title: PBMC-T24_AO-rep2

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description: PBMC gene expression of mouse after injection of oleic acid

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: PBMC, T24, AO, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Each group of mice was sacrificed 1h, 1h30, 3h, 4h, 18h or 24h after injection of OA or physiological serum by exsanguination through the eye vein. 200 to 900 µL of whole blood was collected in tubes containing 100µL EDTA 0.5M. PBMC were isolated using a ficoll gradient 1.084 (Ficoll-Paque Premium 1.084, GE Healthcare #17-5446-02). Cells were resuspended in 500 µL PBS and counted, allowed us to recover an average quantity of 1.9x106 PBMC for 600 µl of blood. Total RNA from PBMC was isolated using the Mouse RiboPure-Blood RNA isolation kit (Ambion, #AM1951). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Female C57Bl/6J mice were anesthetized with 5% Xylazine – 20% Ketamine (0,1ml/10g). We injected 200 µl of physiological serum in the control mouse at each time-point and 200 µl of OA (1,2 µl/g body weight, sigma #27728-1L-R) in the other mice of our study. Administration of physiological serum and OA was done through the tail vein with a 0.3-ml insulin syringe (BD #320837).

value: oleic acid

tag: time (h)

value: Female

tag: age (week)

value: PBMC


title: DMSO_rep1

status: Public on Jan 01 2015

type: RNA

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

description: Gene expression data from ESCs cultured withour treatment

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: Images were scanned using the high sensitivity protocol (AgilentG3_HiSen_GX_1color) on a SureScan microarray scanner (Agilent Technologies) and probe intensities were obtained by taking the gProcessedSignal from the output of Agilent feature extraction software using default settings.

data_processing: Probe intensities were analysed using the NIA Array Analysis tool (http://lgsun.grc.nia.nih.gov/ANOVA/).

molecule: total RNA

organism: Mus musculus

source_name: Cultured embryonic stem cells

label_protocol: RNA was amplified into cRNA and 150ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies- 5190-2305).

growth_protocol: E14 ESCs were cultured in GMEM (Sigma) supplemented with 10% FBS (Gibco), 100 μM 2-mercaptoethanol (Sigma), 1xMEM non-essential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate (all from Gibco), and 1000 units/ml LIF (made in-house) on gelatinised tissue culture flasks (Coring)

extract_protocol: Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).

treatment_protocol: Pre-treated with 250nM PD173074 for 24 hours, and then stimulated for the indicated times with 250nM 4OHT

tag: cell type

value: E14tg2a ESCs

tag: agent

value: DMSO

tag: time point


title: control_8 [miRNA]

city: Leuven

first: Jan

last: Van der Goten

address: Herestraat 49 bus 701

department: Clinical and Experimental Medicine

country: Belgium

institute: KU Leuven

description: colonic mucosal microRNA expression data from control individual

hyb_protocol: Incubation at 99°C for 5 minutes, followed by 45°C for another 5 minutes. Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix) was performed under rotation (60 rpm) at 48°C for 16 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality control of the array data was performed with the Affymetrix miRNA QC Tool, version 1.1.1.0. Data were analyzed using RMA method in Bioconductor (R version 2.15.0).

label: biotin

organism: Homo sapiens

source_name: colonic mucosal biopsy from control individual

label_protocol: Total RNA (250 ng) was used in a tailing reaction followed by ligation of the biotinylated signal molecule, using the FlashTag™ Biotin HSR RNA Labeling Kit (Genesphere) protocol for Affymetrix GeneChip miRNA arrays. As recommended, the labeling efficiency is verified with the ELOSA QC assay (Genesphere).

extract_protocol: Total RNA was extracted using the miRVAna miRNA isolation Kit (Ambion), according to the manufacturer's instructions. The integrity and quantity of total RNA and small RNA were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit and the Agilent Small RNA kit, respectively.

tag: tissue

value: colon

tag: disease

value: control

tag: disease activity

value: not applicable


title: 2h_rep1

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 2 hours with 4OHT to activate c-Raf


title: PBMC-T24_AO-rep3

source_name: PBMC, T24, AO, rep3

tag: treatment

tag: gender

tag: strain


title: PBMC-T24_Phi-rep2

description: PBMC gene expression of mouse after injection of physiological serum

source_name: PBMC, T24, Phi, rep2

value: physiological serum


title: PBMC-T24_Phi-rep1

source_name: PBMC, T24, Phi, rep1


title: PBMC-T18_Phi-rep2

source_name: PBMC, T18, Phi, rep2


title: PBMC-T3_AO-rep2

source_name: PBMC, T3, AO, rep2


title: PBMC-T4_AO-rep2

source_name: PBMC, T4, AO, rep2


title: PBMC-T18_AO-rep1

source_name: PBMC, T18, AO, rep1


title: PBMC-T4_Phi-rep1

source_name: PBMC, T4, Phi, rep1


title: PBMC-T18_Phi-rep1

source_name: PBMC, T18, Phi, rep1


title: PBMC-T4_AO-rep1

source_name: PBMC, T4, AO, rep1


title: PBMC-T24_AO-rep1

source_name: PBMC, T24, AO, rep1


title: PBMC-T3_AO-rep3

source_name: PBMC, T3, AO, rep3


title: PBMC-T18_AO-rep3

source_name: PBMC, T18, AO, rep3


title: PBMC-T18_AO-rep2

source_name: PBMC, T18, AO, rep2


title: PBMC-T3_Phi-rep1

source_name: PBMC, T3, Phi, rep1


title: PBMC-T1h30_AO-rep2

source_name: PBMC, T1h30, AO, rep2


title: PBMC-T3_AO-rep1

source_name: PBMC, T3, AO, rep1


title: PBMC-T1h30_AO-rep1

source_name: PBMC, T1h30, AO, rep1


title: PBMC-T1h30_AO-rep3

source_name: PBMC, T1h30, AO, rep3


title: PBMC-T3_Phi-rep2

source_name: PBMC, T3, Phi, rep2


title: PBMC-T1h30_Phi-rep1

source_name: PBMC, T1h30, Phi, rep1


title: brain-T24_Phi-rep1

description: Brain gene expression of mouse after injection of physiological serum

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: brain, T24, Phi, rep1

extract_protocol: Total RNA from brain were isolated using trizol.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: brain


title: PBMC-T1_AO-rep2

source_name: PBMC, T1, AO, rep2


title: brain-T18_AO-rep2

description: Brain gene expression of mouse after injection of oleic acid

source_name: brain, T18, AO, rep2


title: PBMC-T1_AO-rep1

source_name: PBMC, T1, AO, rep1


title: brain-T18_Phi-rep2

source_name: brain, T18, Phi, rep2


title: brain-T24_AO-rep2

source_name: brain, T24, AO, rep2


title: brain-T18_AO-rep1

source_name: brain, T18, AO, rep1


title: PBMC-T1_Phi-rep2

source_name: PBMC, T1, Phi, rep2


title: brain-T4_Phi-rep1

source_name: brain, T4, Phi, rep1


title: brain-T4_AO-rep1

source_name: brain, T4, AO, rep1


title: PBMC-T1h30_Phi-rep2

source_name: PBMC, T1h30, Phi, rep2


title: brain-T4_AO-rep2

source_name: brain, T4, AO, rep2


title: brain-T4_AO-rep3

source_name: brain, T4, AO, rep3


title: brain-T24_Phi-rep2

source_name: brain, T24, Phi, rep2


title: PBMC-T1h30_Phi-rep3

source_name: PBMC, T1h30, Phi, rep3


title: brain-T18_Phi-rep1

source_name: brain, T18, Phi, rep1


title: PBMC-T1_Phi-rep3

source_name: PBMC, T1, Phi, rep3


title: PBMC-T1_AO-rep3

source_name: PBMC, T1, AO, rep3


title: brain-T24_AO-rep1

source_name: brain, T24, AO, rep1


title: brain-T24_AO-rep3

source_name: brain, T24, AO, rep3


title: brain-T4_Phi-rep2

source_name: brain, T4, Phi, rep2


title: PBMC-T1_Phi-rep1

source_name: PBMC, T1, Phi, rep1


title: brain-T3_AO-rep3

source_name: brain, T3, AO, rep3


title: brain-T3_AO-rep2

source_name: brain, T3, AO, rep2


title: brain-T3_AO-rep1

source_name: brain, T3, AO, rep1


title: brain-T1h30_AO-rep2

source_name: brain, T1h30, AO, rep2


title: brain-T1h30_AO-rep3

source_name: brain, T1h30, AO, rep3


title: brain-T3_Phi-rep2

source_name: brain, T3, Phi, rep2


title: brain-T3_Phi-rep1

source_name: brain, T3, Phi, rep1


title: brain-T1h30_Phi-rep1

source_name: brain, T1h30, Phi, rep1


title: brain-T1h30_Phi-rep2

source_name: brain, T1h30, Phi, rep2


title: brain-T1h30_AO-rep1

source_name: brain, T1h30, AO, rep1


title: brain-T1_AO-rep1

source_name: brain, T1, AO, rep1


title: brain-T1h30_Phi-rep3

source_name: brain, T1h30, Phi, rep3


title: brain-T1_AO-rep3

source_name: brain, T1, AO, rep3


title: lung-T24_AO-rep1

description: Lung gene expression of mouse after injection of oleic acid

source_name: lung, T24, AO, rep1

extract_protocol: Total RNA from lung were isolated using trizol.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: lung


title: brain-T1_Phi-rep3

source_name: brain, T1, Phi, rep3


title: brain-T1_AO-rep2

source_name: brain, T1, AO, rep2


title: lung-T24_AO-rep3

source_name: lung, T24, AO, rep3


title: brain-T1_Phi-rep2

source_name: brain, T1, Phi, rep2


title: lung-T18_AO-rep3

source_name: lung, T18, AO, rep3


title: brain-T1_Phi-rep1

source_name: brain, T1, Phi, rep1


title: lung-T18_AO-rep1

source_name: lung, T18, AO, rep1


title: lung-T4_Phi-rep2

description: Lung gene expression of mouse after injection of physiological serum

source_name: lung, T4, Phi, rep2


title: lung-T4_AO-rep3

source_name: lung, T4, AO, rep3


title: lung-T24_AO-rep2

source_name: lung, T24, AO, rep2


title: lung-T24_Phi-rep2

source_name: lung, T24, Phi, rep2


title: lung-T18_Phi-rep2

source_name: lung, T18, Phi, rep2


title: lung-T18_Phi-rep1

source_name: lung, T18, Phi, rep1


title: CEN-glucose-round2

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: CEN-glucose-round2 sample vs. FY4

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2010-11-09 Scan Time : 11:29:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file
Data normalization : default Agilent settings

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : DNA
Extraction method : Nib and Grab

tag: strain/background

tag: genotype

value: wild type

growth_protocol: limiting nutrient : glucose

value: CEN library

tag: limiting nutrient

value: glucose

tag: replicate


title: lung-T18_AO-rep2

source_name: lung, T18, AO, rep2


title: lung-T3_AO-rep3

source_name: lung, T3, AO, rep3


title: lung-T4_AO-rep1

source_name: lung, T4, AO, rep1


title: CEN-glucose-round1

description: CEN-glucose-round1 pDNA from sample collected at generation 50 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2010-10-19 Scan Time : 09:57:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf


title: lung-T4_Phi-rep1

source_name: lung, T4, Phi, rep1


title: lung-T3_AO-rep2

source_name: lung, T3, AO, rep2


title: lung-T3_AO-rep1

source_name: lung, T3, AO, rep1


title: lung-T4_AO-rep2

source_name: lung, T4, AO, rep2


title: CEN-phosphate-round2

description: CEN-phosphate-round2 final vs. FY4

growth_protocol: limiting nutrient : phosphate

value: phosphate


title: CEN-phosphate-round1

description: CEN-phosphate-round1, pDNA from sample collected at generation 50 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2010-10-12 Scan Time : 11:34:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: CEN-sulfate-round2

description: CEN-sulfate-round2 vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2010-11-23 Scan Time : 09:21:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

growth_protocol: limiting nutrient : sulfate

value: sulfate


title: lung-T24_Phi-rep1

source_name: lung, T24, Phi, rep1


title: mutant, biological rep3

city: Wuhan

first: Xiaolei

last: Fan

state: Hubei

address: Shizishan Street, Hongshan District

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Expression measures for each probe set were obtained by employing the robust multi-array average (RMA) method in R environment with Bioconductor Affy package.

label: Biotin

organism: Oryza sativa

source_name: japonica rice cultivar Zhonghua11, OsSLAC7 T-DNA insertion mutant

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

growth_protocol: Both the mutant and widetype plants were planted in a greenhouse (14 h day 28°C; 10 h night 20°C) before being moved to the field (Wuhan).

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

treatment_protocol: Untreated

tag: cultivar

value: flag leaves

tag: genotype/variation

value: OsSLAC7 T-DNA insertion mutant


title: lung-T1h30_AO-rep2

source_name: lung, T1h30, AO, rep2

value: oleic acid

tag: time (h)

value: Female


title: lung-T1h30_Phi-rep1

source_name: lung, T1h30, Phi, rep1

tag: age (week)


title: S6 evolution Pop12-day33

description: S61233pop (rad51 evolved mutant in sulfate) DNA vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-02-28 Scan Time : 09:56:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: S6 evolution Pop12-day33


title: lung-T3_Phi-rep2

source_name: lung, T3, Phi, rep2


title: CEN-sulfate-round1

description: CEN-sulfate-round1 pDNA from sample collected at generation 50 vs. FY4


title: lung-T1h30_AO-rep3

source_name: lung, T1h30, AO, rep3


title: wildtype, biological rep1

source_name: japonica rice cultivar Zhonghua11, wildtype

value: wildtype


title: S61133pop vs. FY4

description: S61133pop (rad51 evolved mutant in sulfate) vs. FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-05 Scan Time : 08:45:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: wildtype, biological rep3


title: wildtype, biological rep2


title: lung-T1_AO-rep3

source_name: lung, T1, AO, rep3


title: mutant, biological rep1


title: mutant, biological rep2


title: DEX::CRL1 line 3, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after dexamethasone treatment

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 3, 4 hours after dexamethasone treatment.

hyb_protocol: All steps of Microarray hybridization and data processing were performed according manufacturer’s instructions (Affymetrix). Equipments were provided by Affymetrix Company. Twelve μg of biotin-labelled antisens RNAs were fragmented and hybridized to GeneChip Rice Genome Arrays (Affymetrix) for 16h at 45°C and 60rpm in a Hybridization Oven 645.

scan_protocol: Arrays were washed, labeled with phycoerythrin on the Fluidic Station 450 and read with the Scanner 3000 7G.

data_processing: Data acquisition was done with the GeneChip Command Console. Array pictures were analyzed with MAS5 algorithm of the Expression Console software (Affymetrix).

source_name: crl1 mutant transformed with pINDEX2-CRL1 plasmid, genetic transformation event 3

label_protocol: Antisense RNA strand were biotynilated according the Affymetrix (Affymetrix, CA, USA) IVT Express protocol.

growth_protocol: Dehulled and surface sterilized seeds of Oryza sativa, cv. Taichung65 were cultured in sterile closed pots containing half strength Murashige and Skoog (MS) medium  and were incubated at 26°C under a 12h light/12h dark photoperiod. Seven day-old seedlings were transferred in flasks containing half strength MS liquid medium.

extract_protocol:
The full-length CRL1 (Os03g05510) cDNA was amplified by RT-PCR from RNA extracted from stem base and roots of Oryza sativa cv Taichung 65. CRL1-specific primers containing sequences of restriction sites adapted for the clonings. The obtained CRL1 amplicon was cloned in the SpeI/XhoI restriction sites of the binary vector pINDEX2 (Ouwerkerk et al., 2001, Planta 213, 370-378) to generate the pINDEX2-CRL1. This plasmid was transferred into Agrobacterium tumefaciens strain EHA105. Genetic transformation was performed as previously described (Sallaud et al., 2003, Theor Appl Genet 106, 1396_1408). Single locus and homozygous T2 lines were selected on the basis of the segregation of the antibiotic resistance gene carried by the T-DNA. The induction of CRL1 by dexamathasone was checked by northern blot. The capacity of transgenic lines to produce crown roots 48h after dexamethasone treatment was evaluated. On this base three independent lines expressing CRL1 after dexamethasone treatment (called DXC1, DXC2 and DXC3) were selected. One line transformed with pINDEX2 empty plasmid (called DX) was used as control.
Total RNA was extracted from frozen twenty stem bases using a RNeasy Plant Mini Kit (Quiagen) according to manufacturer’s instructions. Residual genomic DNA was removed with the RNAse-Free DNase Set (Quiagen) during RNA purification. They were quantified with a NanoQuant at 260nm wavelength and analyzed for quality on a BioAnalyzer 2100 (Agilent, CA, USA).

treatment_protocol: One day after transfer of seedlings in liquid culture medium, the medium was supplemented with 10 µM dexamethasone or mock (0,5‰ v:v ethanol). Stem bases were collected 4 and 8 hours after dexamethasone treatment and immediately frozen in liquid nitrogen for RNA extraction.

value: stem bases of 8 day old seedlings

value: Taichung 65

tag: line

value: 4 hours after dexamethasone treatment


title: lung-T1h30_AO-rep1

source_name: lung, T1h30, AO, rep1


title: DEX::CRL1 line 3, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 3, 8 hours after dexamethasone treatment.

value: 8 hours after dexamethasone treatment


title: lung-T1_Phi-rep3

source_name: lung, T1, Phi, rep3

value: physiological serum


title: lung-T1_AO-rep1

source_name: lung, T1, AO, rep1

value: lung


title: lung-T1_AO-rep2

source_name: lung, T1, AO, rep2


title: DEX::CRL1 line 3, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 3, 8 hours after mock treatment.

value: 8 hours after mock treatment


title: DEX::CRL1 line 3, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 3, 4 hours after mock treatment.

value: 4 hours after mock treatment


title: lung-T3_Phi-rep1

source_name: lung, T3, Phi, rep1


title: DEX::CRL1 line 2, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 2, 8 hours after dexamethasone treatment.

source_name: crl1 mutant transformed with pINDEX2-CRL1 plasmid, genetic transformation event 2


title: lung-T1_Phi-rep1

source_name: lung, T1, Phi, rep1


title: DEX::CRL1 line 2, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 2, 8 hours after mock treatment.


title: DEX::CRL1 line 2, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 2, 4 hours after dexamethasone treatment.


title: lung-T1h30_Phi-rep2

source_name: lung, T1h30, Phi, rep2


title: DEX::CRL1 line 1, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 1, 8 hours after dexamethasone treatment.

source_name: crl1 mutant transformed with pINDEX2-CRL1 plasmid, genetic transformation event 1


title: lung-T1_Phi-rep2

source_name: lung, T1, Phi, rep2


title: control line 2, crl1 mutant transformed with empty pINDEX2, 8 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with an empty pINDEX2 plasmid,  8 hours after dexamethasone treatment.


title: DEX::CRL1 line 2, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 2, 4 hours after mock treatment.


title: DEX::CRL1 line 1, crl1 mutant transformed with pINDEX2-CRL1, 8 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 1, 8 hours after mock treatment.


title: DEX::CRL1 line 1, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 1, 4 hours after dexamethasone treatment.


title: HCC017T

city: Taipei

last: Kao

state: Taiwan

address: 125 Lih-Der Road, Peitou District

department: Research

country: Taiwan

institute: Koo Foundation SYS Cancer Center

hyb_protocol: A cocktail was prepared by combining the specific amounts of fragmented cRNA, probe array controls, bovine serum albumin, and herring sperm DNA according to the protocol of the manufacturer. The cRNA cocktail was hybridized to oligonucleotide probes on the U133A array for 16 hours at 45˚C according to the Affymetrix protocol. Immediately following hybridization, the hybridized probe array underwent an automated washing and staining in an Affymetrix GeneChip Fluidics Station 450 using the protocol EukGE-WS2v5.

scan_protocol: U133A arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The expression intensity of each gene was determined by scaling to a trimmed-mean of 500 using the Affymetrix Microarray Analysis Suite (MAS) 5.0 software. The scaled expression intensities of all human genes on a U133A array were logarithmically transformed to the base 2, and normalized using quantile normalization.

source_name: hepatocellular carcinoma

label_protocol: Biotin-labeled complementary RNA (cRNA) hybridization targets were prepared from 5 ug total RNA by in vitro transcription from cDNA templates according to the Affymetrix protocol. The cRNA was purified and chemically fragmented before hybridization.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: tissue type

value: hepatocellular carcinoma


title: HCC015N

source_name: adjacent non-tumorous liver

value: adjacent non-tumorous liver


title: control line 1, crl1 mutant, 8 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant 8 hours after mock treatment.

source_name: crl1 mutant

value: crl1 mutant


title: HCC016N


title: DEX::CRL1 line 1, crl1 mutant transformed with pINDEX2-CRL1, 4 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with pINDEX2-CRL1 plasmid, line 1, 4 hours after mock treatment.


title: HCC017N


title: control line 2, crl1 mutant transformed with empty pINDEX2, 8 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with an empty pINDEX2 plasmid,  8 hours after mock treatment.


title: control line 2, crl1 mutant transformed with empty pINDEX2, 4 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with an empty pINDEX2 plasmid,  4 hours after dexamethasone treatment.


title: HCC018N


title: HCC014T


title: control line 1, crl1 mutant, 4 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant 4 hours after dexamethasone treatment.


title: HCC018T


title: control line 1, crl1 mutant, 4 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant 4 hours after mock treatment.


title: HCC013T


title: H9 PluriSIn#2 (20uM)

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

description: Gene expression data from undifferentiated pluripotent stem cells grown on matrigel with mTeSR1 and exposed to PluriSIn#2 for 12 h.

hyb_protocol: Affymetrix protocol, 11ug cRNA.

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4.

data_processing: Affymetrix Expression Console MAS5.

source_name: H9, PluriSIn#2 (20uM)

label_protocol: 200ng total RNA, Affymetrix protocol.

growth_protocol: Cells were grown on matrigel-coated plates using mTeSR1 defined medium (Invitrogen). Cultures were passaged every 4-6 days enzymatically with trypsin-EDTA.

extract_protocol: Total RNA was isolated using 5 Prime RNA isolation kit.

treatment_protocol: Undifferentiated pluripotent stem cells were grown on matrigel with mTeSR1 and exposed to PluriSIn#2 at 20uM with 0.02% DMSO for 12 h.

tag: cell line

tag: cell type

value: undifferentiated human embryonic stem cells


title: HCC012N


title: Normal_IGD_3

type: SRA

city: New York

first: Dan

last: Landau

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
WGBS Alignment: bisulfite-convereted WGBS reads were aligned to the hg19 genome with bsMap using the following parameters -v 10 -f 40 -q 5 -S 1
RRBS Alignment: bisulfite-converted reads were aligned to a MspI-digested hg19 genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Genome_build: hg19
Supplementary_files_format_and_content: extended bed file. [Sample].hg.bed.txt contains counts of high-quality CG and TG at each sampled CpG in [Sample]. Format:<CpG chr hg19>  <CpG position hg19> < CpG strand hg19> <Unmethylated read count  is the number of TGs observed> <Concordantly unmethylated reads in the number of reads supporting the particular CpG that are fully unmethylated in all CpGs covered by the read> <Concordantly unmethylated reads in the number of reads supporting the particular CpG that are fully unmethylated in all CpGs covered by the read> <Discordant reads is the number of reads supporting the particular CpG that are neither fully methylated nor fully unmethylated in all CpGs covered by the read>

source_name: Normal CD19+CD27-IgD+

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing. Each library was aligned to the HG19 (human genome version nineteen) and the original methylation sites were inferred based on cytosine-to-thymine conversion.  WGBS library generation was performed as previously described (Gifford et al., 2013)

value: Normal CD19+CD27-IgD+

tag: disease status

value: healthy


title: CLL007

source_name: CLL cells

value: CLL cells

value: CLL


title: control line 1, crl1 mutant, 8 hours after dexamethasone treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant 8 hours after dexamethasone treatment.

tag: tissue


title: control line 2, crl1 mutant transformed with empty pINDEX2, 4 hours after mock treatment

description: Gene expression data from stem bases of 8 days old seedlings of crl1 mutant transformed with an empty pINDEX2 plasmid,  4 hours after mock treatment.

tag: treatment


title: HCC016T


title: HCC015T


title: HCC010T


title: Normal_IGD_6


title: HCC012T


title: HCC013N


title: HCC014N


title: HCC009N


title: HCC010N


title: Normal_IGD_8


title: HCC008T


title: HCC008N


title: HCC011T


title: HCC011N


title: HCC009T


title: HCC006T


title: Normal_CD19_1

source_name: Normal CD19+ cells

value: Normal CD19+ cells


title: HCC007N


title: CLL169_TP1

source_name: CLL cells time point 1


title: Normal_IGD_3_RRBS


title: HCC007T


title: Normal_IGD_2


title: HCC006N


title: Normal_IGD_11


title: HCC005T


title: Normal_IGD_10


title: Normal_IGD_12


title: HCC005N


title: HCC004T


title: HCC002N


title: Normal_CD27_6

source_name: Normal CD19+CD27+ cells

value: Normal CD19+CD27+ cells


title: HCC003N


title: Normal_CD27_3


title: HCC001N


title: HCC002T


title: Normal_CD27_8


title: Roots Myc -S [MtChip2-12]

city: Dijon

first: Leonardo

last: Casieri

address: 17, rue Sully

institute: INRA

description: Roots Myc -S

hyb_protocol: Microarrays were hybridized at 38°C during 16 to 18 h with 6 μg of Cy3 labelled ds-cDNA in Nimblegen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (Nimblegen Systems, Inc., Madison, WI, USA) for grid alignment and expression data analyses. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

organism: Medicago truncatula

source_name: Roots, mycorrhized, sulfur deficient condition

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 10 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 250 ng random hexamer primers. ds-cDNA was cleaned and labeled in accordance with the Nimblegen Gene Expression Analysis protocol (Nimblegen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A (Promega) at 37°C for 10 min and cleaned using 25:24:1 phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. For Cy3 labeling of cDNA, the Nimblegen One-Color DNA labeling kit was used according to the manufacturer’s guideline detailed in the Gene Expression Analysis protocol (Nimblegen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 2 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, Ipswich, MA, USA) were added and the mix incubated at 37°C for 2h302.5 h. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol/ethanol precipitation.

growth_protocol: Plants were grown in 16 h/8 h day/night cycle at of 23/21°C, respectively. Modified Long Ashton solution was used to fertilize the plants every second day.

extract_protocol: Colected leaf and root samples were immediately frozen in liquid nitrogen and stored at -80°C.  Hundred mg of frozen samples were ground in liquid nitrogen using the Trizol method (Invitrogen, Carlsbad, CA). Total RNAs were purified using the RNeasy Plant kit (Qiagen) according to the manufacturer’s instructions. The genomic DNA was eliminated after treatment with Dnase I for 20 min at 37°C using the DNA-free kit (Ambion, Austin, TX, USA). RNA was checked for purity and degradation by capillary electrophoresis using the Bio-Analyzer Experion (Bio-Rad; RNA Standard Sens kit; RNA StdSens chips). RNA concentration was also determined by spectrometry and only RNAs with an OD260:OD280 ratio of ≥ 1.8 and no discernable degradation were used for microarray experiments.

treatment_protocol: The mycorrhizal fungus Rhizophagus irregularis (ex Glomus intraradices BEG141) was maintained on leek. Leek roots with a mycorhization rate of at least 85% (M value, Trouvelot et al., 1986) were thoroughly washed to remove any trace of soil, cut in 1 cm long pieces and used (50 mg FW/plant) to inoculate the mycorrhized (Myc) plants. Non colonized leek roots were used to inoculate non-mycorrhized (NM) plants

value: Jemalong line A17


title: HCC004N


title: Osmotic stressed replicate 1, dye swap

first: Jonathan

middle: A.

last: Miller

address: 616 NE Northlake Place

department: Microbiology

description: Biological replicate 1 of 3; dye swap

hyb_protocol: Hybridization was performed as per the Agilent 60-mer processing protocol (Sure-Hyb chamber/SSPE wash with the Agilent Stabilization and Drying Solution) using a microhybridization oven (Bellco Biotechnology, Vienland, NJ). 40 pmol Alexa Fluor 555- and Alexa Fluor 647-labeled cDNAs were cohybridized. Following hybridization, slides were washed and dried and stored in nitrogen-purged SmartDesiccator (Terra Universal, Fullerton, CA) until scanning.

scan_protocol: Slides were sent to Center for Array Technologies at the University of Washington (Seattle, WA) and scanned using an Agilent G2565AA microarray scanner.

data_processing: Scanned images were processed by Agilent Feature Extraction software Ver. 7.5.1. using default settings for Agilent arrays, Linear & Lowess method for normalization, and PMT setting of 10, 50, and 100.

label: Alexa Fluor 647

organism: Methylorubrum extorquens AM1

source_name: 5 M sodium chloride-stressed cells, 10 minutes

label_protocol: 5 ug DNase-I treated total RNA and 4 ug random decamers were used for cDNA synthesis incorporating amino allyl dUTP as per Amino Allyl cDNA Labelling Kit (Ambion, Austin, TX). Following overnight ethanol precipitation at -80C and 45 min microcentrifugation at 20,800 x g at 4C, cDNA was coupled to either Alexa Fluor 555 ot Alexa Fluor 647 reactive dye dissolved in 3 uL high quality DMSO.

growth_protocol: Cells were grown on minimal salts medium containing 25 mM methanol in a chemostat (BioFlo 110 Modular Fermentor, New Brunswick Scientific, Edison, NJ) under steady-state conditions at 28C.

extract_protocol: Samples were placed into 1/10 volume ice-cold "Stop Solution" (5% v/v water saturated phenol at pH 7.0, 95% v/v absolute ethanol). Cells were extracted via centrifugation at 4C for 8 min at 4500 x g. RNA was extracted using Qiagen's RNeasy Mini Kit (yeast protocol). Cells were lysed with a Mini-beadbeater 8 (BioSpec Products, Bartlesville, OK) at 4C with 600 uL 0.1-mm zirconium-silica beads (BioSpec Products).

treatment_protocol: 40 ml samples were removed, transferred to 250 ml flasks, and exposed to appropriate stressor; duplicate control samples were removed and left untreated. Samples were placed in shaker at 28C for 10 minutes.

value: Wild type

label: Alexa Fluor 555

source_name: Unstressed cells, 10 minutes


title: Oxidative stressed replicate 2, dye swap

description: Biological replicate 2 of 3; dye swap

source_name: 100 mM hydrogen peroxide-stressed cells, 10 minutes


title: Roots Myc -S [MtChip2-9rew]

description: Roots Myc -S


title: Osmotic stressed replicate 2

description: Biological replicate 2 of 3


title: Osmotic stressed replicate 3, dye swap

description: Biological replicate 3 of 3; dye swap


title: Oxidative stressed replicate 3, dye swap

description: Biological replicate 3 of 3; dye swap


title: Osmotic stressed replicate 1

description: Biological replicate 1 of 3


title: Normal_CD27_4


title: Osmotic stressed replicate 2, dye swap

description: Biological replicate 2 of 3; dye swap


title: Oxidative stressed replicate 1, dye swap

description: Biological replicate 1 of 3; dye swap


title: Oxidative stressed replicate 3

description: Biological replicate 3 of 3


title: HCC003T


title: Roots Myc -S [MtChip2-11]

description: Roots Myc -S


title: Roots Myc -S [MtChip2-8]

description: Roots Myc -S


title: Roots Myc -S [MtChip2-10]

description: Roots Myc -S


title: Normal_CD27_2


title: Normal_CD19_7


title: Normal_CD27_10


title: HCC001T


title: Osmotic stressed replicate 3

description: Biological replicate 3 of 3


title: Formaldehyde stressed replicate 3

description: Biological replicate 3 of 3

source_name: 15 mM formaldehyde-stressed cells, 10 minutes


title: Roots Myc +S [MtChip2-5]

description: Roots Myc +S

source_name: Roots, mycorrhized, normal sulfur condition


title: Normal_CD27_12


title: Formaldehyde stressed replicate 2, dye swap

description: Biological replicate 2 of 3; dye swap


title: Oxidative stressed replicate 2

description: Biological replicate 2 of 3


title: Formaldehyde stressed replicate 1, dye swap

description: Biological replicate 1 of 3; dye swap


title: Roots Myc -S [MtChip2-7rew]

description: Roots Myc -S


title: Formaldehyde stressed replicate 1

description: Biological replicate 1 of 3


title: Oxidative stressed replicate 1

description: Biological replicate 1 of 3


title: Roots Myc +S [MtChip2-6]

description: Roots Myc +S


title: Roots Myc +S [MtChip2-1]

description: Roots Myc +S


title: Normal_CD19_4


title: Normal_CD27_11


title: Normal_CD19_6


title: Normal_CD19_8


title: Normal_CD19_3


title: Formaldehyde stressed replicate 3, dye swap

description: Biological replicate 3 of 3; dye swap


title: Normal_CD19_12


title: GICLRefMIX vs. OE19 GICL

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

department: Medicine

institute: UCLA

hyb_protocol: In comparison of expression between each gastric cancer cell line and a reference mix pool composed of equal amount of all the gastric cancer cell lines list under column Sample name plus IM98m. 825 ng each of labeled reference mix  (GICLRefMix, cy3 label) and individual gastric cancer cell  line (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent G2505C scanner with extended dynamic range. Images were quantified using Agilent Feature Extraction Software version A.9.5.1 or version  10.7.3.1 refer to raw data file column.

data_processing:
Agilent Feature Extraction Software was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used  to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging.
In Rosetta analysis, setting for cluster Algoritm is list here and applies to both sample experiment and sequence.  Algorithm=Agglomerative, Algorithm parameters: Heuristic criteria=Average link, Similarity measure metric type=Cosine correlation.
In Rosetta analysis, setting for statistical cuts is list here to generate the cluster.  Thresholds=equal or bigger than 2 fold change with P-value equal or less than 0.01. Number of experiment cut is not applied.

source_name: GICL Reference Mix

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

growth_protocol:
Gastric cancer cell lines were cultured in recommended media following manufacture's instruction.
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were characterized using mtDNA sequence prior to use.

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

value: gastric cancer cell lines

source_name: OE19 GICL

value: Gastric cancer cell line


title: GICLRefMIX vs. SNU-1 GICL

source_name: SNU-1 GICL


title: GICLRefMIX vs. NUGC3 GICL

source_name: NUGC3 GICL


title: Roots Myc +S [MtChip2-2]

description: Roots Myc +S


title: GICLRefMIX vs. OE33 GICL

source_name: OE33 GICL


title: Formaldehyde stressed replicate 2

description: Biological replicate 2 of 3


title: Roots NM -S [MtChip1-10]

description: Roots NM -S

source_name: Roots, non-mycorrhized, sulfur deficient condition


title: GICLRefMIX vs. SNU-16 GICL

source_name: SNU-16 GICL


title: Roots NM -S [MtChip1-11]

description: Roots NM -S


title: GICLRefMIX vs. SNU-5 GICL

source_name: SNU-5 GICL


title: GICLRefMIX vs. NCI N87 GICL

source_name: NCI N87 GICL

value: NCI N87


title: Roots NM -S [MtChip1-9]

description: Roots NM -S


title: GICLRefMIX vs. NUGC4 GICL

source_name: NUGC4 GICL


title: Roots Myc +S [MtChip2-3]

description: Roots Myc +S


title: GICLRefMIX vs. MKN74 GICL

source_name: MKN74 GICL


title: Normal_CD19_10

source_name: Normal CD19+ cells


title: Normal_CD19_11


title: Normal_CD19_2


title: NORMAL_9


title: GICLRefMIX vs. MKN45 GICL

source_name: MKN45 GICL


title: NORMAL_8


title: CLL090

source_name: CLL cells


title: Roots NM -S [MtChip1-8]

description: Roots NM -S


title: GICLRefMIX vs. KATO III GICL

source_name: KATO III GICL

value: KATO III


title: Roots NM -S [MtChip1-7]

description: Roots NM -S


title: GICLRefMIX vs. FU97 GICL

source_name: FU97 GICL


title: GICLRefMIX vs. MKN1 GICL

source_name: MKN1 GICL


title: CLL036


title: Roots NM +S [MtChip1-1]

description: Roots NM +S

source_name: Roots, non-mycorrhized, normal sulfur condition


title: GICLRefMIX vs. AGS GICL

source_name: GICL Reference Mix

source_name: AGS GICL

value: AGS


title: GICLRefMIX vs. IM95 GICL

source_name: IM95 GICL


title: CLL035


title: CLL060


title: Leaves NM -S [MtChip3-11]

description: Leaves NM -S

source_name: Leaves, non-mycorrhized, sulfur deficient condition


title: Roots NM +S [MtChip1-2]

description: Roots NM +S


title: Leaves NM -S [MtChip3-12]

description: Leaves NM -S


title: MDA-MB-468_rep2

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

description: gene expression in  cancer cell lines

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 7.3.1 and default normalization procedures were used.

source_name: breast cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated an Rneasy kit (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: ZR75-1_rep3

description: gene expression in  cancer cell lines


title: SKBR-3_rep2

description: gene expression in  cancer cell lines


title: MCF-7_rep1

description: gene expression in  cancer cell lines


title: SKBR-3_rep3

description: gene expression in  cancer cell lines


title: Leaves NM -S [MtChip3-10]

description: Leaves NM -S


title: Leaves NM -S [MtChip3-9]

description: Leaves NM -S


title: MCF-7_rep3

description: gene expression in  cancer cell lines


title: Leaves NM -S [MtChip3-8]

description: Leaves NM -S


title: ZR75-1_rep1

description: gene expression in  cancer cell lines


title: MDA-MB-468_rep1

description: gene expression in  cancer cell lines


title: MDA-MB-468_rep3

description: gene expression in  cancer cell lines


title: ZR75-1_rep2

description: gene expression in  cancer cell lines


title: MCF-7_rep2

description: gene expression in  cancer cell lines


title: SKBR-3_rep1

description: gene expression in  cancer cell lines


title: CLL030_TP2

source_name: CLL cells time point 2

value: CLL cells time point 2


title: CLL030_TP1

source_name: CLL cells time point 1

value: CLL cells time point 1


title: CLL027


title: CLL028


title: MDA-MB-435_rep3

description: gene expression in  cancer cell lines


title: CLL024


title: Leaves NM -S [MtChip3-7]

description: Leaves NM -S


title: Leaves NM +S [MtChip3-6]

description: Leaves NM +S

source_name: Leaves, non-mycorrhized, normal sulfur condition


title: Roots Myc +S [MtChip2-4]

description: Roots Myc +S

source_name: Roots, mycorrhized, normal sulfur condition


title: MDA-MB-435_rep1

description: gene expression in  cancer cell lines


title: Leaves NM +S [MtChip3-2]

description: Leaves NM +S


title: Leaves NM +S [MtChip3-3]

description: Leaves NM +S


title: SK-EV-C4._rep1

description: gene expression in  cancer cell lines


title: Leaves NM +S [MtChip3-4]

description: Leaves NM +S


title: MDA-MB-231_rep1

description: gene expression in  cancer cell lines


title: SKBR-3/ b1_rep1

description: gene expression in  cancer cell lines

value: SKBR-3/ b1


title: Leaves NM +S [MtChip3-1]

description: Leaves NM +S


title: Leaves Myc -S [MtChip4-12]

description: Leaves Myc -S

source_name: Leaves, mycorrhized, sulfur deficient condition


title: MDA-MB-231_rep3

description: gene expression in  cancer cell lines


title: SKBR-3/ b1_rep3

description: gene expression in  cancer cell lines


title: MDA-MB-231_rep2

description: gene expression in  cancer cell lines


title: MDA-MB-435_rep2

description: gene expression in  cancer cell lines


title: SK-EV-C4._rep2

description: gene expression in  cancer cell lines


title: SK-EV-C4._rep3

description: gene expression in  cancer cell lines


title: SK-B1-C1_rep1

description: gene expression in  cancer cell lines


title: SKBR-3/ EV_rep3

description: gene expression in  cancer cell lines

value: SKBR-3/ EV


title: CLL020_TP2


title: CLL023


title: CLL022


title: CLL020_TP1


title: CLL169_TP2


title: CLL032


title: SK-B1-C1_rep2

description: gene expression in  cancer cell lines


title: CLL169_TP1_RRBS


title: SK-B1-C1_rep3

description: gene expression in  cancer cell lines


title: Leaves Myc -S [MtChip4-10rew]

description: Leaves Myc -S


title: SKBR-3/ EV_rep1

description: gene expression in  cancer cell lines


title: SKBR-3/ b1_rep2

description: gene expression in  cancer cell lines


title: CLL019_TP2


title: SKBR-3/ EV_rep2

description: gene expression in  cancer cell lines


title: Leaves Myc -S [MtChip4-8]

description: Leaves Myc -S


title: Leaves Myc -S [MtChip4-9]

description: Leaves Myc -S


title: GICLRefMIX vs. MKN7 GICL

source_name: MKN7 GICL


title: Leaves Myc -S [MtChip4-7]

description: Leaves Myc -S


title: 7750

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 14 pmol; Cy5 label: 10 pmol) was hybridised on the array followed by (manual) washing, according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with SureScan High-Resolution Technology and probe signals were quantified using Agilent's Feature Extraction software (version 10.1.1.1).

data_processing: Within arrays: The analysis is based on the expression values as obtained from the Agilent Feature Extraction (FE) Software. We use feature gProcessedSignal for the Cy3 signal and feature rProcessedSignal for the Cy5 signal. The intensities are log2-transformed. Between arrays: Since we assume that the expression of the majority of the probes should stay more or less the same on all arrays and channels (such that the global distributions of expression values hardly differ), we normalize the data by quantile normalization (Bolstad et al. (2003)) of the intensities, using the R package preprocessCore. From these normalized intensities, we compute the log-ratios (Cy5/Cy3).

source_name: 57-MT4 IFNa 6h

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 500 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

extract_protocol: QIAgen RNeasy kit. Protocols were carried out according to the manufacturer's instructions.

value: HTLV-1-infected CD4+ T cells

value: IFN-a (1000 IU/ml) for 6 hours

source_name: 58-MT4 A+IFNa 6h

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 500 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer's protocol (Agilent).

value: A + IFN-a for 6 hours


title: Leaves Myc +S [MtChip4-6]

description: Leaves Myc +S

source_name: Leaves, mycorrhized, normal sulfur condition


title: 7748

source_name: 52-MT2 A+IFNa 6h

value: A (5 µg/ml) for 6 hours


title: Leaves Myc +S [MtChip4-5]

description: Leaves Myc +S


title: 7744

source_name: 45-MT4 IFNa 6h

source_name: 46-MT4 A+IFNa 6h


title: CLL019_TP1

value: CLL


title: Leaves Myc +S [MtChip4-4]

description: Leaves Myc +S


title: 7749


title: 7747

source_name: 51-MT2 IFNa 6h


title: 7746


title: 7751


title: CLL018_TP2


title: 7745


title: CLL018_TP1


title: CLL016_TP2


title: CLL168

source_name: CLL cells

value: CLL cells


title: 7739

value: Q3 (1 µg/ml) for 6 hours

value: untreated for 6 hours


title: Leaves Myc +S [MtChip4-2]

description: Leaves Myc +S

value: Jemalong line A17


title: 7742

source_name: 40-MT2 A+IFNa 6h


title: 7743


title: 7741

source_name: 39-MT2 IFNa 6h


title: 7738

value: Q2 (10 µg/ml) for 6 hours


title: Leaves Myc +S [MtChip4-3]

description: Leaves Myc +S


title: 7736

source_name: JVW 49-MT2 C 6h


title: CLL014_TP2

source_name: CLL cells time point 2


title: CLL016_TP1

source_name: CLL cells time point 1


title: Leaves Myc +S [MtChip4-1]

description: Leaves Myc +S


title: 7740


title: 7735


title: CLL015


title: Leaves NM +S [MtChip3-5]

description: Leaves NM +S

source_name: Leaves, non-mycorrhized, normal sulfur condition


title: 7733


title: 7729


title: 7737


title: 7728


title: 255290910120_1_4

city: Beijing

first: Qingsheng

last: Yu

address: No 2, East Yinghua Rd, Chaoying District

institute: China-Japan Friendship Institute of Clinical Medical Sciences

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: cells cultured in vitro_untreated

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

growth_protocol: Cells were cultured in Dulbecco's phosphate-buffered saline (D-PBS; Solarbio Life Sciences, Beijing, China) , and plated in 100mm gelatin-coated culture dishes (Corning, New York, NY) containing M199 medium supplemented with 2 mM L-glutamine, 100 μg/mL streptomycin and 100 IU/mL penicillin (AMRESCO LLC, Solon, OH), 20% fetal bovine serum (FBS, Gibco), and recombinant human vascular endothelial growth factor 165 (rhVEGF 165, Sino Biological Inc., Beijing, China). Medium was changed after 24 h to remove nonadherent cells and then two times per week.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: At day 15, cells were detached using 0.25% trypsin/EDTA at 37°C and duplicated to 60mm gelatin-coated culture dishes. After 7 days, one copy of cells were treated with 0.1 mg/ml hydrocortisone (Tianjin Kingyork Group Co. Ltd., Tianjin, China) for 24 hours as experimental study. The other copy of cells from the same subject were left untreated as paired control.

tag: gender

value: female

tag: age

value: bone microcirculatory endothelial cell

tag: treated with

value: none (control)

source_name: cells cultured in vitro_hydrocortisone-treated

value: 0.1 mg/ml hydrocortisone for 24hr


title: 255290910150_1_4


title: 7732


title: 7734


title: CLL167_TP2

value: CLL cells time point 2


title: CLL167_TP1

value: CLL cells time point 1


title: 7731


title: CLL025


title: CLL012


title: CLL001_TP1


title: 7177

source_name: 11-MT4 A+IFNa 6h

extract_protocol: Norgen's Total RNA Purification kit, followed by re-purification with the QIAgen RNeasy kit. Protocols were carried out according to the manufacturer's instructions.

source_name: 9-MT4 IFNa 6h


title: 255290910132_1_4


title: 7043

source_name: 15-MT4 IFNa 6h


title: 7042

source_name: 17-MT4 A+IFNa 6h


title: 7176


title: 7175

source_name: 10-MT4 IFNb 6h

value: IFN-b (1000 IU/ml) for 6 hours

source_name: 7-MT4 C 6h


title: 7174

source_name: 3-MT2 IFNa 6h

value: HTLV-1-infected CD4+ T cells

source_name: 1-MT2 C 6h


title: 255290910117_1_4


title: 7730


title: 255290910120_1_3


title: 255290910114_1_4

value: male


title: 255290910049_1_2


title: 7041

value: A + IFN-a for 6 hours


title: CLL001_TP2


title: CLL011_TP2


title: 7040

value: IFN-a (1000 IU/ml) for 6 hours


title: 7035

source_name: 8-MT4 A 6h

value: A (5 µg/ml) for 6 hours


title: CLL093

source_name: CLL cells

value: CLL cells

value: CLL


title: CLL011_TP1


title: 255290910049_1_1


title: PVX infected chrysanthemum sample_3

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Samples were harvested at three days after virus infection

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

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

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

organism: Chrysanthemum

source_name: One-month old chrysanthemum plants which were propaged by cutting

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

growth_protocol: Plants were grown in green house with normal growth condition.

extract_protocol: Total RNAs were extracted by using Qiagen RNeasy Mini Kit.

treatment_protocol: Virus infection was performed by sap inoculation.

tag: infection

value: PVX infected

value: whole plant

tag: strain

value: Chrysanthemum (Dendranthema X grandiflora)


title: PVX infected chrysanthemum sample_2


title: 7036


title: 7038

source_name: 16-MT4 IFNb 6h

value: untreated for 6 hours


title: CLL161


title: PVX infected chrysanthemum sample_1


title: 7037


title: CLL160


title: 7033


title: 7032


title: CLL159


title: TSWV infected chrysanthemum sample_2

value: TSWV infected


title: 7039


title: TSWV infected chrysanthemum sample_1


title: 7026

source_name: 4-MT2 IFNb 6h


title: 7028


title: 7029

source_name: 5-MT2 A+IFNa 6h

source_name: 2-MT2 A 6h


title: 7030


title: 7027


title: TSWV infected chrysanthemum sample_3


title: CMV infected chrysanthemum sample_2

value: CMV infected


title: CLL158


title: CLL008


title: CLL157


title: CLL092


title: CMV infected chrysanthemum sample_1


title: CLL156


title: CMV infected chrysanthemum sample_3


title: CLL155


title: CLL154


title: Mock (buffer) treated chrysanthemum sample_2

description: Samples were harvested at three days after treatment

value: Mock (buffer) treated


city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: Gene expression data whole blood rituximab treated week 24 sample 95 non-responder

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The data were preprocessed and analyzing using Partek Genomic Suite.

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

tag: tissus

value: whole blood

value: rituximab treated week 24

tag: sample

tag: response

value: non-responder


description: Gene expression data whole blood rituximab treated baseline sample 91 moderate-responder

value: rituximab treated baseline

value: moderate-responder


title: CLL153


title: Mock (buffer) treated chrysanthemum sample_3


description: Gene expression data whole blood rituximab treated baseline sample 95 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 86 responder

value: responder


title: CLL152


description: Gene expression data whole blood rituximab treated baseline sample 86 responder


title: Leaf-ZC_spring_rep3

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

description: Gene expression in spring

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Camellia sinensis 44K custom array (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as "Detected" were maintained.

organism: Camellia sinensis

source_name: fresh shoots, Zhongcha 108, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Four tea plant cultivars, "Longjing 43", "Zhongcha 108", "Zhonghuang 1" and "Zhonghuang 2" were grown in the China National Germplasm Hangzhou Tea Repository (CNGHTR) at the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS).

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's.

treatment_protocol: In the spring, the fresh shoots (two and a bud) were sampled from the four cultivars.

value: fresh shoots (two and a bud)

tag: sampling season

value: spring


title: Mock (buffer) treated chrysanthemum sample_1


description: Gene expression data whole blood rituximab treated week 24 sample 83 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 91 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 7 responder


description: Gene expression data whole blood rituximab treated week 24 sample 78 moderate-responder


title: 7031

value: HTLV-1-infected CD4+ T cells

value: A (5 µg/ml) for 6 hours

value: IFN-a (1000 IU/ml) for 6 hours


description: Gene expression data whole blood rituximab treated baseline sample 7 responder


description: Gene expression data whole blood rituximab treated baseline sample 78 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 76 non-responder


title: Leaf-ZC_spring_rep1

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

description: Gene expression in spring

source_name: fresh shoots, Zhongcha 108, replicate 1


description: Gene expression data whole blood rituximab treated baseline sample 83 moderate-responder


title: Leaf-ZH1_spring_rep3

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 1, replicate 3


title: CLL014_TP1

source_name: CLL cells time point 1

value: CLL cells time point 1

value: CLL


title: CLL150

value: CLL cells


title: 7034

value: untreated for 6 hours

source_name: 9-MT4 IFNa 6h


title: CLL151


title: Leaf-ZH1_spring_rep2

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 1, replicate 2


description: Gene expression data whole blood rituximab treated week 24 sample 68 responder


description: Gene expression data whole blood rituximab treated baseline sample 68 responder


description: Gene expression data whole blood rituximab treated week 24 sample 67 non-responder


title: CLL007_RRBS


description: Gene expression data whole blood rituximab treated week 24 sample 63 non-responder


title: Leaf-ZH2_spring_rep3

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 2, replicate 3


description: Gene expression data whole blood rituximab treated baseline sample 67 non-responder


title: Leaf-ZH1_spring_rep1

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 1, replicate 1


title: CLL148


description: Gene expression data whole blood rituximab treated week 24 sample 60 responder


description: Gene expression data whole blood rituximab treated baseline sample 63 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 60 responder


title: CLL146


title: CLL147


title: CLL145


title: CLL144


title: CLL141


title: Leaf-ZH2_spring_rep2

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 2, replicate 2


description: Gene expression data whole blood rituximab treated baseline sample 54 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 54 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 45 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 53 responder


description: Gene expression data whole blood rituximab treated baseline sample 76 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 47 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 53 responder


description: Gene expression data whole blood rituximab treated week 24 sample 52 non-responder


title: Leaf-LJ_spring_rep3

description: Gene expression in spring

source_name: fresh shoots, Longjing 43, replicate 3


description: Gene expression data whole blood rituximab treated baseline sample 52 non-responder


title: Leaf-ZH2_spring_rep1

description: Gene expression in spring

source_name: fresh shoots, Zhonghuang 2, replicate 1


description: Gene expression data whole blood rituximab treated baseline sample 47 non-responder


title: Leaf-LJ_spring_rep1

description: Gene expression in spring

source_name: fresh shoots, Longjing 43, replicate 1


title: Leaf-LJ_spring_rep2

description: Gene expression in spring

source_name: fresh shoots, Longjing 43, replicate 2


title: CLL140

source_name: CLL cells


title: CLL170


description: Gene expression data whole blood rituximab treated week 24 sample 3 responder


description: Gene expression data whole blood rituximab treated baseline sample 3 responder


description: Gene expression data whole blood rituximab treated baseline sample 323 non-responder


title: CLL139


title: CLL138


title: CLL088_TP2

source_name: CLL cells time point 2

value: CLL cells time point 2


description: Gene expression data whole blood rituximab treated baseline sample 45 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 323 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 320 responder


description: Gene expression data whole blood rituximab treated baseline sample 320 responder


title: CLL088_TP1


description: Gene expression data whole blood rituximab treated baseline sample 314 moderate-responder


description: Gene expression data whole blood rituximab treated week 24 sample 313 non-responder


title: CLL137


description: Gene expression data whole blood rituximab treated week 24 sample 314 moderate-responder


title: CLL133


title: HSF-G

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: ChIP-chip HSF-G cells CENP-A

hyb_protocol: Manufacturer's NimbleScan Protocol.

scan_protocol: Manufacturer's NimbleScan Protocol.

data_processing: Manufacturer's NimbleScan Protocol.

organism: Equus caballus

source_name: CENP-A ChIP DNA from HSF-G cells

label_protocol: Standard NimbleGen protocol.

extract_protocol: 2x10E6 cells were harvested using trypsin and washed in PBS. The cells were lysed in 5ml of Buffer I (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 0.5 mM Spermidine, 0.2 mM EDTA, 250 uM PMSF) and 5 ml of Buffer II (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 0.5 mM Spermidine, 0.2 mM EDTA, 250 uM PMSF, 0.1% NP-40). Nuclei were washed and resuspended in Buffer III (85 mM KCl, 5.5% sucrose, 10 mM Tris pH 7.6, 1.5 mM CaCl2, 3 mM MgCl2, 250 uM PMSF). Nuclei were digested with MNase (60 units/ml) and RNase A (3ug/ml) for 20 minutes at room temperature. Digestion was stopped adding EDTA (10mM final concentration). The supernatant containing the first soluble fraction of chromatin was recovered by centrifugation. After over-night incubation of chromatin in 5 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 5 mM NaCl) on ice, the supernatant containing the second soluble fraction of chromatin was recovered. The chromatin was diluted in 50 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 50 mM NaCl) and pre-cleared with protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 1 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of anti-CENP-A antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 4 h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 15 min at 4C: 140 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 140 mM NaCl) and 200 mM NaCl buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 200 mM NaCl). The protein-DNA complexes were eluted from the beads in 400 µl elution buffer (10 mM Tris pH 7.5, 0.5 mM EDTA, 0.5 mM EGTA, 250 uM PMSF, 0.05% NP-40, 50 mM NaCl, 1% SDS) at room temperature for 30 min. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input using Qiagen PCR Purification kit and was amplified using the Sigma-Aldrich Whole Genome Amplification kit.

value: fibroblasts

source_name: Input DNA from HSF-G cells


description: Gene expression data whole blood rituximab treated week 24 sample 261 moderate-responder

value: whole blood


description: Gene expression data whole blood rituximab treated week 24 sample 307 responder

value: rituximab treated week 24


description: Gene expression data whole blood rituximab treated baseline sample 307 responder


description: Gene expression data whole blood rituximab treated baseline sample 259 moderate-responder


description: Gene expression data whole blood rituximab treated baseline sample 261 moderate-responder


description: Gene expression data whole blood rituximab treated baseline sample 313 non-responder

value: non-responder


title: Leaf-ZC_spring_rep2

description: Gene expression in spring

source_name: fresh shoots, Zhongcha 108, replicate 2


title: CLL136


title: HSF-E

description: ChIP-chip HSF-E cells CENP-A

source_name: CENP-A ChIP DNA from HSF-E cells

source_name: Input DNA from HSF-E cells


title: HSF-C

description: ChIP-chip HSF-C cells CENP-A

source_name: CENP-A ChIP DNA from HSF-C cells

source_name: Input DNA from HSF-C cells


title: CLL134


description: Gene expression data whole blood rituximab treated baseline sample 245 responder

value: rituximab treated baseline


title: CLL130


title: HSF-D

description: ChIP-chip HSF-D cells CENP-A

source_name: CENP-A ChIP DNA from HSF-D cells

source_name: Input DNA from HSF-D cells


description: Gene expression data whole blood rituximab treated week 24 sample 255 moderate-responder

value: moderate-responder


description: Gene expression data whole blood rituximab treated baseline sample 271 responder

value: responder


description: Gene expression data whole blood rituximab treated week 24 sample 271 responder


description: Gene expression data whole blood rituximab treated week 24 sample 251 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 245 responder


description: Gene expression data whole blood rituximab treated week 24 sample 242 responder


title: CLL126


description: Gene expression data whole blood rituximab treated week 24 sample 244 responder


description: Gene expression data whole blood rituximab treated baseline sample 255 moderate-responder


description: Gene expression data whole blood rituximab treated baseline sample 251 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 244 responder


title: CLL129


title: CLL128


description: Gene expression data whole blood rituximab treated week 24 sample 259 moderate-responder


title: CLL125


description: Gene expression data whole blood rituximab treated week 24 sample 230 moderate-responder


description: Gene expression data whole blood rituximab treated baseline sample 242 responder


title: CLL124


description: Gene expression data whole blood rituximab treated baseline sample 229 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 230 moderate-responder


title: HSF-B

description: ChIP-chip HSF-B cells CENP-A

source_name: CENP-A ChIP DNA from HSF-B cells

source_name: Input DNA from HSF-B cells


title: CLL006_TP2


title: CLL006_TP1

source_name: CLL cells time point 1


title: 254606412359_2_2

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

source_name: bone microcirculatory endothelial cell_hydrocortisone treated

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

tag: subject age

tag: subject gender

value: female

value: bone microcirculatory endothelial cells

tag: culture type

value: cells cultured in vitro

value: 0.1 mg/ml hydrocortisone for 24hrs


title: CLL123


title: 254606412359_2_1

source_name: bone microcirculatory endothelial cell_untreated

value: none (untreated control)


title: 254606412359_1_1


description: Gene expression data whole blood rituximab treated baseline sample 227 non-responder


title: CLL105


title: 254606412358_2_4


description: Gene expression data whole blood rituximab treated week 24 sample 229 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 21 moderate-responder


title: 254606412358_2_3


description: Gene expression data whole blood rituximab treated week 24 sample 227 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 217 responder


description: Gene expression data whole blood rituximab treated baseline sample 220 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 21 moderate-responder


title: 254606412359_1_2


description: Gene expression data whole blood rituximab treated week 24 sample 211 responder


title: CLL104


description: Gene expression data whole blood rituximab treated baseline sample 217 responder


title: CLL083


description: Gene expression data whole blood rituximab treated baseline sample 211 responder


title: 254606412358_2_1


description: Gene expression data whole blood rituximab treated week 24 sample 215 responder


title: CLL087


description: Gene expression data whole blood rituximab treated week 24 sample 209 non-responder


description: Gene expression data whole blood rituximab treated week 24 sample 220 non-responder


title: CLL103


description: Gene expression data whole blood rituximab treated baseline sample 215 responder


description: Gene expression data whole blood rituximab treated week 24 sample 207 responder


title: CLL080


title: CLL077


title: 254606412358_1_3


title: 254606412358_1_4


title: CLL075


description: Gene expression data whole blood rituximab treated baseline sample 209 non-responder


description: Gene expression data whole blood rituximab treated baseline sample 207 responder


title: 254606412358_1_2

value: male


title: CLL131

value: CLL


description: Gene expression data from whole blood rituximab treated baseline sample 206 responder


description: Gene expression data from whole blood rituximab treated week 24 sample 206 responder


description: Gene expression data from whole blood rituximab treated baseline sample 19 responder


title: CLL074

value: CLL cells


title: CLL044


description: Gene expression data from whole blood rituximab treated week 24 sample 196 non-responder


title: 254606412358_1_1


title: CLL073


description: Gene expression data from whole blood rituximab treated week 24 sample 19 responder


title: CLL100


title: CLL120


description: Gene expression data from whole blood rituximab treated week 24 sample 191 non-responder


description: Gene expression data from whole blood rituximab treated baseline sample 186 moderate-responder


title: 254606411733_2_4


title: 254606411733_1_4


title: CLL070


title: 254606411733_1_3


description: Gene expression data from whole blood rituximab treated baseline sample 182 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 174 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 185 moderate-responder


title: 8Gy FLASH

city: Fontenay-aux-roses

first: Nathalie

last: Gault

address: 18 rue de Panorama

institute: CEA

description: LT-HSC 15 days post TBI

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: LT-HSC 15 days post TBI

extract_protocol: Total RNA was extracted using Rneasy plus micro kit Qqiagen) according the manufacturer's instructions.

treatment_protocol: 10000 LT-HSCs  were isolated from bone marrow of irradiated and non-irradiated mice  15 days post TBI

value: bone marrow

value: LT-HSC

value: 8-10 weeks


description: Gene expression data from whole blood rituximab treated baseline sample 196 non-responder

value: whole blood


title: CLL119

source_name: CLL cells


description: Gene expression data from whole blood rituximab treated week 24 sample 174 moderate-responder

value: rituximab treated week 24


description: Gene expression data from whole blood rituximab treated baseline sample 171 responder


title: 8Gy CDR

description: LT-HSC 15 days post TBI


description: Gene expression data from whole blood rituximab treated week 24 sample 168 non-responder

value: non-responder


description: Gene expression data from whole blood rituximab treated baseline sample 168 non-responder

value: rituximab treated baseline


title: 254606411733_2_3


description: Gene expression data from whole blood rituximab treated baseline sample 169 non-responder


title: CLL118


description: Gene expression data from whole blood rituximab treated baseline sample 191 non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 182 moderate-responder

value: moderate-responder


title: myoblasts-APC siRNA-biological repl 03

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA was hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix)

scan_protocol: GeneChips were scanned using the affymetrix GCS3000 7G system

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. Affymetrix probe-set data were normalized using the robust multi-array average (RMA) method using R

source_name: siAPC-treated proliferating myoblasts

label_protocol: 2.5μg of Sens Target DNA were fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

growth_protocol: satellite cells-derived myoblasts were cultured on collagen-coated dishes in Ham's-F10 nutrient mix supplemented with 20% FBS and 2.5ng/ul basic FGF

extract_protocol: RNA extraction was performed by using the TRIzol Reagent (Life Technologies) according to manufacturer's instructions. 50 ng of total RNA was reverse transcribed following the Ovation PicoSL WTA System (Nugen). The resulting double strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5ug of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen).

treatment_protocol: Proliferating myoblasts were transfected with siRNA by using Lipofectamine 2000 and Optimem (Life Technologies) following manufacturer's protocol

value: skeletal muscle

value: satellite cells-derived myoblasts


title: CLL069


title: 254606412358_2_2

value: female

value: bone microcirculatory endothelial cells


title: CLL117


description: Gene expression data from whole blood rituximab treated week 24 sample 163 non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 169 non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 171 responder

value: responder


title: CLL068


title: myoblasts-APC siRNA-biological repl 02


title: non-irradiated

description: LT-HSC 15 days post TBI


description: Gene expression data from whole blood rituximab treated week 24 sample 185 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 161 non-responder


title: CLL066_TP2

source_name: CLL cells time point 2

value: CLL cells time point 2


title: CLL067


description: Gene expression data from whole blood rituximab treated baseline sample 163 non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 152 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 161 non-responder


title: CLL066_TP1

value: CLL cells time point 1


title: CLL065

value: CLL


title: myoblasts-control siRNA-biological repl 01

source_name: mock-treated proliferating myoblasts


title: myoblasts-control siRNA-biological repl 03


description: Gene expression data from whole blood rituximab treated baseline sample 148 non-responder


title: myoblasts-control siRNA-biological repl 02


description: Gene expression data from whole blood rituximab treated baseline sample 140 moderate-responder


title: myoblasts-APC siRNA-biological repl 01


description: Gene expression data from whole blood rituximab treated baseline sample 126 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 148 non-responder


description: Gene expression data from whole blood rituximab treated baseline sample 152 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 126 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 1333 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 125 responder


title: CLL062

value: CLL cells


description: Gene expression data from whole blood rituximab treated week 24 sample 140 moderate-responder


title: Seedlings-SWCNHs (25 ug/ml) rep.2

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

description:
Gene expression data from seedlings of 11 day-old tomato - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_280575_Tomato_NL-8

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 11 day old ssedlings of wild type tomato

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)

growth_protocol: Tomato seeds were germinated on MS medium (Magenta boxes) in light and harvested after 1 day and 11 days of cultivation.

extract_protocol: Seeds and seedlings were isolated and immediately frozen in liquid nitrogen. The harvested seeds and seedlings  were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special treatments before harvesting were carried out.

tag: cultivar

value: Micro-Tom

tag: genotype/variation

value: wild type

tag: growth protocol

value: SWCNHs

value: seedlings of 11 day-old tomato


title: Seedlings-SWCNHs (25 ug/ml) rep.3

description:
Gene expression data from seedlings of 11 day-old tomato - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_280576_Tomato_NL-9

tag: tissue


title: CLL005

tag: cell type

tag: disease status


title: CLL061


title: CLL099


title: Seedlings-SWCNHs (25 ug/ml) rep.1

description:
Gene expression data from seedlings of 11 day-old tomato - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_280574_Tomato_NL-7


title: CLL098


description: Gene expression data from whole blood rituximab treated baseline sample 122 non-responder

value: whole blood

tag: treatment


description: Gene expression data from whole blood rituximab treated week 24 sample 122 non-responder

value: rituximab treated week 24

value: non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 115 responder


title: CLL097


description: Gene expression data from whole blood rituximab treated baseline sample 125 responder

value: rituximab treated baseline


title: Seeds-SWCNHs (25 ug/ml) rep.3

description:
Gene expression data from tomato seeds (1 day on SWCNHs medium) - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_278474_Tomato_NS-9

source_name: Seeds of wild type tomato (1 day on SWCNHs medium)

value: seeds


description: Gene expression data from whole blood rituximab treated week 24 sample 117 non-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 1333 moderate-responder

value: moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 102 responder


description: Gene expression data from whole blood rituximab treated week 24 sample 113 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 113 moderate-responder


title: Seeds-SWCNHs (25 ug/ml) rep.1

description:
Gene expression data from tomato seeds (1 day on SWCNHs medium) - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_278472_Tomato_NS-7


description: Gene expression data from whole blood rituximab treated baseline sample 103 responder


description: Gene expression data from whole blood rituximab treated week 24 sample 1041 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 115 responder


description: Gene expression data from whole blood rituximab treated week 24 sample 104 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 1013 moderate-responder


description: Gene expression data from whole blood rituximab treated baseline sample 117 non-responder


description: Gene expression data from whole blood rituximab treated baseline sample 104 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 103 responder


description: Gene expression data from whole blood rituximab treated week 24 sample 186 moderate-responder


title: Seeds-SWCNHs (25 ug/ml) rep.2

description:
Gene expression data from tomato seeds (1 day on SWCNHs medium) - Wild type (cv. Micro-Tom) grown on 25 ug/ml of SWCNHs
EA09092_278473_Tomato_NS-8


title: CLL063


description: Gene expression data from whole blood rituximab treated week 24 sample 102 responder


title: CLL057


description: Gene expression data from whole blood rituximab treated baseline sample 1013 moderate-responder


title: CLL054


description: Gene expression data from whole blood rituximab treated baseline sample 1041 moderate-responder


description: Gene expression data from whole blood rituximab treated week 24 sample 1011 non-responder


title: CLL053


title: HeLa c-miR TNF I vs. HeLa miR133b TNF I

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 1.25 µg of each labeled cRNA was fragmented and subsequent hybridized to whole human genome 44k microarrays (AMADID-012391) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Hybridized microarrays were washed using the SSC washing protocol (Agilent Technologies). Scanning of microarrays was performed with extended mode (100% and 10%) at 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: he extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2 (Rosetta Biosoftware, Seattle, WA, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: HeLa c-miR TNF

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled with either Cyanine 3-CTP or Cyanine 5-CTP according the suppliers instructions

extract_protocol: total RNA was extracted with Trizol (invitrogen) according the suppliers instructions using Glycogen as carrier

tag: cell line

value: HeLa

tag: time

value: control miR transfection 48h before stimulation

tag: stimulation

value: TNF alpha stimulation for 6 h prior to RNA collection

source_name: HeLa miR133b TNF

value: miR-133b transfection 48h before stimulation


description: Gene expression data from whole blood rituximab treated baseline sample 1011 non-responder

tag: tissus


title: CLL042


title: HeLa miR133b TNF I vs. HeLa c-mir TNF I


title: CLL043


title: CLL096


title: CLL003


title: CLL113


title: CLL041


title: CLL040_TP2

value: CLL cells time point 2


title: NTERA2 pl [gene-level]

city: Oslo

first: Sharmini

last: Alagaratnam

address: Radiumhospitalet, Montebello

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
H25 [gene-level]
H25_HuEx.CEL (see Series record)
H25_HuEx.rma-gene-core.chp

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned in-house.

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

data_processing:
RMA expression value derived from Expression Console software; core-gene and core-exon analyses
CHP files were generated from raw CEL files by Expression Console software. Both CEL and CHP files were used as input for data analysis, specifically PCA in Qlucore (CHP), gene- and exon-level expression differences by XRAY (CEL files) and limma (CHP files), and two-class pair-wise Significance of Microarrays (CHP files).

source_name: EC cell line

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

growth_protocol: All ES lines and the three EC lines marked 'fe' were grown on mitomycin C-inactivated mouse embryo fibroblasts in knock-out DMEM with 10% Serum Replacement and 4 ng/ml FGF. All EC cells were grown in plastic flasks in high-glucose DMEM with 10% FCS.

extract_protocol: Total RNA was isolated from the cell lines using the AllPrep DNA/RNA Mini kit (Qiagen).

treatment_protocol: All cells were FACS sorted for the surface marker SSEA3 before storage in RNAlater (Qiagen).

value: EC cell line

value: plastic-grown


title: Shef7 [gene-level]

description:
H24 [gene-level]
H24_HuEx.CEL (see Series record)
H24_HuEx.rma-gene-core.chp

source_name: ES cell line

value: ES cell line

value: feeder-grown