title: Islets Nkx6.1 Mutant B

city: La Jolla

first: Brandon

last: Taylor

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego

description: Gene expression of islets at 6 weeks of age after deletion of Nkx6.1

hyb_protocol: Standard Agilent hybridization with 1650 ng cRNA. 17-19 hrs @ 65°C. Standard Agilent wash including Stabilization & Drying Solution.

scan_protocol: Model G2505B Agilent Scanner. One color. 100% and 10% PMT settings for Extended Dynamic Range. 5µm resolution.

data_processing: Raw Data extraction using Agilent Feature Extraction Software v10.7.3.1 using protocol GE1_107_Sep09 . Normalization, a modified LOESS.

source_name: Isolated islets, mutant mice, pooled sample 2

label_protocol: QuickAmp Low Input labelling: 150 ng total RNA labeled with Cy3. Specific Activity of > 6 pmol dye/µg cRNA accepted.

growth_protocol: All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees.

extract_protocol: Islets were isolated and stored in 350 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from two pancreata of the same genotype as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of RNase free water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male mice were injected with 2 mg/25 g tamoxifen in corn oil four times between 4 and 6 weeks of age.

tag: strain

value: Nkx6.1-flox [mixed FVB/N x C57Bl/6J] X Pdx1-CreERTM [mixed Cd1 X C57Bl/6J background]

tag: tissue

value: Pancreatic islets

tag: gender

value: male

tag: age

value: 6 weeks

value: Tamoxifen

tag: genotype

value: Nkx6.1fl/-;Pdx1-CreERTM Mutant


title: Islets Nkx6.1 Mutant C

status: Public on Sep 12 2013

type: RNA

state: CA

country: USA

molecule: total RNA

organism: Mus musculus

source_name: Isolated islets, mutant mice, pooled sample 3

tag: treatment


title: Bp22_RAW_1 (Cy3)

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: SAMPLE 69

hyb_protocol: Microarray hybridizations were performed at 65°C in a MAUI hybridization station (BioMicro Systems, USA) for 17hrs.

scan_protocol: The slides were washed, dried in a centrifuge at 600rpm for 4mins, and scanned on an Axon Genepix 4000B scanner (Molecular Devices, USA) at a resolution of 5 microns

data_processing: The raw data (.pair file) was subjected to Lowess within-chip normalization as implemented in GeneSpring GX11 , and cross-chip median normalization using R, .

organism: Burkholderia pseudomallei Bp22

source_name: Burkholderia pseudomallei Bp22 wild type

label_protocol: Sample cDNAs were labeled with Cy3 (Cy3-ULS, Kreatech Diagnostics, USA) and a universal hybridization reference (K9LBS) was similarly labeled with Cy5.

growth_protocol: Reference sample used (Cy5) is common to all - Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).

extract_protocol: Bacterial cells in liquid cultures were isolated by centrifugation at 3500rpm at 4°C for 15mins, washed with 1xDPBS, and re-pelleted. Cell pellets were mixed with 4-8ml TRIZOL reagent (Invitrogen, USA) and maintained at room temperature for 10mins. For bacterial cells on plate cultures, bacterial colonies were harvested using sterile inoculation loops directly into 4ml TRIZOL. One-tenth the volume of 1-bromo-3-chloro-propane (Sigma, USA) was then added, and the entire mixture vortexed for 15s. The mixture was incubated at room temperature for 3mins and centrifuged at 9,000rpm at 4°C for 30mins. The aqueous phase was transferred to a fresh tube containing an equal volume of isopropanol, mixed well, and maintained at room temperature for 10mins. The tube was then centrifuged at 9,000rpm at 4°C for 30mins to obtain the total RNA pellet. The pellet was washed with 1ml 75% ethanol, dried at room temperature for 5mins, and resuspended in 30ul of RNase-free water. Bp-infected RAW264.7 cells were lysed with TRIZOL and both murine and bacterial total RNAs were extracted using a PureLink RNA mini kit (Invitrogen, USA). Bp-infected murine lungs from infected BALB/c mice were treated with 2ml TRIZOL, homogenized using a Polytron homogenizer (maximum speed, two bursts 10–15s each), and processed for RNA extraction. Extracted RNAs were treated with DNase I (DNA-free; Ambion, USA) to remove contaminating genomic DNA, according to the manufacturer’s instructions.

treatment_protocol: RNA samples were further enriched for bacterial mRNAs using a MICROBExpress kit (Ambion, USA) to deplete bacterial 16S and 23S rRNAs, according to the manufacturer’s instructions. For RNA samples comprising both bacterial and mammalian RNAs, bacterial RNAs were separated from mammalian 18S and 28S rRNAs using a MICROBEnrich kit (Ambion, USA), according to the manufacturer’s instructions. The MICROBEnrich kit uses a Capture Oligo Mix of capture oligonucleotides homologous to mammalian 18S and 28S rRNAs. After processing, bacterial mRNA samples were quantified by spectrophotometry, and electrophoresed in TAE/formamide agarose gels to assess overall mRNA quality and integrity.

tag: genotype/variation

value: wild type

tag: infection

value: Bp-infected RAW264.7 cell line

tag: condition

value: Extracellular bacteria killed by 250ug/ml kanamycin 2 hrs p.i.  Infected cells lysed for intracellular bacteria harvest after 5 hrs.


title: Bp22_RAW_1 (Cy5)

description: SAMPLE 70

organism: Burkholderia pseudomallei K96243

source_name: Burkholderia pseudomallei K96243 wild type

value: Not applicable

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: HUVEC2 [Nov 2012]

city: Atlanta

first: Young-sup

last: Yoon

state: Georgia

address: 101 Woodruff Cir

department: Medicine

institute: Emory University

description: Gene expression data from HUVECs

hyb_protocol: Samples were hybridized according to the GeneChip® PrimeView™ Human Gene Expression Array protocol by the Core Genomics Facility, University of Illinois at Chicago.

scan_protocol: Samples were scanned according to the GeneChip® PrimeView™ Human Gene Expression Array protocol by the Core Genomics Facility, University of Illinois at Chicago.

data_processing: Partek Genomics Suite was used for data processing. RMA was used for normalization algorithm and background corrected log2 transformed signals for all samples.

label: biotin

organism: Homo sapiens

label_protocol: Samples are labeled according to the GeneChip® PrimeView™ Human Gene Expression Array labeling protocol by the Core Genomics Facility, University of Illinois at Chicago.

growth_protocol: Standard mammalian cell cultrure methods

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: Lentiviral transduction of ER71/ETV2

tag: cell type

value: Human umbilical venous endothelial cells


title: Bp22_LBML_2 (Cy3)

description: SAMPLE 67

value: Bacteria subjected to growth in LB. Harvested at log phase (OD600 = 0.8).


title: Bp22_LBML_1 (Cy5)

description: SAMPLE 66


title: E-2 [Nov 2012]

description: Gene expression data from KDR+ cells derived from ER71 transduced HDFs

source_name: long term cultured KDR+ cells from ER71 transduced HDF at D8

value: reprogrammed cells


title: Bp22_LBML_1 (Cy3)

description: SAMPLE 65


title: Bp22_LB4hr_1 (Cy5)

description: SAMPLE 58


title: Bp22_LB4hr_2 (Cy5)

description: SAMPLE 60


title: Bp22_LBES_1 (Cy5)

description: SAMPLE 62


title: E-1 [Nov 2012]

source_name: long term cultured KDR+ cells from ER71 transduced HDF at D7


title: Bp22_LBES_2 (Cy3)

description: SAMPLE 63

value: Bacteria subjected to growth in LB. Harvested at early-stationary phase (OD600 = 1.8).


title: Bp22_VirAGRAW_1 (Cy3)

description: SAMPLE 73

source_name: Burkholderia pseudomallei Bp22 virAG mutant

value: virAG mutant


title: Bp22_LBES_2 (Cy5)

description: SAMPLE 64


title: Bp22_LB4hr_2 (Cy3)

description: SAMPLE 59

value: Bacteria (wild type) grown to 4 hrs (log phase) in LB.


title: Bp22_LB3hr_2 (Cy5)

description: SAMPLE 56


title: Bp22_LBES_1 (Cy3)

description: SAMPLE 61


title: Islets Nkx6.1 Mutant A

source_name: Isolated islets, mutant mice, pooled sample 1

value: Nkx6.1-flox [mixed FVB/N x C57Bl/6J] X Pdx1-CreERTM [mixed Cd1 X C57Bl/6J background]


title: Bp22_LB4hr_1 (Cy3)

description: SAMPLE 57


title: Bp22_LB3hr_1 (Cy3)

description: SAMPLE 53

value: Bacteria (wild type) grown to OD600=0.6 (log phase) in LB.


title: Islets Control B

description: Gene expression of control islets at 6 weeks of age

source_name: Isolated islets, control mice, pooled sample 2

value: Pancreatic islets

value: male

value: Nkx6.1fl/+;Pdx1-CreERTM Control


title: TM-human-1

city: Amsterdam

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Biological TM replicate 1 of 2 of healthy human eyes

hyb_protocol: Labeled human TM RNA and labeled human common reference sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.
Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next, we normalized within arrays (method 'loess', resulating in MA) and between arrays (method aquantile). In the matrix table, we listed these normilized red channels of each human TM sample (log2).

source_name: healthy human trabecular meshwork

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.

growth_protocol: not applicable

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

treatment_protocol: TM tissue was dissected from healthy human donor eyes (<24h post mortem time)

value: trabecular meshwork

source_name: Total RNA from pooled healthy human RPE/choroid cells

value: RPE/choroid


title: Islets Control A

source_name: Isolated islets, control mice, pooled sample 1

value: 6 weeks

value: Tamoxifen


title: HDF 1 [Nov 2012]

description: Gene expression data from HDFs

source_name: HDF 1

value: Human dermal fibroblasts


title: KDR+ cells-1 [June 2012]

source_name: KDR+ cells from ER71 transduced HDF at D7


title: HDF 2 [Nov 2012]

description: Gene expression data from HDFs

source_name: HDF 2


title: KDR+ cells-2 [June 2012]


title: Bp22_LB3hr_2 (Cy3)

description: SAMPLE 55

value: wild type

value: Not applicable


title: Bp22_LB3hr_1 (Cy5)

description: SAMPLE 54

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: TM-human-2

description: Biological TM replicate 2 of 2 of healthy human eyes


title: HFHFr-NA

city: Kyoto

first: Hiroyuki

last: Tsuchiya

state: Kyoto

address: Nakauchi-cho 5, Misasagi, Yamashina-ku

department: Department of Biophysical Chemistry

country: Japan

institute: Kyoto Pharmaceutical University

hyb_protocol: Labeled cRNA was fragmented and hybridized to Agilent Technologies Whole Mouse Genome Microarray 4x44K (G4122F) according to manufacturers instructions

scan_protocol: Signals were scanned on Agilent Technologies Microarray Scanner.

data_processing: Signals were imported into GeneSpring software, and normalized to facilitate comparison among arrays.

source_name: HFHFr-NA

label_protocol: Labeled cRNA was prepared using Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: RNA was extracted using RNeasy PLUS Mini kit (Qiagen)

treatment_protocol: Mice were fed a high-fat, high-fructose (HFHFr) diet for 16 weeks, and subsequently were fed an all-trans retinoic acid-supplemented normal diet for further 4 weeks.

tag: Sex

value: 25 weeks

value: liver

value: HFHFr diet 16 weeks, all-trans retinoic acid-supplemented normal diet 4 weeks

tag: phenotype

value: normal (recovered from insulin resistance)


title: Bp22_CDMML_2 (Cy3)

description: SAMPLE 51

value: Bacteria subjected to growth in CDM. Harvested at log phase (OD600 = 0.2).


title: HUVEC2 [June 2012]

description: Gene expression data from HUVECs

value: Human umbilical venous endothelial cells


title: HUVEC 1 [Nov 2012]

description: Gene expression data from HUVECs

source_name: HUVEC 1


title: Bp22_LBML_2 (Cy5)

description: SAMPLE 68


title: HFHFr-F

source_name: HFHFr-F

treatment_protocol: Mice were fed a high-fat, high-fructose (HFHFr) diet for 20 weeks.

value: HFHFr diet 20 weeks

value: severe insulin resistance


title: HFHFr-FA

source_name: HFHF-FA

treatment_protocol: Mice were fed a high-fat, high-fructose (HFHFr) diet for 16 weeks, and subsequently were fed an all-trans retinoic acid-supplemented HFHFr diet for further 4 weeks.

value: male

value: HFHFr diet 16 weeks, all-trans retinoic acid-supplemented HFHFr diet 4 weeks

value: not insulin resistant, but slight liver steatosis


title: HDF 1 [June 2012]

description: Gene expression data from HDFs


title: Bp22_CDMML_1 (Cy3)

description: SAMPLE 49

source_name: Burkholderia pseudomallei Bp22 wild type


title: Bp22_CDMML_1 (Cy5)

description: SAMPLE 50

source_name: Burkholderia pseudomallei K96243 wild type


title: Bp22_CDMML_2 (Cy5)

description: SAMPLE 52


title: Bp22_CDMES_2 (Cy5)

description: SAMPLE 48


title: Bp22_CDMES_1 (Cy5)

description: SAMPLE 46


title: HFHFr-N

source_name: HFHFr-N

treatment_protocol: Mice were fed a high-fat, high-fructose (HFHFr) diet for 16 weeks, and subsequently were fed a normal diet for further 4 weeks.

value: HFHFr diet 16 weeks, normal diet 4 weeks

value: insulin resistant


title: Control

source_name: control

treatment_protocol: Untreated.

value: untreated


title: Cotton_alkalinity-2

city: Beijing

first: Weicai

last: Yang

address: No.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description:
seedlings treated with alkalinity, biological rep2
Gene expression data from cotton seedlings 14-day after germation treated under pH=11

hyb_protocol: Cleaned total RNAs from each of the six samples, including control, ABA, cold, Mannitol, NaCl as well as pH treatment were sent to CapitalBio Corporation in Beijing for microarray hybridization and preliminary data analysis.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

organism: Gossypium hirsutum

source_name: Cotton seedings under pH=11 treatment

label_protocol: The arrays were hybridized with Cy3 and Cy5 fluorescently labeled probe pairs of ABA treated plants plus control, cold-treated plants plus control, mannitol-treated plants plus control, NaCl-treated plants plus control, and pH-treated plants plus control. (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The sterilized seeds were germinated and grown on half-strength MS solid medium for 4 days in a growth chamber maintained at 25℃, 12h photoperiod (white fluorescent light at 500–600 μm m-2s-1). For abiotic stress treatment, the seeds were raised on the corresponding medium.

extract_protocol: A Modified LiCl method was used for RNA isolation.

treatment_protocol: For ABA treatment, seeds were kept in 1/2 MS+1μM ABA, PH 5.8 for ten days; for cold treatment, seeds were first kept in 1/2 MS, PH 5.8, and 25℃ for 8 days, and then exposed to 4℃ for 2 days; for drought stress, seeds were treated with 200mM mannitol, PH 5.8, and 25℃ for ten days; for salinity stress, seeds were treated with 200mM NaCl, PH 5.8, and 25℃ for ten days; for alkalinity (high pH, hereinafter referred to pH) stress, seeds were kept in 1/2 MS, pH 11, and 25℃ for 10 days.

value: seeding

value: 14-day after germination


title: Cotton_alkalinity-1

description:
seedlings treated with alkalinity, biological rep1
Gene expression data from cotton seedlings 14-day after germation treated under pH=11


title: Islets Control C

source_name: Isolated islets, control mice, pooled sample 3

value: Nkx6.1-flox [mixed FVB/N x C57Bl/6J] X Pdx1-CreERTM [mixed Cd1 X C57Bl/6J background]

value: Pancreatic islets

value: 6 weeks

value: Tamoxifen

value: Nkx6.1fl/+;Pdx1-CreERTM Control


title: Bp22_RAW_2 (Cy3)

description: SAMPLE 71

value: wild type

value: Bp-infected RAW264.7 cell line

value: Extracellular bacteria killed by 250ug/ml kanamycin 2 hrs p.i.  Infected cells lysed for intracellular bacteria harvest after 5 hrs.


title: Bp22_CDMES_1 (Cy3)

description: SAMPLE 45

value: Not applicable

value: Bacteria subjected to growth in CDM. Harvested at early-stationary phase (OD600 = 0.5).


title: Cotton_salinity-2

description:
seedlings treated with NaCl, biological rep2
Gene expression data from cotton seedlings 14-day after germation treated with 200mM NaCl

source_name: Cotton seedings under 200mM NaCl treatment


title: Cotton_salinity-1

description:
seedlings treated with NaCl, biological rep1
Gene expression data from cotton seedlings 14-day after germation treated with 200mM NaCl


title: Bp22_bsaN_2 (Cy3)

description: SAMPLE 43

source_name: Burkholderia pseudomallei Bp22 bsaN mutant

value: bsaN mutant

value: Bacteria (bsaN mutant) grown to OD600=0.6 (log phase) in LB.


title: Cotton_salinity-3

description:
seedlings treated with NaCl, biological rep3
Gene expression data from cotton seedlings 14-day after germation treated with 200mM NaCl


title: Cotton_drought-3

description:
seedlings treated with mannitol, biological rep3
Gene expression data from cotton seedlings 14-day after germation treated with 200mM mannitol

source_name: Cotton seedings under 200mM mannitol treatment


title: Bp22_bsaN_1 (Cy5)

description: SAMPLE 42

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: Bp22_BprP_2 (Cy3)

description: SAMPLE 39

source_name: Burkholderia pseudomallei Bp22 bprP mutant

value: bprP mutant

value: Bacteria (bprP mutant) grown to OD600=0.6 (log phase) in LB.


title: Bp22_bsaN_1 (Cy3)

description: SAMPLE 41


title: Cotton_drought-2

description:
seedlings treated with mannitol, biological rep2
Gene expression data from cotton seedlings 14-day after germation treated with 200mM mannitol

value: seeding


title: Cotton_cold-2

description:
seedlings treated under low trmperature, biological rep2
Gene expression data from cotton seedlings 14-day after germation treated under 4℃

source_name: Cotton seedings under 4℃

value: 14-day after germination


title: Bp22_bsaN_2 (Cy5)

description: SAMPLE 44


title: Bp22_BprP_2 (Cy5)

description: SAMPLE 40


title: Cotton_cold-3

description:
seedlings treated under low trmperature, biological rep3
Gene expression data from cotton seedlings 14-day after germation treated under 4℃


title: Bp22_BprP_1 (Cy5)

description: SAMPLE 38


title: Cotton_drought-1

description:
seedlings treated with mannitol, biological rep1
Gene expression data from cotton seedlings 14-day after germation treated with 200mM mannitol


title: Bp22_CDMES_2 (Cy3)

description: SAMPLE 47


title: Bp22_BprCRAW_2 (Cy3)

description: SAMPLE 35

source_name: Burkholderia pseudomallei Bp22 bprC mutant

value: bprC mutant


title: Cotton_ABA-1

description:
seedlings treated with ABA, biological rep1
Gene expression data from cotton seedlings 14-day after germation treated with 1μM ABA

source_name: Cotton seedings under 1μM ABA treatment


title: Bp22_BprP_1 (Cy3)

description: SAMPLE 37


title: Cotton_cold-1

description:
seedlings treated under low trmperature, biological rep1
Gene expression data from cotton seedlings 14-day after germation treated under 4℃


title: Bp22_BprCRAW_1 (Cy3)

description: SAMPLE 33

value: Extracellular bacteria killed by 250ug/ml kanamycin 2 hrs p.i. Infected cells lysed for intracellular bacteria harvest after 5 hrs.


title: Cotton_CK-2

description:
seedlings under normal condition, biological rep2
Gene expression data from cotton seedlings 14-day after germation under normal growth condition

source_name: Cotton seedings under normal growth condition


title: Bp22_BprCRAW_2 (Cy5)

description: SAMPLE 36


title: Cotton_CK-3

description:
seedlings under normal condition, biological rep3
Gene expression data from cotton seedlings 14-day after germation under normal growth condition


title: HDF 2 [June 2012]

description: Gene expression data from HDFs

source_name: HDF 2

value: Human dermal fibroblasts


title: Bp22_BprC_2 (Cy5)

description: SAMPLE 32


title: Bp22_BprC_1 (Cy5)

description: SAMPLE 30


title: Bp008_pmlITc_2 (Cy5)

description: SAMPLE 28


title: Bp22_BprCRAW_1 (Cy5)

description: SAMPLE 34


title: Bp22_BprC_2 (Cy3)

description: SAMPLE 31

value: Bacteria ( bprC mutant) grown to 4 hrs (log phase) in LB.


title: suture_patent_7

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

description:
biological replicate 7
REEF 007P

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in GenomeStudio and then exported in text format followed by upload to Partek Genomics Suite for statistical analysis

source_name: Cranial suture

label_protocol: Illumina DASL Assay

extract_protocol: RNA was extracted with Trizol reagent followed by isoproponal precipitation and 70% ethanol wash

value: patent


title: suture_patent_5

description:
biological replicate 5
REEF 005P


title: Cotton_ABA-2

description:
seedlings treated with ABA, biological rep2
Gene expression data from cotton seedlings 14-day after germation treated with 1μM ABA


title: Cotton_ABA-3

description:
seedlings treated with ABA, biological rep3
Gene expression data from cotton seedlings 14-day after germation treated with 1μM ABA


title: suture_patent_3

description:
biological replicate 3
REEF 003P


title: suture_patent_2

description:
biological replicate 2
REEF 002P


title: suture_patent_4

description:
biological replicate 4
REEF 004P


title: suture_patent_1

description:
biological replicate 1
REEF 001P


title: suture_fused_7

description:
biological replicate 7
REEF 007F

value: synostosed


title: preeclampsia 86

city: Nanchang

first: xiaoju

last: He

address: Bayi Road 318#

department: Department of Obstetrics

institute: Jiangxi Maternal and Child Health Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 11 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: preeclampsia 86

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

extract_protocol: 1*1*1cm3 Placenta tissues in the middle of maternal placenta were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA integrity was evaluated by Nano Drop ND-1000 spectrophotometer. 1 ug of total RNA was used for the construction of sequencing libraries.

tag: mean arterial pressure (mmhg)

tag: urine protein

value: placenta

tag: disease state

value: preeclampsia


title: suture_patent_6

description:
biological replicate 6
REEF 006P


title: suture_fused_6

description:
biological replicate 6
REEF 006F


title: suture_fused_5

description:
biological replicate 5
REEF 005F


title: HUVEC 1 [June 2012]

description: Gene expression data from HUVECs

source_name: HUVEC 1

value: Human umbilical venous endothelial cells


title: suture_fused_3

description:
biological replicate 3
REEF 003F


title: suture_fused_4

description:
biological replicate 4
REEF 004F


title: Bp008_2 (Cy5)

description: SAMPLE 24

source_name: Burkholderia pseudomallei K96243 wild type

value: wild type

value: Not applicable


title: preeclampsia 34

source_name: preeclampsia 34


title: suture_fused_2

description:
biological replicate 2
REEF 002F


title: preeclampsia 42

source_name: preeclampsia 42


title: Bp008_pmlITc_1 (Cy3)

description: SAMPLE 25

organism: Burkholderia pseudomallei

source_name: Burkholderia pseudomallei Bp008 pmlI mutant

value: pmlI mutant

value: Mutant grown for 24 hrs for maximal MprA expression difference.


title: Bp008_pmlITc_2 (Cy3)

description: SAMPLE 27


title: suture_fused_1

description:
biological replicate 1
REEF 001F


title: Bp22_BprC_1 (Cy3)

description: SAMPLE 29


title: preeclampsia 81

source_name: preeclampsia 81


title: Bp008_pmlITc_1 (Cy5)

description: SAMPLE 26

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: preeclampsia 71

source_name: preeclampsia 71


title: Bp008_1 (Cy5)

description: SAMPLE 22


title: Bp008_2 (Cy3)

description: SAMPLE 23

source_name: Burkholderia pseudomallei Bp008 wild type

value: Bacteria grown for 24 hrs for maximal MprA expression.


title: Bp008_1 (Cy3)

description: SAMPLE 21


title: preeclampsia 63

source_name: preeclampsia 63


title: AL30_H2O2ref_1 (Cy5)

description: SAMPLE 20


title: AL30_37C30mins_1 (Cy3)

description: SAMPLE 13

source_name: Burkholderia pseudomallei K96243 rpoE mutant

value: rpoE mutant

value: Bacteria grown to log phase, pelleted and resuspended in warmed LB medium for 30 minutes


title: AL30_37C30mins_2 (Cy3)

description: SAMPLE 15


title: AL30_H2O2ref_1 (Cy3)

description: SAMPLE 19

value: Bacteria grown in LB, reference condition for hydrogen peroxide perturbation.


title: Cotton_CK-1

description:
seedlings under normal condition, biological rep1
Gene expression data from cotton seedlings 14-day after germation under normal growth condition

value: seeding

value: 14-day after germination


title: AL30_37C30mins_1 (Cy5)

description: SAMPLE 14


title: normal 50

source_name: normal 50

value: normal


title: AL30_37C30mins_2 (Cy5)

description: SAMPLE 16


title: mouse_lung_WT_F_Rep 4

status: Public on Sep 11 2013

city: Trento

first: Valerio

last: Del Vescovo

state: Trentino Alto Adige

address: via delle Regole 101

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

hyb_protocol: Purified Cy3 labeled RNA was hybridized accordingly to the manufacturer protocol. 20 Rotation x min 16h 60C

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner G2505C with default protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.1.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. In order to normalize data was used Quantile normalization funcion.

source_name: mouse, lung, WT, Female, Replicate 4

label_protocol: One hundred nanograms of total RNA samples was dephosphorylated, 3′ end-labeled with Cy3-pCp, purified on Micro Bio-Spin columns, dried, and hybridized onto arrays using the miRNA Microarray System labeling kit V2 according to the manufactures instructions (5190-0456)

extract_protocol: Total RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction.

treatment_protocol: SP-C/c-raf transgenic mice were obtained from the laboratory of Prof. Ulf Rapp (University of Würzburg, Germany). Lung tissue from n=6 male and n=6 females SP-C/c-Raf transgenic mice (aged 4–6 months) and n= 6 male and n= 6 female normal lung tissue from type mice (aged 4-6 months) were sacrificed and the lung tissues were immediately frozen on dry ice and stored at - 80° until further analysis.From each frozen lung tissue 10-mm thick sections were prepared and transferred on polyethylene napthalate foil-covered slides (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). The sections were fixed in methanol/acetic acid and stained in hematoxylin. The desired cells were microdissected using the PALM MicroLaser systems (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany) and collected in an adhesive cap (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). Microdissected cells were resuspended in a guanidine isothiocyanate containing buffer (RLT buffer from RNeasy MikroKit, Qiagen, Santa Clarita, CA, USA) with 10 ml/ml ß-mercaptoethanol to ensure isolation of intact RNA.

value: lung adenocarcinoma

value: female


title: normal 32

source_name: normal 32

value: placenta


title: mouse_lung_WT_F_Rep 3

source_name: mouse, lung, WT, Female, Replicate 3


title: AL30_H2O210mins_1 (Cy3)

description: SAMPLE 17

value: Bacteria grown in LB with hydrogen peroxide treatment for 10mins.


title: AL30_37C16hr_2 (Cy3)

description: SAMPLE 11

value: Bacteria grown to log phase, pelleted and resuspended in warmed LB medium for 16 hours


title: AL30_H2O210mins_1 (Cy5)

description: SAMPLE 18

value: wild type


title: normal 114

source_name: normal 114


title: AL30_37C16hr_2 (Cy5)

description: SAMPLE 12

value: Not applicable


title: mouse_lung_WT_F_Rep 6

source_name: mouse, lung, WT, Female, Replicate 6


title: AL30_37C16hr_1 (Cy3)

description: SAMPLE 9


title: normal 90

source_name: normal 90


title: AL30_37C16hr_1 (Cy5)

description: SAMPLE 10


title: mouse_lung_WT_F_Rep 2

source_name: mouse, lung, WT, Female, Replicate 2


title: mouse_lung_WT_M_Rep 6

source_name: mouse, lung, WT, Male, Replicate 6

value: male


title: mouse_lung_WT_M_Rep 5

source_name: mouse, lung, WT, Male, Replicate 5


title: normal 95

source_name: normal 95


title: mouse_lung_WT_M_Rep 4

source_name: mouse, lung, WT, Male, Replicate 4


title: AL30_04C30mins_2 (Cy3)

description: SAMPLE 7

value: Bacteria grown to log phase, pelleted and resuspended in cold LB medium for 30 minutes.


title: mouse_lung_WT_F_Rep 5

source_name: mouse, lung, WT, Female, Replicate 5


title: mouse_lung_WT_M_Rep 2

source_name: mouse, lung, WT, Male, Replicate 2


title: AL30_04C30mins_2 (Cy5)

description: SAMPLE 8

source_name: Burkholderia pseudomallei K96243 wild type

value: Bacteria subjected to growth in LB. Harvested at stationary phase (OD600 = 2.0).


title: mouse_lung_WT_F_Rep 1

source_name: mouse, lung, WT, Female, Replicate 1


title: mouse_lung_cRaf_F_Rep 5

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 5

value: cRaf overexpressing


title: mouse_lung_cRaf_F_Rep 6

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 6


title: mouse_lung_cRaf_F_Rep 4

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 4


title: mouse_lung_WT_M_Rep 1

source_name: mouse, lung, WT, Male, Replicate 1


title: AL30_04C16hr_2 (Cy3)

description: SAMPLE 3

source_name: Burkholderia pseudomallei K96243 rpoE mutant

value: rpoE mutant

value: Bacteria grown to log phase, pelleted and resuspended in cold LB medium for 16 hours


title: mouse_lung_cRaf_F_Rep 2

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 2


title: mouse_lung_cRaf_F_Rep 1

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 1


title: mouse_lung_cRaf_F_Rep 3

source_name: mouse, lung, cRaf overexpressing, Female, Replicate 3


title: AL30_04C30mins_1 (Cy3)

description: SAMPLE 5


title: mouse_lung_cRaf_M_Rep 6

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 6


title: mouse_lung_cRaf_M_Rep 2

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 2


title: mouse_lung_cRaf_M_Rep 5

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 5


title: mouse_lung_cRaf_M_Rep 3

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 3


title: mouse_lung_cRaf_M_Rep 4

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 4


title: AL30_04C30mins_1 (Cy5)

description: SAMPLE 6


title: mouse_lung_cRaf_M_Rep 1

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 1


title: mouse_lung_WT_M_Rep 3

source_name: mouse, lung, WT, Male, Replicate 3


title: AL30_04C16hr_1 (Cy5)

description: SAMPLE 2

source_name: Burkholderia pseudomallei K96243 wild type


title: AL30_04C16hr_2 (Cy5)

description: SAMPLE 4


title: Let1_GFP_1h.4

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Gene expression in GFP expressing cells infected with PR8 influenza for 1 hour

hyb_protocol: 600ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 C and 10rpm. The arrays were washed for 1 minute in Agilent GE Wash Buffer 1 and then for another minute in Agilent GE Wash Buffer 2.

scan_protocol: Scanning was performed using an Agilent High-Resolution DNA Microarray Scanner, with 3 micron resolution and 20-bit dynamic range. The resulting images were processed with Agilent Feature Extraction version 10.7.3.1 to generate raw probe intensity data.

data_processing: Arrays were quantile normalized using the normalizeBetweenArrays function from the Bioconductor marray package.

source_name: immortalized airway epithelial cells, expressing GFP, infected with PR8 influenza 1 hour

label_protocol: Labeling was performed with the One-Color Microarray-Based Gene Expression Analysis protocol version 6.5 (Agilent). Briefly, double-stranded cDNA was synthesized from 200ng of total RNA using a T7-oligo(dT) primer, followed by in vitro transcription by T7 RNA polymerase with incorporation of Cy3-labeled CTP.

growth_protocol: To generate LET1 cells, lung cells were isolated from C57Bl/6 mice using a modified dispase-agarose protocol (Herold et al., 2006), cultured to yield lung epithelial type I cells (LET1) trans-differentiated from type II epithelial cells, then immortalized by transduction with MSCV-SV40 large T antigen and used after a minimal number of passages. LET1 cells were cultured in DMEM containing 10% heat-inactivated FBS, 2 mM L-glutamine, and penicillin-streptomycin (complete DMEM), incubated at 37oC 5% CO2., passaged using a brief trypsinization, and sub-cultured 1:20 every 3 days.

extract_protocol: Total RNA was isolated from bone-marrow-derived macrophages using TRIzol (Invitrogen) according to the manufacturer's instructions. Prior to labeling, the integrity of samples was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were infected with influenza A (A/Puerto Rico/8/34) (PR8) at MOI=5 in OptiMEM in the absence of trypsin, the inoculum removed by washing, and cells cultured in OptiMEM.

value: immortalized airway epithelial cells

tag: transgene

value: GFP

tag: time

value: 1 hour

value: PR8 influenza


title: Let1_GFP_1h.5

tag: strain


title: Let1_GFP_18h.1

description: Gene expression in GFP expressing cells infected with PR8 influenza for 18 hours

source_name: immortalized airway epithelial cells, expressing GFP, infected with PR8 influenza 18 hours

value: 18 hours


title: Let1_miR451_1h.1

description: Gene expression in miR-451 expressing cells infected with PR8 influenza for 1 hour

source_name: immortalized airway epithelial cells, expressing miR-451, infected with PR8 influenza 1 hour


title: Let1_miR144_1h.2

description: Gene expression in miR-144 expressing cells infected with PR8 influenza for 1 hour

source_name: immortalized airway epithelial cells, expressing miR-144, infected with PR8 influenza 1 hour


title: Let1_miR144_18h.2

description: Gene expression in miR-144 expressing cells infected with PR8 influenza for 18 hours

source_name: immortalized airway epithelial cells, expressing miR-144, infected with PR8 influenza 18 hours


title: Let1_miR144_1h.4


title: Let1_GFP_18h.2


title: Let1_miR144_18h.1


title: Let1_miR144_1h.5


title: Let1_miR451_1h.2


title: Let1_GFP_1h.1


title: Let1_GFP_1h.3


title: Let1_miR144_1h.1


title: Let1_GFP_1h.2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 96h, biological rep2

city: Freising

first: Susanne

last: Procopio

address: Weihenstephanersteig 20

department: Lehrstuhl für Brau- und Getränketechnologie

country: Germany

institute: Technische Universität München

description: Gene expression data from Saccharomyces pastorianus var. Carlsbergensis

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using the Robust Multi-array Average (RMA) algorithm. RMA is an algorithm used to create an expression matrix from Affymetrix data. The raw intensity values are background corrected, log2 transformed and then quantile normalized. Next a linear model is fit to the normalized data to obtain an expression measure for each probe set on each array.

organism: Saccharomyces pastorianus

source_name: Yeast cells 96h after pitching

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix user Maunal (3´IVT Express Kit) from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Cropped yeast cells were used to inoculate fresh synthetic medium (pH level 5,4) with a pitching rate of 15 x 106 viable cells/ml for strain S23 and 10 x 106 viable cells/ml for strain S81. Fermentations were carried out in tall 2-liter EBC tubes. These experiments were done in triplicate for both yeasts. Static fermentation was carried out at typical industrial temperature conditions 12°C for the strain S23 and 20°C for the strain S81.

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

treatment_protocol: Yeast cells were taken at intervals for up to 120 h after pitching and immediately cooled on ice


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 120h, biological rep3

source_name: Yeast cells 120h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 96h, biological rep1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 120h, biological rep1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 96h, biological rep3


title: liver tumor 1 from female F1

type: genomic

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

hyb_protocol: Hybridization procedure was performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol V5.0 using the Agilent Oligo aCGH Hybridization Kit (Agilent Technologies).  The corresponding Cy3- and Cy5-labelled DNA were combined and hybridized at 65 degrees C for 24 hrs to an Agilent Mouse Genome CGH Microarray 4x44K chip.

scan_protocol: Fluorescence signals of the microarrays were detected using Agilent's DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image file. Further analysis and visualization of the hybridization result was performed with the Agilent CGH Analytics software (V 3.5).

molecule: genomic DNA

source_name: tumor from FIV transduced mouse

label_protocol: Digested DNA was used as template for a genomic DNA labelling reaction using the Genomic DNA Labeling Kit PLUS (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Pregnant mice (16 days gestation) were anaesthetized using isoflurane. Fetuses were removed from the womb and FIV-based viral particles were administered to the yolk sac vein of each fetus. The fetuses were then returned to the womb and were delivered naturally. Mice were kept under normal conditions until they were sacrificed.

extract_protocol: Genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega, Madison, WI)

treatment_protocol: liver tissue and tumors were flash frozen in liquid nitrogen and stored at -80 degrees until DNA extraction.

value: FIV-based lentiviral viral particles containing the gene encoding EGFP

value: female

tag: tissue

value: liver tumor

source_name: liver tissue surrounding tumors

value: liver


title: liver tumor 1 from male M1

tag: gender


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 72h, biological rep3

source_name: Yeast cells 72h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 120h, biological rep2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 72h, biological rep1


title: liver tumor 2 from female F1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 72h, biological rep2


title: liver tumor 2 from female F2


title: liver tumor 1 from female F2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 24h, biological rep2

source_name: Yeast cells 24h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 24h, biological rep1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 12h, biological rep3

source_name: Yeast cells 12h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 12h, biological rep1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 24h, biological rep3


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 48h, biological rep3

source_name: Yeast cells 48h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 48h, biological rep2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 48h, biological rep1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 0h, biological rep3

description: Gene expression data from Saccharomyces pastorianus var. Carlsbergensis before pitching (control)

source_name: Yeast cells before pitching


title: Let1_miR144_1h.3


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 8h, biological rep2

source_name: Yeast cells 8h after pitching


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 0h, biological rep2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 8h, biological rep3


title: liver tumor 2 from male M1


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 12h, biological rep2


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 8h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 120h, biological rep2

description: Gene expression data from Saccharomyces cerevisiae

organism: Saccharomyces cerevisiae


title: Saccharomyces cerevisiae strain S81 at 96h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 120h, biological rep3


title: Saccharomyces cerevisiae strain S81 at 96h, biological rep3


title: Saccharomyces cerevisiae strain S81 at 72h, biological rep3


title: Saccharomyces pastorianus var. Carlsbergensis strain S23 at 0h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 72h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 72h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 48h, biological rep3


title: Saccharomyces cerevisiae strain S81 at 48h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 24h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 48h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 24h, biological rep3


title: Saccharomyces cerevisiae strain S81 at 12h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 8h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 12h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 24h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 8h, biological rep3


title: Saccharomyces cerevisiae strain S81 at 0h, biological rep3

description: Gene expression data from Saccharomyces cerevisiae before pitching (control)


title: Saccharomyces cerevisiae strain S81 at 8h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 0h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 0h, biological rep2


title: Saccharomyces cerevisiae strain S81 at 96h, biological rep1


title: Saccharomyces cerevisiae strain S81 at 120h, biological rep1


title: Ezh2 KO Th2 cells

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

description: Gene expression data from Ezh2 KO Th2 cells

hyb_protocol: cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using Affymetrix GeneChip Command Console Software (AGCC) and Console Software (Expression Console).

source_name: Ezh2 KO naïve CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions

label_protocol: Total RNA was labeled using the GeneChip 3' IVT Express Kit

growth_protocol: CD4 T cell cultures. Naïve (CD44lowCD62Lhigh) CD4+ T cells were purified from spleens of mice as described in the Supplementary Experimental Procedures. For Th1, Th2 and non-polarized Th cell cultures, 7.5 × 10^5 naïve CD4 T cells were plated onto 48 well tissue culture plates (Costar) pre-coated with 10 μg/ml agonistic anti-TCRβ antibody (clone H57-597) with 1 μg/ml agonistic anti-CD28 antibody (clone 37.51, Biolegend) and 15 ng/ml IL-2. In addition, Th1 cultures contained 1 ng/ml recombinant mouse IL-12 (Wako) and anti-IL-4 antibody (clone 11B11), Th2 cultures contained 10 ng/ml recombinant mouse IL-4 (Peprotech) and anti-IFN-γ antibody (clone R4-6A2), and non-polarized Th cell cultures contained anti-IL-4 antibody (Clone 11B11) and anti-IFN-γ antibody (clone R4-6A2). After two days, the cells were recultured for an additional three days in the same culture medium with cytokines but without anti-TCRβ or anti-CD28 antibody stimulation

treatment_protocol: Th cells were harvested and RNA was immediately isolated

value: CD4 T cell


title: Saccharomyces cerevisiae strain S81 at 12h, biological rep3


title: Wild type Th2 cells

description: Gene expression data from wild type Th2 cells

source_name: Wild type naïve CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions


title: Wild type Th1 cells

description: Gene expression data from wild type Th1 cells

source_name: Wild type naïve CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions


title: Ezh2 KO Th1 cells

description: Gene expression data from Ezh2 KO Th1 cells

source_name: Ezh2 KO naïve CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions


title: Wild type unpolarized Th cells

description: Gene expression data from wild type unpolarized Th cells

source_name: Wild type naïve CD4 T cells from spleen cultured for 5 days in Non-polarizing conditions


title: MDA_male_4day_rep6MDA_G86M_D4_6

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

description: Gene expression data from liver samples of male CD1 mice treated with Methylendianiline up to 4 days.

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software GCOS (Genechip Operating Software) version 1.4.0

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: Methylendianiline, male mice, 4 days

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

growth_protocol: CD-1 male and female mice were orally treated with a set of genotoxic carcinogens (CIDB, DMN and MDA), nongenotoxic carcinogens (DCB, PB and PBO), non-hepatocarcinogens (CFX, Nif, Praz and Prop) and a group of undefined compounds (CPA, Wy-14643 and TAA) over a period of 3 and 14 days.

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany).

treatment_protocol: After 3 and 14 days of compound treatment mice were anaesthetized in isoflurane and exsanguinated from the heart and subjected to necropsy. The left lateral liver lobe was extracted and snap frozen under -80°C conditions.

value: CD-1 mouse

value: Liver

value: Methylendianiline

value: 4 days


title: MDA_male_4day_rep5MDA_G86M_D4_5

value: male


title: MDA_female_15day_rep3MDA_G89F_D15_3

description: Gene expression data from liver samples of female CD1 mice treated with Methylendianiline up to 15 days.

source_name: Methylendianiline, female mice, 15 days

value: 15 days


title: MDA_female_15day_rep4MDA_G89F_D15_4


title: MDA_female_15day_rep5MDA_G89F_D15_5


title: MDA_female_15day_rep3MDA_G88F_D15_3


title: MDA_female_15day_rep1MDA_G89F_D15_1


title: MDA_female_15day_rep1MDA_G88F_D15_1


title: MDA_female_15day_rep2MDA_G88F_D15_2


title: MDA_female_4day_rep5MDA_G87F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Methylendianiline up to 4 days.

source_name: Methylendianiline, female mice, 4 days


title: MDA_female_15day_rep6MDA_G88F_D15_6


title: MDA_female_15day_rep5MDA_G88F_D15_5


title: MDA_female_15day_rep6MDA_G89F_D15_6


title: MDA_female_15day_rep2MDA_G89F_D15_2


title: MDA_female_15day_rep4MDA_G88F_D15_4


title: MDA_female_4day_rep4MDA_G87F_D4_4


title: MDA_female_4day_rep2MDA_G86F_D4_2


title: MDA_female_4day_rep6MDA_G86F_D4_6


title: MDA_female_4day_rep1MDA_G87F_D4_1


title: MDA_female_4day_rep3MDA_G87F_D4_3


title: Ezh2 KO unpolarized Th cells

description: Gene expression data from Ezh2 KO unpolarized Th cells

source_name: Ezh2 KO naïve CD4 T cells from spleen cultured for 5 days in Non-polarizing conditions


title: MDA_female_4day_rep3MDA_G86F_D4_3


title: MDA_female_4day_rep5MDA_G86F_D4_5


title: MDA_female_4day_rep6MDA_G87F_D4_6


title: MDA_female_4day_rep4MDA_G86F_D4_4


title: MDA_female_4day_rep2MDA_G87F_D4_2


title: MDA_female_4day_rep1MDA_G86F_D4_1


title: DCB_female_15day_rep3DCB_G85F_D15_3

description: Gene expression data from liver samples of female CD1 mice treated with 1,4-Dichlorobenzene up to 15 days.

source_name: 1,4-Dichlorobenzene, female mice, 15 days


title: DCB_female_15day_rep6DCB_G85F_D15_6


title: DCB_female_15day_rep1DCB_G85F_D15_1


title: DCB_female_4day_rep5DCB_G83F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with 1,4-Dichlorobenzene up to 4 days.

source_name: 1,4-Dichlorobenzene, female mice, 4 days


title: DCB_female_15day_rep2DCB_G85F_D15_2


title: DCB_female_15day_rep4DCB_G85F_D15_4


title: DCB_female_15day_rep5DCB_G85F_D15_5


title: DCB_female_4day_rep1DCB_G83F_D4_1


title: DCB_female_4day_rep6DCB_G83F_D4_6


title: DCB_female_4day_rep2DCB_G83F_D4_2


title: CPA_female_15day_rep5CPA_G80F_D15_5

description: Gene expression data from liver samples of female CD1 mice treated with Cyproterone acetate up to 15 days.

source_name: Cyproterone acetate, female mice, 15 days

value: Cyproterone acetate


title: CPA_female_15day_rep3CPA_G80F_D15_3


title: CPA_female_4day_rep3CPA_G78F_D4_3

description: Gene expression data from liver samples of female CD1 mice treated with Cyproterone acetate up to 4 days.

source_name: Cyproterone acetate, female mice, 4 days


title: CPA_female_15day_rep2CPA_G80F_D15_2


title: CPA_female_4day_rep1CPA_G78F_D4_1


title: CPA_female_4day_rep2CPA_G78F_D4_2


title: CPA_female_4day_rep4CPA_G78F_D4_4


title: CO_female_15day_rep6CO_G77F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Corn oil up to 15 days.

source_name: Corn oil, female mice, 15 days

value: Corn oil


title: DCB_female_4day_rep4DCB_G83F_D4_4


title: CPA_female_15day_rep4CPA_G80F_D15_4


title: CO_female_15day_rep5CO_G77F_D15_5


title: CPA_female_4day_rep5CPA_G78F_D4_5


title: CPA_female_15day_rep6CPA_G80F_D15_6


title: CPA_female_15day_rep1CPA_G80F_D15_1


title: CPA_female_4day_rep6CPA_G78F_D4_6


title: CO_female_4day_rep4CO_G76F_D4_4

description: Gene expression data from liver samples of female CD1 mice treated with Corn oil up to 4 days.

source_name: Corn oil, female mice, 4 days


title: H2O_female_15day_rep6H2O_G75F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Water up to 15 days.

source_name: Water, female mice, 15 days

value: Water


title: CO_female_15day_rep3CO_G77F_D15_3


title: CO_female_15day_rep2CO_G77F_D15_2


title: CO_female_4day_rep1CO_G76F_D4_1


title: CO_female_4day_rep6CO_G76F_D4_6


title: CO_female_4day_rep5CO_G76F_D4_5


title: CO_female_4day_rep2CO_G76F_D4_2


title: H2O_female_15day_rep3H2O_G75F_D15_3


title: H2O_female_4day_rep5H2O_G74F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Water up to 4 days.

source_name: Water, female mice, 4 days


title: H2O_female_4day_rep3H2O_G74F_D4_3


title: CO_female_15day_rep1CO_G77F_D15_1


title: H2O_female_15day_rep2H2O_G75F_D15_2


title: CO_female_15day_rep4CO_G77F_D15_4


title: H2O_female_4day_rep2H2O_G74F_D4_2


title: H2O_female_15day_rep1H2O_G75F_D15_1


title: H2O_female_4day_rep6H2O_G74F_D4_6


title: DCB_female_4day_rep3DCB_G83F_D4_3


title: H2O_female_4day_rep1H2O_G74F_D4_1


title: MDA_male_15day_rep2MDA_G89M_D15_2

description: Gene expression data from liver samples of male CD1 mice treated with Methylendianiline up to 15 days.

source_name: Methylendianiline, male mice, 15 days


title: MDA_male_15day_rep6MDA_G88M_D15_6


title: MDA_male_15day_rep3MDA_G89M_D15_3


title: MDA_male_15day_rep5MDA_G89M_D15_5


title: MDA_male_15day_rep4MDA_G89M_D15_4


title: H2O_female_15day_rep4H2O_G75F_D15_4


title: H2O_female_15day_rep5H2O_G75F_D15_5


title: H2O_female_4day_rep4H2O_G74F_D4_4


title: MDA_male_15day_rep4MDA_G88M_D15_4


title: MDA_male_4day_rep6MDA_G87M_D4_6


title: MDA_male_4day_rep2MDA_G87M_D4_2


title: MDA_male_15day_rep2MDA_G88M_D15_2


title: MDA_male_4day_rep2MDA_G86M_D4_2


title: MDA_male_15day_rep1MDA_G88M_D15_1


title: MDA_male_15day_rep5MDA_G88M_D15_5


title: MDA_male_4day_rep3MDA_G86M_D4_3


title: DCB_male_15day_rep5DCB_G85M_D15_5

description: Gene expression data from liver samples of male CD1 mice treated with 1,4-Dichlorobenzene up to 15 days.

source_name: 1,4-Dichlorobenzene, male mice, 15 days


title: MDA_male_4day_rep4MDA_G86M_D4_4


title: DCB_male_15day_rep4DCB_G85M_D15_4


title: MDA_male_4day_rep3MDA_G87M_D4_3


title: DCB_male_4day_rep6DCB_G83M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with 1,4-Dichlorobenzene up to 4 days.

source_name: 1,4-Dichlorobenzene, male mice, 4 days


title: DCB_male_15day_rep6DCB_G85M_D15_6


title: MDA_male_15day_rep3MDA_G88M_D15_3


title: MDA_male_4day_rep5MDA_G87M_D4_5


title: CO_female_4day_rep3CO_G76F_D4_3


title: DCB_male_4day_rep3DCB_G83M_D4_3


title: DCB_male_4day_rep4DCB_G83M_D4_4


title: DCB_male_15day_rep1DCB_G85M_D15_1


title: MDA_male_15day_rep1MDA_G89M_D15_1


title: MDA_male_4day_rep1MDA_G86M_D4_1


title: DCB_male_15day_rep3DCB_G85M_D15_3


title: miRNA expression profiling of pediatric AML patients [7250071]

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

institute: Heinrich-Heine University Düsseldorf

description: miRNA expression profiling of pediatric AML patients compared to CD34+ cells and adult AML patients

hyb_protocol: The corresponding Cy3 and Cy5 labled miRNAs were combined and hybridized overnight (16 hours, 42°C) to a miRXplore microarray (MACS molecular Miltenyi Biotec) using an a-Hyb Hybridization Station (MACS molecular Miltenyi Biotec). The microarrays were washed five times with distilled water (at room temperature) and dried with compressed, dry air.

scan_protocol: miRXplore microarrays were scanned using the Axon GenePix 4200A Microarray Scanner

data_processing: Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered with respect to background-subtracted signal intensity, signal to noise ratio and spot diameter. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity of the miRNAs derived from the samples of interest was two-fold the mean background value. The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 18 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes. Signal intensities of miRNAs without the corresponding miRNA in the synthetic miRNA pool were divided by the mean value of signal intensities of all detected miRNAs in the pool.

organism: synthetic construct

source_name: synthetic miRNA pool (universal reference)

label_protocol: miRNAs were 3' end labeled using a truncated and mutated RNA ligase Rnl2(1-249)K227Q

extract_protocol: The 4 Ago antibodies were obtained from our cooperation partner Prof. Dr. Gunter Meister from University Regensburg and were manufactured in house. TRIzol extraction of Ago- / isotype control-associated and total RNA was performed according to the manufacturer's instructions.

tag: reference

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled

value: BM (bone marrow)

tag: age

tag: rna sybtype

value: miRNAs


title: MDA_male_15day_rep6MDA_G89M_D15_6

tag: treatment


title: miRNA expression profiling of pediatric AML patients [7370063]

source_name: healthy control

tag: genotype


title: DCB_male_4day_rep5DCB_G83M_D4_5


title: miRNA expression profiling of pediatric AML patients [7250070]


title: CPA_male_15day_rep4CPA_G80M_D15_4

description: Gene expression data from liver samples of male CD1 mice treated with Cyproterone acetate up to 15 days.

source_name: Cyproterone acetate, male mice, 15 days


title: DCB_male_4day_rep2DCB_G83M_D4_2


title: miRNA expression profiling of pediatric AML patients [7510007]


title: miRNA expression profiling of pediatric AML patients [7250068]


title: CPA_male_15day_rep5CPA_G80M_D15_5


title: CPA_male_15day_rep2CPA_G80M_D15_2


title: CPA_male_4day_rep4CPA_G78M_D4_4

description: Gene expression data from liver samples of male CD1 mice treated with Cyproterone acetate up to 4 days.

source_name: Cyproterone acetate, male mice, 4 days


title: CPA_male_15day_rep6CPA_G80M_D15_6


title: CPA_male_15day_rep1CPA_G80M_D15_1


title: DCB_male_4day_rep1DCB_G83M_D4_1


title: miRNA expression profiling of pediatric AML patients [7250067]


title: miRNA expression profiling of pediatric AML patients [7250066]


title: CPA_male_4day_rep1CPA_G78M_D4_1


title: CPA_male_15day_rep3CPA_G80M_D15_3


title: CPA_male_4day_rep2CPA_G78M_D4_2


title: CO_male_15day_rep6CO_G77M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Corn oil up to 15 days.

source_name: Corn oil, male mice, 15 days


title: miRNA expression profiling of pediatric AML patients [7250064]

value: PB (peripheral blood)


title: miRNA expression profiling of pediatric AML patients [7250063]


title: miRNA expression profiling of pediatric AML patients [7250061]


title: miRNA expression profiling of pediatric AML patients [7250055]


title: miRNA expression profiling of pediatric AML patients [7250056]


title: miRNA expression profiling of pediatric AML patients [7250053]


title: miRNA expression profiling of pediatric AML patients [7250054]


title: miRNA expression profiling of pediatric AML patients [7250052]


title: CO_male_15day_rep5CO_G77M_D15_5


title: miRNA expression profiling of pediatric AML patients [7250051]


title: miRNA expression profiling of pediatric AML patients [7250050]


title: miRNA expression profiling of pediatric AML patients [7250049]


title: CO_male_15day_rep4CO_G77M_D15_4


title: CO_male_15day_rep3CO_G77M_D15_3


title: CO_male_15day_rep2CO_G77M_D15_2


title: CO_male_15day_rep1CO_G77M_D15_1


title: CO_male_4day_rep4CO_G76M_D4_4

description: Gene expression data from liver samples of male CD1 mice treated with Corn oil up to 4 days.

source_name: Corn oil, male mice, 4 days


title: CO_male_4day_rep1CO_G76M_D4_1


title: CO_male_4day_rep3CO_G76M_D4_3


title: CO_male_4day_rep5CO_G76M_D4_5


title: CO_male_4day_rep6CO_G76M_D4_6


title: miRNA expression profiling of pediatric AML patients [7250043]


title: CO_male_4day_rep2CO_G76M_D4_2


title: miRNA expression profiling of pediatric AML patients [7250041]

source_name: AML inv(16)


title: miRNA expression profiling of pediatric AML patients [7250065]


title: miRNA expression profiling of pediatric AML patients [7250040]


title: H2O_male_15day_rep6H2O_G75M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Water up to 15 days.

source_name: Water, male mice, 15 days


title: miRNA expression profiling of pediatric AML patients [7250039]


title: H2O_male_15day_rep4H2O_G75M_D15_4


title: H2O_male_15day_rep5H2O_G75M_D15_5


title: miRNA expression profiling of pediatric AML patients [7250037]


title: H2O_male_15day_rep3H2O_G75M_D15_3


title: miRNA expression profiling of pediatric AML patients [7250036]


title: miRNA expression profiling of pediatric AML patients [7250033]


title: miRNA expression profiling of pediatric AML patients [7250032]


title: miRNA expression profiling of pediatric AML patients [7250031]


title: miRNA expression profiling of pediatric AML patients [7250030]


title: miRNA expression profiling of pediatric AML patients [7250029]


title: H2O_male_15day_rep2H2O_G75M_D15_2


title: H2O_male_4day_rep6H2O_G74M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Water up to 4 days.

source_name: Water, male mice, 4 days


title: H2O_male_15day_rep1H2O_G75M_D15_1


title: H2O_male_4day_rep5H2O_G74M_D4_5


title: H2O_male_4day_rep1H2O_G74M_D4_1


title: MDA_male_4day_rep4MDA_G87M_D4_4

description: Gene expression data from liver samples of male CD1 mice treated with Methylendianiline up to 4 days.

source_name: Methylendianiline, male mice, 4 days


title: miRNA expression profiling of pediatric AML patients [7250034]


title: H2O_male_4day_rep3H2O_G74M_D4_3


title: miRNA expression profiling of pediatric AML patients [7250028]


title: DCB_male_15day_rep2DCB_G85M_D15_2


title: H2O_male_4day_rep2H2O_G74M_D4_2


title: H2O_male_4day_rep4H2O_G74M_D4_4


title: miRNA expression profiling of pediatric AML patients [7250026]


title: miRNA expression profiling of pediatric AML patients [7250025]


title: MDA_male_4day_rep1MDA_G87M_D4_1


title: miRNA expression profiling of pediatric AML patients [7250024]


title: DMN_female_15day_rep6DMN_G72F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Dimethylnitrosamine up to 15 days.

source_name: Dimethylnitrosamine, female mice, 15 days

value: female

value: Dimethylnitrosamine


title: DMN_female_15day_rep5DMN_G72F_D15_5


title: DMN_female_15day_rep4DMN_G72F_D15_4


title: miRNA expression profiling of pediatric AML patients [7250023]


title: miRNA expression profiling of pediatric AML patients [7250027]


title: DMN_female_15day_rep3DMN_G72F_D15_3


title: DMN_female_15day_rep2DMN_G72F_D15_2


title: DMN_female_4day_rep6DMN_G70F_D4_6

description: Gene expression data from liver samples of female CD1 mice treated with Dimethylnitrosamine up to 4 days.

source_name: Dimethylnitrosamine, female mice, 4 days


title: DMN_female_15day_rep1DMN_G72F_D15_1


title: miRNA expression profiling of pediatric AML patients [7250022]


title: DMN_female_4day_rep5DMN_G70F_D4_5


title: miRNA expression profiling of pediatric AML patients [7250019]


title: miRNA expression profiling of pediatric AML patients [7250020]


title: miRNA expression profiling of pediatric AML patients [7250015]


title: miRNA expression profiling of pediatric AML patients [7250018]


title: DMN_female_4day_rep2DMN_G70F_D4_2


title: miRNA expression profiling of pediatric AML patients [7250014]


title: DMN_female_4day_rep3DMN_G70F_D4_3


title: CIDB_female_15day_rep6CIDB_G69F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with C.I. Direct Black up to 15 days.

source_name: C.I. Direct Black, female mice, 15 days

value: C.I. Direct Black


title: miRNA expression profiling of pediatric AML patients [7250013]


title: DMN_female_4day_rep1DMN_G70F_D4_1


title: miRNA expression profiling of pediatric AML patients [7250012]


title: miRNA expression profiling of pediatric AML patients [7250010]


title: CIDB_female_15day_rep5CIDB_G69F_D15_5


title: miRNA expression profiling of pediatric AML patients [7250009]


title: miRNA expression profiling of pediatric AML patients [7250006]


title: miRNA expression profiling of pediatric AML patients [7250007]


title: CIDB_female_15day_rep4CIDB_G69F_D15_4


title: CIDB_female_15day_rep1CIDB_G69F_D15_1


title: CIDB_female_4day_rep5CIDB_G67F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with C.I. Direct Black up to 4 days.

source_name: C.I. Direct Black, female mice, 4 days


title: miRNA expression profiling of pediatric AML patients [7250005]


title: miRNA expression profiling of pediatric AML patients [7150024]


title: DMN_female_4day_rep4DMN_G70F_D4_4


title: CPA_male_4day_rep3CPA_G78M_D4_3


title: miRNA expression profiling of pediatric AML patients [6810031]


title: CIDB_female_4day_rep4CIDB_G67F_D4_4


title: miRNA expression profiling of pediatric AML patients [7150016]

source_name: normal


title: miRNA expression profiling of pediatric AML patients [7150017]


title: miRNA expression profiling of pediatric AML patients [7150014]


title: miRNA expression profiling of pediatric AML patients [7120041]


title: CIDB_female_4day_rep1CIDB_G67F_D4_1


title: miRNA expression profiling of pediatric AML patients [7120039]

source_name: other


title: CIDB_female_4day_rep2CIDB_G67F_D4_2


title: CO_female_15day_rep5CO_G65F_D15_5

description: Gene expression data from liver samples of female CD1 mice treated with Corn oil up to 15 days.

source_name: Corn oil, female mice, 15 days


title: CO_female_15day_rep6CO_G65F_D15_6


title: CO_female_15day_rep2CO_G65F_D15_2


title: CO_female_4day_rep5CO_G64F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Corn oil up to 4 days.

source_name: Corn oil, female mice, 4 days


title: CIDB_female_4day_rep3CIDB_G67F_D4_3


title: CPA_male_4day_rep6CPA_G78M_D4_6


title: CIDB_female_15day_rep3CIDB_G69F_D15_3


title: CIDB_female_15day_rep2CIDB_G69F_D15_2


title: CO_female_15day_rep3CO_G65F_D15_3


title: CPA_male_4day_rep5CPA_G78M_D4_5


title: CO_female_4day_rep6CO_G64F_D4_6


title: miRNA expression profiling of pediatric AML patients [7120038]

source_name: synthetic miRNA pool (universal reference)


title: CO_female_15day_rep1CO_G65F_D15_1


title: miRNA expression profiling of pediatric AML patients [7120025]


title: miRNA expression profiling of pediatric AML patients [7120040]


title: miRNA expression profiling of pediatric AML patients [7120024]


title: miRNA expression profiling of pediatric AML patients [7120023]


title: CO_female_4day_rep3CO_G64F_D4_3


title: CO_female_4day_rep2CO_G64F_D4_2


title: CO_female_15day_rep4CO_G65F_D15_4


title: DMN_male_15day_rep5DMN_G72M_D15_5

description: Gene expression data from liver samples of male CD1 mice treated with Dimethylnitrosamine up to 15 days.

source_name: Dimethylnitrosamine, male mice, 15 days


title: CO_female_4day_rep4CO_G64F_D4_4


title: CO_female_4day_rep1CO_G64F_D4_1


title: DMN_male_4day_rep5DMN_G70M_D4_5

description: Gene expression data from liver samples of male CD1 mice treated with Dimethylnitrosamine up to 4 days.

source_name: Dimethylnitrosamine, male mice, 4 days


title: DMN_male_4day_rep4DMN_G70M_D4_4


title: DMN_male_15day_rep4DMN_G72M_D15_4


title: DMN_male_15day_rep6DMN_G72M_D15_6


title: miRNA expression profiling of pediatric AML patients [6810073]


title: DMN_male_4day_rep6DMN_G70M_D4_6


title: DMN_male_4day_rep2DMN_G70M_D4_2


title: miRNA expression profiling of pediatric AML patients [6810072]


title: miRNA expression profiling of pediatric AML patients [6810071]


title: DMN_male_4day_rep3DMN_G70M_D4_3


title: miRNA expression profiling of pediatric AML patients [7120022]


title: CIDB_male_15day_rep2CIDB_G69M_D15_2

description: Gene expression data from liver samples of male CD1 mice treated with C.I. Direct Black up to 15 days.

source_name: C.I. Direct Black, male mice, 15 days


title: CIDB_male_15day_rep4CIDB_G69M_D15_4


title: miRNA expression profiling of pediatric AML patients [6810070]

description: miRNA expression profiling of pediatric AML patients compared to CD34+ cells and adult AML patients


title: ~17d gestation mouse_liver tissue_untreated_5d, biological rep5

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

description: Gene expression data from liver tissue harvested from ~17d pregnant untreated SKH:QS mouse

hyb_protocol: Following fragmentation, ~600-700 ng of single-stranded DNA were hybridised on Affymetric 1.0 ST human gene arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G GeneChip® Scanner.

data_processing: The data was processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.

label: Biotin

source_name: SKH:QS mouse liver tissue from untreated pregnant mouse, day 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual, Affymetrix).

growth_protocol: Mice were individually housed in polycarbonate cages in an isolated temperature (~21˚C) and moisture (~55-65% relative humidity) controlled room with a 14-hr light/10-hr dark cycle, with ad libitum access to food and water

extract_protocol: Total RNA was extracted from liver tissue using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.

treatment_protocol: Mice were fitted with Elizabethan collars to minimise oral ingestion of sunscreens.  Mice were treated six times over four days with sunscreen containing 68ZnO microparticles, 68ZnO nanoparticles, or no ZnO particles at all (formulation-only), or were untreated.  Mice were sacrificed on day five by intraperitoneal injection of Xylase (50mg/kg)/ketamine (50mg/kg) followed by cervical dislocation.

value: ~17d gestation liver


title: ~17d gestation mouse_liver tissue_untreated_5d, biological rep4


title: miRNA expression profiling of pediatric AML patients [6810067]


title: CIDB_male_15day_rep5CIDB_G69M_D15_5

value: CD-1 mouse


title: CIDB_male_15day_rep3CIDB_G69M_D15_3

value: Liver


title: CIDB_male_15day_rep6CIDB_G69M_D15_6


title: DMN_male_4day_rep1DMN_G70M_D4_1


title: CIDB_male_15day_rep1CIDB_G69M_D15_1


title: ~17d gestation mouse_liver tissue_untreated_5d, biological rep2


title: miRNA expression profiling of pediatric AML patients [6810066]


title: ~17d gestation mouse_liver tissue_untreated_5d, biological rep3


title: CIDB_male_4day_rep5CIDB_G67M_D4_5

description: Gene expression data from liver samples of male CD1 mice treated with C.I. Direct Black up to 4 days.

source_name: C.I. Direct Black, male mice, 4 days


title: miRNA expression profiling of pediatric AML patients [6810065]


title: miRNA expression profiling of pediatric AML patients [6810063]


title: ~17d gestation mouse_liver tissue_untreated_5d, biological rep1


title: CO_male_15day_rep6CO_G65M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Corn oil up to 15 days.

source_name: Corn oil, male mice, 15 days


title: CIDB_male_4day_rep3CIDB_G67M_D4_3


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 6

description: Gene expression data from liver tissue harvested from ~17d pregnant SKH:QS mouse topically treated with a sunscreen containing ZnO nanoparticles six times over four days

source_name: SKH:QS mouse liver tissue from ZnO nanoparticle sunscreen-treated pregnant mouse, day 5


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 5


title: CO_male_15day_rep5CO_G65M_D15_5


title: CO_male_15day_rep4CO_G65M_D15_4


title: CO_male_15day_rep3CO_G65M_D15_3


title: CIDB_male_4day_rep6CIDB_G67M_D4_6


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 4


title: miRNA expression profiling of pediatric AML patients [6810064]

source_name: AML inv(16)


title: CIDB_male_4day_rep4CIDB_G67M_D4_4


title: miRNA expression profiling of pediatric AML patients [6810061]


title: miRNA expression profiling of pediatric AML patients [6810062]


title: miRNA expression profiling of pediatric AML patients [6810060]


title: miRNA expression profiling of pediatric AML patients [6810059]

value: t(1,11) is a seldom form of  11q23 aberration (MLL abberation)


title: miRNA expression profiling of pediatric AML patients [6810058]


title: CO_male_15day_rep2CO_G65M_D15_2


title: CO_male_4day_rep4CO_G64M_D4_4

description: Gene expression data from liver samples of male CD1 mice treated with Corn oil up to 4 days.

source_name: Corn oil, male mice, 4 days

value: 4 days


title: ~17d gestation mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  4

description: Gene expression data from liver tissue harvested from ~17d pregnant SKH:QS mouse topically treated with a sunscreen containing ZnO microparticles six times over four days

source_name: SKH:QS mouse liver tissue from ZnO microparticle sunscreen-treated pregnant mouse, day 5


title: CO_male_4day_rep5CO_G64M_D4_5

value: male


title: PB_female_15day_rep2PB_G62F_D15_2

description: Gene expression data from liver samples of female CD1 mice treated with Phenobarbital up to 15 days.

source_name: Phenobarbital, female mice, 15 days

value: Phenobarbital

value: 15 days


title: PB_female_15day_rep3PB_G62F_D15_3


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 3


title: CO_male_15day_rep1CO_G65M_D15_1

value: Corn oil


title: PB_female_15day_rep6PB_G62F_D15_6


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 2


title: CO_male_4day_rep6CO_G64M_D4_6


title: PB_female_15day_rep5PB_G62F_D15_5


title: PB_female_15day_rep4PB_G62F_D15_4


title: ~17d gestation mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  5


title: ~17d gestation mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 1


title: miRNA expression profiling of pediatric AML patients [6810056]


title: miRNA expression profiling of pediatric AML patients [6810055]


title: ~17d gestation mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  3


title: PB_female_4day_rep6PB_G60F_D4_6

description: Gene expression data from liver samples of female CD1 mice treated with Phenobarbital up to 4 days.

source_name: Phenobarbital, female mice, 4 days


title: ~17d gestation mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  2


title: PB_female_4day_rep4PB_G60F_D4_4


title: PB_female_4day_rep5PB_G60F_D4_5


title: PB_female_4day_rep3PB_G60F_D4_3


title: ~17d gestation mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  1


title: miRNA expression profiling of pediatric AML patients [6810057]


title: PB_female_15day_rep1PB_G62F_D15_1


title: CIDB_male_4day_rep2CIDB_G67M_D4_2


title: miRNA expression profiling of pediatric AML patients [6810053]


title: miRNA expression profiling of pediatric AML patients [6810054]

source_name: normal


title: miRNA expression profiling of pediatric AML patients [6810048]


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 6

description: Gene expression data from liver tissue harvested from ~17d pregnant SKH:QS mouse topically treated with a sunscreen formulation-only six times over four days

source_name: SKH:QS mouse liver tissue from formulation-only-treated pregnant mouse, day 5


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 4


title: TAA_female_15day_rep4TAA_G59F_D15_4

description: Gene expression data from liver samples of female CD1 mice treated with Thioacetamid up to 15 days.

source_name: Thioacetamid, female mice, 15 days

value: Thioacetamid


title: miRNA expression profiling of pediatric AML patients [6810051]

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled


title: PB_female_4day_rep2PB_G60F_D4_2


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 3


title: TAA_female_15day_rep3TAA_G59F_D15_3


title: TAA_female_4day_rep6TAA_G57F_D4_6

description: Gene expression data from liver samples of female CD1 mice treated with Thioacetamid up to 4 days.

source_name: Thioacetamid, female mice, 4 days


title: miRNA expression profiling of pediatric AML patients [6810052]

source_name: synthetic miRNA pool (universal reference)

value: BM (bone marrow)


title: miRNA expression profiling of pediatric AML patients [6810047]

value: miRNAs


title: PB_female_4day_rep1PB_G60F_D4_1


title: Virgin mouse_liver tissue_untreated_5d, biological rep6

description: Gene expression data from liver tissue harvested from virgin untreated SKH:QS mouse

source_name: SKH:QS mouse liver tissue from untreated virgin mouse, day 5

value: Virgin liver


title: miRNA expression profiling of pediatric AML patients [6810043]


title: TAA_female_15day_rep2TAA_G59F_D15_2

value: female


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 2

source_name: SKH:QS mouse liver tissue from formulation-only-treated pregnantmouse, day 5


title: TAA_female_15day_rep5TAA_G59F_D15_5


title: TAA_female_15day_rep1TAA_G59F_D15_1


title: TAA_female_15day_rep6TAA_G59F_D15_6


title: TAA_female_4day_rep4TAA_G57F_D4_4


title: TAA_female_4day_rep2TAA_G57F_D4_2


title: WY_female_15day_rep6WY_G54F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Wy-14643 up to 15 days.

source_name: Wy-14643, female mice, 15 days


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 1


title: ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 5


title: TAA_female_4day_rep1TAA_G57F_D4_1


title: WY_female_15day_rep5WY_G54F_D15_5


title: TAA_female_4day_rep3TAA_G57F_D4_3


title: TAA_female_4day_rep5TAA_G57F_D4_5


title: WY_female_15day_rep4WY_G54F_D15_4


title: Virgin mouse_liver tissue_untreated_5d, biological rep5


title: miRNA expression profiling of pediatric AML patients [6810041]

source_name: other


title: miRNA expression profiling of pediatric AML patients [6810040]


title: miRNA expression profiling of pediatric AML patients [6810039]


title: WY_female_15day_rep3WY_G54F_D15_3


title: miRNA expression profiling of pediatric AML patients [6810036]


title: WY_female_4day_rep6WY_G52F_D4_6

description: Gene expression data from liver samples of female CD1 mice treated with Wy-14643 up to 4 days.

source_name: Wy-14643, female mice, 4 days


title: WY_female_15day_rep1WY_G54F_D15_1


title: Virgin mouse_liver tissue_untreated_5d, biological rep4


title: miRNA expression profiling of pediatric AML patients [6810038]


title: miRNA expression profiling of pediatric AML patients [6810032]


title: WY_female_4day_rep5WY_G52F_D4_5


title: WY_female_15day_rep2WY_G54F_D15_2


title: WY_female_4day_rep4WY_G52F_D4_4


title: Virgin mouse_liver tissue_untreated_5d, biological rep3


title: Virgin mouse_liver tissue_untreated_5d, biological rep1


title: WY_female_4day_rep1WY_G52F_D4_1


title: WY_female_4day_rep3WY_G52F_D4_3


title: miRNA expression profiling of pediatric AML patients [6810030]


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 6

description: Gene expression data from liver tissue harvested from virgin SKH:QS mouse topically treated with a sunscreen containing ZnO nanoparticles six times over four days

source_name: SKH:QS mouse liver tissue from ZnO nanoparticle sunscreen-treated virgin mouse, day 5


title: WY_female_4day_rep2WY_G52F_D4_2


title: PBO_female_15day_rep4PBO_G50F_D15_4

description: Gene expression data from liver samples of female CD1 mice treated with Piperonyl-butoxide up to 15 days.

source_name: Piperonyl-butoxide, female mice, 15 days

value: Piperonyl-butoxide


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 3


title: PBO_female_15day_rep5PBO_G50F_D15_5


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 5


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 4


title: miRNA expression profiling of pediatric AML patients [6810035]

description: miRNA expression profiling of pediatric AML patients compared to CD34+ cells and adult AML patients


title: miRNA expression profiling of pediatric AML patients [6810029]


title: PBO_female_15day_rep2PBO_G50F_D15_2


title: Virgin mouse_liver tissue_untreated_5d, biological rep2


title: miRNA expression profiling of pediatric AML patients [6810027]


title: PBO_female_15day_rep1PBO_G50F_D15_1


title: miRNA expression profiling of pediatric AML patients [6810022]

source_name: AML inv(16)

value: PB (peripheral blood)


title: miRNA expression profiling of pediatric AML patients [6810019]


title: PBO_female_15day_rep3PBO_G50F_D15_3


title: miRNA expression profiling of pediatric AML patients [6810018]


title: CMC_female_15day_rep6CMC_G41F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Carboxymethyl cellulose up to 15 days.

source_name: Carboxymethyl cellulose, female mice, 15 days

value: Carboxymethyl cellulose


title: miRNA expression profiling of pediatric AML patients [6810013]


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  5

description: Gene expression data from liver tissue harvested from virgin SKH:QS mouse topically treated with a sunscreen containing ZnO microparticles six times over four days

source_name: SKH:QS mouse liver tissue from ZnO microparticle sunscreen-treated virgin mouse, day 5


title: PBO_female_15day_rep6PBO_G50F_D15_6

value: CD-1 mouse


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 2


title: miRNA expression profiling of pediatric AML patients [6810008]


title: PBO_female_4day_rep4PBO_G48F_D4_4

description: Gene expression data from liver samples of female CD1 mice treated with Piperonyl-butoxide up to 4 days.

source_name: Piperonyl-butoxide, female mice, 4 days

value: Liver


title: PBO_female_4day_rep6PBO_G48F_D4_6


title: PBO_female_4day_rep5PBO_G48F_D4_5


title: PBO_female_4day_rep1PBO_G48F_D4_1


title: miRNA expression profiling of pediatric AML patients [6810004]


title: Virgin mouse_liver tissue_nano ZnO sunscreen_5d, biological rep 1


title: CMC_female_15day_rep5CMC_G41F_D15_5


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  6


title: PBO_female_4day_rep2PBO_G48F_D4_2


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  3


title: CMC_female_15day_rep3CMC_G41F_D15_3


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  4


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  2


title: CMC_female_15day_rep1CMC_G41F_D15_1


title: CMC_female_4day_rep5CMC_G40F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Carboxymethyl cellulose up to 4 days.

source_name: Carboxymethyl cellulose, female mice, 4 days


title: CMC_female_4day_rep6CMC_G40F_D4_6


title: CMC_female_15day_rep4CMC_G41F_D15_4


title: CMC_female_4day_rep4CMC_G40F_D4_4


title: CMC_female_15day_rep2CMC_G41F_D15_2


title: PBO_female_4day_rep3PBO_G48F_D4_3


title: CMC_female_4day_rep3CMC_G40F_D4_3


title: Virgin mouse_liver tissue_ micro ZnO sunscreen_5d, biological rep  1


title: miRNA expression profiling of pediatric AML patients [6400059]


title: miRNA expression profiling of pediatric AML patients [6400060]


title: miRNA expression profiling of pediatric AML patients [6400057]


title: miRNA expression profiling of pediatric AML patients [6400058]


title: CMC_female_4day_rep2CMC_G40F_D4_2


title: miRNA expression profiling of pediatric AML patients [6400028]


title: miRNA expression profiling of pediatric AML patients [6400027]


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 6

description: Gene expression data from liver tissue harvested from virgin SKH:QS mouse topically treated with a sunscreen formulation-only six times over four days

source_name: SKH:QS mouse liver tissue from formulation-only-treated virgin mouse, day 5


title: CMC_female_4day_rep1CMC_G40F_D4_1


title: PB_male_4day_rep4PB_G60M_D4_4

description: Gene expression data from liver samples of male CD1 mice treated with Phenobarbital up to 4 days.

source_name: Phenobarbital, male mice, 4 days


title: miRNA expression profiling of pediatric AML patients [6160031]


title: PB_male_4day_rep1PB_G60M_D4_1


title: PB_male_15day_rep1PB_G62M_D15_1

description: Gene expression data from liver samples of male CD1 mice treated with Phenobarbital up to 15 days.

source_name: Phenobarbital, male mice, 15 days


title: PB_male_15day_rep4PB_G62M_D15_4


title: PB_male_15day_rep2PB_G62M_D15_2


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 1


title: TAA_male_15day_rep6TAA_G59M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Thioacetamid up to 15 days.

source_name: Thioacetamid, male mice, 15 days


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 2


title: PB_male_4day_rep2PB_G60M_D4_2


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 4


title: PB_male_15day_rep3PB_G62M_D15_3


title: PB_male_4day_rep6PB_G60M_D4_6


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 5


title: Virgin mouse_liver tissue_formulation-only_5d, biological rep 3


title: PB_male_4day_rep5PB_G60M_D4_5


title: NB4, Identified miRNAs of total RNA, biological rep2

description: Gene expression data from miRNAs of total RNA of NB4 cells

source_name: synthetic miRNA pool (universal reference)

source_name: NB4 cell line, 4'-thiouridine and UV treated

value: human acute promyelocytic leukemia

value: cells carry the t(15;17) PML-RARA fusion gene

value: cells were harvested after 48 - 72 h

tag: rna subtype

value: total RNA


title: TAA_male_15day_rep5TAA_G59M_D15_5

value: male

value: 15 days


title: NB4, Identified miRNAs of total RNA, biological rep3


title: NB4, Identified miRNAs of total RNA, biological rep1


title: TAA_male_15day_rep4TAA_G59M_D15_4

value: Thioacetamid


title: NB4, Isotype control detected miRNAs, biological rep3

description: Isotype control detected miRNAs

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled

value: unspecific bound miRNAs of isotype control


title: hONS cells_MAX-treated_ 6h, biological rep 3

description: Gene expression data from MAX hONS cells at 6h

source_name: MAX-treated hONS cells at 6h

growth_protocol: hONS cells derived from adult olfactory mucosa were propagated as adherent monolayers in DMEM/F12 (1:1, Gibco) containing 10% FBS, at 37˚C, 10% CO2.

extract_protocol: Total RNA was extracted from cells using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.

treatment_protocol: Cells were treated with medium containing 25ug/ml of ZnO nanoparticles (Nanosun, Z-COTE, HP1 or MAX), or medium containing no nanoparticles (untreated) and incubated at 37˚C, 10% CO2 for 2h or 6h.

tag: cell type

value: hONS

value: 25ug/ml of ZnO nanoparticles (MAX)

tag: incubated


title: TAA_male_15day_rep3TAA_G59M_D15_3


title: PB_male_4day_rep3PB_G60M_D4_3

value: Phenobarbital

value: 4 days


title: hONS cells_MAX-treated_ 6h, biological rep 4


title: NB4, Isotype control detected miRNAs, biological rep2

description: Isotype control detected miRNAs


title: NB4, Isotype control detected miRNAs, biological rep4

description: Isotype control detected miRNAs


title: hONS cells_MAX-treated_ 6h, biological rep 2


title: TAA_male_15day_rep2TAA_G59M_D15_2


title: NB4, Isotype control detected miRNAs, biological rep1

description: Isotype control detected miRNAs


title: TAA_male_4day_rep6TAA_G57M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Thioacetamid up to 4 days.

source_name: Thioacetamid, male mice, 4 days


title: TAA_male_4day_rep4TAA_G57M_D4_4


title: hONS cells_MAX-treated_ 6h, biological rep 1


title: TAA_male_15day_rep1TAA_G59M_D15_1


title: TAA_male_4day_rep5TAA_G57M_D4_5


title: WY_male_15day_rep6WY_G54M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Wy-14643 up to 15 days.

source_name: Wy-14643, male mice, 15 days


title: TAA_male_4day_rep3TAA_G57M_D4_3


title: WY_male_15day_rep5WY_G54M_D15_5


title: hONS cells_HP1-treated_ 6h, biological rep 2

description: Gene expression data from HP1-treated hONS cells at 6h

source_name: HP1-treated hONS cells at 6h

value: 25ug/ml of ZnO nanoparticles (HP1)


title: PB_male_15day_rep5PB_G62M_D15_5


title: WY_male_15day_rep4WY_G54M_D15_4


title: NB4, Ago4-associated miRNAs, biological rep3

description: Identification of Ago4-associated miRNAs

value: Ago4-associated miRNAs


title: hONS cells_HP1-treated_ 6h, biological rep 4


title: hONS cells_HP1-treated_ 6h, biological rep 1


title: TAA_male_4day_rep2TAA_G57M_D4_2

value: CD-1 mouse


title: WY_male_15day_rep3WY_G54M_D15_3

value: Liver


title: NB4, Ago4-associated miRNAs, biological rep2

value: human acute promyelocytic leukemia


title: NB4, Ago4-associated miRNAs, biological rep1

value: cells carry the t(15;17) PML-RARA fusion gene


title: NB4, Ago3-associated miRNAs, biological rep3

description: Identification of Ago3-associated miRNAs

value: cells were harvested after 48 - 72 h

value: Ago3-associated miRNAs


title: NB4, Ago3-associated miRNAs, biological rep2


title: WY_male_4day_rep6WY_G52M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Wy-14643 up to 4 days.

source_name: Wy-14643, male mice, 4 days

value: male


title: WY_male_4day_rep4WY_G52M_D4_4


title: hONS cells_Z-COTE-treated_ 6h, biological rep 3

description: Gene expression data from Z-COTE-treated hONS cells at 6h

source_name: Z-COTE-treated hONS cells at 6h

value: 25ug/ml of ZnO nanoparticles (Z-COTE)


title: hONS cells_Z-COTE-treated_ 6h, biological rep 4


title: WY_male_15day_rep1WY_G54M_D15_1

value: 15 days


title: WY_male_15day_rep2WY_G54M_D15_2


title: hONS cells_Z-COTE-treated_ 6h, biological rep 2


title: WY_male_4day_rep5WY_G52M_D4_5


title: WY_male_4day_rep3WY_G52M_D4_3


title: PBO_male_15day_rep6PBO_G50M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Piperonyl-butoxide up to 15 days.

source_name: Piperonyl-butoxide, male mice, 15 days

value: Piperonyl-butoxide


title: WY_male_4day_rep1WY_G52M_D4_1


title: hONS cells_Nanosun-treated_ 6h, biological rep 4

description: Gene expression data from Nanosun-treated hONS cells at 6h

source_name: Nanosun-treated hONS cells at 6h

value: 25ug/ml of ZnO nanoparticles (Nanosun)


title: NB4, Ago2-associated miRNAs, biological rep2

description: Identification of Ago2-associated miRNAs

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled

value: Ago2-associated miRNAs


title: NB4, Ago2-associated miRNAs, biological rep3


title: NB4, Ago3-associated miRNAs, biological rep1


title: PBO_male_15day_rep5PBO_G50M_D15_5


title: WY_male_4day_rep2WY_G52M_D4_2


title: hONS cells_Z-COTE-treated_ 6h, biological rep 1

value: hONS


title: PBO_male_15day_rep4PBO_G50M_D15_4


title: PBO_male_15day_rep2PBO_G50M_D15_2


title: PBO_male_15day_rep1PBO_G50M_D15_1


title: hONS cells_Nanosun-treated_ 6h, biological rep 2


title: hONS cells_Nanosun-treated_ 6h, biological rep 3


title: PBO_male_4day_rep6PBO_G48M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Piperonyl-butoxide up to 4 days.

source_name: Piperonyl-butoxide, male mice, 4 days

value: 4 days


title: hONS cells_Nanosun-treated_ 6h, biological rep 1


title: PBO_male_4day_rep5PBO_G48M_D4_5


title: PBO_male_4day_rep4PBO_G48M_D4_4


title: PBO_male_4day_rep3PBO_G48M_D4_3


title: NB4, Ago1-associated miRNAs, biological rep3

description: Identification of Ago1-associated miRNAs

value: Ago1-associated miRNAs


title: NB4, Ago2-associated miRNAs, biological rep1


title: NB4, Ago1-associated miRNAs, biological rep2


title: NB4, Ago1-associated miRNAs, biological rep1


title: KASUMI-1, Identified miRNAs of total RNA, biological rep3

description: Gene expression data from miRNAs of total RNA of KASUMI-1 cells

source_name: KASUMI-1 cell line, 4'-thiouridine and UV treated

value: human acute myeloid leukemia

value: cells carry the t(8;21) AML1-ETO fusion gene

value: total RNA


title: KASUMI-1, Identified miRNAs of total RNA, biological rep1


title: KASUMI-1, Identified miRNAs of total RNA, biological rep2


title: CMC_male_15day_rep6CMC_G41M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Carboxymethyl cellulose up to 15 days.

source_name: Carboxymethyl cellulose, male mice, 15 days

value: CD-1 mouse

value: Liver

value: Carboxymethyl cellulose


title: CMC_male_15day_rep5CMC_G41M_D15_5


title: hONS cells_MAX-treated_ 2h, biological rep 4

description: Gene expression data from MAX hONS cells at 2h

source_name: MAX-treated hONS cells at 2h

value: 25ug/ml of ZnO nanoparticles (MAX)


title: hONS cells_unntreated_ 6h, biological rep 3

description: Gene expression data from untreated hONS cells at 6h

source_name: Untreated hONS cells at 6h


title: hONS cells_unntreated_ 6h, biological rep 2


title: hONS cells_MAX-treated_ 2h, biological rep 3


title: CMC_male_15day_rep3CMC_G41M_D15_3

value: male


title: hONS cells_MAX-treated_ 2h, biological rep 2


title: hONS cells_unntreated_ 6h, biological rep 1


title: CMC_male_4day_rep5CMC_G40M_D4_5

description: Gene expression data from liver samples of male CD1 mice treated with Carboxymethyl cellulose up to 4 days.

source_name: Carboxymethyl cellulose, male mice, 4 days


title: CMC_male_4day_rep6CMC_G40M_D4_6


title: CMC_male_15day_rep1CMC_G41M_D15_1


title: CMC_male_4day_rep4CMC_G40M_D4_4


title: PBO_male_4day_rep1PBO_G48M_D4_1


title: hONS cells_unntreated_ 6h, biological rep 4


title: CMC_male_15day_rep2CMC_G41M_D15_2


title: PBO_male_4day_rep2PBO_G48M_D4_2


title: CMC_male_15day_rep4CMC_G41M_D15_4


title: KASUMI-1, Isotype control detected miRNAs, biological rep4

description: Isotype control detected miRNAs

value: cells were harvested after 48 - 72 h

value: unspecific bound miRNAs of isotype control


title: KASUMI-1, Isotype control detected miRNAs, biological rep3

description: Isotype control detected miRNAs


title: hONS cells_MAX-treated_ 2h, biological rep 1


title: CMC_male_4day_rep3CMC_G40M_D4_3


title: CMC_male_4day_rep1CMC_G40M_D4_1


title: CMC_male_4day_rep2CMC_G40M_D4_2


title: Praz_female_15day_rep6Praz_G39F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Prazosin up to 15 days.

source_name: Prazosin, female mice, 15 days

value: female

value: Prazosin

value: 15 days