title: p-Coumaric 10 min replicate 1

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

institute: ICTAN-CSIC

description: Biological replicate 1 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned.

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C / GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes.

organism: Lactiplantibacillus plantarum

source_name: Untreated cells: Control

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking p-CA to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to p-CA to bring their final concentration to 1.5 mM. Cell cultures were centrifuged after 10 minutes of exposure to p-CA and RNA was extracted and purified.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in the Mini-BeadBeather (BIOSPEC Products, INC.) using three treatments of 4600 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

tag: compound

value: without p-coumaric acid

source_name: Treated cells: Experimental

value: p-coumaric acid 1.5 mM


title: healthy adult control JR TRAPS 2007 Sample 31

status: Public on Jan 16 2013

type: RNA

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

country: USA

institute: nih

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs was hybridized  to Affymetrix U133A_2.0 GeneChips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: Fluorescent intensities were measured with an Affymetrix GeneChip Scanner 3000.

data_processing:
Prior to statistical analysis of the MAS5 data, all probe sets for each microarray were globally scaled to a target intensity of 500 in the Affymetrix software (GCOS v1.4). Only transcripts with a present (P) flag in 75% or more of the chips from a given class were analyzed.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HG-U133A_2
program-name = Expression Console
program-version = 1.2.1.20
program-company = Affymetrix
affymetrix-algorithm-param-apt-engine = ProbesetSummarizeEngine
affymetrix-algorithm-param-apt-program-name = Expression Console
affymetrix-algorithm-param-apt-opt-analysis-name = rma
affymetrix-algorithm-param-apt-opt-set-analysis-name = rma
affymetrix-algorithm-param-apt-opt-analysis-spec = rma-bg,quant-norm.sketch=0.bioc=true.lowprecision=false.usepm=true.target=0.doavg=f
alse.subsetmd5=37a9e6fae3eaa22bda0bb220c6bc054d,pm-only,med-polish.FixFeatureEffect=false.UseInputModel=false.FitFeatureResponse=true.
expon=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.allele-a=false
affymetrix-algorithm-param-apt-opt-do-residuals = false
affymetrix-algorithm-param-apt-opt-do-feature-effects = false
affymetrix-algorithm-param-apt-opt-write-sketch = false
affymetrix-algorithm-param-apt-opt-write-profile = false
affymetrix-algorithm-param-quantification-name = med-polish
affymetrix-algorithm-param-quantification-version = 1.0
affymetrix-algorithm-param-quantification-scale = log2
affymetrix-algorithm-param-quantification-type = signal

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: 1.5 μg of total RNA was used for standard target preparation and hybridization (Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents). 10 ug of labeled cRNA was fragmented according to the protocol recommendations.

extract_protocol: PBMCs were isolated from whole blood using ficoll-based Lymphocyte Separation Medium (MP Biomedicals). The cell pellets were resuspended in Trizol (Invitrogen Corp.) for 5 min and stored at -80oC until the samples from this study could be processed together. Total RNA was isolated from the PBMC lysates by alcohol precipitation and the RNA samples were subject to further purification via RNEasy columns (Qiagen, Inc.). The concentration and quality of RNA samples was determined using spectrophotometry and the 2100 Bioanalyzer (Agilent Technlogies, Inc.). The RNA samples all had 260:280 ratios between 1.8 and 2.1 and were of good quality as evidenced by intact 18S and 28S rRNA bands

treatment_protocol: All blood specimens were processed within 60 minutes of drawing to minimize ex vivo changes in gene expression

tag: cell type

value: peripheral blood mononuclear cells

tag: genotype

value: healthy adult control

tag: disease state


title: NLRP3 mutation carrier 08_12_05 Sample 4

description: total RNA from patient with active disease

value: NLRP3 mutation carrier

tag: disease causing mutation

value: heterozygous for G569R

value: CAPS


title: NLRP3 mutation carrier 08_12_05 Sample 2

value: mosaic for K355N


title: MGE_Lhx6-GFP+

city: San Francisco

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

description: Gene expression in embryonic Lhx6-GFP+ cells

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: Dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

organism: Mus musculus

source_name: FACS purified Lhx6-GFP+ cells from E12.5 brain medial ganglionic eminence

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

growth_protocol: For MGE-Lhx6-GFP+ cells, there is no growth protocol. Cells were isolated fresh from sacrificed embryos. For differentiated ES cells, ES cells were subjected to MGE-differentiated protocol as described in Chen et al., 2013 (PLOS ONE) manuscript. Briefly, ES cells were dissociated into single cells with 0.25% trypsin-EDTA (Invitrogen) and quickly re-aggregated in the differentiation media (GMEM medium supplemented with 10% KSR, 1 mM sodium pyruvate, 0.1 mM NEAA, 0.1 mM 2-ME) containing 100 ng/ml Dkk-1 (5000 cells/100 µl/well) using 96-well low cell adhesion plates (Lipidure-coat plate A-U96, NOF America). On day 3 of differentiation (D3), 20 µl of differentiation media containing SAG (Alexis Biochemicals) was added into each well so that the final concentration of SAG was 6 nM. On D6, ES cell aggregates (embryoid body (EB) aggregates) were transferred to a 10-cm bacterial-grade dish with DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and 6 nM SAG.

extract_protocol: RNA was prepared using QIAGEN RNeasy Micro kit according to the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For MGE-Lhx6-GFP+ cells, embryonic 12.5 (E12.5) MGE from Lhx6-GFP transgenic mouse (in CD-1 background) brains were dissected and dissociated into single cells with 0.05% ypsin/EDTA (UCSF CCF) with 10 µg/ml DNase I (Roche) at 37C for 15 min. For differentiated ES cells, On day 12 of MGE differentiation protocol, ES embroic body aggregates from 20 96-wells plates were collected (1920 aggregates) and dissociated with the enzyme solution of the Neural Tissue Dissociation Kit (Sumitomo Bakelite, MB-X9901). Rock inhibitor Y-27632 (10 µM) was added in all the solutions to prevent cell death. Cells were stained with Sytox Blue (Invitrogen, to eliminate dead cells) in 1% BSA/HBSS 15 minutes before FACsorting to distinguish dead vs. live cells. Lhx6-GFP+ cells were sorted with BD FACSAria II using 100µm nozzle and collected in 10% FBS/DMEM/F-12.

tag: strain background

tag: genotype/variation

value: carrying Lhx6-GFP BAC

tag: gender

value: female

tag: tissue

value: brain

tag: developmental stage

tag: gfp marker

value: GFP positive


title: p-Coumaric 10 min replicate 2

city: Madrid

country: Spain

description: Biological replicate 2 of 3

treatment_protocol: Cell cultures were centrifuged after 10 minutes of exposure to p-CA and RNA was extracted and purified.

tag: strain


title: p-Coumaric 10 min replicate 3

description: Biological replicate 3 of 3


title: healthy adult control JR TRAPS 2007 Sample 11


title: NLRP3 mutation carrier 08_12_05 Sample 3

value: heterozygous for F523C


title: NLRP3 mutation carrier 08_12_05 Sample 1

value: heterozygous for D303N


title: Mammary tumor RNA from AKXD RI Strain 20

status: Public on Jan 15 2013

city: Bethesda

first: Natalie

last: Goldberger

address: 9000 Rockville Pike

institute: NCI

hyb_protocol: Slides were hybridized at 56C for 16 hrs following the miRCURY LNA microRNA Array Power Labeling kit (Exiquon Inc) instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Agilent Feature Extraction Software (version A.7.5) was used for LOWESS normalized and background subtraction.

source_name: mammary tumor

label_protocol: Total RNA (1 ug) was labeled using the miRCURY LNA microRNA Array Power Labeling kit (Exiquon Inc) following manufacturer's instructions.

extract_protocol: Total RNA was extracted using the mirVana Isolation Kit (Ambion) following manufacturer's instructions.

value: [FVB/N-TgN(MMTV-PyVT)634Mul x AKXD R1]F1 sublines

value: mammary tumor

source_name: FirstChoice Total RNA Ambion (AM7800)

value: Swiss Webster mice

value: various


title: SCC of the vulva 04-1190 aCGH

type: genomic

city: oslo

first: Francesca

last: Micci

address: Ullernchausseen 70

department: Institute for medical informatics

country: Norway

institute: Oslo Universitetssykehus

hyb_protocol: aCGH was performed using Agilent SurePrint G3 Human CGH Microarray 4 x 180K arrays (Agilent Technologies Inc., Palo Alto, CA, USA).

scan_protocol: All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.

data_processing: Genomic Workbench software (Agilent Technologies Inc.) was used with design file 022060.xml.

molecule: genomic DNA

source_name: tumor tissue

label_protocol: DNA was labeled according to the manufacturer’s instructions.

extract_protocol: Genomic DNA was extracted from fresh-frozen tissue using the MagAttract DNA Mini M48 kit (Qiagen Inc., Valencia, CA, USA).

tag: differentiation

value: poorly differentiated

value: squamous cell carcinoma tumor

tag: individual

source_name: control DNA (supplied by Agilent)

tag: sample type

value: Cat nr G1521 Human Genomic DNA Female from Promega


title: Mammary tumor RNA from AKXD RI Strain 18


title: Mammary tumor RNA from AKXD RI Strain 16


title: Mammary tumor RNA from AKXD RI Strain 14


title: Mammary tumor RNA from AKXD RI Strain 7


title: Mammary tumor RNA from AKXD RI Strain 9


title: Mammary tumor RNA from AKXD RI Strain 13


title: Mammary tumor RNA from AKXD RI Strain 22


title: Mammary tumor RNA from AKXD RI Strain 2


title: Mammary tumor RNA from AKXD RI Strain 11


title: Mammary tumor RNA from AKXD RI Strain 10


title: Mammary tumor RNA from AKXD RI Strain 21


title: San Quintin, Baja California 18 hour  desiccation Organ pipe cactus BC_SQ_OP_18_R-3

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. 18 hour desiccation treatment.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

value: Wild-type

tag: phenotype

value: normal

tag: origin

value: San Quintin, Baja California

tag: time

value: 18 hour

tag: treatment

value: desiccation treatment

tag: media

value: prepared from Organ pipe cactus

tag: status

value: virgin

value: whole organism


title: San Quintin, Baja California 9 hour  desiccation Organ pipe cactus BC_SQ_OP_9_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. 9 hour desiccation treatment.

tag: genotype

value: female

value: 9 hour


title: San Quintin, Baja California 18 hour  desiccation Organ pipe cactus BC_SQ_OP_18_R-1


title: San Quintin, Baja California 18 hour  desiccation Organ pipe cactus BC_SQ_OP_18_R-2


title: San Quintin, Baja California 9 hour  desiccation Organ pipe cactus BC_SQ_OP_9_R-1


title: Mammary tumor RNA from AKXD RI Strain 3

value: [FVB/N-TgN(MMTV-PyVT)634Mul x AKXD R1]F1 sublines


title: San Quintin, Baja California 9 hour  desiccation Organ pipe cactus BC_SQ_OP_9_R-4


title: San Quintin, Baja California 0 hour  desiccation Organ pipe cactus BC_SQ_OP_0_R-1

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. Zero hour desiccation treatment.

value: 0 hour


title: San Quintin, Baja California 9 hour  desiccation Organ pipe cactus BC_SQ_OP_9_R-2


title: San Quintin, Baja California 18 hour  desiccation Agria cactus BC_SQ_AG_18_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Agria cactus. 18 hour desiccation treatment.

value: prepared from Agria cactus


title: San Quintin, Baja California 18 hour  desiccation Agria cactus BC_SQ_AG_18_R-1


title: San Quintin, Baja California 18 hour  desiccation Agria cactus BC_SQ_AG_18_R-2


title: San Quintin, Baja California 0 hour  desiccation Organ pipe cactus BC_SQ_OP_0_R-2


title: San Quintin, Baja California 0 hour  desiccation Agria cactus BC_SQ_AG_0_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Agria cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.97


title: San Quintin, Baja California 9 hour  desiccation Agria cactus BC_SQ_AG_9_R-2

description: This sample is of wild-type Drosophila mojavensis virgin females originated from San Quintin, Baja California. These females were raised on lab-media prepared from Agria cactus. 9 hour desiccation treatment.


title: San Quintin, Baja California 9 hour  desiccation Agria cactus BC_SQ_AG_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.99


title: San Quintin, Baja California 9 hour  desiccation Agria cactus BC_SQ_AG_9_R-3


title: San Quintin, Baja California 0 hour  desiccation Organ pipe cactus BC_SQ_OP_0_R-4


title: Punta Prieta, Baja California 18 hour  desiccation Organ pipe cactus BC_PP_OP_18_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.94

value: Punta Prieta, Baja California


title: Punta Prieta, Baja California 18 hour  desiccation Organ pipe cactus BC_PP_OP_18_R-3

source_name: Drosophila mojavensis TSC#15081-1352.93


title: San Quintin, Baja California 0 hour  desiccation Agria cactus BC_SQ_AG_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.95


title: Punta Prieta, Baja California 9 hour  desiccation Organ pipe cactus BC_PP_OP_9_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.90


title: San Quintin, Baja California 0 hour  desiccation Agria cactus BC_SQ_AG_0_R-4

source_name: Drosophila mojavensis TSC#15081-1352.98


title: Punta Prieta, Baja California 18 hour  desiccation Organ pipe cactus BC_PP_OP_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.91


title: San Quintin, Baja California 0 hour  desiccation Organ pipe cactus BC_SQ_OP_0_R-3


title: San Quintin, Baja California 18 hour  desiccation Agria cactus BC_SQ_AG_18_R-4


title: San Quintin, Baja California 0 hour  desiccation Agria cactus BC_SQ_AG_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.96


title: Punta Prieta, Baja California 18 hour  desiccation Organ pipe cactus BC_PP_OP_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.92


title: Punta Prieta, Baja California 9 hour  desiccation Organ pipe cactus BC_PP_OP_9_R-2

source_name: Drosophila mojavensis TSC#15081-1352.88


title: Punta Prieta, Baja California 9 hour  desiccation Organ pipe cactus BC_PP_OP_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.89


title: Punta Prieta, Baja California 9 hour  desiccation Organ pipe cactus BC_PP_OP_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.87


title: Punta Prieta, Baja California 0 hour  desiccation Organ pipe cactus BC_PP_OP_0_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Organ pipe cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.85


title: Punta Prieta, Baja California 0 hour  desiccation Organ pipe cactus BC_PP_OP_0_R-4

source_name: Drosophila mojavensis TSC#15081-1352.86


title: Punta Prieta, Baja California 18 hour  desiccation Agria cactus BC_PP_AG_18_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Agria cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.81


title: Punta Prieta, Baja California 0 hour  desiccation Organ pipe cactus BC_PP_OP_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.84


title: Punta Prieta, Baja California 18 hour  desiccation Agria cactus BC_PP_AG_18_R-3

source_name: Drosophila mojavensis TSC#15081-1352.80


title: Punta Prieta, Baja California 18 hour  desiccation Agria cactus BC_PP_AG_18_R-5

source_name: Drosophila mojavensis TSC#15081-1352.82


title: Punta Prieta, Baja California 18 hour  desiccation Agria cactus BC_PP_AG_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.78


title: Punta Prieta, Baja California 9 hour  desiccation Agria cactus BC_PP_AG_9_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Agria cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.77


title: Punta Prieta, Baja California 9 hour  desiccation Agria cactus BC_PP_AG_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.76


title: Punta Prieta, Baja California 0 hour  desiccation Agria cactus BC_PP_AG_0_R-2

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Prieta, Baja California. These females were raised on lab-media prepared from Agria cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.71


title: Punta Prieta, Baja California 0 hour  desiccation Agria cactus BC_PP_AG_0_R-3

source_name: Drosophila mojavensis TSC#15081-1352.72


title: Punta Prieta, Baja California 0 hour  desiccation Organ pipe cactus BC_PP_OP_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.83


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Organ pipe cactus SO_OPNM_OP_9_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.65


title: Punta Prieta, Baja California 0 hour  desiccation Agria cactus BC_PP_AG_0_R-4

source_name: Drosophila mojavensis TSC#15081-1352.73


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Organ pipe cactus SO_OPNM_OP_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.62


title: Punta Prieta, Baja California 18 hour  desiccation Agria cactus BC_PP_AG_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.79


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Organ pipe cactus SO_OPNM_OP_18_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.69


title: Punta Prieta, Baja California 0 hour  desiccation Agria cactus BC_PP_AG_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.70


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Organ pipe cactus SO_OPNM_OP_0_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.61


title: Punta Prieta, Baja California 9 hour  desiccation Agria cactus BC_PP_AG_9_R-2

source_name: Drosophila mojavensis TSC#15081-1352.75


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Organ pipe cactus SO_OPNM_OP_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.59


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Organ pipe cactus SO_OPNM_OP_18_R-3

source_name: Drosophila mojavensis TSC#15081-1352.68


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Organ pipe cactus SO_OPNM_OP_0_R-3

source_name: Drosophila mojavensis TSC#15081-1352.60


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Agria cactus SO_OPNM_AG_18_R-5

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Agria cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.57


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Organ pipe cactus SO_OPNM_OP_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.67


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Organ pipe cactus SO_OPNM_OP_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.66


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Organ pipe cactus SO_OPNM_OP_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.58


title: Punta Prieta, Baja California 9 hour  desiccation Agria cactus BC_PP_AG_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.74


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Organ pipe cactus SO_OPNM_OP_9_R-2

source_name: Drosophila mojavensis TSC#15081-1352.63


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Organ pipe cactus SO_OPNM_OP_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.64


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Agria cactus SO_OPNM_AG_18_R-3

source_name: Drosophila mojavensis TSC#15081-1352.55


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Agria cactus SO_OPNM_AG_18_R-4

source_name: Drosophila mojavensis TSC#15081-1352.56


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Agria cactus SO_OPNM_AG_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.54


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Agria cactus SO_OPNM_AG_9_R-2

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Agria cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.50


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Agria cactus SO_OPNM_AG_9_R-4

source_name: Drosophila mojavensis TSC#15081-1352.52


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Agria cactus SO_OPNM_AG_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.51


title: Organ Pipe National Manument, Sonora desert 18 hour  desiccation Agria cactus SO_OPNM_AG_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.53


title: Punta Onah, Sonora desert 18 hour  desiccation Organ pipe cactus SO_PO_OP_18_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.43

value: Punta Onah, Sonora desert


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Agria cactus SO_OPNM_AG_0_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Organ Pipe National Manument, Sonora desert. These females were raised on lab-media prepared from Agria cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.48


title: Punta Onah, Sonora desert 18 hour  desiccation Organ pipe cactus SO_PO_OP_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.41


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Agria cactus SO_OPNM_AG_0_R-3

source_name: Drosophila mojavensis TSC#15081-1352.47


title: Organ Pipe National Manument, Sonora desert 9 hour  desiccation Agria cactus SO_OPNM_AG_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.49


title: Punta Onah, Sonora desert 18 hour  desiccation Organ pipe cactus SO_PO_OP_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.42


title: Punta Onah, Sonora desert 9 hour  desiccation Organ pipe cactus SO_PO_OP_9_R-4

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.40


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Agria cactus SO_OPNM_AG_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.45


title: Punta Onah, Sonora desert 18 hour  desiccation Organ pipe cactus SO_PO_OP_18_R-4

source_name: Drosophila mojavensis TSC#15081-1352.44


title: Punta Onah, Sonora desert 18 hour  desiccation Agria cactus SO_PO_AG_18_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Agria cactus. 18 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.32


title: Punta Onah, Sonora desert 0 hour  desiccation Organ pipe cactus SO_PO_OP_0_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Organ pipe cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.36


title: Punta Onah, Sonora desert 18 hour  desiccation Agria cactus SO_PO_AG_18_R-4

source_name: Drosophila mojavensis TSC#15081-1352.33


title: Punta Onah, Sonora desert 0 hour  desiccation Organ pipe cactus SO_PO_OP_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.35


title: Punta Onah, Sonora desert 9 hour  desiccation Organ pipe cactus SO_PO_OP_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.37


title: Punta Onah, Sonora desert 0 hour  desiccation Agria cactus SO_PO_AG_0_R-3

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Agria cactus. Zero hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.24


title: Punta Onah, Sonora desert 0 hour  desiccation Organ pipe cactus SO_PO_OP_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.34


title: Punta Onah, Sonora desert 18 hour  desiccation Agria cactus SO_PO_AG_18_R-1

source_name: Drosophila mojavensis TSC#15081-1352.30


title: Punta Onah, Sonora desert 9 hour  desiccation Agria cactus SO_PO_AG_9_R-2

description: This sample is of wild-type Drosophila mojavensis virgin females originated from Punta Onah, Sonora desert. These females were raised on lab-media prepared from Agria cactus. 9 hour desiccation treatment.

source_name: Drosophila mojavensis TSC#15081-1352.27


title: Punta Onah, Sonora desert 0 hour  desiccation Agria cactus SO_PO_AG_0_R-4

source_name: Drosophila mojavensis TSC#15081-1352.25


title: Punta Onah, Sonora desert 9 hour  desiccation Organ pipe cactus SO_PO_OP_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.39


title: Organ Pipe National Manument, Sonora desert 0 hour  desiccation Agria cactus SO_OPNM_AG_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.46


title: Punta Onah, Sonora desert 9 hour  desiccation Agria cactus SO_PO_AG_9_R-4

source_name: Drosophila mojavensis TSC#15081-1352.29


title: Punta Onah, Sonora desert 9 hour  desiccation Agria cactus SO_PO_AG_9_R-3

source_name: Drosophila mojavensis TSC#15081-1352.28


title: Punta Onah, Sonora desert 0 hour  desiccation Agria cactus SO_PO_AG_0_R-2

source_name: Drosophila mojavensis TSC#15081-1352.23


title: Punta Onah, Sonora desert 9 hour  desiccation Organ pipe cactus SO_PO_OP_9_R-2

source_name: Drosophila mojavensis TSC#15081-1352.38


title: Punta Onah, Sonora desert 18 hour  desiccation Agria cactus SO_PO_AG_18_R-2

source_name: Drosophila mojavensis TSC#15081-1352.31


title: Punta Onah, Sonora desert 9 hour  desiccation Agria cactus SO_PO_AG_9_R-1

source_name: Drosophila mojavensis TSC#15081-1352.26


title: SJ_CRLF-3

city: Memphis

first: Linda

last: Holmfeldt

state: Tennessee

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

description: Sample name: SJBALL179

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array.  GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: CRLF diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from ALL cases

extract_protocol: Trizol

tag: all subtype

value: B-lineage ALL with CRLF2 rearrangement


title: Punta Onah, Sonora desert 0 hour  desiccation Agria cactus SO_PO_AG_0_R-1

source_name: Drosophila mojavensis TSC#15081-1352.22


title: SJ_TCF3-3

description: Sample name: SJE2A012

source_name: TCF3 diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: B-lineage ALL with TCF3-PBX1 rearrangement


title: 44-45chr-101

description: Sample name: SJHYPO101

value: Near diploid karyotype


title: SJ_CRLF-1

description: Sample name: SJBALL191


title: SJ_MLL-4

description: Sample name: SJMLL026

source_name: MLL diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: B-lineage ALL with MLL rearrangement


title: SJ_MLL-3

description: Sample name: SJMLL029


title: SJ_MLL-1

description: Sample name: SJMLL028


title: SJ_MLL-2

description: Sample name: SJMLL025


title: SJ_PH-1

description: Sample name: SJPHALL011

source_name: PH diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: B-lineage ALL with BCR-ABL1 rearrangement


title: SJ_ETV6-4

description: Sample name: SJETV005

source_name: ETV6 diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: B-lineage ALL with ETV6-RUNX1 rearrangement


title: SJ_TCF3-2

description: Sample name: SJE2A010


title: SJ_ETV6-5

description: Sample name: SJETV004


title: SJ_PH-3

description: Sample name: SJPHALL013


title: SJ_ETV6-2

description: Sample name: SJETV002


title: SJ_PH-4

description: Sample name: SJPHALL008


title: SJ_H50-2

description: Sample name: SJHYPER002

source_name: H50 diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: B-lineage ALL with high hyperdiploid karyotype


title: SJ_ETV6-1

description: Sample name: SJETV001


title: SJ_ETV6-3

description: Sample name: SJETV003


title: SJ_TCF3-4

description: Sample name: SJE2A011


title: SJ_TCF3-1

description: Sample name: SJE2A003


title: SJ_CRLF-2

description: Sample name: SJDOWN013


title: SJ_PH-2

description: Sample name: SJPHALL010


title: SJ_H50-1

description: Sample name: SJHYPER001


title: SJ_H50-3

description: Sample name: SJHYPER028


title: 44-45chr-115

description: Sample name: SJHYPO115

source_name: 44-45chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.


title: 44-45chr-114

description: Sample name: SJHYPO114


title: 44-45chr-113

description: Sample name: SJHYPO113


title: 44-45chr-112

description: Sample name: SJHYPO112


title: 44-45chr-111

description: Sample name: SJHYPO111


title: 44-45chr-110

description: Sample name: SJHYPO110


title: 44-45chr-104

description: Sample name: SJHYPO104


title: 44-45chr-108

description: Sample name: SJHYPO108


title: 2x32-39chr-55

description: Sample name: SJHYPO055

source_name: 2x32-39chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: Masked low hypodiploid karyotype


title: 44-45chr-109

description: Sample name: SJHYPO109


title: 44-45chr-107

description: Sample name: SJHYPO107


title: 44-45chr-105

description: Sample name: SJHYPO105


title: 44-45chr-102

description: Sample name: SJHYPO102


title: 44-45chr-100

description: Sample name: SJHYPO100


title: 44-45chr-106

description: Sample name: SJHYPO106


title: 44-45chr-97

description: Sample name: SJHYPO097


title: 44-45chr-103

description: Sample name: SJHYPO103


title: 2x32-39chr-83

description: Sample name: SJHYPO083


title: 44-45chr-98

description: Sample name: SJHYPO098


title: 2x32-39chr-79

description: Sample name: SJHYPO079


title: 2x32-39chr-84

description: Sample name: SJHYPO084


title: 2x32-39chr-53

description: Sample name: SJHYPO053


title: 44-45chr-95

description: Sample name: SJHYPO095


title: 40-43chr-1

description: Sample name: SJHYPO121

source_name: 40-43chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: High hypodiploid karyotype


title: 32-39chr-120

description: Sample name: SJHYPO120

source_name: 32-39chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: Low hypodiploid karyotype


title: 32-39chr-80

description: Sample name: SJHYPO080


title: 32-39chr-77

description: Sample name: SJHYPO077


title: 32-39chr-78

description: Sample name: SJHYPO078


title: 32-39chr-52

description: Sample name: SJHYPO052


title: 32-39chr-68

description: Sample name: SJHYPO068


title: 32-39chr-64

description: Sample name: SJHYPO064


title: 32-39chr-14

description: Sample name: SJHYPO014


title: 32-39chr-26

description: Sample name: SJHYPO026


title: 32-39chr-63

description: Sample name: SJHYPO063


title: 32-39chr-61

description: Sample name: SJHYPO061


title: 32-39chr-22

description: Sample name: SJHYPO022


title: 32-39chr-9

description: Sample name: SJHYPO009


title: 32-39chr-12

description: Sample name: SJHYPO012


title: 32-39chr-51

description: Sample name: SJHYPO051


title: Keloid Skin

type: other

city: Kumamoto

first: Katsunari

last: Makino

state: Kumamoto

address: 1-1-1 Honjo

department: Dermatology and Plastic Surgery

country: Japan

institute: Kumamoto University

description: Test

data_processing: The raw threshold cycle (Ct) was normalized using the value of housekeeping gene, U6.

label: SYBR Green

molecule: other

source_name: Human skin obtained by involved skin biopsy from patients with Keloid.

label_protocol: For PCR array, miRNAs were reverse-transcribed into first strand cDNA using RT2 miRNA First Strand Kit (SABiosciences). A mixture of equal amounts of miRNAs from 3 normal skins, 3 SSc, 3 LSc or 3 keloid were prepared, and miRNA expression profile in each disease in vivo was evaluated using RT2 Profiler PCR Array. The cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix and the mixture was added into 96-well RT2 miRNA PCR Array that includes primer pairs for 88 human miRNAs (SABiosciences).

extract_protocol: The microRNA (miRNA) isolation from human skin tissue was performed using miRNeasy FFPE kit (Qiagen).

value: involved skin of Keloid


title: LSc Skin

description: Test

source_name: Human skin obtained by involved skin biopsy from patients with LSc.

value: involved skin of LSc


title: SSc Skin

description: Test

source_name: Human skin obtained by involved skin biopsy from patients with diffuse cutaneous SSc.

value: involved skin of SSc


title: Leaf-Alethea-salt-rep3

city: Lancaster

first: Michael

middle: R

last: Roberts

address: Bailrigg

department: Lancaster Environment Centre

country: United Kingdom

institute: Lancaster University

hyb_protocol: Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Probe signal intensities were extracted from .CEL files and normalised using the GC-RMA method (default settings) in the R Bioconductor suite.

organism: Solanum lycopersicum

source_name: Tomato leaf, Alethea pre-treatment, salt main treatment

label_protocol: Labelled using protocol described in Affymetrix manual 3' IVT Express Kit User Manual

growth_protocol: Tomato seed (cv. Ailsa Craig, Moles Seeds Ltd, Colchester, UK) were sown and germinated in Levington M3 compost (Henry Alty Ltd., Preston, UK), prior to individual transplantation into 2 L pots. Seedlings were maintained in glasshouse conditions supplemented with high pressure sodium lighting, supplying a background Photosynthetically Active Radiation (PAR) photon flux density of approximately μmol m-2 s-1, with a photoperiod of 14 h/10 h light/dark, and air temperatures of 22°C/18°C day/night. Plants were arranged randomly according to treatment, and were grown for four weeks prior to establishment of experimental treatments (approximately 6th true leaf stage).

extract_protocol: For each treatment, a single RNA extract was made from leaf 3 pooled from 3 individual plants. Frozen plant tissue was ground to a fine powder in a pre-cooled pestle and mortar with liquid nitrogen and acid-washed sand, and transferred to a 15 mL polypropylene centrifuge tube. 2 ml well mixed RNA extraction buffer (1:1 mix of phenol and 0.1 M LiCl, 0.1 M Tris.Cl pH 8.0, 10 mM EDTA and 1% SDS) at 95ºC was added per gram of fresh weight plant material and tubes vortexed until thoroughly mixed. Half a volume of chloroform/isoamyl alcohol (24:1) was added and mixed well by vortexing. After centrifugation in a bench top centrifuge at 3500 x g for 10 min at 4ºC, the upper aqueous phase was removed to a new 15 ml centrifuge tube and re-extracted with chloroform/isoamyl alcohol before centrifugation for a further 10 min as before. The aqueous phase was removed to a new centrifuge tube and mixed with an equal volume of 4 M LiCl and incubated overnight at 4ºC. Tubes were then centrifuged for 15 min at 3500 x g at 4ºC to pellet precipitated RNA. The supernatant was removed and the pellet drained and resuspended in 300 µl 0.3 M NaOAc pH 5.2, before being transferred to an Eppendorf tube. RNA was re-precipitated by the addition of 750 µl cold ethanol, followed by centrifugation in a microcentrifuge for 10 min at 14000 rpm. Pellets were drained and rinsed in 70% ethanol and left to dry on the bench, for ~ 30 min, under a 60 W lamp, after which pellets were resuspended in 50-100 µl ddH2O. 100 μg of RNA was purified using a Qiagen RNeasy kit, using the specified protocol (RNeasy® Mini Handbook, Fourth Edition, April 2006).

treatment_protocol: An experimental formula of the ‘Alethea’ technology (Plant Impact PLC, Harpenden, UK) was applied to four-week old tomato seedlings at a concentration of 99:1 v/v (distilledH2O:Alethea) as per manufacturer’s instructions. Control plants, were sprayed with distilled H2O. Alethea solution was sprayed onto leaves until run-off using a pressurized airbrush. Plants were air-dried and then returned to the glasshouse. 24 h following Alethea application, a salinity treatment of 100 mM NaCl was applied to plants via pot-watering until maximum soil saturation was reached (~ 3 h), with control plants fed with H2O only. 24 h following salinity treatment (48 h following Alethea treatment), 3rd true leaves of plants were snap frozen in liquid nitrogen for subsequent RNA extraction.

tag: cultivar

value: Ailsa Craig

value: Leaf

tag: age

value: 4 weeks


title: 32-39chr-74

description: Sample name: SJHYPO074


title: 2x24-31chr-116

description: Sample name: SJHYPO116

source_name: 2x24-31chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: Masked near haploid karyotype


title: 32-39chr-25

description: Sample name: SJHYPO025


title: 2x24-31chr-118

description: Sample name: SJHYPO117

source_name: 2x24-31chr relapse sample. RNA extracted from tumor cells obtained at diagnosis.


title: Normal Skin

description: Control

source_name: Human skin obtained by skin biopsy from healthy donors

tag: tissue

value: normal skin


title: 2x24-31chr-89

description: Sample name: SJHYPO089


title: Leaf-Alethea-water-rep2

source_name: Tomato leaf, Alethea pre-treatment, water main treatment


title: Leaf-Alethea-water-rep3

value: Alethea pre-treatment, water main treatment


title: Leaf-water-salt-rep3

source_name: Tomato leaf, water pre-treatment, salt main treatment


title: 2x24-31chr-88

description: Sample name: SJHYPO088


title: 2x24-31chr-91

description: Sample name: SJHYPO091


title: 2x24-31chr-81

description: Sample name: SJHYPO081


title: Leaf-water-salt-rep2

value: water pre-treatment, salt main treatment


title: Leaf-Alethea-water-rep1


title: Leaf-Alethea-salt-rep2

value: Alethea pre-treatment, salt main treatment


title: Leaf-Alethea-salt-rep1


title: Leaf-water-salt-rep1


title: Leaf-water-water-rep1

source_name: Tomato leaf, water pre-treatment, water main treatment


title: Leaf-water-water-rep2

value: water pre-treatment, water main treatment


title: 2x24-31chr-87

description: Sample name: SJHYPO087


title: 2x24-31chr-72

description: Sample name: SJHYPO072


title: 2x32-39chr-71

description: Sample name: SJHYPO071


title: 2x24-31chr-50

description: Sample name: SJHYPO050


title: 2x24-31chr-42

description: Sample name: SJHYPO042


title: 2x24-31chr-45

description: Sample name: SJHYPO045


title: 24-31chr-90

description: Sample name: SJHYPO090

source_name: 24-31chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.

value: Near haploid karyotype


title: Leaf-water-water-rep3


title: 2x24-31chr-29

description: Sample name: SJHYPO029


title: 2x24-31chr-54

description: Sample name: SJHYPO054


title: subcutaneous adipose tissue needle biopsy Participant 1 control group 6 month visit (technical rep2)

city: Seattle

first: Karen

middle: Weber

last: Makar

state: WA

address: 1100 Fairview Ave N Po box 19024

institute: Fred Hutchinson Cancer Research Center

description:
technical replicate 2
971065-702

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and quantile normalized in GenomeStudio (V2011.1, Gene Expression Module v1.9.0).

source_name: adipose tissue_control_6 month

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

extract_protocol: Qiagen adipose tissue Rneasy kit

tag: gender

value: female

tag: sample group

value: control

tag: time point

value: 6 month


title: 24-31chr-123

description: Sample name: SJHYPO123


title: 2x24-31chr-41

description: Sample name: SJHYPO041


title: subcutaneous adipose tissue needle biopsy Participant 47 diet+exercise group baseline visit

source_name: adipose tissue_diet+exercise_baseline

value: diet+exercise

value: baseline


title: subcutaneous adipose tissue needle biopsy Participant 1 control group baseline visit (technical rep2)

description:
technical replicate 2
971116-702

source_name: adipose tissue_control_baseline


title: 2x24-31chr-43

description: Sample name: SJHYPO043


title: 2x24-31chr-44

description: Sample name: SJHYPO044


title: 24-31chr-85

description: Sample name: SJHYPO085


title: subcutaneous adipose tissue needle biopsy Participant 45 diet group 6 month visit

source_name: adipose tissue_diet_6 month

value: diet


title: subcutaneous adipose tissue needle biopsy Participant 47 diet+exercise group 6 month visit

source_name: adipose tissue_diet+exercise_6 month


title: subcutaneous adipose tissue needle biopsy Participant 45 diet group baseline visit

source_name: adipose tissue_diet_baseline


title: subcutaneous adipose tissue needle biopsy Participant 46 exercise group 6 month visit

source_name: adipose tissue_exercise_6 month

value: exercise


title: subcutaneous adipose tissue needle biopsy Participant 46 exercise group baseline visit

source_name: adipose tissue_exercise_baseline


title: 2x24-31chr-32

description: Sample name: SJHYPO032


title: subcutaneous adipose tissue needle biopsy Participant 44 control group baseline visit


title: subcutaneous adipose tissue needle biopsy Participant 44 control group 6 month visit


title: 24-31chr-69

description: Sample name: SJHYPO069


title: subcutaneous adipose tissue needle biopsy Participant 42 exercise group 6 month visit


title: 24-31chr-66

description: Sample name: SJHYPO066


title: Healthy Monocyte rep2

city: Stockholm

first: Elham

last: Dadfar

country: Sweden

institute: Karolinska Institutet

description: SAMPLE 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U113A GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix scanner GS 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Healthy Monocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Midi Macs CD14 purified perpheral blood monocytes

tag: subject

value: healthy control

tag: cell type

value: CD14 purified perpheral blood monocytes


title: Uremic Monocyte rep1

description: SAMPLE 1

source_name: Uremic Monocyte

value: Uremic patient


title: 24-31chr-75

description: Sample name: SJHYPO075


title: 24-31chr-67

description: Sample name: SJHYPO067


title: 24-31chr-82

description: Sample name: SJHYPO082


title: Uremic Monocyte rep2

description: SAMPLE 2


title: Healthy Monocyte rep1

description: SAMPLE 4


title: 24-31chr-65

description: Sample name: SJHYPO065


title: subcutaneous adipose tissue needle biopsy Participant 41 diet+exercise group baseline visit


title: Uremic Monocyte rep3

description: SAMPLE 3


title: STING-/- + ssDNA90 rep 1

city: Miami

first: Tianli

last: Xia

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

description:
replicate 1
SAMPLE 19

data_processing: Data was Quantile normalized and log2 transformed to median of samples using GeneSpring GX (V.12.5).

label: Biotin

growth_protocol: DMEM suppliemented with 10% DMEM, 37 °C, 5% CO2

extract_protocol: total RNA extraction using QIAGEN RNeasy mini kit following kit instruction

treatment_protocol: lipofectamin 2000 (invitrogen) standard transfection protocol

tag: strain background

tag: genotype/variation

value: STING knock-out; STING-/-

value: primary mouse embryonic fibroblasts (MEFs)

tag: treated with

value: ssDNA90 for 3 h


title: 24-31chr-60

description: Sample name: SJHYPO060


title: subcutaneous adipose tissue needle biopsy Participant 40 diet+exercise group 6 month visit


title: 24-31chr-56

description: Sample name: SJHYPO056


title: STAT1-/- + dsDNA90 rep 2

description:
replicate 2
SAMPLE 16

value: STAT1 knock-out; STAT1-/-

value: dsDNA90 for 3 h


title: subcutaneous adipose tissue needle biopsy Participant 41 diet+exercise group 6 month visit


title: Healthy Monocyte rep3

description: SAMPLE 6


title: 24-31chr-62

description: Sample name: SJHYPO062


title: STING-/- + ssDNA90 rep 2

description:
replicate 2
SAMPLE 20


title: STING+/+ + ssDNA90 rep 1

description:
replicate 1
SAMPLE 17

value: wild type; STING+/+


title: STING+/+ + ssDNA90 rep 2

description:
replicate 2
SAMPLE 18


title: subcutaneous adipose tissue needle biopsy Participant 43 diet+exercise group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 43 diet+exercise group baseline visit


title: subcutaneous adipose tissue needle biopsy Participant 42 exercise group baseline visit


title: STAT1-/- rep 2

description:
replicate 2
SAMPLE 14


title: STAT1-/- rep 1

description:
replicate 1
SAMPLE 13


title: 24-31chr-49

description: Sample name: SJHYPO049

value: Near haploid karyotype


title: subcutaneous adipose tissue needle biopsy Participant 40 diet+exercise group baseline visit

value: female


title: STAT1+/+ + dsDNA90 rep 2

description:
replicate 2
SAMPLE 12

value: wild type; STAT1+/+


title: 24-31chr-46

description: Sample name: SJHYPO046


title: STAT1+/+ + dsDNA90 rep 1

description:
replicate 1
SAMPLE 11


title: 24-31chr-47

description: Sample name: SJHYPO047


title: STAT1+/+ rep 1

description:
replicate 1
SAMPLE 9


title: subcutaneous adipose tissue needle biopsy Participant 39 exercise group 6 month visit

value: 6 month


title: subcutaneous adipose tissue needle biopsy Participant 38 diet group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 37 control group 6 month visit

value: control


title: STING+/+ rep 2

description:
replicate 2
SAMPLE 2


title: 24-31chr-39

description: Sample name: SJHYPO039


title: subcutaneous adipose tissue needle biopsy Participant 39 exercise group baseline visit

value: baseline


title: subcutaneous adipose tissue needle biopsy Participant 38 diet group baseline visit

value: diet


title: STING-/- + dsDNA90 rep 1

description:
replicate 1
SAMPLE 7


title: STAT1+/+ rep 2

description:
replicate 2
SAMPLE 10


title: STING-/- + dsDNA90 rep 2

description:
replicate 2
SAMPLE 8


title: STING-/- rep 1

description:
replicate 1
SAMPLE 5


title: STING+/+ + dsDNA90 rep 2

description:
replicate 2
SAMPLE 4


title: 24-31chr-37

description: Sample name: SJHYPO037


title: STING-/- rep 2

description:
replicate 2
SAMPLE 6


title: subcutaneous adipose tissue needle biopsy Participant 37 control group baseline visit


title: 24-31chr-40

description: Sample name: SJHYPO040


title: STING+/+ rep 1

description:
replicate 1
SAMPLE 1


title: STING+/+ + dsDNA90 rep 1

description:
replicate 1
SAMPLE 3


title: 24-31chr-35

description: Sample name: SJHYPO035


title: 24-31chr-31

description: Sample name: SJHYPO031


title: subcutaneous adipose tissue needle biopsy Participant 36 exercise group baseline visit

value: exercise


title: STING-/-

description: SAMPLE 3

source_name: mouse embryonic fibroblasts

treatment_protocol: primary MEFs were infected with γ34.5 deleted HSV1 at M.O.I. 1 for 1 hour, washed and incubated in fresh medium for another 3 hours


title: STING-/- + HSV1

description: SAMPLE 4

tag: infected with

value: γ34.5 deleted HSV1 at M.O.I. 1 for 1 h


title: STING+/+

description: SAMPLE 1


title: subcutaneous adipose tissue needle biopsy Participant 36 exercise group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 35 diet+exercise group 6 month visit

value: diet+exercise


title: subcutaneous adipose tissue needle biopsy Participant 35 diet+exercise group baseline visit


title: STING+/+ + HSV1

description: SAMPLE 2


title: 24-31chr-34

description: Sample name: SJHYPO034


title: 24-31chr-28

description: Sample name: SJHYPO028


title: subcutaneous adipose tissue needle biopsy Participant 34 diet+exercise group 6 month visit


title: 24-31chr-30

description: Sample name: SJHYPO030


title: Trachea E18_5 WT2

city: Irvine

first: Denise

last: Stephens

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

description: Mouse trachea, embryonic day 18.5

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: Mouse trachea, embryonic day 18.5

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Tissues from mice were collected at respective ages.

extract_protocol: Tissues were homogenized and total RNA extracted with Trizol.  RNA samples were cleaned up with Invitrogen Pure Link kit.

value: trachea

value: wildtype CB6 mice


title: Trachea E18_5 WT1

description: Mouse trachea, embryonic day 18.5


title: Cornea P28 9a

description: Whole mouse cornea, postnatal day 28, rep3

source_name: Whole mouse cornea, postnatal day 28

value: whole cornea


title: 24-31chr-24

description: Sample name: SJHYPO024


title: Trachea E18_5 WT3

description: Mouse trachea, embryonic day 18.5


title: Lung E18_5 WT2

description: Mouse lung, embryonic day 18.5

source_name: Mouse lung, embryonic day 18.5

value: lung


title: 24-31chr-23

description: Sample name: SJHYPO023


title: Lung E18_5 WT3

description: Mouse lung, embryonic day 18.5


title: Cornea P28 7a

description: Whole mouse cornea, postnatal day 28, rep2


title: Cornea P28 3a

description: Whole mouse cornea, postnatal day 28, rep1


title: subcutaneous adipose tissue needle biopsy Participant 34 diet+exercise group baseline visit


title: Lung E18_5 WT1

description: Mouse lung, embryonic day 18.5


title: subcutaneous adipose tissue needle biopsy Participant 33 exercise group 6 month visit


title: Cornea P14 05a

description: Whole mouse cornea, postnatal day 14, rep3

source_name: Whole mouse cornea, postnatal day 14


title: Cornea P7 10a

description: Whole mouse cornea, postnatal day 7, rep3

source_name: Whole mouse cornea, postnatal day 7


title: 24-31chr-21

description: Sample name: SJHYPO021

source_name: 24-31chr diagnosis sample. RNA extracted from tumor cells obtained at diagnosis.


title: Cornea P14 03b

description: Whole mouse cornea, postnatal day 14, rep2


title: Cornea P14 01a

description: Whole mouse cornea, postnatal day 14, rep1


title: subcutaneous adipose tissue needle biopsy Participant 33 exercise group baseline visit


title: Cornea P7 7b

description: Whole mouse cornea, postnatal day 7, rep2


title: Cornea P7 4b

description: Whole mouse cornea, postnatal day 7, rep1


title: 24-31chr-19

description: Sample name: SJHYPO019


title: subcutaneous adipose tissue needle biopsy Participant 32 diet group 6 month visit


title: 24-31chr-20

description: Sample name: SJHYPO020


title: 24-31chr-18

description: Sample name: SJHYPO018


title: Cornea P3 7b

description: Whole mouse cornea, postnatal day 3, rep2

source_name: Whole mouse cornea, postnatal day 3


title: subcutaneous adipose tissue needle biopsy Participant 32 diet group baseline visit


title: Cornea P3 9a

description: Whole mouse cornea, postnatal day 3, rep3


title: subcutaneous adipose tissue needle biopsy Participant 31 control group 6 month visit

source_name: adipose tissue_control_6 month


title: Cornea P3 2a

description: Whole mouse cornea, postnatal day 3, rep1


title: Cornea E17_5 5R

description: Whole mouse cornea, embryonic day 17.5, rep2

source_name: Whole mouse cornea, embryonic day 17.5


title: Cornea E17_5 6L

description: Whole mouse cornea, embryonic day 17.5, rep3


title: Cornea E15_5 7b

description: Whole mouse cornea, embryonic day 15.5, rep3

source_name: Whole mouse cornea, embryonic day 15.5


title: 24-31chr-16

description: Sample name: SJHYPO016


title: 24-31chr-15

description: Sample name: SJHYPO015


title: STAT1-/- + dsDNA90 rep 1

description:
replicate 1
SAMPLE 15

value: STAT1 knock-out; STAT1-/-

value: primary mouse embryonic fibroblasts (MEFs)


title: 24-31chr-8

description: Sample name: SJHYPO008


title: subcutaneous adipose tissue needle biopsy Participant 31 control group baseline visit

source_name: adipose tissue_control_baseline


title: subcutaneous adipose tissue needle biopsy Participant 30 diet+exercise group 6 month visit

source_name: adipose tissue_diet+exercise_6 month


title: Cornea E15_5 6a

description: Whole mouse cornea, embryonic day 15.5, rep2


title: Cornea E14_5 13a

description: Whole mouse cornea, embryonic day 14.5, rep3

source_name: Whole mouse cornea, embryonic day 14.5


title: Ikaros transduced cells 48h, biological rep3  [primary pre-B cells]

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description:
Gene expression data from 48h Ikaros transduced primary pre-B cells
Ikaros-48h_3

hyb_protocol: Fragmented and labelled cDNA from three biological replicates was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Gene 1.0 ST arrays were normalised using rma-sketch implemented in Expression Consol Software 1.2.1

source_name: primary pre-B cell

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) for hybridization on MoGene 1.0 ST v1 arrays was used according to Affymetrix protocol.

growth_protocol: Primary pre-B cells were established from fetal liver cells plated on irradiated ST2 stromal cells in IMDM, 10% FCS, 1% penicillin-streptomycin, 2 mM 2-mercaptoethanol, and 5 ng/ml IL-7.

extract_protocol: RNA was isolated with RNAbee (Ambion). Total RNA was amplified using GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix).

treatment_protocol: Primary pre-B cells were transduced as described  (Thompson et al., 2007, Immunity 26:335-344) with mouse stem cell virus (MSCV) vectors encoding wild-type Ikaros tagged with a haemagglutinin (HA) epitope followed by an internal ribosomal entry site (IRES) and GFP (HA-Ikaros-IRES-GFP), or the IRES-GFP control vector.

tag: strain

value: a mix of C57BL/6 and 129

value: Fetal liver

value: primary pre-B cell

tag: transduced with

value: wild type Ikaros (HA-Ikaros-IRES-GFP)


title: Cornea E14_5 4a

description: Whole mouse cornea, embryonic day 14.5, rep1


title: Cornea E14_5 8a

description: Whole mouse cornea, embryonic day 14.5, rep2


title: Cornea E17_5 3L

description: Whole mouse cornea, embryonic day 17.5, rep1


title: subcutaneous adipose tissue needle biopsy Participant 30 diet+exercise group baseline visit

source_name: adipose tissue_diet+exercise_baseline

value: female


title: subcutaneous adipose tissue needle biopsy Participant 29 exercise group baseline visit

source_name: adipose tissue_exercise_baseline


title: Ikaros transduced cells 48h, biological rep2  [primary pre-B cells]

description:
Gene expression data from 48h Ikaros transduced primary pre-B cells
Ikaros-48h_2


title: control vector transduced cells 48h, biological rep2  [primary pre-B cells]

description:
Gene expression data from 48h control vector transduced primary pre-B cells
control vector-48h_2

value: control vector (IRES-GFP)


title: control vector transduced cells 48h, biological rep3  [primary pre-B cells]

description:
Gene expression data from 48h control vector transduced primary pre-B cells
control vector-48h_3


title: subcutaneous adipose tissue needle biopsy Participant 29 exercise group 6 month visit

source_name: adipose tissue_exercise_6 month

value: 6 month


title: 24-31chr-1

description: Sample name: SJHYPO001

value: Near haploid karyotype


title: Ikaros transduced cells 48h, biological rep1  [primary pre-B cells]

description:
Gene expression data from 48h Ikaros transduced primary pre-B cells
Ikaros-48h_1


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_microRNA_rep3

city: Beijing

first: Yong

last: Yang

address: baijiazhuang street 8

country: China

institute: ccmu

description: microRNA expression data of A549/CDDP rep 3.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Background detection was followed by RMA global background correlation, quantile normalization, median estimation and log2-transformation using the miRNA QC software tool (Affymetrix).

source_name: cisplatin-resistant A549/CDDP lung cancer cell line

label_protocol: miRNA microarray target labeling was conducted using 1000 ng of total RNA and the FlashTag Biotin HSR kit (Genisphere, Hatfield, PA).

growth_protocol: Cells were maintained in RPMI-1640 medium (Life Technologies) supplemented with 10% fetal calf serum (Gibco, Grand Island, NY, USA) in a humid atmosphere containing 5% CO2 at 37°C. The A549/CDDP cell medium additionally contained 2 mg/L cisplatin in order to maintain its drug-resistant phenotype.

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

tag: cell line

value: A549/CDDP (A549 derivative)

value: lung adenocarcinoma cells

tag: cisplatin sensitivity

value: resistant


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_microRNA_rep2

description: microRNA expression data of A549/CDDP rep 2.


title: 24-31chr-2

description: Sample name: SJHYPO002

tag: all subtype


title: subcutaneous adipose tissue needle biopsy Participant 28 diet+exercise group 6 month visit

value: diet+exercise


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_microRNA_rep3

description: microRNA expression data of A549 rep 3.

source_name: parental A549 lung cancer cell line

value: A549 (parental)

value: sensitive


title: vector-ERt2 cells 6h OHT, biological rep2

description:
Gene expression data from 6h 4-OHT-treated vector control B3 cells
vector-ERt2_2

hyb_protocol: cRNA from two biological replicates per condition was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) and Fragmented and labelled cDNA from three biological replicates per condition was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Genome 4302 arrays were normalised using GCRMA within the GCRMA R/Bioconductor package (v.2.20.0) and hybridisation batch effects removed using the Limma R/Bioconductor package. Mouse Gene 1.0 ST arrays were normalised using RMA implemented in the Affy R/Bioconductor package (v.1.26.1).

source_name: vector-ERt2 cells 6h OHT

label_protocol: GeneChip IVT labelling kit (Affymetrix) for hybridization on 430 2.0 arrays and GeneChip WT Terminal Labeling Kit (Affymetrix) for hybridization on MoGene 1.0 ST v1 arrays were used according to Affymetrix protocol.

growth_protocol: Mouse pre-B cell line B3 was grown in IMDM, 10% FCS and  1% penicillin-streptomycin.

extract_protocol: RNA was isolated with RNAbee (Ambion). Total RNA was amplified using either GeneChip Two-Cycle cDNA synthesis kit (Affymetrix) or GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix).

treatment_protocol: B3 cells were transduced as described  (Thompson et al., 2007, Immunity 26:335-344) with mouse stem cell virus (MSCV) vectors encoding wild-type Ikaros tagged with a haemagglutinin (HA) epitope followed by an internal ribosomal entry site (IRES) and GFP (HA-Ikaros-IRES-GFP), or the DNA binding-deficient Ikaros mutant 159A (HA-159A Ikaros-IRES-GFP). Ikaros inducible cells were generated by transducing B3 cells with a construct encoding a fusion protein of HA-tagged Ikaros and the estrogen receptor hormone-binding domain (HA-Ikaros-ERt2-IRES-GFP) or an ERt2-IRES-GFP control vector.

value: pre-B cells

value: Vector (ERt2-IRES-GFP)

value: 4-hydroxytamoxifen for 6h


title: control vector transduced cells 48h, biological rep1  [primary pre-B cells]

description:
Gene expression data from 48h control vector transduced primary pre-B cells
control vector-48h_1

value: a mix of C57BL/6 and 129


title: vector-ERt2 cells 6h OHT, biological rep1

description:
Gene expression data from 6h 4-OHT-treated vector control B3 cells
vector-ERt2_1


title: subcutaneous adipose tissue needle biopsy Participant 27 exercise group baseline visit

value: exercise

value: baseline


title: vector-ERt2 cells 6h OHT, biological rep3

description:
Gene expression data from 6h 4-OHT-treated vector control B3 cells
vector-ERt2_3


title: Cornea E15_5 1a

description: Whole mouse cornea, embryonic day 15.5, rep1

value: whole cornea

tag: genotype

value: wildtype CB6 mice


title: subcutaneous adipose tissue needle biopsy Participant 28 diet+exercise group baseline visit

value: female


title: 24-31chr-6

description: Sample name: SJHYPO006


title: Ikaros-ERt2 cells 6h OHT, biological rep3

description:
Gene expression data from 6h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-6h_3

source_name: Ikaros-ERt2 cells 6h OHT


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_microRNA_rep1

description: microRNA expression data of A549/CDDP rep 1.


title: subcutaneous adipose tissue needle biopsy Participant 27 exercise group 6 month visit

value: 6 month


title: 7 days post-amputation wildtype adult zebrafish, sample 3

city: Montpellier

first: Chris

last: Jopling

address: 141 rue de la Cardonille

department: Physiologie

country: France

institute: Institut de Génomique Fonctionnelle

description:
WT3_7
Gene expression data from 7 day post-amputation wildtype adult zebrafish hearts.

hyb_protocol: Samples were hybridized to GeneChip Zebrafish Genome Arrays (Affymetrix) using a GeneChip Hybridization Oven 640.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed using the RMA algorithm. Then, LIMMA was applied to calculate significant differential expression between samples.

organism: Danio rerio

label_protocol: 200 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix).

tag: line

value: AB

value: wildtype

value: heart

tag: developmental stage

value: adult, sexually mature

tag: treatment

value: amputation

tag: time post-treatment

value: 7 days


title: Ikaros-ERt2 cells 6h OHT, biological rep2

description:
Gene expression data from 6h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-6h_2


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_lncRNA_rep3

description: lncRNA and mRNA expression data of A549/CDDP rep 3.

hyb_protocol: Hybridization was performed in Agilent's SureHyb Hybridization Chambers.

scan_protocol: Data was extracted using Agilent Feature Extraction software.

data_processing: Raw signal intensities were normalized by the quantile method using Agilent GeneSpring GX v11.5.1. Low intensity lncRNAs and mRNAs were filtered out.

label_protocol: The Agilent Quick Amp Labeling Kit was used for sample labeling.

value: A549/CDDP (A549 derivative)

value: lung adenocarcinoma cells

value: resistant


title: Ikaros-ERt2 cells 2h OHT, biological rep3

description:
Gene expression data from 2h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-2h_3

source_name: Ikaros-ERt2 cells 2h OHT

value: pre-B cells

value: 4-hydroxytamoxifen for 2h


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_lncRNA_rep3

description: lncRNA and mRNA expression data of A549 rep 3.

value: A549 (parental)

value: sensitive


title: subcutaneous adipose tissue needle biopsy Participant 26 diet group baseline visit

source_name: adipose tissue_diet_baseline

tag: gender

tag: tissue

tag: sample group

value: diet

tag: time point

value: baseline


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_microRNA_rep2

description: microRNA expression data of A549 rep 2.

tag: cell type


title: 7 days post-amputation wildtype adult zebrafish, sample 2

description:
WT2_7
Gene expression data from 7 day post-amputation wildtype adult zebrafish hearts.


title: subcutaneous adipose tissue needle biopsy Participant 26 diet group 6 month visit

source_name: adipose tissue_diet_6 month

value: female


title: 7 days post-amputation dnHIF1a-expressing adult zebrafish, sample 2

description:
HIF2_7
Gene expression data from 7 day post-amputation dnHIF1a-expressing adult zebrafish hearts.


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_microRNA_rep1

description: microRNA expression data of A549 rep 1.


title: Ikaros-ERt2 cells 2h OHT, biological rep2

description:
Gene expression data from 2h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-2h_2

tag: treated with


title: 7 days post-amputation wildtype adult zebrafish, sample 1

description:
WT1_7
Gene expression data from 7 day post-amputation wildtype adult zebrafish hearts.


title: 7 days post-amputation dnHIF1a-expressing adult zebrafish, sample 1

description:
HIF1_7
Gene expression data from 7 day post-amputation dnHIF1a-expressing adult zebrafish hearts.


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_lncRNA_rep2

description: lncRNA and mRNA expression data of A549/CDDP rep 2.


title: A549/CDDP cisplatin-resistant non-small cell lung cancer cell line_lncRNA_rep1

description: lncRNA and mRNA expression data of A549/CDDP rep 1.


title: Unamputated wildtype adult zebrafish, sample 3

description:
WT3_0
Gene expression data from unamputated wildtype adult zebrafish hearts.

source_name: unamputated wildtype adult zebrafish


title: Ikaros-ERt2 cells 6h OHT, biological rep1

description:
Gene expression data from 6h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-6h_1

value: 4-hydroxytamoxifen for 6h


title: Ikaros-ERt2 cells 2h OHT, biological rep1

description:
Gene expression data from 2h 4-OHT-treated Ikaros inducible B3 cells
Ikaros-ERt2-2h_1


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_lncRNA_rep2

description: lncRNA and mRNA expression data of A549 rep 2.


title: Unamputated wildtype adult zebrafish, sample 2

description:
WT2_0
Gene expression data from unamputated wildtype adult zebrafish hearts.

value: AB


title: 7 days post-amputation dnHIF1a-expressing adult zebrafish, sample 3

description:
HIF3_7
Gene expression data from 7 day post-amputation dnHIF1a-expressing adult zebrafish hearts.


title: subcutaneous adipose tissue needle biopsy Participant 24 diet+exercise group baseline visit

value: diet+exercise


title: mammary tumor after orthotopic injection of 6dt1 cells expressing negative control rep4

description: Mammary tumor RNA collected 30 days after orthotopic injection of 6dt1 cells in female FVB/N mice.

hyb_protocol: Samples were hybridized in the GeneChip Hybridization Oven 645 while shaking at 60 rpm at 45C for 16 hrs.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were collected using the GeneChip Command Console Software (AGCC).
MoEx-1_0-st-v1.r2.pgf
MoGene-1_0-st-v1.na32.mm9.transcript

label: Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

source_name: mammary tumor

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

growth_protocol: Mammary tumors were collected 30 days after orthotopic injection of 6dt1 cells.

extract_protocol: Samples were snap frozen in liquid N2. Total RNA was isolated using RNAeasy Kit (Qiagen).  RNA (100 ng) was reverse transcribed and amplified using WT Expression Kit (Ambion).

treatment_protocol: not applicable

value: FVB/N

value: mammary tumor


title: subcutaneous adipose tissue needle biopsy Participant 24 diet+exercise group 6 month visit

value: 6 month


title: subcutaneous adipose tissue needle biopsy Participant 25 control group 6 month visit

source_name: adipose tissue_control_6 month

value: control


title: subcutaneous adipose tissue needle biopsy Participant 25 control group baseline visit

source_name: adipose tissue_control_baseline


title: A549 cisplatin-sensitive non-small cell lung cancer cell line_lncRNA_rep1

description: lncRNA and mRNA expression data of A549 rep 1.


title: subcutaneous adipose tissue needle biopsy Participant 23 exercise group baseline visit

value: exercise


title: mammary tumor after orthotopic injection of 6dt1 cells expressing negative control rep3


title: subcutaneous adipose tissue needle biopsy Participant 23 exercise group 6 month visit


title: Unamputated dnHIF1a-expressing adult zebrafish, sample 3

description:
HIF3_0
Gene expression data from unamputated dnHIF1a-expressing adult zebrafish hearts.

value: heart

value: adult, sexually mature


title: Unamputated dnHIF1a-expressing adult zebrafish, sample 1

description:
HIF1_0
Gene expression data from unamputated dnHIF1a-expressing adult zebrafish hearts.


title: Unamputated wildtype adult zebrafish, sample 1

description:
WT1_0
Gene expression data from unamputated wildtype adult zebrafish hearts.

value: wildtype


title: subcutaneous adipose tissue needle biopsy Participant 21 exercise group baseline visit


title: P0_Ovary_TNF_biological rep2

city: Pullman

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from rat P0 Ovary incubated in the presence of 1 ng/ml TNF for 24 hours

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

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

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software  (Partek Inc., St. Louis, MO) uing RMA, GC-content adjusted algorithm background correction, quantile normalization, median polish methos for probesets summarization, and log values of probes signals using base 2.

organism: Rattus norvegicus

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Zero-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured for 24 hours in the absence  (controls) or presence (treated) of either Amh (human Anti-Mülerian hormone)(50ng/mL), CTGF (connective tissue growth factor )(500 ng/mL), progesterone (P4) (10E-6 M),  estradiol (E2) (10E-6 M), TNF (tumor necrosis factor ) (1ng/mL), FGF2 (fibroblast growth factor 2) (50 ng/mL), Inhba (inhibin, beta A) (10 ng/mL).   Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.  On any given day a culture experiment was performed, the treatment groups included untreated control ovaries and one to three different growth factor treatments.

tag: organ culture batch

tag: rna prep batch

tag: scan date

value: Sprague-Dawley rat

value: Female

value: Rat ovary

value: Rat ovary  at day P0 incubated for 1 more day


title: Unamputated dnHIF1a-expressing adult zebrafish, sample 2

description:
HIF2_0
Gene expression data from unamputated dnHIF1a-expressing adult zebrafish hearts.


title: subcutaneous adipose tissue needle biopsy Participant 22 diet+exercise group 6 month visit

source_name: adipose tissue_diet+exercise_6 month


title: P0_Ovary_TNF_biological rep3

source_name: P0 Ovary incubated in the presence of 1 ng/ml TNF for 24 hours


title: P0_Ovary_P4_biological rep2

description: Gene expression data from rat P0 Ovary incubated in the presence of 10E-6M progesterone (P4) for 24 hours


title: P0_Ovary_TNF_biological rep1

value: incubated in the presence of 1 ng/ml TNF for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 21 exercise group 6 month visit

value: female


title: mammary tumor after orthotopic injection of 6dt1 cells expressing miR-290 rep2

tag: strain


title: P0_Ovary_Inhba_biological rep3

description: Gene expression data from rat P0 Ovary incubated in the presence of 100 ng/ml Inhba for 24 hours


title: P0_Ovary_Inhba_biological rep2

source_name: P0 Ovary incubated in the presence of 100 ng/ml Inhba for 24 hours


title: P0_Ovary_Inhba_biological rep1

value: incubated in the presence of 100 ng/ml Inhba for 24 hours


title: P0_Ovary_P4_biological rep1

source_name: P0 Ovary incubated in the presence of 10E-6M progesterone (P4) for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 19 control group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 20 diet group 6 month visit

value: diet


title: subcutaneous adipose tissue needle biopsy Participant 19 control group baseline visit

value: baseline


title: mammary tumor after orthotopic injection of 6dt1 cells expressing miR-290 rep3

value: FVB/N


title: subcutaneous adipose tissue needle biopsy Participant 17 exercise group baseline visit

source_name: adipose tissue_exercise_baseline


title: subcutaneous adipose tissue needle biopsy Participant 17 exercise group 6 month visit

source_name: adipose tissue_exercise_6 month


title: subcutaneous adipose tissue needle biopsy Participant 22 diet+exercise group baseline visit

source_name: adipose tissue_diet+exercise_baseline

value: diet+exercise


title: subcutaneous adipose tissue needle biopsy Participant 16 diet+exercise group 6 month visit

value: 6 month


title: subcutaneous adipose tissue needle biopsy Participant 20 diet group baseline visit


title: mammary tumor after orthotopic injection of 6dt1 cells expressing negative control rep2

value: mammary tumor


title: subcutaneous adipose tissue needle biopsy Participant 18 diet+exercise group baseline visit


title: mammary tumor after orthotopic injection of 6dt1 cells expressing miR-290 rep1


title: subcutaneous adipose tissue needle biopsy Participant 18 diet+exercise group 6 month visit


title: mammary tumor after orthotopic injection of 6dt1 cells expressing negative control rep1


title: P0_Ovary_FGF2_biological rep2

description: Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml FGF2 for 24 hours


title: P0_Ovary_FGF2_biological rep3

source_name: P0 Ovary incubated in the presence of 50 ng/ml FGF2 for 24 hours


title: bmhhdac-1

first: Kenneth

middle: M

last: Dombek

address: 1959 Pacific St. N.E.

department: Biochemistry

institute: University of Washington

hyb_protocol: Fragmented cRNAs were loaded into Yeast 2.0 arrays and rotated at 60 rpm for 16 h in an Affymetrix hybridization oven set at 45˚C. Hybridized arrays were then stained and washed using an Affymetrix Fluidics Station 450 as described in the Fluidics Station manual for Yeast 2.0 arrays.

scan_protocol: The stained arrays were scanned using an Affymetrix GeneChip scanner.

data_processing: The data were analyzed using various Bioconductor packages for the R statistical analysis programming environment. First, all S. pombe probe sets, individual S. cerevisiae probes whose sequence contains a SNP in the W303 genome sequence as determined by the Saccharomyces Genome Resequencing Project (Sanger Institute in Cambridge, U.K.), and probes from probe sets that overlapped deletions present in the W303 genome as determined by Schacherer et al. (Nature. 2009. 458:342-5) were filtered from the cdf environment created from the information in the yeast2cdf package. This was accomplished using the Bioconductor altcdfenvs and makecdfenv packages. Then, the probe intensities were summarized using the Bioconductor affy package. Background was corrected using RMA, and then the data was normalized by Quantiles and summarized by Median polish.

organism: Saccharomyces cerevisiae

source_name: Exponentially growing cells, CTY-TY44

label_protocol: Biotinylated cRNAs were prepared from 250 ng of each total RNA and fragmented using the Affymetrix 3' IVT Express Kit.

growth_protocol: Cells were incubated overnight in YP medium containing 5% glucose on a flask shaker at 30˚C until they reached an optical density at 600 nm of between 0.7 and 1.3.

extract_protocol: RNA was isolated by the standard hot acid phenol method for yeast.

treatment_protocol: Growth in YP medium with 5% glucose as the carbon source.

tag: genetic background

tag: genotype/variation

value: bmh1-170ts bmh2∆ hda1∆ rpd3∆

tag: carbon source

value: 5% glucose

tag: growth phase

value: exponential


title: hdac-3

source_name: Exponentially growing cells, KBY3

value: hda1∆ rpd3∆


title: P0_Ovary_E2_biological rep3

description: Gene expression data from rat P0 Ovary incubated in the presence of 10E-6M estradiol (E2) for 24 hours

tag: genotype

value: Sprague-Dawley rat

tag: developmental stage


title: hdac-2


title: bmhhdac-2


title: hdac-1


title: P0_Ovary_FGF2_biological rep1

value: Female

tag: treatment

value: incubated in the presence of 50 ng/ml FGF2 for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 14 diet group 6 month visit

tag: gender


title: subcutaneous adipose tissue needle biopsy Participant 14 diet group baseline visit

tag: tissue


title: subcutaneous adipose tissue needle biopsy Participant 13 control group 6 month visit

tag: sample group

value: control


title: bmhhdac-3


title: P0_Ovary_CTGF_biological rep3 2

description: Gene expression data from rat P0 Ovary incubated in the presence of 500 ng/ml CTGF for 24 hours

value: Rat ovary

value: Rat ovary  at day P0 incubated for 1 more day


title: P0_Ovary_E2_biological rep1

source_name: P0 Ovary incubated in the presence of 10E-6M estradiol (E2) for 24 hours


title: bmh-3

source_name: Exponentially growing cells, YLL1087

value: bmh1-170ts bmh2∆


title: subcutaneous adipose tissue needle biopsy Participant 16 diet+exercise group baseline visit

value: female

tag: time point


title: P0_Ovary_CTGF_biological rep2 2

source_name: P0 Ovary incubated in the presence of 500 ng/ml CTGF for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 15 exercise group baseline visit

value: exercise

value: baseline


title: P0_Ovary_CTGF_biological rep1 2

value: incubated in the presence of 500 ng/ml CTGF for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 15 exercise group 6 month visit

value: 6 month


title: subcutaneous adipose tissue needle biopsy Participant 13 control group baseline visit


title: P0_Ovary_E2_biological rep2

value: incubated in the presence of 10E-6M estradiol (E2) for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 12 exercise group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 11 diet+exercise group baseline visit

value: diet+exercise


title: subcutaneous adipose tissue needle biopsy Participant 12 exercise group baseline visit


title: P0_Ovary_AMH_biological rep3

description: Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours


title: subcutaneous adipose tissue needle biopsy Participant 11 diet+exercise group 6 month visit


title: bmh-2

value: 5% glucose


title: bmh-1

value: exponential


title: W303-2

source_name: Exponentially growing cells, W303-1A

value: wild type


title: W303-1


title: P0_Ovary_Control_biological rep6

description: Gene expression data from rat P0 Ovary incubated for 24 hours with no treatmnet

value: Sprague-Dawley rat


title: P0_Ovary_AMH_biological rep1

source_name: P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours

value: Female


title: W303-3


title: P0_Ovary_Control_biological rep2 2

source_name: P0 Ovary incubated for 24 hours with no treatmnet


title: P0_Ovary_Control_biological rep5

value: incubated for 24 hours with no treatmnet


title: P0_Ovary_Control_biological rep3 2


title: Sto E18_5 WT4

description: Mouse stomach, embryonic day 18.5

source_name: Mouse stomach, embryonic day 18.5

value: stomach

value: wildtype CB6 mice


title: P0_Ovary_Control_biological rep8

value: Rat ovary

value: Rat ovary  at day P0 incubated for 1 more day


title: Sto E18_5 WT1

description: Mouse stomach, embryonic day 18.5


title: subcutaneous adipose tissue needle biopsy Participant 10 diet+exercise group baseline visit

value: female


title: siSTING+dsDNA90-2

description:
replicate 2
SAMPLE 8

growth_protocol: DMEM:Medium 199 at 1:4 suppliemented with 4 mM L-Glutamine, 1mM sodium pyruvate and 10% DMEM, 37 °C, 5% CO2

treatment_protocol: siRNA transfect using lipofectamin RNAimax and DNA transfection using lipofectamin 2000 following invitrogen standard transfection protocols

tag: cell line

tag: cell type

value: foreskin fibroblast cells

tag: transfected with

value: STING siRNA for 72 h

tag: stimulated with

value: dsDNA90  for 3 hrs


title: Sto E18_5 WT2

description: Mouse stomach, embryonic day 18.5


title: subcutaneous adipose tissue needle biopsy Participant 10 diet+exercise group 6 month visit

source_name: adipose tissue_diet+exercise_6 month

value: 6 month


title: E18.5 WT Dorsal Skin 6-4

description: Dorsal skin, embryonic day 18.5

source_name: Dorsal skin, embryonic day 18.5

value: dorsal skin


title: E18.5 WT Dorsal Skin 5-5

description: Dorsal skin, embryonic day 18.5


title: subcutaneous adipose tissue needle biopsy Participant 7 control group 6 month visit

source_name: adipose tissue_control_6 month

value: control


title: P0_Ovary_Control_biological rep7

tag: organ culture batch

tag: rna prep batch

tag: scan date


title: siSTING+dsDNA90-1

description:
replicate 1
SAMPLE 7


title: subcutaneous adipose tissue needle biopsy Participant 7 control group baseline visit

source_name: adipose tissue_control_baseline

value: baseline


title: subcutaneous adipose tissue needle biopsy Participant 9 exercise group baseline visit

source_name: adipose tissue_exercise_baseline

value: exercise


title: siSTING-2

description:
replicate 2
SAMPLE 6


title: subcutaneous adipose tissue needle biopsy Participant 8 diet group 6 month visit

source_name: adipose tissue_diet_6 month

value: diet


title: P0_Ovary_Control_biological rep1 2

value: Sprague-Dawley rat


title: subcutaneous adipose tissue needle biopsy Participant 9 exercise group 6 month visit

source_name: adipose tissue_exercise_6 month


title: subcutaneous adipose tissue needle biopsy Participant 8 diet group baseline visit

source_name: adipose tissue_diet_baseline


title: subcutaneous adipose tissue needle biopsy Participant 6 diet group 6 month visit


title: E18.5 WT Dorsal Skin 1-4

description: Dorsal skin, embryonic day 18.5


title: siSTING-1

description:
replicate 1
SAMPLE 5


title: E16.5 WT Dorsal Skin 8

description: Dorsal skin, embryonic day 16.5

source_name: Dorsal skin, embryonic day 16.5


title: subcutaneous adipose tissue needle biopsy Participant 6 diet group baseline visit


title: Skin E14_5 1-2_re

description: Dorsal skin, embryonic day 14.5

source_name: Dorsal skin, embryonic day 14.5


title: E16.5 WT Dorsal Skin 7

description: Dorsal skin, embryonic day 16.5


title: si-NS-2

description:
replicate 2
SAMPLE 2

value: non-specific siRNA for 72 h


title: si-NS+dsDNA90-2

description:
replicate 2
SAMPLE 4


title: E16.5 WT Dorsal Skin 6

description: Dorsal skin, embryonic day 16.5


title: si-NS+dsDNA90-1

description:
replicate 1
SAMPLE 3


title: subcutaneous adipose tissue needle biopsy Participant 5 diet+exercise group baseline visit

source_name: adipose tissue_diet+exercise_baseline

value: diet+exercise


title: si-NS-1

description:
replicate 1
SAMPLE 1


title: subcutaneous adipose tissue needle biopsy Participant 4 diet+exercise group 6 month visit


title: SI E18_5 WT4

description: Mouse proximal small intestine, embryonic day 18.5

value: proximal small intestine


title: E14.5 WT Dorsal Skin 1-3

description: Dorsal skin, embryonic day 14.5

value: wildtype CB6 mice


title: Skin E14_5 1-2_5

description: Dorsal skin, embryonic day 14.5


title: subcutaneous adipose tissue needle biopsy Participant 5 diet+exercise group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 3 exercise group 6 month visit


title: subcutaneous adipose tissue needle biopsy Participant 4 diet+exercise group baseline visit


title: CPCs passage 15 rep1

city: Tehran

first: SeyedAhmad

last: Mousavi

state: Tehran

address: Bani hashem st - Resalat hw

department: Molecular systems biology

country: Iran

institute: Royan institute

hyb_protocol: 750 ng of each cRNA sample was hybridized into Illumina’s Sentrix HumanHT-12 v4 Expression Bead Chips at 58 °C overnight according to Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (part # 11322355, rev.A).

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%)

data_processing: The data were normalised using Robust Spline Normalization normalisation with lumi in R

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 15

label_protocol: From 200 ng total RNA, generation of biotin-labeled cRNA was done using Illumina® TotalPrep™ RNA amplification Kit (Applied Biosystems, AMIL1791).

growth_protocol: cardiac precursor cells isolated from human heart right atria and ventricle were cultured in qrowth medium IMDM, 15% FBS, 1% l-glutamine and 1% peniciline/streptomycine supplemented with 10g/ml bFGF.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer instructions. Briefly, cells were dissolved in 1ml TRIzol reagent. Then they were lysed by vortexing and incubation for 5-10 min, after that 200 µl chloroform was added per 1 ml TRIzol and mixed by inversion. The sample was centrifuged at 12000×g for 15 min at 4°C. The upper layer was carefully removed and stored for RNA isolation. RNA was precipitated by adding 0.5 ml Isopropyl alcohol per 1 ml TRIzol reagent used for the initial homogenization. Samples were incubated at room temperature for 10 minutes and centrifuged at no more than 12,000 x g for 10 minutes at 4°C. Supernatant was carefully removed and the RNA pellet was washed once with 75% ethanol. The sample was vortexed and centrifuged at no more than 7,500 x g for 5 minutes at 4°C. After brief air drying, the RNA pellet was dissolved in RNase-free water and incubated for 10 min at 55°C. The quantity and quality of isolated RNA was evaluated by spectrophotometry.

value: heart tissue

value: cardiac precursor cells

tag: passage


title: SI E18_5 WT3

source_name: Mouse proximal small intestine, embryonic day 18.5


title: CPCs passage 12 rep3

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 12


title: CPCs passage 15 rep3


title: subcutaneous adipose tissue needle biopsy Participant 2 diet group baseline visit

value: female