC_LF_rep5

description: Gene expression


title: 05PBMC_HF_rep2

description: Gene expression


title: 23PBMC_LF_rep6

description: Gene expression


title: 31PBMC_LF_rep8

description: Gene expression


title: 07PBMC_LF_rep2

description: Gene expression


title: 02PBMC_LF_rep1

description: Gene expression


title: 49Mu_HF_rep12

description: Gene expression

value: Pectoralis major muscle


title: 08PBMC_LF_rep2

description: Gene expression


title: 46Mu_LF_rep12

description: Gene expression


title: 06PBMC_HF_rep2

description: Gene expression


title: 47Mu_HF_rep12

description: Gene expression


title: 04PBMC_HF_rep1

description: Gene expression


title: 40Mu_LF_rep10

description: Gene expression


title: 03PBMC_HF_rep1

description: Gene expression


title: 43Mu_HF_rep11

description: Gene expression


title: 01PBMC_LF_rep1

description: Gene expression


title: 36Mu_HF_rep8

description: Gene expression


title: 35Mu_HF_rep9

description: Gene expression


title: 37Mu_HF_rep9

description: Gene expression


title: 34Mu_LF_rep9

description: Gene expression


title: 44Mu_HF_rep10

description: Gene expression


title: 24Mu_LF_rep6

description: Gene expression


title: 27Mu_HF_rep7

description: Gene expression


title: 31Mu_LF_rep8

description: Gene expression


title: 26Mu_LF_rep7

description: Gene expression


title: 33Mu_LF_rep9

description: Gene expression


title: 28Mu_HF_rep6

description: Gene expression


title: 39Mu_LF_rep10

description: Gene expression


title: 30Mu_HF_rep8

description: Gene expression


title: 32Mu_LF_rep8

description: Gene expression


title: 42Mu_LF_rep11

description: Gene expression


title: 25Mu_LF_rep7

description: Gene expression


title: 38Mu_HF_rep10

description: Gene expression


title: 23Mu_LF_rep6

description: Gene expression


title: 29Mu_HF_rep7

description: Gene expression


title: 21Mu_HF_rep5

description: Gene expression


title: 22Mu_HF_rep6

description: Gene expression


title: 18Mu_LF_rep5

description: Gene expression


title: 17Mu_LF_rep5

description: Gene expression


title: 14Mu_HF_rep4

description: Gene expression


title: 08Mu_LF_rep2

description: Gene expression


title: 20Mu_HF_rep4

description: Gene expression


title: 09Mu_LF_rep3

description: Gene expression


title: 19Mu_HF_rep5

description: Gene expression


title: 11Mu_HF_rep3

description: Gene expression


title: 06Mu_HF_rep2

description: Gene expression


title: 05Mu_HF_rep2

description: Gene expression


title: 04Mu_HF_rep1

description: Gene expression


title: 02Mu_LF_rep1

description: Gene expression


title: 47Adip_HF_rep12

description: Gene expression

value: Abdominal fat


title: 16Mu_LF_rep4

description: Gene expression


title: 49Adip_HF_rep12

description: Gene expression


title: 48Adip_HF_rep11

description: Gene expression


title: 07Mu_LF_rep2

description: Gene expression


title: 01Mu_LF_rep1

description: Gene expression


title: 44Adip_HF_rep10

description: Gene expression


title: 03Mu_HF_rep1

description: Gene expression


title: 46Adip_LF_rep12

description: Gene expression


title: 42Adip_LF_rep11

description: Gene expression


title: 43Adip_HF_rep11

description: Gene expression


title: 45Adip_LF_rep12

description: Gene expression


title: 38Adip_HF_rep10

description: Gene expression


title: 13Mu_HF_rep3

description: Gene expression


title: 41Adip_LF_rep11

description: Gene expression


title: 15Mu_LF_rep4

description: Gene expression


title: 39Adip_LF_rep10

description: Gene expression


title: 34Adip_LF_rep9

description: Gene expression


title: 29Adip_HF_rep7

description: Gene expression


title: 36Adip_HF_rep8

description: Gene expression


title: 35Adip_HF_rep9

description: Gene expression


title: 25Adip_LF_rep7

description: Gene expression


title: 30Adip_HF_rep8

description: Gene expression


title: 31Adip_LF_rep8

description: Gene expression


title: 26Adip_LF_rep7

description: Gene expression


title: 22Adip_HF_rep6

description: Gene expression


title: 18Adip_LF_rep5

description: Gene expression


title: 27Adip_HF_rep7

description: Gene expression


title: 15Adip_LF_rep4

description: Gene expression


title: 14Adip_HF_rep4

description: Gene expression


title: 37Adip_HF_rep9

description: Gene expression


title: 13Adip_HF_rep3

description: Gene expression


title: 33Adip_LF_rep9

description: Gene expression


title: 28Adip_HF_rep6

description: Gene expression


title: 24Adip_LF_rep6

description: Gene expression


title: 21Adip_HF_rep5

description: Gene expression


title: 20Adip_HF_rep4

description: Gene expression


title: 16Adip_LF_rep4

description: Gene expression


title: 40Adip_LF_rep10

description: Gene expression


title: 11Adip_HF_rep3

description: Gene expression


title: 19Adip_HF_rep5

description: Gene expression


title: 10Adip_LF_rep3

description: Gene expression


title: 17Adip_LF_rep5

description: Gene expression


title: 23Adip_LF_rep6

description: Gene expression


title: 09Adip_LF_rep3

description: Gene expression


title: 08Adip_LF_rep2

description: Gene expression


title: 05Adip_HF_rep2

description: Gene expression


title: 03Adip_HF_rep1

description: Gene expression


title: 49Li_HF_rep12

description: Gene expression

value: Liver


title: 06Adip_HF_rep2

description: Gene expression


title: 48Li_HF_rep11

description: Gene expression


title: 47Li_HF_rep12

description: Gene expression


title: 42Li_LF_rep11

description: Gene expression


title: 43Li_HF_rep11

description: Gene expression


title: 45Li_LF_rep12

description: Gene expression


title: 07Adip_LF_rep2

description: Gene expression


title: 39Li_LF_rep10

description: Gene expression


title: 41Li_LF_rep11

description: Gene expression


title: 01Adip_LF_rep1

description: Gene expression


title: 38Li_HF_rep10

description: Gene expression


title: 32Li_LF_rep8

description: Gene expression


title: 35Li_HF_rep9

description: Gene expression


title: 27Li_HF_rep7

description: Gene expression


title: 46Li_LF_rep12

description: Gene expression


title: 29Li_HF_rep7

description: Gene expression


title: 37Li_HF_rep9

description: Gene expression


title: 28Li_HF_rep6

description: Gene expression


title: 40Li_LF_rep10

description: Gene expression


title: 33Li_LF_rep9

description: Gene expression


title: 44Li_HF_rep10

description: Gene expression


title: 24Li_LF_rep6

description: Gene expression


title: 25Li_LF_rep7

description: Gene expression


title: 30Li_HF_rep8

description: Gene expression


title: 36Li_HF_rep8

description: Gene expression


title: 26Li_LF_rep7

description: Gene expression


title: 21Li_HF_rep5

description: Gene expression


title: 20Li_HF_rep4

description: Gene expression


title: 22Li_HF_rep6

description: Gene expression


title: 17Li_LF_rep5

description: Gene expression


title: 23Li_LF_rep6

description: Gene expression


title: 19Li_HF_rep5

description: Gene expression


title: 10Mu_LF_rep3

description: Gene expression


title: 16Li_LF_rep4

description: Gene expression


title: 10Li_LF_rep3

description: Gene expression


title: 08Li_LF_rep2

description: Gene expression


title: 13Li_HF_rep3

description: Gene expression


title: 14Li_HF_rep4

description: Gene expression


title: 03Li_HF_rep1

description: Gene expression


title: 18Li_LF_rep5

description: Gene expression


title: 04Li_HF_rep1

description: Gene expression


title: 09Li_LF_rep3

description: Gene expression


title: 05Li_HF_rep2

description: Gene expression


title: 15Li_LF_rep4

description: Gene expression


title: 07Li_LF_rep2

description: Gene expression


title: 11Li_HF_rep3

description: Gene expression


title: 01Li_LF_rep1

description: Gene expression


title: 06Li_HF_rep2

description: Gene expression


title: 02Li_LF_rep1

description: Gene expression