title: MMN+Glucose+NH4/36hrs (R3)

description: Treat MMN+Glucose+NH4/36hrs; Replicate 3 (subarray A12)


title: MMN+Glucose+NH4/14hrs (R2)

status: Public on Sep 01 2013

type: RNA

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

description: Treat MMN+Glucose+NH4/14hrs; Replicate 2 (subarray A05)

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 40% PMT.

data_processing: The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).

molecule: total RNA

organism: Paxillus involutus

source_name: Treat MMN+Glucose+NH4/14hrs

label_protocol: Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).

growth_protocol: Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in medium. The fungus was first grown for 9 days on a Minimum Melin Norkrans (MMN)+glucose medium (in RT and in the dark). The cultures were then starved for nitrogen during 24 hrs, by replacing the medium by the same medium but excluding the nitrogen source (NH4Cl).

extract_protocol: Harvest mycelium was immediately dropped into liquid nitrogen and homogenized in a mortar on dry ice. Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MinElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).

treatment_protocol: After starvation the medium was replaced with BSA dissolved in MMN+glucose (inorganic N source excluded) and followed by incubation for 4 days. After this period of time there was either no addition or addition of 5mg of NH4Cl and continued incubation for either 14 or 36 hrs prior harvest (3 replicates for each).

tag: strain

tag: tissue

value: mycelium patch


title: Healthy 01 KH01_02

type: mixed

city: Chicago

first: Nathan

last: Schoettler

state: IL

address: 924 E 57th Street, R402

country: USA

institute: University of Chicago

hyb_protocol: Prior to hybridization, microarrays were re-hydrated, washed (Wash Buffers A, B and C, ArrayIt), prehybridized for two hours (BlockIt Blocking Buffer, ArrayIt) and washed again. Hybridizations were performed with 10 ng of the labeled reference sample added to 1.5 μg labeled cDNA and 2 μg human Cot-1 DNA (Invitrogen). DNA was mixed with HybIt 2 hybridization buffer (ArrayIt) at 1x concentration to a final volume of 20 μL, denatured at 80°C for 3 minutes and hybridized overnight at 37.0°C for 14-16 hours.

scan_protocol: Following hybridization, microarrays were washed with Wash Buffers A, B and C for 2 minutes each, dried and scanned using an Axon GenePix 4000B scanner (Molecular Devices). All amplified and labeled cDNA samples were hybridized two times as technical replicates. cDNA labeling, prehybridization, hybridization, washing and scanning were all performed by the same individual at approximately the same time of the day.

data_processing:
Image analysis was performed using GenePix Pro 6.0 (Molecular Devices). Spot recognition and flags were checked for each spot and manually adjusted when appropriate. Because the reference sample was co-hybridized with all samples, hybridization quality could be readily observed and missing spots could be easily detected. Missing spots were consistent between arrays, and no more than 3 of 12 replicate spots per gene were missing. Therefore, only 9 replicate spots were used for analysis even though the majority of probes were spotted 12 times per array. Log2 background subtracted values (for both red and green channels) for the human light chain V genes were normalized using the LOWESS function of the MAANOVA 2.0 software (Xiangqin Cui, Hao Wu, Gary A. Churchill, The Jackson Lab) in Matlab (Mathworks).
Normalized log2 for the red channel and green channel are reported on two separate sheets.

label: Alexa 647

organism: Homo sapiens

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa+IgLambda- phenotype

label_protocol: Ulysis Alexa-Fluor 647 (Ch1) and Ulysis Alexa-Fluor 555 (Ch2)

extract_protocol: Total RNA was extracted using TRIZOL according to the recommended protocol

tag: disease state

value: Healthy

tag: individual

tag: cell type

label: Alexa 555

molecule: other

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)

tag: components

tag: sample type

value: Synthesized DNA (oligonucleotides)


title: SLE 06 LSLE06_01

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype

value: SLE

value: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: MMN+Glucose+NH4/14hrs (R1)

description: Treat MMN+Glucose+NH4/14hrs; Replicate 1 (subarray A04)


title: Healthy 01 KH01_01

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa+IgLambda- phenotype


title: Berry_DMR-B_vs_TH_BioRepSWAP

city: Legnaro

first: Massimiliano

last: Corso

state: Padova

address: Viale dell'Università 16

country: Italy

institute: University of Padova

description: Comparison between gene expression profiles of DMR-B and TH berries - Biological replicate swap

hyb_protocol: The pre-hybridization and hybridization steps were carried out in Corning® hybridization chambers with some drops of 0.3× SSC to maintain internal humidity and salts concentration, immersed in a water bath at 48 °C. The microarray was pre-hybridized for 2 h with a solution containing 5× SSC, 0.1% SDS, 1× Denhardt's, and 100 ng/μl DNA carrier. Then the slides were washed once with 0.2× SSC solution and isopropanol, and dried by centrifuging for 2 min at 2000 rpm. Before hybridization, probes were mixed to have an equal amount of each fluorescent dye, ethanol precipitated with ammonium acetate (final 2 M) and resuspended in 37 μl of hybridization solution (5× SSC, 0.1% SDS, 25% formamide, and 40 ng/μl DNA carrier). The probe was denaturated for 30 s, distributed on the spotted area of the slide, and covered with a glass cover slip. After 48 h of hybridization the slides were washed once in 1× SSC 0.2% SDS and in 0.1× SSC 0.2% SDS for 5 min and twice in 0.2× SSC for 5 min to eliminate completely SDS residues that may cause shadows on the spotted area.

scan_protocol: The microarrays were scanned with a two-channel confocal microarray scanner (ScanArray® Lite, Perkin-Elmer) using its dedicated software (ScanArray Express 3.0.0., Perkin-Elmer). The laser power was set between 67 and 79% of maximum and the photomultiplier tube (PMT) was set between 69 and 79% of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing: Raw hybridization data were quality-filtered and background-subtracted by using TIGR Spotfinder software (www.tm4.org/spotfinder) as described by Ziliotto et al., 2012 [19]. Resulted data were intra-array normalized using the median method. MeV software (www.tm4.org/mev) (www.tm4.org/mev) was used for discovering differentially gene expression among the comparisons (t-test).

organism: Vitis vinifera

source_name: Whole berry, DMR-B

label_protocol: Total RNA was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following the manufacturer's instructions.

extract_protocol: Total RNA for both microarray and real-time PCR experiments was extracted from whole berries using the perchlorate method as reported by Ziliotto et al., 2012

treatment_protocol: One-hundred bunches from sixty homogeneous plants (two bunches per plant) were collected at different times: a) at traditional grape harvest named Traditional Harvest (TH), occurred at 27 of October, b) late harvest (LH) berries over-ripened in plant, at 20 days after TH (DATH), c) DMR, berries collected both from clusters located above the cut (DMR-A) and below the cut (DMR-B) (vintage date: 36 and 45 DATH).

tag: harvest technique

value: DMR-B

value: whole berry

source_name: Whole berry, TH (control)

value: TH


title: Berry_LH_vs_TH_BioRep1

description: Comparison between gene expression profiles of LH and TH berries - Biological replicate 1

source_name: Whole berry, LH

value: LH


title: MMN+Glucose-NH4/14hrs (R1)

description: Treat MMN+Glucose-NH4/14hrs; Replicate 1 (subarray A01)

source_name: Treat MMN+Glucose-NH4/14hrs


title: Berry_LH_vs_TH_BioRep2

description: Comparison between gene expression profiles of LH and TH berries - Biological replicate 2


title: MMN+Glucose+BSA (R3)

description: Treat MMN+Glucose+BSA; Replicate 3 (subarray A12)

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 20% PMT.

source_name: Treat MMN+Glucose+BSA

treatment_protocol: After N starvation there were 3 different treatments (each with 3 replicates) and involved the addition of either pollen, gliadin or BSA dissolved in MMN+glucose (inorganic N source excluded). Plates were then incubated for 7 days prior harvest.


title: MMN+Glucose-NH4/14hrs (R3)

description: Treat MMN+Glucose-NH4/14hrs; Replicate 3 (subarray A03)


title: SN-CCs-2

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Rank invariant normalization using Illumina BeadStudio software version 3

label: biotin

organism: Mus musculus

source_name: cumulus cells (CCs) from antral mouse oocytes of known developmental competence

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: gender

value: female

tag: age

value: six weeks

value: oocytes


title: SN-CCs-1

description: replicate 1


title: NSN-CCs-1

description: replicate 1

source_name: cumulus cells (CCs) from antral mouse oocytes of known developmental incompetence


title: Berry_DMR-A_vs_TH_BioRepSWAP

description: Comparison between gene expression profiles of DMR-A and TH berries - Biological replicate swap

source_name: Whole berry, DMR-A

value: DMR-A


title: Berry_DMR-A_vs_TH_BioRep2

description: Comparison between gene expression profiles of DMR-A and TH berries - Biological replicate 2


title: Berry_DMR-B_vs_TH_BioRep1

description: Comparison between gene expression profiles of DMR-B and TH berries - Biological replicate 1


title: MMN+Glucose-NH4/14hrs (R2)

description: Treat MMN+Glucose-NH4/14hrs; Replicate 2 (subarray A02)


title: MMN+Glucose+BSA (R2)

description: Treat MMN+Glucose+BSA; Replicate 2 (subarray A11)


title: MMN+Glucose+BSA (R1)

description: Treat MMN+Glucose+BSA; Replicate 1 (subarray A10)


title: Berry_DMR-B_vs_TH_BioRep2

description: Comparison between gene expression profiles of DMR-B and TH berries - Biological replicate 2


title: NSN-CCs-2

description: replicate 2


title: HAN-72h-rep4

city: Beijing

first: Xiaolan

last: Zhang

address: No.2 Yuanmingyuan Xi Lu Haidian District

department: Vegetable Science

country: China

institute: China Agricultural University

description: Biological replicate 4 of 4.

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.

data_processing: Data were processed using lowess normalization with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA).

organism: Arabidopsis thaliana

source_name: RNA from 72h mock

label_protocol: RNA was dye-labeled as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: Plants used for microarray experiments were 35S:HAN-GR lines in the Landsberg erecta (Ler) background.Plants were grown on a soil:vermiculite:perlite mixture under continuous illumination with a light intensity range of 80 to 100 µmol•m–2•s–1 at 20°C.

extract_protocol: Total RNA were extracted using Qiagen RNeasy according to the manufacturer's instructions

tag: genotype/variation

value: control

tag: time

source_name: RNA from 72h DEX treatment

value: HAN overexpression


title: MMN+Glucose+Gliadin (R3)

description: Treat MMN+Glucose+Gliadin; Replicate 3 (subarray A06)

source_name: Treat MMN+Glucose+Gliadin


title: HAN-72h-rep1

description: Biological replicate 1 of 4.


title: Berry_DMR-A_vs_TH_BioRep1

description: Comparison between gene expression profiles of DMR-A and TH berries - Biological replicate 1


title: HAN-72h-rep3

description: Biological replicate 3 of 4.


title: HUVEC_VEGF_60min plus CsA

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyorin University School of Medicine

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

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

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

source_name: HUVEC, VEGF+CSA

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

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were purchased from Ronza and cultured in EGM-2 MV complete medium (Ronza).

extract_protocol: Total RNA was extracted with TRIzol reagents (Invitrogen) according to manufacturer's protocol.

treatment_protocol: HUVEC were serum-starved overnight, pretreated with 1mM cyclosporine A (calbiochem) for 30 min, and then stimulated by 50ng/mL VEGF (R&D systems) for 1 hour. Adenovirus expressing the control or CA-NFATc1 infected HUVEC for 24 hours in EGM-2 MV complete medium.

value: human umbilical vein endothelial cells (HUVECs)

tag: treatment

value: VEGF + CsA

tag: adenovirus infection


title: MMN+Glucose+Gliadin (R1)

description: Treat MMN+Glucose+Gliadin; Replicate 1 (subarray A04)

value: mycelium patch


title: HUVEC_Ad-NFATc1

source_name: HUVEC, Ad-NFATc1


title: HUVEC_Ad-control

source_name: HUVEC, Ad-control

value: Ad-control


title: HAN-72h-rep2

description: Biological replicate 2 of 4.


title: MMN+Glucose+Pollen (R3)

description: Treat MMN+Glucose+Pollen; Replicate 3 (subarray A03)

source_name: Treat MMN+Glucose+Pollen


title: HAN-12h-rep4

description: Biological replicate 4 of 4.

source_name: RNA from 12h DEX treatment

source_name: RNA from 12h mock


title: MMN+Glucose+Pollen (R2)

description: Treat MMN+Glucose+Pollen; Replicate 2 (subarray A02)


title: HAN-4h-rep4

description: Biological replicate 4 of 4.

source_name: RNA from 4h DEX treatment

source_name: RNA from 4h mock


title: MMN+Glucose+Gliadin (R2)

description: Treat MMN+Glucose+Gliadin; Replicate 2 (subarray A05)


title: HAN-12h-rep2

description: Biological replicate 2 of 4.


title: HAN-12h-rep1

description: Biological replicate 1 of 4.


title: HAN-12h-rep3

description: Biological replicate 3 of 4.


title: HUVEC_VEGF_0min

source_name: HUVEC, untreated


title: Pfeiffer BCL6siRNA 3

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

description: Gene expression data from Pfeiffer DLBCL cell line 48h after transfection with BCL6 targeting siRNA oligos

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip H-GU-133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix scanner.

data_processing: Data was normalized and probe-sets summarized with the MAS5 algorithm implemented in the R-system affy package and the variance was stabilized by performing a log-base2 transformation.

source_name: Pfeiffer BCL6siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix, Santa Clara, CA).

growth_protocol: Cell lines were maintained in 10% FBS supplemented IMDM medium

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

treatment_protocol: Cells were transiently transfected with either a BCL6-specific or a non-target control siRNA

value: B-cell

tag: cell line

value: Pfeiffer DLBCL


title: HAN-4h-rep3

description: Biological replicate 3 of 4.


title: Pfeiffer BCL6siRNA 2


title: Pfeiffer NTshRNA 3

description: Gene expression data from Pfeiffer DLBCL cell line 48h after transfection with NT-control siRNA oligos

source_name: Pfeiffer NTshRNA


title: Pfeiffer BCL6siRNA 1


title: HUVEC_VEGF_60min

source_name: HUVEC, VEGF

value: VEGF


title: Pfeiffer NTshRNA 2


title: Teratoma, mouse embryonic stem cells electroporated with R167Q VHL cDNA, biological rep 3

city: Raleigh

first: Michelle

middle: C

last: DeSimone

state: NC

address: 112 Derieux Place

department: Genetics

institute: NCSU

description: Gene expression data from VHL mutant ES cell teratoma

hyb_protocol: Biotinylated cRNA targets were then purified, fragmented, and hybridized to GeneChip® array during the overnight incubation at 45 °C in a rotating hybridization oven.

scan_protocol: After hybridization, the arrays were stained with streptavidin-phycoerythrin in the GeneChip® Fluidics 450 station and then scanned using Affymetrix GeneChip® Scanner 3000 7G Plus Targeted Genotyping System with Autoloader (laser filter set at 570 nm; pixel size 2.5 μm). The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® GCOS v. 1.2 software with following settings of quantitation parameters: Alpha1 = 0.05, Alpha2 = 0.065, Tau = 0.015, Gamma1H = 0.0045, Gamma1L = 0.0045, Gamma2H = 0.006, Gamma2L = 0.006, Perturbation = 1.1, Target Intensity = 150.

data_processing:
Gene expression data (CEL files) were analyzed using Partek® Genomic Suite, version 6.5 (Partek Inc., St. Louis MO) by robust multi-array analysis (RMA).
The sequences from which the array probe sets were derived from GenBank®, Ensembl, dbEST, and RefSeq. Gene expression data (CEL files) were analyzed using Partek® Genomic Suite, version 6.5 (Partek Inc., St. Louis MO). Gene expression data were normalized by robust multi-array analysis (RMA) and analysis of variance was performed using Partek® software. We identified differentially expressed genes between classes using the non-parametric rank-product method (p-value <0.05 and 0.01) and log2 expression values for each gene were generated.

source_name: mouse embryonic stem cell teratoma

label_protocol: Total RNA samples were processed following a standard one-cycle eukaryotic target preparation protocol from Affymetrix. Briefly, total RNA was first reverse-transcribed using T7-oligo(dT) promoter primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

growth_protocol: Vhl-/- mouse embryonic stem (ES) cells expressing wildtype, P81S or R167Q human VHL gene cDNA were grown to 70% confluency, trypsinized and suspended in 100uL of sterile PBS prior to injection.

extract_protocol: Total RNA was isolated from frozen teratoma samples using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were assessed using ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

treatment_protocol: Female nude mice were injected subcutaneously in bilateral flanks with 1x10^6 cells of each VHL ES cell line. When tumors reached a maximum dimension of 1cm, mice were sacrificed by CO2, and tumors were excised and flash frozen in liquid nitrogen.

tag: genotype

value: human VHL R167Q transgene in Vhl-/- mouse ES cells injected into nude mouse host

tag: phenotype

value: apoptotic

value: teratoma

tag: host strain

value: *nu/nu* mice (Taconic Labs, Hudson, NY, USA)

tag: donor strain

value: wild-type J1 strain Sv/129 ES cells


title: MMN+Glucose+Pollen (R1)

description: Treat MMN+Glucose+Pollen; Replicate 1 (subarray A01)

tag: strain

tag: tissue


title: Pfeiffer NTshRNA 1

tag: cell type


title: Teratoma, mouse embryonic stem cells electroporated with R167Q VHL cDNA, biological rep 2


title: HAN-4h-rep1

description: Biological replicate 1 of 4.


title: Teratoma, mouse embryonic stem cells electroporated with R167Q VHL cDNA, biological rep 1


title: OCI-Ly7 BCL6siRNA 1

description: Gene expression data from OCI-Ly7 DLBCL cell line 48h after transfection with BCL6 targeting siRNA oligos

source_name: OCI-Ly7 BCL6siRNA

value: OCI-Ly7 DLBCL


title: T84 first

city: Sendai

first: Yasufumi

last: Matsuda

state: Miyagi

address: 1-1 seiryouchou aobaku

department: Surgery

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 10 µg of fragmented cRNA was applied to each bioarray. Bioarrays were hybridized overnight at 37 ºC at 300 rpm in an incubator, then washed in stringent TNT buffer at 46 ºC for 1 h followed by incubation with streptavidin-Cy5 at room temperature for 30 min in the dark. Bioarrays were washed in TNT buffer twice each followed by a rinse in 0.05% Tween-20 in water and then dried.

scan_protocol: Glass slides were scanned using a GenePix 4000A scanner.

data_processing: The grids of the image spots were adjusted and their signals were analyzed using the CodeLink System Software, version 5.0, which produces both a raw and a normalized hybridization signal for each spot on the array.

source_name: colorectal cancer cell line

label_protocol: From 2 µg of total RNA, double-stranded cDNA and subsequent biotinlabeled cRNA were synthesized using the CodeLink Expression Assay Kit according to the manufacturer’s instructions.

growth_protocol: RPMI 1640, Leibovitz's L-15 Medium, McCoy's 5A, or D-MEM/F-12, containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. The cell lines were cultured at 37°C in a humidified atmosphere of 5% CO2 and 95% air in a plastic flask.

extract_protocol: Samples were extracted using Qiagen Rneasy kit.


title: OCI-Ly7 BCL6siRNA 2


title: Jurkat-anti-miR-Control

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

description: Jurkat cells electroporated with synthetic RNA molecules corresponding to miR-29a inhibitors (anti-miR), and profiled after 48 hours post-transfections.

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the Gene Expression Hybridization Kit (Agilent, 5188-5242). After posthybridization washes (Wash Buffers 1 and 2 Kit, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies).

data_processing: Images were analyzed with the software Agilent Feature Extraction 11.5 and extracted expression values (gProcessedSignal) were further normalized to the 75 percentile expression value, considering all non-control features (ControlType=0). Following normalization, replicate probes were averaged, resulting in the final set of 41,000 unique probes.

source_name: T-cell acute lymphoblastic leukemia Jurkat cell line, anti-miR control

label_protocol: Cy3-labelled cRNA was generated using the Quick Amp Labeling Kit, one-color (Agilent, 5190-0442), following the manufacturer's protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (One Color RNA Spike-In Kit, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: The human Jurkat T cell line was grown in RPMI 1640 (Gibco, Invitrogen, Merelbeke, Belgium) supplemented with 20% Fetal Calf Serum (FCS) (Hyclone, Perbio, Belgium) 50U/ml penicillin and 50µg/ml streptomycin at 37ºC and 5% CO2.

extract_protocol: Total RNA of transfected Jurkat cells was extracted using the Trizol LS reagent, according to the manufacturer's instructions (Invitrogen, Carlsbad, CA, USA), and quantified by a NanoVue Spectrophotometer (GE Healthcare, London, UK) at 260nM. RNA samples used for the microarrays experiments were purified with RNeasy Kit (Quiagen, Valencia, CA, USA) and RNA quality was assessed by agarose gel electrophoresis through 28S and 18S ribosomal RNA visualization.

treatment_protocol: After four days in culture, 1x10^6 cells were electroporated with synthetic RNA molecules corresponding to miR-29a mimics (pre-miR) or inhibitors (anti-miR), or corresponding negative controls (Ambion, Austin, TX, USA). Molecules were electroporated at a final concentration of 100 nM, using the Neon transfection System (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's protocol and with the following settings: three 10 msec pulses of 1400 V, resulting in an efficiency and viability of 80%. Cells were maintained in RPMI medium +10% FCS without antibiotics, and harvested after 48 hours post-transfections for RNA extraction.

value: Jurkat

value: T-cell acute lymphoblastic leukemia cells

value: male

tag: synthetic rna

value: anti-miR negative control


title: HAN-4h-rep2

description: Biological replicate 2 of 4.

value: control

value: HAN overexpression


title: OCI-Ly7 BCL6siRNA 3


title: OCI-Ly7 NTsiRNA 2

description: Gene expression data from OCI-Ly7 DLBCL cell line 48h after transfection with NT-control siRNA oligos

source_name: OCI-Ly7 NTsiRNA


title: SW948 first


title: Jurkat-anti-miR-29a

description: Jurkat cells electroporated with synthetic RNA molecules corresponding to anti-miR negative control, and profiled after 48 hours post-transfections.

source_name: T-cell acute lymphoblastic leukemia Jurkat cell line, anti-miR-29a


title: T84 second


title: Jurkat-pre-miR-Control

description: Jurkat cells electroporated with synthetic RNA molecules corresponding to miR-29a mimics (pre-miR), and profiled after 48 hours post-transfections.

source_name: T-cell acute lymphoblastic leukemia Jurkat cell line, pre-miR control

value: pre-miR negative control


title: OCI-Ly7 NTsiRNA 3


title: Jurkat-pre-miR-29a

description: Jurkat cells electroporated with synthetic RNA molecules corresponding pre-miR negative control, and profiled after 48 hours post-transfections.

source_name: T-cell acute lymphoblastic leukemia Jurkat cell line, pre-miR-29a


title: Teratoma, mouse embryonic stem cells electroporated with wildtype VHL cDNA, biological rep 3

description: Gene expression data from wild-type VHL ES cell teratoma

value: human VHL WT transgene in Vhl-/- mouse ES cells injected into nude mouse host


title: Teratoma, mouse embryonic stem cells electroporated with P81S VHL cDNA, biological rep 2

value: human VHL P81S transgene in Vhl-/- mouse ES cells injected into nude mouse host

value: apoptosis-resistant


title: SW948 second


title: Teratoma, mouse embryonic stem cells electroporated with wildtype VHL cDNA, biological rep 2


title: OCI-Ly7 NTsiRNA 1

value: B-cell


title: Teratoma, mouse embryonic stem cells electroporated with wildtype VHL cDNA, biological rep 1


title: AD-III-13

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

description: Gene expression data from fresh frozen stage 3 lung adenocarcinoma tissue

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

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

data_processing: The data were analyzed with 'justGCRMA' function in R (http://www.r-project.org/).

source_name: lung adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA.

extract_protocol: RNA was isolated using RNeasy (Qiagen) following manufacture's protocol.

tag: tissue collection

value: Bulk

value: M

tag: Stage

value: IIIA

tag: smokingstat

value: former

tag: packyrs

tag: age at surgery

tag: disease state

value: stage 3 lung adenocarcinoma tissue


title: Teratoma, mouse embryonic stem cells electroporated with P81S VHL cDNA, biological rep 3

value: teratoma

value: *nu/nu* mice (Taconic Labs, Hudson, NY, USA)

value: wild-type J1 strain Sv/129 ES cells


title: AD-III-12

tag: gender


title: SW620 first


title: Teratoma, mouse embryonic stem cells electroporated with P81S VHL cDNA, biological rep 4


title: SW480 second


title: SW620 second


title: HT-29 first


title: AD-III-10

value: F

value: current


title: AD-III-7


title: HT-29 second


title: AD-III-2


title: LoVo first

value: LoVo


title: SW480 first


title: LS180 first


title: SW48 first


title: LS180 second


title: Teratoma, mouse embryonic stem cells electroporated with P81S VHL cDNA, biological rep 1


title: LoVo second


title: AD-II-12

description: Gene expression data from fresh frozen stage 2 lung adenocarcinoma tissue

value: stage 2 lung adenocarcinoma tissue


title: AD-III-5


title: AD-III-11


title: AD-III-1


title: AD-III-9


title: AD-III-4


title: AD-II-11


title: SW48 second


title: AD-III-6


title: AD-III-8


title: AD-II-10

value: IIA


title: HCT-15 second


title: HCT-15 first


title: HCT116 second


title: HCT116 first


title: AD-III-3


title: AD-II-9


title: DLD-1 second


title: CX-1 first


title: COLO205 first


title: HCT-8 first


title: CX-1 second


title: HCT-8 second


title: COLO320 first


title: COLO320 second


title: COLO205 second


title: AD-II-4

value: never


title: DLD-1 first


title: AD-II-6


title: AD-I-69

description: Gene expression data from fresh frozen stage 1 lung adenocarcinoma tissue

value: stage 1 lung adenocarcinoma tissue


title: CloneA second

value: CloneA


title: AD-II-7


title: AD-I-67


title: AD-II-5


title: CloneA first


title: AD-II-3

value: IIB


title: AD-I-68

value: Bulk


title: AD-II-1

value: M

value: some smoking


title: HETp 43d Biological rep2

city: Cambridge

first: D. R.

last: Mani

state: MA

address: 7 Cambridge Center

institute: The Broad Institute of MIT and Harvard

description: Gene expression data from the heart from 43 day old HET mouse treated with probucol

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MGU74Av2 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station FS400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2005A.

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

source_name: HET heart at 43d Probucol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug of total RNA.

growth_protocol: Mice were fed with either Chow diet or Probucol diet

value: SR-BI+/- apoE-/-

tag: age

value: 43 days

value: heart

tag: diet

value: Probucol diet


title: AD-II-2


title: AD-I-65

value: IA

value: former


title: AD-I-63


title: AD-I-64


title: HETp 43d Biological rep1

tag: genotype


title: HETp 31d Biological rep3

description: Gene expression data from the heart from 31 day old HET mouse treated with probucol

source_name: HET heart at 31d Probucol

value: 31 days


title: AD-I-66

value: F


title: AD-I-62

value: IB


title: HETp 31d Biological rep2


title: dKOp 43d Biological rep6

description: Gene expression data from the heart from 43 day old dKO mouse treated with probucol

source_name: dKO heart at 43d Probucol

value: SR-BI-/- apoE-/-


title: HETp 21d Biological rep1

description: Gene expression data from the heart from 21 day old HET mouse treated with probucol

source_name: HET heart at 21d Probucol

value: 21 days


title: dKOp 43d Biological rep3


title: Arabidopsis, whole root, 140mM NaCl for 4 days, replicate 2

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science, Department of Plant Biology

description: Gene expression data from whole roots on 140mM NaCl for 4 day treatment

hyb_protocol: Arrays were hybridized, blocked, washed, and post processed with Agilent One Color RNA Spike-In Kit. And the procesures were performed in the microarray facilities located at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore

scan_protocol: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_10 and Grid:021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: Genespring GX10 for data normalization

source_name: whole root

label_protocol: Fluorescent cRNA were generated using Agilent's Quick Amp Labeling Kit

growth_protocol: Seeds were surface sterilized with 20% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water.  Seeds were stratified at 4˚C for 2 days before being planted on standard media.  Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Salt media is standard media with 140mM NaCl added.  Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh at a density of ~20 seeds/cm in two rows.

extract_protocol: RNA was extracted using the RNAeasy Mini Kit (Qiagen GmbH).

treatment_protocol: Wild type plants of columbia were germinated and grown for 5 days, and then they were transferred to standard or salt media (standard media with 140mM NaCl added) for 1hr, 3hrs, 20hrs, 2days, 4days and 8days before harvesting.

tag: ecotype

value: Columbia

value: Seedling roots, 9 days after germination

tag: growth media

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 4 day


title: dKOp 43d Biological rep2


title: dKOp 43d Biological rep4


title: dKOp 43d Biological rep5


title: AD-I-57

value: Bulk

value: current

value: stage 1 lung adenocarcinoma tissue


title: Arabidopsis, whole root, 140mM NaCl for 2 days, replicate 2

description: Gene expression data from whole roots on 140mM NaCl for 2 day treatment

value: Seedling roots, 7 days after germination

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 2 day


title: AD-I-58

value: M


title: AD-I-56


title: AD-I-54


title: Arabidopsis, whole root, standard conditions for 8 days, replicate 2

description: Gene expression data from whole roots on standard condition for 8 day control

value: Seedling roots, 11 days after germination

value: Standard media for 5 days, transferred to standard media for 8 day


title: AD-I-61

value: IA

value: never


title: AD-I-55

value: F

value: former


title: Arabidopsis, whole root, standard conditions for 4 days, replicate 1

description: Gene expression data from whole roots on standard condition for 4 day control

value: Standard media for 5 days, transferred to standard media for 4 day


title: AD-I-53


title: Arabidopsis, whole root, 140mM NaCl for 4 days, replicate 1


title: Arabidopsis, whole root, standard conditions for 4 days, replicate 2


title: HETp 31d Biological rep1

value: SR-BI+/- apoE-/-

value: 31 days

value: heart

value: Probucol diet


title: HETp 21d Biological rep2

value: 21 days


title: Arabidopsis, whole root, 140mM NaCl for 8 days, replicate 2

description: Gene expression data from whole roots on 140mM NaCl for 8 day treatment

value: Columbia

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 8 day


title: HETp 21d Biological rep3


title: AD-I-59

value: Bulk

value: IB

value: stage 1 lung adenocarcinoma tissue


title: Arabidopsis, whole root, 140mM NaCl for 8 days, replicate 1

value: Seedling roots, 11 days after germination


title: AD-I-60

value: M


title: Arabidopsis, whole root, standard conditions for 8 days, replicate 1

value: Standard media for 5 days, transferred to standard media for 8 day


title: AD-I-52

value: IA


title: AD-II-8

value: F

value: IIA

value: stage 2 lung adenocarcinoma tissue


title: dKOp 43d Biological rep1

value: SR-BI-/- apoE-/-

value: 43 days


title: Arabidopsis, whole root, 140mM NaCl for 2 days, replicate 1

value: Seedling roots, 7 days after germination

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 2 day


title: dKOp 31d Biological rep7

description: Gene expression data from the heart from 31 day old dKO mouse treated with probucol

source_name: dKO heart at 31d Probucol

value: 31 days

value: heart

value: Probucol diet


title: AD-I-51

value: Bulk

value: current


title: dKOp 31d Biological rep8


title: dKOp 31d Biological rep6


title: dKOp 31d Biological rep5


title: AD-I-49

value: stage 1 lung adenocarcinoma tissue


title: AD-I-50

value: IB

value: former


title: Arabidopsis, whole root, 140mM NaCl for 20 hours, replicate 1

description: Gene expression data from whole roots on 140mM NaCl for 20 hour treatment

value: Columbia

value: Seedling roots, 6 days after germination

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 20 hour


title: dKOp 31d Biological rep4


title: dKOp 31d Biological rep3


title: Arabidopsis, whole root, 140mM NaCl for 20 hours, replicate 2


title: dKOp 31d Biological rep2


title: dKOp 21d Biological rep6

description: Gene expression data from the heart from 21 day old dKO mouse treated with probucol

source_name: dKO heart at 21d Probucol

value: 21 days


title: Arabidopsis, whole root, standard conditions for 20 hours, replicate 2

description: Gene expression data from whole roots on standard condition for 20 hour control

value: Standard media for 5 days, transferred to standard media for 20 hour


title: Arabidopsis, whole root, standard conditions for 2 days, replicate 2

description: Gene expression data from whole roots on standard condition for 2 day control

value: Standard media for 5 days, transferred to standard media for 2 day


title: AD-I-46

value: F

value: IA

value: never


title: dKOp 31d Biological rep1

value: SR-BI-/- apoE-/-

value: 31 days


title: AD-I-48

value: M


title: AD-I-45

value: Bulk


title: Arabidopsis, whole root, 140mM NaCl for 3 hours, replicate 1

description: Gene expression data from whole roots on 140mM NaCl for 3 hour treatment

value: Seedling roots, 5 days after germination

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 3 hour


title: Arabidopsis, whole root, standard conditions for 2 days, replicate 1

value: Seedling roots, 7 days after germination


title: AD-I-47

value: former

value: stage 1 lung adenocarcinoma tissue


title: AD-I-43


title: Arabidopsis, whole root, 140mM NaCl for 3 hours, replicate 2

value: Columbia


title: AD-I-44


title: Arabidopsis, whole root, standard conditions for 20 hours, replicate 1

value: Seedling roots, 6 days after germination


title: dKOp 21d Biological rep5

value: 21 days

value: heart

value: Probucol diet


title: Arabidopsis, whole root, standard conditions for 3 hours, replicate 1

description: Gene expression data from whole roots on standard condition for 3 hour control

value: Standard media for 5 days, transferred to standard media for 3 hour


title: AD-I-41

description: Gene expression data from fresh frozen stage 1 lung adenocarcinoma tissue


title: dKOp 21d Biological rep4


title: AD-I-42

value: F

value: current


title: Arabidopsis, whole root, 140mM NaCl for 1 hour, replicate 2

description: Gene expression data from whole roots on 140mM NaCl for 1 hour treatment

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 1 hour


title: Arabidopsis, whole root, standard conditions for 3 hours, replicate 2


title: dKOp 21d Biological rep2

value: SR-BI-/- apoE-/-


title: Arabidopsis, whole root, 140mM NaCl for 1 hour, replicate 1


title: dKOp 21d Biological rep3


title: dKOp 21d Biological rep1


title: AD-I-40


title: HET 43d Biological rep9

description: Gene expression data from the heart from 43 day old HET mouse

source_name: HET heart at 43d

value: SR-BI+/- apoE-/-

value: 43 days

value: Chow diet


title: Untreated Replicate 1

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

country: Canada

institute: McGill University

hyb_protocol: The Hy3TM and Hy5TM labelled samples were mixed pairwise and hybridization was performed according to the miRCURYTM LNA array manual (Exiqon) using a Tecan HS4800 hybridization station

scan_protocol: Microarray slides were scanned using the Agilent G2565BA Microarray Scanner System.  Image Analysis used ImaGene 8.0 software.

data_processing: LOWESS normalized and background corrected (Normexp with offset value 10)

source_name: Lung, untreated

label_protocol: 1 μg of total RNA from sample and reference was labelled with Hy3TM and Hy5TM respectively using miRCURYTM LNA Array power labelling kit from Exiqon according to the manufacturer's protocol.

extract_protocol: Total RNA from mouse left lung was extracted using miRNeasy Mini kits from Qiagen according to manufacturer's protocol.

treatment_protocol: C57Bl/6 mice were purchased from Jackson Labortory and housed at the Meakins-Christie Laboratories. Mice were treated at 8 weeks of age and killed 6 weeks post treatment.

value: Male

value: Lung

tag: treatment

value: Untreated

tag: treatment delivery

tag: euthanasia day post treatment

source_name: reference sample

tag: sample type

value: reference


title: Untreated Replicate 4

tag: strain

tag: tissue


title: Untreated Replicate 3


title: AD-I-39

tag: tissue collection

value: Bulk

tag: Stage

value: stage 1 lung adenocarcinoma tissue


title: Bleomycin Replicate 2

source_name: Lung, bleomycin treated

value: 100 Units/Kg Bleomycin

value: Subcutaneous with Osmotic Pump


title: HET 43d Biological rep8

value: heart


title: Arabidopsis, whole root, standard conditions for 1 hour, replicate 1

description: Gene expression data from whole roots on standard condition for 1 hour control

value: Columbia

value: Seedling roots, 5 days after germination

value: Standard media for 5 days, transferred to standard media for 1 hour


title: HET 43d Biological rep7


title: Arabidopsis, whole root, standard conditions for 1 hour, replicate 2


title: HET 43d Biological rep6


title: AD-I-38

value: F

tag: smokingstat

value: current

tag: packyrs


title: AD-I-36

value: former

tag: age at surgery

tag: disease state


title: AD-I-35

tag: gender

value: M


title: AD-I-33


title: AD-I-34


title: AD-I-37


title: Bleomycin Replicate 3


title: Bleomycin Replicate 1


title: HET 43d Biological rep5

value: SR-BI+/- apoE-/-

tag: age

value: 43 days

tag: diet

value: Chow diet


title: HET 43d Biological rep2

tag: genotype


title: HET 31d Biological rep9

description: Gene expression data from the heart from 31 day old HET mouse

source_name: HET heart at 31d

value: 31 days


title: HET 43d Biological rep1


title: Control vs tellurite/CTX replicate 1

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

description: Biological replicate 1 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min simultaneously to tellurite 0.05 μg/ml and cefotaxime 0.13 μg/ml.

hyb_protocol: Hybridization buffer (6X SSC buffer; 0.2 % SDS; 5 % Denhardt's solution; Salmon sperm DNA 13 µg/ml; 25 % deionized formamide; 23 µl of tagged cDNA) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an ScanArray Gx scanner (PerkinElmer).

data_processing: LOESS normalized, Normexp background subtracted data obtained from log2 of processed Red signal/processed Green signal. Bioconductor package used

label: Alexa Fluor 647

organism: Escherichia coli K-12

source_name: Total RNA extracted from tellurite and CTX exposed cultures

label_protocol: 20 µg of total RNA were primed with 2 µl of 3 µg/µl Random primer at 80°C for 5 min, then reversed transcribed at 42°C for 2.5 h in the presence of 200 U SuperScript II Reverse transcriptase (Invitrogen), and 10 mM each dATP, dCTP, dGTP, with 4 mM dTTP, 1 mM Alexa fluor 555 aha dUTP (or 1mM Alexa fluor 647 aha dUTP)

growth_protocol: An overnight E. coli culture was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cultures were exposed to tellurite (0.05 µg/ml), CTX (0.13 µg/ml) or simultaneously to tellurite (0.05 µg/ml) and CTX (0.13 µg/ml) during 15 min.

label: Alexa Fluor 555

source_name: Total RNA extracted from untreated cultures


title: HET 31d Biological rep10


title: HET 31d Biological rep7


title: AD-I-32


title: HET 43d Biological rep4


title: HET 43d Biological rep3


title: AD-I-29


title: AD-I-28


title: Control vs tellurite/CTX replicate 2

description: Biological replicate 2 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min simultaneously to tellurite 0.05 μg/ml and cefotaxime 0.13 μg/ml.


title: HET 31d Biological rep8


title: AD-I-27


title: Control vs CTX replicate 2

description: Biological replicate 2 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to cefotaxime 0.13 μg/ml.

source_name: Total RNA extracted from CTX exposed cultures


title: Control vs CTX replicate 3

description: Biological replicate 3 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to cefotaxime 0.13 μg/ml.


title: Control vs CTX replicate 1

description: Biological replicate 1 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to cefotaxime 0.13 μg/ml.


title: AD-I-30


title: HET 31d Biological rep6


title: AD-I-26


title: Control vs. Tellurite replicate 3

description: Biological replicate 3 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to tellurite 0.05 μg/ml.

source_name: Total RNA extracted from tellurite exposed cultures


title: Control vs tellurite/CTX replicate 3

description: Biological replicate 3 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min simultaneously to tellurite 0.05 μg/ml and cefotaxime 0.13 μg/ml.


title: AD-I-24

source_name: lung adenocarcinoma


title: AD-I-31


title: Control vs. Tellurite replicate 2

description: Biological replicate 2 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to tellurite 0.05 μg/ml.


title: AD-I-23


title: HET 31d Biological rep5


title: HET 31d Biological rep3


title: Control vs. Tellurite replicate 1

description: Biological replicate 1 of 3. Exponential growing cultures (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.4 and were exposed during 15 min to tellurite 0.05 μg/ml.


title: HET 31d Biological rep4


title: HET 31d Biological rep2


title: HET 31d Biological rep1


title: HET 21d Biological rep9

description: Gene expression data from the heart from 21 day old HET mouse

source_name: HET heart at 21d

value: 21 days


title: AD-I-25

value: Bulk


title: HET 21d Biological rep6


title: HET 21d Biological rep8


title: HET 21d Biological rep5


title: AD-I-20

value: stage 1 lung adenocarcinoma tissue


title: HET 21d Biological rep7


title: AD-I-17


title: Peripheral blood samples collected from patient with Klinefelter's Syndrome, replicate 3

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

description: test replicate 3

hyb_protocol: Hybridization were carried out on Agilent’s Microarray Platform according to Agilent’s standard protocols.

scan_protocol: scanning were carried out on Agilent’s Microarray Platform according to Agilent’s standard protocols. The array data were extracted with Agilent Feature Extraction software.

data_processing: After global mean normalization, probes with an intensity <400 were filtered out for further analysis. Differentially expressed genes were further analyzed based on a significant enrichment of GO terms using hyper geometric distribution in the R language package software.

source_name: Peripheral blood

label_protocol: labelled with cy3-dCTP or cy5-dCTP using Klenow enzyme.

growth_protocol: Ten peripheral blood samples were collected from five patients with Klinefelter’s Syndrome and five normal controls .

extract_protocol: Total RNA was extracted from 0.2 ml of peripheral blood according to the manufacturer’s protocol (Bio chain, Beijing, China). RNA quality was evaluated using formaldehyde agarose gel electrophoresis and was quantified via spectrophotometry (Nano drop, Wilmington, DE).

treatment_protocol: A 0.2ml of whole blood for each subjects were mixed with the 0.6ml RNA lysis buffer (Bio chain, Beijing, China) and stored at -80°C until the RNA was isolated.

value: blood

value: Klinefelter's Syndrome

tag: process

value: test


title: AD-I-22

value: some smoking


title: AD-I-18


title: Peripheral blood samples collected from patient with normal control, replicate 4

description: reference replicate 4

value: normal

value: reference


title: Peripheral blood samples collected from patient with normal control, replicate 3

description: reference replicate 3


title: Peripheral blood samples collected from patient with Klinefelter's Syndrome, replicate 2

description: test replicate 2


title: PSP7-dependent host transcriptional responses in mouse BMDM infected with T. gondii [Pru_PSP7-KO]

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

description: Gene expression data from BMDM infected with indicated T. gondii strain, 18 h post-infection

hyb_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies).

scan_protocol: After washing, slides were scanned with the Agilent DNA microarray Scanner. Data was extracted and normalized using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 9 samples have flags in Detected or Not Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.

source_name: mouse BMDM infected with T. gondii Pru_PSP7-KO

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.  Dyes used were Cy5

growth_protocol:
Bone marrow-derived macrophages were obtained from 8-10-week  old C57BL/6 mice purchased from JANVIER (France). Bone marrow
was isolated by flushing hind tibias and femurs using a 25-gauge needle and DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin. ~5 x 10^6 cells were resuspended in DMEM supplemented with 20 ng/mL M-CSF (Invitrogen)and plated in 10-cm nontissue culture-treated dishes (Corning). Cells were incubated at 37°C, with 5% CO2 in humidified air for 6 days. Adherent cells were harvested in cold-PBS(4°C) using a cell scraper, and replated at 8 x 10e6 cells per 10-cm2 plate for the assay.

treatment_protocol: Mouse BMDM were infected with Toxoplasma gondii tachyzoites (prepared from infected HFFs and washed in PBS) of the indicated strain at multiplicity of infection ~3; 18 hours post-infection, adherent cells and cells in the supernatent were harvested and lysed in Trizol reagent for RNA extraction.

tag: host cell

value: Mouse bone marrow-derived macrophages (BMDM)

tag: parasite

value: Pruku80(deltaPSP7) mutant

tag: time point

value: 18 h post-infection


title: Peripheral blood samples collected from patient with Klinefelter's Syndrome, replicate 4

description: test replicate 4


title: AD-I-14

value: M

value: former


title: AD-I-15


title: Peripheral blood samples collected from patient with Klinefelter's Syndrome, replicate 5

description: test replicate 5


title: AD-I-16


title: Peripheral blood samples collected from patient with Klinefelter's Syndrome, replicate 1

description: test replicate 1


title: AD-I-19

value: current


title: Peripheral blood samples collected from patient with normal control, replicate 5

description: reference replicate 5


title: AD-I-21

value: F


title: AD-I-13


title: HET 21d Biological rep4

value: SR-BI+/- apoE-/-

value: heart

value: Chow diet


title: HET 21d Biological rep3

value: 21 days


title: PSP7-dependent host transcriptional responses in mouse BMDM infected with T. gondii [RH_PSP7-KO]

source_name: mouse BMDM infected with T. gondii RH_PSP7-KO

value: RHku80(deltaPSP7) mutant


title: Peripheral blood samples collected from patient with normal control, replicate 1

description: reference replicate 1

value: blood


title: AD-I-11

value: Bulk

value: stage 1 lung adenocarcinoma tissue


title: HET 21d Biological rep1


title: HET 21d Biological rep2


title: AD-I-12


title: dKO 43d Biological rep11

description: Gene expression data from the heart from 43 day old dKO mouse

source_name: dKO heart at 43d

value: SR-BI-/- apoE-/-

value: 43 days


title: ZT16_GI_3

city: Pohang

first: Seungmin

last: Han

state: Gyeongbuk

address: Hyojadong

department: School of Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: POSTECH

description:
SAMPLE 30
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT16 [rep3]

hyb_protocol: Standard Agilent  hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Scanned signal intensity is log2-transformed. The log2-transformed data for ZT1 and ZT16 were quantile-normalized separately. The data processing including quantile normalization was done using MATLAB 7.7.0 (R2008b)

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: 16L/8D-grown seedlings for 7 days

extract_protocol: Total mRNA was extracted using WelPrepTM (JOIN BIO-INNOVATION, Daegu, Korea), and DNA was digested by treatment with DNase I (Ambion, Austin, TX).

treatment_protocol: Seven-day-old seedlings grown under LD were harvested at ZT1 and ZT16.

tag: ecotype/cultivar

tag: genotype/variation

value: transgenic gi-2 plants expressing GIpro::GI-GFP (GI plants)

value: 7-day-old seedlings

tag: sampling time


title: dKO 43d Biological rep12

tag: tissue


title: Heat_Tolerant_Mouse-5, biological rep9

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description: microRNA gene expression data in Heat Tolerant mouse

hyb_protocol: 21.5ul of each high-quality biotin-labeled miRNA sample was hybridized to Affymetrix Gene-Chip®  miRNA 2.0 Array for 16 hours according  to Affymetrix protocol. The arrays were washed and stained on the Affymetrix Fluidics station 400.

scan_protocol: The arrays were scanned with a Hewlett Packard G2500A gene Array Scanner.

data_processing: Affymetrix® miRNA QC Tool v 1.1.1.0 (Affymetrix, Santa Clara, CA) was used for the data summarization and  microarrays quality control. Gene expression values were obtained using Affymetric Expression Console program, RMA-DABG option.

source_name: Heat Tolerant mouse after heat exposures

label_protocol: Total RNA samples, containing low molecular weight RNA, were biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit (Genisphere LLC, Hatfield, PA). The quality of the biotin labeling process was confirmed by using Enzyme Linked Oligosorbent Assay (ELOSA) protocol (Genisphere LLC, Hatfield, PA).

growth_protocol: All mice were maintained in conventional animal facilities (~21°C) with ad libitum food and water at the Uniformed Services University (USU) Laboratory Animal Medicine facility. The USU Institutional Animal Care and Use Committee approved all procedures performed on animals. All experimental mice were surgically implanted with a temperature transponder (Model G2 E-Mitter, Mini Mitter Corp, Bend, OR). At least two weeks were allowed for recovery. At the time of the experimental protocols, all mice were healthy as evidenced by body weight gains (≥ presurgical levels), normal behavior and no sign of infection.

extract_protocol: Mouse muscle tissue samples were subjected to total RNA isolation procedure using  mirVana™ miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX). Concentration of each RNA sample was determined by NanoDrop® spectrophotometer ND-1000 (NanoDrop Technologies, Wilmington, DE). The quality of RNA samples was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

treatment_protocol: Heat tests were conducted in an environmental chamber (Model 3950, Thermo Forma, Marietta, OH). Mice were placed in the chamber at ~21°C (relative humidity: ~22-30%) a day before experimentation. Heat exposures began the following morning after stable baseline data were obtained. Food and water were removed from cages before exposure. We used a modifiedheat protocol  from the laboratory of Michel et al. (2007) such that heat exposure continued a maximum of 3 h, including ,1 h of heating the chamber to a predetermined temperature (39.5 ^ 0.28C). Heat exposure was terminated at core temperature (Tc) of ,42.48C or 3 h into heat exposure, whichever happened first. Based on our preliminary data, this protocol allowed sufficient heat exposure to test sensitivity to heat stress without any risk to the animals. All heat tests and telemetry measurements made to identify TOL and INT mice were performed after.

tag: strain

value: Gastrocnemius muscle

value: 10-12 weeks

tag: weigh

tag: Sex

value: male


title: dKO 43d Biological rep10


title: AD-I-10

description: Gene expression data from fresh frozen stage 1 lung adenocarcinoma tissue

tag: tissue collection

value: M

tag: Stage

tag: smokingstat

value: former

tag: packyrs

tag: age at surgery


title: Heat_Tolerant_Mouse-9, biological rep11

tag: age


title: dKO 43d Biological rep9

tag: genotype

tag: diet


title: ZT16_GI_1

description:
SAMPLE 28
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT16 [rep1]


title: Heat_Tolerant_Mouse-4, biological rep8


title: Peripheral blood samples collected from patient with normal control, replicate 2

description: reference replicate 2

tag: disease state

value: normal

tag: process

value: reference


title: AD-I-8

tag: gender

value: F

value: current


title: AD-I-9


title: Heat_Tolerant_Mouse-3, biological rep7


title: Heat_Tolerant_Mouse-7, biological rep10


title: ZT16_GI-NES_3

description:
SAMPLE 27
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT16 [rep3]

tag: ecotype/cultivar

tag: genotype/variation

value: transgenic gi-2 plants expressing GIpro::GI-GFP-NES (GI-NES plants)


title: ZT16_GI-NLS_3

description:
SAMPLE 24
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT16 [rep3]

value: transgenic gi-2 plants expressing GIpro::GI-GFP-NLS (GI-NLS plants)

tag: tissue

tag: sampling time


title: ZT16_GI_2

description:
SAMPLE 29
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT16 [rep2]


title: Heat_Intolerant_Mouse-11, biological rep6

description: microRNA gene expression data in Heat Intolerant mouse

source_name: Heat Intolerant mouse after heat exposures

tag: strain

tag: weigh


title: ZT16_GI-NES_1

description:
SAMPLE 25
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT16 [rep1]


title: AD-I-6

tag: tissue collection

value: Bulk


title: AD-I-7

tag: Stage

value: stage 1 lung adenocarcinoma tissue


title: Heat_Intolerant_Mouse-9, biological rep5

tag: Sex


title: dKO 43d Biological rep8

value: SR-BI-/- apoE-/-

value: heart

value: Chow diet


title: AD-I-4

tag: smokingstat

tag: packyrs


title: dKO 43d Biological rep7

tag: age

value: 43 days


title: ZT16_GI-NES_2

description:
SAMPLE 26
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT16 [rep2]

value: 7-day-old seedlings


title: AD-I-5

tag: age at surgery


title: dKO 43d Biological rep6

tag: genotype

tag: diet


title: ZT16_GI-NLS_2

description:
SAMPLE 23
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT16 [rep2]


title: AD-I-3

tag: disease state


title: AD-I-2

tag: gender


title: Heat_Tolerant_Mouse-11, biological rep12

value: Gastrocnemius muscle

value: 10-12 weeks


title: Heat_Intolerant_Mouse-5, biological rep3

value: male


title: dKO 43d Biological rep3


title: Heat_Intolerant_Mouse-7, biological rep4


title: ZT16_gi-2_1

description:
SAMPLE 19
re-analysis of GSM815827
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT16 [rep1]

tag: ecotype/cultivar

value: GI-null mutants (gi-2)


title: ZT16_GI-NLS_1

description:
SAMPLE 22
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT16 [rep1]

tag: genotype/variation


title: dKO 43d Biological rep2

tag: tissue


title: dKO 31d Biological rep10

description: Gene expression data from the heart from 31 day old dKO mouse

source_name: dKO heart at 31d

value: 31 days


title: ZT16_gi-2_2

description:
SAMPLE 20
re-analysis of GSM815828
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT16 [rep2]

tag: sampling time


title: Heat_Intolerant_Mouse-3, biological rep1

tag: strain


title: N-98

description: Gene expression data from fresh frozen normal lung tissue

source_name: normal lung

value: M

value: normal lung tissue


title: dKO 43d Biological rep4

description: Gene expression data from the heart from 43 day old dKO mouse


title: N-100


title: ZT16_gi-2_3

description:
SAMPLE 21
re-analysis of GSM815829
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT16 [rep3]


title: N-99

value: F


title: ZT16_col_2

description:
SAMPLE 17
re-analysis of GSM815822
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep2]

value: wild type


title: N-97


title: ZT16_col_1

description:
SAMPLE 16
re-analysis of GSM815821
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep1]


title: ZT1_GI_3

description:
SAMPLE 15
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT1 [rep3]

value: transgenic gi-2 plants expressing GIpro::GI-GFP (GI plants)


title: ZT16_col_3

description:
SAMPLE 18
re-analysis of GSM815823
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep3]


title: AD-I-1

description: Gene expression data from fresh frozen stage 1 lung adenocarcinoma tissue

value: Bulk

value: former


title: N-96


title: dKO 43d Biological rep1

value: SR-BI-/- apoE-/-


title: N-95


title: dKO 31d Biological rep8

value: heart


title: dKO 31d Biological rep9

value: Chow diet


title: Heat_Intolerant_Mouse-4, biological rep2

tag: weigh


title: dKO 31d Biological rep7


title: N-94

tag: tissue collection


title: dKO 31d Biological rep6


title: N-93


title: dKO 31d Biological rep5


title: dKO 31d Biological rep4


title: dKO 31d Biological rep3


title: ZT1_GI_2

description:
SAMPLE 14
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT1 [rep2]


title: ZT1_GI-NLS_3

description:
SAMPLE 9
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT1 [rep3]

value: transgenic gi-2 plants expressing GIpro::GI-GFP-NLS (GI-NLS plants)


title: dKO 31d Biological rep2


title: ZT1_GI-NES_1

description:
SAMPLE 10
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT1 [rep1]

value: transgenic gi-2 plants expressing GIpro::GI-GFP-NES (GI-NES plants)

value: 7-day-old seedlings


title: dKO 31d Biological rep1


title: ZT1_GI-NES_2

description:
SAMPLE 11
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT1 [rep2]


title: N-90


title: N-89


title: N-91


title: ZT1_GI-NES_3

description:
SAMPLE 12
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NES grown under LD were harvested at ZT1 [rep3]


title: ZT1_gi-2_3

description:
SAMPLE 6
re-analysis of GSM815817
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT1 [rep3]


title: dKO 21d Biological rep10

description: Gene expression data from the heart from 21 day old dKO mouse

source_name: dKO heart at 21d

value: 21 days


title: dKO 21d Biological rep9


title: N-88


title: ZT1_GI-NLS_1

description:
SAMPLE 7
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT1 [rep1]


title: N-86


title: N-87


title: ZT1_gi-2_2

description:
SAMPLE 5
re-analysis of GSM815816
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT1 [rep2]


title: ZT1_gi-2_1

description:
SAMPLE 4
re-analysis of GSM815815
7-day-old seedlings of gi-2 null mutant grown under LD were harvested at ZT1 [rep1]


title: N-85

description: Gene expression data from fresh frozen normal lung tissue


title: dKO 21d Biological rep7


title: dKO 21d Biological rep8


title: dKO 21d Biological rep5


title: N-84


title: ZT1_col_3

description:
SAMPLE 3
re-analysis of GSM815811
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep3]


title: dKO 21d Biological rep6


title: ZT1_col_2

description:
SAMPLE 2
re-analysis of GSM815810
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep2]


title: N-83


title: ZT1_col_1

description:
SAMPLE 1
re-analysis of GSM815809
7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep1]


title: dKO 21d Biological rep4


title: dKO 21d Biological rep3


title: dKO 21d Biological rep2

description: Gene expression data from the heart from 31 day old dKO mouse


title: ZT1_GI_1

description:
SAMPLE 13
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP grown under LD were harvested at ZT1 [rep1]


title: Pax6 KO2, E9.5 (3)

city: Saint Louis

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

description:
5355492022_D
Total RNA amplified as cDNA.

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v2.0 bead arrays by the Genome Technology Access Center (GTAC) at Washington University.

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing:
Background subtraction and cubic spline normalization and differential expression performed using Illumina Genome Studio software.
Value is the mean hybridization intensity for all beads (usually 25-50 per array) containing the indicated oligonucleotide probe.

source_name: Pax6-/- surface ectoderm

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice euthanized and embryos removed at E9.5.

extract_protocol: Total RNA was extracted and purified from the tissue obtained from three mouse embryos. Samples from each genotype were pooled and triplicate samples were amplified using a Qiagen RNeasy Microkit (Qiagen# 74004). Total RNA was amplified to produce ~6 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos frozen in OCT and sectioned at 10 microns. Laser microdissection of the lens placode on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene.

tag: strain/background

value: mixed (FVB; 129)

value: surface ectoderm


title: N-79


title: dKO 21d Biological rep1


title: Pax6 KO3, E9.5 (3)

description:
5355492022_A
Total RNA amplified as cDNA.


title: N-77


title: N-78


title: N-81


title: WT3, E9.5 (3)

description:
5355492022_F
Total RNA amplified as cDNA.

source_name: WT lens placode

value: lens placode


title: Pax6 KO1, E9.5 (3)

description:
5355492023_F
Total RNA amplified as cDNA.


title: WT2, E9.5 (3)

description:
5355492023_D
Total RNA amplified as cDNA.


title: N-80


title: N-76

value: M


title: N-82

value: normal lung tissue


title: WT1, E9.5 (3)

description:
5355492022_E
Total RNA amplified as cDNA.


title: N-73


title: N-74

value: F


title: N-72


title: N-75


title: Pax6 KO1, E9.5 (2)

description:
4661295049_A
Total RNA amplified as cDNA.


title: WT2, E9.5 (2)

description:
4661295071_A
Total RNA amplified as cDNA.

value: wild type


title: dKO 43d Biological rep5

description: Gene expression data from the heart from 43 day old dKO mouse

value: 43 days


title: WT3, E9.5 (2)

description:
4661295071_D
Total RNA amplified as cDNA.


description: mRNA gene expression data in Heat Intolerant mouse

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The arrays were scanned using HiScanSQ System.

data_processing: In Genome Studio the data were normalised (quantile normalisation) and background was subtracted

label_protocol: Biotinylated cRNA were prepared with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

value: Gastrocnemius muscle

value: 10-12 weeks

tag: Sex

value: male


title: Pax6 KO3, E9.5 (2)

description:
4661295071_E
Total RNA amplified as cDNA.


title: N-69

description: Gene expression data from fresh frozen normal lung tissue

value: Bulk


title: Pax6 KO2, E9.5 (2)

description:
4661295049_F
Total RNA amplified as cDNA.


title: N-71


title: WT1, E9.5 (2)

description:
4661295049_D
Total RNA amplified as cDNA.


title: N-70


title: N-67


title: N-68


title: Heat_Tolerant_Mouse-9, biological rep11


title: Heat_Tolerant_Mouse-7, biological rep10


title: N-65


title: N-66


title: N-64


title: Heat_Tolerant_Mouse-4, biological rep8


title: Heat_Tolerant_Mouse-3, biological rep7


title: N-63


title: liver_aflibercept_rep3

first: Kevin

last: Wei

state: CA

address: CCSR 3105a  269 Campus Drive

department: Hematology Division

institute: Stanford University School of Medicine

hyb_protocol: Hybridization was done on MEEBO oligonucleotide arrays printed at the Stanford Functional Genomic Facility.  MEEBO slides were post-processed the same day of hybridization.  Fluorescently labeled amplified RNA samples were hybridized on the array with an amplified reference RNA sample at 16 hours at 65 degrees C.

scan_protocol: Arrays were scanned on an Agilent G2565AA scanner

data_processing: Data processing was carried out using LIMMA.  The mean values from each channel were Log2 transformed and normalized using print-tip LOESS to minimize printing effects

source_name: Universal Reference RNA

label_protocol: Total RNA was amplified and coupled to Cy3/Cy5 using amino allyl MessageAmp II aRNA amplification kit (ambion) according to the manufacturer's protocols.  Labeled RNA was then fragmented using RNA Fragmentation Reagent (Ambion)

growth_protocol: All mice were on a 12 h light-dark cycle in a pathogen free animal facility

extract_protocol: On average, mouse liver tissue was harvested and homogenized.  Total RNA was isolated using Trizol (Invitrogen). RNA samples were reverse transcribed into cDNA using a Reverse Transcription Kit (Invitrogen).

treatment_protocol: Mice received VEGF Trap protein (aflibercept) subcutaneously two times per week at 25 mg per kg body weight. For control groups, mice were treated with humanized Fc (Regeneron)

tag: cell line

value: embryo, embryonic fibroblast, kidney, liver hepatocyte, lung alveolar macrophage, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis

source_name: mouse liver 9 weeks after treatment with aflibercept

value: liver

tag: treatment

value: aflibercept


title: liver_aflibercept_rep4


tag: age


title: liver_aflibercept_rep2


title: liver_control_rep5

source_name: mouse liver 9 weeks after treatment with humanized Fc

value: humanized Fc


title: liver_aflibercept_rep1


title: N-61


title: ZT1_GI-NLS_2

description:
SAMPLE 8
7-day-old seedlings of transgenic gi-2 plants expressing GIpro::GI-GFP-NLS grown under LD were harvested at ZT1 [rep2]

value: transgenic gi-2 plants expressing GIpro::GI-GFP-NLS (GI-NLS plants)

value: 7-day-old seedlings


title: N-62


title: Heat_Tolerant_Mouse-5, biological rep9


title: liver_control_rep4


title: N-60


title: N-59


title: N-92


title: N-56


title: liver_control_rep2


title: liver_control_rep3


title: N-57


title: NKT-cells_NK1.1+_CD103-_replicate2

city: Oxford

first: Richard

last: Cornall

address: Roosevelt Drive

department: Centre of Cellular and Molecular Physiology

country: United Kingdom

institute: University of Oxford

description: CD103- replicate2

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using the BioConductor package VSN (variance stabilisation and normalisation)  in R

label: Biotin

source_name: mature (CD44+, NK1.1+) thymic natural killer T cells

label_protocol: Standard Illumina labelling protocol was used to prepare biotinylated cRNA

extract_protocol: RNA was extracted using the RNAqueous®-Micro Kit from Ambion in accordance with manufacturers protocols. RNA quantity and quality was assessed by spectral density.

tag: cell type

value: Male


title: liver_control_rep1


title: N-55


title: N-58


title: N-54


title: N-53


title: N-49


title: NKT-cells_NK1.1+_CD103+_replicate3

description: CD103+ replicate3


title: N-48


title: NKT-cells_NK1.1+_CD103-_replicate3

description: CD103- replicate3


title: NKT-cells_NK1.1+_CD103+_replicate1

description: CD103+ replicate1


title: N-50


title: N-46


title: NKT-cells_NK1.1+_CD103+_replicate2

description: CD103+ replicate2


title: Wildtype, thymic, NK1.1+ NKT cells replicate3

description: wildtype replicate3

tag: genotype

value: wildtype


title: NKT-cells_NK1.1+_CD103-_replicate1

description: CD103- replicate1


title: Wildtype, thymic, NK1.1+ NKT cells replicate1

description: wildtype replicate1


title: N-45

value: M


title: N-51

value: normal lung tissue


title: Wildtype, thymic, NK1.1+ NKT cells replicate2

description: wildtype replicate2


title: DOCK8 knockout, thymic, NK1.1+ NKT cells replicate3

description: DOCK8 ko replicate3

value: Captain Morgan (DOCK8 deficient animal strain)


title: N-52


title: N-43


title: N-44


title: Malt1 -/- TH17 Cells  48 hours after induction from Naïve T cells Replicate 5

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description: Malt1 -/- TH17 Induced Cells

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 2011.1)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.0) followed by median centered normalization

source_name: Malt1 -/- TH17 Cells

label_protocol: Biotinylated cDNA were prepared with the Illumina 96 RNA prep Kit (LifeTech)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser using RNA Nano Kit (Agilent).

tag: genetic background

value: 8-12 weeks

tag: source cell

value: Naïve (CD4+CD62L+) T cells from lymph nodes and spleens

value: Malt1 -/-

value: TH17 cell

tag: time

value: 48 hours

value: induction of differentiation of Naïve T cells


title: WT TH17 Cells  72 hours after induction from Naïve T cells Replicate 5

description: WT TH17 Induced Cells

source_name: WT TH17 Cells

value: WT

value: 72 hours


title: N-42

value: Bulk

tag: gender

value: F

tag: disease state


title: Malt1 -/- TH1 Cells  72 hours after induction from Naïve T cells Replicate 5

description: Malt1 -/- TH1 Induced Cells

source_name: Malt1 -/- TH1 Cells

value: TH1 cell


title: DOCK8 knockout, thymic, NK1.1+ NKT cells replicate2

description: DOCK8 ko replicate2


title: N-40


title: WT TH1 Cells  72 hours after induction from Naïve T cells Replicate 5

description: WT TH1 Induced Cells

source_name: WT TH1 Cells


title: WT TH1 Cells  48 hours after induction from Naïve T cells Replicate 5

description: WT TH1 Induced Cells


title: Malt1 -/- TH1 Cells  48 hours after induction from Naïve T cells Replicate 5

description: Malt1 -/- TH1 Induced Cells


title: Malt1 -/- TH17 Cells  48 hours after induction from Naïve T cells Replicate 4

description: Malt1 -/- TH17 Induced Cells


title: WT TH1 Cells  72 hours after induction from Naïve T cells Replicate 4

description: WT TH1 Induced Cells


title: WT TH17 Cells  48 hours after induction from Naïve T cells Replicate 5

description: WT TH17 Induced Cells


title: N-41


title: N-36


title: N-39


title: N-38


title: N-37


title: N-34


title: N-32


title: Malt1 -/- TH17 Cells  72 hours after induction from Naïve T cells Replicate 5

description: Malt1 -/- TH17 Induced Cells


title: WT TH1 Cells  72 hours after induction from Naïve T cells Replicate 3

description: WT TH1 Induced Cells


title: WT TH1 Cells  72 hours after induction from Naïve T cells Replicate 2

description: WT TH1 Induced Cells


title: Malt1 -/- TH1 Cells  48 hours after induction from Naïve T cells Replicate 4

description: Malt1 -/- TH1 Induced Cells


title: N-33


title: WT TH17 Cells  48 hours after induction from Naïve T cells Replicate 4

description: WT TH17 Induced Cells


title: WT TH1 Cells  48 hours after induction from Naïve T cells Replicate 4

description: WT TH1 Induced Cells


title: Malt1 -/- TH1 Cells  48 hours after induction from Naïve T cells Replicate 3

description: Malt1 -/- TH1 Induced Cells


title: N-30


title: N-29


title: N-31


title: N-47


title: N-35


title: N-27


title: DOCK8 knockout, thymic, NK1.1+ NKT cells replicate1

description: DOCK8 ko replicate1


title: N-28


title: Malt1 -/- TH17 Cells  48 hours after induction from Naïve T cells Replicate 3

description: Malt1 -/- TH17 Induced Cells


title: WT TH1 Cells  72 hours after induction from Naïve T cells Replicate 1

description: WT TH1 Induced Cells


title: WT TH1 Cells  48 hours after induction from Naïve T cells Replicate 3

description: WT TH1 Induced Cells


title: Malt1 -/- TH17 Cells  48 hours after induction from Naïve T cells Replicate 1

description: Malt1 -/- TH17 Induced Cells


title: N-23


title: Malt1 -/- TH17 Cells  72 hours after induction from Naïve T cells Replicate 4

description: Malt1 -/- TH17 Induced Cells


title: N-25


title: N-24


title: WT TH17 Cells  72 hours after induction from Naïve T cells Replicate 3

description: WT TH17 Induced Cells


title: WT1 Hippocampus

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression profile of Tet1 WT1 Hippocampus

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 1.65ug cy3-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetronitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Arrays were normalized using limma R package with across-array quantile normalization and within-array LOESS

source_name: mouse hippocampus

label_protocol: Cy3 or Cy5-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 0.5 µg total RNA.

growth_protocol: All mice used for microarray analysis were naïve and housed in standard laboratory conditions and mouse cages before harvest of tissues.

extract_protocol: RNA used for microarray was extracted from snap frozen cotex or hippocampus tissue using RNAeasy Kit (Qaigen).

tag: tissue

value: hippocampus

value: wild type


title: WT TH17 Cells  72 hours after induction from Naïve T cells Replicate 4

description: WT TH17 Induced Cells


title: Malt1 -/- TH17 Cells  48 hours after induction from Naïve T cells Replicate 2

description: Malt1 -/- TH17 Induced Cells


title: KO1 Hippocampus

description: Gene expression profile of Tet1 KO1 Hippocampus

treatment_protocol: All mice used for microarray analysis were naïve and housed in standard laboratory conditions and mouse cages before harvest of tissues.

value: Tet1 KO


title: WT TH1 Cells  48 hours after induction from Naïve T cells Replicate 2

description: WT TH1 Induced Cells


title: Malt1 -/- TH1 Cells  72 hours after induction from Naïve T cells Replicate 4

description: Malt1 -/- TH1 Induced Cells


title: Malt1 -/- TH1 Cells  72 hours after induction from Naïve T cells Replicate 3

description: Malt1 -/- TH1 Induced Cells


title: KO2 Hippocampus

description: Gene expression profile of Tet1 KO2 Hippocampus


title: N-20

value: M


title: N-18

value: normal lung tissue


title: N-26


title: N-21


title: N-22


title: Malt1 -/- TH17 Cells  72 hours after induction from Naïve T cells Replicate 3

description: Malt1 -/- TH17 Induced Cells


title: N-17


title: WT2 Cortex

description: Gene expression profile of Tet1 WT2 Cortex

source_name: mouse cortex

value: brain cortex


title: Malt1 -/- TH1 Cells  72 hours after induction from Naïve T cells Replicate 2

description: Malt1 -/- TH1 Induced Cells

value: 8-12 weeks


title: N-16


title: WT TH17 Cells  72 hours after induction from Naïve T cells Replicate 2

description: WT TH17 Induced Cells

value: Naïve (CD4+CD62L+) T cells from lymph nodes and spleens


title: WT TH17 Cells  48 hours after induction from Naïve T cells Replicate 3

description: WT TH17 Induced Cells


title: KO2 Cortex

description: Gene expression profile of Tet1 KO2 Cortex


title: N-15


title: WT1 Cortex

description: Gene expression profile of Tet1 WT1 Cortex


title: Malt1 -/- TH1 Cells  48 hours after induction from Naïve T cells Replicate 2

description: Malt1 -/- TH1 Induced Cells

value: Malt1 -/-


title: Malt1 -/- TH17 Cells  72 hours after induction from Naïve T cells Replicate 2

description: Malt1 -/- TH17 Induced Cells

value: TH17 cell


title: N-12


title: N-10

tag: smokingstat

value: never

tag: age at surgery


title: R1-D567 + siARexon 3

city: Minneapolis

first: Michael

middle: David

last: Nyquist

address: Masonic Cancer Center, University of Minnesota, Mayo Mail Code 806 420 Delaware St SE

department: Genetics Cell Developmental Bio

institute: University of Minnesota

hyb_protocol: 150ng of biotin-labeled cRNA was hybridized with Illumina Beadchips using the HumanHT-12 v4 Expression Beadchip Kit in accordance with the manufacturer's specifications

scan_protocol: Hybridized Beadchips were scanned with an Illumina iScan.

data_processing: Average probe intensity data was extracted from iScan image files using the Partek Report Plug-in for Illumina GenomeStudio and then imported to Partek Genomics Suite 6.6.  Raw intensity data was log2 transformed and quantile normalized using Partek GS 6.6.

source_name: R1-D567 prostate cancer cells

label_protocol: Total RNA was converted to amplified, biotinylated, antisense cRNA using the Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies) in accordance with the manufacturer's specifications.

growth_protocol: Cells were grown in RPMI-1640 with 10% FBS on tissue culture treated plastic.

extract_protocol: Total RNA was extracted using Trizol and column purified using Qiagen RNA purification columns.

treatment_protocol: Cells were electroporated with either siCNTL or siAR-exon1.  R1-AD1 cells were electroporated with siCNTL.  Electroporated cells were plated in RPMI 1640 medium supplemented with 10% CSS.  After 48h, cells were switched to serum free RPMI-1640 medium supplemented with 1nM DHT or 0.1% (v/v) ethanol (vehicle control) for 24 hours.

value: R1-D567 prostate cancer cells

value: Deletion of AR exons 5-12

tag: knockdown

value: EtOH


title: WT TH17 Cells  48 hours after induction from Naïve T cells Replicate 2

description: WT TH17 Induced Cells

value: WT

value: 48 hours

value: induction of differentiation of Naïve T cells


title: N-11

tag: tissue collection

value: Bulk


title: R1-D567 + siARexon 2

value: Deletion of AR exons 5-11


title: N-13


title: KO1 Cortex

description: Gene expression profile of Tet1 KO1 Cortex

value: Tet1 KO


title: Malt1 -/- TH17 Cells  72 hours after induction from Naïve T cells Replicate 1

description: Malt1 -/- TH17 Induced Cells

value: 72 hours


title: WT TH1 Cells  48 hours after induction from Naïve T cells Replicate 1

description: WT TH1 Induced Cells

value: TH1 cell


title: R1-D567 + siCNTL 3

value: Deletion of AR exons 5-9

value: siCNTL


title: N-9

value: F

value: normal lung tissue


title: N-14


title: R1-AD1 + EtOH 3

source_name: R1-AD1 prostate cancer cells

value: R1-AD1 prostate cancer cells

value: Full length AR


title: R1-D567 + siARexon 1

value: R1-D567 prostate cancer cells

value: Deletion of AR exons 5-10


title: WT TH17 Cells  48 hours after induction from Naïve T cells Replicate 1

description: WT TH17 Induced Cells

value: 8-12 weeks

value: Naïve (CD4+CD62L+) T cells from lymph nodes and spleens

value: TH17 cell


title: N-7

value: never


title: N-6

value: Bulk

value: M


title: N-8


title: R1-AD1 + EtOH 1

value: EtOH


title: R1-D567 + siCNTL 2

value: Deletion of AR exons 5-8


title: Malt1 -/- TH1 Cells  72 hours after induction from Naïve T cells Replicate 1

description: Malt1 -/- TH1 Induced Cells

value: Malt1 -/-

value: TH1 cell

value: 72 hours

value: induction of differentiation of Naïve T cells


title: R1-D567 + siCNTL 1

value: Deletion of AR exons 5-7

value: siCNTL


title: WT TH17 Cells  72 hours after induction from Naïve T cells Replicate 1

description: WT TH17 Induced Cells

value: WT


title: N-5

value: normal lung tissue


title: R1-AD1 + EtOH 2

value: R1-AD1 prostate cancer cells

value: Full length AR


title: R1-AD1 + DHT 3

value: 1nM DHT


title: wound day 14 skin

first: Denise

last: Gay

address: 550 1st avenue

institute: NYU langone

description: Gene expression data from wound tissue taken at wound day 14.

hyb_protocol: 5.5ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0ST GeneChips (Affymetrix Inc., Santa Clara CA)

scan_protocol: Gene chips were scanned using a GeneChip 3000 7G scanner.

data_processing: CEL files were normalized with RMA in Partek Genomics Suite v6.6

source_name: wound tissue taken at wound day 14 from three adult C57Bl/6 mice

label_protocol: cRNA, amplified from 250ng total RNA, was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: Large 1.5cm2 full thickness excision wounds, removing both epidermis and underlying dermis, were created on the backs of adult C57Bl/6 mice. Following surgery, animals were housed in barrier facility conditions and observed daily for normal healing.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Plus kit

treatment_protocol: Animals were sacrificed and wound tissue, both dermis and any overlying epidermis, was dissected out and flash frozen in liquid nitrogen. Care was taken to avoid surrounding unwounded skin and hair follicles at the wound edge. Wound tissue from three adult C57Bl/6 mice was combined for each time point analyzed.

tag: strain

value: 6 weeks

tag: stress

value: large full thickness skin excision

value: healing wound epidermis and dermis

value: wound day 14


title: WT2 Hippocampus

description: Gene expression profile of Tet1 WT2 Hippocampus

value: hippocampus

value: wild type


title: wound day 12 skin

description: Gene expression data from wound tissue taken at wound day 12.

source_name: wound tissue taken at wound day 12 from three adult C57Bl/6 mice

value: wound day 12


title: N-4

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

data_processing: The data were analyzed with 'justGCRMA' function in R (http://www.r-project.org/).

source_name: normal lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA.

value: Bulk

value: M

value: never


title: N-3

value: F


title: N-2


title: bone_del175k mutant_rep3

city: beijing

first: xiaoquan

last: zhu

address: N01 dahua road dongdan beijing

institute: beijing hospital

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST (Affymetrix) and scanned at the UCLA Microarray Core Facility.

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

data_processing: The raw data were processed using SUM software 3.02.

source_name: bone of newbone mice

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: 3 paires of  newbone mice radii and ulnae from Tnni2del175k mutant mice and their wild-type littermates were collected

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.recoveries of long transcripts.

value: bone

tag: genotype/variation

value: del175k mutant


title: R1-AD1 + DHT 1

value: siCNTL

tag: treatment


title: wound day 10 skin

city: New York

description: Gene expression data from wound tissue taken at wound day 10.

source_name: wound tissue taken at wound day 10 from three adult C57Bl/6 mice

tag: age

value: wound day 10


title: N-1

last: Leontovich

address: 200 First street

institute: Mayo Clinic

value: normal lung tissue


title: bone_wild-type_rep3

value: wild-type


title: bone_del175k mutant_rep2


title: bone_del175k mutant_rep1


title: bone_wild-type_rep1


title: bone_wild-type_rep2


title: R1-AD1 + DHT 2

tag: cell type

value: R1-AD1 prostate cancer cells

value: Full length AR

value: 1nM DHT


title: N-19


title: C98S1R_1 with array type SUNFLOWER from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: The early sowing constitutes an alternative strategy to avoid drought occurring during flowering and post-flowering periods and responsible for decrease in sunflower production. In French cropping system, early sowing is associated to low temperature period and frost during first development stages in sunflower. Knowledge about metabolism of frost acclimation must be performed to supply tools for breeding programs in sunflower. The aim of our experiment is to unravel the transcriptional regulation underpinning frost tolerance in sunflower

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: aerial - - Plants were grown in growth chambers from September 6th to October 12th. Tissue collection (leaf) was carried out the 6th of October and the 11th of October. - October 6th, plants C1 and S1, 65% hygrometry, 4°C air temperature, 150 micromol/m-2/s-1 PPFD, in growth chamber; - October 11th, plants C2 and S2, 65% hygrometry, 4°C air temperature, 150 micromol/m-2/s-1 PPFD, in growth chamber.

treatment_protocol: Name:FROST - environmental treatment - frost,temperature,frost:. C1 C2 S1 S2

value: 30 day

value: chamber 2 cold acclimation then frost

value: leaf


title: C98S2R_3 with array type SUNFLOWER from Affymetrix

value: 35 day

value: chamber 1 control condition then frost