title: Cyanothece sp. ATCC 51142_time_38.08_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 2, sampled at 38.08 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_41.75_biorep1_techrep1

status: Public on Feb 03 2015

type: RNA

city: East Lansing

first: Sandeep

middle: B.

last: Gaudana

state: MI

address: 612 Wilson Road

country: USA

institute: Michigan State University

description: Bilogical replicate 1 of 2, technical replicate 1 of 3, sampled at 41.75 h into constant light cultivation

hyb_protocol: 300ng of each labeled sample to be co-hybridized was fragmented and hybridized on custom array:  Agilent Custom GE, 8x15K Microarray - AMADID 018970.

scan_protocol: Agilent Technologies Scanner G2505C was used

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Crocosphaera subtropica ATCC 51142

source_name: Cyanothece sp. ATCC 51142_time_41.75

label_protocol: 1ug of total RNA was labeled using Kreatech ULS labeling system each sample was labeled with Cy5 a pool of the samples was used as a control - this was labeled with Cy3

growth_protocol: Axenic cultures of Cyanothece 51142 were cultivated in ASP2 medium without nitrate in air-sparged and stirred bioreactor with external illumination of 230 µmol photons.

extract_protocol: Samples were drawn to extract RNA for microarray analysis such that the product of volume and OD730nm was 50.0.  Total RNA was extracted from the samples using TRI reagent (Sigma–Aldrich).

treatment_protocol: The culture was entrained under light/dark cycles (12 h /12 h) (LD) for 4 days and then released into continuous light (LL)

tag: sample

tag: time in constant light (hours)

source_name: Cyanothece sp. ATCC 51142

value: Pool 1-18

tag: time point

value: Control:equimolar pool of all samples


title: BY4742_2pct_Glu.3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: BY4742 Wild Type

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

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

data_processing: RMA normalization log2

organism: Saccharomyces cerevisiae

source_name: BY4742 Wild Type

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Yeast_2 Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

growth_protocol: Cultures were grown at 30°C overnight in a 96 well plate in YPD and then 2.5µl of the overnight culture was inoculated into 147.5µl of culture media in 100 well Bioscreen plates. Yeast growth rates were analyzed in the OD420-580 range in the Bioscreen C MBR machine (Growth Curves USA) as previously described using the Yeast Outgrowth Data Analyzer (YODA)

extract_protocol: Wild type and los1∆ cells were inoculated in 5ml YEPD overnight culture.  Three isolates of each strain were tested, with six cultures (duplicates) for wild type cells and three cultures for los1∆ cells.  Overnight cultures were then diluted to <0.05 OD600 in 50ml YEPD and shaken at 225 rpm at 30°C until exactly 0.5 OD600 was reached.    The entire cuture was then transferred to conical tubes and centrifuged at 4°C for 2 minutes at 3000g in a counter top centrifuge.  Supernatant was removed and resuspended in 1 ml ice cold Martin Lysis buffer (40mM KCl, 7.5 mM MgCl2, 1 mM DTT, 25 mM Tris-HCl pH7.5, 0.5 mg/ml heparin, 100µg/ml cycloheximide, in ddH2O).  Suspensions were transferred to microfuge tubes containing 0.4g glass beads (Sigma) and vortexed for 30 seconds, 8 times with 30 seconds on ice between vortex steps.  10µl of 20% triton X-100 and 10µl 20% Na deoxycholate  were added to each tube and vortexed for 15 seconds.  Lysate was cleared of debris by centrifugation at 17k g in a microcentrifuge at 4°C for 2 minutes.  Cleared lysate was then treated by the RNeasy Qiagen RNA prep following the manufacturer’s protocol.

tag: strain


title: Cyanothece sp. ATCC 51142_time_36.415_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 3, sampled at 36.415 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_36.415


title: Cyanothece sp. ATCC 51142_time_41.75_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 3, sampled at41.75 h into constant light cultivation


title: BY4742_2pct_Glu.5

description: BY4742 Wild Type


title: Primary human monocytes from patient with metastatic breast cancer #1

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was handled and normalized in BASE (https://casa4.bmc.lu.se/onk/). All data was mean background corrected followed by quantile normalization. Array control probes were removed.

label: biotin

organism: Homo sapiens

source_name: Primary human monocytes

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

extract_protocol: Total RNA was extracted with TRIZOL. Quality control was performed with Agilent 2100 Bioanalyser.

tag: cell type

value: primary monocyte

tag: disease state

value: Metastatic breast cancer


title: BY4742_2pct_Glu.6

description: BY4742 Wild Type


title: Cyanothece sp. ATCC 51142_time_Control_pool_techrep1

description: Control: equimolar pool of RNA from all 9 time points and their biological replicates, so a total of 18 samples

source_name: Cyanothece sp. ATCC 51142_time_Control

value: Control


title: Cyanothece sp. ATCC 51142_time_31.125_biorep1_techrep3

description: Bilogical replicate 1 of 2, technical replicate 3 of 3, sampled at 31.125 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_31.125


title: BY4742_2pct_Glu.2

description: BY4742 Wild Type


title: Cyanothece sp. ATCC 51142_time_34.96_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 2, sampled at 34.96 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_34.96


title: Cyanothece sp. ATCC 51142_time_25.915_biorep1_techrep3

description: Bilogical replicate 1 of 2, technical replicate 3 of 3, sampled at 25.915 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_25.915


title: Cyanothece sp. ATCC 51142_time_27.83_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 2, sampled at 27.83 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_27.83


title: BY4742_2pct_Glu.1

description: BY4742 Wild Type


title: Cyanothece sp. ATCC 51142_time_38.08_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 2, sampled at 38.08 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_38.08


title: Cyanothece sp. ATCC 51142_time_41.75_biorep2_techrep1

description: Bilogical replicate 2 of 2, technical replicate 1 of 3, sampled at 41.75 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_27.83_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 2, sampled at 27.83 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_31.125_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 3, sampled at 31.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_21.125_biorep1_techrep3

description: Bilogical replicate 1 of 2, technical replicate 3 of 3, sampled at 21.125 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_21.125


title: Cyanothece sp. ATCC 51142_time_31.125_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 3, sampled at 31.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_24.54_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 2, sampled at 24.54 h into constant light cultivation

source_name: Cyanothece sp. ATCC 51142_time_24.54


title: Cyanothece sp. ATCC 51142_time_34.96_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 2, sampled at 34.96 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_24.54_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 2, sampled at 24.54 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_21.125_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 3, sampled at 21.125 h into constant light cultivation


title: Cyanothece sp. ATCC 51142_time_25.915_biorep1_techrep2

description: Bilogical replicate 1 of 2, technical replicate 2 of 3, sampled at 25.915 h into constant light cultivation


title: Col-0_+CK1hr_2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with cytokinin treatment [rep2]

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Scanned signal intensity was log2-transformed. The log2-transformed data for two comparisons (1. untreated mutants (single, double, or triple mutant of ARR1, 10, and 12 genes) versus untreated Col-0; and 2. CK-treated Col-0 versus mock-treated Col-0) were quantile-normalized separately. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011b).

organism: Arabidopsis thaliana

source_name: Root tissues of Arabidopsis 10-day-old seedlings

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Arabidopsis seedlings were grown on vertically oriented 1/2 MS agar plates in an environmentally controlled growth room (Korea Instruments, Seoul, Korea) at 22 °C with continuous light for 10 days.

extract_protocol: Total RNA was isolated from root tissues using WelPrepTM (Welgene, Daegu, Korea), and the integrity of the total RNA was checked using a Bioanalyzer 2100.

treatment_protocol: For the comparison untreated mutants (single, double, or triple mutant of ARR1, 10, and 12 genes) versus untreated Col-0, there was no treatment. For the comparison CK-treated Col-0 versus mock-treated Col-0, 10-day-old seedlings were mock-treated or treated with 5uM N6-benzyladenine (BA, Sigma B 3408) for 1 hour.

tag: tissue

value: root

tag: age

tag: developmental stage

value: seedling

tag: ecotype

tag: genotype/variation

value: wild type

tag: treatment

value: cytokinin treatment


title: Cyanothece sp. ATCC 51142_time_25.915_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 3, sampled at 25.915 h into constant light cultivation


title: Col-0_+CK1hr_1

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with cytokinin treatment [rep1]


title: Col-0_-1hr_1

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with mock treatment [rep1]

value: mock treatment


title: Col-0_-1hr_2

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with mock treatment [rep2]


title: arr1/10/12_0hr_2

description: Root tissues of 10-day-old seedlings of arr1/10/12 triple mutant with no treatment [rep2]

value: arr1/10/12 triple mutant

value: no treatment


title: arr1/10_0hr_1

description: Root tissues of 10-day-old seedlings of arr1/10 double mutant with no treatment [rep1]

value: arr1/10 double mutant


title: 16 week ApoE 4681

city: Oxford

first: Keith

last: Channon

address: Roosevelt Drive

department: Radcliffe Department of Medicine

country: United Kingdom

institute: Oxford University

hyb_protocol: The Lucidea slide pro was used for hybridisation and washing

scan_protocol: The arrays were scanned using the Axon 4000B scanner, where the red and green lasers were adjusted to provide similar global counts across the array, to alleviate any technical difference within the dyes themselves. GenePix software for the Axon 4000B performed the data extraction using the GAL file to generate the raw data files.

data_processing: Raw data was analysed using GeneSpring Software for lowess normalisation

organism: Mus musculus

source_name: thoracic aorta from 16 week old ApoE mouse

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions.

extract_protocol: Thoracic aortas were homogenised in TriZol reagent (Sigma) and total RNA extracted using Rneasy kits (Qiagen)

treatment_protocol: ApoE knockout mice were fed a western type diet to develop atherosclerosis. Thoracic aortas were dissected from 8 week old or 16 week old mice.

tag: diet

value: western-type diet

source_name: Reference

value: chow fed


title: arr1/12_0hr_2

description: Root tissues of 10-day-old seedlings of arr1/12 double mutant with no treatment [rep2]

value: arr1/12 double mutant


title: 16 week ApoE 4681 dyeswap


title: arr10/12_0hr_2

description: Root tissues of 10-day-old seedlings of arr10/12 double mutant with no treatment [rep2]

value: arr10/12 double mutant


title: Cyanothece sp. ATCC 51142_time_21.125_biorep1_techrep1

description: Bilogical replicate 1 of 2, technical replicate 1 of 3, sampled at 21.125 h into constant light cultivation

value: Pool 1-18


title: arr1/10/12_0hr_1

description: Root tissues of 10-day-old seedlings of arr1/10/12 triple mutant with no treatment [rep1]


title: 16 week ApoE 4680


title: arr1/10_0hr_2

description: Root tissues of 10-day-old seedlings of arr1/10 double mutant with no treatment [rep2]


title: 16 week ApoE 4680 dyeswap


title: arr10/12_0hr_1

description: Root tissues of 10-day-old seedlings of arr10/12 double mutant with no treatment [rep1]


title: 16 week ApoE 4628 dyeswap


title: 16 week ApoE 4628


title: arr1/12_0hr_1

description: Root tissues of 10-day-old seedlings of arr1/12 double mutant with no treatment [rep1]


title: arr12_0hr_1

description: Root tissues of 10-day-old seedlings of arr12 single mutant with no treatment [rep1]

value: arr12 single mutant


title: miR-155KO_MOG35-55

city: Lodz

first: Marcin

middle: P

last: Mycko

address: Kopcinskiego 22

department: Department of Neurology

country: Poland

institute: Medical University of Lodz

description: Test

data_processing:
endogenous control Hprt1 oraz 18-s; Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)];
DataAssist (Life Technologies) software performed all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data; Matrix normalized worksheet reports normalized signal (against housekeeping genes); Fold Change worksheet reports test/control ratios.

label: TaqMan probes (FAM)

source_name: T helper cells from murine splenocytes

label_protocol: PCR assays were performed using the TaqMan probes (Life Technologies).

growth_protocol: 72 hrs in 37C in IMDM/10% FCS medium 1x10e6 cells/ml

extract_protocol: Total RNA isolation with miRVana

treatment_protocol: 20 ug/ml of MOG peptide 35-55 or untreated

value: T helper cells

tag: activation

value: MOG peptide 35-55 20 ug/ml

tag: time of stimulation

value: 72 hrs

value: miR-155 deficient


title: 8 week ApoE 5079 dyeswap

source_name: thoracic aorta from 8 week old ApoE mouse


title: 8 week ApoE 5079


title: P13_adeno

type: genomic

city: Salt Lake City

first: Joshua

middle: D

last: Schiffman

state: Utah

address: 2000 Circle of Hope Dr

department: Pediatric Oncology/Hematology

institute: Huntsman Cancer Institute

description: Hybridized to Oncoscan FFPE Array (v3)

hyb_protocol: Arrays were hybridized overnight, Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing: CEL files are combined by OncoScan Console software to generate OSCHP files which are analyzed by Nexus Express for Oncoscan software, using the TuScan algorithm

label: Biotin

molecule: genomic DNA

source_name: FFPE

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan.

extract_protocol: Genomic DNA was extracted from FFPE using the Ambion Recover All Total Nucleic Acid Isolation Kit. DNA quantity was assessed with a Qubit using the Quant-it DNA High Sensitivity kit from Invitrogen

tag: diagnosis

value: Li-Fraumeni Syndrome tumors

tag: tumor type

value: lung adenocarcinoma


title: H1_met2

description: Hybridized to Oncoscan FFPE Array (v3)

value: osteosarcoma lung metastasis


title: arr10_0hr_1

description: Root tissues of 10-day-old seedlings of arr10 single mutant with no treatment [rep1]

value: root

value: seedling

value: arr10 single mutant


title: 8 week ApoE 5078 dyeswap


title: arr10_0hr_2

description: Root tissues of 10-day-old seedlings of arr10 single mutant with no treatment [rep2]

value: no treatment


title: arr1_0hr_2

description: Root tissues of 10-day-old seedlings of arr1 single mutant with no treatment [rep2]

value: arr1 single mutant


title: 8 week ApoE 5078

value: western-type diet

value: chow fed


title: B6_MOG35-55

description: Test


title: arr12_0hr_2

description: Root tissues of 10-day-old seedlings of arr12 single mutant with no treatment [rep2]


title: 8 week ApoE 5077


title: B6_unstim

description: Control

value: unstimulated


title: Col-0_0hr_1

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with no treatment [rep1]

value: wild type


title: H1_met1

description: Hybridized to Oncoscan FFPE Array (v3)


title: miR-155KO_unstim

description: Test


title: P13_meningioma

description: Hybridized to Oncoscan FFPE Array (v3)

value: meningioma


title: Col-0_0hr_2

description: Root tissues of 10-day-old seedlings of wild type (Col-0) with no treatment [rep2]


title: arr1_0hr_1

description: Root tissues of 10-day-old seedlings of arr1 single mutant with no treatment [rep1]


title: R.sphaeroides 2.4.1 ∆iscR vs. R.sphaeroides 2.4.1 wildtype replicate 2

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: biological sample 4-6

hyb_protocol: Total RNA of three independent experiments of an iscR deletion strain (2.4.1∆iscR) and a control strain (wild type 2.4.1) were pooled and hybridized to one array. Two arrays werehybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: R with Limma package was used for data evaluation. LOESS normalized and background subtracted.

organism: Cereibacter sphaeroides 2.4.1

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

growth_protocol: R. sphaeroides strains grown microaerobically

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

tag: genotype

value: ∆iscR


title: R.sphaeroides 2.4.1 ∆iscR vs. R.sphaeroides 2.4.1 wildtype replicate 1

description: biological sample 1-3


title: 8 week ApoE 5077 dyeswap


title: 15-08-039-3_Nonasthmatic

status: Public on Feb 02 2015

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

hyb_protocol: Nimblegen-recommended protocol on the Maui 12-bay hyb station.

scan_protocol: Nimblegen-recommended settings on the Nimblegen’s scanner (Roche Nimblegen, Madison, WI)

data_processing: Images were processed using RMA normalization with Nimblegen’s DEVA software.

source_name: PBMC

label_protocol: RNA was reverse transcribed and amplified using the TransPlex Whole Transcriptome Amplification (WTA) Kit (Sigma-Aldrich, St. Louis, MO) followed by Cy3 labeling using Nimblegen one-color labeling kits.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using the Ficoll density gradient separation. DNA and RNA were isolated simultaneously from the PBMCs using the AllPrep DNA/RNA kit (Qiagen, Germantown, MD), DNA and RNA samples were quantified and purity assessed using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was determined using the Bioanalyzer (Agilent, Santa Clara, CA).

tag: asthma

value: FALSE

tag: subtype

value: non

value: PBMC


title: 15-08-044-9_Nonasthmatic


title: 15-08-035-5_Asthmatic

value: TRUE


title: 15-08-033-8_Nonasthmatic


title: 15-08-042-0_Nonasthmatic


title: 15-08-038-6_Nonasthmatic


title: 15-08-043-1_Asthmatic


title: 15-08-032-9_Nonasthmatic


title: 15-08-037-2_Nonasthmatic


title: 15-08-045-4_Nonasthmatic


title: 15-08-036-4_Nonasthmatic


title: 15-08-040-8_Nonasthmatic


title: 15-08-027-0_Nonasthmatic


title: 15-08-024-3_Nonasthmatic


title: 15-08-023-6_Nonasthmatic


title: 15-08-031-7_Nonasthmatic


title: 15-08-020-4_Nonasthmatic


title: 15-08-026-2_Nonasthmatic


title: 15-08-022-7_Nonasthmatic


title: 15-08-029-1_Nonasthmatic


title: 15-08-018-4_Asthmatic

value: reversible


title: 15-08-019-7_Nonasthmatic


title: 15-08-025-8_Nonasthmatic


title: 15-08-021-5_Nonasthmatic


title: 15-08-028-9_Asthmatic


title: 15-08-017-8_Nonasthmatic


title: 15-08-034-0_Nonasthmatic


title: 15-08-014-5_Nonasthmatic


title: 15-08-016-6_Nonasthmatic


title: 15-08-013-2_Nonasthmatic


title: 15-08-009-9_Nonasthmatic


title: 15-08-006-8_Asthmatic


title: 15-08-002-3_Asthmatic


title: 15-08-015-0_Asthmatic


title: 15-08-007-5_Asthmatic


title: 15-08-011-3_Asthmatic


title: 15-07-031-8_Asthmatic


title: 15-07-035-6_Nonasthmatic


title: 15-07-028-5_Nonasthmatic


title: 15-08-005-2_Nonasthmatic


title: 15-08-001-0_Asthmatic


title: 15-07-033-9_Asthmatic


title: 15-07-037-3_Nonasthmatic


title: 15-08-004-7_Asthmatic


title: 15-08-010-9_Nonasthmatic


title: 15-07-029-2_Nonasthmatic


title: 15-08-008-1_Nonasthmatic


title: 15-07-034-1_Nonasthmatic


title: 15-07-030-2_Nonasthmatic


title: 15-08-012-1_Asthmatic


title: 15-07-027-1_Asthmatic


title: 15-07-032-5_Asthmatic


title: 15-07-036-0_Nonasthmatic


title: 15-08-003-4_Nonasthmatic


title: 15-07-024-4_Nonasthmatic


title: 15-07-019-8_Asthmatic


title: 15-07-020-0_Asthmatic


title: 15-07-016-7_Nonasthmatic


title: 15-07-025-9_Nonasthmatic


title: 15-07-023-7_Asthmatic


title: 15-07-026-3_Asthmatic


title: 15-07-021-6_Asthmatic


title: 15-07-006-9_Asthmatic


title: 15-07-009-5_Nonasthmatic


title: 15-07-015-1_Asthmatic


title: 15-07-017-9_Asthmatic


title: 15-07-001-1_Asthmatic


title: 15-07-010-5_Nonasthmatic


title: 15-07-003-0_Asthmatic


title: 15-07-013-3_Asthmatic


title: 15-07-002-4_Asthmatic


title: 15-07-005-3_Asthmatic


title: 15-07-018-0_Asthmatic


title: 15-07-022-8_Nonasthmatic


title: 15-07-014-6_Asthmatic


title: 15-07-007-6_Asthmatic


title: 15-07-008-2_Asthmatic


title: 15-07-004-8_Asthmatic


title: 15-06-010-8_Nonasthmatic


title: 15-06-003-3_Nonasthmatic


title: 15-06-006-7_Asthmatic


title: 15-06-008-0_Nonasthmatic


title: 15-06-007-9_Asthmatic


title: 15-06-004-6_Asthmatic


title: 15-06-002-2_Asthmatic


title: 15-05-040-4_Asthmatic


title: 15-05-042-7_Nonasthmatic


title: 15-05-037-5_Asthmatic


title: 15-05-041-5_Nonasthmatic


title: 15-05-038-1_Nonasthmatic


title: 15-06-009-8_Nonasthmatic


title: 15-05-033-4_Nonasthmatic


title: 15-05-025-4_Nonasthmatic


title: 15-05-036-8_Asthmatic


title: 15-05-027-7_Asthmatic


title: 15-05-029-6_Nonasthmatic


title: 15-05-035-2_Asthmatic


title: 15-07-011-4_Nonasthmatic


title: 15-06-001-4_Nonasthmatic


title: 15-05-031-0_Nonasthmatic


title: 15-05-030-6_Nonasthmatic


title: 15-05-026-5_Asthmatic


title: 15-05-032-3_Asthmatic


title: 15-05-034-7_Asthmatic


title: 15-05-023-1_Asthmatic


title: 15-05-039-9_Asthmatic


title: 15-05-028-3_Asthmatic


title: 15-05-020-8_Asthmatic


title: 15-05-012-6_Asthmatic


title: 15-05-024-9_Asthmatic


title: 15-05-016-1_Asthmatic


title: 15-05-008-6_Nonasthmatic


title: 15-05-018-8_Asthmatic


title: 15-05-022-0_Asthmatic


title: 15-05-014-2_Asthmatic


title: 15-05-010-3_Asthmatic


title: 15-05-017-4_Nonasthmatic


title: 15-05-013-5_Nonasthmatic


title: 15-05-021-2_Asthmatic


title: 15-05-011-9_Asthmatic


title: 15-05-015-7_Asthmatic


title: 15-05-019-0_Asthmatic


title: 15-05-009-3_Asthmatic


title: 15-06-005-1_Nonasthmatic


title: 15-05-006-4_Nonasthmatic


title: 15-05-002-9_Asthmatic


title: 15-05-001-7_Nonasthmatic


title: 15-04-008-7_Asthmatic


title: 15-04-004-1_Nonasthmatic


title: 15-04-005-6_Asthmatic


title: 15-04-010-4_Asthmatic


title: 15-05-004-0_Asthmatic


title: 15-04-002-5_Asthmatic


title: 15-04-006-0_Nonasthmatic


title: 15-05-005-5_Asthmatic


title: 15-02-053-1_Nonasthmatic


title: 15-02-049-9_Asthmatic


title: 15-04-007-3_Asthmatic


title: 15-04-003-9_Asthmatic


title: 15-02-054-9_Nonasthmatic


title: 15-02-050-8_Asthmatic


title: 15-02-055-4_Nonasthmatic


title: 15-02-047-5_Nonasthmatic


title: 15-04-009-4_Asthmatic


title: 15-02-051-2_Nonasthmatic


title: 15-05-003-8_Asthmatic


title: 15-04-001-8_Asthmatic


title: 15-02-052-0_Nonasthmatic


title: 15-02-046-8_Nonasthmatic


title: 15-02-048-1_Nonasthmatic


title: 15-02-045-2_Nonasthmatic


title: 15-02-041-0_Nonasthmatic


title: 15-02-026-0_Nonasthmatic


title: 15-02-043-4_Nonasthmatic


title: 15-02-035-8_Nonasthmatic


title: 15-02-039-1_Nonasthmatic


title: 15-02-030-4_Nonasthmatic


title: 15-02-042-3_Asthmatic


title: 15-02-018-2_Asthmatic


title: 15-02-022-5_Asthmatic


title: 15-02-027-3_Nonasthmatic


title: 15-02-040-6_Nonasthmatic


title: 15-02-044-7_Asthmatic


title: 15-02-031-5_Asthmatic


title: 15-02-038-9_Asthmatic


title: 15-02-033-6_Nonasthmatic


title: 15-02-036-2_Asthmatic


title: 15-02-023-9_Nonasthmatic


title: 15-02-019-5_Nonasthmatic


title: 15-02-029-4_Nonasthmatic


title: 15-02-020-2_Asthmatic


title: 15-02-024-1_Nonasthmatic


title: 15-02-028-7_Nonasthmatic


title: 15-02-015-3_Asthmatic


title: 15-02-025-6_Nonasthmatic


title: 15-02-037-0_Asthmatic


title: 15-02-021-8_Nonasthmatic


title: 15-02-032-7_Nonasthmatic


title: 15-02-017-6_Asthmatic


title: 15-02-013-0_Nonasthmatic


title: 15-02-016-9_Nonasthmatic


title: 15-02-012-4_Asthmatic


title: 15-02-011-1_Asthmatic


title: 15-02-007-8_Nonasthmatic


title: 15-02-001-3_Asthmatic


title: 15-02-009-7_Asthmatic


title: 15-02-005-0_Asthmatic


title: 15-02-008-4_Nonasthmatic


title: 15-02-004-5_Asthmatic


title: 15-02-003-2_Asthmatic


title: 15-02-014-8_Nonasthmatic


title: 15-02-010-7_Asthmatic


title: 15-02-006-6_Asthmatic


title: 15-02-002-1_Asthmatic


title: 15-08-014-5_Nonasthmatic

hyb_protocol: Illumina Infinium protocol

scan_protocol: Illumina iScan

data_processing:
normalized using the SWAN method contained in the R package minfi; the normalized M-values were used in all downstream analyses
Unmethylated and methylated signal intensities are reported in matrix-raw-values.txt which is linked as a supplementary file on the Series record.

label_protocol: 0.85-1.00 µg DNA were bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research, Orange, CA). Each conversion assay included a commercially available positive and negative control (Universal Methylation DNA Standard, Zymo Research, Orange, CA).  Bisulfite converted samples formed the input for the Illumina Infinium Methylation assay


title: 15-08-027-0_Nonasthmatic


title: 15-02-024-1_Nonasthmatic


title: 15-02-002-1_Asthmatic


title: 15-06-001-4_Nonasthmatic


title: 15-08-034-0_Nonasthmatic


title: 15-07-001-1_Asthmatic


title: 15-05-039-9_Asthmatic


title: 15-05-022-0_Asthmatic


title: 15-04-010-4_Asthmatic


title: 15-07-030-2_Nonasthmatic


title: 15-06-009-8_Nonasthmatic


title: 15-05-029-6_Nonasthmatic


title: 15-07-014-6_Asthmatic


title: 15-02-007-8_Nonasthmatic


title: 15-05-004-0_Asthmatic


title: 15-07-024-4_Nonasthmatic


title: 15-07-031-8_Asthmatic


title: 15-02-006-6_Asthmatic


title: 15-02-020-2_Asthmatic


title: 15-07-033-9_Asthmatic


title: 15-02-023-9_Nonasthmatic


title: 15-05-018-8_Asthmatic


title: 15-07-037-3_Nonasthmatic


title: 15-02-031-5_Asthmatic


title: 15-08-022-7_Nonasthmatic


title: 15-05-019-0_Asthmatic


title: 15-08-004-7_Asthmatic


title: 15-05-025-4_Nonasthmatic


title: 15-02-047-5_Nonasthmatic


title: 15-04-002-5_Asthmatic


title: 15-06-006-7_Asthmatic


title: 15-05-035-2_Asthmatic


title: 15-08-012-1_Asthmatic


title: 15-06-008-0_Nonasthmatic


title: 15-05-021-2_Asthmatic


title: 15-08-018-4_Asthmatic


title: 15-08-011-3_Asthmatic


title: 15-08-002-3_Asthmatic


title: 15-07-002-4_Asthmatic


title: 15-02-045-2_Nonasthmatic


title: 15-08-008-1_Nonasthmatic


title: 15-08-019-7_Nonasthmatic


title: 15-08-015-0_Asthmatic


title: 15-02-053-1_Nonasthmatic


title: 15-08-024-3_Nonasthmatic


title: 15-07-020-0_Asthmatic


title: 15-05-009-3_Asthmatic


title: 15-08-032-9_Nonasthmatic


title: 15-05-011-9_Asthmatic


title: 15-05-028-3_Asthmatic


title: 15-05-014-2_Asthmatic


title: 15-05-001-7_Nonasthmatic


title: 15-05-041-5_Nonasthmatic


title: 15-07-036-0_Nonasthmatic


title: 15-06-005-1_Nonasthmatic


title: 15-07-029-2_Nonasthmatic


title: 15-05-032-3_Asthmatic


title: 15-08-029-1_Nonasthmatic


title: 15-05-013-5_Nonasthmatic


title: 15-02-001-3_Asthmatic


title: 15-08-016-6_Nonasthmatic


title: 15-08-035-5_Asthmatic


title: 15-05-002-9_Asthmatic


title: 15-02-040-6_Nonasthmatic


title: 15-08-013-2_Nonasthmatic


title: 15-08-036-4_Nonasthmatic


title: 15-05-015-7_Asthmatic


title: 15-02-048-1_Nonasthmatic


title: 15-02-043-4_Nonasthmatic


title: 15-08-040-8_Nonasthmatic


title: 15-02-041-0_Nonasthmatic


title: 15-02-039-1_Nonasthmatic


title: 15-07-005-3_Asthmatic


title: 15-02-014-8_Nonasthmatic


title: 15-07-034-1_Nonasthmatic


title: 15-08-023-6_Nonasthmatic


title: 15-04-005-6_Asthmatic


title: 15-05-040-4_Asthmatic


title: 15-07-013-3_Asthmatic


title: 15-06-007-9_Asthmatic


title: 15-02-019-5_Nonasthmatic


title: 15-02-037-0_Asthmatic


title: 15-05-024-9_Asthmatic


title: 15-05-037-5_Asthmatic


title: 15-05-010-3_Asthmatic


title: 15-05-008-6_Nonasthmatic


title: 15-02-018-2_Asthmatic


title: 15-02-035-8_Nonasthmatic


title: NM-401_3_162 [701]

city: Roskilde

first: Sarah

middle: Søs

last: Poulsen

state: Denmark

address: Knud den Stores Vej 39B, 2.MF

country: Denmark

institute: The National Research Centre for the Working Environment

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Female C57BL/6 mice at the age of 5–7 weeks were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the experiment. All mice were fed on Altromin (no. 1324, Christian Petersen, Denmark) and had access to water ad libitum during the whole experiment. The mice were housed in groups of 10 animals in polypropylene cages with sawdust bedding and enrichment at controlled temperature 21±1°C and humidity 50±10% with a 12-h light/12-h dark cycle. Experiments were initiated at 8 weeks of age. All procedure complied with EC Directive 86/609/EEC and Danish laws regulating experiments on animals (permit 2010/561-1779). Mice did not display any signs of respiratory distress, lethargy or any other physical symptoms following exposure.

extract_protocol: At 1, 3 or 28 days post-instillation, the mice were anaesthetized as described above and killed by exsanguination via intracardiac puncture. Immediately after withdrawing the heart blood, the liver tissue were snap frozen in cryotubes in liquid N2 and stored at –80°C. Total RNA was extracted (n=6 per group) using Trizol reagent and further purified using the RNeasy Mini Kit with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios between 2.0 and 2.15 and RINs above 7.0.

treatment_protocol: The C57BL/6 mice were exposed in groups of 6 to 162 ug of NRCWE-26 or NM-401 via intratracheal instillation. In brief, mice were anesthetised with 4 % isoflurane until fully relaxed and 2.5 % during the instillation The mice were kept on their back at a 40-degree angle on a hot plate (37°C) during the entire procedure. 162 μg of NRCWE-26 or NM-401 was administered via a single intratracheal instillation. A 40 μl suspension was instilled followed by 150 μl air with a 250 μl SGE glass syringe. Control animals were instilled with vehicle (NanoPure water with 2% serum). After the instillation catheter was removed, breathing was observed in order to assure that the delivered material did not block the airways.

tag: sampleID

tag: time point (days)

tag: dose

tag: particle

tag: strain

tag: gender

value: female

source_name: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)

tag: reference


title: Control NM-401_3_0 [756]

source_name: Control NM-401

value: Control NM-401

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Control NCRWE-026_28_0 [372]

source_name: Control NCRWE-026

value: Control NCRWE-026


title: NM-401_28_162 [721]


title: Control NM-401_28_0 [767]


title: 15-07-017-9_Asthmatic

tag: cell type


title: 15-08-026-2_Nonasthmatic


title: NM-401_1_162 [685]


title: Control NCRWE-026_3_0 [358]


title: NCRWE-026_28_162 [162]


title: 15-07-019-8_Asthmatic


title: 15-05-017-4_Nonasthmatic


title: 15-02-021-8_Nonasthmatic


title: NCRWE-026_1_162 [791]


title: 15-02-012-4_Asthmatic


title: Control NCRWE-026_1_0 [347]


title: Control NM-401_1_0 [747]


title: NCRWE-026_3_162 [143]


title: 15-06-003-3_Nonasthmatic


title: Control NCRWE-026_28_0 [376]


title: 15-05-016-1_Asthmatic


title: NCRWE-026_28_162 [161]


title: Control NM-401_28_0 [766]


title: NCRWE-026_3_162 [141]


title: 15-02-027-3_Nonasthmatic


title: NCRWE-026_3_162 [144]


title: 15-07-010-5_Nonasthmatic


title: NM-401_28_162 [718]


title: Control NM-401_3_0 [754]


title: NM-401_1_162 [682]


title: 15-02-042-3_Asthmatic


title: NM-401_28_162 [720]


title: 15-02-003-2_Asthmatic


title: 15-05-006-4_Nonasthmatic


title: Control NM-401_28_0 [769]


title: NCRWE-026_28_162 [158]


title: NM-401_3_162 [704]


title: NCRWE-026_1_162 [795]


title: Control NCRWE-026_3_0 [359]


title: 15-05-042-7_Nonasthmatic


title: Control NM-401_1_0 [749]


title: 15-04-001-8_Asthmatic


title: Control NCRWE-026_28_0 [375]


title: 15-04-007-3_Asthmatic


title: 15-05-038-1_Nonasthmatic


title: 15-07-009-5_Nonasthmatic


title: 15-05-034-7_Asthmatic


title: Control NCRWE-026_3_0 [357]


title: 15-08-033-8_Nonasthmatic


title: Control NM-401_3_0 [761]


title: NCRWE-026_1_162 [790]


title: NM-401_3_162 [703]


title: NM-401_1_162 [686]


title: Control NM-401_1_0 [742]


title: Control NCRWE-026_3_0 [356]


title: NM-401_28_162 [723]


title: Control NCRWE-026_1_0 [346]


title: Control NCRWE-026_28_0 [373]


title: NM-401_3_162 [705]


title: NCRWE-026_3_162 [139]


title: Control NM-401_28_0 [771]


title: Control NM-401_3_0 [758]


title: 15-05-033-4_Nonasthmatic


title: 15-07-027-1_Asthmatic


title: 15-02-011-1_Asthmatic


title: 15-02-009-7_Asthmatic


title: Control NCRWE-026_1_0 [348]


title: Control NCRWE-026_28_0 [374]


title: NCRWE-026_28_162 [270]


title: Control NCRWE-026_1_0 [345]


title: Control NM-401_1_0 [744]


title: Control NM-401_28_0 [770]


title: NCRWE-026_1_162 [792]


title: NM-401_1_162 [687]


title: 15-08-031-7_Nonasthmatic


title: 15-02-025-6_Nonasthmatic


title: Control NM-401_3_0 [755]


title: 15-06-010-8_Nonasthmatic


title: 15-07-004-8_Asthmatic


title: NM-401_28_162 [722]


title: 15-07-023-7_Asthmatic


title: 15-05-003-8_Asthmatic


title: NCRWE-026_28_162 [160]


title: Control NM-401_1_0 [743]


title: Control NCRWE-026_1_0 [344]


title: NM-401_1_162 [684]


title: 15-02-028-7_Nonasthmatic


title: NM-401_3_162 [700]


title: Control NCRWE-026_3_0 [355]


title: 15-02-046-8_Nonasthmatic


title: NCRWE-026_1_162 [793]


title: 15-08-003-4_Nonasthmatic


title: 15-02-016-9_Nonasthmatic


title: NCRWE-026_3_162 [142]


title: 15-02-036-2_Asthmatic


title: 15-08-010-9_Nonasthmatic


title: 15-02-008-4_Nonasthmatic


title: 15-07-003-0_Asthmatic


title: 15-04-004-1_Nonasthmatic


title: 15-02-004-5_Asthmatic


title: 15-04-006-0_Nonasthmatic


title: 15-08-020-4_Nonasthmatic


title: 15-05-031-0_Nonasthmatic


title: 15-02-044-7_Asthmatic


title: 15-07-015-1_Asthmatic


title: 15-08-001-0_Asthmatic


title: 15-07-016-7_Nonasthmatic


title: 15-07-021-6_Asthmatic


title: 15-02-013-0_Nonasthmatic


title: KO_KA_rep.5

city: Krakow

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were preprocessed using beadarray R package and normalized using quantile normalization.

source_name: denate gyrus of hippocampus

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

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

tag: time

value: 6 hrs

tag: drug

value: Kainic acid

value: KO ( Srf f/f;CaMKCreERT2)


title: 15-02-055-4_Nonasthmatic


title: 15-08-021-5_Nonasthmatic


title: 15-07-026-3_Asthmatic


title: KO_KA_rep.1


title: KO_KA_rep.3


title: KO_KA_rep.2


title: KO_KA_rep.4


title: 15-02-017-6_Asthmatic


title: 15-08-009-9_Nonasthmatic


title: KO_SAL_rep.6

value: Saline


title: 15-08-025-8_Nonasthmatic


title: 15-05-023-1_Asthmatic


title: 15-02-029-4_Nonasthmatic


title: KO_SAL_rep.3


title: 15-08-017-8_Nonasthmatic


title: KO_SAL_rep.4


title: 15-08-006-8_Asthmatic


title: KO_SAL_rep.1


title: 15-08-007-5_Asthmatic


title: 15-08-037-2_Nonasthmatic


title: 15-08-043-1_Asthmatic


title: CTR_KA_rep.5

value: CTR (SRF f/f)


title: 15-02-026-0_Nonasthmatic


title: 15-02-052-0_Nonasthmatic


title: CTR_KA_rep.4


title: CTR_KA_rep.3


title: 15-06-002-2_Asthmatic


title: KO_SAL_rep.5


title: 15-02-022-5_Asthmatic


title: CTR_KA_rep.2


title: KO_SAL_rep.2


title: CTR_SAL_rep.6


title: CTR_KA_rep.1


title: 15-07-025-9_Nonasthmatic


title: CTR_SAL_rep.4


title: 15-08-038-6_Nonasthmatic


title: 15-07-007-6_Asthmatic


title: 15-08-028-9_Asthmatic


title: 15-02-051-2_Nonasthmatic


title: CTR_SAL_rep.3


title: CTR_SAL_rep.1


title: 15-02-010-7_Asthmatic


title: CTR_SAL_rep.2


title: 15-02-005-0_Asthmatic


title: 15-05-020-8_Asthmatic


title: 15-05-005-5_Asthmatic


title: 15-05-012-6_Asthmatic


title: MLO-Y4 cell cultured under normal earth gravity level (control), biological rep 2

city: Xi'an

first: Yang

last: Wang

state: Shaanxi

address: 127 Youyi Xilu

department: Biology

country: China

institute: Northwestern Polytechnical University

description: genome gene expression data from MOL-Y4 cell cultured under normal earth gravity level (control)

hyb_protocol: Array hybridization was performed using GeneChip Hybridization, Wash and Stain Kit in Hybridization Oven 645 at 45℃ for 16 hours, and then array was washed in Fluidics Station 450 followed the manufacturer's instructions( Affymetrix, Santa Clara, CA, US).

scan_protocol: Arrat slides were scanned by GeneChip Scanner 3000

data_processing: Scan results were readed by using Command Console Software3.1 and then data were normalized by Rubust Multi-Chip Average (RMA) algorithm.

source_name: MLO-Y4 cell cultured under normal earth gravity level (control), 48h,

label_protocol: RNA was amplified, labeled and purified by using Ambion WT expression Kit (Amnion,US) and GeneChip WT Terminal Labeling Kit( Affymetrix, Santa Clara, CA, US) followed the manufactuere's instructions to obtain biotin labeled cDNA.

growth_protocol: MLO-Y4 osteocyte-like cell were cultured in α-Modified Eagle's Medium(α-MEM) containing 5% fetal bovine serum, 5% calf serum, 1% benzylpenicillin and 1% streptomycin. MLO-Y4 cells grew on culture flask coated with collagen (rat tail collagen type1, 0.15mg/ml) and cells were incubated at 37℃ with 5% CO2 before treated under LG-HMF.

extract_protocol: Total RNA was extracted by using Trizol reagent with the protocol given by the manufacturer.

treatment_protocol: MLO-Y4 cells were digested by trypsin containing 0.03% EDTA, and seeded onto 96-well plates with a density of 30000 per well, then ten wells were placed into a 35-mm tissue-culture plate. Then the plate was delivered to the bore of the superconducting magnet with three different apparent gravity levels  (μ-g,1-g and 2-g). Thses three plates  were fixed on a object holder, and continuously 37℃ and 5%CO2 were supplied to the magnet bore. Control group was incubated at 37℃ and 5%CO2 under normal earth gravity condition. After 48 hours culture, cells were collected for further research.

tag: tissue

value: long bone

tag: age

value: 14 days

tag: cell line

tag: treatment

value: normal earth gravity level (control)


title: NEGCONT-Input_rep2

city: Saint Louis

first: Tarik

last: Hadzic

state: MO

address: 660 S. Euclid Ave

department: Psychiatry

institute: Washington University in St Louis School of Medicine

description: 2 repeats of a control anti-MYC ChIP-chip (test=ChIP sample; control: Input)

hyb_protocol: ChIP samples were hybridized to Drosophila 2.0 Tiling Arrays exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

scan_protocol: Drosophila 2.0 Tiling Arrays were scanned via a Gene CHIP Scanner 3000 (Affymetrix) and the GeneCHIP Operating Software version 1.4.

data_processing:
To detect statistically significant DIMM binding peaks throughout the genome we used the Model-based Analysis of Tiling arrays (MAT; Johnson et al. 2006 PNAS vol. 103 (33)). The following settings were used: MAT version 06022009 with BandWidth = 300, Max- Gap = 300 and MinProbe = 8. The resulting MAT score, which is calculated from normalized probe intensities, represents a statistical likelihood that a particular genomic region is enriched in the immunoprecipitated relative to the control sample.
Bed and wig files generated by MAT version 06022009 (BandWidth = 300, Max-Gap = 300 and MinProbe = 8). Files titled Final_Normalization generated by: 1.) first normalizing DIMM-MYC anti-MYC ChIP to its input (#1 - #2), and Negative Control anti-MYC ChIP to its input (#3 - #4)             2.) Subtracting (#3 - #4) from (#1 - #2)            3.) Normalizing DIMM-MYC anti-MYC ChIP to Negative Control anti-MYC ChIP (#1 - #3)            4.) Adding product from part two and part three [(1-2)-(3-4)]+(1-3)            5.) Running a Cistrome tool naive peak caller on wig file from part four with a p-value of 1e-4

organism: Drosophila melanogaster

source_name: Input DNA from control heads

label_protocol: ChIP samples were labeled exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

growth_protocol: Drosophila were grown at 18 degree Celsius. Two-to-three-day-old adults were shifted to 30 degrees Celsius for 72 hours, then harvested.

extract_protocol: ChIP was performed as described by Menet et al. (Genes Dev. 2010 24: 358-367). w1118; c929-GAL4;tub-GAL80ts females were crossed to w1; UAS-dimm-myc; males at 18°C. To control for non-specific antibody binding, non-specific DNA enrichment (through binding to sepharose beads, reaction surfaces etc. [13]), ChIPs were also performed on the w1118; c929-GAL4; tub-GAL80ts parental strain that lacks the dimm::myc transgene. Progeny developed at 18oC through adult eclosion. Two to three day old adults of the following two genotypes (w1/ +; c929-GAL4/UAS-dimm-myc; tub- GAL80ts/+ and w1118; c929-GAL4; tub-GAL80ts) were shifted to 30°C for 3 days. Flies were collected on dry ice, and heads were sieved the following day through 25 and 40 micron sieves. One milliliter of fly heads was homogenized in 7 ml Wheaton-Dounce homogenizers with the type B (tight) pestle in 3 mL of NEB buffer (10 mM HEPES-Na at pH 8.0, 10 mM NaCl, 0.1 mM EGTA-Na at pH 8.0, 0.5 mM EDTA-Na at pH 8.0, 1 mM DTT, 0.5% Tergitol NP-10, 0.5 mM Spermidine, 0.15 mM Spermine plus protease inhibitor cocktail [Roche mini]) for a total of 30 min (alternating 2-min homogenization 10 times, 1 min on ice 10 times). Homogenate was dumped into a 70-mm cell strainer placed in a 50-mL falcon tube and centrifuged at 300g for 2 min. Filtered homogenate was split into three fractions, transferred to microfuge tubes and centrifuged at 6,000 x g for 10 min. The nuclei-containing pellets were resuspended in 1 mL of NEB and centrifuged at 20,000 x g for 20 min on sucrose gradient (0.65 mL of 1.6 M sucrose in NEB, 0.35 mL of 0.8 M sucrose in NEB). The pellet was resuspended in 1 mL of NEB and 11% formaldehyde (diluted in Schneider’s media; Sigma) was added to a final concentration of 1%. Nuclei were cross-linked for 10 min at room temperature on a rotator before cross-linking was quenched by adding 1/10 vol of 1.375 M glycine for 5 min. The nuclei were collected by centrifugation at 6,000 x g for 5 min. All centrifugations steps were carried out at 4oC. Nuclei were washed twice in 1 mL of NEB and resuspended in 450 mL of Sonication buffer (10 mM HEPES-Na at pH 7.5, 2 mM EDTA at pH 8.0, 1% SDS, 0.2% Trition X-100, 0.5 mM Spermidine, 0.15 mM Spermine plus Roche mini protease inhibitor cocktail). Two biological replicates of nuclei were sonicated using a Fisherbrand Sonic Dismembranator at setting 2 (57 W) five times for 15 sec on and 2 min off (set on ice). Sonicated nuclei were centrifuged at 15,000 x g for 10 min and frozen at -80°C in 150 μl aliquots. The majority of the sonicated chromatin had a unimodal sequence length distribution with a peak around 500 base pairs. Twenty-five microliters of sonicated chromatin were removed for the input sample. The remaining 125μl of chromatin was diluted in 1.1 mL of IP buffer (50 mM HEPES/KOH at pH 7.6, 2 mM EDTA, 1% Triton, 0.1% NaDeoxycholate in PBS). Samples were rotated overnight at 4°C after adding antibodies: 15 μl of anti-c-MYC tag goat antibody (Abcam ab9132). Protein G- Sepharose beads (Zymed) were blocked overnight in 0.1 mg/mL yeast tRNA and 1 mg/mL BSA in IP buffer. After overnight incubation, the beads were washed once in IP buffer, added to the chromatin/antibody mixture, and then incubated for an additional 2 h at 4°C. Beads were spun down at 10,000 rpm for 20 sec and were washed once in 1.5 mL of ChIP Wash buffer (50 mM HEPES-KOH at pH 7.6, 1 mM EDTA, 1% Triton, 0.1% NaDeoxycholate, 0.1% Sarkosyl, 0.1% BSA, 0.5 M KCl in PBS). Beads were resuspended in 1 mL of ChIP Wash buffer and rotated for 30 min at 4°C. Beads were then washed once in Li Wash Buffer (10 mM Tris-Cl at pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% NaDeooxychoalte, 1 mM EDTA) and once in cold TE (pH 8.0) before being eluted with 150 mL of ChIP Elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1% SDS, 1 mM DTT, 0.1 mg/mL Proteinase K). ChIP Elution buffer (150 mL) was also added to the input sample. Both IP and input samples were incubated for 2 h at 37°C. The sepharose beads were removed from the IP samples and then all samples were decrosslinked overnight at 65°C. DNA was isolated from the samples using PCR purification kit (Qiagen).

treatment_protocol: Flies were frozen on dry ice and heads isolated.

tag: genotype

value: w;c929-GAL4; tubgal80ts

value: whole fly heads

tag: chip antibody

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: 15-07-022-8_Nonasthmatic

tag: asthma

value: FALSE

tag: subtype

value: non

value: PBMC


title: 15-07-032-5_Asthmatic

value: TRUE


title: 15-04-003-9_Asthmatic


title: 15-07-006-9_Asthmatic


title: NEGCONT-Input_rep1

value: Flies were frozen on dry ice and heads isolated.


title: MLO-Y4 cell cultured under normal earth gravity level (control), biological rep 3


title: MLO-Y4 cell cultured under normal earth gravity level (control), biological rep 1


title: 15-08-039-3_Nonasthmatic


title: MLO-Y4 cell cultured under LG-HMF 2-g, biological rep 3

description: genome gene expression data from MOL-Y4 cell cultured under LG-HMF 2-g

source_name: MLO-Y4 cell cultured under LG-HMF 2-g, 48h,

value: LG-HMF 2-g


title: NEGCONT-IP_rep2

source_name: MYC ChIP DNA from control heads

value: MYC

value: Abcam


title: CTR_SAL_rep.5

value: 6 hrs


title: MLO-Y4 cell cultured under LG-HMF 2-g, biological rep 1


title: NEGCONT-IP_rep1

description:
CONTROL_ChIP_versus_INPUT_3-4.bed
CONTROL_ChIP_versus_INPUT_3-4.wig
2 repeats of a control anti-MYC ChIP-chip (test=ChIP sample; control: Input)


title: 15-08-045-4_Nonasthmatic


title: DIMM-MYC-Input_rep2

description: 2 repeats of a DIMM::MYC anti-MYC ChIP-chip (test=ChIP sample; control: Input)

source_name: Input DNA from DIMM::MYC fly heads


title: 15-04-008-7_Asthmatic


title: DIMM-MYC-Input_rep1


title: 15-02-054-9_Nonasthmatic


title: 15-07-035-6_Nonasthmatic


title: MLO-Y4 cell cultured under LG-HMF 1-g, biological rep 3

description: genome gene expression data from MOL-Y4 cell cultured under LG-HMF 1-g

source_name: MLO-Y4 cell cultured under LG-HMF 1-g, 48h,

value: LG-HMF 1-g


title: 15-05-030-6_Nonasthmatic


title: MLO-Y4 cell cultured under LG-HMF 1-g, biological rep 1


title: 15-05-026-5_Asthmatic


title: 15-02-015-3_Asthmatic


title: MLO-Y4 cell cultured under LG-HMF 1-g, biological rep 2


title: MLO-Y4 cell cultured under LG-HMF 2-g, biological rep 2


title: DIMM-MYC-IP_rep2

description:
DIMM-MYC_ChIP_versus_CONTROL_ChIP_1-3.bed
DIMM-MYC_ChIP_versus_CONTROL_ChIP_1-3.wig
2 repeats of a DIMM::MYC anti-MYC ChIP-chip (test=ChIP sample; control: Input)

source_name: MYC ChIP DNA from DIMM::MYC fly heads


title: 15-02-033-6_Nonasthmatic


title: 15-07-008-2_Asthmatic

value: reversible


title: DIMM-MYC-IP_rep1

description:
DIMM-MYC_ChIP_versus_INPUT_1-2.bed
DIMM-MYC_ChIP_versus_INPUT_1-2.wig
2 repeats of a DIMM::MYC anti-MYC ChIP-chip (test=ChIP sample; control: Input)


title: MLO-Y4 cell cultured under LG-HMF μ-g, biological rep 3

description: genome gene expression data from MOL-Y4 cell cultured under LG-HMF μ-g

source_name: MLO-Y4 cell cultured under LG-HMF μ-g, 48h,

value: LG-HMF μ-g


title: 15-02-050-8_Asthmatic


title: RSP_0981+pIND5-RSP_0981_Rep2

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

description: Gene expression data from a ΔRSP_0981 (ΔCcmR) overexpressing RSP_0981 obtained under aerobic conditions.

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization.  Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package.  Correction for multiple testing was done using Benjamini-Hochberg correction. All analyses were conducted in the R statistical programming environment.

organism: Cereibacter sphaeroides

source_name: ΔRSP_0981 (ΔAkgR) cells overexpression RSP_0981 from an IPTG inducible plasmid (pIND5) grown aerobically

label_protocol: Synthesized cDNA was labeled with BioArray™ Terminal labeling kit with biotin-ddUTP

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase.

extract_protocol: RNA was extracted from R. sphaeroides cells by hot acid phenol extraction.

value: ΔRSP_0981 (ΔAkgR)


title: 15-07-028-5_Nonasthmatic


title: MLO-Y4 cell cultured under LG-HMF μ-g, biological rep 1

value: long bone

value: 14 days


title: 15-08-044-9_Nonasthmatic


title: 15-07-011-4_Nonasthmatic


title: RSP_0981+pIND5-RSP_0981_Rep1


title: RSP_1663+pIND5-RSP_1663_Rep2

description: Gene expression data from a ΔRSP_1663 (ΔCcmR) overexpressing RSP_1663 obtained under aerobic conditions.

source_name: ΔRSP_1663 (ΔCcmR) cells overexpression RSP_1663 from an IPTG inducible plasmid (pIND5) grown aerobically

value: ΔRSP_1663 (ΔCcmR)


title: 15-05-036-8_Asthmatic


title: RSP_1663+pIND5-RSP_1663_Rep1


title: iNOSKO CON-2

city: manhattan

first: Geming

last: Lu

state: New York

address: 1425 madison ave

institute: mount sinai school of medicine

description: Bone marrow derived macrophages cultured in GM-CSF medium for 7 days

hyb_protocol: standard illumina hybridization protocol

scan_protocol: standard illumina scanning protocol

data_processing: Raw data files were converted using GenomeStudio and further processed using using lumi v2.10.0 Bioconductor/R and limma v3.14.4 Bioconductor/R.

source_name: Macrophage purified

label_protocol: RNA microarray was performed using RNA isolated from M1 polarized macrophages from WT and iNOS deficient mice stimulated with LPS/IFNγ for 6 hours. Total RNA was extracted using a RNeasy plus kit (QIAGEN, Valencia, CA), and the array was performed on an Illumina MouseWG-8 v2.0 expression beadchip (Illumina, USA) by the Genomics Core Facility at the Mount Sinai School of Medicine. Microarray data was normalized with background subtraction and rank invariant normalization.

growth_protocol: Bone marrow (BM) cells were isolated from tibias and femurs of C57BL/6 mice and the cells were cultured in the complete DMEM medium supplemented with GM-CSF (10 ng/ml)or M-CSF (10 ng/ml). On day 6 or 7, bone marrow derived macrophages (BMDMs) were harvested and then seeded in fresh complete DMEM medium at a density of 2 x 106 cells/ml for experiments.

extract_protocol: Total RNA was extracted using an RNeasy plus kit (QIAGEN, Valencia, CA)

treatment_protocol: Bone marrow derived macrophages were  activated with LPS (200 ng/ml) plus IFN-γ (10 ng/ml)

value: female

value: 8 weeks

tag: genotype/variation

value: iNOS deficient

value: cultured in GM-CSF medium for 7 days


title: MLO-Y4 cell cultured under LG-HMF μ-g, biological rep 2


title: WT M1-2

description: Bone marrow derived macrophages cultured in GM-CSF medium for 7 days, stimulated with LPS(200ng/ml) and IFNg (10ng/ml) for 6 hours

tag: strain

value: wild type


title: iNOSKO M1-2

tag: gender

value: cultured in GM-CSF medium for 7 days, stimulated with LPS(200ng/ml) and IFNg (10ng/ml) for 6 hours


title: RSP_0981_Rep2

description: Gene expression data from a ΔRSP_0981 markerless deletion strain obtained under aerobic conditions.

source_name: ΔRSP_0981 (ΔAkgR) deletion cells grown aerobically


title: Streptococcus mutans Δ835np mutant Cell Replicate 4

status: Public on Feb 01 2015

city: Gainesville

first: Sang-Joon

last: Ahn

state: FL

address: 1395 Center Dr.

department: Department of Oral Biology

institute: University of Florida

hyb_protocol: The Cy5-labeled experimental samples were mixed in equal quantity to the Cy3-labeled reference RNA and hybridized to the microarray slides using a Maui four-chamber hyrbidization system (BioMicro Systems) for 16 h at 42°C.  The slides were washed according to the TIGR protocol

scan_protocol: The slides were scanned using a GenePix scanner (Axon Instruments). The scanned images were loaded into TIGR Spotfinder software and overlaid. A spot grid was created according to TGIR specifications and adjusted manually to fit all spots to the grid and intensity for each spot determined.

data_processing: Data was normalized using Microarray Data Analysis Software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate anaylsis

organism: Streptococcus mutans

source_name: S. mutans Δ835np mutant

label_protocol: 2 ug of RNA was primed with 6 ug of random hexamer primer (Invitrogen) at 70°C for 10 mins and reverse transcribed at 42°C overnight using SuperScript III (Invitrogen ) and 2:1 dTTP:aminoacyl-dUTP and 100mM dATP, dCTP, dGTP, dTTP.  Purified cDNA samples were coupled with Cy3 or Cy5.

growth_protocol: All samples were grown in BHI medium to OD600 = 0.5

extract_protocol: Total RNA was extracted using phenol (pH 4.3), DNase I treated and purified using RNAse mini kit (Qiaigen)

treatment_protocol: Cells were harvested and treated with RNA protect reagent

value: Δ835np mutant

source_name: Reference S. mutans UA159 RNA

tag: sample type

value: reference


title: Streptococcus mutans Δ835np mutant Cell Replicate 2


title: Streptococcus mutans Δ835np mutant Cell Replicate 3


title: 15-02-038-9_Asthmatic

source_name: PBMC

value: TRUE

tag: cell type

value: PBMC


title: Streptococcus mutans UA159 Cell Replicate 1

source_name: S. mutans wild-type

value: wild-type


title: Streptococcus mutans UA159 Cell Replicate 3


title: Streptococcus mutans UA159 Cell Replicate 4


title: Streptococcus mutans UA159 Cell Replicate 2


title: 15-02-030-4_Nonasthmatic

value: FALSE

value: non


title: RSP_0981_Rep1

value: ΔRSP_0981 (ΔAkgR)


title: RSP_1663_Rep3

description: Gene expression data from a ΔRSP_1663 markerless deletion strain obtained under aerobic conditions.

source_name: ΔRSP_1663 (ΔCcmR) deletion cells grown aerobically


title: Streptococcus mutans Δ835np mutant Cell Replicate 1


title: WT M1


title: 15-07-018-0_Asthmatic

value: reversible


title: 15-02-032-7_Nonasthmatic


title: iNOSKO CON


title: RSP_1663_Rep1


title: RSP_1663_Rep2


title: 15-08-005-2_Nonasthmatic


title: WT CON


title: WT CON-2


title: Primary Human Hepatocytes in Random Pure Culture at Day 6, Biological Rep2

city: Fort Collins

first: Salman

last: Khetani

state: Colorado

address: 1301 Campus Delivery, 200 West Lake Street

department: Department of Mechanical Engineering, School of Biomedical Engineering

institute: Colorado State University

description: Gene expression from PHHs in Random Pure Culture

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized with rotation at 60 rpm for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array using Affymetrix's FS450_0001 fluidics protocol.

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

data_processing: Raw intensity values on the microarrays were normalized, modeled, and compared using default options within the dChip (DNA Chip Analyzer) software package. The invariant set normalization method was used to compare arrays to a selected baseline array (GeneChip with median intensity) and the PM-MM model-based expression index (MBEI) analysis was used for computing expression values for gene comparison.

source_name: Primary human hepatocytes in random pure culture at day 6, donor #2

label_protocol: Biotinylated cRNA from iHeps were prepared according to the standard Affymetrix protocol using the GeneChip 3' IVT Plus Reagent Kit (Expression Analysis Technical Manual, 2001, Affymetrix). Primary Hepatocyte double-stranded cDNA was synthesized using a T7- (dt)24 primer (Oligo) and reverse transcription (Invitrogen). Biotin-labeled cRNA was synthesized using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences).

extract_protocol: iHep RNA was prepared using the RNeasy Mini Kit (Qiagen) and treated with Optizyme Recombinant DNase I to remove genomic DNA (Fisher Bioreagents). Primary Hepatocyte RNA was extracted via TRIzol (Invitrogen) and purified using the RNeasy Kit (Qiagen) as per manufacturer’s instructions.

value: Primary Human Hepatocytes (PHHs)

tag: commercial vendor

value: CellzDirect

tag: days of culture

value: day 6

tag: individual

value: donor 2


title: MPCC at Day 6, Biological Rep2

description: Gene expression from PHHs in the MPCC Platform

source_name: Primary human hepatoytes in the MPCC platform at day 6, donor #2


title: iNOSKO M1

value: female

tag: age

value: 8 weeks

value: iNOS deficient


title: MPCC at Day 18, Biological Rep2

source_name: Primary human hepatoytes in the MPCC platform at day 18, donor #2

value: day 18


title: Fresh Primary Human Hepatocytes at Day 0, Biological Rep1

description: Gene expression from freshly isolated PHHs

source_name: Freshly isolated primary human hepatocytes, donor #1

value: ADMET Technologies

value: day 0

value: donor 1


title: RE550_KPL4_6-Medi5117

city: Gaithersburg

first: Zheng

last: Liu

address: One Medimmune Way

institute: Medimmune LLC

hyb_protocol: Fifteen micrograms of each biotin-labeled cRNA was fragmented for hybridization on Affymetrix Human Genome U133 Plus 2.0 GeneChip® arrays.

scan_protocol: All GeneChip® washing, staining, and scanning procedures were performed with Affymetrix standard equipment.

data_processing: Data capture and initial array quality assessments were performed with the GeneChip Operating Software (GCOS) tool.

source_name: KPL4 + Medi5117

label_protocol: Generating biotin-labeled amplified cRNA from 75 ng of total RNA was accomplished using the MessageAmpTM Premier RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Cancer cell lines were purchased from the American Type Culture Collection (Manassas, VA) and grew according to protocols of the vendor. Cell line authentication was conducted by STR-based DNA fingerprinting and multiplex PCR.  IMPACT tests were also performed on all cell lines.

extract_protocol: Total RNA was extracted from snap-frozen xenograft tumor samples using the ZR RNA MicroPrep kit (Zymo Research, Orange, CA)

treatment_protocol: Xenograft tumors from DU145, KPL4, and NCI-H1650 were treated with 30 mg/kg of MEDI5117 or IgG isotype control IgG1 for a total of two doses.

tag: tissue

value: xenograft tumor


title: 15-02-049-9_Asthmatic

value: TRUE

value: PBMC


title: RE550_KPL4_5-Medi5117


title: RE550_KPL4_un3

source_name: KPL4, Untreated


title: RE550_H1650_Un1_REHYB

source_name: NCI-H1650, Untreated


title: 15-05-027-7_Asthmatic


title: MPCC at Day 42, Biological Rep1

source_name: Primary human hepatoytes in the MPCC platform at day 42, donor #1

value: day 42


title: 15-08-042-0_Nonasthmatic

value: FALSE

value: non


title: RE550_H1650_4-Medi5117


title: 15-06-004-6_Asthmatic


title: iMPCC at Day 9

description: Gene expression from iHeps in the iMPCC Platform

source_name: iHeps in the iMPCC platform at day 9 of culture

value: iPSC-Derived Hepatocytes (iHeps)

value: Cellular Dynamics International

value: day 9


title: Fresh Primary Human Hepatocytes at Day 0, Biological Rep2

source_name: Freshly isolated primary human hepatocytes, donor #2

value: Primary Human Hepatocytes (PHHs)

value: CellzDirect

value: donor 2


title: RE550_H1650_un2


title: RE550_KPL4_8-Medi5117


title: RE550_KPL4_un1


title: RE550_KPL4_un2


title: Raji BCL11A-XS - repeat 2 - mAdbID:77955

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 77955

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 720 ScanPower: 100;; 100 LaserPower: 3.03;; 2.68 Temperature: 28.8

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Raji pXY-PURO Negative Control

label_protocol:
Cy3 Sample Labeling Protocol
Other: Labeled using amino allyl conjugation method.

extract_protocol:
TRIzol Extraction
Other: Total RNA was extracted using TRIzol reagent according to manufacturer's instructions.

tag: cell line

value: Raji

value: B cell

tag: disease state

value: Human Burkitt's Lymphoma

tag: protocol

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-PURO (negative control vector) using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.

source_name: Raji pXY-BCL11A-XS

label_protocol:
Cy5 Sample Labeling Protocol
Other: Labeled using amino allyl conjugation method.

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-BCL11A-XS using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.


title: iMPCC at Day 21

source_name: iHeps in the iMPCC platform at day 21 of culture

value: day 21


title: 15-04-009-4_Asthmatic

value: TRUE


title: RE550_H1650_un3

value: xenograft tumor


title: RE550_H1650_5-Medi5117


title: RE550_H1650_6-Medi5117


title: Tlr3-/- irradiated 6hr

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: TLR3 6hr

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

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

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

source_name: small intestine, Tlr3-/-, g-irradiated, 6hr

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

extract_protocol: RNA samples were extracted from small intestines using the miRNeasy mini kit (Qiagen).

treatment_protocol: Small intestines were collected from Tlr3+/+ and Tlr3-/- mice at 0 and 6 hr after exposure to 10 Gy of total body g-irradiation.

value: small intestine

tag: treatment

value: g-irradiated

tag: time point


title: Fresh Universal Mixture of Liver Cells at Day 0, Biological Rep1

description: Gene expression from freshly isolated liver cells

source_name: Freshly isolated mixture of liver cells (hepatocytes + nonparenchymal cells), donor #1

value: Universal Mixture of Liver Cells

value: ADMET Technologies

value: day 0

value: donor 1


title: Tlr3+/+ irradiated 6hr

description: WT 6hr

source_name: small intestine, WT, g-irradiated, 6hr


title: Tlr3+/+ non-treated 0hr

description: WT 0hr

source_name: small intestine, WT, non-treated, 0hr

value: non-treated


title: mt_Cortex, 4 weeks old, biological replicate 2 [PAMM-085A]

city: Phoenix

first: Garilyn

last: Jentarra

state: AZ

address: 350 W. Thomas Rd

department: Neurology Research

institute: Barrow Neurological Institute

description: MeCP2 A140V mouse 412 (test)

data_processing:
Experiments used an MJ Research Chromo4 RT-PCR machine. Ct thresholds were manually set within the linear phase of the logarithmic amplification plots using Opticon Monitor 3 software. Data from the logarithmic plots was exported and analyzed using the downloadable Excel PCR Array Data Analysis Template version 2.0 provided by SA Biosciences (http://sabiosciences.com/pcrarraydataanalysis.php). This template uses the ΔΔCt method to establish the fold change between control and experimental groups. It also uses a two-tailed student’s t test to establish statistical significance using p<0.05. A set of 5 housekeeping genes (Gapdh, Actb, HSP90ab1, Hprt1, and Gusb), which are included on the array plates, was used for normalization. This was done by subtracting the average Ct value of the housekeeping genes in each sample from the Ct values of the genes of interest in that sample.
The 'non-normalized.txt' reports raw Ct values before normalization. The 'fold_change.txt' reports test/control (i.e., MeCP2 A140V/wildtype) ratios [available as Series supplementary files]

label: SYBR green

source_name: somatosensory/motor cortex

label_protocol: PCR assays were performed using the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences (Frederick, MD) following the manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR using the cDNA was then performed on an MJ Research Chromo4 RT-PCR machine using this protocol: 10 minutes at 95ºC followed by 40 cycles of (95ºC for 15 seconds, 55ºC for 40 seconds, and 72ºC for 30 seconds).

growth_protocol: Heterozygous MeCP2 A140V females produced in our mouse colony were bred with wild type male C57BL/6 mice to produce the male MeCP2 A140V hemizygous and wild type littermate mice used in these experiments. All breeding and experimentation was conducted in accordance with IACUC-approved protocols.

extract_protocol: RNA was extracted from the somatosensory/motor cortex of 4 week old male MeCP2 A140V mutant mice and their male wild type littermates (n=3 for each group). TRIzol Reagent (Invitrogen, Carlsbad, California) was used to extract the RNA from homogenized brain tissue. RNA was then purified using the SA Biosciences (Frederick, Maryland) RT2 qPCR-Grade RNA Isolation Kit. Turbo DNA-free from Ambion (Austin, Texas) was used to remove residual genomic DNA from the samples. cDNA was synthesized from 1 µg total RNA for each sample using SA Biosciences RT2 First-Strand Kit.

treatment_protocol: no treatment

tag: strain background

value: [Heterozygous MeCP2 A140V female] X [wild type C57BL/6 male]

value: mutant MeCP2 A140V

value: male

value: 4 weeks

value: somatosensory/motor cortex


title: mt_Cortex, 4 weeks old, biological replicate 3 [PAMM-085A]

description: MeCP2 A140V mouse 413 (test)


title: WT_Cortex, 4 weeks old, biological replicate 1 [PAMM-060A]

description: Wild type mouse 406 (control)

label_protocol: PCR assays were performed using the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A) from SABiosciences (Frederick, MD) following the manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR using the cDNA was then performed on an MJ Research Chromo4 RT-PCR machine using this protocol: 10 minutes at 95ºC followed by 40 cycles of (95ºC for 15 seconds, 55ºC for 40 seconds, and 72ºC for 30 seconds).

value: wild type


title: WT_Cortex, 4 weeks old, biological replicate 2 [PAMM-085A]

description: Wild type mouse 408 (control)


title: WT_Cortex, 4 weeks old, biological replicate 3 [PAMM-085A]

description: Wild type mouse 409 (control)


title: WT_Cortex, 4 weeks old, biological replicate 2 [PAMM-060A]

description: Wild type mouse 408 (control)


title: WT_Cortex, 4 weeks old, biological replicate 1 [PAMM-085A]

description: Wild type mouse 406 (control)


title: mt_Cortex, 4 weeks old, biological replicate 1 [PAMM-060A]

description: MeCP2 A140V mouse 410 (test)


title: RE550_DU145_Un3

source_name: DU145, Untreated


title: WT_Cortex, 4 weeks old, biological replicate 3 [PAMM-060A]

description: Wild type mouse 409 (control)


title: mt_Cortex, 4 weeks old, biological replicate 1 [PAMM-085A]

description: MeCP2 A140V mouse 410 (test)


title: mt_Cortex, 2 weeks old, biological replicate 3 [PAMM-085A]

description: MeCP2 A140V mouse 6 (test)

extract_protocol: RNA was extracted from the somatosensory/motor cortex of 2 week old male MeCP2 A140V mutant mice and their male wild type littermates (n=3 for each group). TRIzol Reagent (Invitrogen, Carlsbad, California) was used to extract the RNA from homogenized brain tissue. RNA was then purified using the SA Biosciences (Frederick, Maryland) RT2 qPCR-Grade RNA Isolation Kit. Turbo DNA-free from Ambion (Austin, Texas) was used to remove residual genomic DNA from the samples. cDNA was synthesized from 1 µg total RNA for each sample using SA Biosciences RT2 First-Strand Kit.

value: 2 weeks


title: mt_Cortex, 4 weeks old, biological replicate 2 [PAMM-060A]

description: MeCP2 A140V mouse 412 (test)


title: mt_Cortex, 4 weeks old, biological replicate 3 [PAMM-060A]

description: MeCP2 A140V mouse 413 (test)


title: mt_Cortex, 2 weeks old, biological replicate 3 [PAMM-060A]

description: MeCP2 A140V mouse 6 (test)


title: mt_Cortex, 2 weeks old, biological replicate 1 [PAMM-060A]

description: MeCP2 A140V mouse 2 (test)


title: mt_Cortex, 2 weeks old, biological replicate 2 [PAMM-060A]

description: MeCP2 A140V mouse 3 (test)


title: RE550_DU145_Un2


title: RE550_DU145_Un1


title: RE550_DU145_9-Medi5117


title: RE550_DU145_7-Medi5117


title: mt_Cortex, 2 weeks old, biological replicate 2 [PAMM-085A]

description: MeCP2 A140V mouse 3 (test)


title: mt_Cortex, 2 weeks old, biological replicate 1 [PAMM-085A]

description: MeCP2 A140V mouse 2 (test)


title: RE550_DU145_8-Medi5117


title: WT_Cortex, 2 weeks old, biological replicate 2 [PAMM-060A]

description: Wild type mouse 4 (control)


title: mt_cerebellum_4 wks old_biological rep 2 [PAMM-085A]

description: MeCP2 A140V mouse 412 (test)

source_name: mutant_Cerebellum_4 wk old

extract_protocol: RNA was extracted from the cerebella of 4 week old male MeCP2 A140V mutant mice and their male wild type littermates (n=3 for each group). TRIzol Reagent (Invitrogen, Carlsbad, California) was used to extract the RNA from homogenized brain tissue. RNA was then purified using the SA Biosciences (Frederick, Maryland) RT2 qPCR-Grade RNA Isolation Kit. Turbo DNA-free from Ambion (Austin, Texas) was used to remove residual genomic DNA from the samples. cDNA was synthesized from 1 µg total RNA for each sample using SA Biosciences RT2 First-Strand Kit.

value: [Heterozygous MeCP2 A140V female] X [wild type C57BL/6  male]

value: MeCP2 A140V hemizygous

value: whole cerebellum


title: mt_cerebellum_4 wks old_biological rep 1 [PAMM-085A]

description: MeCP2 A140V mouse 410 (test)


title: WT_Cortex, 2 weeks old, biological replicate 1 [PAMM-085A]

description: Wild type mouse 1 (control)


title: WT_cerebellum_4 wks old_biological rep 2 [PAMM-085A]

description: Wild type mouse 408 (control)

source_name: WT_Cerebellum_4 wk old


title: WT_Cortex, 2 weeks old, biological replicate 3 [PAMM-060A]

description: Wild type mouse 5 (control)


title: WT_Cortex, 2 weeks old, biological replicate 2 [PAMM-085A]

description: Wild type mouse 4 (control)


title: WT_Cortex, 2 weeks old, biological replicate 1 [PAMM-060A]

description: Wild type mouse 1 (control)


title: WT_cerebellum_4 wks old_biological rep 3 [PAMM-085A]

description: Wild type mouse 409 (control)


title: WT_cerebellum_4 wks old_biological rep 1 [PAMM-060A]

description: Wild type mouse 406 (control)

data_processing:
Experiments used an MJ Research Chromo4 RT-PCR machine. Ct thresholds were manually set within the linear phase of the logarithmic amplification plots using Opticon Monitor 3 software. Data from the logarithmic plots was exported and analyzed using the downloadable Excel PCR Array Data Analysis Template version 2.0 provided by SA Biosciences (http://sabiosciences.com/pcrarraydataanalysis.php). This template uses the ΔΔCt method to establish the fold change between control and experimental groups. It also uses a two-tailed student’s t test to establish statistical significance using p<0.05. A set of 5 housekeeping genes (Gapdh, Actb, HSP90ab1, Hprt1, and Gusb), which are included on the array plates, was used for normalization. This was done by subtracting the average Ct value of the housekeeping genes in each sample from the Ct values of the genes of interest in that sample. Raw Ct values exceeding 35 are set to 35 for calculations.
The 'non-normalized.txt' reports raw Ct values before normalization. The 'fold_change.txt' reports test/control (i.e., MeCP2 A140V/wildtype) ratios [available as Series supplementary files]


title: mt_cerebellum_4 wks old_biological rep 3 [PAMM-085A]

description: MeCP2 A140V mouse 413 (test)


title: WT_cerebellum_4 wks old_biological rep 2 [PAMM-060A]

description: Wild type mouse 408 (control)


title: WT_Cortex, 2 weeks old, biological replicate 3 [PAMM-085A]

description: Wild type mouse 5 (control)


title: Control siRNA transfected hTERT-RPE1 cell spheroids/YAP1 siRNA transfected  hTERT-RPE1 cell spheroids

description: Comparison biological replicate of Control siRNA transfected human hTERT-RPE1 cell spheroids with that of YAP1 siRNA transfected spheroids.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Control siRNA

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: DMEM supplemented with 10 % Fetal Bovine Serum

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

treatment_protocol: hTERT-RPE1 cells transfected with either Control siRNA or YAP1 siRNA seeded in 12 well-plates (Hydrocell; CellSeed) were incubated to form spheroids for 48 hr at 37°C

value: retina pigmented epithelial cells

tag: transfection

value: control siRNA

source_name: YAP1 siRNA

value: YAP1 siRNA


title: WT_cerebellum_4 wks old_biological rep 1 [PAMM-085A]

description: Wild type mouse 406 (control)

tag: genotype/variation


title: mt_cerebellum_4 wks old_biological rep 1 [PAMM-060A]

description: MeCP2 A140V mouse 410 (test)


title: mt_cerebellum_4 wks old_biological rep 2 [PAMM-060A]

description: MeCP2 A140V mouse 412 (test)


title: mt_cerebellum_4 wks old_biological rep 3 [PAMM-060A]

description: MeCP2 A140V mouse 413 (test)


title: WT_cerebellum_4 wks old_biological rep 3 [PAMM-060A]

description: Wild type mouse 409 (control)


title: mt_cerebellum_2 wks old_biological rep 3 [PAMM-060A]

description: MeCP2 A140V mouse 6 (test)

source_name: mutant_Cerebellum_2 wk old

extract_protocol: RNA was extracted from the cerebella of 2 week old male MeCP2 A140V mutant mice and their male wild type littermates (n=3 for each group). TRIzol Reagent (Invitrogen, Carlsbad, California) was used to extract the RNA from homogenized brain tissue. RNA was then purified using the SA Biosciences (Frederick, Maryland) RT2 qPCR-Grade RNA Isolation Kit. Turbo DNA-free from Ambion (Austin, Texas) was used to remove residual genomic DNA from the samples. cDNA was synthesized from 1 µg total RNA for each sample using SA Biosciences RT2 First-Strand Kit.


title: mt_cerebellum_2 wks old_biological rep 2 [PAMM-060A]

description: MeCP2 A140V mouse 3 (test)


title: mt_cerebellum_2 wks old_biological rep 1 [PAMM-060A]

description: MeCP2 A140V mouse 2 (test)


title: mt_cerebellum_2 wks old_biological rep 2 [PAMM-085A]

description: MeCP2 A140V mouse 3 (test)

label_protocol: PCR assays were performed using the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences (Frederick, MD) following the manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR using the cDNA was then performed on an MJ Research Chromo4 RT-PCR machine using this protocol: 10 minutes at 95C followed by 40 cycles of (95C for 15 seconds, 55C for 40 seconds, and 72C for 30 seconds).


title: WT_cerebellum_2 wks old_biological rep 3 [PAMM-060A]

description: Wild type mouse 5 (control)

source_name: WT_Cerebellum_2 wk old


title: mt_cerebellum_2 wks old_biological rep 3 [PAMM-085A]

description: MeCP2 A140V mouse 6 (test)


title: mt_Cortex, 4 weeks old, biological replicate 3 [PAMM-088A]

description: MeCP2 A140V mouse 413 (test)

label_protocol: PCR assays were performed using the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A) from SABiosciences (Frederick, MD) following the manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR using the cDNA was then performed on an MJ Research Chromo4 RT-PCR machine using this protocol: 10 minutes at 95ºC followed by 40 cycles of (95ºC for 15 seconds, 55ºC for 40 seconds, and 72ºC for 30 seconds).


title: WT_cerebellum_2 wks old_biological rep 1 [PAMM-085A]

description: Wild type mouse 1 (control)


title: mt_Cortex, 4 weeks old, biological replicate 2 [PAMM-088A]

description: MeCP2 A140V mouse 412 (test)


title: mt_Cortex, 2 weeks old, biological replicate 2 [PAMM-088A]

description: MeCP2 A140V mouse 3 (test)


title: mt_cerebellum_2 wks old_biological rep 1 [PAMM-085A]

description: MeCP2 A140V mouse 2 (test)


title: mt_Cortex, 2 weeks old, biological replicate 3 [PAMM-088A]

description: MeCP2 A140V mouse 6 (test)


title: WT_Cortex, 2 weeks old, biological replicate 2 [PAMM-088A]

description: Wild type mouse 4 (control)


title: WT_Cortex, 2 weeks old, biological replicate 3 [PAMM-088A]

description: Wild type mouse 5 (control)


title: mt_Cortex, 2 weeks old, biological replicate 1 [PAMM-088A]

description: MeCP2 A140V mouse 2 (test)


title: WT_cerebellum_2 wks old_biological rep 2 [PAMM-060A]

description: Wild type mouse 4 (control)


title: WT_cerebellum_2 wks old_biological rep 1 [PAMM-060A]

description: Wild type mouse 1 (control)


title: WT_cerebellum_2 wks old_biological rep 2 [PAMM-085A]

description: Wild type mouse 4 (control)


title: WT_cerebellum_2 wks old_biological rep 3 [PAMM-085A]

description: Wild type mouse 5 (control)


title: WT_Cortex, 4 weeks old, biological replicate 1 [PAMM-088A]

description: Wild type mouse 406 (control)


title: WT_Cortex, 4 weeks old, biological replicate 2 [PAMM-088A]

description: Wild type mouse 408 (control)


title: Raji BCL11A-XS - repeat 1 - mAdbID:77951

description: mAdb experiment ID: 77951

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 690 ScanPower: 100;; 100 LaserPower: 3.03;; 3.1 Temperature: 28.77

value: Raji

value: B cell

value: Human Burkitt's Lymphoma

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-PURO (negative control vector) using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-BCL11A-XS using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.


title: WT_Cortex, 2 weeks old, biological replicate 1 [PAMM-088A]

description: Wild type mouse 1 (control)

value: [Heterozygous MeCP2 A140V female] X [wild type C57BL/6 male]


title: WT_Cortex, 4 weeks old, biological replicate 3 [PAMM-088A]

description: Wild type mouse 409 (control)

value: male


title: mt_cerebellum_4 wks old_biological rep 3 [PAMM-088A]

description: MeCP2 A140V mouse 413 (test)

value: 4 weeks


title: mt_Cortex, 4 weeks old, biological replicate 1 [PAMM-088A]

description: MeCP2 A140V mouse 410 (test)

value: mutant MeCP2 A140V

value: somatosensory/motor cortex


title: WT_cerebellum_4 wks old_biological rep 1 [PAMM-088A]

description: Wild type mouse 406 (control)

value: wild type


title: mt_cerebellum_2 wks old_biological rep 2 [PAMM-088A]

description: MeCP2 A140V mouse 3 (test)

value: [Heterozygous MeCP2 A140V female] X [wild type C57BL/6  male]

value: 2 weeks


title: mt_cerebellum_2 wks old_biological rep 3 [PAMM-088A]

description: MeCP2 A140V mouse 6 (test)

value: MeCP2 A140V hemizygous

value: whole cerebellum


title: WT_cerebellum_4 wks old_biological rep 2 [PAMM-088A]

description: Wild type mouse 408 (control)


title: WT_cerebellum_4 wks old_biological rep 3 [PAMM-088A]

description: Wild type mouse 409 (control)


title: mt_cerebellum_4 wks old_biological rep 1 [PAMM-088A]

description: MeCP2 A140V mouse 410 (test)


title: Tlr3-/- non-treated 0hr

description: TLR3 0hr

source_name: small intestine, Tlr3-/-, non-treated, 0hr

value: small intestine

value: non-treated


title: Muscle_sedentary_group1_animal5

city: Nuthetal

first: Timo

last: Kanzleiter

address: Arthur-Scheunert-Alle 114

department: Experimental Diabetology

institute: DIfE

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

scan_protocol: Slides were scanned using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: RNA from quadriceps muscle of sedentary mice

label_protocol: Cy3 labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using TRIzol reagent according to the manufacturers instruction. RNA was subjeted to DNAase digestion to remove genomic DNA. Quantification of RNA was performed on a Nanodrop-1000 and RNA integrity was measured on Agilents Bioanalyzer

treatment_protocol: Exercised mice received four 4 weeks of regular exercise training on a motorized treadmill and were compared to sedentary controls

tag: strain

value: 13 weeks

value: quadriceps muscle


title: mt_cerebellum_4 wks old_biological rep 2 [PAMM-088A]

description: MeCP2 A140V mouse 412 (test)

tag: gender


title: WT_cerebellum_2 wks old_biological rep 3 [PAMM-088A]

description: Wild type mouse 5 (control)


title: mt_cerebellum_2 wks old_biological rep 1 [PAMM-088A]

description: MeCP2 A140V mouse 2 (test)


title: Muscle_sedentary_group1_animal6


title: Muscle_sedentary_group1_animal1


title: Muscle_exercised_group2_animal3

source_name: RNA from quadriceps muscle of exercised mice


title: Muscle_exercised_group2_animal4


title: Muscle_sedentary_group2_animal5


title: WT_cerebellum_2 wks old_biological rep 1 [PAMM-088A]

description: Wild type mouse 1 (control)


title: WT_cerebellum_2 wks old_biological rep 2 [PAMM-088A]

description: Wild type mouse 4 (control)


title: Muscle_sedentary_group2_animal4


title: 46T-Dry, biological rep1

city: Hangzhou

first: Shao Jian

last: Zheng

address: Yuhangtang Rd 866#

department: College Life Sciences

institute: Zhejiang University

description: Gene expression from 46T seedlings with dehydration treatment 1h

hyb_protocol: Array hybridization and wash were performed using the Genechip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix) and Fluidics Station 450 (Cat#00-0079, Affymetrix) following the manufacturer’s instructions

scan_protocol: Hybridized slides were scanned by GeneChip.Scanner 3000 (Cat00-00212, Affimetrix)

data_processing: Raw data were normalized by the MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, USA)

label_protocol: Total RNA was amplified, labeled, and purified with the Genechip 3’IVT Express Kit (Cat#901229, Afftnetrix, Santa Clara, CA, USA) following the manufacturer’s instructions to obtain biotin labeled cRNA

growth_protocol: Arabidopsis thaliana seedlings were grown in an environmental controlled growth chamber programmed for a 16-h-ight/8-h-dark cycle with daytime temperature of 24℃ and a night temperature of 21℃

extract_protocol: Total RNA was isolated using the RNase kit (Qiagen) from three replicate samples of the 1-week-old wild-type and OV46 seedling under normal and dehydration treatment for 1 h

treatment_protocol: 1-week-old seedlings were dehydrated on Whatman 3MM paper at 22℃ and 60% humidity under dim light for 1h for drought treatment

tag: line

value: dehydration treatment 1h

tag: developmental stage

value: 1-week-old seedlings


title: 46T-Dry, biological rep2

source_name: 46T seedlings with dehydration treatment 1h


title: WT-Dry, biological rep3

description: Gene expression from wild-type seedlings with dehydration treatment 1h

source_name: Wild-type seedlings with dehydration treatment 1h


title: Muscle_sedentary_group2_animal2


title: 46T-Dry, biological rep3


title: Muscle_exercised_group1_animal5


title: WT-Dry, biological rep1


title: Muscle_exercised_group2_animal5


title: WT-CK, biological rep3

description: Gene expression from wild-type seedlings without treatment

source_name: Wild-type seedlings without treatment


title: WT-Dry, biological rep2


title: Muscle_exercised_group1_animal1


title: 46T-CK, biological rep1

description: Gene expression from OV46 seedlings without treatment

source_name: 46T seedlings without treatment


title: 46T-CK, biological rep3


title: WT-CK, biological rep2


title: WT-CK, biological rep1


title: SH-290

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was normalized by neqc (Shi et al., Nucleic Acids Res. 2010), and its batch effect (day of experiment) was adjusted by ComBat (Johnson et al., Biostatistics. 2007)

source_name: PBMC

label_protocol: Standard Illumina label protocol

extract_protocol: PBMCs were prepared from 20 mL of peripheral blood by density gradient centrifugation using Ficoll-Paque (GEHealthcare Life Sciences, Uppsala, Sweden). All samples were cryopreserved until RNA extraction. Total RNA was isolated using TRIzol LS reagent (Invitrogen, Carlsbad, Calif) and purified using RNeasy Mini Kit (Qiagen, Valencia, Calif), according to the manufacturer’s instructions. Quality and integrity of the purified total RNA were confirmed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif) and Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, Del).

treatment_protocol: This is a retrospective analysis with peripheral blood samples from a subset of 112 patients with metastatic CRPC, who were positive for human leukocyte antigen (HLA)-A2, A24, A3 super type (-A3, -A11, -A30, -A31 and -A33) or -A26 and enrolled in phase 1, 1-2, and 2 clinical trials for PPV between February 2001 and April 2008. These studies were approved by the ethics review committee at the participating hospitals in Japan (Kurume University Hospital, Kinki University Hospital, Okayama University Hospital, and Nara Medical University Hospital). The detailed method of clinical trials was described in our previous reports.

tag: os

tag: event


title: Muscle_exercised_group2_animal1


title: SH-293


title: Mutant Huntingtin sorted cells replicate-3

city: Paris

first: Christian

last: Neri

address: 9 quai St Bernard

department: CNRS UMR 8256, Inserm ERL U1164

country: France

institute: Sorbonne Université, CNRS, INSERM

description:
128Q-19Q-rep3
biological replicate 3 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.

hyb_protocol: probes were hybridized on dual-color Agilent 22k microarrays following manufacturer's protocol.

scan_protocol: Scanned on an Genepix 4000B scanner (Axon).Images were quantified using GenePix Pro Software.

data_processing: Goulphar was used for background subtraction and LOWESS normalization.

organism: Caenorhabditis elegans

source_name: 128Q embryonic purified touch-receptor cells

label_protocol: After a one-round linear amplification with MessageAmp kit (Ambion), RNAs were labelled with the CyScribe Post-labelling kit (Amersham) following manufacturer's instructions.

growth_protocol: embryonic cells were isolated from gravid adults following lysis in a hypochloride solution. Embryos were dissociated with treatement using chitinase/chymotrypsine then trypsine. Cells were then grown overnight on TESPA-coated glass plate.

extract_protocol: Total RNA extracted using Trizol LS (Invitrogen) following manufacturer's instructions

treatment_protocol: Cells were  sorted on a Moflo flow cytometer (Dako) based on GFP fluorescence, recovered in Trizol

tag: cell type

value: embryonic touch-receptor cells

tag: polyq

value: mutant Huntingtin (128Q)

source_name: 19Q embryonic purified touch-receptor cells

value: normal Huntingtin (19Q)


title: SH-286

tag: age


title: SH-227


title: SH-284


title: 46T-CK, biological rep2


title: SH-288


title: Normal Huntingtin sorted cells replicate-2

description:
19Q-GFPonly-rep2
biological replicate 2 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.

source_name: GFP only embryonic purified touch-receptor cells

value: GFP only


title: SH-223


title: Mutant Huntingtin sorted cells replicate-1

description:
128Q-19Q-rep1
biological replicate 1 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.


title: SH-217


title: Mutant Huntingtin sorted cells replicate-2

description:
128Q-19Q-rep2
biological replicate 2 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.


title: SH-213


title: Normal Huntingtin sorted cells replicate-3

description:
19Q-GFPonly-rep3
biological replicate 3 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.


title: SH-205


title: SH-225


title: SH-221


title: Normal Huntingtin sorted cells replicate-1

description:
19Q-GFPonly-rep1
biological replicate 1 of 3. Embryonic cells purified by cell sorting based on GFP fluorescence.


title: SH-204


title: SH-207


title: SH-215


title: SH-203


title: SH-200


title: SH-219