title: hypoxia control (no ketamine) replicate 2

description: SAMPLE 9; HC2


title: optA1_0_Hx Rep3

status: Public on Apr 06 2016

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Gene expression from optA1 strain with hypoxanthine

hyb_protocol: 1 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

label: biotin

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: optA1 strain with hypoxanthine

label_protocol: Total RNA was amplified as directed in the Affymetrix Prokaryotic Target Labeling Assay protocol.

growth_protocol: The strains were grown exponentially (after initiation by a 1,000-fold dilution from overnight cultures) for ~5 generations at 37°C in Vogel-Bonner (VB) minimal medium supplemented with glucose (0.4%), pantothenic acid (5 µg/ml), casamino acids (Becton-Dickenson) (1%), and hypoxanthine (50 µg/ml).

extract_protocol: At each time point, 15 ml of each culture was mixed with 30 ml of RNAprotect Bacteria Reagent (Qiagen), vortexed for 5s, incubated for 5 min at room temperature, and centrifuged for 10 min at 5000g.  The pellet was processed using a Qiagen RNeasy Midi kit with on-column DNase digestion using Qiagen DNase.  The final elution of RNA from the column was with 160 μl RNase-free water.

treatment_protocol: At OD630nm = 0.1, the cultures were filtered through 47-mm diameter polycarbonate membrane filter (0.4 µm pore size; Millipore), washed with the same medium without hypoxanthine (Hx), and then resuspended at the same cell density (OD630 = 0.1) in the medium without Hx, and growth was continued as before.  The OD630 was followed closely during the next two hours, and the cells were periodically diluted with fresh, pre-warmed medium without Hx to keep OD between values 0.1 and 0.3 (low-dilution protocol).  Samples were taken for microarray analysis (see below) at 0, 15, 30, 45, 60 and 120 minutes.  In a parallel procedure, the optA1 gpt double mutant was also followed in a near-identical manner using a more highly diluted culture over a six-hour incubation period in the absence of hypoxanthine (high-dilution protocol).  The effectiveness of the latter treatment was followed microscopically by observing the extensive cellular filamentation associated with dGTP starvation.

tag: strain


title: hypoxia ketamine replicate 2

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

description: SAMPLE 14; HK2

hyb_protocol: This was performed following protocols from Agilent. Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and  hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida. Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis, resulting in 9301 data rows.

data_processing: Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays.  To identify the genes that were differentially regulated (DR) between groups, the normalized and transformed intensities were analyzed by moderated t-test using empirical Bayes method for small sample size per group (p<0.05).   Analyses were carried out using Bioconductor's Limma Package for R software v. 2.15.1.

organism: Ovis aries

source_name: fetal cerebral cortex 24 hrs after onset of 30 min hypoxia and intravenous injection of ketamine

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.4 to 14.4 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the cerebral cortex using Trizol (Invitrogen, Carlsbad, CA) , followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA).The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.  RNA Integrity Number (RIN) values ranged from 7.7 to 9.2.

treatment_protocol: Chronically catheterized late gestation fetal sheep were subjected to transient (30 min) maternal ventilatory hypoxia without (n=5) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) or to normoxia without (n=3) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) followed by 23.5 h normoxia.  Fetal frontal cerebral cortex was collected at the end of normoxia recovery period.

tag: age

value: late gestation fetal sheep

tag: pretreated with

value: ketamine (3 mg/kg, iv)

tag: subjected to

tag: time point

value: 24 hours after onset of 30 min hypoxia

tag: tissue

value: fetal frontal cerebral cortex


title: optA1_60 (Low Dilution) Rep2

description: Gene expression from optA1 strain w/o hypoxanthine 60 min at low dilution protocol


title: Monocytes, 6hr after incubation with live E. coli, subject 27

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

label: Biotin

organism: Homo sapiens

source_name: CD14+CD16- human monocytes, incubation with live E. coli, 6hr

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Human monocytes used in this study were isolated from buffy coats obtained from the German Red Cross Blood Transfusion Service, Berlin, Germany. Permission for experiments with human primary cells was obtained from the local ethic committee. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation over Histopaque-1077 (Sigma-Aldrich; Steinheim, Germany). CD14+CD16- monocytes were purified by negative selection via immunomagnetic separation using EasySep monocyte isolation kits with CD16 depletion (Stemcell Technologies; Grenoble, France) according to the manufacturer's instructions. Isolated monocytes were cultured at a density of 10 x 10^6 cells/ml in RPMI1640 supplemented with 10% fetal calf serum (FCS), 1% glutamine, 1% HEPES buffer, 1% non-essential amino acids (all from Sigma-Aldrich; Steinheim, Germany) at 37°C, 5% CO2 in a humidified incubator.

extract_protocol: CD14+CD16- human monocytes were sorted by flow cytometry and were infected with EC HKEC at MOI 10. After 6 hours, cells were harvested, washed once in PBS, and lysed in Trizol (Life Technologies, Karlsruhe, Germany). Total RNA was prepared from four independent experiments (= four separate donors) according to the Trizol manufacturer’s protocol. RNA was purified using a Qiagen RNeasy microkit according to manufacturer’s protocol.

treatment_protocol: Escherichia coli K12, strain DH5α, thymidine auxotrophs (ThyA-) were selected as previously described (Sander et al.; PubMed ID: 21602824). Auxotrophy was confirmed by inoculation and overnight culture of single colonies in LB medium. ThyA- E. coli (hereafter referred to as EC) grew only in the presence of thymidine and were resistant to trimethoprim. For heat killing, EC were grown to log phase, washed and re-suspended in PBS at an optical density at 600 nm (OD600) of 0.6, and subsequently incubated at 60 °C for 60 min. Heat-killed ThyA- E. coli (HKEC) were used immediately after killing or stored at -80 °C for up to three months. Efficient killing was confirmed by overnight plating on thymidine/trimethoprim-supplemented LB-agar plates. Infection of human monocytes was performed at the multiplicity of infection (MOI) = 1.

tag: treatment

value: incubation with live E. coli


title: hypoxia ketamine replicate 1

description: SAMPLE 13; HK1

value: transient (30 min) maternal ventilatory hypoxia


title: hypoxia control (no ketamine) replicate 5

description: SAMPLE 12; HC5

source_name: fetal cerebral cortex 24 hrs after onset of 30 min hypoxia


title: hypoxia control (no ketamine) replicate 1

description: SAMPLE 8; HC1

source_name: fetal cerebral cortex 24 hrs after onset of 30 min normoxia and intravenous injection of ketamine

value: normoxia

value: 24 hours after onset of 30 min normoxia


title: Monocytes, 6hr after control incubation, subject 27

source_name: CD14+CD16- human monocytes, control incubation, 6hr

value: control incubation


title: optA1_45 (Low Dilution) Rep3

description: Gene expression from optA1 strain w/o hypoxanthine 45 min at low dilution protocol


title: normoxia ketamine replicate 4

description: SAMPLE 7; NK4


title: Monocytes, 6hr after incubation with heat-killed E. coli, subject 35

source_name: CD14+CD16- human monocytes, incubation with heat-killed E. coli, 6hr

value: incubation with heat-killed E. coli


title: optA1_45 (Low Dilution) Rep2

source_name: optA1 strain w/o hypoxanthine 45 min at low dilution protocol


title: hypoxia control (no ketamine) replicate 4

description: SAMPLE 11; HC4


title: normoxia ketamine replicate 2

description: SAMPLE 5; NK2


title: normoxia ketamine replicate 3

description: SAMPLE 6; NK3


title: Monocytes, 6hr after incubation with live E. coli, subject 35


title: optA1_30 (Low Dilution) Rep2

description: Gene expression from optA1 strain w/o hypoxanthine 30 min at low dilution protocol


title: normoxia ketamine replicate 1

description: SAMPLE 4; NK1


title: optA1_15 (Low Dilution) Rep2

description: Gene expression from optA1 strain w/o hypoxanthine 15 min at low dilution protocol


title: Monocytes, 6hr after incubation with heat-killed E. coli, subject 23


title: wt MEFs PREX2 Q1430*

city: Houston

first: Lynda

last: Chin

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: MD Anderson Cancer Center

hyb_protocol: Performed according to Affymetrix protocols. Affmetrix GeneChip mouse genome 430 Plus2 arrays containing probe sets for >45,000 characterized genes and expressed sequence tags, were used. Approximately 12.5 μg of fragmented cRNA was used in a 250-μl hybridization mixture containing herring-sperm DNA (0.1 mg/ml; Promega), plus bacterial and phage cRNA controls (1.5 pM BioB, 5 pM BioC, 25 pM BioD, and 100 pM Cre) to serve as internal controls for hybridization efficiency. Aliquots (200 μl) of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin– phycoerythrin (Life Technologies) and amplified with biotinylated anti-streptavidin antibody (Vector Laboratories) on the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Performed according to Affymetrix protocols. Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities.

data_processing: Signal intensity and presence call data were derived with the MAS5 (Affymetrix) algorithm.

organism: Mus musculus

source_name: MEFS isolated from wt E13.5 embryos and ectopically expressing PREX2 Q1430* mutant

label_protocol: Performed according to Affymetrix protocols. Briefly, double-stranded cDNA was synthesized from total RNA with GeneChip 3’ IVT express kit (Affmetrix), with a T7 RNA polymerase promoter site added to its 3′ end (Genset, La Jolla, CA). Biotinylated cRNAs were generated from cDNAs in vitro and amplified by using GeneChip 3’ IVT express kit. After purification of cRNAs by the RNeasy mini kit (Qiagen, Hilden, Germany), 15 μg of cRNA was fragmented at 94°C for 35 min.

extract_protocol: Total RNA isolation was performed with the Qiagen RNeasy kit, according to the manufacturer’s instructions.

treatment_protocol: Spontaneously immortalized MEFs from either wt or Suv420h1 knockout mice were used. Wt MEFs were transduced with lentivirus to express indicated PREX2 mutants. Suv420h1 ko MEFs were reconstituted either with control GFP or Suv420h1-GFP fusion. Total RNA was isolated and subjected to analysis

value: mouse embryonic fibroblasts


title: optA1_120 (Low Dilution) Rep1

description: Gene expression from optA1 strain w/o hypoxanthine 120 min at low dilution protocol


title: optA1_60 (Low Dilution) Rep1

source_name: optA1 strain w/o hypoxanthine 60 min at low dilution protocol


title: wt MEFs PREX2 E824*

source_name: MEFS isolated from wt E13.5 embryos and ectopically expressing PREX2 E824* mutant


title: optA1_0_Hx Rep2


title: normoxia control (no ketamine) replicate 2

description: SAMPLE 2; NC2

source_name: fetal cerebral cortex 24 hrs after onset of 30 min normoxia


title: normoxia control (no ketamine) replicate 3

description: SAMPLE 3; NC3


title: normoxia control (no ketamine) replicate 1

description: SAMPLE 1; NC1


title: Monocytes, 6hr after control incubation, subject 35


title: optA1_45 (Low Dilution) Rep1


title: Plasma_sub_5_hr_3

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

description: Total RNA was reverse-transcribed, pre-amplified with feature-specific primers, and loaded onto custom OpenArrays by liquid handling robot in the Johns Hopkins University DNA Analysis Facility. Quantitative real-time PCR was performed for 220 features.

hyb_protocol: Pre-amplified cDNA was loaded onto custom OpenArray chips by AccuFill liquid handling robot in the Johns Hopkins University DNA Analysis facility. qRT-PCR was performed by a QuantStudio 12K Flex instrument (Thermo Fisher) per manufacturer's recommendations.

data_processing:
ExpressionSuite software (Thermo Fisher) was used to collect Crt data.
Data were processed using ExpressionSuite (Applied Biosystems/Thermo Fisher), Microsoft Excel, and R/Bioconductor. Crts with amplification score > 1.15 were retained for further analysis. Quantile normalization was conducted with the affy package (R/Bioconductor) for features detected in at least 9 of 10 samples. Missing values indicate wells that did not amplify or did not satisfy the amplification score criterion (raw data) or that were not expressed in at least 9 of 10 samples (Matrix, normalized data).

label: FAM

source_name: plasma

extract_protocol:
Total RNA was obtained from plasma using the Exiqon Biofluids protocol as modified by McAlexander, et al., PMID 23720669.
3 microliters total RNA per sample was reverse-transcribed using Megaplex primers (Applied Biosystems/ThermoFisher). cDNA was pre-amplified for 14 cycles with Mexaplex Pre-Amp primers (Applied Biosystems/Thermo Fisher).

value: plasma


title: Plasma_sub_5_hr_0


title: wt MEFs PREX2 K278*

source_name: MEFS isolated from wt E13.5 embryos and ectopically expressing PREX2 K278* mutant


title: wt MEFs plus PREX2 wt

source_name: MEFS isolated from wt E13.5 embryos and ectopically overexpressing PREX2 wt


title: Monocytes, 6hr after incubation with live E. coli, subject 23


title: optA1_30 (Low Dilution) Rep1

source_name: optA1 strain w/o hypoxanthine 30 min at low dilution protocol


title: optA1_0_Hx Rep1


title: Monocytes, 6hr after incubation with live E. coli, subject 21


title: Monocytes, 6hr after incubation with heat-killed E. coli, subject 27


title: wt MEFs plus GFP

source_name: MEFS isolated from wt E13.5 embryos and ectopically expressing GFP


title: Monocytes, 6hr after control incubation, subject 21


title: wt MEFs plus LacZ

source_name: MEFS isolated from wt E13.5 embryos and ectopically expressing LacZ


title: Suv420h1 -/- + GFP MEFs

source_name: MEFs isolated from E13.5 Suv420h1 knockout embryos plus GFP reconstitution


title: MML18

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: b-Catenin (t = 24h) - C

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: raw data were processed using the R/Bioconductor package limma; background correction: normexp; quantile normalization: VSN

label_protocol: Not provided

extract_protocol: Trizol extraction / Qiagen RNeasy Micro cleanup

treatment_protocol: Migr1 vector or β-cat-S33Y infected PUER cells were treated with  10 nM 4-OHT for induction of PU.1 expression.

value: PUER cell line (myeloid)

tag: genotype

value: MIGR1/ β-catenin-S33Y


title: Monocytes, 6hr after control incubation, subject 23


title: Plasma_sub_4_hr_3


title: Monocytes, 6hr after incubation with heat-killed E. coli, subject 21


title: Plasma_sub_4_hr_0


title: Plasma_sub_3_hr_3


title: MML16

description: b-Catenin (t = 24h) - A

source_name: bCat-A 24h


title: Plasma_sub_3_hr_0


title: Suv420h1 -/- MEFs

source_name: MEFs isolated from E13.5 Suv420h1 knockout embryos


title: MML17

description: b-Catenin (t = 24h) - B


title: MML15

description: b-Catenin (t = 0h) - C

source_name: bCat-C  0h


title: MML13

description: b-Catenin (t = 0h) - A

source_name: bCat-A  0h


title: Suv420h1 -/- + Suv420h1-GFP MEFs

source_name: MEFs isolated from E13.5 Suv420h1 knockout embryos plus Suv420h1-GFP fusion reconstitution


title: WT_60 (Low Dilution) Rep3

description: Gene expression from control strain w/o hypoxanthine 60 min at low dilution protocol


title: WT_30 (Low Dilution) Rep3

description: Gene expression from control strain w/o hypoxanthine 30 min at low dilution protocol


title: WT_120 (Low Dilution) Rep3

description: Gene expression from control strain w/o hypoxanthine 120 min at low dilution protocol


title: MML6

description: GFP control (t = 24h) - C

source_name: GFP-C 24h


title: Plasma_sub_2_hr_0


title: Plasma_sub_2_hr_3


title: MML14

description: b-Catenin (t = 0h) - B

source_name: bCat-B  0h


title: Plasma_sub_1_hr_3


title: optA1_15 (Low Dilution) Rep1

source_name: optA1 strain w/o hypoxanthine 15 min at low dilution protocol


title: WT_120 (Low Dilution) Rep2

source_name: control strain w/o hypoxanthine 120 min at low dilution protocol


title: WT_15 (Low Dilution) Rep3

description: Gene expression from control strain w/o hypoxanthine 15 min at low dilution protocol


title: 1/3PH 36H (s04m46)

city: Hangzhou

first: Zhikun

last: Liu

address: Qingchun Road 79#

country: China

institute: Zhejiang University

hyb_protocol: Each slide was hybridized with 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit in hybridization Oven (Agilent Technologies) at 55°C, 20rpm for 20 hours according to the manufacturer’s instructions for hybridization.

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent Technologies), and Feature Extraction software 10.7 (Agilent Technologies) was used with the default settings.

data_processing: Raw data were normalized against the Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies).

organism: Rattus norvegicus

source_name: 1/3PH 37H remnant liver

label_protocol: The molecular miRNA within the total RNA was labeled by the miRNA Complete Labeling and Hyb Kit (Agilent Technologies) followed the manufacturer’s instructions for labeling.

growth_protocol: remnant liver after partial hepatectomy

extract_protocol: Total RNA was extracted and purified using the mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions and was confirmed for the RIN number to inspect RNA integration using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The left lateral lobe, which accounts for 30% of the total liver mass, was removed for 1/3 PH. In addition, 2/3 PH surgeries were performed as originally described. The regenerating lobes (right lobes) were harvested 6, 12, 24, or 36 hours after surgery. The right lobes of 3 rats without PH were also harvested as the normal controls. To avoid differences related to circadian rhythms in miRNA expression, liver harvest was performed between 8 a.m. and 12 p.m.

tag: gender

value: male

tag: protocol

tag: time

value: 36 hours after surgery

value: liver


title: MML4

description: GFP control (t = 24h) - A

source_name: GFP-A 24h


title: Plasma_sub_1_hr_0

source_name: plasma


title: MML3

description: GFP control (t = 0h) - C

source_name: GFP-C 0h


title: MML2

description: GFP control (t = 0h) - B

source_name: GFP-B 0h


title: PBMC_sub_5_hr_0

hyb_protocol: qRT-PCR protocol: Pre-amplified cDNA was loaded onto custom OpenArray chips by AccuFill liquid handling robot in the Johns Hopkins University DNA Analysis facility. qRT-PCR was performed by a QuantStudio 12K Flex instrument (Thermo Fisher) per manufacturer's recommendations.

source_name: PBMC

extract_protocol:
Total RNA was extracted from human PBMC as described by Baier, et al., J Nutr, 2014, PMID 25122645, and sent on dry ice by overnight delivery.
100 ng total RNA per sample was reverse-transcribed using Megaplex primers (Applied Biosystems/ThermoFisher). cDNA was pre-amplified for 12 cycles with Mexaplex Pre-Amp primers (Applied Biosystems/Thermo Fisher).

value: PBMC


title: PBMC_sub_4_hr_6


title: MML5

description: GFP control (t = 24h) - B

source_name: GFP-B 24h


title: WT_0_Hx Rep3

description: Gene expression from control strain with hypoxanthine

source_name: control strain with hypoxanthine


title: 133B_Human Peripheral blood NK cells CD56Bright CD16-  Donor B

description: Corresponds to sample 14 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p5 Dim.

hyb_protocol: cRNA were hybridized on GeneChip Human HG-U133B arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

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.  D-chip software was used to analyze the data for the manuscript but the D-chip output was lost due to hard drive damage.

source_name: Human Peripheral blood NK cells CD56Bright CD16-  Donor A - Single donor

label_protocol: Fragmented and biotinylated cRNAhybridized and eluted from HGU95Av2 arrays ( Koopman et al JEM 2003) were kept frozen at -80C for 16 monrths and hybridized to HG-U133B arrays

extract_protocol: Trizol extraction as described in Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12

treatment_protocol: Ex vivo Decidual NK cells were extracted from 1rst trimester decidual samples by DNAse-Collagenase digestion  and Flow Cytometry sorted as CD3- CD56Bright CD16- cells, Peripheral blood NK cells were isolated from leucopack  by enrichment with negatrive enrichment  antibody cocktail Rosette Sep NK ( Milteny Biotech) followed by flow cytometry sorting as CD3- CD56Bright CD16- cells (Peripheral blood NK cells CD56Bright CD16-) or CD3- CD56Dim CD16+ cells (Peripheral blood NK cells CD56Dim CD16+). For detailed methods see Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12.

tag: cell type

value: NK cells

value: peripheral blood

tag: cell markers

value: CD56[Bright], CD16-


title: WT_45 (Low Dilution) Rep2

description: Gene expression from control strain w/o hypoxanthine 45 min at low dilution protocol


title: PBMC_sub_4_hr_0


title: 133B_Human Peripheral blood NK cells CD56Bright CD16-  pooled from 3 donors

description: Corresponds to sample 13 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donors are the same as sample p1p Dim.


title: 133B_Human Peripheral blood NK cells CD56Dim CD16+  Donor B

description: Corresponds to sample 19 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample  p6 Bright.

source_name: Human Peripheral blood NK cells CD56Dim CD16+  Donor A - Single donor


title: WT_15 (Low Dilution) Rep2

source_name: control strain w/o hypoxanthine 15 min at low dilution protocol


title: PBMC_sub_3_hr_6


title: WT_120 (Low Dilution) Rep1


title: WT_60 (Low Dilution) Rep2

source_name: control strain w/o hypoxanthine 60 min at low dilution protocol


title: PBMC_sub_5_hr_6


title: WT_30 (Low Dilution) Rep2

source_name: control strain w/o hypoxanthine 30 min at low dilution protocol


title: PBMC_sub_2_hr_0


title: PBMC_sub_2_hr_6


title: 133B_Human Peripheral blood NK cells CD56Dim CD16+  pooled from 3 donors

description: Corresponds to sample18 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12).  Donors are the same as sample  p3p Bright.


title: WT_0_Hx Rep2


title: WT_60 (Low Dilution) Rep1


title: WT_45 (Low Dilution) Rep1

source_name: control strain w/o hypoxanthine 45 min at low dilution protocol


title: WT_30 (Low Dilution) Rep1


title: MML1

description: GFP control (t = 0h) - A

source_name: GFP-A 0h


title: 133B_Human Peripheral blood NK cells CD56Bright CD16-  Donor A

description: Corresponds to sample 12 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p10Dim.


title: 133B_Human Peripheral blood NK cells CD56Dim CD16+  Donor A

description: Corresponds to sample 17 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12). Donor is the same as sample p11Bright.


title: 133B_Human Decidual NK cells sample 8

description: Corresponds to sample 9 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 5 to 6  weeks  Single donor

value: Decidual NK cells

value: uterine endometrium


title: 133B_Human Decidual NK cells sample 7

description: Corresponds to sample 8 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 6 weeks + 2 days pregnancy Single donor


title: PBMC_sub_3_hr_0


title: WT_15 (Low Dilution) Rep1


title: 133B_Human Decidual NK cells sample 3

description: Corresponds to sample 5 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 7 weeks + 5 days pregnancy Single donor


title: PBMC_sub_1_hr_0


title: 133B_Human Decidual NK cells sample 4

description: Corresponds to sample 6 in (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-12)

source_name: Human Decidual NK cells from ~ 7 weeks + 1 day pregnancy Single donor


title: Post fracture day 5 sample c

status: Public on Apr 05 2016

city: Old Westbury

first: Michael

last: Hadjiargyrou

state: New York

address: New York Institute of Technology

department: Department of Life Sciences

institute: New York Institute of Technology

description:
miRNA expression in day 5 femur fracture callus
PFD5c

hyb_protocol: Each sample was resuspended in 17ml nuclease free water. A master hybridization master mix was made consisting of diluted Hyb Spike-In controls, Agilent 10X blocking agent and Agilent Hi-RPM hybridization buffer.  Aliquots of the master mix were added to each resuspended sample to a final volume of 45ml.  The hybridization mix was incubated for 5 min at 1000C and then transferred to an ice/water bath to be incubated for 5 min.  The samples were then briefly centrifuged to collect any condensation from the tube caps. The entire amount for each sample was dispensed into the center of a gasket well of an Agilent Mouse miRNA Release 21.0, 8x60K microarray slide (8 samples/slide).  Once all samples were applied to the gasket slide, the chamber cover was clamped in place.  The assembled slide cassette was placed into the hybridization oven and hybridized for 20 hrs at 550C at 20 rpm.

scan_protocol: The array was scanned using Agilent Scan Control vA.8.5.1 with the AgilentG3_miRNA protocol at a resolution of 5mm.

data_processing: miRNAs with Absent calls across all samples were filtered out. Quantile normalization was used to normalize the remaining miRNAs.

source_name: Post fracture femur, day 5, replicate 3

label_protocol: Total RNA (100ng) from each sample (3 samples/time point) was labeled using the Agilent miRNA Complete Labeling and Hybridization kit.

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen) per manufacturer’s instructions.

treatment_protocol: Not applicable

tag: stress

value: fracture

value: day 5

value: femur fracture callus


title: Post fracture day 11 sample a

description:
miRNA expression in day 11 femur fracture callus
PFD11a

source_name: Post fracture femur, day 11, replicate 1

value: day 11


title: Post fracture day 1 sample c

description:
miRNA expression in day 1 femur fracture callus
PFD1c

source_name: Post fracture femur, day 1, replicate 3

value: day 1


title: Post fracture day 3 sample b

description:
miRNA expression in day 3 femur fracture callus
PFD3b

source_name: Post fracture femur, day 3, replicate 2

value: day 3


title: Post fracture day 5 sample b

description:
miRNA expression in day 5 femur fracture callus
PFD5b

source_name: Post fracture femur, day 5, replicate 2


title: Post fracture day 7 sample c

description:
miRNA expression in day 7 femur fracture callus
PFD7c

source_name: Post fracture femur, day 7, replicate 3

value: day 7


title: Post fracture day 7 sample b

description:
miRNA expression in day 7 femur fracture callus
PFD7b

source_name: Post fracture femur, day 7, replicate 2


title: Post fracture day 7 sample a

description:
miRNA expression in day 7 femur fracture callus
PFD7a

source_name: Post fracture femur, day 7, replicate 1


title: Post fracture day 11 sample b

description:
miRNA expression in day 11 femur fracture callus
PFD11b

source_name: Post fracture femur, day 11, replicate 2


title: Post fracture day 14 sample b

description:
miRNA expression in day 14 femur fracture callus
PFD14b

source_name: Post fracture femur, day 14, replicate 2

value: day 14


title: Post fracture day 11 sample c

description:
miRNA expression in day 11 femur fracture callus
PFD11c

source_name: Post fracture femur, day 11, replicate 3

value: male


title: Post fracture day 14 sample a

description:
miRNA expression in day 14 femur fracture callus
PFD14a

source_name: Post fracture femur, day 14, replicate 1


title: Post fracture day 14 sample c

description:
miRNA expression in day 14 femur fracture callus
PFD14c

source_name: Post fracture femur, day 14, replicate 3


title: Post fracture day 5 sample a

description:
miRNA expression in day 5 femur fracture callus
PFD5a

source_name: Post fracture femur, day 5, replicate 1


title: Post fracture day 1 sample a

description:
miRNA expression in day 1 femur fracture callus
PFD1a

source_name: Post fracture femur, day 1, replicate 1


title: WT_0_Hx Rep1

description: Gene expression from control strain with hypoxanthine

source_name: control strain with hypoxanthine


title: Post fracture day 1 sample b

description:
miRNA expression in day 1 femur fracture callus
PFD1b

source_name: Post fracture femur, day 1, replicate 2


title: Post fracture day 3 sample a

description:
miRNA expression in day 3 femur fracture callus
PFD3a

source_name: Post fracture femur, day 3, replicate 1


title: gpt_30 (Low Dilution) Rep2

description: Gene expression from gpt strain w/o hypoxanthine 30 min at low dilution protocol


title: PBMC_sub_1_hr_6

description: Total RNA was reverse-transcribed, pre-amplified with feature-specific primers, and loaded onto custom OpenArrays by liquid handling robot in the Johns Hopkins University DNA Analysis Facility. Quantitative real-time PCR was performed for 220 features.

source_name: PBMC


title: Post fracture day 3 sample c

description:
miRNA expression in day 3 femur fracture callus
PFD3c

source_name: Post fracture femur, day 3, replicate 3


title: Intact control sample b

description:
miRNA expression in intact femur
Intact_b

source_name: Contralateral (intact) femur, replicate 2

value: control

value: femur


title: Intact control sample a

description:
miRNA expression in intact femur
Intact_a

source_name: Contralateral (intact) femur, replicate 1


title: Intact control sample c

description:
miRNA expression in intact femur
Intact_c

source_name: Contralateral (intact) femur, replicate 3


title: Colon_KO_Day12_rep3

city: Paris

first: Bruno

last: LAMAS

address: 27 rue Chaligny

department: CHU St Antoine

country: France

institute: Unité INSERM 1157/UMR 7203

description: Gene expression in colon from Card9-/- mouse 12 days after DSS

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes and hybridized to the microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed and then dried immediately.

scan_protocol: After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies), with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing: The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE1_107_Sep09 protocol.

source_name: Colon, KO, Day12, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: female C57BL/6j mice and female Card9-/- mice on the background C57BL/6j were bred in specific-pathogen–free facilities.

extract_protocol: Total RNA was isolated from colon samples using RNeasy® Mini Kit (Qiagen), according to the manufacturer's instructions. RNA integrity was checked onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) and all of the samples showed a RIN score higher than 7.

treatment_protocol: For the induction of colitis, mice were given drinking water supplemented with 2% (w/v) Dextran sulphate sodium (DSS) for 7 days, then allowed to recover by drinking water alone for 5 additional days. Mice were euthanized before (Day0), 7 and 12 days after DSS administration and colon samples were taken.

value: colon

value: female

value: 8 weeks


title: wild type RAW264.7 cells, untreated

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression data from wild type RAW264.7 cells

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

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The genes in each Matrix template are arranged according to affymetrix probe set id.

source_name: wild type RAW264.7 cells, untreated

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

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

treatment_protocol: RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h.

value: macrophage

tag: cell line


title: Colon_WT_Day12_rep5

description: Gene expression in colon from WT mouse 12 days after DSS

source_name: Colon, WT, Day12, replicate 5

value: wildtype


title: Colon_KO_Day12_rep2

source_name: Colon, KO, Day12, replicate 2


title: Colon_KO_Day12_rep5

source_name: Colon, KO, Day12, replicate 5


description: Gene expression data from wild type RAW264.7 cells infected with VSV


title: Colon_WT_Day12_rep3

source_name: Colon, WT, Day12, replicate 3


title: Colon_WT_Day12_rep2

source_name: Colon, WT, Day12, replicate 2


title: Colon_KO_Day12_rep4

source_name: Colon, KO, Day12, replicate 4


description: Gene expression data from wild type RAW264.7 cells infected with HSV-1


title: Colon_KO_Day12_rep1

source_name: Colon, KO, Day12, replicate 1


title: Colon_WT_Day7_rep5

description: Gene expression in colon from WT mouse 7 days after DSS

source_name: Colon, WT, Day7, replicate 5


title: Colon_WT_Day7_rep4

source_name: Colon, WT, Day7, replicate 4


title: Colon_WT_Day12_rep4

source_name: Colon, WT, Day12, replicate 4


title: Colon_KO_Day7_rep3

description: Gene expression in colon from Card9-/- mouse 7 days after DSS

source_name: Colon, KO, Day7, replicate 3


title: Colon_WT_Day12_rep1

source_name: Colon, WT, Day12, replicate 1


title: Colon_KO_Day7_rep2

source_name: Colon, KO, Day7, replicate 2


title: Colon_KO_Day7_rep1

source_name: Colon, KO, Day7, replicate 1


title: WT_45 (Low Dilution) Rep3

description: Gene expression from control strain w/o hypoxanthine 45 min at low dilution protocol


title: Colon_WT_Day7_rep3

source_name: Colon, WT, Day7, replicate 3


title: Colon_WT_Day7_rep1

source_name: Colon, WT, Day7, replicate 1


title: Colon_KO_Day0_rep2

description: Gene expression in colon from Card9-/- mouse before DSS

source_name: Colon, KO, Day0, replicate 2


title: Colon_KO_Day7_rep4

source_name: Colon, KO, Day7, replicate 4


title: Rat cortical microvessels, HEP, sample 5

city: Barcelona

first: Teresa

last: García-Lezana

address: Paseo de la Vall d'hebron 119-129

country: Spain

institute: Vall d'Hebron Research Institute

hyb_protocol: Approximately 5μg of fragmented and labeled ssDNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 17 hours at 45° at Gene Titan platform

scan_protocol: Arrays were scanned on an Affymetrix Gene Titan platform

data_processing: RMA algorithm was used to normalize the arrays and summarized the probes.

source_name: Rat brain cortex microvasculature after PCA+HEP

label_protocol: 5.5µg of ssDNA were fragmented and labeled using the WT Plus kit (Affymetrix) following protocol guides.

extract_protocol: none provided by submitter

value: Brain cortex microvasculature

tag: surgery

value: Portocaval anatomosis surgery (PCA) + total hepatectomy (HEP) 24h later


title: Colon_WT_Day7_rep2

source_name: Colon, WT, Day7, replicate 2


title: Colon_KO_Day0_rep3

source_name: Colon, KO, Day0, replicate 3


title: Rat cortical microvessels, HEP, sample 8


title: Colon_WT_Day0_rep1

description: Gene expression in colon from WT mouse before DSS

source_name: Colon, WT, Day0, replicate 1


title: Rat cortical microvessels, HEP, sample 3


title: Colon_KO_Day0_rep1

source_name: Colon, KO, Day0, replicate 1


title: Rat cortical microvessels, HEP, sample 4


title: Rat cortical microvessels, HEP, sample 1


title: Rat cortical microvessels, HAL, sample 6

source_name: Rat brain cortex microvasculature after PCA+HAL

value: Portocaval anatomosis surgery (PCA) + Hepatic artery ligation (HAL) 24h later


title: Colon_WT_Day0_rep2

source_name: Colon, WT, Day0, replicate 2


title: Rat cortical microvessels, HEP, sample 2


title: Rat cortical microvessels, HEP, sample 6


title: Rat cortical microvessels, HEP, sample 7


title: Rat cortical microvessels, HAL, sample 2


title: Rat cortical microvessels, HAL, sample 1


title: Rat cortical microvessels, Sham, sample 8

source_name: Rat brain cortex microvasculature sham surgery control

value: Sham


title: Colon_WT_Day0_rep3

source_name: Colon, WT, Day0, replicate 3


title: Rat cortical microvessels, HAL, sample 5


title: Rat cortical microvessels, HAL, sample 4


title: Rat cortical microvessels, HAL, sample 3


title: Rat cortical microvessels, Sham, sample 2


title: Rat cortical microvessels, HAL, sample 8


title: Rat cortical microvessels, Sham, sample 4


title: Rat cortical microvessels, HAL, sample 7


title: Rat cortical microvessels, Sham, sample 3


title: Rat cortical microvessels, Sham, sample 7


title: MPLA+MDP_3hours_rep2

city: Moscow

first: Amir

last: Tukhvatulin

address: Gamaleya str, 18

department: Medical microbiology

country: Russia

institute: N.F. Gamaleya Research Center for Epidemiology and Microbiology

description: cells 3 hours after combined stimulation of TLR4 and NOD2 with MPLA 1μg/ml and MDP 20μg/ml, correspondingly, biological rep2

hyb_protocol: Sample hybridization was performed using  GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) in according with GeneChip® WT Terminal Labeling and Hybridization User Manual (Affymetrix Manual P/N 702880 Rev. 4).  Following fragmentation, 5 ug of cDNA were hybridized for 18 hr at 45C on  GeneChip Human Gene 1.0 ST Array.Wash, Stain and Scan of arrays were performed in according with GeneChip® Expression Wash, Stain and Scan User Manual (Affymetrix Manual P/N 702731 Rev. 3). GeneChips were washed and stained using in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 151 GeneChip 3000 7G scanner.

data_processing: Arrays were preprocessed in GeneChip Command Console Software (AGCC, Affymetrix, version 1.4.1.46) and Affymetrix Transriptome Analysis Console (version 3.0.0.466) using RMA-sketch option.

source_name: cell culture derived from human peripheral blood

label_protocol: Samples for whole genome expression analysis using Affymetrix microarrays were prepared according to the manufacturer’s recommendations (Affymetrix Manual User Manual P/N 702808 Rev. 4). 0.5μg of each total RNA sample was used for cDNA synthesis using the Ambion WT Expression Kit (Thermo Fisher Scientific). Sample labeling was performed using the GeneChip® WT Terminal Labeling Kit (Affymetrix) according manufacturer’s protocol (P/N 702808 Rev. 4).

growth_protocol: THP-1 cells (Invivogen, USA) were cultured in RPMI medium (GE Healthcare, USA) supplemented with 10% fetal calf serum (FCS, Thermo Scientific, USA), 50 U/ml penicillin, 50 μg/ml streptomycin, 2 mM glutamine, and 0.1 M NaHCO3 (all PanEco, Russia) at 37°C with 5% CO2. Every 2-3 days cells were centrifugated (1000 rpm, 10 min) with subsequent resuspension at 1-2 x 105 viable cells/mL in fresh medium. For microarray-based gene expression analysis cells were seeded  3-cm culture dishes at 1x10^6 cells per dish in RPMI medium.

extract_protocol: QIAzol lysis reagent (Qiagen, USA) was added and the samples were centrifuged through a QIAshredder column (Qiagen, Germany). Total RNA was extracted from the eluate by the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions. Genomic DNA contamination was removed by performing DNaseI digestion on the RNA binding column for 15 min. Total RNA was eluted in 50 μl of RNase-free H2O and stored at −80°C. RNA yield and purity was assessed spectrophotometrically by measuring OD260 and OD260/280 ratio respectively in RNase-free H2O using NanoDrop ND-1000 (NanoDrop Technologies, USA). For all samples  OD260/280 ratio was between 2.0 and 2.2.  RNA integrity was determined using the RNA 6000 Nano kit and Agilent Bioanalyser 2100 System (all, Agilent Technologies, USA). Values of RNA quality indicator (RIN) generated by Bioanalyser system’s software ranged from 7.7 to 9.1.

treatment_protocol: Next day, cells were treated with MDP (20μg/ml, Invivogen) and MPLA (1μg/ml, Invivogen) individually or in combination or left untreated. 3 hours afer cells were harvested  by centrifugation (1000rpm, 10min) and lyzed by Qiazol reagent (Qiagen, USA)

value: human monocytic cell culture line


title: Rat cortical microvessels, Sham, sample 1


title: MDP_3hours_rep1

description: cells 3 hours after individual stimulation of NOD2 with MDP 20μg/ml, biological rep1


title: intact cells_rep1

description: intact cells, biological rep1


title: MDP_3hours_rep2

description: cells 3 hours after individual stimulation of NOD2 with MDP 20μg/ml, biological rep2


title: MPLA+MDP_3hours_rep1

description: cells 3 hours after combined stimulation of TLR4 and NOD2 with MPLA 1μg/ml and MDP 20μg/ml, correspondingly, biological rep1


title: MPLA_3hours_rep2

description: cells 3 hours after individual stimulation of TLR4 with MPLA 1μg/ml, biological rep2


title: intact cells_rep2

description: intact cells, biological rep2


title: MPLA_3hours_rep1

description: cells 3 hours after individual stimulation of TLR4 with MPLA 1μg/ml, biological rep1


title: [Human fibroblasts]-[untreated]-[patient 3 rep3]

city: New York

first: Gaurav

last: Pandey

address: 1 Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Fibroblast Patient 3 sample 3

hyb_protocol: Standard Illumina Whole Genome Gene Expression Direct Hybridization protocol

scan_protocol: Standard Illumina Hiscan protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

source_name: Human fibroblasts_untreated_patient 3

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: Comparison of untreated HUVECs grown in regular EGM-2 media, HUVECs treated with TGF-B, HUVECS treated with TGF-B and oxidative stress, and comparator human dermal fibroblasts

extract_protocol: RNeasy mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions. Residual DNA was removed using the RNase-Free DNase Set (Qiagen) on-column DNase treatment during RNeasy preparation. RNA was amplified by Illumina TotalPrep RNA Amplification Kit

treatment_protocol: Huvecs were either treated with TGF-B or TGF-B plus oxidative stress

tag: patient id

value: patient 3

value: Patient-derived primary cell line

value: human dermal fibroblasts

tag: stimulated with

value: none (untreated)


title: Rat cortical microvessels, Sham, sample 5


title: [Human fibroblasts]-[untreated]-[patient 3 rep1]

description: Fibroblast Patient 3 sample 1


title: [Human fibroblasts]-[untreated]-[patient 3 rep2]

description: Fibroblast Patient 3 sample 2


title: [Human fibroblasts]-[untreated]-[patient 2 rep4]

description: Fibroblast Patient 2 sample 4

source_name: Human fibroblasts_untreated_patient 2

value: patient 2


title: [Human fibroblasts]-[untreated]-[patient 1 rep3]

description: Fibroblast Patient 1 sample 3

source_name: Human fibroblasts_untreated_patient 1

value: patient 1


title: [Human fibroblasts]-[untreated]-[patient 2 rep2]

description: Fibroblast Patient 2 sample 2


title: [Human fibroblasts]-[untreated]-[patient 1 rep4]

description: Fibroblast Patient 1 sample 4


title: [Human fibroblasts]-[untreated]-[patient 2 rep3]

description: Fibroblast Patient 2 sample 3


title: [Human fibroblasts]-[untreated]-[patient 1 rep1]

description: Fibroblast Patient 1 sample 1


title: [Human fibroblasts]-[untreated]-[patient 1 rep2]

description: Fibroblast Patient 1 sample 2


title: [HUVECS]-[treated with TGF-b and H2O2]-[rep3]

description: HUVECs with TGF-b + H2O2 sample 3

source_name: HUVECS_treated with TGF_b and H2O2

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: TGF-b + H2O2


title: [Human fibroblasts]-[untreated]-[patient 2 rep1]

description: Fibroblast Patient 2 sample 1


title: [HUVECS]-[treated with TGF-b and H2O2]-[rep1]

description: HUVECs with TGF-b + H2O2 sample 1


title: [HUVECS]-[treated with TGF-b and H2O2]-[rep2]

description: HUVECs with TGF-b + H2O2 sample 2


title: [HUVECS]-[treated with TGF-b and H2O2]-[rep4]

description: HUVECs with TGF-b + H2O2 sample 4


title: [HUVECS]-[treated with TGF-b]-[rep2]

description: HUVECs with TGF-b only sample 2

source_name: HUVECS_treated with TGF_b

value: TGF-b


title: [HUVECS]-[treated with TGF-b]-[rep4]

description: HUVECs with TGF-b only sample 4


title: [HUVECS]-[unstimulated]-[rep3]

description: HUVECs - unstimulated sample 3

value: none (unstimulated control)


title: [HUVECS]-[unstimulated]-[rep2]

description: HUVECs - unstimulated sample 2


title: [HUVECS]-[treated with TGF-b]-[rep1]

description: HUVECs with TGF-b only sample 1


title: [HUVECS]-[treated with TGF-b]-[rep3]

description: HUVECs with TGF-b only sample 3


title: CD8+4-1BB+LAG3+_Exp1

city: Chicago

first: Jason

middle: B

last: Williams

state: Illinois

address: 929 E. 57th St GCIS W423H

department: Pathology

institute: University of Chicago

hyb_protocol: Hypridization step was performed according to the University of Chicago Genomice Core facility protocol

scan_protocol: Scanning step was performed according to the University of Chicago Genomice Core facility protocol

data_processing: Quantile Normalization

source_name: CD8+ Tumor Infiltrating Lymphocytes

label_protocol: Labeling step was performed according to the University of Chicago Genomice Core facility protocol

growth_protocol: Mice were purchased from Taconic Farms and maintained on a normal diet

extract_protocol: B16.SIY.dsRed tumors, from d14 tumor bearing mice, were smashed through a 50 micron filter, washed 3 times with PBS and Ficolled. A second ficoll step from performed on the pellet from the first ficoll. Cells were stained with Live/Dead eF780, CD8a, CD4, CD3, 4-1BB, LAG3, PD1

treatment_protocol: No Treatment was performed on the mice or on the cells

value: Female

tag: strain

value: B16.SIY.dsRed Tumor

value: CD8+ Tumor Infiltrating Lymphocytes

tag: day

value: Day 14 post tumor inoculation


title: CD8+4-1BB–LAG3+_Exp1


title: CD8+4-1BB+LAG3+_Exp2


title: 550cGy, repeat 4

city: Los Angeles

first: Xiao

last: Yan

state: CA

address: 615 Charles E. Young Dr. S

institute: UCLA

description:
gene expression data from KSL cells
550cGy-4

hyb_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared from total RNA with the NuGen WT-Ovation Pico RNA Amplification kit (NuGen Technologies, San Carlos, CA)

scan_protocol: Amplified, labeled cDNA was then hybridized to GeneChip® Mouse Genome 430A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: Quantile normalization method was used to normalize the gene expression and raw data was log2 transformed. Differentially expressed genes were identified using the Partek software. ANOVA (Analysis of variance) was used to calculate the p value.  Genes showing altered expression with p < 0.05 and more than 2 fold changes were considered differentially expressed. The pathway and network analysis was performed using Ingenuity (IPA). IPA computes a score for each network according to the fit of the set of supplied focus genes. These scores indicate the likelihood of focus genes to belong to a network versus those obtained by chance. A score > 2 indicates a <= 99% confidence that a focus gene network was not generated by chance alone. The canonical pathways generated by IPA are the most significant for the uploaded data set. Fischer’s exact test with FDR option was used to calculate the significance of the canonical pathway.

source_name: Mouse BM KSL cells, 550cGy

label_protocol: Samples were labeled with NuGen FL-Ovation Biotin Module V2 (Nugen Technologies, San Carlos, CA)

growth_protocol: Mice were raised until 10 wks old

extract_protocol: Bone marrow ckit+sca1+lineage- cells were isolated using a FACS Aria cell sorter, and RNA from KSL cells were isolated using Rneasy micro kit.

treatment_protocol: Mice were irradiated for 550cGy with a Cesium 137 irradiator

value: 550cGy irradiation

value: Bone Marrow

value: KSL cells


title: CD8+4-1BB–LAG3–PD-1–_Exp1


title: CD8+4-1BB–LAG3+_Exp2


title: 550cGy, repeat 6

description:
gene expression data from KSL cells
550cGy-6


title: 550cGy, repeat 3

description:
gene expression data from KSL cells
550cGy-3


title: ColonicEpithelium_HighProteinDiet_rep4

city: Nanjing

first: Weiyun

last: Zhu

state: Jiangsu

address: No.1, Weigang, Xuanwu District

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

description: Gene expression after dietary high protein diet for six weeks in rat colon

hyb_protocol: The fragmented cRNA was then mixed with 55 μL 2× GEx Hybridization buffer. 100 μL of the mixture was used to the Agilent Rat Whole Genome 4×44K Array Chip (Agilent Technologies), and hybridized at 65 °C for 17 hours in an Agilent Microarray Hybridization Chamber (Agilent, G2534A) in rotating Hybridization Oven (Agilent, G2545A). After hybridization, array slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature and followed by a 1 min wash with Agilent Gene expression Wash Buffer II (Agilent, 5188-5327) at 37 °C. Slides were finally rinsed with acetonitrile for cleaning up and drying.

scan_protocol: Hybridized arrays were scanned at 5 μm resolution on a Genepix 4000B Microarray Scanner (Axon Instruments, Sunnyvale, CA).

data_processing: Expression data were normalized through quantile normalization using the Robust Multichip Average algorithm. Array data were normalized to the global median signal intensity value and values were log base 2 transformed. Low-intensity and unreliable results were removed using a filter on flags feature, with standardized software algorithms

source_name: Colonic Epithelium,High Protein Diet,rep4

label_protocol: 4 μg cRNA were labelled with fluorescent dye Cy3 and purified. 875 ng of each Cy3 labeled cRNA in a volume of 41.8 μL were combined with 11 μL of 10× Blocking agent and 2.2 μL 25× Fragmentation buffer, and incubated at 60 °C for 30 minutes.

extract_protocol: cRNA synthesis, in vitro transcription, labelling and microarray hybridization were performed as described by manufacture’s protocol (Agilent Technologies). In brief, total RNA was first purified using QIAGEN RNeasy Mini Kit (QIAGEN). For each sample, 2 μg RNA was used for reverse transcribed with T7 Promotor primer, second strand synthesis, and cRNA synthesis, and cRNA purification, to produce high quality cRNA.

value: wistar

value: colonic epithelium

value: male


title: ColonicEpithelium_HighProteinDiet_rep6

source_name: Colonic Epithelium,High Protein Diet,rep6


title: 550cGy, repeat 2

description:
gene expression data from KSL cells
550cGy-2


title: CD8+4-1BB–LAG3–PD-1+_Exp1


title: 550cGy, repeat 5

description:
gene expression data from KSL cells
550cGy-5


title: ColonicEpithelium_HighProteinDiet_rep5

source_name: Colonic Epithelium,High Protein Diet,rep5


title: ColonicEpithelium_HighProteinDiet_rep3

source_name: Colonic Epithelium,High Protein Diet,rep3


title: CD8+4-1BB–LAG3–PD-1+_Exp2


title: Rat cortical microvessels, Sham, sample 6

value: Brain cortex microvasculature

value: Sham


title: CD8+4-1BB–LAG3–PD-1–_Exp2


title: ColonicEpithelium_HighProteinDiet_rep2

source_name: Colonic Epithelium,High Protein Diet,rep2


title: ColonicEpithelium_HighProteinDiet_rep1

source_name: Colonic Epithelium,High Protein Diet,rep1


title: 0cGy, repeat 1

description:
gene expression data from KSL cells
0cGy-1

source_name: Mouse BM KSL cells, 0cGy

value: control


title: 0cGy, repeat 4

description:
gene expression data from KSL cells
0cGy-4


title: ColonicEpithelium_NormalProteinDiet_rep5

description: Gene expression after dietary normal protein diet for six weeks in rat colon

source_name: Colonic Epithelium,Normal Protein Diet,rep5


title: 0cGy, repeat 2

description:
gene expression data from KSL cells
0cGy-2


title: 0cGy, repeat 6

description:
gene expression data from KSL cells
0cGy-6


title: 550cGy, repeat 1

description:
gene expression data from KSL cells
550cGy-1


title: 0cGy, repeat 3

description:
gene expression data from KSL cells
0cGy-3


title: Wnt-medulloblastoma endothelial cells biological rep8

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

source_name: Wnt-medulloblastoma endothelial cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

growth_protocol: Hindbrain and tumors were collected directly from mice, and immediately processed for cell dissociation and sorting

extract_protocol: Qiagen RNAeasy Micro Kit RNA isolation was performed according to the manufacture's instructions

treatment_protocol: Isolated hindbrains and tumors were dissociated in papain solution (5 units/ml) for 30 minutes, then dissociated and washed in neurobasal media. Dissociated cells were filtered through a 30 micron nylon filter, then resuspended in Miltenyi MACS sorting buffer with Fc blocking solution. Anti- Cd105 and Cd144-PE conjugated antibodies (eBioscience) were added and subsequently sorted for with Anti-PE bound Miltenyi MACS magnetic beads. Purification was performed following Miltenyi MACS instructions

tag: strain background

value: mixed

value: Blbp-Cre; Ctnnb1 +/Exon3 flox; Trp53 flox/flox; Pik3ca +/flox

tag: tissue type

value: Wnt-medulloblastoma mouse tumor

value: Cd144/Cd105 cells by magnetic sorting


title: ColonicEpithelium_NormalProteinDiet_rep3

source_name: Colonic Epithelium,Normal Protein Diet,rep3

tag: tissue


title: ColonicEpithelium_NormalProteinDiet_rep2

source_name: Colonic Epithelium,Normal Protein Diet,rep2


title: ColonicEpithelium_NormalProteinDiet_rep6

source_name: Colonic Epithelium,Normal Protein Diet,rep6


title: Wnt-medulloblastoma endothelial cells biological rep6


title: Wnt-medulloblastoma endothelial cells biological rep7


title: ColonicEpithelium_NormalProteinDiet_rep1

source_name: Colonic Epithelium,Normal Protein Diet,rep1


title: [HUVECS]-[unstimulated]-[rep1]

description: HUVECs - unstimulated sample 1

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: none (unstimulated control)


title: Wnt-medulloblastoma endothelial cells biological rep4


title: 0cGy, repeat 5

description:
gene expression data from KSL cells
0cGy-5


title: Wnt-medulloblastoma endothelial cells biological rep2


title: Trained; 8 weeks vol running; rep 6

city: Washington

first: Jon-Philippe

middle: K.

last: Hyatt

state: DC

address: 3700 Reservoir Rd.

institute: Georgetown University

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR6

hyb_protocol: 0.6 ug of Cy3-labelled fragmented cRNA was hybridized overnight (17 h; 65° C) to Whole rat genome oligo arrays (8x60k) per the manufacturer's instructions (Agilent). Following hybridization, the microarrays were washed 1X in Aglient Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated (37° C) Buffer 2 for 1 min.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray scanner (G2565AA) using one color scan setting for 8x60k array slides.

data_processing: Agilent Feature Extraction Software 11.5.11.1 (Agilent) was used to read and process microarray image files for intensities.

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug total RNA using the Agilent One-Color Low RNA Input Linear Amp labeling kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from a mid-bely muscle chunk using RNeasy Plus Universal Mini Kit (Qiagen, Valencia, CA). RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Aglent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Following 8-week sedentary, detraining, or training periods, soleus muscles were harvested and flash frozen in isopentane cooled by liquid nitrogen 24 hours following an acute exercise challenge lasting 1 hr.

value: skeletal muscle

value: female

tag: age

value: ~14 weeks


title: Trained; 8 weeks vol running; rep 7

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR7

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 7


title: Trained; 8 weeks vol running; rep 4

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR4

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 4


title: Wnt-medulloblastoma endothelial cells biological rep5

tag: genotype


title: Trained; 8 weeks vol running; rep 5

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR5

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 5

tag: gender


title: Wnt-medulloblastoma endothelial cells biological rep3


title: Trained; 8 weeks vol running; rep 2

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR2

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 2


title: Shh-medulloblastoma endothelial cells, biological rep6

source_name: Shh-medulloblastoma endothelial cells

value: Ptch+/-; Ink4c-/-

value: Shh-medulloblastoma mouse tumor


title: Trained; 8 weeks vol running; rep 3

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR3

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 3


title: Trained; 8 weeks vol running; rep 1

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR1

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 1


title: 9857_SNP6.0

type: genomic

city: Newcastle upon Tyne

first: Claire

middle: Joanne

last: Schwab

state: Tyne and Wear

address: Level 5, Sir James Spence Institute, Queen Victoria Rd

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL and CHP files were generated using Affymetrix Genotyping Console using HapMap collection as reference.

molecule: genomic DNA

source_name: Bone Marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from leukemic blasts obtained from peripheral blood or bone marrow at diagnosis, relapse or at remission using the Qiagen Dneasy Blood and Tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: disease

value: acute lymphoblastic leukemia

tag: Stage

value: Diagnostic sample


title: Shh-medulloblastoma endothelial cells, biological rep7

tag: cell type


title: Shh-medulloblastoma endothelial cells, biological rep8


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 8

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR8

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 8


title: Wnt-medulloblastoma endothelial cells biological rep1


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 7

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR7

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 7


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 6

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR6

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 6


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 5

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR5

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 5


title: 11535_SNP6.0


title: ColonicEpithelium_NormalProteinDiet_rep4

description: Gene expression after dietary normal protein diet for six weeks in rat colon

source_name: Colonic Epithelium,Normal Protein Diet,rep4

value: wistar

value: colonic epithelium

value: male


title: 21550_SNP6.0


title: Shh-medulloblastoma endothelial cells, biological rep2

value: mixed


title: Shh-medulloblastoma endothelial cells, biological rep4


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 4

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR4

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 4


title: Shh-medulloblastoma endothelial cells, biological rep5


title: adult hindbrain endothelial cells, biological rep8

source_name: adult hindbrain endothelial cells

value: wild type (normal)

value: Adult mouse hindbrain


title: Trained; 8 weeks vol running; rep 8

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
TR8

source_name: Soleus muscle (mid-belly sample); 8 weeks voluntary wheel running; replicate 8


title: adult hindbrain endothelial cells, biological rep5

value: Cd144/Cd105 cells by magnetic sorting


title: Shh-medulloblastoma endothelial cells, biological rep3


title: adult hindbrain endothelial cells, biological rep7


title: Sedentary; 8 weeks; rep 7

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED7

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 7


title: Sedentary; 8 weeks; rep 8

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED8

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 8


title: 21347_SNP6.0


title: Shh-medulloblastoma endothelial cells, biological rep1


title: 26681_SNP6.0


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 2

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR2

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 2


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 1

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR1

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 1


title: adult hindbrain endothelial cells, biological rep4


title: Sedentary; 8 weeks; rep 5

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED5

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 5


title: 11959_remission_SNP6.0

value: Remission sample


title: 5630_diag_SNP6.0


title: adult hindbrain endothelial cells, biological rep6


title: 5630_relapse_SNP6.0

value: Relapse sample


title: 23029_SNP6.0


title: 11959_diag_SNP6.0


title: adult hindbrain endothelial cells, biological rep2


title: Sedentary; 8 weeks; rep 6

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED6

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 6


title: Sedentary; 8 weeks; rep 2

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED2

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 2


title: adult hindbrain endothelial cells, biological rep3


title: Sedentary; 8 weeks; rep 3

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED3

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 3


title: IL-10 producing TFR2 cells 3

city: canberra

first: Pablo

last: Fernandez De Canete Nieto

address: building 131 garran road

country: Australia

institute: JCSMR,ANU

description: FITC,PE,APC,PECy7,APCCy7,a700,Bv421,7AAD

hyb_protocol: samples were sent to the Ramaciotti Centre for Genomics (Sydney, Australia) for analysis with Affymetrix GeneChip® Human Gene 2.0 ST microarrays (http://sydney.edu.au/science/molecular_bioscience/tools/micro_array/dicy.php)

data_processing: CEL files were imported into Partek Genomics Suite (Version 6.6) using the RMA algorithm with RMA background correction, quantile normalization and median polish probeset summarization. Differentially-expressed probesets were identified in Partek GS using a 2-factor ANOVA model with the factors being “SubjectID”.

source_name: Tonsil cell suspension (stimulated with PMA and Ionomycin)

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

treatment_protocol: Tonsillar cell suspensions were stimulated with PMA (50ng/ml) and Ionomycin (1µg/ml) for 6 hours prior to FACS sort purification

tag: individual

value: donor 3

value: tonsil

tag: treatment

value: tonsil cell suspension stimulated with PMA and Ionomycin

tag: cell subset

value: IL-10 producing TFR2 cells


title: Sedentary; 8 weeks; rep 4

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED4

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 4

value: skeletal muscle

value: female

value: ~14 weeks


title: Sedentary; 8 weeks; rep 1

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
SED1

source_name: Soleus muscle (mid-belly sample); 8 weeks sedentary; replicate 1


title: IL-10 negative TFR2 cells 3

scan_protocol: samples were sent to the Ramaciotti Centre for Genomics (Sydney, Australia) for analysis with Affymetrix GeneChip® Human Gene 2.0 ST microarrays (http://sydney.edu.au/science/molecular_bioscience/tools/micro_array/dicy.php)

value: IL-10 negative TFR2 cells


title: WT_oviduct

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

description:
WT mouse
WT_oviduct

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul, denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Mouse Transcriptome Array 1.0 was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip®  Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis

data_processing: Files imported to R applying RMA background correction and summarization

source_name: oviduct

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix

growth_protocol: the samples come from tissue that was freshly isolated and not cultured.

extract_protocol: Dissected tissues were collected on ice, washed in PBS and frozen. Tissues were disrupted in Tri-reagent by zirconium beads in a mechanical tissue disruptor (Precellys 24, Bertin technologies). RNA was isolated according to manufacturer recommendations (PureLink RNA mini kit, Ambion).

treatment_protocol: no treatments were applied.

value: mixed C57BL/6 x 129

value: 65 days

value: WT

value: oviduct


title: buccal cells_52_rep_2

status: Public on Apr 04 2016

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

description:
Duke Twins Study of Memory in Aging twin9a vs. common reference pool
BUCCAL_9B

hyb_protocol: The enriched PCR products were hybridized overnight at 48°C onto the 12.1k human CpG island microarray (Microarray Facility, University Health Network, Toronto) as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .

scan_protocol: The arrays were scanned using the Genepix 4000B scanner and Genepix Pro 6.0 (Axon Instruments).

data_processing: Linear Models for Microarray Data (LIMMA) package (Bioconductor) for R was used for background correction, normalization, and to extract the signal intensities. Briefly, normexp was used for background correction, loess was used for within-array normalization, and Rquantile was used for between-array normalization.

source_name: buccal cells, control

label_protocol: 1 μg of purified enriched PCR products were fluorescently labelled with Cy5 (Roche) for the reference and with Cy3 (Roche) for the sample, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.).  Each sample was independently enriched and hybridized twice to produce two technical replicates.

extract_protocol: The samples were first digested using proteinase K (20mg/ml) and lysis buffer mixture at 55°C overnight.  A mixture of phenol, chloroform, and iso-amyl alcohol (in ratios of 25:24:1) was used to remove the proteins, followed by two times chloroform wash, precipitation of DNA using cold isopropanol, and a final wash using 70% ethanol.  After the extraction, the DNA samples were suspended in 0.1M Tris-EDTA buffer and were kept in -80°C for storage prior to use.  The purity and the concentrations of DNA were checked using a UV spectrophotometer.

value: buccal cells

tag: disease status

value: control

source_name: white blood cells, common reference pool

value: white blood cells


title: Dahl-S_colon_tumor-induced_rep2

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

description:
S2
Gene expression in colon of 30-week-old Dahl salt-sensitive rat receiving Azoxymethane to induce colon tumors at 6 weeks of age

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (All Targets Value) were chosen for further data analysis.

source_name: Dahl salt-senstive rat, colon tissue, Azoxymethane-induced colon tumors

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA from colons of 3 S and 3 S.LEW congenic rats were prepared for microarray study using TRIzol Reagent (Life Technologies) following the manufacturer's protocol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Dahl salt-sensitive rats (SS/Jr) were from our colony and will be referred to S. The congenic rat strain we used in this study is the S.LEW(10)x12x2x3x5 (S.LEW) congenic strain and will be referred to S.LEW congenic rat [Hypertension. 2007 Nov;50(5):891-8]. All the experimental rats were weaned at 28-30 d of age and fed with a low salt (0.3% NaCl) Harlan Teklad diet after weaning. At six weeks of age, both S and S.LEW congenic rats received intraperitoneal (IP) injection of AOM in sterial saline at a dose of 15mg/kg body weight once a week for two consecutive weeks. Then two animals per plastic cage, one S rat and one congenic rat, were housed in barrier-sustained animal room with a 12-h light/dark cycle. At 30 weeks of age, all the rats were euthanized through carbon dioxide inhalation. The colon tissue was harvested, dissected longitudinally, and washed with saline.

value: S

value: Azoxymethane

value: colon

value: male

value: 30 weeks


title: Gemc1 KO oviduct

description:
GEMC1 null mouse
KO_oviduct

value: GEMC1 null


title: Dahl-S_colon_tumor-induced_rep1

description:
S1
Gene expression in colon of 30-week-old Dahl salt-sensitive rat receiving Azoxymethane to induce colon tumors at 6 weeks of age


title: WT trachea

description:
WT mouse
WT_trachea

source_name: trachea

value: 39 days

value: trachea


title: IL-10 negative TFR2 cells 4

label_protocol: samples were sent to the Ramaciotti Centre for Genomics (Sydney, Australia) for analysis with Affymetrix GeneChip® Human Gene 2.0 ST microarrays (http://sydney.edu.au/science/molecular_bioscience/tools/micro_array/dicy.php)

value: donor 4

value: tonsil

value: tonsil cell suspension stimulated with PMA and Ionomycin


title: IL-10 negative TFR2 cells 2

value: donor 2

value: IL-10 negative TFR2 cells


title: Detraining; 4 wk voluntary running; 4 wk sedentary; rep 3

description:
Gene expression 24 hr post-acute exercise (1hr forced wheel running)
DETR3

source_name: Soleus muscle (mid-belly sample); 4 weeks voluntary running + 4 weeks sedentary; replicate 3

value: skeletal muscle

value: female

value: ~14 weeks


title: Gemc1 KO trachea

description:
GEMC1 null mouse
KO_trachea

value: mixed C57BL/6 x 129


title: IL-10 producing TFR2 cells 4

value: IL-10 producing TFR2 cells


title: buccal cells_51_rep_1

description:
Duke Twins Study of Memory in Aging twin9a vs. common reference pool
BUCCAL_9A

value: buccal cells

value: control

value: white blood cells


title: IL-10 producing TFR2 cells 2


title: S.LEW(10)x12x2x3x5_colon_tumor-induced_rep3

description:
C3
Gene expression in colon of 30-week-old S.LEW(10)x12x2x3x5 congenic strain receiving Azoxymethane to induce colon tumors at 6 weeks of age

source_name: S.LEW(10)x12x2x3x5 congenic strain, colon tissue, Azoxymethane-induced colon tumors

value: Azoxymethane

value: colon

value: male

value: 30 weeks


title: 4607_SNP6.0

source_name: Bone Marrow

value: acute lymphoblastic leukemia

value: Diagnostic sample


title: buccal cells_49_rep_1

description:
Duke Twins Study of Memory in Aging twin8b vs. common reference pool
BUCCAL_8A


title: buccal cells_47_rep_1

description:
Duke Twins Study of Memory in Aging twin8a vs. common reference pool
BUCCAL_7A

source_name: buccal cells, Alzheimer's disease

value: Alzheimer's disease


title: buccal cells_50_rep_2

description:
Duke Twins Study of Memory in Aging twin8b vs. common reference pool
BUCCAL_8B


title: buccal cells_46_rep_2

description:
Duke Twins Study of Memory in Aging twin7b vs. common reference pool
BUCCAL_6B


title: buccal cells_48_rep_2

description:
Duke Twins Study of Memory in Aging twin8a vs. common reference pool
BUCCAL_7B


title: buccal cells_43_rep_1

description:
Duke Twins Study of Memory in Aging twin7a vs. common reference pool
BUCCAL_5A


title: S.LEW(10)x12x2x3x5_colon_tumor-induced_rep2

description:
C2
Gene expression in colon of 30-week-old S.LEW(10)x12x2x3x5 congenic strain receiving Azoxymethane to induce colon tumors at 6 weeks of age


title: Data 223 Area4

city: Milann

first: Cecilia

last: Dieci

address: Via Celoria 10

department: Department of Health, Animal Science and Food Safety

country: Italy

institute: University of Milan

description: Array 12

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 10x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 60°C for 15 minutes and then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 60°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilization solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal.

organism: Bos taurus

label_protocol: Samples were labeled using the Universal Linkage System (ULS)  Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule. The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Cumulus cells were collected from slaughterhouse-derived ovaries and grouped according to the oocyte chromatin configuration as described by Lodde et al. 2007.

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 13.5 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HSPlus RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification. Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol:
Procedures used for the collection of Cumulus Cells and Oocytes from a single COC for mRNA extraction for microarray analysis
•Collect COCs as usual (see R&DBIO lab IVP procedure) in Hepes buffered collection medium (M199D)
Cumulus Cells collection
•Put a single COC in 300 µl of pre-warmed (37°C) M199D in a numbered eppendorf tube (RNAase free). Vortex 35 Hz for 1 min
•Rinse the tube walls and the cap with 300 µl of pre-warmed M199D and allow the oocyte to settle.
•Put the content of the tube in a 35 mm petri dish and remove the oocyte.
• Put the denuded oocyte (DO) in a numbered 5µl drop of M199D containing 1µg/ml Hoechst 33342 in a 60 mm dish covered with pre-warmed mineral oil (embryo culture grade). Keep the petri dish on a thermostatic plate set at 37-38°C. (6 drops/oocytes per dish) until reading.
NOTE: the number of the oocyte in the drop MUST BE the same as the number corresponding cumulus cells in the 1.7 ml tube
•Put the remained cell suspension in the same tube from where it belongs.
•Rinse the petri dish with 300 µl of cold PBS, put it in the same tube and keep it on ice.
•Immediately centrifuge the cell suspension 10000 rpm for 1 min at 4°C.
•Remove the supernatant and wash the cell pellet in 1 ml of cold PBS.
•Centrifuge 10000 rpm for 1 min at 4°C.
•Remove the supernatant as much as possible (leave 5µl maximum).
•Freeze the cell pellet by putting the bottom of the tube directly in liquid nitrogen.
•Store in a box at -80°C.
NOTE: for RNA extraction pool 10 tubes with cumulus cells of the same GV stage

value: cumulus cell

tag: oocyte chromatin configuration


title: Data 223 Area1

description: Array 9


title: buccal cells_44_rep_2

description:
Duke Twins Study of Memory in Aging twin7a vs. common reference pool
BUCCAL_5B


title: S.LEW(10)x12x2x3x5_colon_tumor-induced_rep1

description:
C1
Gene expression in colon of 30-week-old S.LEW(10)x12x2x3x5 congenic strain receiving Azoxymethane to induce colon tumors at 6 weeks of age


title: buccal cells_41_rep_1

description:
Duke Twins Study of Memory in Aging twin6b vs. common reference pool
BUCCAL_4A


title: Data 223 Area3

description: Array 11


title: buccal cells_42_rep_2

description:
Duke Twins Study of Memory in Aging twin6b vs. common reference pool
BUCCAL_4B


title: Data 223 Area2

description: Array 10


title: adult hindbrain endothelial cells, biological rep1

source_name: adult hindbrain endothelial cells

value: mixed

value: wild type (normal)

value: Adult mouse hindbrain

value: Cd144/Cd105 cells by magnetic sorting


title: buccal cells_40_rep_2

description:
Duke Twins Study of Memory in Aging twin6a vs. common reference pool
BUCCAL_3B


title: buccal cells_39_rep_1

description:
Duke Twins Study of Memory in Aging twin6a vs. common reference pool
BUCCAL_3A


title: buccal cells_45_rep_1

description:
Duke Twins Study of Memory in Aging twin7b vs. common reference pool
BUCCAL_6A


title: Data 222 Area2

description: Array 6


title: Data 222 Area4

description: Array 8


title: Data 222 Area3

description: Array 7


title: Dahl-S_colon_tumor-induced_rep3

description:
S3
Gene expression in colon of 30-week-old Dahl salt-sensitive rat receiving Azoxymethane to induce colon tumors at 6 weeks of age

value: S


title: Data 221 Area4

description: Array 4


title: Data 221 Area3

description: Array 3


title: buccal cells_37_rep_1

description:
Duke Twins Study of Memory in Aging twin17b vs. common reference pool
BUCCAL_38A


title: buccal cells_35_rep_1

description:
Duke Twins Study of Memory in Aging twin17a vs. common reference pool
BUCCAL_37A


title: buccal cells_36_rep_2

description:
Duke Twins Study of Memory in Aging twin17a vs. common reference pool
BUCCAL_37B


title: buccal cells_33_rep_1

description:
Duke Twins Study of Memory in Aging twin16b vs. common reference pool
BUCCAL_34A


title: buccal cells_32_rep_2

description:
Duke Twins Study of Memory in Aging twin16a vs. common reference pool
BUCCAL_33B


title: Data 221 Area1

description: Array 1


title: buccal cells_34_rep_2

description:
Duke Twins Study of Memory in Aging twin16b vs. common reference pool
BUCCAL_34B


title: buccal cells_38_rep_2

description:
Duke Twins Study of Memory in Aging twin17b vs. common reference pool
BUCCAL_38B


title: buccal cells_27_rep_1

description:
Duke Twins Study of Memory in Aging twin5b vs. common reference pool
BUCCAL_2A


title: buccal cells_28_rep_2

description:
Duke Twins Study of Memory in Aging twin5b vs. common reference pool
BUCCAL_2B


title: buccal cells_24_rep_2

description:
Duke Twins Study of Memory in Aging twin14b vs. common reference pool
BUCCAL_26B


title: buccal cells_23_rep_1

description:
Duke Twins Study of Memory in Aging twin14b vs. common reference pool
BUCCAL_26A


title: buccal cells_22_rep_2

description:
Duke Twins Study of Memory in Aging twin14a vs. common reference pool
BUCCAL_25B


title: Data 222 Area1

description: Array 5


title: buccal cells_26_rep_2

description:
Duke Twins Study of Memory in Aging twin15a vs. common reference pool
BUCCAL_29B


title: buccal cells_25_rep_1

description:
Duke Twins Study of Memory in Aging twin15a vs. common reference pool
BUCCAL_29A


title: buccal cells_21_rep_1

description:
Duke Twins Study of Memory in Aging twin14a vs. common reference pool
BUCCAL_25A


title: buccal cells_29_rep_1

description:
Duke Twins Study of Memory in Aging twin15b vs. common reference pool
BUCCAL_30A


title: buccal cells_20_rep_2

description:
Duke Twins Study of Memory in Aging twin13b vs. common reference pool
BUCCAL_24B


title: buccal cells_30_rep_2

description:
Duke Twins Study of Memory in Aging twin15b vs. common reference pool
BUCCAL_30B


title: buccal cells_18_rep_2

description:
Duke Twins Study of Memory in Aging twin13a vs. common reference pool
BUCCAL_23B


title: buccal cells_14_rep_2

description:
Duke Twins Study of Memory in Aging twin12a vs. common reference pool
BUCCAL_21B


title: buccal cells_13_rep_1

description:
Duke Twins Study of Memory in Aging twin12a vs. common reference pool
BUCCAL_21A


title: buccal cells_15_rep_1

description:
Duke Twins Study of Memory in Aging twin12b vs. common reference pool
BUCCAL_22A


title: buccal cells_19_rep_1

description:
Duke Twins Study of Memory in Aging twin13b vs. common reference pool
BUCCAL_24A


title: Data 221 Area2

description: Array 2


title: buccal cells_11_rep_1

description:
Duke Twins Study of Memory in Aging twin5a vs. common reference pool
BUCCAL_1A


title: buccal cells_9_rep_1

description:
Duke Twins Study of Memory in Aging twin11b vs. common reference pool
BUCCAL_18A


title: buccal cells_16_rep_2

description:
Duke Twins Study of Memory in Aging twin12b vs. common reference pool
BUCCAL_22B


title: buccal cells_5_rep_1

description:
Duke Twins Study of Memory in Aging twin10b vs. common reference pool
BUCCAL_12A


title: buccal cells_6_rep_2

description:
Duke Twins Study of Memory in Aging twin10b vs. common reference pool
BUCCAL_12B


title: buccal cells_3_rep_1

description:
Duke Twins Study of Memory in Aging twin10a vs. common reference pool
BUCCAL_11A


title: buccal cells_4_rep_2

description:
Duke Twins Study of Memory in Aging twin10a vs. common reference pool
BUCCAL_11B


title: buccal cells_2_rep_2

description:
Duke Twins Study of Memory in Aging twin9b vs. common reference pool
BUCCAL_10B


title: buccal cells_1_rep_1

description:
Duke Twins Study of Memory in Aging twin9b vs. common reference pool
BUCCAL_10A


title: frontal cortex_20_rep_2

description:
Duke Twins Study of Memory in Aging twin4a vs. common reference pool
BRAIN_9A_2

source_name: frontal cortex, Later age of onset AD

value: frontal cortex

value: Later age of onset AD


title: buccal cells_31_rep_1

description:
Duke Twins Study of Memory in Aging twin16a vs. common reference pool
BUCCAL_33A

value: buccal cells


title: cerebellum_8_rep_2

description:
Duke Twins Study of Memory in Aging twin4b vs. common reference pool
BRAIN_9B_CB_2

source_name: cerebellum, Later age of onset AD

value: cerebellum

value: white blood cells


title: frontal cortex_21_rep_1

description:
Duke Twins Study of Memory in Aging twin4b vs. common reference pool
BRAIN_9B_1

source_name: frontal cortex, Earlier age of onset AD

value: Earlier age of onset AD


title: frontal cortex_22_rep_2

description:
Duke Twins Study of Memory in Aging twin4b vs. common reference pool
BRAIN_9B_2


title: buccal cells_10_rep_2

description:
Duke Twins Study of Memory in Aging twin11b vs. common reference pool
BUCCAL_18B


title: D2_ww_PBS, replicate 3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
replicate 3
9371989048_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

source_name: MCA 215 fibrosarcoma

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

value: 10-12 weeks

value: wt

value: PBS


title: D2_ww_PBS, replicate 1

description:
replicate 1
9341927055_B

source_name: MCA 213 fibrosarcoma


title: D2_ww_PBS, replicate 2

description:
replicate 2
9341927106_A

source_name: MCA 214 fibrosarcoma


title: cerebellum_7_rep_1

description:
Duke Twins Study of Memory in Aging twin4b vs. common reference pool
BRAIN_9B_CB_1


title: D2_ww_DX, replicate 2

description:
replicate 2
9341927101_D

source_name: MCA 211 fibrosarcoma

value: DX


title: D2_ww_DX, replicate 3

description:
replicate 3
9371989048_C

source_name: MCA 212 fibrosarcoma


title: D2_ww_DX, replicate 1

description:
replicate 1
9322863008_B

source_name: MCA 210 fibrosarcoma


title: buccal cells_7_rep_1

description:
Duke Twins Study of Memory in Aging twin11a vs. common reference pool
BUCCAL_17A

source_name: buccal cells, control

value: control

source_name: white blood cells, common reference pool


title: cerebellum_5_rep_1

description:
Duke Twins Study of Memory in Aging twin3b vs. common reference pool
BRAIN_8B_CB_1


title: frontal cortex_19_rep_1

description:
Duke Twins Study of Memory in Aging twin4a vs. common reference pool
BRAIN_9A_1


title: frontal cortex_16_rep_2

description:
Duke Twins Study of Memory in Aging twin3b vs. common reference pool
BRAIN_8B_2


title: cerebellum_6_rep_2

description:
Duke Twins Study of Memory in Aging twin3b vs. common reference pool
BRAIN_8B_CB_2


title: D2_fw_PBS, replicate 3

description:
replicate 3
9371989048_A

source_name: MCA 209 fibrosarcoma


title: D2_fw_PBS, replicate 2

description:
replicate 2
9341927055_E

source_name: MCA 208 fibrosarcoma


title: D2_fw_DX, replicate 2

description:
replicate 2
9341927106_E

source_name: MCA 206 fibrosarcoma


title: D2_fw_PBS, replicate 1

description:
replicate 1
9322863008_C

source_name: MCA 207 fibrosarcoma


title: D2_fw_DX, replicate 1

description:
replicate 1
9341927106_C

source_name: MCA 205 fibrosarcoma


title: frontal cortex_15_rep_1

description:
Duke Twins Study of Memory in Aging twin3b vs. common reference pool
BRAIN_8B_1


title: cerebellum_4_rep_2

description:
Duke Twins Study of Memory in Aging twin2b vs. common reference pool
BRAIN_11B_CB_2


title: frontal cortex_13_rep_1

description:
Duke Twins Study of Memory in Aging twin3a vs. common reference pool
BRAIN_8A_1


title: frontal cortex_14_rep_2

description:
Duke Twins Study of Memory in Aging twin3a vs. common reference pool
BRAIN_8A_2