title: 1 dpp Non-translating, biological rep1

description: Gene expression data from 1 dpp mouse testes non-translating mRNAs

source_name: Mouse 1 dpp testes non-translating mRNAs


title: 1 dpp Non-translating, biological rep3

status: Public on Jul 27 2013

type: RNA

city: Greenville

first: Christopher

middle: B

last: Geyer

state: NC

address: 600 Moye Boulevard, Mail Stop 620

department: Anatomy and Cell Biology

country: USA

institute: East Carolina University

hyb_protocol: Hybridized to the Affymetrix 430 2.0 mouse expression array at the core facility at the University of North Carolina, Neuroscience Research Center, Chapel Hill, NC.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotin-labeled amplified antisense RNA was synthesized from 5 ug of RNA by the standard Affymetrix 3’ IVT procedure

growth_protocol: All animal procedures were performed in accordance with the National Research Council Guide for the Care and Use of Laboratory Animals and approved by the Animal Care and Use Committee of East Carolina University. CD-1 mice were used for all analyses. Euthanasia was performed by decapitation, and testes were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated from polysome sucrose fractions by TRIzol extraction (Invitrogen) using manufacturer’s instructions

treatment_protocol: Testes were harvested and washed with 1X ice-cold phosphate-buffered saline (PBS) containing cycloheximide to freeze polysomes, then immediately snap-frozen in liquid nitrogen, and stored at -80°C. Testes were pulverized under liquid nitrogen and lysed in 1 ml polysome lysis. Lysates were homogenized and nuclei were pelleted by centrifugation. Cytoplasmic extracts were layered onto a linear sucrose density gradient in polysome gradient and then centrifuged at 210,000 x g at 4°C for 2 h without braking. Gradients were then fractionated using an ISCO gradient fractionation system equipped with a UA-6 detector. RNP fractions, 40S, 60S, 80S, light polysomes, and heavy polysomes were monitored by continuous UV absorption profiles at 254 nm. Fourteen successive 750 μl fractions were collected and stored at -80°C.

tag: tissue

value: Testis

tag: genotype

tag: age

value: 1 day post partium


title: Luminal progenitors_Patient9

status: Public on Jul 26 2013

city: Vancouver

first: Connie

last: Eaves

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

description: Patient-9, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1ul Agilent fragmentation buffer and 5ul of 10X Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60K Microarrays (Design ID 028004) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried for 1min in acetonitrile.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution.

data_processing: Data was processed with Agilent Feature Extraction 10.10.

organism: Homo sapiens

source_name: Luminal progenitors

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from about 25ng RNA using Agilent One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling v1.0 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
Human breast tissues obtained from reduction mammoplasty surgeries were collected, processed and single cells FACS purified as described by Eirew et al Nature Medicine (PMID 19029987).
RNA was isolated from approximately a million cells in Trizol (Invitrogen), re-purified using the RNeasy Micro kit (Qiagen), and total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis.  Samples with a RIN value of greater than or equal to 8.0 were deemed to be acceptable for microarray analysis.

tag: gender

value: Female

tag: cell type


title: 1 dpp Non-translating, biological rep2


title: Luminal progenitors_Patient2

description: Patient-2, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Basal cells_Patient6

description: Patient-6, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)

source_name: Basal cells


title: Basal cells_Patient5

description: Patient-5, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)


title: Luminal cells-mature_Patient1

description: Patient-1, Lin-CD49fnegEpCAMpos (mature luminal cells)

source_name: Luminal cells-mature


title: Basal cells_Patient7

description: Patient-7, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)


title: Luminal progenitors_Patient1

description: Patient-1, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal progenitors_Patient6

description: Patient-6, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal cells-mature_Patient7

description: Patient-7, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Basal cells_Patient3

description: Patient-3, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)


title: Luminal progenitors_Patient7

description: Patient-7, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal progenitors_Patient3

description: Patient-3, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal progenitors_Patient5

description: Patient-5, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal cells-mature_Patient6

description: Patient-6, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Luminal cells-mature_Patient4

description: Patient-4, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Basal cells_Patient2

description: Patient-2, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)


title: Luminal progenitors_Patient8

description: Patient-8, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: Luminal cells-mature_Patient8

description: Patient-8, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Basal cells_Patient4

description: Patient-4, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)


title: Mutant AteIF(iso)4E-1 polysomes versus Wt polysomes rep 2

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

description: Translational effect in polysomal fractions Experimental replicate 2 of 2

hyb_protocol: Equal quantities of labeled cDNA were hybridized using UniHyb (TeleChem International INC) to the arrays for 14 h at 42°C.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate.

data_processing:
For each spot the Alexa555 and Alexa647 density mean value and the background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/).
Values for P_, NP_, and Total_RNA_(ISO/WT) rep were Lowess normalized background intensity subtracted ratios (ISO/WT) representing test/reference
Values for P_, NP_, and total_RNA_z-score represent the z-score, where zi measures the number of standard deviations from the mean: zi = [Ri – mean(R)] / sd(R), where Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. Z-scores are available in the supplementary file on the Series record.

organism: Arabidopsis thaliana

source_name: AteIF(iso)4E-1 polysomes 15 days old seedlings

label_protocol: Ten µg of RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 by the First-Strand cDNA labeling kit (Invitrogen). Incorporation of the fluorophores (dUTP-CY5 and dUTP-CY3) was analyzed by the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: The sterilized seeds were spread on 0.7% (w/v) agar (Becton Dickinson, Mexico) containing Gamborg’s B5 minimal medium (Sigma-Aldrich Quimica, Mexico) with 1% sucrose (Sigma). The seeds were stratified at 4 °C in the dark (Petri dish wrapped in two layers of aluminium foil) for two days and then grown for 15 days at 20 °C under 100 µmol m-2 sec-1 light intensity in a 8/16 light/dark photoperiod.

extract_protocol:
For total RNA isolation, 100 mg of 15 day-old seedlings were crushed with liquid N2 and homogenized in Trizol ® Reagent (Invitrogen). Chloroform was added at 1/6 (v/v), the mixture was vortexed and then centrifuged at 12,000 g for 15 min at 4 °C. The colorless upper aqueous phase was carefully collected and precipitated with 1 volume of isopropanol at room temperature. After centrifugation at 12,000 g for 20 min at 4 °C, the RNA pellet was washed with 75% ethanol, the ethanol removed by additional round of centrifugation and the RNA dissolved in 50 µl of diethyl pyrocarbonate (DEPC)-treated water.
For RNA isolation from sucrose gradient fractions, each fraction was treated with 0.5% sodium dodecyl sulfate (SDS) and 20 ug/ml proteinase K (Sigma), then extracted twice with equal volume of phenol/chloroform/isoamyl alcohol [25:24:1 (v/v/v)] by vortexing. The mixture was centrifuged at 10,000 g for 5 min at 4 °C and the aqueous phase was added with LiCl 1.5 M final concentration and equal volume of cold isopropanol. The RNA was precipitated at -20 ºC during 1 h and centrifuged at 12,000 g for 15 min at 4 °C. The pellet was washed with 70% ethanol and dissolved in 30 µl of DEPC-treated water.

treatment_protocol: For translational analysis, two grams of 15 day-old Arabidopsis thaliana seedlings were crushed with liquid nitrogen and homogenized in 2 ml of lysis buffer consisting of 200 mM Tris-HCl, 50 mM KAc, 25 mM MgAc, 2 mM EGTA 2, 2% PTE (10 Tridecyl Polyoxyethylene ether), 1% IGEPAL (Sigma) and 50mg/ml cycloheximide (Sigma). After lysis, samples were centrifuged for 15 min at 12,000 g at 4 °C. The supernatant was placed on 60% sucrose in gradient buffer containing 50 mM Tris-HCl, 20 mM KAc, 2 mM EGTA and 50 mg/ml cycloheximide and centrifuged in a Beckman 75Ti rotor at 50,000 rpm for 3 hours at 4 °C. The pellet was dissolved in 400 µl of DEPC water, layered onto 20 to 60% sucrose continuous gradient and centrifuged in a Beckman SW40 rotor at 36,000 rpm for 2.5 h at 4 °C. The gradient was fractionated with continuous monitoring of the absorbance at 260 nm.

tag: development stage

value: seedlings

value: 15 days old

tag: rna type

value: Polysomal RNA

source_name: Wt polysomes 15 days old seedlings


title: Mutant AteIF(iso)4E-1 polysomes versus Wt polysomes rep 1

description: Translational effect in polysomal fractions Experimental replicate 1 of 2


title: Mutant AteIF(iso)4E-1 non-polysomes versus Wt non-polysomes rep 2

description: Translational effect in non-polysomal fractions Experimental replicate 2 of 2

source_name: AteIF(iso)4E-1 non-polysomes 15 days old seedlings

value: Non-polysomal RNA

source_name: Wt non-polysomes 15 days old seedlings


title: Luminal cells-mature_Patient2

description: Patient-2, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Luminal cells-mature_Patient5

description: Patient-5, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: Mutant AteIF(iso)4E-1 versus Wt rep 2

description: Transcriptional effect Experimental replicate 2 of 2.

source_name: AteIF(iso)4E-1 15 days old seedlings

value: Total RNA

source_name: Wt 15 days old seedlings


title: Mutant AteIF(iso)4E-1 non-polysomes versus Wt non-polysomes rep 1

description: Translational effect in non-polysomal fractions Experimental replicate 1 of 2


title: Luminal progenitors_Patient4

description: Patient-4, Lin-CD49fposEpCAMpos (luminal progenitor-enriched)


title: H9 (DK_C7_31)

city: Philadelphia

first: Jason

last: Mills

state: PA

address: 3501 Civic Center Blvd, CTRB, RM5100

department: Laboratory Medicine

institute: The Children's Hospital of Philadelphia

hyb_protocol: Three biological replicates were prepared for all iPSC and hESC-derived samples. Quantified RNA samples were hybridized to Affymetrix GeneChip Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix protocol

data_processing: All gene array data obtained from Affymetrix passed quality control steps and were sent to RMA normalization and log transformation by Affymetrix Expression Console.

source_name: Human ES

label_protocol: Affymetrix protocol

growth_protocol: Human fibroblast lines CHOPWT1 (Coriell GM00969), CHOPWT2 (Coriell GM05565), and BMC (ATCC CRL-2097) were cultured in IMDM (Mediatech) containing 10% FBS at 37°C and 5% CO2 in a humidified incubator. The iPSCs were maintained in HES media: DMEM/F12 containing 2 mM of glutamine, 20% Knockout Serum Replacement (KO), 1X NEAA, 0.1 mM β-mercaptoethanol, and 10 ng/ml of bFGF (Roche, Indianapolis, IN) on 0.1% gelatin (Sigma, Inc.) coated plates with irradiated mouse embryonic fibroblast (MEFs)

extract_protocol: Total RNA and miRNA were isolated from cells using the miRNeasy kit (Qiagen, Inc), with the optional column RNAse-free DNase treatment, according to the manufacturer’s instructions.

treatment_protocol: iPSCs were enriched by FACS sorted for pluripotency markers SSEA3-FITC (1:100; Biolegend) and Tra-1-81-APC (1:100; Biolegend)

value: embryonic stell cells

tag: cell line


title: H9 (DK_C9_33)


title: BMC3 (DK_C2_26)

source_name: wild type hiPS

value: Induced pluripotent stem cells


title: CHB8 (DK_C12_36)


title: Luminal cells-mature_Patient3

description: Patient-3, Lin-CD49fnegEpCAMpos (mature luminal cells)


title: CHB8 (DK_C11_35)


title: BMC1 (DK_B12_24)


title: H1 (DK_C4_28)


title: H1 (DK_C5_29)


title: H1 (DK_C6_30)


title: BMC3 (DK_C3_27)


title: CHB8 (DK_C10_34)


title: H9 (DK_C8_32)


title: BMC3 (DK_C1_25)


title: BMC2 (DK_B9_21)


title: BMC1 (DK_B11_23)


title: BMC1 (DK_B10_22)


title: BMC2 (DK_B7_19)


title: HIV-1 Vpr SH-SY5Y (miRNA)

first: Bassel

middle: E

last: Sawaya

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

hyb_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

scan_protocol: Array chips were scanned using Axon GenePix Scanner (Molecular Devices, Downingtown, PA) and Genepix 4000 image capture software (Molecular Devices, Downingtown, PA).

data_processing: Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control.

label: Hy5 Power labeling

source_name: SH-SY5Y neuronal cell line

growth_protocol: Neuronal cell line, SH-SY5Y (5 x 105) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).

treatment_protocol: Cells were treated with 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada for 24 hours.

tag: treatment

value: 10 pg/ml of Vpr protein


title: 7F-iCM-12W (Reprogrammed -> cardiomyocyte) 1

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 20 hr at 45C on Affymetrix GeneChip  Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Expression Analysis Technical Manual 701021 Rev. 3

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000

data_processing: Arrays were normalized with the RMA normalization method, using the Affymetrix Power Tools suite, version 1.12.0.

source_name: Induced cardiomyocyte (reprogrammed cell)

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen Ovation Pico WTA System and Encore Biotin Module protocol from 2-5 ng total RNA

growth_protocol: Cells were growing in M106plus  LGSC from Invitrogen, and were cultured in DMEM/M199 with 10% FBS after retrovirus infection.

extract_protocol: Total RNA extraction was performed by using Qiagen Rneasy Plus Micro Kit according to the manufacturer's instructions.

treatment_protocol: Cells were infected with retrovirus. Cells were digested with 0.05% Trypsion, and sorted out by FACS at the time indicated.

tag: group

value: Group S

tag: source

value: H9F cell line


title: NMuMG cells treated by 11 days with 4ng/ml TGF-β, replicate 1

city: Worcester

first: cheng

last: chang

state: MA

address: 364 Plantation Street, LRB 470X

institute: Umass Medical School

description: gene expression of NMuMG cells undergone MET

hyb_protocol: The aRNA was then purified using aRNA binding magnetic beads and fragmented to a size range of 90-110 nts. The purified aRNA (15ug) was used to hybridize with Mouse Genome 430 2.0 Array (Affymetrix).

scan_protocol: Hybridized Mouse Genome 430 2.0 Array (Affymetrix) were scanned by GeneChip Scanner 3000 7G.

data_processing: All samples were run in duplicate. Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (48). The raw array data were normalized using the RMA algorithm.

source_name: NMuMG (immortalized normal murine mammary gland epithelial cells)

label_protocol: 500ng of total RNA with PolyA-RNA control stock was used to synthesize the biotin-labeled antisense RNA (aRNA), following the protocol described in the manual of Affymetrix 3’ IVT Express Kit.

growth_protocol: NMuMG cells were grown in DMEM media with 10% FBS, 1% P/S, and 1% insulin.

extract_protocol: The QIAGEN RNeasy mini-kit was used to extract total RNA from NMuMG cells of different treatment.

treatment_protocol: NMuMG cells were subject to 4ng/ml TGF-β treatment or vehicle for the indicated length of days

value: NMuMG

value: treated by 11 days with 4ng/ml TGF-β


title: 7F-iCM-12W (Reprogrammed -> cardiomyocyte) 3

value: Induced cardiomyocyte (reprogrammed cell)


title: 7F-iCM-12W (Reprogrammed -> cardiomyocyte) 2


title: 5F-iCM-12W (Reprogrammed -> cardiomyocyte) 3

value: Group R


title: 5F-iCM-12W (Reprogrammed -> cardiomyocyte) 2


title: Capan-1_parental_rep 2

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Gene expression (parental line)

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µL of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Human GE 4x44K v2 Microarray (G2519F) for 17 hours at 65 ° C rotating at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile, and 30 seconds with drying solution.

scan_protocol: Slides were scanned immediately after washing on the High-Resolution Microarray Scanner (Agilent, Santa Clara, CA, USA) using one color scan setting for 1x44k array slides.

data_processing: The images were captured by the reader Agilent Bundle according to the parameters recommended for bioarrays and extracted by Agilent Feature Extraction software version 9.5.3. Among the spots present in each array only those with none flag (i.e. low intensity, saturation, controls, etc.) were selected for analysis.

source_name: Parental cell line 1_4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA, USA) according to the manufacturer's instructions, followed by RNAspin column purification (GE Healthcare, Little Chalfont, Buckinghamshire, UK).  Dye incorporation and cRNA yield were checked with the Nanovue Spectrophotometer (GE Healthcare).

growth_protocol: Human pancreatic cancer cell line MIA PaCa-2 was obtained from American Type Culture Collection (ATCC® Number: CRL-1420™, Manassas, VA, USA). The cells were maintained routinely in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen Corporation, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Invitrogen Corporation), 100 U/mL penicillin G (Invitrogen Corporation), and 0.1 mg/mL streptomycin sulfate (Invitrogen Corporation) at 37°C in a humidified, 5% CO2, 95% air atmosphere. Capan-1 cell line established from a hepatic metastasis of a PDAC was also obtained from ATCC (Number: HTB-79™). The cells were grown in IMDM medium (Invitrogen Corporation) supplemented with 20% FBS (Invitrogen Corporation).

extract_protocol: Total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen, Duesseldorf, North Rhine-Westphalia, Germany) according to manufacturer's guidelines.

treatment_protocol: Transfections were performed following the manufacturer’s protocols of the TriFECTa Dicer- Substrate RNAi kit (IDT, Coralville, IA, USA) and Lipofectamine RNAi Max Reagent (Invitrogen Corporation, Carlsbad, CA, USA).  Cells were transfected with a HOXB7-specific siRNA at a final concentration of 10 nM. The mRNA content was measured 48 hours after transfection by RT-qPCR. Each experiment was repeated at least twice.

tag: sample type

value: Cell line derived from pancreatic ductal adenocarcinoma

value: control


title: Basal cells_Patient1

description: Patient-1, Lin-CD49fhiEpCAMneg/low (basal stem/bipotent cell-enriched)

value: Female


title: 7F-HDFiCM-12W (Reprogrammed -> cardiomyocyte) 1

value: Group T

value: Neonatal human tissue


title: Capan-1_parental_rep 1

description: Gene expression (parental line)

source_name: Parental cell line 1_3


title: 7F-HDFiCM-4W (Reprogrammed -> cardiomyocyte) 2

value: Group M


title: Neonatal dermal fibroblast 1

source_name: Dermal Fibroblast

value: Group P

value: Dermal Fibroblast

value: Neonatal human cell line


title: Mutant AteIF(iso)4E-1 versus Wt rep 1

description: Transcriptional effect Experimental replicate 1 of 2.

value: seedlings

value: 15 days old

value: Total RNA


title: Neonatal dermal fibroblast 3


title: Control NMuMG cells, replicate 2

description: gene expression of epithelial NMuMG cells


title: NMuMG cells treated by 11 days with 4ng/ml TGF-β, followed by TGF-β withdrawl for another 13 days, replicate 2

description: gene expression of NMuMG cells undergoing EMT


title: NMuMG cells treated by 11 days with 4ng/ml TGF-β, replicate 2


title: Neonatal dermal fibroblast 2


title: MIA PaCa-2_parental_rep 2

description: Gene expression (parental line)

value: MIA PaCa-2


title: 5F-iCM-12W (Reprogrammed -> cardiomyocyte) 1

value: H9F cell line


title: 7F-HDFiCM-12W (Reprogrammed -> cardiomyocyte) 2


title: 7F-HDFiCM-4W (Reprogrammed -> cardiomyocyte)


title: Capan-1_48h_siRNA anti-HOXB7_rep 1

description: Gene expression  (48 hours after transfection with HOXB7-specific siRNA)

source_name: Capan-1 cell line, 48h, small interfering RNA (siRNA) anti-HOXB7 1_1

value: HOXB7-specific siRNA


title: Control NMuMG cells, replicate 1

value: NMuMG


title: Capan-1_48h_siRNA anti-HOXB7_rep 2

source_name: Capan-1 cell line, 48h, small interfering RNA (siRNA) anti-HOXB7 1_2


title: NMuMG cells treated by 11 days with 4ng/ml TGF-β, followed by TGF-β withdrawl for another 13 days, replicate 1


title: H9F (Cell Line) iCM 7Fs (Reprogrammed -> cardiomyocyte) 2

value: Group I

value: Induced cardiomyocyte (reprogrammed cell)

value: H9F Cell Line


title: H9F (Cell Line) iCM 5Fs (Reprogrammed -> cardiomyocyte) 2

value: Group E


title: Fetal Human Cardiomyocyte 3

source_name: Cardiomyocyte

value: Group C

value: Cardiomyocyte

value: Fetal Human


title: Fetal Human Cardiomyocyte 2


title: H9F (Cell Line) iCM 5Fs (Reprogrammed -> cardiomyocyte) 1


title: H9F (Cell Line) iCM 5Fs (Reprogrammed -> cardiomyocyte) 3


title: MIA PaCa-2_48h_siRNA anti-HOXB7_rep 1

source_name: MIA PaCa-2 cell line, 48h, small interfering RNA (siRNA) anti-HOXB7 1_1

value: Cell line derived from pancreatic ductal adenocarcinoma


title: MIA PaCa-2_48h_siRNA anti-HOXB7_rep 2

source_name: MIA PaCa-2 cell line, 48h, small interfering RNA (siRNA) anti-HOXB7 1_2


title: H9F (Cell line) Cardiac Fibroblast 3

source_name: Cardiac Fibroblast

value: Group A

value: Cardiac Fibroblast


title: H9F (Cell line) Cardiac Fibroblast 2


title: H9F (Cell Line) iCM 7Fs (Reprogrammed -> cardiomyocyte) 1


title: H9 (Cell line) Cardiomyocyte 2

value: Group B

value: H9 Cell Line


title: H9 (Cell line) Cardiomyocyte 1


title: H9 (Cell line) Cardiomyocyte 3


title: H9F (Cell Line) iCM 7Fs (Reprogrammed -> cardiomyocyte) 3


title: MIA PaCa-2_parental_rep 1

description: Gene expression (parental line)

value: control


title: H9F (Cell line) Cardiac Fibroblast 1


title: Fetal Human Cardiomyocyte 1


title: WT_shTLS_3

city: Madrid

first: Maria

last: Monsalve

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description: Gene expression in primary hepatocytes from PGC-1alpha+/+ mice transduced with an adenoviral vector encoding a TLS shRNA

hyb_protocol: Cy3-labeled aRNA (1.65 mg), in a final concentration of 1x GEx HI-RPM hybridization buffer (Agilent Technologies), was hybridized for 17 h at 65ºC in an G2545A hybridization oven (Agilent Technologies) set to 10 rpm. Arrays were washed and dried by centrifugation as indicated in the manufacturer's protocol.

scan_protocol: Arrays were scanned at 5 mm resolution with a G2565BA DNA microarray scanner (Agilent Technologies) at the default settings for 4x44k format one-color arrays.

data_processing: Images were analyzed using Feature Extraction software v10.1.1.1 (Agilent Technologies). Raw signals were thresholded to 1 and normalized by quantile (Bolstad et al., 2003) was performed using GeneSpring software. Data were analyzed on the log2 scale. Default flags were considered as absent, except for saturated spots that were flagged as marginal. Of the initial 41081 probes present in the Agilent 4x44K chip, 25280 satisfied the following criteria (i) their signals were at or above the 80th percentile in at least 50% of the replicates in one condition; (ii) at least 50% of the replicates in one condition were flagged as present or marginal (iii) are not control probes and (iv) have a standard deviation across samples larger than 0.25. Quality Control checks based on the ArrayQualityMetric bioconductor package s (www.bioconductor.org) did not detect any sample as statistical outlier, and therefore all samples were included in statistical analysis done with the limma bioconductor package (Smyth, 2004).

source_name: Hepatocytes from PGC-1alpha+/+ mouse 3 infected with Ad-shTLS/Independent Assay 3

label_protocol: RNA was amplified and labeled with the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA)

growth_protocol: Primary hepatocytes were isolated and cultured as previously described (Bahjat et al., 2000; Rana et al., 1994). Briefly, the liver of anesthesized mice was first perfused with perfusion buffer (150 mM NaCl, 5.5 mM KCl, 10 mM HEPES pH 7.5, 25 mM NaHCO3 0.5 mM EGTA) and then with 0.05 % collagenase for 10 min. Dispersed cells were seeded onto collagen-coated plates (0.2% gelatin, 1% collagen) and cultured in Williams E Medium (Gibco) supplemented with 10% FBS, 2 mM L-glutamine, 100 nM dexamethasone, 100 nM insulin and antibiotics. Fresh medium was added 4 h after plating

extract_protocol: RNA was extracted by Trizol extraction, re-purified with RNAeasy (Invitrogen), and checked for integrity and quantity with the Agilent Bio-Analyzer QC.

treatment_protocol: Hepatocytes were infected overnight with adenoviral vectors at a multiplicity of infection (moi) of 5. Viruses were washed off and cells were harvested 24 h post-infection.

value: Primary Hepatocytes

tag: genotype/variation

tag: adenoviral vector

value: TLS shRNA

tag: strain


title: Cardiac Fibroblast Wildtype Replicate #2

value: Wildtype CF Group

value: Mouse Cardiac Fibroblast


title: Cardiac Fibroblast Wildtype Replicate #3


title: WT_shTLS_2

source_name: Hepatocytes from PGC-1alpha+/+ mouse 2 infected with Ad-shTLS/Independent Assay 2


title: WT_shTLS_1

source_name: Hepatocytes from PGC-1alpha+/+ mouse 1 infected with Ad-shTLS/Independent Assay 1


title: WT_shC_3

description: Gene expression in primary hepatocytes from PGC-1alpha+/+ mice transduced with an adenoviral vector encoding a control shRNA

source_name: Hepatocytes from PGC-1alpha+/+ mouse 3 infected with Ad-shC/Independent Assay 3

value: control shRNA


title: Cardiac Fibroblast Wildtype Replicate #1


title: WT_shC_1

source_name: Hepatocytes from PGC-1alpha+/+ mouse 1 infected with Ad-shC/Independent Assay 1


title: iCM (Reprogrammed -> cardiomyocyte) 2

value: Mouse Group E

value: Induced cardiomyocyte (reprogrammed cell)

value: Induced mouse cardiomyocyte (reprogrammed cell)


title: CAKO_ovoD_rep2

city: Providence

first: Hua

last: Bai

state: RI

address: 34 Olive St, BMC502

department: EEB

institute: Brown University

description: Gene expression data from 15-day-old CAKO with ovoD mutants.

hyb_protocol: 1.5 ug of spin column cleaned cRNA was fragmented by metal inducing hydrolysis, and 1.0 ug of this product was hybridized to arrays overnight at 45°C, 60 rpm. Hybridization, washing and staining were completed on an Affymetrix 450 Fluidics Station

scan_protocol: scan was done on an Affymetrix 3000 G7

data_processing: Quantile normalized data were processed with GCRMA [63] to generate log2 scaled expression values. Probesets with mean expression in the first quartile within a genotype were excluded. Two sided t-tests were used to assess differential expression with individual p < 0.05 and fold change at least 1.5. Probsets were collapsed to genes after differential expression statistics selection.

organism: Drosophila melanogaster

source_name: CAKO with ovoD mutants replicate 2

label_protocol: Double stranded cDNA was amplified overnight at 37°C with the Affymetric IVT labeling protocol to produce biotin labeled cRNA.

growth_protocol: Adults from each genotype were aged to 14 days upon standard media in demography cages (125 females per cage, four cages per genotype).

extract_protocol: For each genotype, total RNA was isolated from 25 whole females with Trizol (Invitrogen) and purified upon RNeasy columns (QIAGEN). Using the Affymetrix One Cycle DNA system, 5 ug total RNA was converted to cDNA.

value: female


title: WT_shC_2

source_name: Hepatocytes from PGC-1alpha+/+ mouse 2 infected with Ad-shC/Independent Assay 2


title: CAKO_ovoD_rep1

source_name: CAKO with ovoD mutants replicate 1


title: CAKO_rep2

description: Gene expression data from 15-day-old CAKO female flies.

source_name: CAKO replicate 2

value: CAKO


title: KO_ShTLS_3

description: Gene expression in primary hepatocytes from PGC-1alpha-/- mice transduced with an adenoviral vector encoding a TLS shRNA

source_name: Hepatocytes from PGC-1alpha-/- mouse 3 infected with Ad-shTLS/Independent Assay 3


title: ovoD mutant_rep3

description: Gene expression data from 15-day-old ovoD female flies.

source_name: ovoD mutants replicate 3

value: ovoD mutant


title: CAKO_ovoD_rep3

source_name: CAKO with ovoD mutants replicate 3


title: iCM (Reprogrammed -> cardiomyocyte) 1

source_name: Induced cardiomyocyte (reprogrammed cell)


title: BMC2 (DK_B8_20)

source_name: wild type hiPS

value: Induced pluripotent stem cells


title: CAKO_rep3

source_name: CAKO replicate 3


title: CAKO_rep1

source_name: CAKO replicate 1


title: KO_ShTLS_2

source_name: Hepatocytes from PGC-1alpha-/- mouse 2 infected with Ad-shTLS/Independent Assay 2


title: ovoD mutant_rep2

source_name: ovoD mutants replicate 2


title: ovoD mutant_rep1

source_name: ovoD mutants replicate 1


title: Dupp_DcyoBACD_vs_Dupp_CSW

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description: normalized Cy3/Cy5 log2 Ratio

hyb_protocol: Preparation of the slides was performed in 50 ml Falcon tubes. All reagents were from the OpArray system from Eurofins MWG Operon. Slides were incubated at 42°C in Pre-Hyb solution for 1 h, then the slides were transferred to Wash 1 solution (1.25 ml Wash B and 48.75 ml H2O) and incubated for 5 min at 37°C. Slides were washed with H2O and dried in a centrifuge (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Hybridization was carried out for 16–18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: For post-hybridization, slides were washed at 37°C in Wash 2 solution (5 ml Wash A, 2.5 ml Wash B and 42.5 ml H2O) and Wash 3 solution (5 ml Wash A and 45 ml H2O) for 10 minutes each. Slides were rotated in Wash 4 solution (1 ml Wash A and 49 ml H2O) for 5 min at room temperature. Finally, the slides were dried by centrifugation (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Fluorescence of the hybridized DNA microarrays was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) at 10 µm resolution with a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The transcriptome comparisons of Δupp ΔcyoBACD vs. Δupp were repeated independently three times in biological replicates. Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (http://www.bioconductor.org). For further analysis, the processed and loess-normalized data as well as detailed experimental information according to MIAME (Brazma et al., 2001) were stored in the in-house microarray database (Polen and Wendisch, 2004). To filter for differentially expressed genes, the following criteria had to be fulfilled: (i) flags ≥0 (GenePix Pro 6.0), (ii) signal/noise ≥5 for Cy5 (F635Median/B635Median, GenePix Pro 6.0) or Cy3 (F532Median/B532Median, GenePix Pro 6.0), (iii) mRNA ratio ≥2.0 or ≤0.5, (iv) in a paired Student’s t test, relative RNA levels had to be significantly different from all spots (p < 0.05).

organism: Gluconobacter oxydans 621H

label_protocol: cDNA synthesis for DNA microarray analysis was performed as described (Polen et al., 2007). 25 µg RNA was used for random hexamer-primed synthesis of fluorescently-labeled cDNA with the fluorescent nucleotide analogues Cy3-dUTP and Cy5-dUTP (GE Healthcare, Freiburg, Germany). The mixture contained 3 µl 1 mM Cy3-dUTP or Cy5-dUTP, 3 µl 0.1 M DTT, 6 µl 5x first strand buffer (Invitrogen, Karlsruhe, Germany), 0.6 µl dNTP-mix (25 mM each of dATP, dCTP, and dGTP and 10 mM dTTP) and 2 µl Superscript II reverse transcriptase (Invitrogen, Darmstadt, Germany). The mixture was incubated for 10 min at room temperature and 110 min at 42 °C, stopped by addition of 10 μl 0.1 N NaOH, incubated for 10 min at 70 °C, and then neutralized by addition of 10 μl 0.1 N HCl. cDNA samples were purified by washing three times with water on a Microcon column (Millipore, YM-30).

growth_protocol: Gluconobacter oxydans ATCC 621H Δupp ΔcyoBACD and reference strain G. oxydans ATCC 621H Δupp were cultivated in baffled shake flasks with mannitol as the carbon source and harvested at OD600 = 1.5 by centrifugation.

extract_protocol: 25 ml of a G. oxydans culture was added to 25 g of crushed ice in a Falcon tube which had been pre-cooled in liquid nitrogen. The cells were sedimented by centrifugation for 3 min at 4 °C and 10,397 x g and after removal of the supernatant the tube with the cell pellet was immersed in liquid nitrogen and then stored at -70°C. For total RNA preparation, the RNeasy system (Qiagen, Hilden, Germany) was used. The cell pellet was resuspended in 700 µl of RLT buffer containing 7 µl ß-mercaptoethanol and transferred to two vials each containing 0.5 g of 0.1-mm diameter zirconium silica beads (Roth, Karlsruhe, Germany). Cells were disrupted by 4 x 30 s bead beating using a Silamat S5 (Ivoclar Vivadent, Ellwangen, Germany). The lysate was centrifuged at 8,000 x g for 2 min and the supernatant was mixed with 250 µl ethanol (-20 °C). RNA was extracted with two RNeasy mini-columns following the manufacturer’s instructions. DNA digestion was performed for 20 min on column by adding 30 Kuniz U RNase-free DNase. RNA concentration and quality were checked photometrically and on formaldehyde gels according to standard procedures (Sambrook and Russell, 2001).

value: G.oxydans 621H Delta-upp (reference)

tag: growth condition

value: Mannitol

value: G.oxydans 621H Delta-upp Delta-cyoBACD


title: KO_ShTLS_1

source_name: Hepatocytes from PGC-1alpha-/-  mouse 1 infected with Ad-shTLS/Independent Assay 1


title: Cardiomyocyte Wildtype Replicate #3

source_name: Cardiomyocyte

value: Wildtype CM Group

value: Cardiomyocyte

value: Mouse Cardiomyocyte


title: KO_shC_3

description: Gene expression in primary hepatocytes from PGC-1alpha-/- mice transduced with an adenoviral vector encoding a control shRNA

source_name: Hepatocytes from PGC-1alpha-/- mouse 3 infected with Ad-shC/Independent Assay 3

value: Primary Hepatocytes


title: Dupp_DcyoBACD_vs_Dupp rep2

description: normalized Cy5/Cy3 log2 Ratio


title: Wildtype_rep1

description: Gene expression data from 15-day-old wildtype female flies.

source_name: Wildtype flies replicate 1

value: Wildtype


title: Wildtype_rep2

source_name: Wildtype flies replicate 2


title: KO_shC_2

source_name: Hepatocytes from PGC-1alpha-/- mouse 2 infected with Ad-shC/Independent Assay 2


title: Dupp_DcyoBACD_vs_Dupp rep1

description: normalized Cy5/Cy3 log2 Ratio


title: Cardiomyocyte Wildtype Replicate #2


title: Wildtype_rep3

source_name: Wildtype flies replicate 3


title: KO_shC_1

source_name: Hepatocytes from PGC-1alpha-/-  mouse 1 infected with Ad-shC/Independent Assay 1


title: Jurkat_rep3_ZnO_24h_10

status: Public on Jul 25 2013

city: Turku

first: Soile

last: Tuomela

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: 0,75 µg of labeled cRNA was hybridized at 58ºC for 18 hours according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridization was detected with 1 µg/ml Cy3-Streptavidin (GE Healthcare)

scan_protocol: The arrays were scanned with Illumina BeadArray Reader, BeadScan software version 3.5 and the numerical results extracted with GenomeStudio 2009.2 without any normalization.

data_processing: The raw data values were pre-processed with the Variance Stabilizing Transform (VST) of Illumina data (Lin et al. 2008 Nucleic Acids Research). Further, the values were between-chip normalized with the quantile normalization method (Bolstad et al. 2003 Bioinformatics). The analysis was done using R and the Bioconductor Lumi package (Du et al. 2008 Bioinformatics). To ensure the independent analyses of EN-specific gene expression changes in MDDC, HMDM, and Jurkat cells, the different cell types were preprocessed separately.

source_name: Jurkat, ZnO, 24h, 10µg/ml

label_protocol: 300 ng of RNA was amplified with Illumina RNA TotalPrep Amplification kit (Ambion). In vitro transcription, during which cRNA was biotinylated, was carried out for 16 hours.

growth_protocol: Jurkat A3 (ATCC, CRL-2570) cells were cultured in Roswell Park Memorial Institute medium (RPMI) 1640 culture medium (Sigma) supplemented with 10% fetal calf serum, 2 mM L-glutamine (Gibco) and 1% penicillin-streptomycin-neomycin (Gibco) as indicated in Buerki-Thurnherr et al. 2012 Nanotoxicology

extract_protocol: Total RNA was isolated with RNAqueous Small Scale Phenol-Free Total RNA Isolation Kit (Ambion)

treatment_protocol: Cells were collected to RNAlater buffer (Ambion)

value: ZnO 10µg/ml

tag: timepoint

value: Jurkat


title: Jurkat_rep3_ZnO_24h_1

source_name: Jurkat, ZnO, 24h, 1µg/ml

value: ZnO 1µg/ml


title: Jurkat_rep3_ZnO_6h_10

source_name: Jurkat, ZnO, 6h, 10µg/ml


title: Jurkat_rep3_TiO2_24h_1

source_name: Jurkat, TiO2, 24h, 1µg/ml

value: TiO2 1µg/ml


title: Jurkat_rep3_ctr_24h_0

source_name: Jurkat, untreated, 24h

value: untreated


title: Cardiomyocyte Wildtype Replicate #1


title: Jurkat_rep2_ZnO_6h_10


title: Jurkat_rep3_ZnO_6h_1

source_name: Jurkat, ZnO, 6h, 1µg/ml


title: Jurkat_rep3_TiO2_6h_1

source_name: Jurkat, TiO2, 6h, 1µg/ml


title: Jurkat_rep3_TiO2_24h_10

source_name: Jurkat, TiO2, 24h, 10µg/ml

value: TiO2 10µg/ml


title: Jurkat_rep2_ZnO_24h_1


title: Jurkat_rep3_TiO2_6h_10

source_name: Jurkat, TiO2, 6h, 10µg/ml


title: Established B-cell precursor cell line REH

type: genomic

city: London

first: Nicola

middle: Emma

last: Potter

state: Sutton, Surrey

address: 15 Cotswold Rd

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using the Birdseed algorithum and Genotyping Console and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in Partek Genomics Suite.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: REH


title: Jurkat_rep3_ctr_6h_0

source_name: Jurkat, untreated, 6h


title: Down syndrome acute lymphoblatic leukaemia

tag: disease state

value: mononuclear cell preparations of leukemic blasts


title: Acute lymphobastic leukaemia Case B remission

tag: subject

value: case B

value: Acute lymphobastic leukaemia remission


title: Jurkat_rep2_TiO2_6h_10


title: Acute lymphobastic leukaemia Case A diagnosis

value: case A

value: Acute lymphobastic leukaemia diagnosis


title: Jurkat_rep2_TiO2_24h_10


title: Jurkat_rep1_ZnO_24h_10


title: Jurkat_rep2_ctr_6h_0


title: Jurkat_rep2_ZnO_6h_1


title: Jurkat_rep2_TiO2_6h_1


title: Jurkat_rep2_ctr_24h_0


title: Jurkat_rep1_TiO2_24h_10


title: Jurkat_rep1_ZnO_6h_1


title: Jurkat_rep1_ZnO_6h_10


title: Jurkat_rep1_TiO2_24h_1


title: Jurkat_rep2_TiO2_24h_1


title: Jurkat_rep1_ZnO_24h_1


title: Acute lymphobastic leukaemia Case B diagnosis


title: Jurkat_rep2_ZnO_24h_10


title: 7F-HDFiCM-4W (Reprogrammed -> cardiomyocyte) 1

source_name: Induced cardiomyocyte (reprogrammed cell)

value: Group M

value: Neonatal human tissue


title: Jurkat_rep1_ctr_6h_0


title: Jurkat_rep1_ctr_24h_0


title: Jurkat_rep1_TiO2_6h_10


title: HMDC_rep3_ZnO_24h_10

source_name: HMDM, ZnO, 24h, 10µg/ml

growth_protocol: Peripheral blood mononuclear cells (PBMC) were prepared from buffy coats obtained from healthy blood donors (Karolinska University Hospital, Stockholm, Sweden) by density gradient centrifugation and positively selected for CD14 expression (CD14 MicroBeads, human (Miltenyi Biotec, Bergisch Gladbach, Germany)). To obtain HMDM, CD14+ monocytes were cultured in supplemented RPMI 1640 medium (Sigma Aldrich) with 50 ng/mL recombinant M-CSF (Novakemi, Handen, Sweden) for three days. See Kunzmann et al. 2011 Toxicology and Applied Pharmacology for further details.

value: HMDM


title: HMDC_rep3_TiO2_24h_10

source_name: HMDM, TiO2, 24h, 10µg/ml


title: HMDC_rep3_ZnO_24h_1

source_name: HMDM, ZnO, 24h, 1µg/ml


title: Acute lymphobastic leukaemia Case A remission


title: Jurkat_rep1_TiO2_6h_1


title: HMDC_rep3_ZnO_6h_1

source_name: HMDM, ZnO, 6h, 1µg/ml


title: HMDC_rep3_TiO2_6h_10

source_name: HMDM, TiO2, 6h, 10µg/ml


title: HMDC_rep3_ctr_24h_0

source_name: HMDM, untreated, 24h


title: HMDC_rep3_ZnO_6h_10

source_name: HMDM, ZnO, 6h, 10µg/ml


title: HMDC_rep3_TiO2_24h_1

source_name: HMDM, TiO2, 24h, 1µg/ml


title: HMDC_rep2_ZnO_6h_10


title: HMDC_rep2_ZnO_6h_1


title: HMDC_rep3_ctr_6h_0

source_name: HMDM, untreated, 6h


title: HMDC_rep3_TiO2_6h_1

source_name: HMDM, TiO2, 6h, 1µg/ml


title: HMDC_rep2_TiO2_6h_1


title: HMDC_rep1_TiO2_24h_10


title: HMDC_rep2_TiO2_24h_10


title: HMDC_rep2_ZnO_24h_1


title: HMDC_rep1_ZnO_6h_10


title: HMDC_rep2_ZnO_24h_10


title: HMDC_rep1_ZnO_24h_1


title: HMDC_rep2_TiO2_6h_10


title: HMDC_rep2_TiO2_24h_1


title: HMDC_rep1_ZnO_6h_1


title: HMDC_rep2_ctr_6h_0


title: HMDC_rep2_ctr_24h_0


title: HMDC_rep1_TiO2_6h_1


title: HMDC_rep1_ZnO_24h_10


title: HMDC_rep1_TiO2_24h_1


title: MDDC_rep3_ZnO_24h_10

source_name: MDDC, ZnO, 24h, 10µg/ml

growth_protocol: Peripheral blood mononuclear cells (PBMC) were prepared from buffy coats obtained from healthy blood donors (Karolinska University Hospital, Stockholm, Sweden) by density gradient centrifugation and positively selected for CD14 expression (CD14 MicroBeads, human (Miltenyi Biotec, Bergisch Gladbach, Germany)). To obtain immature MDDC, CD14+ monocytes were cultured at a density of 4×105 cells/mL at 37 °C in a humidified atmosphere containing 6% CO2 in supplemented RPMI 1640 medium (Sigma Aldrich) with IL-4 (800 IU/mL) and GM-CSF (550 IU/mL) (Biosource International, Camarillo, CA). After three days, half of the culture medium was exchanged with fresh medium containing the cytokines. After 6 days, the cells were collected for analysis. See Kunzmann et al. 2011 Toxicology and Applied Pharmacology for further details.

value: MDDC


title: HMDC_rep1_TiO2_6h_10


title: MDDC_rep3_TiO2_24h_1

source_name: MDDC, TiO2, 24h, 1µg/ml


title: MDDC_rep3_ZnO_24h_1

source_name: MDDC, ZnO, 24h, 1µg/ml


title: HMDC_rep1_ctr_6h_0


title: MDDC_rep3_TiO2_24h_10

source_name: MDDC, TiO2, 24h, 10µg/ml


title: MDDC_rep3_TiO2_6h_10

source_name: MDDC, TiO2, 6h, 10µg/ml


title: MDDC_rep3_ZnO_6h_10

source_name: MDDC, ZnO, 6h, 10µg/ml


title: HMDC_rep1_ctr_24h_0


title: MDDC_rep2_ZnO_24h_10


title: MDDC_rep3_ZnO_6h_1

source_name: MDDC, ZnO, 6h, 1µg/ml


title: MDDC_rep2_ZnO_24h_1


title: MDDC_rep2_TiO2_6h_10


title: MDDC_rep2_ZnO_6h_1


title: MDDC_rep3_ctr_24h_0

source_name: MDDC, untreated, 24h


title: MDDC_rep3_ctr_6h_0

source_name: MDDC, untreated, 6h


title: MDDC_rep2_TiO2_24h_10


title: MDDC_rep2_TiO2_24h_1


title: MDDC_rep3_TiO2_6h_1

source_name: MDDC, TiO2, 6h, 1µg/ml


title: MDDC_rep2_ctr_6h_0


title: MDDC_rep2_ZnO_6h_10


title: MDDC_rep2_ctr_24h_0


title: MDDC_rep2_TiO2_6h_1


title: MDDC_rep1_ZnO_24h_10


title: MDDC_rep1_ZnO_24h_1


title: MDDC_rep1_ZnO_6h_1


title: MDDC_rep1_ZnO_6h_10


title: MDDC_rep1_TiO2_24h_1


title: MDDC_rep1_TiO2_6h_10


title: MEG-01 / GAS2DN

city: ShangHai

first: BaoHong

last: Liu

address: 100 QinZhou Road

country: China

institute: ShangHai center for bioinformation and technology

description: Gene expression data of GAS2DN lentivirus-transduced MEG-01 cells.

hyb_protocol: Array hybridization and wash were performed using GeneChip Hybridization, Wash and Stain Kit in hybridization oven 645 and Fluidics Station 450 following the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip Scanner 3000 and Command Console Software 3.1 with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software 11.0.

label_protocol: Total RNA were labeled with GeneChip 3'IVT express kit following the manufacturer's instruction to obtain biotin-labeled cRNA.

growth_protocol: The cells were cultured with RPMI1640 plus 10% FBS in CO2 incubator.

extract_protocol: Tigen total RNA extraction kit.

treatment_protocol: The cells were transduced with control and GAS2DN lentiviruses and then purified with FACS.

tag: transduction


title: MDDC_rep1_TiO2_6h_1


title: Jurkat_rep3_ZnO-1_6h_10

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (P/N 901530) with GeneTitan Instrument.

scan_protocol: GeneTitan Instrument was used to scan the arrays.

data_processing: Affymetrix GeneChip Command Console 3.1 was used to summarize probe cell intensity data. Hybridization quality was checked with Affymetrix GeneChip Command Console and Expression ConsoleTM 1.1..Samples were preprocessed using the Robust Multi-array Average (RMA) algorithm using the R package affy (Gautier et al. 2004 Bioinformatics). The probe values were linked directly into the ENSEMBL genes with Brainarray CDF-files Version 14 (Dai et al. 2005 Nucleic Acid Reseach).  Samples from each cell type MDDC, HMDM, and Jurkat were pre-processed separately. In addition, series of various NPs (ZnO-2, ZnO-3, ZnO-5, ZnO-9, and ZnO-4 with various doses) are preprocessed as an own group.

source_name: Jurkat, ZnO-1, 6h, 10ug/ml

label_protocol: 250 ng of total RNA was processed with GeneChip 3’ IVT Express Kit (Part no. 901229)

value: Zn0-1 10ug/ml

tag: cell


title: Jurkat_rep3_ZnO-1_24h_10

source_name: Jurkat, ZnO-1, 24h, 10ug/ml


title: Jurkat_rep2_ctr_24h_0

source_name: Jurkat, untreated, 24h


title: MDDC_rep1_ctr_24h_0

tag: cell type


title: Jurkat_rep3_ctr_6h_0

source_name: Jurkat, untreated, 6h


title: MEG-01 / Venus

description: Gene expression data of control lentivirus-transduced MEG-01 cells.

value: control


title: Jurkat_rep1_ZnO-1_6h_10

value: Jurkat


title: Jurkat_rep2_ZnO-1_24h_10


title: Jurkat_rep1_ctr_24h_0


title: Jurkat_rep1_ZnO-1_24h_10


title: Jurkat_rep5_ctr_24h_0


title: MDDC_rep1_TiO2_24h_10


title: Jurkat_rep4_ctr_24h_0


title: Jurkat_rep6_ZnO-4_24h_50

source_name: Jurkat, ZnO-4, 24h, 50ug/ml

value: Zn0-4 50ug/ml


title: Jurkat_rep4_ZnO-4_24h_50


title: Jurkat_rep2_ZnO-1_6h_10


title: Jurkat_rep1_ctr_6h_0


title: Jurkat_rep5_ZnO-4_24h_50


title: Jurkat_rep2_ctr_6h_0


title: Jurkat_rep6_ZnO-4_24h_25

source_name: Jurkat, ZnO-4, 24h, 25ug/ml

value: Zn0-4 25ug/ml


title: MDDC_rep1_ctr_6h_0

value: untreated


title: Jurkat_rep3_ctr_24h_0


title: Jurkat_rep6_ctr_24h_0


title: Clinical case 4 (Mycoplasma case)

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

description: Mycoplasma case

hyb_protocol: Labeled DNA were mixed in 60 ul of hybridization and added to the 8×60K EOPM for hybridization overnight at 65℃ in hybridization oven (Agilent). Then EOPM microarrays were washed with 2×SSC, 0.005%Triton X-100 at room temperature for 1min,and second wash with 0.2×SSC at 37℃ for 1 min

scan_protocol: scanned using a dual-laser scanner (Agilent)

data_processing: the images were extracted and analyzed using Feature Extraction software (Agilent).

source_name: serum

label_protocol: the first cDNA strand was reverse transcribed with a random decamer heeled with a PCR primer (5’- GTTTCCCAGTCACGATCNNNNNNNNN -3'). Then the cDNA was synthesized to double-stranded DNA by using the same primer with Klenow enzyme (Takara, Daian, China). After that, the amplification of the double stranded cDNA of both patients and normal control was performed by PCR utilizing the heel primer. Products of the PCR were then purified and labeled with Cy3-dCTP for normal control and Cy5-dCTP for patient sample, respectively, by using Klenow enzyme (Takara)

extract_protocol: Microbial nucleic acid were extracted using TIANamp Virus DNA/RNA Kit (TIANGEN Biotech., Beijing, China). The carrier RNA from the kit was applied to extract virus nucleic acid with small molecular weight

value: disease

value: healthy control


title: Jurkat_rep4_ZnO-4_24h_25


title: Jurkat_rep6_ZnO-4_24h_10

source_name: Jurkat, ZnO-4, 24h, 10ug/ml

value: Zn0-4 10ug/ml


title: Jurkat_rep5_ZnO-4_24h_25


title: Jurkat_rep4_ZnO-4_24h_10


title: Jurkat_rep5_ZnO-4_24h_10


title: Jurkat_rep5_ZnO-9_24h_10

source_name: Jurkat, ZnO-9, 24h, 10ug/ml

value: Zn0-9 10ug/ml


title: Jurkat_rep4_ZnO-4_24h_100

source_name: Jurkat, ZnO-4, 24h, 100ug/ml


title: Jurkat_rep6_ZnO-9_24h_10


title: Jurkat_rep5_ZnO-4_24h_100


title: Jurkat_rep6_ZnO-4_24h_100


title: Jurkat_rep6_ZnO-2_24h_10

source_name: Jurkat, ZnO-2, 24h, 10ug/ml

value: Zn0-2 10ug/ml


title: Jurkat_rep5_ZnO-2_24h_10


title: Jurkat_rep4_ZnO-9_24h_10


title: Jurkat_rep4_ZnO-3_24h_10

source_name: Jurkat, ZnO-3, 24h, 10ug/ml

value: Zn0-3 10ug/ml


title: Jurkat_rep4_ZnO-2_24h_10


title: MDDC_rep3_ctr_24h_0


title: MDDC_rep3_ZnO-1_24h_10

source_name: MDDC, ZnO-1, 24h, 10ug/ml


title: MDDC_rep2_ZnO-1_6h_10

source_name: MDDC, ZnO-1, 6h, 10ug/ml


title: MDDC_rep3_ctr_6h_0


title: MDDC_rep3_ZnO-1_6h_10


title: Jurkat_rep6_ZnO-3_24h_10


title: MDDC_rep2_ZnO-1_24h_10


title: MDDC_rep2_ctr_6h_0


title: Jurkat_rep5_ZnO-3_24h_10


title: Jurkat_rep6_ZnO-5_24h_10

source_name: Jurkat, ZnO-5, 24h, 10ug/ml

value: Zn0-5 10ug/ml


title: Jurkat_rep4_ZnO-5_24h_10


title: Jurkat_rep5_ZnO-5_24h_10


title: MDDC_rep1_ZnO-1_6h_10


title: MDDC_rep1_ctr_24h_0

source_name: MDDC, untreated, 24h


title: MDDC_rep2_ctr_24h_0


title: MDDC_rep5_ZnO-1_24h_10


title: MDDC_rep7_ctr_24h_0


title: MDDC_rep1_ZnO-1_24h_10


title: MDDC_rep5_ctr_24h_0


title: MDDC_rep4_ctr_24h_0


title: HMDM_rep3_ctr_6h_0

source_name: HMDM, untreated, 6h


title: MDDC_rep6_ZnO-1_24h_10


title: MDDC_rep6_ctr_24h_0


title: HMDM_rep3_ZnO-1_24h_10

source_name: HMDM, ZnO-1, 24h, 10ug/ml


title: HMDM_rep3_ZnO-1_6h_10

source_name: HMDM, ZnO-1, 6h, 10ug/ml


title: HMDM_rep3_ctr_24h_0

source_name: HMDM, untreated, 24h


title: MDDC_rep1_ctr_6h_0

source_name: MDDC, untreated, 6h


title: HMDM_rep2_ZnO-1_24h_10


title: MDDC_rep4_ZnO-1_24h_10


title: HMDM_rep2_ctr_24h_0


title: MDDC_rep7_ZnO-1_24h_10


title: irr_rep3

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.

source_name: NSC 10Gy, d7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement  (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.

extract_protocol: Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.

treatment_protocol: 10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)

value: Murine ES-derived neural stem cells (NSC)


title: HMDM_rep2_ctr_6h_0


title: irr_rep1


title: irr_rep4


title: HMDM_rep2_ZnO-1_6h_10


title: CD2-Lmo2 transgenic, Lyl1 knockout DN thymocytes rep 1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity values were background corrected and normalized by the neqc method. Probes were filtered as ‘not expressed’ if they failed to achieve a BeadStudio detection P value of 0.05 on at least three arrays. Manufacturer probe annotation was used. Linear models were fitted to genes using Bioconductor R package limma. Differences in expression were assessed with empirical Bayes moderated t-statistics. Genes were considered to have different expression if they achieved a false-discovery rate of less than 0.05 and also a fold change of no less than 1.5.

source_name: CD4-CD8 double negative thymocytes

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen).Approximately 300 ng of total RNA was labelled and hybridised to Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) according to Illumina standard protocols.

tag: age

value: 2 months

tag: tissue

value: Thymus


title: irr_rep2


title: CD2-LMO2 transgenic DN tymocytes rep 3

description: replicate 3


title: HMDM_rep1_ZnO-1_6h_10

value: HMDM


title: ctrl_rep4

source_name: NSC not irradiated


title: CD2-Lmo2 transgenic, Lyl1 knockout DN thymocytes rep 2

description: replicate 2


title: CD2-LMO2 transgenic DN tymocytes rep 2

description: replicate 2


title: CD2-LMO2 transgenic DN tymocytes rep 1

description: replicate 1


title: CD2-Lmo2 transgenic, Lyl1 knockout DN thymocytes rep 3

description: replicate 3


title: ctrl_rep3


title: Wild-type DN thymocytes rep 1

description: replicate 1


title: HMDM_rep1_ZnO-1_24h_10

value: Zn0-1 10ug/ml


title: Wild-type DN thymocytes rep 3

description: replicate 3


title: HMDM_rep1_ctr_24h_0


title: Wild-type DN thymocytes rep 6

description: replicate 6


title: HMDM_rep1_ctr_6h_0


title: Wild-type DN thymocytes rep 5

description: replicate 5


title: ctrl_rep2


title: ctrl_rep1


title: Wild-type DN thymocytes rep 4

description: replicate 4


title: Wild-type DN thymocytes rep 2

description: replicate 2


title: 1/10 LC50 ZnO NP replicate 5

status: Public on Jul 24 2013

city: Boston

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: 1/10 LC50 ZnO NP replicate 5

hyb_protocol: Labeled cDNA was hybridized overnight to the custom 133k H. azteca arrays (described in Supporting Information) in a Nimblegen hybridization system following the manufacture’s protocols.  Following hybridization, microarrays were washed with the Nimblegen wash buffer kit (Roche Nimblegen, Madison, WI) according to the manufacturer’s recommendations.

scan_protocol: DNA microarrays were scanned at 3 micron resolution using an Agilent DNA Microarray Scanner G2565CA (Agilent Technologies, Santa Clara, CA) at the University of Massachusetts Medical School in Worchester, MA.  One of the six microarrays performed on the ZnO NP LC25 exposure was removed from down-stream analyses due to technical problems during the hybridization step,  resulting in n=5 for this treatment group.

data_processing:
Feature extraction was performed using Nimblescan software (Roche Nimblegen) and intensity values were normalized by quantile normalization with median polish and log2 transformed in Arraystar (DNAstar, Madison, Wisconsin).
Sequences which were differentially expressed compared to the untreated control or between treatment groups were determined using Statistical Analysis for Microarrays (SAM)24 with a false positive cut-off of 1.
All data normalization and statistical testing were performed at the probe level since a de novo trancriptome assembly of Hyalella azteca was being used.

organism: Hyalella azteca

source_name: 1/10 LC50 ZnO NP

label_protocol: RNA was reverse transcribed and labeled using Nimblegen one-color DNA labeling kit (Roche Nimblegen, Madison, WI) following the manufacturer’s protocols.  RNA was amplified first using TransPlex WTA I Amplification kit (Sigma Aldrich) according to Nimblegen Technical note (Skalitsky and Watt, available at www.nimblegen.com/arraysupport).

growth_protocol: H. azteca were maintained at the US EPA aquatic culturing facility in Cincinnati, OH according to standard methods: U.S. EPA. Methods for Measuring the Toxicity and Bioaccumulation of Sediment-associated Contaminants with Freshwater Invertebrates; EPA 600/R-99/064. U.S. ; U.S. Environmental Protection Agency, Office Research and Development: Duluth, Minnesota, 2000.

extract_protocol: H. azteca were removed from exposure vessels with a pipette and immersed immediately in 0.75 ml of TriReagent (Molecular Research Center, Cincinnati, OH) in a 1.5 ml Eppendorf tube.  All organisms in a single treatment vessel (20 animals) were pooled into one microcentrifuge tube.  H. azteca tissue was homogenized for 5 min. at 30 vibrations/s using a Tissue Lyser bead mill (Qiagen Inc., Valencia, CA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK) and RNA was isolated from the homogenate according to the TriReagent's manufacturer’s methods.  RNA was precipitated on a RNAeasy spin column and treated on the column with DNAse I (Qiagen).  Following DNAse treatment, RNA was eluted from with spin column with RNAse free water.  RNA concentration and quality was assessed using a NanoDrop Spectrophotometer and by visual analysis of RNA on a 1.5 % agarose gel using NorthernMax-Gly buffer (Applied Biosystems/Ambion, Austin, TX).

treatment_protocol: 96-h static, water only exposures were performed as described above for the toxicity bioassays.  Fresh 150 ml of R-MHRW containing the effective concentrations determined through toxicity testing , of metal-based NP or salt was added to each beaker with ten replicate beakers for each exposure concentration (n=6 for microarray analysis, n=4 for RT-qPCR).  Twenty H. azteca, aged 10-days were added to each test beaker with a pipette.  Test vessels were placed in an environmental chamber at 23oC  for 96-h. The media was not agitated by bubbling or stirring during the 96-h exposure to better mimic the natural environment where H. azteca may be exposed to NPs.

value: whole organism

value: 10-day old

value: USEPA Cincinnati strain


title: LC25 ZnO NP replicate 2

description: LC25 ZnO NP replicate 2

source_name: LC25 ZnO NP


title: LC25 ZnO NP replicate 3

description: LC25 ZnO NP replicate 3


title: 1/10 LC50 ZnO NP replicate 2

description: 1/10 LC50 ZnO NP replicate 2


title: LC25 ZnSO4 replicate 3

description: LC25 ZnSO4 replicate 3

source_name: LC25 ZnSO4


title: LC25 ZnSO4 replicate 4

description: LC25 ZnSO4 replicate 4


title: 1/10 LC50 ZnO NP replicate 1

description: 1/10 LC50 ZnO NP replicate 1


title: LC25 ZnSO4 replicate 6

description: LC25 ZnSO4 replicate 6


title: Control replicate 6

description: Control replicate 6

source_name: Control


title: LC25 ZnO NP replicate 4

description: LC25 ZnO NP replicate 4


title: 1/10 LC50 ZnSO4 replicate 1

description: 1/10 LC50 ZnSO4 replicate 1


title: 1/10 LC50 ZnSO4 replicate 2

description: 1/10 LC50 ZnSO4 replicate 2


title: 1/10 LC50 ZnO NP replicate 6

description: 1/10 LC50 ZnO NP replicate 6


title: LC25 ZnSO4 replicate 1

description: LC25 ZnSO4 replicate 1


title: Control replicate 3

description: Control replicate 3


title: LC25 ZnO NP replicate 5

description: LC25 ZnO NP replicate 5


title: 1/10 LC50 ZnSO4 replicate 3

description: 1/10 LC50 ZnSO4 replicate 3


title: 1/10 LC50 ZnSO4 replicate 5

description: 1/10 LC50 ZnSO4 replicate 5


title: LC25 ZnSO4 replicate 5

description: LC25 ZnSO4 replicate 5


title: 1/10 LC50 ZnO NP replicate 3

description: 1/10 LC50 ZnO NP replicate 3


title: LC25 ZnSO4 replicate 2

description: LC25 ZnSO4 replicate 2


title: Control replicate 2

description: Control replicate 2


title: 1/10 LC50 ZnO NP replicate 4

description: 1/10 LC50 ZnO NP replicate 4


title: Control replicate 5

description: Control replicate 5


title: 1/10 LC50 ZnSO4 replicate 4

description: 1/10 LC50 ZnSO4 replicate 4


title: Control replicate 1

description: Control replicate 1


title: Control replicate 4

description: Control replicate 4


title: LC25 ZnO NP replicate 1

description: LC25 ZnO NP replicate 1


title: 1/10 LC50 ZnSO4 replicate 6

description: 1/10 LC50 ZnSO4 replicate 6


title: multiple myeloma bone marrow-derived exosomes #3

first: Aldo

last: Roccaro

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

description: SAMPLE 10

data_processing:
Mean miRNA expression value has been used for miRNA RT-qPCR data normalization, as described (Mestdagh et al., 2009).
Comparison between normal (n=4), and MM- (n=7), MGUS (n=2) BM-MSCs-derived exosomes  was performed by using dChip software (1.5 fold change; P <0.05).
ΔΔCt: one normal control (sample #3) has been used for the calcualtion of the ΔΔCt values
2-ΔΔCt: -[ΔCttest -ΔCtcontrol]

label: FAM

source_name: MM #3

label_protocol: Total RNA is converted into cDNA using a single "megaplex" reverse transcriptase reaction. The megaplex reaction contains a specific stem-loop primer for each of the mature target microRNA's (Each stem-loop primer is designed to hybridize to only the fully mature microRNA, and not to precursor forms of its target.). The cDNA is subjected to a "pre-amplification" PCR.   Sixty nanograms of RNA is used in the reverse transcription reaction. A stem-loop primer for each target miRNA is present in the reaction. The 3' region of each primer is complementary to the 3' region of its target miRNA. The 5' region of the primer is a non-miRNA "tail" and contains a sequence that will serve as the reverse primer in the pre-amplification and RT-PCR reactions.   A portion of the cDNA reaction is added to a "pre-amplification" PCR reaction. The primers in the pre-amplification reaction consist of  (1) a mixture of forward primers, each of which anneals to a specific miRNA cDNA, and (2) a single reverse primer sequence that anneals to the complement of the stem/loop primer "tail", a sequence that is present in every miRNA cDNA.   The pre-amplification reaction is diluted, and a portion of it is added to a solution containing Taq polymerase and deoxynucleotide triphosphates. This solution is distributed to the wells of a 384-well plate via microfluidic channels in the card rather than by pipetting into individual wells. The 384-well plates are called TaqMan Low Density Array (TLDA) cards. Each well contains a specific miRNA forward primer, a specific miRNA TaqMan® probe, and a reverse "tail" primer.  Thermocycling and data collection are carried out on an Applied Biosystems 7900HT instrument.

growth_protocol: Exosomes were purified from cell culture supernatant of BM-MSCs. FBS used in culture media for exosome isolation was pre-cleared by ultracentrifugation at 100,000× g for 3 hr at 4°C. Supernatant fractions collected from 48 hours BM-MSC cultures were filtered using a filtration on 0.22 m pore filters, as previously described (Valadi et al., 2007; Ostrowski et al., 2010), followed by ultracentrifugation at 20,000g for 20 min, and incubation with an exosome precipitation solution (ExoQuick, System Biosciences, Mountain View, CA) (Karolina et al., 2011). Exosomes were then harvested by ultracentrifugation at 100,000g for 70 min, as previously described (Pelinado et al., 2012).

extract_protocol: RNA was isolated using RNeasy mini kit (Qiagen, Valencia, CA), according to manufacturer’s protocol and as previously described (Valadi Nature Cell Biol, 2007).

value: multiple myeloma patient


title: multiple myeloma bone marrow-derived exosomes #2

description: SAMPLE 8

source_name: MM #2


title: MGUS bone marrow-derived exosomes #2

description: SAMPLE 9

source_name: MGUS #2

value: MGUS patient


title: MGUS bone marrow-derived exosomes #1

description: SAMPLE 7

source_name: MGUS #1


title: normal bone marrow-derived exosomes #3

description: SAMPLE 3

source_name: NBM #3

value: healthy donor


title: multiple myeloma bone marrow-derived exosomes #6

description: SAMPLE 6

source_name: MM #6


title: multiple myeloma bone marrow-derived exosomes #1

description: SAMPLE 5

source_name: MM #1


title: normal bone marrow-derived exosomes #4

description: SAMPLE 4

source_name: NBM #4


title: normal bone marrow-derived exosomes #2

description: SAMPLE 2

source_name: NBM #2


title: normal bone marrow-derived exosomes #1

description: SAMPLE 1

source_name: NBM #1


title: MSC from OF2

city: Los Angeles

first: Cunye

last: Qu

address: 2250 Alcazar st., CSA103

institute: University of Southern California

description:
Gene expression data from MSC of ossifying fibroma
OFMSC2

hyb_protocol: Following fragmentation, 6 microg of cRNA were hybridized to the Affymetrix HG-U133A_2 chip according to the protocols provided by the manufacturer.

scan_protocol: The chips were scanned using a GeneArray Scanner.

data_processing: The data was pre-processed with GC-RMA using Partek Genome Suite 6.0.

source_name: Cultured MSCs of ossifying fibroma2

label_protocol: Biotinylated cRNA were prepared from 1 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY)

growth_protocol: Mesenchymal stem cells were cultured in α-MEM containing 15% FBS, 100 mΜ L-ascorbic acid, 100 U/ml penicillin, 100 μg ml-1 streptomycin and 2 mM L-glutamine.

extract_protocol: RNA from mesenchymal stem cells was extracted using a Qiagen Rneasy Mini-kit according to the manufacturer's instructions.

treatment_protocol: Wild type cells were used for comparision.

value: cultured MSC at p1

tag: cell source

value: ossifying fibroma


title: MSC from OF1

description:
Gene expression data from MSC of ossifying fibroma
OFMSC1

source_name: Cultured MSCs of ossifying fibroma1


title: MSC from jawbone

description:
Gene expression data from MSC of jawbone
JMSC

source_name: Cultured MSCs of normal jawbone

value: normal jawbone


title: multiple myeloma bone marrow-derived exosomes #5

description: SAMPLE 13

source_name: MM #5


title: CMP2 [miRNA]

city: Baltimore

first: Curt

middle: I

last: Civin

state: Maryland

address: BRB 14-021, 655 W Baltimore St

department: Center for Stem Cell Biology & Regenerative Medicine

institute: University of Maryland School of Medicine

description:
miR expression in CMPs
Sample name: 251911910232_2_3

hyb_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

data_processing: normalization was performed via the quantile method in the limma bioconductor package in R

source_name: CMP

extract_protocol: RNA was isolated from Trizol using a miRNeasy Micro kit according to manufacturer’s instructions (Qiagen)

value: Bone marrow

value: CMP

tag: gender

value: female


title: MEP2 [miRNA]

description:
miR expression in MEPs
Sample name: 251911910232_2_4

scan_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

source_name: MEP

value: MEP


title: Control siRNA TGFbeta 1

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

hyb_protocol: Hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: probesets were summarized and probeset-level values normalized with rma(target=core) function from R/Bioconductor package oligo (version 1.14.0)

source_name: NMuMG_TGFβ treated

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: NMuMG cells were transfected with control siRNA (siControl) or siRNA against Klf4 (siKlf4) in the presence (2 days) and absence of TGFβ

extract_protocol: RNA was extracted using Rneasy kit (Qiagen)

treatment_protocol: Cells were either kept untreated or treated with TGFβ (2ng/ml)

value: NMuMG

tag: sirna

value: control

tag: treatment

value: TGFβ (2ng/ml)


title: GMP2 [miRNA]

description:
miR expression in GMPs
Sample name: 251911910232_2_2

source_name: GMP

label_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

value: GMP


title: T98G cell BAP-PCBP2 Replicate 3

first: zhong

middle: xiao

last: peng

address: 5 Dong Dan San Tiao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

description: three  replicates of BAP-PCBP2 vs. control BAP-GFP for each dye orientation

hyb_protocol: Mix 55 μL 2x GE Hybridization Buffer HI-RPM to 55 μL cRNA from Fragmentation Mix. Take the chip with 100 μL of the sample, 10rpm rolling hybridization for 17 hours at 65°C. Remove the chip to lotion 1, washing for 1 minutes. And take the chip into the lotion 2, washing for 1 minutes (37°C).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software (v 7.0) was used for background subtraction and LOWESS normalization.

source_name: T98G BAP-PCBP2 cells

label_protocol: Add 2 μg of total RNA to a 1.5-mL microcentrifuge tube. Add 5 μL of T7 Primer into the tube that contain each tube now contains a total volume of 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Add 60 μL of Transcription Mix and incubate samples in a circulating water bath at 40°C for 2 hours. Add 10 μL DMSO to 4 μg above purified cRNA (6.6 μL), and add 3.4 μL 0.3M sodium bicarbonate (PH 9.0). Add the the 20 μL cRNA mixture to a fluorescent dye (Cy3 or Cy5), 25°C for 1 hours. Add 9 μL 4M Hydroxylamine, incubate for 15min at 25°C.

growth_protocol: T98G cells were cultured in minimum essential medium and Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum, respectively. All cells were maintained at 37°C with 5% CO2.

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

value: brain

tag: tumor

value: glioma

source_name: T98G BAP-GFP cells


title: Dumbo retina, biological rep4

city: SION

first: Arnaud

last: Boulling

address: Avenue de Grand-Champsec 64

institute: Institute for Research in Ophthalmology

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data were extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA normalization method.

source_name: Dumbo retina at P15

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affimetryx). The resulting sense cDNA was fragmented by UDG and APE 1 and biotin-labelled with TdT using the GeneChip® WT Terminal labelling kit (Affymetrix).

growth_protocol: Dmbo mice were backcrossed with C57BL/6JWT to remove the Rd1 mutation. Wild-type and dumbo mice were maintained in a 12-hours light/12-hours dark cycle with free access to food and water. Animals were killed at P15 by cervical dislocation.

extract_protocol: Retinas were isolated under a microscope to remove extra retinal tissue and snap-frozen at -80°C. Total RNA was individually isolated from each whole retina and purified using the RNeasy minikit as described by the manufacturer. RNA quantities were assessed by NanoDrop®ND-1000 spectrophotometer

tag: genotype

value: Homozygous dumbo

tag: developmental stage


title: Klf4 siRNA 2

source_name: NMuMG_No treatment

value: against Klf4 (siKlf4)


title: Control siRNA 2


title: Control siRNA TGFbeta 2


title: Wild-type retina, biological rep4

source_name: Wild-type retina at P15

tag: strain

value: Homozygous Wild-type


title: GMP1 [miRNA]

description:
miR expression in GMPs
Sample name: 251911910232_1_2


title: Control siRNA 1


title: MEP1 [miRNA]

description:
miR expression in MEPs
Sample name: 251911910232_1_4


title: Klf4 siRNA TGFbeta 1


title: T98G cell BAP-PCBP2 Replicate 2


title: Dumbo retina, biological rep1


title: Wild-type retina, biological rep3


title: Dumbo retina, biological rep3


title: ST-HSC 3 [miRNA]

description:
miR expression in ST-HSCs
Sample name: 251911910564_2_2

source_name: ST-HSC

value: ST-HSC


title: Klf4 siRNA 1


title: Wild-type retina, biological rep1


title: T98G cell BAP-PCBP2 Replicate 1


title: Klf4 siRNA TGFbeta 2


title: CMP1 [miRNA]

description:
miR expression in CMPs
Sample name: 251911910232_1_3


title: Dumbo retina, biological rep2


title: Wild-type retina, biological rep2


title: multiple myeloma bone marrow-derived exosomes #4

description: SAMPLE 12

source_name: MM #4

tag: group

value: multiple myeloma patient


title: MPP 3 [miRNA]

description:
miR expression in MPPs
Sample name: 251911910564_2_4

source_name: MPP

value: MPP


title: MPP 2 [miRNA]

description:
miR expression in MPPs
Sample name: 251911910564_2_3


title: MEP [miRNA]

description:
miR expression in MEPs
Sample name: 251911910363_1_4


title: GMP [miRNA]

description:
miR expression in GMPs
Sample name: 251911910363_1_2


title: CMP [miRNA]

description:
miR expression in CMPs
Sample name: 251911910363_1_3


title: multiple myeloma bone marrow-derived exosomes #7

description: SAMPLE 11

source_name: MM #7


title: MPP [miRNA]

description:
miR expression in MPPs
Sample name: 251911910564_1_2


title: LT-HSC [miRNA]

description:
miR expression in LT-HSCs
Sample name: 251911910363_2_1

source_name: LT-HSC

value: LT-HSC


title: CMP [mRNA]

description:
Sample name: 251486821355_3
mRNA expression in CMPs

value: Bone marrow


title: MEP [mRNA]

description:
Sample name: 251486821356_1
mRNA expression in MEPs


title: MEP2 [mRNA]

description:
Sample name: 251486819723_1_4
mRNA expression in MEPs


title: MPP [mRNA]

description:
Sample name: 251486821355_4
mRNA expression in MPPs


title: GMP2 [mRNA]

description:
Sample name: 251486819723_1_2
mRNA expression in GMPs


title: MPP 3 [mRNA]

description:
Sample name: 251486823190_1_4
mRNA expression in MPPs


title: MPP 2 [mRNA]

description:
Sample name: 251486823190_1_3
mRNA expression in MPPs


title: GMP1 [mRNA]

description:
Sample name: 251486819774_1_2
mRNA expression in GMPs


title: wild-type mouse at week 11 - mouse number 33

city: Paris

first: Morwena

last: Latouche

address: 47 Bd de l'Hôpital

country: France

institute: CRICM

hyb_protocol: Mix of Cy3 and Cy5-Labeled aRNAs were fragmented according to the manufacturer instructions (Agilent, Two-Color Microarray-Based gene expression analysis Protocol). The fragments were hybridized to 4x44k whole mouse genome’s microarrays (GE2-v5_95 Agilent® chips, > 38,000 probes )

scan_protocol: Images were quantified using Agilent Feature Extraction Software (procedure GE2-v5_95_Feb07).

data_processing: BRB array tools (v4.2.1) was used for normlization (by lowess smoother). Minimum intensity was threshold at 100 and spots with both green and red intensities below 100 were considered as absent. Genes with less than 50% present call were filtered out and excluded from further analysis.

source_name: Cerebellum week 11, wild-type mouse

label_protocol: 5 µg of aRNA of each sample was labeled by coupling with cyanine-5 and reference sample (a pool of all WT and KI P10 samples) with cyanine-3 (two-color-method)

growth_protocol: female mice were killed by decapitation on post natal days 10 and 22 and 11 weeks female mice were killed by cervical dislocation. Cerebella were harvested and immediately submerged in RNA stabilization reagent (RNAlater, Qiagen, Valencia, CA) and then flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction

extract_protocol: Using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX), 400ng of total RNA from each sample was reverse transcribed and linearly amplified using a primer containing oligo(dT) and a T7 RNA polymerase promoter. After synthesis of the first and second strands of cDNA and purification on cDNA Filter Cartridge, the product was used in an in vitro transcription reaction to generate purified Amino Allyl-Modified aRNA

treatment_protocol: Total RNAs were extracted from each frozen cerebellum using RNeasy Protect Mini Kit (Qiagen) following the manufacturer’s instruction

value: wild-type

value: Week 11

value: cerebellum

source_name: Pooled total cerebellar RNA from WT and KI mice at P10

value: SCA7 KI + wild-type (pooled)


title: wild-type mouse at week 11 - mouse number 23

value: female


title: LT-HSC2-3 Pool [mRNA]

description:
Sample name: 251486823194_1_2
mRNA expression in LT-HSCs


title: testis of op_sample2

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

country: Japan

institute: Research Organization of Information and Systems

description: Gene expression in 3day fifth instar larvae in op mutant

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies). 1.65ug of Cy3-labelled cRNA was mixed, fragmented and hybridized to the silkworm 4 x 44 K oligo-microarray slide at 65 degrees Celsius for 17 hours with shaking at 10 rpm. The array was washed in Agilent Gene Expression Wash Buffer 1 for 1min at room temperature and Agilent Gene Expression Wash Buffer 2 for 1min at 37 degrees Celsius.

scan_protocol: Intensities of the hybridized probes were detected with an Agilent G2565B Microarray Scanner at 10-mm scan resolution.

data_processing: Signals were extracted with G2565AA Feature Extraction Software v.9.5 (Agilent Techonologies). The raw data in text files were normalized 'per spot' and 'per chip' using GeneSpring GX v.10.3 (Agilent Techonologies).

organism: Bombyx mori

source_name: Testis, 3day of fifth instar larvae, op mutant

label_protocol: Total RNA(300ng) was processed for Cy3-labelled cRNA synthesis using the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions (Agilent Technologies). The Cy3-labelled cRNA was purified using RNeasy Mini Kit (Qiagen) and quantified on an Agilent 2100 and Nano Drop 1000 Spectrophotometer.

extract_protocol: Total RNA from wild type or op testis were isolated using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Total RNA was quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)

treatment_protocol: Silkworms were reared on fresh mulberry leaves and kept at 25 degrees Celsius on a 12-hour light/12-hour dark cycle.

value: testis

tag: genotype/variation

value: op mutant

value: 3 day of fifth instar larvae


title: CMP2 [mRNA]

description:
Sample name: 251486819723_1_3
mRNA expression in CMPs

source_name: CMP

value: CMP


title: testis of op_sample1


title: testis of wild type_sample2

description: Gene expression in 3day fifth instar larvae in wild type

source_name: Testis, 3day of fifth instar larvae, wild type

value: wild type


title: ST-HSC 3 [mRNA]

description:
Sample name: 251486823190_1_2
mRNA expression in ST-HSCs


title: wild-type mouse at week 11 - mouse number 18


title: wild-type mouse at P22 - mouse number 31

source_name: Cerebellum P22, wild-type mouse


title: wild-type mouse at P22 - mouse number 30


title: MEP1 [mRNA]

description:
Sample name: 251486819774_1_4
mRNA expression in MEPs

source_name: MEP

value: MEP


title: wild-type mouse at week 11 - mouse number 32


title: ST-HSC 2 [mRNA]

description:
Sample name: 251486823190_1_1
mRNA expression in ST-HSCs


title: LT-HSC [mRNA]

description:
Sample name: 251486823194_1_3
mRNA expression in LT-HSCs


title: wild-type mouse at week 11 - mouse number 20


title: CMP1 [mRNA]

description:
Sample name: 251486819774_1_3
mRNA expression in CMPs


title: ST-HSC [mRNA]

description:
Sample name: 251486821356_2
mRNA expression in ST-HSCs


title: wild-type mouse at P22 - mouse number 26


title: wild-type mouse at P10 - mouse number 5

source_name: Cerebellum P10, wild-type mouse


title: wild-type mouse at P10 - mouse number 7


title: wild-type mouse at P22 - mouse number 29


title: wild-type mouse at P10 - mouse number 2


title: testis of wild type_sample1


title: wild-type mouse at P10 - mouse number 10


title: wild-type mouse at P10 - mouse number 1


title: SCA7 KI mouse at P22 - mouse number 13

source_name: Cerebellum P22, SCA7 KI mouse

value: SCA7 KI


title: SCA7 KI mouse at week 11 - mouse number 15

source_name: Cerebellum week 11, SCA7 KI mouse


title: SCA7 KI mouse at P22 - mouse number 17


title: SCA7 KI mouse at week 11 - mouse number 21


title: SCA7 KI mouse at week 11 - mouse number 19


title: wild-type mouse at P22 - mouse number 27


title: SCA7 KI mouse at week 11 - mouse number 16


title: SCA7 KI mouse at P10 - mouse number 6

source_name: Cerebellum P10, SCA7 KI mouse


title: SCA7 KI mouse at P10 - mouse number 8


title: SCA7 KI mouse at P10 - mouse number 9


title: SCA7 KI mouse at P22 - mouse number 12


title: SCA7 KI mouse at P22 - mouse number 11


title: SCA7 KI mouse at week 11 - mouse number 22


title: SCA7 KI mouse at P10 - mouse number 3


title: SCA7 KI mouse at P10 - mouse number 4


title: Splenic NK cells selenium 4

city: Sao Paulo

first: Andreia

middle: Oliveira

last: Latorre

state: SP

address: 87, Prof. Dr. Orlando Marques de Paiva

department: Pathology

institute: University of Sao Paulo

description: Gene expression of splenic NK cells from mice treated with selenium for 14 days

hyb_protocol: Cy3-labeled cRNA (1.65 µg) was fragmented and hybridized to Whole Mouse Genome 4x44k arrays at 10 rpm/17 h at 65 °C.

scan_protocol: Hybridized arrays were washed with the Gene Expression Wash Buffer Kit (Agilent) and scanned using Agilent Microarray scanner.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software using default parameters (protocol GE1-v5_95 and Grid: 014868_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Splenic NK Cells, selenium, mouse 4

label_protocol: Double-stranded cDNA was synthesized from 200 ng of total RNA with the Agilent One-Color Spike-Mix as positive controls and cDNA Master Mix (Agilent). cRNA was transcribed and labeled from the cDNA using the Quick Amp Labeling Kit (Agilent).  Cyanine 3-labeled and amplified cRNA was purified using RNAspin mini columns (GE Healthcare) and Cy3 concentration was evaluated with a spectrophotometer NanoVue™ Plus (GE Healthcare).

extract_protocol: Total RNA was isolated with RNAspin Mini RNA Isolation Kit (GE Healthcare, Buckinghamshire) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and integrity was assessed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: isolated splenic NK cells

value: male

value: selenium


title: Splenic NK cells ptaquiloside+selenium 5

description: Gene expression of splenic NK cells from mice treated with ptaquiloside and selenium for 14 days

source_name: Splenic NK Cells, ptaquiloside and selenium, mouse 5

value: ptaquiloside + selenium


title: Splenic NK cells selenium 5

source_name: Splenic NK Cells, selenium, mouse 5


title: Splenic NK cells ptaquiloside+selenium 3

source_name: Splenic NK Cells, ptaquiloside and selenium, mouse 3


title: Splenic NK cells ptaquiloside+selenium 4

source_name: Splenic NK Cells, ptaquiloside and selenium, mouse 4


title: Splenic NK cells selenium 2

source_name: Splenic NK Cells, selenium, mouse 2


title: Splenic NK cells ptaquiloside 5

description: Gene expression of splenic NK cells from mice treated with ptaquiloside for 14 days

source_name: Splenic NK Cells, ptaquiloside, mouse 5

value: ptaquiloside


title: Splenic NK cells selenium 3

source_name: Splenic NK Cells, selenium, mouse 3


title: Splenic NK cells selenium 1

source_name: Splenic NK Cells, selenium, mouse 1


title: SCA7 KI mouse at week 11 - mouse number 34

source_name: Pooled total cerebellar RNA from WT and KI mice at P10


title: Splenic NK cells ptaquiloside+selenium 1

source_name: Splenic NK Cells, ptaquiloside and selenium, mouse 1


title: Splenic NK cells ptaquiloside+selenium 2

source_name: Splenic NK Cells, ptaquiloside and selenium, mouse 2


title: Splenic NK cells ptaquiloside 1

source_name: Splenic NK Cells, ptaquiloside, mouse 1


title: Splenic NK cells control 3

description: Gene expression of splenic NK cells from mice treated with water for 14 days

source_name: Splenic NK Cells, control, mouse 3

value: control


title: Splenic NK cells ptaquiloside 3

source_name: Splenic NK Cells, ptaquiloside, mouse 3


title: GMP [mRNA]

description:
Sample name: 251486821355_2
mRNA expression in GMPs

source_name: GMP

value: Bone marrow

value: GMP


title: Splenic NK cells control 2

source_name: Splenic NK Cells, control, mouse 2


title: Splenic NK cells ptaquiloside 2

source_name: Splenic NK Cells, ptaquiloside, mouse 2


title: Splenic NK cells control 4

source_name: Splenic NK Cells, control, mouse 4


title: Splenic NK cells control 5

source_name: Splenic NK Cells, control, mouse 5


title: Splenic NK cells ptaquiloside 4

source_name: Splenic NK Cells, ptaquiloside, mouse 4


title: ST-HSC [miRNA]

description:
miR expression in ST-HSCs
Sample name: 251911910363_2_2

source_name: ST-HSC

value: ST-HSC


title: G1E-ER-GATA-1 - SetD8 siRNA - Replicate 1of3

city: Madison

first: Andrew

last: DeVilbiss

state: WI

address: 1111 Highland Ave, WIMR 4028

department: Cell and Regenerative Biology

institute: UW-Madison

description: siSetD8 01

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Mouse GE 8x60 Microarray (GPL13912), 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), both containing 0.005% Triton X-102Slides were air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the 8x60K G3 one color Microarray format. Dye channel is green, scan area 61x21.65 mm, scan resolution 3 um, Tiff is 20 bit.

data_processing: Data was processed using Edge3 one color limma differential expression analysis. FDR = 10%

source_name: G1E-ER-GATA-1 - SetD8 siRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: G1E-ER-GATA-1 cells were maintained at a density of 0.5x10^6 cells / ml in IMDM (Gibco) containing 15% FBS (Gemini) 1% penicillin-streptomycin (Gemini), 2 U/ml erythropoietin, 120 nM monothioglycerol (Sigma), 0.6% conditioned medium from a Kit ligand-producing CHO cell line, and 1mg/ml puromycin (Gemini).

extract_protocol: Total RNA from 1 million G1E-ER-GATA-1 cells was isolated using Trizol (Invitrogen). RNA was purified using Rneasy Micro Kit (Qiagen), per manufacture instructions.

treatment_protocol: 3x10^6 cells were transfected at 0 h and 24 h with 240nmol siRNA (non-targeting or SetD8-specific) using an Amaxa Nucleofector II system, along with Lonza kit R. At 24 h, cells were treated with 1mm ß-estradiol. Cells were harvested for RNA extraction at 48 h.

tag: cell line

value: SetD8 knockdown

value: ß-Estradiol (24 h)


title: MCF-7, H2ac knockdown in E2-treatment

city: Taipei

first: CH

last: Su

address: Li-Long

country: Taiwan

institute: YMGC

description: Gene expression data from knockdown of H2ac in E2-treated MCF-7.

hyb_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to manufacturer's instructions.

data_processing: Using scaling factor. The default settings are "scaling all probe sets to target signal: "500" and "normalization by user defined in value: 1.

source_name: Knockdown of H2ac in E2-treated MCF-7 cell line

growth_protocol: MCF-7 cells were grown in RPMI media 1640 medium without phenol red (Gibco) and supplemented with 5% charcoal–dextran-treated FBS for at least 3 days.

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

treatment_protocol: Cells were transfected with sacrombled or H2ac siRNA  for 72 hours, and then treated with or without 10 nM E2 for 4 hours.

tag: knockdown


title: G1E-ER-GATA-1 - SetD8 siRNA - Replicate 2of3

description: siSetD8 02


title: G1E-ER-GATA-1 - SetD8 siRNA - Replicate 3of3

description: siSetD8 03


title: MCF-7, H2ac knockdown

description: Gene expression data from knockdown of H2ac in MCF-7.

scan_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to manufacturer's instructions.

source_name: Knockdown of H2ac in  MCF-7 cell line


title: MCF-7, control knockdown in E2-treatment

description: Gene expression data from scrambled siRNA Knockdown in E2-treated MCF-7 cells.

source_name: Knockdown of scrambled RNA in E2-treated MCF-7 cell line

label_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to manufacturer's instructions.

value: scrambled siRNA


title: G1E-ER-GATA-1 - Control siRNA - Replicate 2of3

description: siControl 02

source_name: G1E-ER-GATA-1 - Control siRNA


title: G1E-ER-GATA-1 - Control siRNA - Replicate 3of3

description: siControl 03


title: OCILY18-anti-IgG-4h-rep2

status: Public on Jul 23 2013

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

institute: Roche Pharma

description: Gene expression data from human cell lines

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

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

data_processing:
The MAS5.0 normalized data for each unicate provided in the Sample table.
The data were further analyzed with In-house tools. We generated data sets consisting of "mean values" for the three replicates and "change factors" to the appropriate control experiment supplied in the GSE23394_Matrix_triplicates.xls file. Our in-house tool is called Race-A (Roche Affymetrix Chip Experiment - Analysis). The method is MAS5.0 and the scaling factor was adjusted for a scaling mean of 158. The CHGF=change factors are relative ratios (-1 for up regulation and +1 for down regulation to avoid the gap between -1 and +1), i.e. chgf=1 means double signal, chgf=-1 means half signal.

source_name: Human cell line,  4h

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard procedures of cell culture according to the guidelines of suppliers

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

treatment_protocol: cells were treated for 4h

value: anti-IgG

tag: dose

tag: unit

value: µg/ml


title: MCF-7, control knockdown

description: Gene expression data from scrambled siRNA Knockdown MCF-7 cells.

source_name: Knockdown of scrambled RNA in  MCF-7 cell line


title: Splenic NK cells control 1

source_name: Splenic NK Cells, control, mouse 1

tag: cell type


title: Z138-anti-IgG-4h-rep3


title: OCILY18-anti-IgG-4h-rep1


title: Z138-Control-4h-rep5

value: Control


title: Z138-Control-4h-rep6


title: OCILY18-Control-4h-rep4


title: SUDHL4-Control-4h-rep6


title: SUDHL4-Control-4h-rep4


title: G1E-ER-GATA-1 - Control siRNA - Replicate 1of3

description: siControl 01


title: OCILY18-Control-4h-rep5


title: Z138-anti-IgG-4h-rep1


title: Clinical case 3 (Streptococcus case)

description: Streptococcus case

source_name: serum

tag: sample type

value: disease

value: healthy control


title: Z138-anti-IgG-4h-rep2


title: OCILY18-anti-IgG-4h-rep3


title: SUDHL4-Control-4h-rep5


title: OCILY18-Control-4h-rep6


title: Z138-Control-4h-rep4


title: SUDHL4-anti-IgG-4h-rep2


title: SUDHL4-anti-IgG-4h-rep3


title: SUDHL4-anti-IgG-4h-rep1


title: REC1-anti-IgMFab2-4h-rep2


title: REC1-anti-IgMFab2-4h-rep3


title: REC1-anti-IgG-4h-rep2


title: REC1-RituximabFab2-4h-rep3


title: REC1-anti-IgMFab2-4h-rep1


title: REC1-RituximabFab2-4h-rep1


title: REC1-anti-IgG-4h-rep1


title: REC1-RituximabFab2-4h-rep2


title: REC1-LT20-4h-rep1


title: REC1-anti-IgG-4h-rep3