title: pYES2 5h

city: Bangalore

first: Ram

last: Rajasekharan

state: Karnataka

address: Sir CV Raman Avenue

department: Biochemistry

country: India

institute: Indian Institute of Science

description: Gene expression after 5 hour

hyb_protocol: 600ng of cy3 labeled samples were  fragmented and hybridized .  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C  and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX V 11 75th Percentile Normalization

source_name: pYES2 5h

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Cells were grown in synthetic minimal medium containing 0.67% yeast nitrogen base (Difco) supplemented with the appropriate amino acids, adenine and no uracil, and induced with 2% galactose for two or five hours as indicated.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit as per 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).

treatment_protocol: Cell were harvested by centrifugation and stored in sigma RNAlater solution.

tag: plasmid

value: pYES2 control

tag: time

value: 5h induction


title: MPH_24h_D5_2

status: Public on Apr 24 2012

type: RNA

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Treatment with MPH 24h

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: All samples were normalized by MAS 5 algorithm

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Treatment with MPH 24h

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: Hepatocytes were isolated by using a two-step collagenase perfusion technique . The viability was assessed by trypan blue exclusion and the cells (≥85% viability) were cultured as a monolayer at a density of 0.57x105 cells/cm2 in William’s E medium supplemented with 10%v/v fetal bovine serum, 292mg/ml L-glutamine, 7ng/ml glucagon and antibiotics (7.33IU/ml benzylpenicillin sodium, 50µg/ml kanamycin monosulphate, 50µg/ml streptomycin sulphate, and 10µg/ml ampicillin sodium) in an incubator at 37°C (5% CO2 and 95% air, 100% humidity). After 4 hours, the medium was renewed with serum-free culture medium, supplemented with 25µg/ml hydrocortisone hemisuccinate and 1mg/ml bovine insulin.

extract_protocol: Samples for RNA isolation were collected after 24 hours and 72 hours of exposure. Three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: At 18-20 hours post-plating, exposure to 2-Nitrofluorene  (78 µM), Aflatoxin B (19 nM), Clonidine hydrochloride (277 µM), Methapyrilene hydrichloride (8.5 µM), Nifedipine (156 µM), 4(methylnitrosamino)-1-(3-pyridyl)-1 –butanone (625 µM), Piperonyl butoxide (13.4 µM), Wy-14,643 (250 µM) was initiated.

tag: cell type

value: primary hepatocytes

tag: exposure time

tag: replicate


title: MPH_24h_D6_3

description: Treatment with MPH 24h


title: C(MPH)_24h_D5_2

description: Control for MPH 24h

source_name: Control for MPH 24h


title: MPH_24h_D4_1

description: Treatment with MPH 24h


title: C(NNK)_24h_D9_3

description: Control for NNK 24h

source_name: Control for NNK 24h


title: NNK_24h_D8_2

description: Treatment with NNK 24h

source_name: Treatment with NNK 24h


title: rPLC-pYES2 2h

description: Gene expression after 2 hour

organism: Saccharomyces cerevisiae

source_name: rPLC-pYES2 2h

tag: strain

value: rPLC-pYES2 Phospholipase C

value: 2h induction


title: C(MPH)_24h_D6_3

description: Control for MPH 24h


title: NNK_24h_D7_1

description: Treatment with NNK 24h


title: C(NNK)_24h_D8_2

description: Control for NNK 24h


title: pYES2 2h

description: Gene expression after 2 hour

source_name: pYES2 2h


title: rPLC-pYES2 5h

description: Gene expression after 5 hour

source_name: rPLC-pYES2 5h


title: NIF_24h_D9_3

description: Treatment with NIF 24h

source_name: Treatment with NIF 24h


title: NIF_24h_D8_2

description: Treatment with NIF 24h


title: C(MPH)_24h_D4_1

description: Control for MPH 24h


title: PIPB_24h_D9_3

description: Treatment with PIPB 24h

source_name: Treatment with PIPB 24h


title: C(NNK)_24h_D7_1

description: Control for NNK 24h


title: NIF_24h_D7_1

description: Treatment with NIF 24h


title: AFB_72h_D1_1

description: Treatment with AFB 72h

source_name: Treatment with AFB 72h


title: NNK_24h_D9_3

description: Treatment with NNK 24h


title: WYE_72h_D1_1

description: Treatment with WYE 72h

source_name: Treatment with WYE 72h


title: 2NF_24h_D8_2

description: Treatment with 2NF 24h

source_name: Treatment with 2NF 24h


title: C(2NF_PIPB_NIF)_24h_D8_2

description: Control for 2NF, PIPB and NIF 24h

source_name: Control for 2NF, PIPB and NIF 24h


title: PIPB_24h_D8_2

description: Treatment with PIPB 24h


title: 500mM NaCl-rep4

city: Corvallis

first: Markael

middle: D.

last: Luterra

state: OR

address: 116 Gilmore Hall

department: Biological and Ecological Engineering

country: USA

institute: Oregon State University

hyb_protocol: Performed by Oregon State University Core Laboratories as described in the NimbleGen Array User's Guide: Gene Expression Arrays, vol. 5.0.  Four-plex arrays hybridized using NimbleGen Hybridization System 4.

scan_protocol: Performed by Oregon State University Core Laboratories as described in the NimbleGen Array User's Guide: Gene Expression Arrays, vol. 5.0.  Scanner: Axon GenePix 4200A Pro.  PMT=450.  Laser power=100.  Pixel size=5.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization, and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).  Log(2)-transformed, normalized signal intensities were averaged across technical replicate blocks.

organism: Synechocystis sp. PCC 6803

source_name: liquid media with 500 mM NaCl

label_protocol: Performed by Oregon State University Core Laboratories as described in the NimbleGen Array User's Guide: Gene Expression Arrays, vol. 5.0.  Method: Random 9-mer.  Label: Cy3

growth_protocol: Wild-type Synechocystis sp. PCC 6803 cells were grown in 500 ml volumes of BG-11 media (35 mM HEPES, pH 7.8) in 1 ml Erlenmeyer flasks bubbled with sterile air under illumination of approximately 50 µE/m2/S.

extract_protocol: Multiple 500 µL aliquots from each sample were scraped (gel samples) or pipetted (control and salt-exposed samples) into 2 mL microtubes and flash frozen in liquid nitrogen to preserve RNA expression profiles. Samples were stored at -80°C.   The following were added directly to each 500 L frozen aliquot:  100 µL extraction buffer (120 mM sodium acetate, 60 mM EDTA, 3% SDS, pH 5.2), 500 µL phenol (buffer saturated, pH 4.5, Amresco, Solon, OH), approximately 500 µL 0.1 mm diameter glass beads (BioSpec, Bartlesville, OK), and sufficient 1 M HCl to bring the final pH to 5.2 (14.5 µL for liquid samples, 10 µL for TEOS gel samples, and 4.1 µL for aqueous gel samples). Following homogenization in a bead beater (BioSpec, four 30-s cycles with 30-s rest periods between), tubes were incubated at 65°C for 10 minutes, with occasional mixing to prevent phase separation. At this point, 100 mL chloroform with 4% isoamyl alcohol was added and tubes were vortexed for 15 s, placed on ice for three minutes, and centrifuged for 10 minutes at 20,000g to achieve phase separation.  The aqueous phase was further extracted with 300 µL each phenol and chloroform (to remove residual protein) and 600 µL chloroform (to remove residual phenol), and RNA was precipitated by addition of 1/10 volume 10 M lithium chloride and 1 volume isopropanol, incubation at -20°C for 30 minutes, and centrifugation (15,000g) at 4°C for 15 minutes. RNA pellets were washed with 75% ethanol and resuspended in 50 µL nuclease-free water (Amresco).  RNA was purified and concentrated using RNeasy Mini spin columns (Qiagen, Germantown, MD), with on-column DNase treatment following the protocol provided. To maximize final yield and concentration, 30 µL RNase-free water was heated to 50°C prior to addition to the column, and eluate was returned to the column for a second elution. RNA yield was measured by absorbance at 260 nm (NanoDrop ND-1000, Thermo Fisher Scientific, Wilmington, DE), both before and after purification. RNA purity was assessed by examining A260/A280 and A260/A230 ratios; both of these measures exceeded 1.8 in all samples before and after purification. RNA integrity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and all samples exhibited sharp rRNA bands with no evidence of RNA degradation.

treatment_protocol:
Cells were harvested by centrifugation in late log phase and resuspended in BG-11 media (35 mM HEPES, pH 7.8) at an OD730 of 8.0.  Encapsulation in aqueous and alkoxide sol-gels was performed as described below.  Liquid controls were prepared by mixing 2 ml resuspended cells with 2 ml BG-11 media.   500 mM salt-treated cells were prepared by mixing 2 ml resuspended cells with 2 ml BG-11 media containing 1 M NaCl.  All samples totaled 4 ml in 35 mm petri dishes, with an OD730 of 4.0.  All samples were incubated under continuous light (80 µE/m2/s) for 24 hours prior to freezing and RNA extraction.
Aqueous encapsulation protocol: Aqueous gels were made by first pre-hydrolyzing a 6.3 M aqueous solution of sodium silicate (Fisher Scientific, Fair Lawn, NJ) with hydrochloric acid in the presence of an ion exchange resin. In a 125 mL Erlenmeyer flask, 57.8 mL deionized water, 920 mL of 1.0 M hydrochloric acid, 4.0 mL 6.3 M sodium silicate, and 11.6 g Amberlite™ IR-120 H ion exchange resin (Sigma Aldrich, St. Louis, MO) were combined and vigorously stirred with a magnetic stir bar for approximately 2 hours prior to vacuum filtering, to remove the resin, and sterile filtering through a 0.22 mm filter.  Gels with a volume of 4.0 mL were prepared by combining 2.0 mL of cell suspension in buffered BG-11 (35 mM HEPES, pH 7.8) at an OD730 of approximately 8.0 with 2.0 mL of the pre-hydrolyzed aqueous sol, 30 mL of 1.0 M potassium hydroxide, and 40 mL 5.0 M sodium chloride solution in a 35 mm Petri dish.
Alkoxide encapsulation protocol: Alkoxide gels were prepared by first pre-hydrolyzing a solution of tetraethoxysilane (TEOS) (Alfa Aesar, Ward Hill, MA) in the presence of deionized water and acid catalyst. In a 50 mL Erlenmeyer flask, 5.0 mL TEOS was combined with 8.08 mL 18.2 MW deionized water (Millipore, Billerica, MA) and 112 mL 1.0 M nitric acid (molar ratio of 1:20:0.005, silicon:water:acid) and stirred vigorously with a magnetic stir bar on a heated stir plate at approximately 60°C for 2 hours. The elevated temperature promoted hydrolysis and the evaporation of ethanol. Stirring continued for an additional hour at room temperature prior to filtering the sol through a 0.22 mm sterile filter before encapsulation.  Gels with a volume of 4.0 mL were prepared by combining 2.0 mL of cell suspension in buffered BG-11 (35 mM HEPES, pH 7.8) at an OD730 of approximately 8.0 with 1.2 mL additional BG-11, 800 L of the pre-hydrolyzed alkoxide sol, and 8.0 L of 1.0 M potassium hydroxide in a 35 mm Petri dish.

tag: treatment

value: liquid media with 500 mM NaCl

tag: treatment duration

value: 24 hours


title: AFB_24h_D3_3

description: Treatment with AFB 24h

source_name: Treatment with AFB 24h


title: CND_24h_D3_3

description: Treatment with CND 24h

source_name: Treatment with CND 24h


title: 2NF_24h_D7_1

description: Treatment with 2NF 24h


title: C(2NF_PIPB_NIF)_24h_D7_1

description: Control for 2NF, PIPB and NIF 24h


title: 500mM NaCl-rep3


title: C(2NF_PIPB_NIF)_24h_D9_3

description: Control for 2NF, PIPB and NIF 24h


title: 500mM NaCl-rep2


title: 500mM NaCl-rep1


title: WYE_24h_D2_2

description: Treatment with WYE 24h

source_name: Treatment with WYE 24h


title: C(WYE_CND_AFB)_24h_D3_3

description: Control for WYE, CND and AFB 24h

source_name: Control for WYE, CND and AFB 24h


title: WYE_24h_D3_3

description: Treatment with WYE 24h


title: AFB_24h_D1_1

description: Treatment with AFB 24h


title: PIPB_24h_D7_1

description: Treatment with PIPB 24h


title: WYE_24h_D1_1

description: Treatment with WYE 24h


title: C(WYE_CND_AFB)_24h_D1_1

description: Control for WYE, CND and AFB 24h


title: AFB_24h_D2_2

description: Treatment with AFB 24h


title: 2NF_24h_D9_3

description: Treatment with 2NF 24h


title: CND_24h_D2_2

description: Treatment with CND 24h


title: C(WYE_CND_AFB)_24h_D2_2

description: Control for WYE, CND and AFB 24h


title: CND_24h_D1_1

description: Treatment with CND 24h


title: Alkoxide gel-rep4

source_name: TEOS alkoxide sol-gel

value: TEOS alkoxide sol-gel


title: LNCaP sphere-forming cell R1881 1hr

city: Frederick

first: Ji

last: Zheng

state: MD

address: 1050 Boyles St.

institute: National Cancer Institute

description: LNCaP cells were grown in stem cell medium for 5 days to form prostaspheres. Sphere-forming cells were treated with 0.02 nM R1881 for 1hr and harvested.

hyb_protocol: Samples were incubated with Agilent Blocking buffer and Fragmentation buffer at 60°C for 30 minutes. Agilent hybridization buffer were added, and samples were hybridized to an Agilent whole genome gene expression array following manufacturer's directions.

scan_protocol: Scanned on an GenePix® 4000B scanner. Images were quantified using GenePix Pro 6.1 Software. Image file (.jpg) and data file (.gpr) were uploaded into mAdb system.

data_processing: Data was extracted in mAdb system. Signal calculation: Mean Intensity minus Median Background. Normalization method: Local Mean Across Element Signal Intensity (LOESS).

organism: Homo sapiens

source_name: LNCaP sphere-forming cell R1881 1hr

label_protocol: 7 µg of total RNA from different samples were reversed transcribed at 42°C for 75 minutes in the presence of 400 U SuperScript III Reverse Transcriptase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM Cy5-dUTP. 7 µg of total universal reference RNA were reversed transcribed at same condition with 25 µM Cy3-dUTP.

growth_protocol: LNCaP cells were dissociated to single cells and plated at low density (3000 cells/mL). Cells were grown in stem-cell medium (DMEM/F12 plus 10 ng/mL bFGF, 20 ng/mL EGF, 5 mg/mL insulin, and 0.4% BSA) supplemented with serum replacement (1% Knockout) for 5 days before hormone treatment.

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

tag: cell line

value: LNCaP clone FGC (CRL-1740)

tag: age

value: 50 years adult

tag: organ

value: prostate

tag: disease

value: carcinoma

tag: gender

value: male

source_name: Agilent's Universal Human Reference RNA

value: 10 human cell lines


title: Alkoxide gel-rep3


title: LNCaP sphere-forming cell R1881 24hr

description: LNCaP cells were grown in stem cell medium for 5 days to form prostaspheres. Sphere-forming cells were treated with 0.02 nM R1881 for 24hr and harvested.

source_name: LNCaP sphere-forming cell R1881 24hr


title: Alkoxide gel-rep2


title: Alkoxide gel-rep1


title: LNCaP sphere-forming cell estradiol 24hr

description: LNCaP cells were grown in stem cell medium for 5 days to form prostaspheres. Sphere-forming cells were treated with 50 nM estradiol for 24hr and harvested.

value: 50 nM estradiol for 24hr


title: Aqueous gel-rep4

source_name: aqueous sol-gel

value: aqueous sol-gel


title: LNCaP sphere-forming cell estradiol 1hr

description: LNCaP cells were grown in stem cell medium for 5 days to form prostaspheres. Sphere-forming cells were treated with 50 nM estradiol for 1hr and harvested.

source_name: LNCaP sphere-forming cell estradiol 1hr

value: 50 nM estradiol for 1hr


title: Control-rep3

source_name: liquid media

value: liquid media


title: Aqueous gel-rep1


title: Control-rep4


title: Aqueous gel-rep2


title: Aqueous gel-rep3


title: Control-rep2


title: E11.5PGCs_2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal. The raw Red signal data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.The raw Red signal data intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. Detected signals for each gene were normalized by global normalization method (the median of the detected signal intensity was adjusted to 20).

organism: Mus musculus

source_name: primordial germ cell

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

growth_protocol: Knockout DMEM supplemented with 15% KSR (Invitrogen), 2 mM glutamine, 1 mM nonessential amino acids, 2-ME, LIF, and bFGF.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

value: primordial germ cell

tag: variation

value: Nanog-GFP

tag: treatment group


title: EG(2i+A83)_2


title: RA 34 FLS Dex

city: University of Birmingham

first: Rowan

middle: Samuel

last: Hardy

state: West Midlands

address: 2nd floor IBR

department: Clinical and Experimental Medicine

country: United Kingdom

institute: University oif Birmingham

description: SAMPLE 11

data_processing: Data were obtained as Ct values (the cycle number at which logarithmic PCR plots cross a calculated threshold line) and used to determine ΔCt values (Ct of target gene - Ct of housekeeping gene) as raw data for gene expression (high ΔCt = low gene expression). The fold change in gene expression was determined by subtracting ΔCt values for treated cells from their respective control samples. The resulting ΔΔCt values were then used to calculate fold change in gene expression according to the equation 2-ΔΔCt.

label: FAM

source_name: Synovial tissue from RA, dexamethasone

label_protocol: RNA was reverse transcribed using random hexamers (Promega, Madison, WI, USA).

growth_protocol: Grown to confluence in 75-cm2 flasks in normal RPMI 10% FCS, 1%p/s.

extract_protocol: Sigma Tri Reagent extraction from 75-cm2 flasks as per manufacturer's guidelines.

treatment_protocol: Treated for 16 hr in low-serum media.

value: cultured primary synovial fibroblasts

tag: Sex

value: female

tag: disease status

value: rheumatoid arthritis (RA)

value: dexamethasone (100nmol/l)

tag: patient identifier


title: Day3(2i+A83)_1


title: RA 38 FLS Dex

description: SAMPLE 12


title: EG(2i+A83)_1


title: LNCaP sphere-forming cell ethanol 1hr

description: LNCaP cells were grown in stem cell medium for 5 days to form prostaspheres. Sphere-forming cells were treated with ethanol (vehicle) for 1hr and harvested.

source_name: LNCaP sphere-forming cell ethanol 1hr

value: ethanol (vehicle) for 1hr


title: Day6(2i+A83)_1


title: Day6(2i+A83)_2


title: E11.5PGCs_1


title: Testis rep 2 (Cy5)

type: genomic

city: Cambridge

first: Bettina

last: Fischer

address: Tennis Court Road

department: Systems Biology Centre

institute: Unversity of Cambridge

description: Testis rep2 vs Sperm rep3 dye-swap

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: RNA samples were amplified using SMART method. Briefly, RNA was treated with RQ1 DNase (Promega).  Reverse transcription was performed with 1 ?M 3’SMART CDS Primer IIA (5’ AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-VN 3’, V = G+A+C, N = A+C+G+T), 1 ?M SMART IIA chimeric oligo (5’ AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CGC-888 3’, 8 = riboG), 1x First-Strand Buffer, 0.25 mM of each nucleotide, 2 mM DTT and 1 ?l PowerScript Reverse Transcriptase (Clontech) for 1.5 hours at 42 ºC, then snap cool on ice. Amplification of 5 ?l cDNA was performed with 1 ?l 50x Advantage 2 Polymerase Mix (Clontech) in 1x Advantage 2 PCR buffer, 0.05 mM of each nucleotide, 0.8 ?M 5’ PCR Primer II (5’AAG-CAG-TGG-TAT-CAA-CGC-AGA-GT 3’) in 50 ?l total volume.  The cycling conditions were: initiation 95°C for 1 min, followed by 20 cycles of 95°C for 5sec, 65°C for 5 sec, extension at 68°C for 6 min.  The optimal number of cycles was determined taking aliquots from every second cycle between cycles 18 to 28 and visualising these by electrophoresis in a 1% agarose gel.  For all samples 20 cycles (two cycles less than saturation) were used to stay within the exponential phase. 1 ?g of amplified DNA was labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Invitrogen) in the presence of fluorescently labeled Cy3- or Cy5-dCTP (GE Healthcare) at 37°C for 2 hours and the product purified using Sephadex G50 columns (GE Healthcare).

growth_protocol: All fly stocks were maintained at 25°C on standard media.

extract_protocol: 10 adult males were dissected and their testes along with associated accessory glands stored in Trizol (Invitrogen) at -80°C. The RNA was extracted using the Trizol method (Invitrogen).

value: male, tissue:testis with aceesory glands, developmental stage:adult


title: RA 18 FLS Dex

description: SAMPLE 10


title: RA 38 FLS Con2

description: SAMPLE 9

source_name: Synovial tissue from RA, control

value: vehicle


title: Sperm rep 3 (Cy5)

description: Sperm rep3 vs Testis rep1

extract_protocol: Flies were dissected in PBS using fine forceps and a dissecting microscope.  Testes were removed by excision of the male terminalia with forceps and extrusion of the paired testes and attached seminal vesicles from the abdominal cavity.  Seminal vesicles were carefully detached from the testes and moved to a clean drop of PBS.  Seminal vesicles were punctured with a fine needle, allowing sperm to flow outward, and the sperm removed as an intact mass to a microfuge tube containing PBS using forceps and the samples stored on ice.  Routinely 25-50 dissections were performed per session (approximately 60 min) and then centrifuged at 13000 rpm for 2-5 minutes at room temperature.  The sperm pellets were washed twice with 4ºC PBS and excess PBS removed from the final wash before storing frozen at -80ºC. RNA was extracted using the Trizol method (Invitrogen).

value: male, tissue:sperm, developmental stage:adult


title: 6DT1 cells, untransduced, no selection

city: Bethesda

first: Scott

middle: F

last: Winter

address: 37 Convent Dr., Bldg 37 Rm 5046

department: CCR

institute: NCI

hyb_protocol: Mouse Gene 1.0 ST arrays were hybridized at 45C for 16 hours at 60 rpm. Arrays were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Data were collected using Affymetrix AGCC software. CEL files were loaded into Partek using the RMA defaults.

source_name: 6DT1 mouse mammary carcinoma cells

label_protocol: 100 ug of total RNA was reverse transcribed and amplified usint the Ambion WT Expression Kit, and sense strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturers' protocols.

growth_protocol: Cell lines were maintained in DMEM with 10% FBS and pen/strep under standard tissue culture conditions- 37C, 5% CO2

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to manufacturer's instructions. RNA was QC'ed using an Aglient 2100 Bioanalyzer.

treatment_protocol: Lentiviral shRNA particles were produced in 293 cells and used to transduce 6DT1 cells accoring to Open Biosystems standard protocols. Stable cells were selected with 10 ug/ml puromycin. Analysis was performed on pooled clones from each stable line.

value: 6DT1 mouse mammary carcinoma cells

tag: puro selected?

value: no

tag: arid4b level

value: normal

tag: arid4b densitometry


title: 6DT1 cells, pLKO.1 scrambled control

value: yes


title: 6DT1 cells, Arid4b shRNA hairpin 5


title: Day3(2i+A83)_2

tag: cell type


title: Control-rep1

value: 24 hours


title: Testis rep 1 (Cy3)

description: Sperm rep3 vs Testis rep1


title: SEM-K2 obatoclax EC50 rep 2

city: Philadelphia

first: Li-San

last: Wang

state: PA

address: 1424 Blockley Hall, 423 Guardian Drive

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

hyb_protocol: 15 ug of cRNA was hybridized to Affymetrix U133 plus 2.0 Arrays for 16 hours at 45 degrees Celcius

scan_protocol: Microarray chips were scanned using a Affymetrix GeneChip Scanner

data_processing: The data were analyzed using the R/Bioconductor package GC-RMA with default settings.

source_name: Human MLL-AF4 acute lymphoblastic leukemia cell line, 6 hour obatoclax exposure at 72h EC50

label_protocol: Biotin-labeled cRNA was prepared according to Affimetryx protocol (GeneChips Expression Analysis Technical Manual) from 2-2.5 ug of total RNA

growth_protocol: SEM-K2 and RS4:11 cells were plated at 106cell/ml

extract_protocol: Cells were lysed with TRIzol. Total RNA was extracted with chloroform and precipitated with isopropanol.

treatment_protocol: 24 hours after plating, 10x106 cells were treated with vehicle or obatoclax at the 72 hour EC50 or 3xEC50 for 6 hours (2 replicates per condition).

value: Acute Lymphoblastic Leukemia cell line SEM-K2

tag: agent

value: obatoclax

tag: dose


title: RA 18 FLS Con2

description: SAMPLE 7

tag: treatment


title: Sperm rep 3 (Cy3)

description: Testis rep2 vs Sperm rep3 dye-swap


title: 6DT1 cells, Arid4b shRNA hairpin 4

tag: cell line

value: low


title: SEM-K2 obatoclax 3xEC50 rep 2

source_name: Human MLL-AF4 acute lymphoblastic leukemia cell line, 6 hour obatoclax exposure at 3x 72h EC50


title: SEM-K2 Vehcle rep 2

source_name: Human MLL-AF4 acute lymphoblastic leukemia cell line, 6 hour vehicle exposure

value: control


title: Testis rep 1 (Cy5)

description: Testis rep1 dye-swap (genomic DNA only used for spot-finding purpose)

source_name: genomic DNA

label_protocol: 1 µg of genomic DNA was labelled using the BioPrime DNA labelling kit (Invitrogen) in the presence of fluorescently labeled Cy3- or Cy5-dCTP (GE Healthcare) at 37°C for 2 hours and the product purified using Sephadex G50 columns (GE Healthcare).

extract_protocol: 15 flies were homogenised in 300 µl Buffer A (100mM Tris-HCl pH 7.7, 100mM EDTA, 100mM NaCl, 0.5% SDS) and incubated at 65°C for 30 minutes. 600 µl 6M LiCl/5MKAc (ratio 2.5:1) added, mixed and incubated on ice for 20min. The cell debris was pelleted at 13000rpm for 15 minutes and supernatant transferred to new tube. The DNA was then precipitated with 0.75 volumes of ice-cold isopropanol at 13000 rmp for 30 minutes and washed with 70% ethanol. Then the genomic DNA was RNase treated for 20 minutes.

value: female, strain:w1118, tissue:whole fly, developmental stage:adult


title: RA 38 FLS TNF

description: SAMPLE 6

source_name: Synovial tissue from RA, TNF

value: cultured primary synovial fibroblasts

value: female

value: TNF (10ng/ml)


title: RA 34 FLS TNF

description: SAMPLE 5

value: rheumatoid arthritis (RA)


title: 6DT1 cells, Arid4b shRNA hairpin 3


title: RA 18 FLS TNF

description: SAMPLE 4


title: Relative miRNA expression_CTX in vivo_day21 versus Baseline

city: San Antonio

first: Yongxin

last: Chen

state: TX

address: 7703 Floyd Curl Drive

department: Surgery

institute: University of Texas Health Science Center at San Antonio

description: Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

data_processing: Cycle threshold (Ct) values were calculated with SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. The comparative Ct method was used to calculate the relative miRNA expression. The Ct value of an endogenous control gene (MammU6, snRNA) was subtracted from the corresponding Ct value for the target gene resulting in the ΔCt value. Relative miRNA expression was determined by 2^-ΔΔCt.

source_name: Cardiotoxin muscle injury mouse model

extract_protocol: Total RNA was isolated using miRNeasy Minikit (QIAGEN) according to manufacturer’s instructions. RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA samples with RNA integrity number (RIN) > 9 were used in the array studies.

treatment_protocol: Mice were anesthetized with inhalation of 1-2% isoflurane (Vedco Inc) and placed on a warming pad to maintain body temperature during the procedure. CTX (Calbiochem) (2.5 μM in pyrogen-free saline) was injected intramuscularly below the knee into the anterior (100 μl) compartments of both hind limbs. TA muscles were collected at baseline (no injections) and at days 1-5, 7 and 21 after CTX injection (n=4 mice/time point). The tissues were weighed; half of the muscle was homogenized in QIAzolLysis Reagent (QIAGEN) using TissueRuptor (QIAGEN) and stored at -80°C until use; the other half was placed in 10% neutral buffered formalin for histological examination to confirm the extent and time course of muscle injury and regeneration.

tag: time point

tag: tissue

value: hind limb muscle

tag: strain

value: Male

tag: age

value: 4-6 months


title: RS4:11 obatoclax 3xEC50 rep 2

value: Acute Lymphoblastic Leukemia cell line RS4:11


title: SEM-K2 obatoclax 3xEC50 rep 1


title: WYE_72h_D2_2

description: Treatment with WYE 72h

source_name: Treatment with WYE 72h

value: primary hepatocytes

tag: exposure time

tag: replicate


title: RA 38 FLS Con

description: SAMPLE 3

tag: Sex

value: vehicle


title: Sperm rep 2 (Cy5)

description: Sperm rep2 (genomic DNA only used for spot-finding purpose)

tag: gender

value: male, tissue:sperm, developmental stage:adult


title: RS4:11 Vehicle rep 2


title: RA 34 FLS Con

description: SAMPLE 2

tag: disease status

tag: patient identifier


title: Sperm rep 2 (Cy3)

type: mixed

description: Sperm rep2 dye-swap (genomic DNA only used for spot-finding purpose)

value: female, tissue:whole fly, developmental stage:adult


title: Relative miRNA expression_CTX in vivo_day4 versus Baseline


title: Testis rep 2 (Cy3)

description: Testis rep2 (genomic DNA only used for spot-finding purpose)

value: male, tissue:testis with aceesory glands, developmental stage:adult


title: Relative miRNA expression_CTX in vivo_day7 versus Baseline


title: Relative miRNA expression_CTX in vivo_day3 versus Baseline


title: Sperm rep 1 (Cy3)

description: Sperm rep1 dye-swap (genomic DNA only used for spot-finding purpose)


title: SEM-K2 Vehcle rep 1

value: Acute Lymphoblastic Leukemia cell line SEM-K2


title: RS4:11 obatoclax EC50 rep 2

value: obatoclax


title: Sperm rep 1 (Cy5)

description: Sperm rep1 (genomic DNA only used for spot-finding purpose)


title: Control, biological rep 3

first: Jonathan

middle: Lee

last: Jesneck

state: MA

address: 77 Massachusetts Ave., 35-208

department: Lab for Manufacturing and Productivity

institute: MIT

description: Six-week-old littermateOtt1 wild type mice

hyb_protocol: Ovation RNA amplification system V2 (Nugen, San Carlos, CA)

scan_protocol: Affymetrix Mouse expression array 430A2.0 chips

data_processing: robust multi-array analysis (RMA) algorithm using BioConductor software

source_name: Control

label_protocol: RNAse-free DNAse (Qiagen, Valencia, CA)

extract_protocol: RNeasy Micro kit (Qiagen, Valencia, CA)

value: Lin- Sca-1+ c-Kit+ (LSK)

value: six weeks old

tag: genotype/variation

value: Ott1 wild type


title: Control, biological rep 1


title: SEM-K2 obatoclax EC50 rep 1


title: Control, biological rep 2


title: RA 18 FLS Con

description: SAMPLE 1

value: cultured primary synovial fibroblasts

value: female


title: CW7_rep2_channel2

status: Public on Apr 23 2012

city: Halifax

first: Paul

middle: Vincent

last: Debes

state: NS

address: 1355 Oxford St

department: Biology

country: Canada

institute: Dalhousie University

description: Raw data in A09_Data.txt: (Cy5)

hyb_protocol: As outlined in the Genisphere Array 50 Protocol Revised version 5 available at http://web.uvic.ca/cbr/grasp/microarray/array.html

scan_protocol: Scanned using a ScanArray scanner (PerkinElmer) at a resolution of 10μm and 90%  laser power, manually equilibrating intensity between dyes for each slide using the photomultiplier tube settings.

data_processing: Spots were localised and quantified with the QuantArray 3.0 software. We only analysed data from spots that fulfilled the following criteria to ensure to analyse genes that are truly transcribed: Spot intensity on a given array higher than the average intensity plus two standard deviations of negative control spots on a given array and this for all individuals of at least one of the six experimental groups. Further analysis was conducted using the R/MAANOVA package, local background was substracted from mean spot intensity, missing data was imputed using the K-nearest neighbor algorithm, for normalisation log2 intensity data data was Joint Lowess corrected and centralised.

organism: Salmo salar

source_name: gill tissue, clear water

label_protocol: Cy5 and Cy3 dyes of the Array50 kit (Genisphere) following the procedures at http://web.uvic.ca/cbr/grasp/microarray/array.html (Genisphere Array 50 Protocol Revised version 5), using 15microgram of RNA per reverse transcription reaction and sunbsequently OPTION 1 – concentration of cDNA using Millipore Microcon YM-30 concentrators.

growth_protocol: Common garden wet lab: the same physical and biological parameters for four similar tanks but two tanks each of two environments (treatments), each tank with 1,790L, flow through system, dechlorinated tab water, varying ambient temperature in the Aquatron Facility of Dalhousie University, Halifax, Canada. Fed with commercial salmon dry fee (Corey).

extract_protocol: Total RNA was extracted from gill tissue following the manufacturer’s manual for purifying RNA from animal tissue (PureLink, Invitrogen) and subsequently treated with DNAse I. For this we added 1μL of a DNase-mix (20μM Tris–HCl (pH 8.4), 2mM MgCl2, and 50μM KCl, 120u*μL-1 DNase I (Invitrogen)) per microgram RNA and incubated the mix for 30min at room temperature followed by an inactivation step that involved adding 1μL of 25mM EDTA and incubating at 65°C for 10min.

treatment_protocol: Daily, for a period of 120 days, water was poured into the middle of each tank containing clear water (control) or 358g dried and ground sediments collected from the upper tidal mudflats in the inner Bay of Fundy, Minas Basin, Canada, were resuspended and poured into the middle of each tank containing suspended sediments (treatment).

tag: sample [environment (c=clear, s=sediments), strain (w=stewiacke river (wild), d=saint john river (domesticated), h=hybrid), individual id]

value: Stewiacke River salmon

tag: environment

value: clear brackish water (S=18PSU)


title: SW2_rep2_channel1

description: Raw data in A09_Data.txt: (Cy3)

source_name: gill tissue, suspended sediments in water

value: brackish water (S=18PSU) containing suspended sediments from the inner Bay of Fundy


title: Relative miRNA expression_CTX in vivo_day1 versus Baseline

value: hind limb muscle

value: Male

value: 4-6 months


title: SD1_rep2_channel2

description: Raw data in A06_Data.txt: (Cy5)

value: Saint John River domesticated salmon


title: Ott1 knock out, biological rep 1

description: Six-week-old Ott1 flox/null Tg-Mx1cre mice

source_name: OTT1 knock out

tag: cell type

value: Ott1 flox/null Tg-Mx1cre


title: SW7_rep1_channel1

description: Raw data in A48_Data.txt: (Cy5)


title: RS4:11 obatoclax EC50 rep 1

value: Acute Lymphoblastic Leukemia cell line RS4:11

tag: agent

tag: dose


title: SD5_rep2_channel1

description: Raw data in A47_Data.txt: (Cy5)


title: SH5_rep1_channel1

description: Raw data in A46_Data.txt: (Cy5)

value: First generation hybrid between Saint John River domesticated and Stewiacke River salmon


title: CH7_rep2_channel2

description: Raw data in A46_Data.txt: (Cy3)


title: CD1_rep2_channel2

description: Raw data in A08_Data.txt: (Cy5)


title: SD1_rep1_channel1

description: Raw data in A08_Data.txt: (Cy3)


title: SW6_rep2_channel2

description: Raw data in A45_Data.txt: (Cy3)


title: CW5_rep1_channel1

description: Raw data in A45_Data.txt: (Cy5)


title: SD4_rep2_channel2

description: Raw data in A44_Data.txt: (Cy3)


title: Ott1 knock out, biological rep 2


title: CD5_rep2_channel1

description: Raw data in A44_Data.txt: (Cy5)


title: CH1_rep2_channel2

description: Raw data in A07_Data.txt: (Cy5)


title: SH1_rep1_channel1

description: Raw data in A07_Data.txt: (Cy3)


title: SD8_rep1_channel1

description: Raw data in A05_Data.txt: (Cy3)


title: CH6_rep2_channel2

description: Raw data in A43_Data.txt: (Cy5)


title: SW1_rep1_channel1

description: Raw data in A06_Data.txt: (Cy3)


title: SH1_rep2_channel2

description: Raw data in A05_Data.txt: (Cy5)


title: CW4_rep2_channel2

description: Raw data in A48_Data.txt: (Cy3)


title: CD6_rep2_channel2

description: Raw data in A47_Data.txt: (Cy3)


title: RS4:11 obatoclax 3xEC50 rep 1

tag: cell line


title: Ott1 knock out, biological rep 3


title: RS4:11 Vehicle rep 1

value: vehicle

value: control


title: SH6_rep2_channel2

description: Raw data in A41_Data.txt: (Cy5)


title: SD4_rep1_channel1

description: Raw data in A42_Data.txt: (Cy5)


title: C(WYE_CND_AFB)_72h_D3_3

description: Control for WYE, CND and AFB 72h

source_name: Control for WYE, CND and AFB 72h

value: primary hepatocytes


title: SD5_rep1_channel1

description: Raw data in A41_Data.txt: (Cy3)


title: RA 34 FLS Con2

description: SAMPLE 8

value: rheumatoid arthritis (RA)

tag: treatment


title: SW2_rep1_channel1

description: Raw data in A04_Data.txt: (Cy5)


title: SH6_rep1_channel1

description: Raw data in A43_Data.txt: (Cy3)


title: SW7_rep2_channel2

description: Raw data in A42_Data.txt: (Cy3)


title: SH5_rep2_channel2

description: Raw data in A40_Data.txt: (Cy3)


title: SH7_rep2_channel2

description: Raw data in A04_Data.txt: (Cy3)


title: CD5_rep1_channel1

description: Raw data in A39_Data.txt: (Cy3)


title: SD3_rep1_channel1

description: Raw data in A35_Data.txt: (Cy5)


title: CH5_rep2_channel2

description: Raw data in A34_Data.txt: (Cy3)


title: CH6_rep1_channel2

description: Raw data in A38_Data.txt: (Cy3)


title: SW5_rep2_channel2

description: Raw data in A33_Data.txt: (Cy3)


title: CW4_rep1_channel2

description: Raw data in A39_Data.txt: (Cy5)


title: CW3_rep1_channel1

description: Raw data in A33_Data.txt: (Cy5)


title: CH7_rep1_channel1

description: Raw data in A37_Data.txt: (Cy5)


title: CD7_rep1_channel1

description: Raw data in A32_Data.txt: (Cy5)


title: CW6_rep2_channel2

description: Raw data in A36_Data.txt: (Cy3)


title: CW5_rep2_channel2

description: Raw data in A37_Data.txt: (Cy3)


title: CD8_rep2_channel2

description: Raw data in A35_Data.txt: (Cy3)


title: SH4_rep1_channel1

description: Raw data in A34_Data.txt: (Cy5)


title: SW4_rep1_channel1

description: Raw data in A36_Data.txt: (Cy5)


title: SH8_rep2_channel2

description: Raw data in A31_Data.txt: (Cy3)


title: SD6_rep2_channel2

description: Raw data in A32_Data.txt: (Cy3)


title: CH4_rep1_channel1

description: Raw data in A31_Data.txt: (Cy5)


title: SW4_rep2_channel2

description: Raw data in A30_Data.txt: (Cy3)


title: SW6_rep1_channel1

description: Raw data in A40_Data.txt: (Cy5)


title: CD6_rep1_channel1

description: Raw data in A38_Data.txt: (Cy5)


title: CW8_rep2_channel2

description: Raw data in A03_Data.txt: (Cy5)


title: SD6_rep1_channel1

description: Raw data in A30_Data.txt: (Cy5)


title: CD7_rep2_channel2

description: Raw data in A27_Data.txt: (Cy3)


title: SD3_rep2_channel2

description: Raw data in A29_Data.txt: (Cy3)


title: SW5_rep1_channel1

description: Raw data in A28_Data.txt: (Cy5)


title: SH8_rep1_channel1

description: Raw data in A29_Data.txt: (Cy5)


title: SH4_rep2_channel2

description: Raw data in A28_Data.txt: (Cy3)


title: CH4_rep2_channel2

description: Raw data in A26_Data.txt: (Cy3)


title: CW6_rep1_channel1

description: Raw data in A27_Data.txt: (Cy5)


title: CH8_rep1_channel1

description: Raw data in A22_Data.txt: (Cy3)


title: CD1_rep1_channel1

description: Raw data in A03_Data.txt: (Cy3)


title: CW3_rep2_channel2

description: Raw data in A25_Data.txt: (Cy3)


title: CH5_rep1_channel1

description: Raw data in A25_Data.txt: (Cy5)


title: CW1_rep2_channel1

description: Raw data in A21_Data.txt: (Cy5)


title: CW2_rep1_channel1

description: Raw data in A24_Data.txt: (Cy3)


title: CD4_rep2_channel2

description: Raw data in A23_Data.txt: (Cy3)


title: SW3_rep2_channel2

description: Raw data in A21_Data.txt: (Cy3)


title: SD7_rep1_channel1

description: Raw data in A23_Data.txt: (Cy5)


title: SH2_rep2_channel2

description: Raw data in A22_Data.txt: (Cy5)


title: CD3_rep2_channel2

description: Raw data in A20_Data.txt: (Cy5)


title: CD2_rep1_channel1

description: Raw data in A02_Data.txt: (Cy5)


title: SD2_rep2_channel1

description: Raw data in A20_Data.txt: (Cy3)


title: SH3_rep2_channel1

description: Raw data in A19_Data.txt: (Cy3)


title: CH1_rep1_channel2

description: Raw data in A02_Data.txt: (Cy3)


title: SW8_rep2_channel2

description: Raw data in A24_Data.txt: (Cy5)


title: SH3_rep1_channel1

description: Raw data in A17_Data.txt: (Cy5)


title: SD7_rep2_channel2

description: Raw data in A17_Data.txt: (Cy3)


title: CD8_rep1_channel1

description: Raw data in A26_Data.txt: (Cy5)


title: CH3_rep2_channel2

description: Raw data in A19_Data.txt: (Cy5)


title: CD2_rep2_channel1

description: Raw data in A11_Data.txt: (Cy3)


title: CH2_rep1_channel2

description: Raw data in A01_Data.txt: (Cy5)


title: CW8_rep1_channel1

description: Raw data in A12_Data.txt: (Cy3)


title: SW1_rep2_channel2

description: Raw data in A12_Data.txt: (Cy5)


title: SD2_rep1_channel1

description: Raw data in A18_Data.txt: (Cy5)


title: SD8_rep2_channel2

description: Raw data in A11_Data.txt: (Cy5)


title: SW8_rep1_channel2

description: Raw data in A18_Data.txt: (Cy3)


title: CH2_rep2_channel2

description: Raw data in A10_Data.txt: (Cy3)


title: CW1_rep1_channel1

description: Raw data in A13_Data.txt: (Cy3)


title: CD3_rep1_channel1

description: Raw data in A15_Data.txt: (Cy3)


title: CH8_rep2_channel2

description: Raw data in A13_Data.txt: (Cy5)


title: CD4_rep1_channel1

description: Raw data in A14_Data.txt: (Cy5)


title: SH2_rep1_channel2

description: Raw data in A16_Data.txt: (Cy3)


title: CW2_rep2_channel2

description: Raw data in A15_Data.txt: (Cy5)


title: SW3_rep1_channel1

description: Raw data in A16_Data.txt: (Cy5)


title: CH3_rep1_channel2

description: Raw data in A14_Data.txt: (Cy3)


title: SH7_rep1_channel1

description: Raw data in A10_Data.txt: (Cy5)


title: CW7_rep1_channel1

description: Raw data in A01_Data.txt: (Cy3)


title: T2D_11

first: Michael

last: Volkmar

address: 808 route de Lennik

department: Faculty of Medicine, C.P. 614

institute: Free University of Brussels (U.L.B.)

hyb_protocol: hybridisation on Infinium HumanMethylation27 BeadChip array was performed according to manufacturer's protocol given in Infinium Assay Methylation Protocol Guide (Illumina, Inc.)

scan_protocol: scanning of Infinium HumanMethylation27 BeadChip array was performed according to manufacturer's protocol given in Infinium Assay Methylation Protocol Guide (Illumina, Inc.)

data_processing: BeadArrayReader and Methylation module of GenomeStudio software (Illumina, Inc.)

source_name: whole blood

label_protocol: labeling was performed according to manufacturer's protocol given in Infinium Assay Methylation Protocol Guide (Illumina, Inc.)

growth_protocol: none, blood was drawn from T2D patients and non-diabetic control donors

extract_protocol: genomic DNAs were isolated using QIAamp DNA Mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Bisulfite treatment was performed as recommended for DNA methylation profiling with Illumina Infinium Beadchip arrays; Bisulfite conversion was performed using EZ DNA Methylation™ Kit (Zymo Research)

value: male


title: CTL_12

value: CTL


title: T2D_3


title: T2D_10


title: T2D_12


title: CTL_9


title: T2D_1


title: T2D_6


title: T2D_4


title: T2D_2


title: T2D_7


title: CTL_11


title: T2D_5


title: CTL_6


title: T2D_9


title: Apical cochlea at postnatal day 0 [P0-Apex_2012]

city: Seoul

first: Heejei

last: Yoon

address: 134 Shinchondong, Seodaemoongu

department: Anatomy

country: South Korea

institute: Yonsei University

description: pooled apical cochlea

hyb_protocol: End-labeled cDNA was hybridized for 16 hours at 45℃ and 60 rpm according to Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: GeneChips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix)

data_processing: Affymetrix Command Console Software version 1.1 was used to process the raw images into CEL files. Gene expression estimates were normalized using the robust multiarray averaging (RMA) method.

source_name: wild-type, apical cochlea

label_protocol: Three hundred nano-gram of high quality total RNA was converted into double-stranded cDNA using a random hexamer conjugated with a T7 promoter sequence. cRNA was generated from the double-stranded cDNA using an in vitro transcription (IVT) reaction and then re-converted into cDNA with dNTPs mix containing dUTP. This cDNA was then fragmented by uracil-DNA glycosylase (UDG) and APE1 restriction endonucleases and labeled with a biotinylated dideoxynucleotide by terminal transferase reaction

growth_protocol: Mouse cochlea dissected from day 0 and 8 pups

extract_protocol: Eighty temporal bones were dissected from mice at P0 and P8. After removing the otic capsule, The cochlear tissues were divided into three equal pieces representing the basal, middle and apical turns, and pooled separately. The pooled cochlear tissues were homogenized with a micro-homogenizer, and total RNA was extracted using an RNeasy Mini Kit.

treatment_protocol: Not applicable

tag: tissue

tag: genetic background


title: HCCLM3-siRNA-CTHRC1

city: Shanghai

first: zhigang

last: zhang

address: No. 800, Dong Chuan Road

department: Shanghai cancer Institute

country: China

institute: Shanghai Jiaotong University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PARTEK Genomics Suite 6.4 using RMA normalization.

source_name: HCCLM3, CTHRC1 siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual Affymetrix).

growth_protocol: Cells were maintained in DMEM (Dulbecco’s Modified Eagle Medium) supplemented with 10% (v/v) fetal calf serum at 37°C in a humidified incubator under 5% CO2 conditions.

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

treatment_protocol: The siRNA duplexes were synthesized by Genepharma Company (Shanghai, China). Transfection of the siRNAs into HCCLM3 was done using X-tremeGENE siRNA Transfection Reagent (Roche Diagnostics GmbH, Penzberg, Germany).

tag: cell line type

value: hepatocellular carcinoma cells

tag: transfected sirna


title: CTL_5


title: CTL_10


title: HCCLM3-siRNA-Scramble

source_name: HCCLM3, scramble siRNA control

value: scramble


title: Middle cochlea at postnatal day 8 [P8-Mid_2012]

description: pooled middle cochlea

source_name: wild-type, middle cochlea

tag: age


title: CTL_8


title: Basal cochlea at postnatal day 0 [P0-Base_2012]

description: pooled basal cochlea

source_name: wild-type, basal cochlea


title: Middle cochlea at postnatal day 0 [P0-Mid_2012]

description: pooled middle cochlea


title: Apical cochlea at postnatal day 8 [P8-Apex_2012]

description: pooled apical cochlea


title: CTL_7


title: CTL_3


title: CTL_4


title: IL-12 Treated - 7 days - repeat 4 - mAdbID:115885

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 115885

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single stranded sense DNA were hybridized to Mouse GeneChip 1.0 ST array (Affymetrix) according to the manufacturers' instructions.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).

source_name: IL-12TD cell Treated - 7 days

label_protocol:
Affymetrix Labeling Protocol
Other: Fragmented single stranded sense DNA were terminal labeled according to the manufacturers' instructions.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated using the RNeasy kit (Qiagen)

treatment_protocol:
Treatment type: adoptive transfer therapy
Treatment dose: 1 x 10(5) IL-12TD cells
Treatment time: 7 days
In-vivo treatment: Six to twelve week old mice were injected subcutaneously with 5 x 10(5) B16 melanoma cells. Ten to fourteen days later, they were irradiated with 5 Gy total body irradiation (TBI) and given 1 x 10(5) IL-12 transduced pmel-1 CD8+ T cells (IL-12TD).

value: subcutaneous B16 melanoma tumor

tag: disease state

value: melanoma

tag: other

value: Subcutaneous B16 tumors were excised from mice 7 days following treatment with 1 x 10(5) IL-12TD pmel-1 CD8+ cells and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: CTL_2

tag: gender

tag: disease status


title: kidney from non-treated control mice

city: Augusta

first: Nino

last: Kvirkvelia

state: GA

department: Medicine

institute: Georgia Health Sciences University

description: Gene expression data from mouse kidney

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The data was analyzed with Expression Console using Robust Multichip Analysis (RMA)

source_name: kidney non-treated

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: Female CBL/6mice, 8-10 week  old, were used for all experiments.

treatment_protocol: Acute nephritis was induced in mice by single injection of sheep nephrotoxic serum (13.5 ug/g body weight), followed by prostaglandin E2 (5 ug/g of body weight) administration daily starting from day 2.  Mice were sacrificed on day 7.

value: Kidney

value: Female

tag: strain

value: 8-10 weeks


title: CTL_1


title: Mock Treated - 7 days - repeat 3 - mAdbID:115880

description: mAdb experiment ID: 115880

source_name: Mock cell Treated - 7 days

treatment_protocol:
Treatment type: adoptive transfer therapy
Treatment dose: 1 x 10(5) Mock cells
Treatment time: 3 days
In-vivo treatment: Six to twelve week old mice were injected subcutaneously with 5 x 10(5) B16 melanoma cells. Ten to fourteen days later, they were irradiated with 5 Gy total body irradiation (TBI) and given 1 x 10(5) un-transduced pmel-1 CD8+ T cells (Mock cells).

value: Subcutaneous B16 tumors were excised from mice 7 days following treatment with 1 x 10(5) Mock pmel-1 CD8+ cells and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: Mock Treated - 7 days - repeat 1 - mAdbID:115878

description: mAdb experiment ID: 115878


title: kidney from NTS treated Mice

description: Gene expression data from mouse kidney

source_name: kidney treated with nephrotoxin


title: kidney from NTS/PGE2 treated mice

description: Gene expression data from mouse kidney

source_name: kidney treated with prostaglandin


title: IL-12 Treated - 7 days - repeat 3 - mAdbID:115884

description: mAdb experiment ID: 115884


title: Mock Treated - 7 days - repeat 2 - mAdbID:115879

description: mAdb experiment ID: 115879


title: Mock Treated - 7 days - repeat 4 - mAdbID:115881

description: mAdb experiment ID: 115881


title: IL-12 Treated - 7 days - repeat 2 - mAdbID:115883

description: mAdb experiment ID: 115883


title: IL-12 Treated - 7 days - repeat 1 - mAdbID:115882

description: mAdb experiment ID: 115882


title: FGFko liver chow-B

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: FGF1 null mouse liver on chow, technical replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: FGF1 null mouse liver on chow

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

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

tag: genotype/variation

value: FGF1 null

value: 24 weeks old

value: Normal chow diet

value: liver


title: Mouse_KO2

city: Ibaraki

first: Ken

last: Matsumoto

address: 1-1-1 Tennodai Tsukuba

institute: University of Tsukuba

description: Gene expression data

data_processing: Affimetrix GeneChip Expression Analysis Technical manual Rev3.

extract_protocol: total RNAs were purified using an RNeasy Micro Kit

value: ICR

tag: developmental stage

value: embryo

value: 8.5dpc（at the 3 to 4 somite stage prior to the start of circulation）


title: No Treatment - 7 days - repeat 4 - mAdbID:115877

description: mAdb experiment ID: 115877

source_name: No Treatment - 7 days

treatment_protocol:
Treatment time: 7 days
In-vivo treatment: Six to twelve week old mice were injected subcutaneously with 5 x 10(5) B16 melanoma cells.

value: Subcutaneous B16 tumors were excised from mice 7 days following no treatment and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: Mouse_WT2

description: Gene expression data

hyb_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3

value: WT


title: T2D islets (4301311023_L)

hyb_protocol: hybridization on Infinium HumanMethylation27 BeadChip array was performed according to manufacturer's protocol given in Infinium Assay Methylation Protocol Guide (Illumina, Inc.)

data_processing: BeadArrayReader and Methylation module of GenomeStudio software (Illumina, Inc.). Image data was analyzed with GenomeStudio Methylation module v1.0.5; no normalisation was performed.  Analyses performed on the non-normalized data.

source_name: human pancreatic islets

extract_protocol: genomic DNAs were isolated using Wizard SV Genomic DNA kit (Promega Corp.) according to manufacturer's protocol

value: diabetic

value: male

tag: age (y)

tag: group

value: CASE

value: type 2 diabetes

tag: cell type

value: pancreatic islets


title: FGFko liver chow-A

description: FGF1 null mouse liver on chow, technical replicate 1


title: Mouse_KO1

description: Gene expression data

scan_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3


title: Mouse_WT1

description: Gene expression data

label_protocol: Affimetrix GeneChip Expression Analysis Technical manual Rev3


title: No Treatment - 7 days - repeat 3 - mAdbID:115876

description: mAdb experiment ID: 115876

value: subcutaneous B16 melanoma tumor

value: melanoma


title: T2D islets (4301311023_F)


title: No Treatment - 7 days - repeat 2 - mAdbID:115875

description: mAdb experiment ID: 115875


title: Mouse_EC2

description: Gene expression data

value: Flk1 positive cell


title: WT liver chow-A

description: wild-type mouse liver on chow, technical replicate 1

source_name: wild-type mouse liver on chow

value: wild-type


title: WT liver chow-B

description: wild-type mouse liver on chow, technical replicate 2

value: 24 weeks old


title: T2D islets (4301311009_C)


title: IL-12 Treated - 3 days - repeat 2 - mAdbID:115871

description: mAdb experiment ID: 115871

source_name: IL-12TD cell Treated - 3 days

treatment_protocol:
Treatment type: adoptive transfer therapy
Treatment dose: 1 x 10(5) IL-12TD cells
Treatment time: 3 days
In-vivo treatment: Six to twelve week old mice were injected subcutaneously with 5 x 10(5) B16 melanoma cells. Ten to fourteen days later, they were irradiated with 5 Gy total body irradiation (TBI) and given 1 x 10(5) IL-12 transduced pmel-1 CD8+ T cells (IL-12TD).

value: Subcutaneous B16 tumors were excised from mice 3 days following treatment with 1 x 10(5) IL-12TD pmel-1 CD8+ cells and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: T2D islets (4301311023_H)


title: CTL islets (4871081068_L)

value: control

value: CTL

value: non-diabetic


title: IL-12 Treated - 3 days - repeat 4 - mAdbID:115873

description: mAdb experiment ID: 115873


title: Mouse_EC1

description: Gene expression data

value: ICR

value: embryo

value: 8.5dpc（at the 3 to 4 somite stage prior to the start of circulation）


title: T2D islets (4301311009_A)

value: diabetic


title: IL-12 Treated - 3 days - repeat 3 - mAdbID:115872

description: mAdb experiment ID: 115872


title: Basal cochlea at postnatal day 8 [P8-Base_2012]

description: pooled basal cochlea


title: No Treatment - 7 days - repeat 1 - mAdbID:115874

description: mAdb experiment ID: 115874

value: Subcutaneous B16 tumors were excised from mice 7 days following no treatment and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: FGFko liver HFD-A

description: FGF1 null mouse liver on HFD, technical replicate 1

source_name: FGF1 null mouse liver on HFD

value: FGF1 null

value: High-fat diet

value: liver


title: FGFko liver HFD-B

description: FGF1 null mouse liver on HFD, technical replicate 2


title: WT liver HFD-B

description: wild-type mouse liver on HFD, technical replicate 2

source_name: wild-type mouse liver on HFD


title: Eng+Flk1+_rep3

city: Minneapolis

first: Rita

last: Perlingeiro

state: MN

address: 312 Church ST SE; NHH 4-124

institute: University of Minnesota

hyb_protocol: The Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K, using Agilent's recommended hybridization chamber and oven.  Finally, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for one minute at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37°C) for one minute.  The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent microarrays were detected using Agilent Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the Microarray Image files.  The software determines feature intensities (including background substraction), rejects outliers, and calculates statistical confidences.
Microarray results were analyzed with GeneSpring GX software. Normalization method: signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.
These normalized signal intensities are joined to a common table the single-experiment normalized data list. The list comprises in addition to the normalized intensity values the feature glsPosAndSignif which indicates with a value=1 that the signal intensity is positive and significant above the background and a value=0 that the signal intensity is not positive and significant above the background.  Table K1099_A3550_intensity_norm.txt is linked as a supplementary file on the Series record.

source_name: E7.5, sorted Eng+Flk1+_replicate 3

label_protocol: 250ng of each of the cDNA were used as a template for Cy3 labeling, which was performed according to Miltenyi Biotec's undisclosed protocol.

growth_protocol: Pool of E7.5 whole embryos were stained for endoglin and Flk-1 using fluorochrome conjugated primary antibodies, and fractions were sorted based on these two markers using BD FACS aria.

extract_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure.  Briefly, the amplification is based on a global PCR protocol mRNA-derived cDNA.  mRNA was isolated via magnetic bead technology.  Amplified cDNA samples were quantified using the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: RNA was prepared using SuperAmpTM lysis buffer (Miltenyi Biotec) and stored appropriately according to the instructions of the SuperAmp preparation kit.

tag: embryo

value: E7.5 embryo (fractionated)

tag: embryo fraction


title: Eng+Flk1-_rep3

source_name: E7.5, sorted Eng+Flk1-_replicate 3


title: Eng+Flk1-_rep2

source_name: E7.5, sorted Eng+Flk1-_replicate 2


title: Eng+Flk1-_rep1

source_name: E7.5, sorted Eng+Flk1-_replicate 1


title: WT liver HFD-A

description: wild-type mouse liver on HFD, technical replicate 1

tag: treatment

tag: tissue


title: IL-12 Treated - 3 days - repeat 1 - mAdbID:115870

description: mAdb experiment ID: 115870

value: subcutaneous B16 melanoma tumor

value: melanoma


title: T2D_8

city: Brussels

source_name: whole blood

value: male


title: Mock Treated - 3 days - repeat 4 - mAdbID:115869

description: mAdb experiment ID: 115869

source_name: Mock cell Treated - 3 days

value: Subcutaneous B16 tumors were excised from mice 3 days following treatment with 1 X 10(5) Mock pmel-1 CD8+ cells and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: CTL islets (4690141078_F)

value: pancreatic islets


title: FGFko eWAT HFD-B

description: FGF1 null mouse eWAT on HFD, technical replicate 2

source_name: FGF1 null mouse eWAT on HFD

value: 24 weeks old

value: epidydimal white adipose tissue


title: Eng+Flk1+_rep2

source_name: E7.5, sorted Eng+Flk1+_replicate 2


title: CTL islets (4564612128_L)

value: control

value: CTL

value: non-diabetic


title: Eng-Flk1-_rep3

source_name: E7.5, sorted Eng-Flk1-_replicate 3


title: FGFko eWAT HFD-A

description: FGF1 null mouse eWAT on HFD, technical replicate 1


title: CTL islets (4301311023_C)


title: No Treatment - 3 days - repeat 2 - mAdbID:115863

description: mAdb experiment ID: 115863

source_name: No Treatment - 3 days

treatment_protocol:
Treatment time: 3 days
In-vivo treatment: Six to twelve week old mice were injected subcutaneously with 5 x 10(5) B16 melanoma cells.

value: Subcutaneous B16 tumors were excised from mice 3 days following no treatment and single cell suspensions were resuspended into RLT buffer (Qiagen) and frozen at -80° F until analysis.


title: Mock Treated - 3 days - repeat 3 - mAdbID:115868

description: mAdb experiment ID: 115868


title: No Treatment - 3 days - repeat 3 - mAdbID:115864

description: mAdb experiment ID: 115864


title: CTL islets (4564612128_J)


title: CTL islets (4690141078_G)


title: WT eWAT HFD-A

description: wild-type mouse eWAT on HFD, technical replicate 1

source_name: wild-type mouse eWAT on HFD

value: wild-type


title: No Treatment - 3 days - repeat 4 - mAdbID:115865

description: mAdb experiment ID: 115865


title: WT eWAT chow-B

description: wild-type mouse eWAT on chow, technical replicate 2

source_name: wild-type mouse eWAT on chow

value: Normal chow diet


title: Eng-Flk1+_rep3

source_name: E7.5, sorted Eng-Flk1+_replicate 3


title: FGFko eWAT chow-A

description: FGF1 null mouse eWAT on chow, technical replicate 1

source_name: FGF1 null mouse eWAT on chow

value: FGF1 null


title: Eng-Flk1+_rep2

source_name: E7.5, sorted Eng-Flk1+_replicate 2


title: WT eWAT HFD-B

description: wild-type mouse eWAT on HFD, technical replicate 2

value: High-fat diet


title: CTL islets (4564612127_K)

source_name: human pancreatic islets


title: CTL islets (4301311023_B)


title: CTL islets (4690141078_H)


title: Eng-Flk1+_rep1

source_name: E7.5, sorted Eng-Flk1+_replicate 1


title: Mock Treated - 3 days - repeat 1 - mAdbID:115866

description: mAdb experiment ID: 115866


title: Eng+Flk1+_rep1

source_name: E7.5, sorted Eng+Flk1+_replicate 1


title: Eng-Flk1-_rep2

source_name: E7.5, sorted Eng-Flk1-_replicate 2


title: WT eWAT chow-A

description: wild-type mouse eWAT on chow, technical replicate 1


title: FGFko eWAT chow-B

description: FGF1 null mouse eWAT on chow, technical replicate 2


title: Mock Treated - 3 days - repeat 2 - mAdbID:115867

description: mAdb experiment ID: 115867


title: CTL islets (4690141078_E)


title: CTL islets (4301311023_A )


title: Eng-Flk1-_rep1

source_name: E7.5, sorted Eng-Flk1-_replicate 1


title: No Treatment - 3 days - repeat 1 - mAdbID:115862

description: mAdb experiment ID: 115862


title: MLL-ENL-ERtm spleen, terminal stage, biological rep 1

status: Public on Apr 22 2012

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Gene expression data from spleen cells derived from mice at the terminal disease stage after 21 months of tamoxifen treatment

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.  The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Differential expression analysis and normalization of chip data was performed in the R statistical environment(2.9.2) using the Limma and Affy packages from Bioconductor project . Raw data were quantile normalized and summarized probe set expression values were computed using the RMA method. Differentially expressed genes were identified using lmFit function (moderated t-statistics) and Benjamini-Hochberg corrected (p<0.05).  Differential expression analysis and normalization of chip data was performed in the R statistical environment(2.9.2) using the Limma and Affy packages from Bioconductor project . Raw data were quantile normalized and summarized probe set expression values were computed using the RMA method. Differentially expressed genes were identified using lmFit function (moderated t-statistics) and Benjamini-Hochberg corrected (p<0.05).

label: Biotin

source_name: MLL-ENL-ERtm spleen with a myeloproliferative phenotype at terminal stage of disease

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: Primary cells derived from mice were used for RNA isolation.

extract_protocol: RNA was isolated using the RNeasy kit according to manufacturer's recommendations (Qiagen).

treatment_protocol: Mice were treated with tamoxifen in concentration of 300 mg/kg chow.

tag: disease stage

value: terminal stage - proliferation, low or absent DDR and no senescence

tag: time of tamoxifen treatment

value: 21 months of tamoxifen treatment in vivo

value: spleen


title: Wild-type spleen, biological rep 5

description: Gene expression data from spleen cells derived from wild-type mice after 11 months of tamoxifen treatment

source_name: Wild-type spleen, age- and time-matched negative control

value: 11 months of tamoxifen treatment in vivo


title: MLL-ENL-ERtm spleen, terminal stage, biological rep 2

description: Gene expression data from spleen cells derived from mice at the terminal disease stage after 23 months of tamoxifen treatment

value: 23 months of tamoxifen treatment in vivo


title: Wild-type bone marrow, biological rep 4

description: Gene expression data from bone marrow cells derived from wild-type mice after 7 months of tamoxifen-treatment

source_name: Wild-type bone marrow, age- and time-matched negative control

value: 7 months of tamoxifen treatment in vivo

value: bone marrow


title: Wild-type spleen, biological rep 3

description: Gene expression data from spleen cells derived from wild-type mice after 9 months of tamoxifen treatment

value: 9 months of tamoxifen treatment in vivo


title: MLL-ENL-ERtm spleen, progression, biological rep 3

description: Gene expression data from spleen cells derived from mice at progressed stage of disease after 9 months of tamoxifen treatment

source_name: MLL-ENL-ERtm spleen with a myeloproliferative phenotype at progressed stage of disease

value: progression - partial senescence and DDR is maintained


title: Wild-type bone marrow, biological rep 2


title: MLL-ENL-ERtm spleen, progression, biological rep 1

description: Gene expression data from spleen cells derived from mice at progressed stage of disease after 10 months of tamoxifen treatment

value: 10 months of tamoxifen treatment in vivo


title: Wild-type spleen, biological rep 4


title: Wild-type spleen, biological rep 2

description: Gene expression data from spleen cells derived from wild-type mice after 8 months of tamoxifen treatment

value: 8 months of tamoxifen treatment in vivo


title: Wild-type spleen, biological rep 1

description: Gene expression data from spleen cells derived from wild-type mice after 24 months of tamoxifen treatment

value: 24 months of tamoxifen treatment in vivo


title: MLL-ENL-ERtm spleen, early stage, biological rep 2

description: Gene expression data from spleen cells derived from mice at the early stage of disease after 7 months of tamoxifen treatment

source_name: MLL-ENL-ERtm spleen with a myeloproliferative phenotype at the early stage of disease

value: early - induced proliferation and DDR


title: Wild-type bone marrow, biological rep 3


title: MLL-ENL-ERtm bone marrow, senescence, biological rep 3

description: Gene expression data from bone marrow cells with signs of senescence derived after 8 months of tamoxifen treatment

source_name: MLL-ENL-ERtm bone marrow with a myeloproliferative phenotype showing signs of senescence

tag: cellular state

value: senescence


title: MLL-ENL-ERtm spleen, early stage, biological rep 3


title: MLL-ENL-ERtm spleen, terminal stage, biological rep 3

description: Gene expression data from spleen cells derived from mice at the terminal disease stage after 19 months of tamoxifen treatment

value: 19 months of tamoxifen treatment in vivo


title: MLL-ENL-ERtm spleen, progression, biological rep 2


title: MLL-ENL-ERtm bone marrow, senescence, biological rep 2


title: MLL-ENL-ERtm spleen, early stage, biological rep 1


title: Wild-type bone marrow, biological rep 1

description: Gene expression data from bone marrow cells derived from wild-type mice after 8 months of tamoxifen-treatment


title: MLL-ENL-ERtm bone marrow, senescence, biological rep 1


title: MLL-ENL-ERtm bone marrow, transition, biological rep 4

description: Gene expression data from bone marrow cells transitting to senescence derived after 7 - 8 months of tamoxifen treatment

source_name: MLL-ENL-ERtm bone marrow with a myeloproliferative phenotype in a transition state from proliferation to senescence

value: the transition period of lower proliferation and high DDR activity

value: from 7 to 8 months of tamoxifen treatment in vivo


title: MLL-ENL-ERtm bone marrow, transition, biological rep 2


title: MLL-ENL-ERtm bone marrow, transition, biological rep 3


title: Caco2_control

first: Satoshi

last: Kondo

institute: Toray Industries,Inc.

description: Caco2 control

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

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

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

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

growth_protocol: Caco2 cell maintained in Dulbecco’s modified Eagle medium,supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extraction of  cell lines was performed according to the manufacturer’s instructions by ISOGEN2.

treatment_protocol: Caco2 cell was treated with 5μM TNFα, 10μM IL1α, 10μM IL1β, or 10μM IL6 for 6 hours.

tag: cell line

value: human epithelial colorectal adenocarcinoma cells


title: Caco2_IL1β 6h

description: Caco2 IL1β

tag: inflammatory cytokines used

value: 10μM IL1β


title: MLL-ENL-ERtm bone marrow, proliferation, biological rep 3

description: Gene expression data from highly proliferating bone marrow cells derived after 7 months of tamoxifen treatment

source_name: MLL-ENL-ERtm bone marrow with a myeloproliferative phenotype in the early proliferation state

value: high proliferation state with low DDR signaling


title: Caco2_TNFα 6h

description: Caco2 TNFα

value: 5μM TNFα


title: Caco2_IL6 6h

description: Caco2 IL6

value: 10μM IL6


title: Caco2_IL1α 6h

description: Caco2 IL1α

value: 10μM IL1α


title: MLL-ENL-ERtm bone marrow, transition, biological rep 1

value: bone marrow


title: MLL-ENL-ERtm bone marrow, proliferation, biological rep 4

value: 7 months of tamoxifen treatment in vivo


title: WAT_ZT13_SR_2

status: Public on Apr 21 2012

city: Göttingen

first: Johanna

last: Barclay

address: Am Fassburg 11

country: Germany

institute: MPI-BPC

hyb_protocol: 17 hours, 60 rpm, 45C

scan_protocol: GeneChip Scanner 3000

data_processing: Data was extracted from CEL files using dChip. Values are MM/PM normalized signal estimates from dChip software.

source_name: epididymal WAT

label_protocol: Labelling was with GeneChip WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen)

treatment_protocol: SR mice were kept awake using 'gentle handing' method from ZT0 until ZT6 for 5 consecutive days, left to sleep ad libitum for 2 days, and sleep restrictiong was repeated for another 5 days.  Control mice were kepts undisturbed in parallel.

tag: gender

value: Male

tag: age

value: 10-12 weeks

value: epididymal WAT

value: sleep restricted

tag: time point


title: WAT_ZT19_SR_2

tag: strain


title: WAT_ZT13_SR_3


title: WAT_ZT19_SR_1


title: WAT_ZT19_SR_3


title: MLL-ENL-ERtm bone marrow, proliferation, biological rep 2


title: WAT_ZT19_Control_1

value: control


title: WAT_ZT1_SR_3


title: WAT_ZT7_SR_3


title: WAT_ZT7_SR_2


title: WAT_ZT1_SR_2


title: WAT_ZT19_Control_2


title: WAT_ZT19_Control_3


title: WAT_ZT13_SR_1


title: WAT_ZT7_Control_3


title: WAT_ZT1_SR_1


title: WAT_ZT7_Control_2


title: WAT_ZT7_SR_1


title: WAT_ZT13_Control_1


title: Liver_ZT19_SR_3

source_name: Liver

value: Liver


title: MLL-ENL-ERtm bone marrow, proliferation, biological rep 1


title: WAT_ZT13_Control_3


title: WAT_ZT13_Control_2


title: WAT_ZT1_Control_1


title: WAT_ZT1_Control_2


title: Liver_ZT19_SR_2


title: 884

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

hyb_protocol: Array slides were washed twice in Wash Buffer II (0.1% SDS, 0.1x SSC), each time for 30S. Then slides were transferred in pre-hybridization buffer (0.1% BSA, 0.1% SDS, 5x SSC) for 120 min. After washing in Wash Buffer II and III (0.1SSC), the denatured hybridization probe mixture (30% formamide, 5x SSC, 0.1% SDS, 0.1mg/ml Salmon sperm DNA, 1x Denhardt’s Solution and 80 pmoles Cy3 and Cy5 probe) was added to slides and incubated for overnight. Next day, the array slides were washed in Wash Buffer I (0.1% SDS, 2x SSC), II and III

scan_protocol: Slides were scanned using an Axon autoloader scanner

data_processing: Data were normailsed by  LOWESS regression using Genespring GX7.3.1

organism: Escherichia coli O157:H7

label_protocol: gDNA was labelled with Cy3&5 using the Bioprime Plus Array CGH Genomic Labelling System (Invitrogen)

growth_protocol: Cultures were grown overnight in LB media

extract_protocol: gDNA was extracted using a ChargeSwitch gDNA Mini Bacteria Kit (Invitrogen)

treatment_protocol: No treatment

tag: phage type

tag: tts (type 3 secretion profile)

value: high

organism: Escherichia coli O157:H7 str. Sakai

source_name: [Universal control] Sakai

value: Sakai

tag: sample type

value: reference


title: 8997

value: low


title: 13425


title: 17489


title: Liver_ZT19_SR_1


title: Liver_ZT13_SR_2


title: WAT_ZT7_Control_1


title: WAT_ZT1_Control_3


title: Liver_ZT7_SR_3


title: 878


title: TUV93

source_name: [test] TUV93

value: unknown


title: Liver_ZT13_SR_1


title: 909


title: Liver_ZT13_SR_3


title: 17478


title: Liver_ZT7_SR_1


title: Liver_ZT1_SR_2


title: Liver_ZT19_Control_1


title: 16438


title: Liver_ZT1_SR_3


title: Liver_ZT7_SR_2


title: Cy5 HUVEC+GATA4 / Cy3 HUVEC rep1

city: paris

first: isabelle

middle: catherine

last: vigon

address: 22 rue Méchain

country: France

institute: Institut Cochin, inserm u1016, cnrs umr8104, Université Paris-Descarte

description: CY5 (HUVEC+GATA4) / CY3 ((HUVEC)

hyb_protocol: After 1H of Pre-hybridization with ethanolamine and NaBorate, an over night direct hybridization sample (Cy5 vs Cy3) in agilent hybridization buffer was realized at 60°C.

scan_protocol: Slides were scanned with DNA Microarray Scanner (Agilent), with 10 µm resolution.The TIFF images were imported into GenePix Pro 6.0.1.00 (Axon, http://www.moleculardevices.com/pages/software/gn_genepix_pro.html)(MDC/Axon Instruments, Sunnyvale, CA, USA). This program was used for image and grid alignment, spot detection and extraction of Cy5 (635 nm) and Cy3 (532 nm) intensities for all detected spots. Spots with little or no signal and obvious defects were flagged as non utilizable spots and labeled ‘not assigned’ (NA), to exclude them from further analysis.

data_processing: Data for each slide were analyzed using the functions of the BioConductor marray package (http://www.bioconductor.org/) to check for the absence of abnormal bias during hybridization. Data were then normalized, using the Loess approach (window of 40%) implemented in the BioConductor marray package (Cleveland WS: Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 1979, 74:829-836. ) comparative analysis were done  with the limma modified t-test package of Bioconductor (Smyth, G. K.2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3. http://www.bepress.com/sagmb/vol3/iss1/art3).

source_name: HUVEC cells

label_protocol: One µg of total RNA was used to generate the double strand cDNA completed with a T7 sequence,  after purification (Qiagen QIAquick PCR Purification,), cDNAs were used for synthesis and amplification  of dye labelled aRNAs. Message RNA amplification was carried out according to the manufacturer's protocol of the Amino Allyl MessageAmpII aRNA Amplificaion kit (Ambion) with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies) .Cy5 or Cy3 mono-reactive Dye Pack GE HEALTHCARE   were conjugated via an amino allyl group. The Cy3 and Cy5 labels were switched, or dye-flipped, between SP and MP aRNA.Labeling were performed using 60 pm of fluorescence for each sample aRNA

growth_protocol: HUVECs were cultured in Endothelial Basal Medium-2 (EBM-2, Lonza, Basel, Switzerland) completed with the Endothelial Growth Medium-2 (EGM-2, Lonza), penicillin (100 U/ml), streptomycin (100 μg/ml), L-Glutamine (2 mM), at 37°C in a fully humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol. The quality of the extracted RNA was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: HUVECs grown to 80% confluence were transduced with 2.5 µg of p24 equivalent recombinant vector (lentivirus containing coding sequence of Nkx2.5, GATA4 or GFP as control) per ml of culture, twice over 24 h. Cells were then washed and cultured in the EBM-2/ EGM-2 medium, 12 days before analysis

tag: cell type

value: Human Umbilical Vein Endothelial Cells

tag: expression


title: 16177


title: Cy5 HUVEC / Cy3 HUVEC+NKX2.5+GATA4

description: CY5 (HUVEC) / CY3 (HUVEC+NKX2.5+GATA4)

value: NKX2,5 and GATA4


title: Liver_ZT19_Control_2


title: Liver_ZT1_SR_1


title: Cy5 HUVEC+GATA4 / Cy3 HUVEC rep2

description: CY5 (HUVEC+GATA4) / CY3 ((HUVEC)


title: 879


title: Liver_ZT13_Control_1


title: Liver_ZT19_Control_3


title: Liver_ZT13_Control_3


title: Liver_ZT7_Control_3


title: Cy5 HUVEC+NKX2.5+GATA4 / Cy3 HUVEC

description: CY5 (HUVEC+NKX2.5+GATA4) / CY3 (HUVEC)


title: 17706


title: Liver_ZT7_Control_2


title: Cy5 HUVEC / Cy3 HUVEC+GATA4 dye-swap rep2

description: CY5 ((HUVEC) / CY3 (HUVEC+GATA4)


title: 888


title: Cy5 HUVEC / Cy3 HUVEC+GATA4 dye-swap rep1

description: CY5 ((HUVEC) / CY3 (HUVEC+GATA4)


title: Liver_ZT1_Control_1


title: Cy5 HUVEC / Cy3 HUVEC+NKX2,5 dye-swap rep1

description: CY5 (HUVEC) / CY3 (HUVEC+NKX2,5)


title: Cy5 HUVEC+NKX2,5 / Cy3 HUVEC rep2

description: CY5 (HUVEC+NKX2,5) / CY3 (HUVEC)


title: P. falciparum-treated-3

status: Public on Apr 20 2012

city: London

first: Sarah

last: Tarr

address: Gower Street

department: ISMB

institute: UCL

description: Gene expression data from LD50 antimycin A-treated Plasmodium falciparum

hyb_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).

data_processing: Raw CEL files were imported into Bioconductor (Gentleman et al., 2004) for data analysis.  Microarrays were analysed for RNA degradation prior to normalisation.  Non-Plasmodium probesets were removed using the altcdfenvs package (Gautier et al., 2004) and microarray data were normalised using GCRMA (Wu et al., 2004).  Differential gene expression was analysed using Linear Models for Microarray Analysis (LIMMA) (Smyth, 2004); the triplicate antimycin A treatment microarrays were contrasted against the triplicate control (DMSO-treated) microarrays.

organism: Plasmodium falciparum

source_name: P. falciparum, treated

growth_protocol: Blood stage P. falciparum 3D7 was maintained in continuous culture in vitro at 37 ºC using the candle-jar method.  Cultures were maintained in citrated human blood at 2 % hematocrit with complete culture media (RPMI 1640 + L-Glutamine (Gibco) with 5 % w/v AlbuMAX I (Invitrogen), 50 μg.ml-1 hypoxanthine, 25 mM HEPES (Gibco) and 25 μg.ml-1 gentamycin (Sigma), pH of 7.6).  Parasitaemia was assessed by thin blood smears stained with Giemsa (Sigma).  Percentage infection of red blood cells was determined by cell counts under an oil immersion light microscope.  Synchronous parasites were obtained by the Stockholm sorbitol method on two consecutive life cycles

extract_protocol: RNA was harvested using Trizol (Invitrogen) as described (Kyes, 2004).  RNA concentration and purity were determined using a NanoDrop (Thermo) and RNA integrity was tested using an Agilent Bioanalyzer (Cambridge Genomic Services, Department of Pathology)

treatment_protocol: Triplicate 15 ml cultures containing synchronous, ring stage parasites at 5 % parasitaemia were treated with 600 nM antimycin A in DMSO (or 1/2000 vol. DMSO for controls) for 24 hours.

tag: agent

value: Antimycin A


title: Liver_ZT13_Control_2

tag: treatment


title: Cy5 HUVEC+NKX2,5 / Cy3 HUVEC rep1

description: CY5 (HUVEC+NKX2,5) / CY3 (HUVEC)


title: Liver_ZT1_Control_2

tag: tissue


title: Liver_ZT7_Control_1


title: C. difficile rep3

city: Coleraine

first: Nigel

middle: G

last: Ternan

state: Co. Londonderry

address: Cromore Road

department: School of Biomedical Sciences

institute: University of Ulster

description: Biological replicate 3 of 3

hyb_protocol: Prior to hybridisation, labelled aRNA was purified using Qiagen’s RNeasy® MinElute Cleanup Kit as per the manufacturer’s instructions.  The labelled probes were then hybridised to a C. difficile strain 630 array (BUGS CD630 gene expression array plus Plasmid pCD630, 8 x 15k array, v2.01) comprising 3,776 genes using the Gene Expression Hybridisation Kit (Agilent Technologies) as described in the manufacturer’s protocol

scan_protocol: The hybridised arrays were subsequently scanned at 532 nm and 635 nm, corresponding to Cy3 and Cy5 excitation maxima, using an Agilent G2505C Microarray Scanner equipped with the extended dynamic range (XDR) software for improved resolution.  The data was then extracted from raw microarray image files and the probe signals were subsequently quantified using Agilent’s Feature Extraction Software version 10.5.1.1.

data_processing: Upon normalisation by the locally weighted scatterplot smoothing (LOWESS) algorithm, the data was imported to GeneSpring GX version 11.0 (Agilent Technologies) where the minimum fluorescence intensity was set to 1.  The mean normalised log2 fluorescence ratios and standard errors of mean were then calculated across all probes for an individual gene.  To test for statistical differences between the heat-stress and control condition, a 5% confidence level was applied in conjunction with the Benjamini-Hochberg False-Discovery Rate (FDR) multiple testing correction.

organism: Clostridioides difficile 630

source_name: C. difficile strain 630, 41°C

label_protocol: Using Ambion’s MessageAmp™ II-Bacteria RNA Amplification Kit, the template mRNA samples were: (a) polyadenylated; (b) the mRNA samples with a stable poly(A) tail were reverse-transcribed into first strand cDNA using an oligo(dT)-primer bearing a T7 promoter; (c) the cDNA samples were then converted into double-stranded DNA (dsDNA); (d) dsDNA was then used as a template for in vitro transcription with T7 RNA polymerase to generate antisense RNA (aRNA); (e) aRNA was then finally labelled with fluorescent dyes (Cy3 and Cy5) to create labelled probes for hybridisation.  In this study, a dye-swap (i.e. control samples labelled with Cy3 and heat-stress samples labelled with Cy5 and vice versa)was performed in order to generate technical replicates and to compensate for any potential bias introduced as a result of inherent discrepancies in Cy dye incorporation.

growth_protocol: Clostridium difficile strain 630 was grown in BHI broth or on BHI agar (Oxoid) at 37°C in a MACS MG500 Anaerobic workstation fitted with an airlock (Don Whitley Scientific, UK).  Three separate colonies on BHI agar were inoculated into three separate BHI starter cultures and incubated overnight.  Each starter was subsequently used to inoculate duplicate fresh BHI broth cultures at 5% v/v.

extract_protocol: Cells were harvested by centrifugation at 9,000 x g for 5 min at 4°C. Total RNA was extracted from aliquots of 4.0 E8 cells using the Qiagen RNAprotect® Bacteria Reagent Handbook Protocol 4: Enzymatic Lysis and Proteinase K Digestion of Bacteria with modifications.  A mechanical lysis step was incorporated – cells in TE buffer with proteinase K and lysozyme were added to a Lysing Matrix A tube (MP Biomedicals) and treated in a Fastprep FP120 machine (MP Biomedicals) at speed 5.5 for 30s.  The Qiagen protocol was then followed and both on-column and in-solution DNAse digestions, with a final on-column cleanup were used to purify the RNA. RNA samples were confirmed free of contaminating genomic DNA by PCR and stored at -70°C until required. For all six RNA samples (3 heat stress, 3 control), an RNA integrity number of >9.6 was obtained, with A260/280 values of > 2.0, and 23S:16S rRNA ratios of ≥ 1.4.

treatment_protocol: Heat stress was induced in one of each of the three sets of duplicate cultures in the early exponential phase (D650nm=0.3) of growth using a water bath set at 41°C and cells were harvested from all six cultures (3 control, 3 heat shock) at late log phase (D650 = 1.1) approximately 3h later.

tag: growth phase

value: late log (D650nm = 1.1)

source_name: C. difficile strain 630, 37°C


title: C. difficile rep1 - dye flip

description: Biological replicate 1 of 3 - dye flip


title: ATRA

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: Gene expression  from primary Wilms tumor cells ws568li, treated with ATRA

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and variance stabilization normalization (VSN) as normalization method

source_name: primary Wilms tumor cells ws568li

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Primary Wilms tumor cells were established from fresh tumor material and maintained in Dulbecco’s Modified Eagle Medium supplemented with 10 % FCS and 1 % penicillin/streptomycin in a humidified chamber at 37C and 5 % CO2.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated with 10 µM all-trans retinoic acid for 4 days, untreated control cells received 1 µl/ml DMSO.

value: primary Wilms tumor cells ws568li

value: ATRA


title: C. difficile rep2 - dye flip

description: Biological replicate 2 of 3 - dye flip


title: Liver_ZT1_Control_3

value: Male


title: P. falciparum-control-3

description: Gene expression data from untreated Plasmodium falciprum

scan_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).

source_name: P. falciparum, control

value: DMSO


title: P. falciparum-control-2

label_protocol: Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).


title: P. falciparum-control-1


title: Cy5 HUVEC / Cy3 HUVEC+NKX2,5 dye-swap rep2

description: CY5 (HUVEC) / CY3 (HUVEC+NKX2,5)


title: untreated

description: Gene expression data from primary Wilms tumor cells ws568li, untreated

value: untreated


title: C. difficile rep3 - dye flip

description: Biological replicate 3 of 3 - dye flip


title: P. falciparum-treated-1


title: P. falciparum-treated-2


title: Emerin-null miRNA, technical rep 2

city: Chicago

first: Jim

last: Holaska

state: IL

address: 5841 S. Maryland Ave, MC 6088

department: Medicine, Section of Cardiology

institute: University of Chicago

hyb_protocol: 1 ug of tailed RNA were hybridized for 16 hr at 48C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Proliferative emerin-null H2K myogenic precursor cells

label_protocol: Biotinylated cRNA was preparedfrom 1ug total RNA according to the FlashTag protocol (Genisphere).

growth_protocol: Cultured in DMEM containing 10% HI-FBS, 2% L-glutamine, 2% Chick embryo extract and 1% Pen/Strep.

extract_protocol: Qiagen miRNeasy kit according to manufacterer's instructions.

treatment_protocol: Cells were collected according to miRNeasy kit protocol.

value: H2K Myoblasts

tag: genotype

value: emerin null


title: larvae_69B>MANF_70

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
LOVER_70
gene expression of MANF ectopic overexpression

hyb_protocol: 5µg of each differentially labelled aaRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's fruit fly Microarray Kit 4x44k, P/N G2519F(Agilent Microarray Design ID 018972) 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 and drying on theAxon 4200AL Scanner using three color scan setting for 4x44k array slides.

data_processing: The microarrays images were segmented and the median intensity of each spot was estimated by the software GenePixPro® 6.0 (Axon). The data were then imported into R software and preprocessed by the BioConductor package Limma.

source_name: larvae 30-44hrs AEL

label_protocol: Diluted spike controls (Agilent) were added to 1µg total RNA and labelled aaRNA was prepared using either cyanine 3 (Cy3) or Cy5 or Alexa 488 dye with Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer's instructions.  Dye incorporation and received aaRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Drosophila melanogaster adults, embryos and larvae were growing at 25 degrees C, adults were laying eggs on apple juice agar plates with yeast paste

extract_protocol: total RNA was extracted with Qiagene RNAeasy extraction Kit (Qiagene) according to manufacturer's recommendations, treated with DNase (Promega) and purified by RNA purification kit (Qiagene). RNA was quantified using a NanoDrop-1000 spectrophotometer,  quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: embryos were collected from apple juice plates, washed with embryowash and dechorionated by routine chlorine treatment and washed carefully, embryos and larvae were picked according to genotypes under microscope into fresh applejuice plates, collected into Eppendorf tubes and snap freezed in liquid nitrogen.

value: whole animal

tag: developmental stage

value: larval

tag: gene expression

value: MANF ectopic overexpression


title: Emerin-null miRNA, technical rep 1

tag: cell line


title: Wildtype miRNA, technical rep 2

source_name: Proliferative wildtype H2K myogenic precursor cells

value: wild type


title: Emerin-null mRNA, technical rep 2


title: C. difficile rep2

description: Biological replicate 2 of 3


title: C. difficile rep1

description: Biological replicate 1 of 3


title: Wildtype miRNA, technical rep 1


title: larvae_MANFdelta96_65

description:
Ldelta96_65
gene expression of zygotic MANF mutant D96

source_name: larvae 30-44 hrs AEL

value: zygotic MANF mutant D96


title: larvae_69B>MANF_69

description:
LOVER_69
gene expression of MANF ectopic overexpression


title: Emerin-null mRNA, technical rep 1


title: Wildtype mRNA, technical rep 2


title: larvae_MANFdelta96_4

description:
Ldelta96_4
gene expression of zygotic MANF mutant D96

source_name: larvae 31-50 hrs AEL