title: cornea vs dermis replicate 2 (dye-swap)

first: Masanari

last: Takamiya

address: Hermann-von-Helmholtz-Platz 1

institute: Karlsruhe Institute of Technology

description:
agilent-051-medium.gpr
biological repeat 2 (dye-swap)

hyb_protocol: Hybridisation of the microarray was done at 65oC for 17 hours, followed by stringency wash.

scan_protocol: Scanning was done with the Axon model 4000B dual-laser scanner and the corresponding GenePix6 software (Molecular Devices, Union City, CA).  Two emission channels for Cy3 and Cy5 dyes were scanned in parallel (16-bit colour depth).

data_processing: The probe sequences commonly found on the Agilent G2518A (design ID:013223 Option 001, 60-mer oligos) and G2519F microarray (design ID: 019161-V2) were re-mapped onto the Zebrafish genome Zv8 and Unigene ESTs by an in-house Perl script after either BLAT- or BLAST-sequence alignment (Altschul, Madden et al. 1997; Kent 2002). 16450 out of 23763 Agilent probes (69.2%) can be re-mapped onto databases of either Unigene (zebrafish build #117), Ensembl genes (Zv8, release 54) or RefSeq genes (zebrafish release 38). BLAT-/BLAST hits within the coding region or within 500 bp range of either 5'- or 3'-flanking region of start or stop codon, respectively, were regarded as the hit (regardless of UTR or not) against the corresponding gene. The open source package for microarray analysis, Limma (Smyth 2004) was used to process the data in the following steps: background correction with the minimum method, within-array normalization, between-array normalization using the Aquantile method, application of linear models for analyzing dye-swap and biological repeats, and finally the assessment of differential expression employing empirical Bayesian for multiple comparisons and the TREAT method (t-test relative to a threshold, (McCarthy and Smyth 2009) for selecting probes with biological meaningful difference).

source_name: dermis

label_protocol: Reverse transcription reaction of the isolated total RNA followed by cRNA probe synthesis were conducted by using Low RNA Input Linear Amplification kit (Cat. No. 51843523, Agilent Technologies).  Synthesized cRNA probes were purified by QIAgen RNeasy purification kit and quantified by NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific).

extract_protocol: Total RNAs from frozen tissues were extracted in Trizol with an electric homogenizer.

value: adult

value: dermis

source_name: cornea

value: cornea


title: WT/WT4

status: Public on Feb 19 2015

type: RNA

city: Baltimore

first: Theodore

last: Kouo

state: MD

address: 733 North Broadway

department: School of Medicine

country: USA

institute: The Johns Hopkins University

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Gal-3 WT T cell adoptively transferred into Gal-3 WT mouse

label_protocol: The NuGEN Ovation Pico WTA Systen V2 Kit (NuGEN Technologies) was used as described in the manufacturer's manual.

growth_protocol: High avidity CD8 T cells were harvested from TCR Transgenic mice bearing the Thy1.2 congenic marker, and purified via negative selection using Dynal beads (Invitrogen).  Cells were adoptively transferred into tumor bearing mice treated with whole cell GM-CSF vaccine and cyclophosphamide, and isolated 5 days post-adoptive transfer from tumors.

extract_protocol: Stratagene Absolutely RNA Nanoprep kit

treatment_protocol: Mice were given 2 simultaneous s.c. injections of 2X10^6 NT2.5 tumor cells in the right and left upper mammary fat pads on day 0, Cyclophosphamide (100 mg/kg) on day 8, GM-CSF vaccine on day 9, and 6x10^6 adoptively transferred Thy1.2+ CD8+ T cells on day 10.  Tumors were dissected from mice 5 days post adoptive transfer when T cell trafficking to the TME is found to be the highest.  Tumor tissue was first mashed through a 40 micron nylon cell strainer before enzymatic digestion with collagenase IV and hyaluronidase.  Adoptively transferred CD8+ T cells were then labeled via antibody staining for the Thy1.2 surface marker which is specific to adoptively transferred cells only, and then purified via fluorescence activated cell sorting.

tag: strain

value: TCR transgenic

tag: cd8 t cell genotype

value: gal-3 WT

tag: host mouse genotype

tag: cell type

value: CD8 T cells

tag: time point

value: 5 days post-adoptive transfer


title: cornea vs dermis replicate 1

city: Kalrsruhe

department: Institute of Toxicology and Genetics

country: Germany

description:
agilent-048-medium.gpr
biological repeat 1

organism: Danio rerio

growth_protocol: Adult zebrafish from the fish facility were used.

treatment_protocol: To prepare total RNA from adult tissues of the cornea and the skin, AB2O2 wild type strain of adult zebrafish was deeply anaesthetised by lethal dose of MESAB.  For each biological repeat of the microarray analysis, 30 globes were removed from the sockets and the cornea was carefully isolated with forceps from the other periocular tissues (the sclera, lens, iris, periocular muscles and retina) in the phosphate-buffered saline. Skin dermis was prepared from ten fish by scraping the scales that hold epidermis on their outer surface with a scalpel that was kept at the right angle moving from tail to head direction. Inevitable minimal amount of fin and muscle tissues that could not be separated was allowed to be included into the dermis preparation. Skin epidermis was prepared from scales as described above. Tissues were immediately chilled on crashed blocks of dry ice and weighted.

tag: age

tag: tissue


title: H2O2

status: Public on Feb 18 2015

city: Guangzhou

first: Qing-Ping

last: Zeng

address: No. 12, Airport Rd.

department: Tropical Medicine Institute

country: China

institute: Guangzhou University of Chinese Medicine

description: Test

data_processing:
ΔΔCt Method
Fold changes (ART/AL; SNP/AL; ARG/AL; CR/AL; H2O2/AL)

label: SYBR

source_name: Muscle, H2O2 injected, six hours

label_protocol: SuperScript. III Reverse Transcriptase (invitrogen)

extract_protocol: TRIZOL® Reagent (Invitrogen)

tag: gender

value: female

value: KM

value: skeletal muscle

value: four-month-old


title: Mut Nr3 -Dox

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: HEK293T-DroshaE1147K -Dox biological replicate to Mut Nr1-Dox

hyb_protocol: miRNA Complete Labeling and Hyb Kit  (Agilent) according to the manufacturers recommendations

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent.  The data were analyzed using the  Bioconductor package VSN (variance stabilizing normalization)

label: Cyanine 3-pcp

organism: Homo sapiens

source_name: HEK293T-DroshaE1147K -Dox

growth_protocol: HEK293T cells were cultivated in DMEM containing 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO2

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the PicoRNA kit (Agilent) on a Bioanalyzer2100.

treatment_protocol: HEK293T expressing wildtype or mutant DROSHA were treated with 1 µg/ml doxycycline for 48h, control cells without doxycycline induction

tag: cell line


title: Mut nr3 +Dox

description: HEK293T-DroshaE1147K +Dox biological replicate to Mut Nr1+Dox

source_name: HEK293T-DroshaE1147K +Dox

label_protocol: miRNA Complete Labeling and Hyb Kit  (Agilent) according to the manufacturers recommendations


title: Mut Nr1 +Dox TR

description: HEK293T-DroshaE1147K +Dox technical replicate to Mut Nr1+Dox


title: Mut nr3 +Dox TR

description: HEK293T-DroshaE1147K +Dox technical replicate to Mut Nr3+Dox


title: Mut Nr3 -Dox TR

description: HEK293T-DroshaE1147K -Dox technical replicate to Mut Nr3-Dox


title: cornea vs dermis replicate 1 (dye-swap)

description:
agilent-049-medium.gpr
biological repeat 1 (dye-swap)


title: cornea vs dermis replicate 2

description:
agilent-050-medium.gpr
biological repeat 2


title: WT/WT3


title: WT nr6+Dox TR

description: HEK293T-DroshaWT +Dox technical replicate to WT Nr6+Dox

source_name: HEK293T-DroshaWT +Dox


title: Mut Nr1 -Dox

description: HEK293T-DroshaE1147K -Dox


title: Mut Nr1 +Dox

description: HEK293T-DroshaE1147K +Dox


title: ART

description: Test

source_name: Muscle, ART injected, daily injection for three days


title: cornea vs dermis replicate 3

description:
agilent-094-medium.gpr
biological repeat 3


title: cornea vs dermis replicate 3 (dye-swap)

description:
agilent-095-medium.gpr
biological repeat 3 (dye-swap)


title: Mj_pbs24_2

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the kuruma shrimp high-density oligonucleotide gene chip array developed by the Laboratory of Genome Science, Tokyo University of Marine Science and Technology. This microarray chip is an 8 x 15 k format, which contains around 13,875 probes. Hybridization was done in a rotating Agilent hybridization oven for 17 hours at 65 °C and then followed by washing in buffers 1 and 2 (Agilent Technologies) for 1 minute each at room temperature and 37 °C, respectively. Slides were immediately dried by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using profile AgilentHD_GX_1color and scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, TIFF file dynamic range is 20 bit and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 040398_D_F_20120424) to obtain background and multiplicatively detrended Processed Signal intensities.  SuBio platform version 1.17 calculated normalized values that the log2 summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Penaeus japonicus

source_name: hemocytes, 24 hours, pbs_2

label_protocol: 200 ng total RNA was reverse-transcribed and labeled with Cy3 using Low Input Quick Amp Labeling kit (Agilent Technologies) followed by RNeasy Mini Kit (Qiagen, Germany) purification.

extract_protocol: Total RNA from hemocytes of control and shrimps injected with PBS, dsGFP and siGFP was extracted using RNAiso reagent (Takara, Japan). The extracted total RNA was then purified by RNeasy Mini Kit (Qiagen, Germany) and the purity was checked by Agilent 2200 TapeStation System (Agilent, USA).

treatment_protocol: After the acclimatization, 4 shrimps in each treatment group (8 for the control group) were intramuscularly injected with 100µl of phosphate buffered saline (PBS) solution, small interferance RNA encoding green fluorecense gene (siGFP) or double stranded RNA encoding green fluorecense gene (dsGFP) at a concentration of 3µg per gram body weight of shrimp. Hemolymph of treated kuruma shrimps were collected at designated time points such as 0, 24, and 48 hours post injection. Approximately 500µl of hemolymph were drawn out from the ventral sinus using 2.5ml sterile syringe with 1ml of filter sterilized and pre-cooled anticoagulant (0.82% NaCl, 0.55% citric acid, 1.98% glucose and 0.88% sodium citrate dissolved in water and adjusted to pH 5.6). Hemocytes were immediately collected by centrifugation at 3,000 x g for 3 minutes and the resulting pellet was washed with 1x PBS.

tag: treatment

value: PBS

tag: time

value: 24 hours


title: WT/WT2


title: WT Nr1+Dox TR

description: HEK293T-DroshaWT +Dox technical replicate to WT Nr1+Dox


title: WT/WT1


title: WT nr6 -Dox TR

description: HEK293T-DroshaWT -Dox technical replicate to WT Nr6-Dox

source_name: HEK293T-DroshaWT -Dox


title: WT Nr1+Dox

description: HEK293T-DroshaWT +Dox


title: WT nr6 -Dox

description: HEK293T-DroshaWT -Dox biological replicate to WT Nr1-Dox


title: WT Nr1-Dox TR

description: HEK293T-DroshaWT -Dox technical replicate to WT Nr1-Dox


title: WT Nr1-Dox

description: HEK293T-DroshaWT -Dox


title: WT nr6+Dox

description: HEK293T-DroshaWT +Dox biological replicate to WT Nr1+Dox


title: female,NON/LtJ,strain, dorsal root ganglion tissue

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: Gene expression data from wildtype mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse MOE_430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were processed using GCRMA in R (version 2.6.2 (2008-02-08)), using packages downloaded from Bioconductor

label_protocol: cDNA and amplified antisense RNA was made from 1.4 mg of pooled total RNA, using the Affymetrix Single Amplification protocol.

growth_protocol: DRGs were dissected from naïve 2-month-old mice of both sexes (n=3 mice/sex/strain) between 09:00–12:00 h

extract_protocol: Total RNA was isolated from tissues using Trizol (Invitrogen) followed by RNeasy (Qiagen, Valencia, CA).

treatment_protocol: wildtype mice

value: dorsal root ganglion

tag: genotype

value: wildtype

value: NON/LtJ

value: 2 months


title: female,SWR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SWR/J


title: female,A/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: A/J


title: female,FVB/NJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: FVB/NJ


title: ccRCC tissue_29

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

institute: Universitätsklinikum Bonn

description: Gene expression in ccRCC tissue

hyb_protocol: Labeled RNA was hybridized to a custom gene expression microarray (AMADID# 041648).

scan_protocol: Arrays were scanned using the Agilent G2565CA Microarray Scanner and Scan Control Software 8.5 according to the manufacturer's instructions.

data_processing: Probe intensities were extracted using Feature Extraction software (Agilent).

source_name: ccRCC tissue

label_protocol: Total RNA (100ng) was labeled using the low input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacturer’s instructions

extract_protocol: Total RNA was  isolated using the mirVana miRNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturers recommendation. To remove residual DNA fragments, we treated the isolate twice with DNase (DNA-free Kit, Ambion).

treatment_protocol: Fresh-frozen tissue samples (approximately 50 mg) were cut on liquid nitrogen and homogenized with Yttrium stabilized Zirkonoxid-Beads (Silibeads, Sigmund-Lindner, Warmensteinach, Germany) using a Precellys24 tissue homogenizer

value: ccRCC tissue

value: male

tag: tnm

tag: pn

tag: cm

tag: grading

tag: ajcc

value: Stage 4

tag: size


title: non pathological renal tissue__30

description: Gene expression in non pathological renal tissue

source_name: non pathological renal tissue

value: non pathological renal tissue


title: non pathological renal tissue__32


title: non pathological renal tissue__24


title: female,MRL/MpJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

tag: strain

value: MRL/MpJ

value: female


title: non pathological renal tissue__28


title: ccRCC tissue_25

description: Gene expression in ccRCC tissue

value: Stage 1


title: female,RIIIS/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: RIIIS/J


title: female,DBA/2J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: female,C3H/HeJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: ccRCC tissue_27

description: Gene expression in ccRCC tissue

value: Stage 3


title: non pathological renal tissue__26


title: female,NOD/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NOD/LtJ


title: non pathological renal tissue__20


title: female,P/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: P/J


title: female,NZO/HILtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: NZO/HILtJ


title: ccRCC tissue_31

description: Gene expression in ccRCC tissue


title: female,C57BR/cdJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: 2 months


title: non pathological renal tissue__18


title: ccRCC tissue_19

description: Gene expression in ccRCC tissue


title: female,SM/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SM/J


title: non pathological renal tissue__22


title: female,PL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: PL/J


title: female,C58/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: ccRCC tissue_17

description: Gene expression in ccRCC tissue

value: ccRCC tissue


title: ccRCC tissue_23

description: Gene expression in ccRCC tissue

value: male


title: female,BTBT T+tf/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BTBT T+tf/J


title: female,SJL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SJL/J


title: non pathological renal tissue__9

value: non pathological renal tissue


title: female,KK/HIJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: KK/HIJ

value: female


title: female,BUB/BnJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BUB/BnJ


title: female,NZW/LacJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZW/LacJ


title: female,CBA/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: CBA/J


title: non pathological renal tissue__14


title: non pathological renal tissue__11


title: non pathological renal tissue__16


title: ccRCC tissue_7

description: Gene expression in ccRCC tissue

value: Stage 1


title: ccRCC tissue_12

description: Gene expression in ccRCC tissue

value: Stage 2


title: male,A/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: wildtype

value: A/J


title: female,c57BL/6J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: 2 months


title: female,AKR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: AKR/J


title: male,SWR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SWR/J


title: ccRCC tissue_10

description: Gene expression in ccRCC tissue

value: ccRCC tissue

value: Stage 3


title: male,NON/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NON/LtJ

value: male


title: ccRCC tissue_5

description: Gene expression in ccRCC tissue


title: female,BALB/CByJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BALB/CByJ


title: non pathological renal tissue__6

value: non pathological renal tissue


title: female,129S1/Sv1mJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: female


title: male,MRL/MpJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: MRL/MpJ


title: ccRCC tissue_3

description: Gene expression in ccRCC tissue


title: male,P/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: P/J


title: ccRCC tissue_1

description: Gene expression in ccRCC tissue


title: non pathological renal tissue__2


title: non pathological renal tissue__4


title: male,NOD/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NOD/LtJ


title: ara6-1, biological rep2

city: Bunkyo-ku

first: Tomokazu

last: Tsutsui

state: Tokyo

address: Room 02 (BF), Faculty of Science Building 2, 7-3-1 Hongo

department: Biological Sciences

institute: The university of tokyo

description: Biological replicate 2 of 3.

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning procedure was conducted with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data processing was performed using Expression Console Version 1.3 (Affymetrix).

organism: Arabidopsis thaliana

label_protocol: Ambion WT Expression Kit (The Ambion) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana (Columbia accession) seeds were sown on MS plates after sterilization. After 1-day incubation at 4ºC, plants were grown at 23ºC under continuous light. After 14 days of incubation on plates, plants were used to the experiment.

extract_protocol: Total RNA was extracted from the whole tissue of 14-day-old plants with the RNeasy Plant Mini Kit (Qiagen).

value: whole tissue


title: male,FVB/NJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: FVB/NJ


title: male,KK/HIJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: KK/HIJ


title: male,PL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: PL/J

value: 2 months


title: ara6-1, biological rep3

description: Biological replicate 3 of 3.


title: male,CBA/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: CBA/J


title: WT, biological rep3

description: Biological replicate 3 of 3.


title: male,SM/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SM/J


title: male,C3H/HeJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,RIIIS/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: RIIIS/J


title: male,NZO/HILtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZO/HILtJ

value: male


title: male,NZW/LacJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZW/LacJ


title: male,C58/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,SJL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SJL/J


title: WT, biological rep1

description: Biological replicate 1 of 3.


title: WT, biological rep2

description: Biological replicate 2 of 3.


title: male,C57BR/cdJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,BTBT T+tf/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BTBT T+tf/J


title: male,BUB/BnJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BUB/BnJ


title: male,BALB/CByJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BALB/CByJ


title: ara6-1, biological rep1

description: Biological replicate 1 of 3.

value: whole tissue


title: male,c57BL/6J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion


title: male,DBA/2J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,129S1/Sv1mJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: Control  90_5

city: Berlin

first: Anke

last: Ehlers

address: Max-Dohrn-Straße 8-10

department: Department of Food Safety

institute: Federal Institute for Risk Assessment

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MouseGenome 430 2.0 (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: liver

label_protocol: Biotinylated cRNA was prepared from 250 ng total RNA according to the 3`IVT express kit Affymetrix protocol.

extract_protocol: Liver tissues were shock-frozen in liquid nitrogen and stored for a few days at -80°C until further processing. Liver organs were ground in a Tissuelyser ball mill (Qiagen, Hilden, Germany) under cooling with liquid nitrogen. The frozen liver tissue was crushed and total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: hemizygous FVB/N-SULT1A1/2

tag: age in weeks

value: no

tag: treatment substance

value: vehicle [glyceryl trioctanoate]

tag: treatment time in days

value: liver


title: Control  90_2


title: Control  90_3


title: Control  90_1


title: 1-MIM-OH 90_4

value: yes


title: male,AKR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: AKR/J

tag: age

value: 2 months


title: Control  21_6

tag: tissue


title: 1-MIM-OH 90_5

tag: gender


title: 1-MIM-OH 90_3


title: Control  21_1


title: Control  21_2


title: 1-MIM-OH 90_6


title: Control  90_4


title: Control  21_3


title: Control  90_6


title: 1-MIM-OH 90_2


title: Control  21_4


title: 1-MIM-OH 90_1


title: 1-MIM-OH 21_4


title: ccRCC tissue_13

description: Gene expression in ccRCC tissue

value: ccRCC tissue

value: Stage 3


title: 1-MIM-OH 21_2

value: male


title: Control  21_5


title: 1-MIM-OH 21_3


title: 1-MIM-OH 21_5


title: Notch3 knockout mouse cerebellar microvascular fragments, biological rep3

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Gene expression data from mouse Notch3 knockout cerebellar microvascular fragments

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 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 7G

data_processing: The data were analyzed with GCRMA package in the bioconductor project (gcrma version 2.32.0).

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix small sample amplification protocol from app. 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed using RNeasy® Mini Kit (Qiagen)

value: cerebellar microvascular fragments

tag: genotype/variation

value: Notch3 knockout


title: 1-MIM-OH 21_1

tag: treatment


title: Notch3 knockout mouse cerebellar microvascular fragments, biological rep2

source_name: Notch3 knockout cerebellar microvascular fragments


title: Notch3 knockout mouse cerebellar microvascular fragments, biological rep1


title: Notch3 knockout mouse cerebral microvascular fragments, biological rep1

description: Gene expression data from mouse Notch3 knockout cerebral microvascular fragments

value: cerebral microvascular fragments


title: control mouse cerebellar microvascular fragments, biological rep2

description: Gene expression data from control mouse cerebellar microvascular fragments

source_name: control cerebellar microvascular fragments


title: Notch3 knockout mouse cerebral microvascular fragments, biological rep2

source_name: Notch3 knockout cerebral microvascular fragments


title: ccRCC tissue_15

description: Gene expression in ccRCC tissue


title: control mouse cerebellar microvascular fragments, biological rep1


title: control mouse cerebral microvascular fragments, biological rep3

description: Gene expression data from control mouse cerebral microvascular fragments

source_name: control cerebral microvascular fragments


title: control mouse cerebellar microvascular fragments, biological rep3


title: Notch3 knockout mouse cerebral microvascular fragments, biological rep3


title: NM-401 Dose 18 Time Point 28 ID 711

city: Roskilde

first: Sarah

middle: Søs

last: Poulsen

state: Denmark

address: Knud den Stores Vej 39B, 2.MF

country: Denmark

institute: The National Research Centre for the Working Environment

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Left lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Female C57BL/6 mice at the age of 5–7 weeks were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the experiment. All mice were fed on Altromin (no. 1324, Christian Petersen, Denmark) and had access to water ad libitum during the whole experiment. The mice were housed in groups of 10 animals in polypropylene cages with sawdust bedding and enrichment at controlled temperature 21±1°C and humidity 50±10% with a 12-h light/12-h dark cycle. Experiments were initiated at 8 weeks of age. All procedure complied with EC Directive 86/609/EEC and Danish laws regulating experiments on animals (permit 2010/561-1779). Mice did not display any signs of respiratory distress, lethargy or any other physical symptoms following exposure.

extract_protocol: At 1, 3 or 28 days post-instillation, the mice were anaesthetized with Hypnorm/Dormicum as described above and killed by exsanguination via intracardiac puncture. Immediately after withdrawing the heart blood, the left lung lobes were snap frozen in cryotubes in liquid N2 and stored at –80°C. Total RNA was extracted (n=6 per group) using Trizol reagent and further purified using the RNeasy Mini Kit with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios between 2.0 and 2.15 and RINs above 7.0.

treatment_protocol: The C57BL/6 mice were exposed in groups of 6 to 18, 54 or 162 ug of NRCWE-26 or NM-401 via intratracheal instillation. In brief, mice were anesthetized by subcutaneous injection of 0.2 ml of Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml,) and Dormicum® (Midazolam 5 mg/ml) in sterile water. The mice were kept on their back at a 40-degree angle on a hot plate (37°C) during the entire procedure. The doses (18, 54 and 162 μg of NRCWE-26 or NM-401) were administered via a single intratracheal instillation. A 40 μl suspension was instilled followed by 150 μl air with a 250 μl SGE glass syringe. Control animals were instilled with vehicle (NanoPure water with 2% serum). After the instillation catheter was removed, breathing was observed in order to assure that the delivered material did not block the airways.

tag: nanomaterial

value: female

tag: dose

tag: time point (day)

tag: ID

source_name: 11 mouse cell lines

tag: reference

value: Universal Mouse Reference RNA

tag: vendor

value: Stratagene, Mississauga, ON, Canada

tag: catelog number


title: NM-401 Dose 54 Time Point 28 ID 717


title: control mouse cerebral microvascular fragments, biological rep2


title: NM-401 Dose repeat Time Point repeat ID 683


title: NRCWE-26 Dose 54 Time Point 28 ID 153


title: NM-401 Dose 164 Time Point 3 ID 700


title: NM-401 Dose 0 Time Point 28 ID 766


title: RPMI8226_shKLF2#2, replicate2

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured according to the manufacturer's instructions.

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.1.187

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg of total RNA

growth_protocol: RPMI8226 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol: After 72 hours of infection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: RPMI8226 cells  were transduced with shRNA by lentivirus.

tag: cell line

tag: cell type

value: Myeloma cells

tag: transduced with

value: shRNAs targeting KLF2


title: NM-401 Dose 164 Time Point 28 ID 718

tag: strain


title: NRCWE-26 Dose 18 Time Point 28 ID 148


title: control mouse cerebral microvascular fragments, biological rep1


title: RPMI8226_shKLF2#1, replicate2


title: NRCWE-26 Dose 164 Time Point 28 ID 160


title: NRCWE-26 Dose 164 Time Point 3 ID 144


title: NM-401 Dose 18 Time Point 3 ID 688


title: NRCWE-26 Dose 54 Time Point 3 ID 137


title: RPMI8226_shLuc2, replicate1

value: shRNAs targeting luciferase (control)


title: RPMI8226_shLuc2, replicate2


title: RPMI8226_shKLF2#2, replicate1


title: RPMI8226_shKLF2#1, replicate1


title: NM-401 Dose repeat Time Point repeat ID 697


title: mock treated with 0.5 mg/ml of histamine

city: Helsinki

first: Maria

last: Anastasina

address: Tukholmankatu 8

department: Institute for Molecular Medicine, Finland

country: Finland

institute: University of Helsinki

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina GenomeStudio Gene Expression Analysis Module 1.9.0;  normalized using Limma package for R from Bioconductor

source_name: macrophages

label_protocol: Standard Illumina label protocol

growth_protocol: Peripheral blood mononuclear cells were isolated form Buffy coats obtained from healthy donors. Macrophages were differentiated from PBMCs in serum-free medium containing granulocyte-macrophage colony stimulating factor for 7 days.

extract_protocol: Total RNA was isolated from infected and non-infected macrophages after 8 hours of infection using Qiagen Rneasy Plus mini kit.

treatment_protocol: Macrophages were infected with Influenza A viruses at indicated multiplicity of infection in serum-free medium.

value: macrophage

tag: time post infection, h


title: infected with A/Udorn/72 (MOI 3) and treated with 0.1 uM SNS-032


title: mock treated with 0.02 mg/ml of dsRNA


title: NRCWE-26 Dose 18 Time Point 3 ID 127


title: infected with A/Udorn/72 (MOI 3)


title: RPMI8226_shKDM3A#2, replicate1

value: shRNAs targeting KDM3A


title: NM-401 Dose 0 Time Point 1 ID 744


title: mock treated with 0.5 mg/ml of histamine and 0.1 uM SNS-032


title: mock treated 0.2 uM of IFNA


title: NM-401 Dose 54 Time Point 1 ID 678


title: mock treated with 0.2 uM LPS and 0.1 uM SNS-032


title: RPMI8226_shKDM3A#1, replicate1


title: mock treated with 0.02 mg/ml of dsRNA nad 0.1 uM SNS-032


title: RPMI8226_shKDM3A#1, replicate2


title: RPMI8226_shKDM3A#2, replicate2


title: mock treated with 0.2 uM LPS


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 6 uM of ASN2


title: Mock treated with 6 uM of ASN2


title: mock treated 0.2 uM of IFNA and 0.1 uM of SNS-032


title: NRCWE-26 Dose 0 Time Point 1 ID 352


title: RPMI8226_shLuc, replicate1


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 2 uM of obatoclax


title: NRCWE-26 Dose 54 Time Point 1 ID 785


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 1 uM of gemcitabine


title: NM-401 Dose 164 Time Point 1 ID 682


title: Mock treated with 1 uM of gemcitabine


title: Wilms_53

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Gene expression data from a Wilms tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Wilms tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: histology

value: blastemal


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 0.1 uM of SNS-032


title: Wilms_51


title: Mock treated with 2 uM of obatoclax


title: Mock treated with 3 uM of saliphenylhalamide


title: RPMI8226_shLuc, replicate2


title: NM-401 Dose 18 Time Point 1 ID 670


title: NRCWE-26 Dose 164 Time Point 1 ID 794


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 3 uM of MK-2206


title: NM-401 Dose 18 Time Point 28 ID 708


title: Wilms_52


title: Mock treated with 3 uM of MK2206


title: NRCWE-26 Dose 18 Time Point 1 ID 781


title: Mock treated with 0.1 uM of SNS-032


title: infected with A/WSN/33 RK/AA mutant (MOI 3)


title: NM-401 Dose 0 Time Point 28 ID 769


title: infected with A/WSN/33 RK/AA mutant (MOI 3), treated with 3 uM of saliphenylhalamide


title: Wilms_50


title: Mock


title: NM-401 Dose 164 Time Point 28 ID 722


title: allergen grain_2

source_name: macrophage donor B


title: Wilms_49

value: regressive


title: histamine 0.5 mg/ml_1

source_name: macrophage donor A


title: control A


title: allergen birch_2


title: Wilms_48


title: control B


title: NRCWE-26 Dose 18 Time Point 28 ID 149


title: Wilms_44


title: allergen birch_1


title: allergen artemisia_2


title: NRCWE-26 Dose 0 Time Point 28 ID 377


title: NM-401 Dose 54 Time Point 28 ID 714


title: histamine 0.5 mg/ml_2


title: allergen artemisia_1


title: allergen grain_1


title: Wilms_46


title: NRCWE-26 Dose 54 Time Point 28 ID 152


title: allergen tick_1


title: NRCWE-26 Dose 164 Time Point 28 ID 162


title: Wilms_43


title: NM-401 Dose 18 Time Point 3 ID 689


title: NM-401 Dose 54 Time Point 3 ID 694


title: allergen tick_2


title: NM-401 Dose 164 Time Point 3 ID 704


title: DOT1L siRNA-1, biological rep.2

city: Houston

first: Yongcheng

last: Song

state: TX

address: One baylor plaza, Baylor College of Medicine

department: PHARMACOLOGY

institute: BAYLOR COLLEGE OF MEDICINE

description:
SAMPLE 12
Replicate 2 of 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The background-subtracted data generated by BeadStudio Software were log2 transformed and then normalised by median centering.

source_name: MDA-MB-231 cells, siDOT1L

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep with QC for Illumina arrays.

growth_protocol: Human cell line MDA-MB-231 was obtained from the American Type Culture Collection (ATCC) and cultured using ATCC recommended culture media in a humidified incubator supplemented with 5% CO2 at 37°C.

extract_protocol: Cells were lysed immediately in TRIzol® Reagent, frozen in liquid nitrogen, and shipped to Asuragen, Inc. (Austin, TX) for microarray experiments.

treatment_protocol: Exponentially growing MDA-MB-231 cells were plated, in duplicate, in 6-well plates at a density of 1 × 10^5 cells/ml in the presence of compounds for 14 days. Compounds and media were refreshed every 3-4 days. siRNA experiments were performed for 7 days by transfecting MDA-MB-231 cells with X-tremeGENE Transfection Reagent (Roche) and 10 nM siRNA (Invitrogen), according to the manufacturer's protocol.

value: breast cancer cell line

value: DOT1L siRNA

tag: treatment duration

value: 7 days


title: T1 (24 hrs)_FGF9, rep 3

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: gene expression data from myelinating cultures 19 DIV treated with FGF9

hyb_protocol: hybridized to Affymetrix Rat Gene 1.0 ST Arrays using manufacturer's protocols using Fluidics Station 450

scan_protocol: Gene Array Scanner 3000-7G

data_processing: Partek Genomics Suite (version 6.6), probeset level data were normalized using GCRMA normalisation and summarised to transcript cluster level using One-Step Tukey's Biweight method.

organism: Rattus norvegicus

source_name: myelinating cultures, 19 DIV

label_protocol: labelled with biotin using Ambion WT Expression Kit following the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol

growth_protocol: Neurospheres were generated from striata of P1 Sprague-Dawley rats by resuspending enzymatically dissociated cells in 20ml neurosphere media [DMEM/F12 (1:1, DMEM containing 4,500 mg/L glucose), supplemented with 0.105 % NaHCO3, 2 mM glutamine, 5,000 IU/ml penicillin, 5µg/ml streptomycin, 5.0mM HEPES, 0.0001% bovine serum albumin, (all from Invitrogen), 25 µg/ml insulin, 100 µg/ml apotransferrin, 60uM putrescine, 20nM progesterone, and 30nM sodium selenite (all from Sigma)] and plating them into a 75 cm3 tissue culture flask. The culture was supplemented with 20ng/ml mouse submaxillary gland epidermal growth factor (R&D Systems) and maintained at 37ºC in a humidified atmosphere of 7% CO2/93% air. Every 2-3 days, 5 ml NSM and 4 µl EGF were added to the flask. Neurosphere-derived astrocytes (NsAs) were obtained by triturating neurospheres and plating them onto Poly-L lysine (PLL, 13ug/ml, Sigma) -coated coverslips (13 mm diameter, VWR International, Leicestershire, UK) in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine (Sigma) until they formed confluent monolayer.      Myelinating spinal cord cultures were derived from E15.5 Sprague-Dawley (SD) embryos. Spinal cords were dissected out, cleared of meninges, minced with a scalpel blade and enzymatically dissociated with 2.5% trypsin (Invitrogen) and 1.33% collagenase (ICN Pharmaceuticals, UK). Enzymatic activity was stopped by adding 1 ml of a solution containing 0.52 mg/ml soybean trypsin inhibitor, 3.0 mg/ml bovine serum albumin, and 0.04 mg/ml DNase (Sigma). The tissue was then triturated, centrifuged and resuspended in plating medium (PM, 50% DMEM, 25% horse serum, 25% HBSS) and 150,000 cells per 100 µl plated on cover slips coated with a confluent monolayer of NsAs. Coverslips were placed in 35-mm Petri dishes (3 per dish) and left in the incubator to attach for 2 hours, after which 300 µl of PM and 500 µl of differentiation medium (DM) [DMEM (4,500 mg/ml glucose), 10 ng/ml biotin, 0.5% hormone mixture (1 mg/ml apotransferrin, 20 mM Putrescine, 4 μM progesterone, and 6 μM selenium; formulation based on Bottenstein and Sato, 197940), 50 nM hydrocortisone, and 0.1 μg/ml insulin (all reagents from Sigma) ] were added. Cultures were fed every 2 days by removing 500 µl of media and replacing it with fresh DM media, after 12 days insulin was removed from the DM used to feed the cultures.  The effect of FGFs or BMP4 on these in vitro myelinating cultures was investigated by adding them to the culture media from day 18 (i.e. when myelination has just begun) to day 28 in vitro.

extract_protocol: RNA was extracted using the Qiagen Rneasy Micro kit according to manufacturer's instructions

treatment_protocol: The in vitro myelinating cultures were either untreated or treated with FGF1, FGF2, FGF9 or BMP4. Samples were collected at 24 hours and 10 days from the untreated and treated myelinating cultures.

value: Sprague-Dawley

value: in vitro myelinating cultures

tag: time


title: NRCWE-26 Dose 54 Time Point 3 ID 135

tag: gender


title: T1 (24 hrs)_FGF2, rep 3

description: gene expression data from myelinating cultures 19 DIV treated with FGF2

tag: treatment


title: 10uM compound [2], biological rep.2

description:
SAMPLE 6
Replicate 2 of 2.
DOT1L inhibitor Compound [2]: Compound 55 (in Anglin et al., 2012).

source_name: MDA-MB-231 cells, 10uM DOT1L inhibitor [2]

value: 10uM DOT1L inhibitor [2]

value: 14 days


title: Wilms_40

value: female


title: Wilms_45


title: 5uM compound [1], biological rep.2

description:
SAMPLE 10
Replicate 2 of 2.
DOT1L inhibitor Compound [1]: EPZ004777 (in Diagle et al., 2011)

source_name: MDA-MB-231 cells, 5uM DOT1L inhibitor [1]

value: 5uM DOT1L inhibitor [1]


title: 1uM compound [1], biological rep.2

description:
SAMPLE 8
Replicate 2 of 2.
DOT1L inhibitor Compound [1]: EPZ004777 (in Diagle et al., 2011)

source_name: MDA-MB-231 cells, 1uM DOT1L inhibitor [1]

value: 1uM DOT1L inhibitor [1]


title: NM-401 Dose 0 Time Point 3 ID 755

tag: nanomaterial

value: Universal Mouse Reference RNA

value: Stratagene, Mississauga, ON, Canada


title: Wilms_41


title: T1 (24 hrs)_FGF2, rep 2


title: Wilms_38


title: 1uM compound [1], biological rep.1

description:
SAMPLE 7
Replicate 1 of 2.
DOT1L inhibitor Compound [1]: EPZ004777 (in Diagle et al., 2011)


title: 5uM compound [1], biological rep.1

description:
SAMPLE 9
Replicate 1 of 2.
DOT1L inhibitor Compound [1]: EPZ004777 (in Diagle et al., 2011)


title: DOT1L siRNA-1, biological rep.1

description:
SAMPLE 11
Replicate 1 of 2.


title: Wilms_42


title: NRCWE-26 Dose 18 Time Point 3 ID 132

tag: dose


title: Wilms_39


title: Wilms_37


title: 10uM compound [2], biological rep.1

description:
SAMPLE 5
Replicate 1 of 2.
DOT1L inhibitor Compound [2]: Compound 55 (in Anglin et al., 2012).


title: NM-401 Dose repeat Time Point repeat ID 691

tag: time point (day)


title: Wilms_36


title: Wilms_35


title: NRCWE-26 Dose 164 Time Point 3 ID 143

tag: ID


title: 2uM compound [2], biological rep.1

description:
SAMPLE 3
Replicate 1 of 2.
DOT1L inhibitor Compound [2]: Compound 55 (in Anglin et al., 2012).

source_name: MDA-MB-231 cells, 2uM DOT1L inhibitor [2]

value: 2uM DOT1L inhibitor [2]


title: T1 (24 hrs)_Control, rep 3

description: gene expression data from myelinating cultures 19 DIV untreated

value: Control


title: T1 (24 hrs)_FGF1, rep 2

description: gene expression data from myelinating cultures 19 DIV treated with FGF1


title: Wilms_34

value: male


title: T1 (24 hrs)_FGF9, rep 2


title: 2uM compound [2], biological rep.2

description:
SAMPLE 4
Replicate 2 of 2.
DOT1L inhibitor Compound [2]: Compound 55 (in Anglin et al., 2012).


title: Control, biological rep.1

description:
SAMPLE 1
Replicate 1 of 2.

source_name: MDA-MB-231 cells, control

value: DMSO control


title: Control, biological rep.2

description:
SAMPLE 2
Replicate 2 of 2.


title: Wilms_33

value: blastemal


title: T1 (24 hrs)_Control, rep 2


title: T1 (24 hrs)_BMP4, rep 3

description: gene expression data from myelinating cultures 19 DIV treated with BMP4


title: NM-401 Dose 54 Time Point 1 ID 677

tag: reference


title: T1 (24 hrs)_FGF1, rep 3


title: T2_FGF2, rep 3

description: gene expression data from myelinating cultures 28 DIV treated with FGF2

source_name: myelinating cultures, 28 DIV

value: T2 (10 days)


title: Wilms_30


title: Wilms_32


title: T2_FGF2, rep 2


title: Wilms_29


title: shHDAC2 SAHA 6h vs shHDAC2 replicate 1

city: Napoli

first: Mariarosaria

last: Conte

address: via De Crecchio

department: Patologia Generale

country: Italy

institute: Second University of Naples

description: Biological replicate 1 of2.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration at 6h.

hyb_protocol: The hybridization of samples was performed with 10X Blocking Agent (Agilent p/n 5188-5281),Fragmentation buffer and GE Hybridization buffer Hi-RPM (Gene expression hybridization Kit-Agilent p/n 5188-5242) at 65 C for 17h,following 2 Wash step (1') were performed with Gene expression wash buffer 1 and 2 (Agilent p/n 5188-5325  and 5188-5325).

scan_protocol: Agilent Microarray Scanner G2565BA Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS and Quantile normalizations.

label_protocol: Diluition of Spike A (Cy3) and Spike B (Cy5) for labeling were performed with Agilent Spike-in Kit two color (Agilent p/n 5188-5279).2500 ng total RNA of each samples were amplied/labeled with Quick Amp Labeling Kit, Two color (Agilentp/n 5190-0444).Qiagen's RNeasy mini spin columns were used for RNA purification (RNeasy Mini Kit p/n 74104)Quantity and quality of RNA  was evalueted by Nanodrop ND-1000 with Microarray measurement program.

growth_protocol: U937 (Human leukemic monocyte lymphoma cell line) scramble and shHDAC2 were cultured in RPMI 1640, containing 10% decomplemented FBS plus G418 0,5 µg/µl

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

value: U937 (Human leukemic monocyte lymphoma cell line ATCC:CRL 1593)

tag: vector

value: untreated

source_name: shHDAC2 (U937 transfected with shHDAC2 vector) treated with SAHA at 5 µM concentration for 6h

treatment_protocol: SAHA treatment at 5 µM concentration for 6 hours


title: shHDAC2 SAHA 24h vs shHDAC2 replicate 4

description: Biological replicate 4 of4.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration for 24h.

source_name: shHDAC2 (U937 transfected with shHDAC2 vector) treated with SAHA at 5 µM concentration for 24h

treatment_protocol: SAHA treatment at 5 µM concentration for 24 hours


title: T2_FGF9, rep 3

description: gene expression data from myelinating cultures 28 DIV treated with FGF9

value: Sprague-Dawley


title: NM-401 Dose 18 Time Point 1 ID 674

tag: vendor

tag: catelog number


title: NM-401 Dose 0 Time Point 1 ID 742


title: T1 (24 hrs)_BMP4, rep 2

tag: cell type

value: in vitro myelinating cultures


title: NRCWE-26 Dose 164 Time Point 1 ID 793


title: shHDAC2 SAHA 6h vs shHDAC2 replicate 2

description: Biological replicate 2 of2.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration for 6h.

source_name: shHDAC2 (U937 transfected with shHDAC2 vector)

tag: cell line

value: treated with SAHA at 5 µM concentration for 6h


title: Wilms_28

description: Gene expression data from a Wilms tumor sample


title: NRCWE-26 Dose 54 Time Point 1 ID 784

source_name: Left lung

tag: strain


title: shHDAC2 SAHA 24h vs shHDAC2 replicate 3

description: Biological replicate 3 of4.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration for 24h.

value: treated with SAHA at 5 µM concentration for 24h


title: NRCWE-26 Dose 18 Time Point 1 ID 780

value: female

source_name: 11 mouse cell lines


title: shHDAC2 SAHA 24h vs shHDAC2 replicate 2

description: Biological replicate 2 of4.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration for 24h.


title: Wilms_31


title: Wilms_47


title: NM-401 Dose 164 Time Point 1 ID 684


title: T2_FGF9, rep 2


title: T2_FGF1, rep 3

description: gene expression data from myelinating cultures 28 DIV treated with FGF1


title: Wilms_26


title: NRCWE-26 Dose 0 Time Point 1 ID 353


title: T2_FGF1, rep 2


title: NM-401 Dose 0 Time Point 28 ID 767


title: NM-401 Dose 164 Time Point 28 ID 723


title: Wilms_25


title: T2_Control, rep 3

description: gene expression data from myelinating cultures 28 DIV untreated


title: Wilms_27


title: NM-401 Dose 18 Time Point 28 ID 706


title: scramble SAHA 6h vs scramble replicate1

description: Biological replicate 1 of2.U937 scramble, untreated, vs U937 scramble SAHA treated at 5 µM concentration at 6h.

value: empty

source_name: U937 scramble (U937 transfected with empty vector) treated with SAHA at 5 µM concentration for 6h


title: shHDAC2 SAHA 24h vs shHDAC2 replicate 1

description: Biological replicate 1 of4.U937 shHDAC2, untreated, vs U937 shHDAC2 SAHA treated at 5 µM concentration at 24h.


title: T2_Control, rep 2


title: T2_BMP4, rep 3

description: gene expression data from myelinating cultures 28 DIV treated with BMP4


title: NM-401 Dose 54 Time Point 28 ID 712


title: Wilms_23

source_name: Wilms tumor tissue


title: scramble SAHA 24h vs scramble replicate 2

description: Biological replicate 2 of2.U937 scramble, untreated, vs U937 scramble SAHA treated at 5 µM concentration at 24h.

source_name: U937 scramble (U937 transfected with empty vector) treated with SAHA at 5 µM concentration for 24h


title: Wilms_22

value: regressive


title: scramble SAHA 24h vs scramble replicate 1

description: Biological replicate 1 of2.U937 scramble, untreated, vs U937 scramble SAHA treated at 5 µM concentration at 24h.

source_name: U937 scramble (U937 transfected with empty vector)


title: scramble SAHA 6h vs scramble replicate 2

description: Biological replicate 2 of2.U937 scramble, untreated, vs U937 scramble SAHA treated at 5 µM concentration at 6h.


title: T1 (24 hrs)_FGF2, rep 1

description: gene expression data from myelinating cultures 19 DIV treated with FGF2


title: Wilms_24


title: Wilms_21


title: shHDAC2 vs scramble replicate 1

description: Biological replicate 1 of2.U937 shHDAC2, untreated, vs U937 scramble


title: shHDAC2 vs scramble replicate 2

description: Biological replicate 2 of2.U937 shHDAC2, untreated, vs U937 scramble


title: NRCWE-26 Dose 164 Time Point 28 ID 161

value: Universal Mouse Reference RNA


title: T1 (24 hrs)_FGF9, rep 1

description: gene expression data from myelinating cultures 19 DIV treated with FGF9


title: T2_BMP4, rep 2


title: NRCWE-26 Dose 0 Time Point 28 ID 373

value: Stratagene, Mississauga, ON, Canada


title: Myoblast-GATA4-OE-day3-3

city: Minneapolis

first: Genomics

last: Center

state: MN

address: 312 Church Street SE

institute: University of Minnesota

data_processing: The data were normalized using mean/median scaling normalization and Welch t test with array track. Signal intensities were normalized by rank invariant method.

source_name: skeletal muscle myoblast_OE_day3

label_protocol: Labeling was performed using TotalPrep RNA Labeling Kit (Ambion).

growth_protocol: Myoblasts isolated from Gata4-loxP mice were cultured in growth medium (Ham’s/F10, 20% FBS, 0.2 μg/ml bFGF) and adenovirally infected with nLacZ or Cre, or retrovirally infected with GATA4.

extract_protocol: Total RNAs were isolated using RNeasy Kit (Qiagen).

treatment_protocol: Infected myoblasts maintained in growth medium were defined as day 0. Infected myoblasts cultured in differentiation medium (DMEM, 5% FBS) for 3 days were defined as day 3.

tag: infection

value: Mouse GATA4

tag: culture

value: Differentiation medium for 3 days


title: NRCWE-26 Dose 18 Time Point 28 ID 145


title: T1 (24 hrs)_Control, rep 1

description: gene expression data from myelinating cultures 19 DIV untreated

source_name: myelinating cultures, 19 DIV

value: Control


title: Myoblast-GATA4-OE-day3-1


title: T1 (24 hrs)_BMP4, rep 1

description: gene expression data from myelinating cultures 19 DIV treated with BMP4


title: Wilms_19

description: Gene expression data from a Wilms tumor sample

tag: histology


title: Wilms_18

value: triphasic


title: T2_FGF2, rep 1

description: gene expression data from myelinating cultures 28 DIV treated with FGF2

tag: time


title: NRCWE-26 Dose 54 Time Point 28 ID 154

tag: gender


title: NM-401 Dose 0 Time Point 3 ID 759


title: Wilms_16

value: male

value: epithelial type


title: NM-401 Dose 54 Time Point 3 ID 695


title: NM-401 Dose 18 Time Point 3 ID 693


title: NM-401 Dose 164 Time Point 3 ID 701


title: Wilms_17


title: Myoblast-GATA4-OE-day3-2


title: T2_FGF9, rep 1

description: gene expression data from myelinating cultures 28 DIV treated with FGF9

tag: treatment

value: T2 (10 days)


title: T1 (24 hrs)_FGF1, rep 1

description: gene expression data from myelinating cultures 19 DIV treated with FGF1


title: Wilms_15


title: Myoblast-GATA4-KO-day3-1

source_name: skeletal muscle myoblast_KO_day3

value: Cre recombinase


title: Myoblast-GATA4-KO-day3-3


title: NRCWE-26 Dose 18 Time Point 3 ID 130

tag: nanomaterial


title: Myoblast-GATA4-KO-day3-2


title: NRCWE-26 Dose 0 Time Point 3 ID 363

tag: dose


title: Myoblast-GATA4-Wt-day3-3

source_name: skeletal muscle myoblast_WT_day3

value: Nuclear β-galactosidase


title: T2_FGF1, rep 1

description: gene expression data from myelinating cultures 28 DIV treated with FGF1

value: Sprague-Dawley

value: in vitro myelinating cultures


title: Myoblast-GATA4-Wt-day3-2


title: Myoblast-GATA4-Wt-day3-1


title: T2_BMP4, rep 1


title: T2_Control, rep 1

description: gene expression data from myelinating cultures 28 DIV untreated


title: Wilms_7

value: diffuse anaplasia


title: Wilms_13

value: female


title: NM-401 Dose 0 Time Point 1 ID 743

tag: time point (day)


title: Wilms_8


title: Wilms_11


title: Myoblast-GATA4-OE-day0-2

source_name: skeletal muscle myoblast_OE_day0

value: Growth medium


title: Wilms_9


title: Wilms_12

value: regressive


title: Wilms_10


title: NRCWE-26 Dose 164 Time Point 3 ID 141

tag: ID

value: Universal Mouse Reference RNA


title: NM-401 Dose 54 Time Point 1 ID 680

tag: reference

value: Stratagene, Mississauga, ON, Canada


title: Myoblast-GATA4-KO-day0-2

source_name: skeletal muscle myoblast_KO_day0


title: Myoblast-GATA4-OE-day0-3

value: Mouse GATA4


title: Myoblast-GATA4-KO-day0-3


title: Myoblast-GATA4-KO-day0-1


title: Myoblast-GATA4-Wt-day0-3

source_name: skeletal muscle myoblast_WT_day0


title: Wilms_6


title: NRCWE-26 Dose 54 Time Point 3 ID 134


title: Wilms_14

value: completely necrotic


title: Wilms_5

value: blastemal


title: NM-401 Dose 18 Time Point 1 ID 673


title: NRCWE-26 Dose 54 Time Point 1 ID 786


title: NRCWE-26 Dose 164 Time Point 1 ID 795


title: NRCWE-26 Dose 18 Time Point 1 ID 779


title: Myoblast-GATA4-Wt-day0-2


title: Wilms_4

value: triphasic


title: Myoblast-GATA4-OE-day0-1


title: Myoblast-GATA4-Wt-day0-1


title: Wilms_3

value: stromal type


title: NM-401 Dose 54 Time Point 28 ID 715


title: NM-401 Dose 18 Time Point 28 ID 707


title: NM-401 Dose 164 Time Point 28 ID 720


title: G2R VZ M 1

city: Grand Rapids

first: Piroska

middle: E

last: Szabo

state: MI

address: 333 Bostwick Ave. NE

department: Center for Epigenetics

institute: Van Andel Research Institute

description: Gene expression data

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.0.

label: Biotin

source_name: G2R VZ M 1

label_protocol: WT Target Labeling Assay was performed using 100ng of total RNA accorind to Affymetrix's 100 ng Total RNA Labeling Protocol.

extract_protocol: RNA was extracted with TRIZOL kit (Qiagen)

treatment_protocol: RNA was prepared from FACS-sorted, EGFP+ cells from mouse fetal prospermatogonia, treated with endocrine disruptors as described in the overall design.

value: primordial germ cells

tag: g0 mother treatment

value: VZ

value: Male

tag: genotype

tag: mother generation

tag: fetus generation

tag: germ cell generation


title: G2R VZ M 2

description: Gene expression data

source_name: G2R VZ M 2

tag: cell type


title: NM-401 Dose 0 Time Point 28 ID 768

tag: strain

tag: vendor

tag: catelog number


title: Wilms_1

tag: histology


title: NRCWE-26 Dose 54 Time Point 28 ID 155

tag: gender


title: G2R DEHP M3

description: Gene expression data

source_name: G2R DEHP M3

value: DEHP


title: NRCWE-26 Dose 0 Time Point 28 ID 375


title: Wilms_2

value: male


title: NRCWE-26 Dose 164 Time Point 28 ID 158


title: shHMGA1 treated cells biological rep2

city: Baltimore

first: Linda

last: Resar

address: 720 Rutland Ave

department: Hematology

institute: Johns Hopkins University

data_processing:
Expression data was pre-processed using the robust microarray (RMA) algorithm, as implemented in the oligo software package available from Bioconductor and annotated to the most recent human genome using the getNetAffx function in the oligo package.  Expression profiles from HMGA1 knock-down cells were compared to control cells treated with the vector RNA using Bayes modified t-tests and the limma package from Bioconductor.  We focused our analysis on the 100 most differentially expressed transcripts.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: MDA-MB-231 siHMGA1 48h

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter random primers for cDNA synthesis, and Invitrogen SuperScript II reverse transcriptase (www.affymetrix.com, GeneChip Expression Analysis, Technicam Manual).

growth_protocol: Cells were grown in DMEM, 10% FBS, 1x NEAA, 1x Glutamax, and 1x Pennicillin/Streptomycin

extract_protocol: RNA was extracted by Trizol using the RNease miniprep kit (Qiagen)

treatment_protocol: Cells were treated by siHMGA1 or control by lipofectamine 2000

tag: cell line

value: triple-negative breast cancer

tag: genotype/variation

value: shHMGA1 knock-down


title: Wilms_20


title: shHMGA1 treated cells biological rep3


title: G2R DEHP M1

description: Gene expression data

source_name: G2R DEHP M1


title: G2R DEHP M2

description: Gene expression data

source_name: G2R DEHP M2


title: RosR_ChIP_noH2O2_rep7_dyeswap

type: genomic

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

hyb_protocol: Labeled samples were hybridized to custom 2 x 105,000 feature 60-mer oligonucleotide microarray (Agilent Technologies, AMADID 026819). On this high-resolution array, the entire H. salinarum genome was tiled every 30 bp in triplicate. Randomly selected regions of the genome were spotted in quadruplicate. Microarray slide hybridization and washing protocols were conducted according to the manufacturer’s instructions (Agilent technologies) with the exception that hybridization was conducted in the presence of 37.5% formamide at 68˚C to ensure proper stringency.

scan_protocol: Slides were scanned on an Agilent G2566AAl scanner using the ChIP-v1_95_May07 protocol.

data_processing: Agilent Feature Extraction was used to map raw spot intensities to microarray grid. Raw probe intensities were normalized first within each array using density-weighted loess (Lickwar et al., 2012). Second, probes were normalized to quantiles across arrays. Binding peaks were detected from normalized data for each replicate independently using MeDiChI in R (Reiss et al., 2008).

molecule: genomic DNA

organism: Halobacterium salinarum NRC-1

source_name: control

label_protocol: DNA fragments were directly labeled with Cy3 and Cy5 dyes (Kreatech) as described previously (Facciotti et al., 2007). Briefly, one µg of each IP sample was labeled with Cy3 or Cy5 dyes from Kreatch corporation according to manufacturer instructions.  Matched, mock-treated controls were oppositely labeled. Dye swaps were conducted to correct for bias in incorporation.

growth_protocol: Halobacterium salinarum NRC-1 harboring VNG0258H(RosR) fused at its C-terminus to the myc epitope was grown to mid-logarithmic phase (OD600 ~ 0.2 - 0.4) in complete medium (CM; 250 g/L NaCl, 20 g/L MgSO4·7H2O, 3 g/L sodium citrate, 2 g/L KCl, 10 g/L peptone) containing 20ug/mL mevinolin.

extract_protocol: Transcription factor-chromatin complexes from each treated time point and untreated cultures were then cross-linked in vivo with 1% formaldehyde for 30 min at room temperature and subjected to immunoprecipitation (IP) by virtue of the myc epitope tag as described previously (Schmid et al. 2011).

treatment_protocol: Cultures were either left untreated or exposed to 25 mM H2O2 for 10, 20, and 60 minutes as indicated in Sample Names

value: NRC-1 transformed with VNG0258H(RosR)::myc

tag: ip

value: mock

tag: condition

value: no H2O2 (non-stress)

value: NRC-1 transformed with RosR::myc

value: myc epitope


title: control treated cells biological rep3

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

source_name: MDA-MB-231 siCon 48h

value: siCon


title: G2R Oil M3

description: Gene expression data

source_name: G2R Oil M3

value: Oil


title: control treated cells biological rep2


title: NRCWE-26 Dose 18 Time Point 28 ID 147

source_name: Left lung

tag: nanomaterial

value: female

tag: dose

tag: time point (day)

tag: ID

source_name: 11 mouse cell lines

value: Universal Mouse Reference RNA

value: Stratagene, Mississauga, ON, Canada


title: NM-401 Dose 0 Time Point 3 ID 754

tag: reference


title: shHMGA1 treated cells biological rep1


title: RosR_ChIP_noH2O2_rep7


title: RosR_ChIP_noH2O2_rep6


title: control treated cells biological rep1


title: G2R Oil M2

description: Gene expression data

source_name: G2R Oil M2

value: primordial germ cells

tag: g0 mother treatment

tag: genotype

tag: mother generation

tag: fetus generation


title: NM-401 Dose 164 Time Point 3 ID 702

tag: strain

tag: vendor


title: G1R VZ M3

description: Gene expression data

source_name: G1R VZ M3

tag: cell type

value: VZ

tag: germ cell generation


title: G1R VZ F3

description: Gene expression data

source_name: G1R VZ F3

tag: gender

value: Female


title: RosR_ChIP_noH2O2_rep6_dyeswap


title: NM-401 Dose 18 Time Point 3 ID 690

tag: catelog number


title: G2R Oil M1

description: Gene expression data

source_name: G2R Oil M1

value: Male


title: NRCWE-26 Dose 0 Time Point 3 ID 364


title: NRCWE-26 Dose 164 Time Point 3 ID 256


title: RosR_ChIP_noH2O2_rep5_dyeswap

tag: ip


title: G1R VZ F2

description: Gene expression data

source_name: G1R VZ F2


title: G1R VZ M2

description: Gene expression data

source_name: G1R VZ M2


title: RosR_ChIP_noH2O2_rep5

tag: condition


title: G1R VZ F1

description: Gene expression data

source_name: G1R VZ F1


title: RosR_ChIP_noH2O2_rep4


title: NRCWE-26 Dose 54 Time Point 3 ID 133

tag: nanomaterial


title: NRCWE-26 Dose 18 Time Point 3 ID 129

tag: dose


title: G1R VZ M1

description: Gene expression data

source_name: G1R VZ M1


title: NM-401 Dose 0 Time Point 1 ID 747

tag: time point (day)


title: NM-401 Dose 18 Time Point 1 ID 671

tag: ID


title: NRCWE-26 Dose 0 Time Point 1 ID 351

tag: reference


title: G2R VZ M 3

description: Gene expression data

source_name: G2R VZ M 3

tag: g0 mother treatment


title: G1R DEHP F2

description: Gene expression data

source_name: G1R DEHP F2

value: DEHP

tag: genotype


title: G1R DEHP M3

description: Gene expression data

source_name: G1R DEHP M3

tag: mother generation


title: RosR_ChIP_noH2O2_rep2_dyeswap


title: RosR_ChIP_noH2O2_rep4_dyeswap


title: RosR_ChIP_noH2O2_rep3_dyeswap


title: NM-401 Dose 164 Time Point 1 ID 685


title: G1R DEHP F1

description: Gene expression data

source_name: G1R DEHP F1

tag: fetus generation


title: RosR_ChIP_noH2O2_rep3

tag: strain

source_name: control


title: NM-401 Dose 54 Time Point 1 ID 679

tag: vendor


title: G1R DEHP M2

description: Gene expression data

source_name: G1R DEHP M2

tag: cell type


title: NRCWE-26 Dose 18 Time Point 1 ID 778


title: NRCWE-26 Dose 0 Time Point 1 ID 349


title: RosR_ChIP_withH2O2_rep3

value: with H2O2


title: G1R DEHP M1

description: Gene expression data

source_name: G1R DEHP M1

tag: germ cell generation


title: RosR_ChIP_withH2O2_rep3_dyeswap


title: RosR_ChIP_noH2O2_rep2


title: G1R BPA M3

description: Gene expression data

source_name: G1R BPA M3

value: BPA

tag: gender


title: RosR_ChIP_withH2O2_rep2_dyeswap

value: NRC-1 transformed with VNG0258H(RosR)::myc


title: NRCWE-26 Dose 164 Time Point 1 ID 791

source_name: Left lung

source_name: 11 mouse cell lines

tag: catelog number


title: RosR_ChIP_withH2O2_rep2

tag: ip

value: mock


title: G1R BPA F3

description: Gene expression data

source_name: G1R BPA F3


title: G1R BPA F2

description: Gene expression data

source_name: G1R BPA F2


title: RosR_ChIP_withH2O2_rep1_dyeswap

tag: condition


title: CpG_G2R_SPERM_OIL_2

description: Chip ID: CpG_G2R_SPERM_OIL_2

hyb_protocol: According to NimbleGen Kit.

scan_protocol: Following NimbleScan's default using Agilent Scanner.

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: MIRA-chip in G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero

label_protocol: According to standard NimbleGen Protocol.

extract_protocol: For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify MIRA-enriched DNA.

tag: epigenetic feature

value: DNA methylation

tag: mouse cross to generate experimental fetus

value: FVBxFVB

tag: age

value: adult

value: mouse adult spermatozoa

tag: generation of germ cell

tag: treatment in utero of g0 mother

value: oil control

source_name: Input DNA of G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero


title: NM-401 Dose 54 Time Point 28 ID 713

tag: nanomaterial

value: female

tag: dose

tag: time point (day)

tag: ID

tag: reference


title: NM-401 Dose 18 Time Point 28 ID 709

tag: strain

value: Universal Mouse Reference RNA

tag: vendor


title: RosR_ChIP_withH2O2_rep1

value: myc epitope


title: G1R BPA M2

description: Gene expression data

source_name: G1R BPA M2

tag: cell type

value: primordial germ cells

tag: g0 mother treatment

tag: genotype

tag: mother generation

tag: fetus generation

tag: germ cell generation


title: NRCWE-26 Dose 54 Time Point 1 ID 789

tag: gender

value: Stratagene, Mississauga, ON, Canada

tag: catelog number


title: RosR_ChIP_noH2O2_rep1_dyeswap

tag: ip

tag: condition

value: no H2O2 (non-stress)


title: G1R BPA F1

description: Gene expression data

source_name: G1R BPA F1

value: Female


title: NM-401 Dose 0 Time Point 28 ID 771

tag: nanomaterial


title: CpG_G2R_SPERM_VZ_1

description: Chip ID: CpG_G2R_SPERM_VZ_1

source_name: MIRA-chip in G2R spermatozoa that was derived from G1R prospermatogonia treatment with VZ in utero

tag: epigenetic feature

tag: mouse cross to generate experimental fetus

tag: age

tag: generation of germ cell

tag: treatment in utero of g0 mother

value: VZ

source_name: Input DNA of G2R spermatozoa that was derived from G1R prospermatogonia treatment with VZ in utero


title: NRCWE-26 Dose 54 Time Point 28 ID 151

tag: strain

tag: dose

tag: time point (day)

tag: ID

tag: reference

tag: vendor


title: NM-401 Dose 164 Time Point 28 ID 719


title: CpG_G2R_SPERM_VZ_2

description: Chip ID: CpG_G2R_SPERM_VZ_2

tag: cell type


title: NRCWE-26 Dose 18 Time Point 28 ID 146

tag: gender


title: G1R BPA M1

description: Gene expression data

source_name: G1R BPA M1

tag: g0 mother treatment

value: Male

tag: genotype

tag: mother generation

tag: fetus generation

tag: germ cell generation


title: CpG_G2R_MGC_DEHP_3

description: Chip ID: CpG_G2R_MGC_DEHP_3

source_name: MIRA-chip in G21R prospermatogonia that was derived from G1R prospermatogonia treated with DEHP in utero

tag: epigenetic feature

tag: mouse cross to generate experimental fetus

value: mouse fetal prospermatogonia

value: DEHP

source_name: Input DNA of G21R prospermatogonia that was derived from G1R prospermatogonia treated with DEHP in utero


title: CpG_G1R_SPERM_OIL_2

description: Chip ID: CpG_G1R_SPERM_OIL_2

source_name: MIRA-chip in G1R spermatozoa after OIL treatment at the spermatogonia stage in utero

tag: age

tag: generation of germ cell

source_name: Input DNA of G1R spermatozoa after OIL treatment at the spermatogonia stage in utero


title: NRCWE-26 Dose 0 Time Point 28 ID 376

tag: nanomaterial

tag: strain

tag: catelog number


title: RosR_ChIP_noH2O2_rep1

value: NRC-1 transformed with VNG0258H(RosR)::myc

tag: ip

tag: condition

source_name: control

value: mock


title: CpG_G2R_SPERM_OIL_1

description: Chip ID: CpG_G2R_SPERM_OIL_1

value: DNA methylation

value: FVBxFVB

tag: treatment in utero of g0 mother


title: G1R Oil F2

description: Gene expression data

source_name: G1R Oil F2

tag: cell type

value: Oil


title: G1R Oil M2

description: Gene expression data

source_name: G1R Oil M2

tag: gender


title: CpG_G2R_MGC_DEHP_2

description: Chip ID: CpG_G2R_MGC_DEHP_2


title: NRCWE-26 Dose 164 Time Point 28 ID 157

source_name: Left lung

tag: dose

tag: time point (day)

tag: ID

source_name: 11 mouse cell lines

tag: reference

tag: vendor


title: NM-401 Dose 164 Time Point 3 ID 703


title: CpG_G2R_MGC_VZ_3

description: Chip ID: CpG_G2R_MGC_VZ_3

source_name: MIRA-chip in G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero

tag: epigenetic feature

source_name: Input DNA of G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero


title: G1R Oil F3

description: Gene expression data

source_name: G1R Oil F3

tag: g0 mother treatment

tag: genotype

tag: mother generation

tag: fetus generation

tag: germ cell generation


title: G1R Oil F1

description: Gene expression data

source_name: G1R Oil F1


title: CpG_G1R_SPERM_VZ_2

description: Chip ID: CpG_G1R_SPERM_VZ_2

source_name: MIRA-chip in G1R spermatozoa after VZ treatment at the spermatogonia stage in utero

tag: mouse cross to generate experimental fetus

tag: age

value: adult

value: mouse adult spermatozoa

tag: generation of germ cell

source_name: Input DNA of G1R spermatozoa after VZ treatment at the spermatogonia stage in utero


title: CpG_G2R_MGC_VZ_2

description: Chip ID: CpG_G2R_MGC_VZ_2

tag: treatment in utero of g0 mother


title: G1R Oil M1

description: Gene expression data

source_name: G1R Oil M1

tag: cell type


title: CpG_G1R_SPERM_OIL_1

description: Chip ID: CpG_G1R_SPERM_OIL_1

value: oil control


title: NM-401 Dose 54 Time Point 3 ID 696

tag: nanomaterial

tag: gender

value: female

tag: strain

value: Universal Mouse Reference RNA

tag: catelog number


title: CpG_G2R_MGC_DEHP_1

description: Chip ID: CpG_G2R_MGC_DEHP_1


title: NM-401 Dose 18 Time Point 3 ID 692

tag: dose

tag: time point (day)

tag: ID

tag: reference

value: Stratagene, Mississauga, ON, Canada


title: CpG_G2R_MGC_VZ_1

description: Chip ID: CpG_G2R_MGC_VZ_1

tag: epigenetic feature


title: NM-401 Dose 0 Time Point 3 ID 758

tag: vendor


title: G1R Oil M3

description: Gene expression data

source_name: G1R Oil M3

value: primordial germ cells

tag: g0 mother treatment

tag: genotype

tag: mother generation

tag: fetus generation


title: NRCWE-26 Dose 164 Time Point 3 ID 139


title: CpG_G2R_MGC_BPA_3

description: Chip ID: CpG_G2R_MGC_BPA_3

source_name: MIRA-chip in G2R prospermatogoniat hat was derived from G1R prospermatogonia treated with BPA in utero

tag: mouse cross to generate experimental fetus

tag: age

tag: generation of germ cell

value: BPA

source_name: Input DNA of G2R prospermatogoniat hat was derived from G1R prospermatogonia treated with BPA in utero


title: CpG_G2R_MGC_BPA_2

description: Chip ID: CpG_G2R_MGC_BPA_2

tag: cell type

tag: treatment in utero of g0 mother


title: CpG_G2R_MGC_OIL_3

description: Chip ID: CpG_G2R_MGC_OIL_3

source_name: MIRA-chip in G2R prospermatogonia that was derived from G1R prospermatogonia treated with OIL in utero

source_name: Input DNA of G2R prospermatogonia that was derived from G1R prospermatogonia treated with OIL in utero


title: CpG_G1R_SPERM_VZ_1

description: Chip ID: CpG_G1R_SPERM_VZ_1

value: VZ


title: CpG_G2R_MGC_BPA_1

description: Chip ID: CpG_G2R_MGC_BPA_1


city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

description:
Sample name: LNP_M
Long term neural precursor cells day 220 negative for HES5

hyb_protocol: For all array hybridizations, GeneChip PrimeView Human Arrays were used according to the manufacturer's instructions

scan_protocol: Imagaing was perforemd according to the manufacturers instructions.

data_processing: CEL file imported by Partek  version 6.6  Probes to Import: Interrogating Probes  Probe filtering: skip  Algorithm: RMA  Background Correction: RMA Background Correction  Normalization: Quantile Normalization  Log Probes using Base: 2  Probeset Summarization: Median Polish

source_name: H9 in vitro derived neural precursor cells day 220

label_protocol: Standard affymetrix protocol

growth_protocol: for detailed description of culture conditions see Edri et al. 2015

extract_protocol: RNA was extracted using miRNeasy kit (Qiagene)

tag: gender

value: Long term neural precursor cells

tag: hes5 status

value: negative for HES5


title: Imprinting_G2R_SPERM_OIL_2

description: Chip ID: Imprinting_G2R_SPERM_OIL_2

source_name: MIRA-chip in G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero

source_name: Input DNA of G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero


title: NRCWE-26 Dose 54 Time Point 3 ID 138

source_name: Left lung

tag: nanomaterial

tag: strain

tag: dose

tag: catelog number


title: CpG_G2R_MGC_OIL_2

description: Chip ID: CpG_G2R_MGC_OIL_2

tag: epigenetic feature

value: mouse fetal prospermatogonia


description:
Sample name: LNP_P
Long term neural precursor cells day 220 positive for HES5

value: positive for HES5


title: NRCWE-26 Dose 0 Time Point 3 ID 365

tag: time point (day)

tag: ID

source_name: 11 mouse cell lines

tag: reference

tag: vendor


title: Imprinting_G2R_SPERM_VZ_1

description: Chip ID: Imprinting_G2R_SPERM_VZ_1

source_name: MIRA-chip in G2R spermatozoa that was derived from G1R prospermatogonia treatment with VZ in utero

source_name: Input DNA of G2R spermatozoa that was derived from G1R prospermatogonia treatment with VZ in utero


title: plasma-treated Sk-Mel-147 (180 s_24 h) 1

city: Greifswald

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

description: gene expression of plasma-treated SK-Mel-147

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides(Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocolGE1_1105 and Grid: 06247_D_F_20131210) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: plasma-treated SK-Mel-147

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop and Bioanalyzer (Agilent, USA).

growth_protocol: SK-Mel-147 were cultured in Dulbecco`s Modified Eagle Medium (DMEM; Lonza, Switzerland) supplemented with 10 % fetal calf serum (FCS; Sigma, USA), 2 mM L-glutamine, 0.1 mg∙L-1 streptomycin and 100 U∙mL-1 penicillin (Lonza, Switzerland).

extract_protocol: After incubating the cells in plasma-treated medium for 2 h, cells were harvested and RNA isolated according to the manufacturer’s instruction (Bio&SELL, Germany). Then, RNA was reversely transcribed using Transcriptor First Strand Synthesis Kit the cDNA synthesis (Roche, Germany). cDNA was conjugated with a fluorescence dye and applied onto whole genome chips (OaksLab, Germnany)

treatment_protocol: For plasma treatment, cells were sub-cultivated and 1×106 cells mL-1 were seeded in a 60 mm-dish 24 h before plasma treatment. Plasma treatment was conducted with the atmospheric pressure argon plasma jet kinpen 09 (neoplas GmbH, Greifswald, Germany) as previously described [29]. A gas flow rate of 3 standard liters per minute was utilized. An indirect treatment regime was chosen to avoid mechanical stress to the cells due to the gas flow. Therefore, 5 mL of DMEM was treated for the indicated time lengths (ranging from 0 s to 180 s) in a meandering pattern. Afterwards, the cells were immediately exposed to the treated medium.

tag: treatment

value: non-thermal plasma treated sample

tag: cell line


title: Imprinting_G2R_SPERM_VZ_2

description: Chip ID: Imprinting_G2R_SPERM_VZ_2

value: DNA methylation

tag: mouse cross to generate experimental fetus

tag: age


title: CpG_G1R_MGC_DEHP_2

description: Chip ID: CpG_G1R_MGC_DEHP_2

source_name: MIRA-chip in G1R prospermatogonia treated with DEHP in utero

tag: cell type

tag: generation of germ cell

value: DEHP

source_name: Input DNA of G1R prospermatogonia treated with DEHP in utero


title: CpG_G2R_MGC_OIL_1

description: Chip ID: CpG_G2R_MGC_OIL_1

tag: treatment in utero of g0 mother


title: plasma-treated Sk-Mel-147 (180 s_24 h) 2


title: NM-401 Dose 164 Time Point 1 ID 687

tag: gender


title: CpG_G1R_MGC_DEHP_3

description: Chip ID: CpG_G1R_MGC_DEHP_3


title: Imprinting_G1R_SPERM_VZ_1

description: Chip ID: Imprinting_G1R_SPERM_VZ_1

source_name: MIRA-chip in G1R spermatozoa after VZ treatment at the spermatogonia stage in utero

value: FVBxFVB

source_name: Input DNA of G1R spermatozoa after VZ treatment at the spermatogonia stage in utero


description:
Sample name: LRG_M
Late radial glial cells day 80 negative for HES5

source_name: H9 in vitro derived neural precursor cells day 80

value: Late radial glial cells

tag: hes5 status


title: plasma-treated Sk-Mel-147 (60 s_24 h) 1


description:
Sample name: LRG_P
Late radial glial cells day 80 positive for HES5


title: NRCWE-26 Dose 18 Time Point 3 ID 131

tag: nanomaterial

tag: strain


title: NM-401 Dose 54 Time Point 1 ID 676

tag: dose

tag: catelog number


title: NM-401 Dose 0 Time Point 1 ID 746

tag: time point (day)


title: plasma-treated Sk-Mel-147 (60 s_24 h) 2


title: CpG_G1R_MGC_VZ_3

description: Chip ID: CpG_G1R_MGC_VZ_3

source_name: MIRA-chip in G1R prospermatogonia treated with VZ in utero

tag: epigenetic feature

source_name: Input DNA of G1R prospermatogonia treated with VZ in utero


title: plasma-treated Sk-Mel-147 (20 s_24 h) 2


description:
Sample name: MRG_M
Mid radial glial cells day 35 negative for HES5

source_name: H9 in vitro derived neural precursor cells day 35

value: Mid radial glial cells


title: Imprinting_G1R_SPERM_VZ_2

description: Chip ID: Imprinting_G1R_SPERM_VZ_2

value: adult

value: mouse adult spermatozoa


title: Imprinting_G1R_SPERM_OIL_1

description: Chip ID: Imprinting_G1R_SPERM_OIL_1

source_name: MIRA-chip in G1R spermatozoa after OIL treatment at the spermatogonia stage in utero

value: oil control

source_name: Input DNA of G1R spermatozoa after OIL treatment at the spermatogonia stage in utero


title: NM-401 Dose 18 Time Point 1 ID 675

value: female

tag: ID

tag: reference

value: Universal Mouse Reference RNA

value: Stratagene, Mississauga, ON, Canada


title: plasma-treated Sk-Mel-147 (20 s_24 h) 1

tag: treatment


title: plasma-treated Sk-Mel-147 (180 s_6 h) 2

tag: cell line


title: CpG_G1R_MGC_VZ_2

description: Chip ID: CpG_G1R_MGC_VZ_2

tag: mouse cross to generate experimental fetus

value: VZ


title: CpG_G1R_MGC_BPA_1

description: Chip ID: CpG_G1R_MGC_BPA_1

source_name: MIRA-chip in G1R prospermatogonia treated with BPA in utero

tag: age

value: BPA

source_name: Input DNA of G1R prospermatogonia treated with BPA in utero


description:
Sample name: ERG_M
Early radial glial cells day 14 negative for HES5

source_name: H9 in vitro derived neural precursor cells day 14

tag: cell type

value: Early radial glial cells

value: negative for HES5


title: NRCWE-26 Dose 0 Time Point 1 ID 354

source_name: Left lung

source_name: 11 mouse cell lines

tag: vendor


title: CpG_G1R_MGC_BPA_2

description: Chip ID: CpG_G1R_MGC_BPA_2

value: mouse fetal prospermatogonia

tag: generation of germ cell

tag: treatment in utero of g0 mother


title: plasma-treated Sk-Mel-147 (180 s_6 h) 1

value: non-thermal plasma treated sample


description:
Sample name: NE_M
Neuroepithelial cells day 12 negative for HES5

source_name: H9 in vitro derived neural precursor cells day 12

tag: gender

value: Neuroepithelial cells

tag: hes5 status


title: plasma-treated Sk-Mel-147 (60 s_6 h) 1

source_name: plasma-treated SK-Mel-147


description:
Sample name: ERG_P
Early radial glial cells day 14 positive for HES5

value: positive for HES5


title: NRCWE-26 Dose 54 Time Point 1 ID 841

tag: nanomaterial

tag: strain


description:
Sample name: NE_P
Neuroepithelial cells day 12 positive for HES5


title: plasma-treated Sk-Mel-147 (20 s_6 h) 2


title: NM-401 Dose 18 Time Point 28 ID 710

tag: dose

tag: catelog number


title: CpG_G1R_MGC_BPA_3

description: Chip ID: CpG_G1R_MGC_BPA_3

tag: epigenetic feature

value: DNA methylation


title: human embryonic stem cell line H9

description:
Sample name: hESC
human embryonic stem cell line H9

source_name: human embryonic stem cells

value: H9 embryonic stem cells


title: Imprinting_G2R_SPERM_OIL_1

description: Chip ID: Imprinting_G2R_SPERM_OIL_1

source_name: MIRA-chip in G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero

value: FVBxFVB

source_name: Input DNA of G2R spermatozoa that was derived from G1R prospermatogonia treatment with OIL in utero


title: NRCWE-26 Dose 164 Time Point 1 ID 790

tag: time point (day)

tag: ID


title: plasma-treated Sk-Mel-147 (60 s_6 h) 2

tag: treatment


title: Imprinting_G2R_MGC_DEHP_2

description: Chip ID: Imprinting_G2R_MGC_DEHP_2

source_name: MIRA-chip in G21R prospermatogonia that was derived from G1R prospermatogonia treated with DEHP in utero

value: DEHP

source_name: Input DNA of G21R prospermatogonia that was derived from G1R prospermatogonia treated with DEHP in utero


title: NM-401 Dose 0 Time Point 28 ID 770

tag: reference


title: CpG_G1R_MGC_VZ_1

description: Chip ID: CpG_G1R_MGC_VZ_1

source_name: MIRA-chip in G1R prospermatogonia treated with VZ in utero

tag: mouse cross to generate experimental fetus


title: Imprinting_G2R_MGC_DEHP_3

description: Chip ID: Imprinting_G2R_MGC_DEHP_3

tag: age


description:
Sample name: MRG_P
Mid radial glial cells day 35 positive for HES5

tag: cell type

value: Mid radial glial cells


title: plasma-treated Sk-Mel-147 (180 s_3 h) 2

tag: cell line


title: CpG_G1R_MGC_OIL_3

description: Chip ID: CpG_G1R_MGC_OIL_3

source_name: MIRA-chip in G1R prospermatogonia treated with OIL in utero

tag: generation of germ cell

value: oil control

source_name: Input DNA of G1R prospermatogonia treated with OIL in utero


title: plasma-treated Sk-Mel-147 (180 s_3 h) 1


title: NM-401 Dose 54 Time Point 28 ID 716

value: female

tag: vendor


title: plasma-treated Sk-Mel-147 (60 s_3 h) 2


title: NRCWE-26 Dose 18 Time Point 28 ID 150

tag: gender

value: Universal Mouse Reference RNA


title: Imprinting_G1R_SPERM_OIL_2

description: Chip ID: Imprinting_G1R_SPERM_OIL_2

source_name: MIRA-chip in G1R spermatozoa after OIL treatment at the spermatogonia stage in utero

value: adult

value: mouse adult spermatozoa

tag: treatment in utero of g0 mother


title: plasma-treated Sk-Mel-147 (60 s_3 h) 1


title: NRCWE-26 Dose 0 Time Point 28 ID 374

tag: nanomaterial

value: Stratagene, Mississauga, ON, Canada


title: plasma-treated Sk-Mel-147 (20 s_6 h) 1


title: NM-401 Dose 164 Time Point 28 ID 721

tag: strain


title: NRCWE-26 Dose 164 Time Point 28 ID 270

tag: dose


title: CpG_G1R_MGC_DEHP_1

description: Chip ID: CpG_G1R_MGC_DEHP_1

source_name: MIRA-chip in G1R prospermatogonia treated with DEHP in utero

source_name: Input DNA of G1R prospermatogonia treated with DEHP in utero


title: CpG_G1R_MGC_OIL_2

description: Chip ID: CpG_G1R_MGC_OIL_2


title: plasma-treated Sk-Mel-147 (20 s_3 h) 2


title: NRCWE-26 Dose 54 Time Point 28 ID 156

tag: catelog number


title: NM-401 Dose 54 Time Point 3 ID 699


title: plasma-treated Sk-Mel-147 (20 s_3 h) 1


title: plasma-treated Sk-Mel-147 (180 s_1 h) 1


title: NM-401 Dose 0 Time Point 3 ID 757


title: NRCWE-26 Dose 18 Time Point 1 ID 783


title: plasma-treated Sk-Mel-147 (60 s_1 h) 2


title: plasma-treated Sk-Mel-147 (60 s_1 h) 1


title: plasma-treated Sk-Mel-147 (180 s_1 h) 2


title: NM-401 Dose 164 Time Point 3 ID 705


title: plasma-treated Sk-Mel-147 (20 s_1 h) 2


title: NRCWE-26 Dose 18 Time Point 3 ID 128


title: NRCWE-26 Dose 164 Time Point 3 ID 142


title: CpG_G1R_MGC_OIL_1

description: Chip ID: CpG_G1R_MGC_OIL_1

tag: epigenetic feature


title: NRCWE-26 Dose 0 Time Point 3 ID 366

tag: time point (day)


title: plasma-treated Sk-Mel-147 (20 s_1 h) 1


title: H2O2-treated Sk-Mel-147 (24 h) 2

description: gene expression of H2O2-treated control

source_name: SK-Mel-147 positive control

value: positive control


title: NRCWE-26 Dose 54 Time Point 3 ID 136

tag: ID


title: H2O2-treated Sk-Mel-147 (24 h) 1

description: gene expression of H2O2-treated control

tag: treatment


title: NM-401 Dose 18 Time Point 1 ID 672

tag: reference


title: H2O2-treated Sk-Mel-147 (6 h) 1

description: gene expression of H2O2-treated control


title: H2O2-treated Sk-Mel-147 (6 h) 2

description: gene expression of H2O2-treated control


title: NM-401 Dose 0 Time Point 1 ID 745


title: NRCWE-26 Dose 164 Time Point 1 ID 792


title: NM-401 Dose 54 Time Point 1 ID 681


title: H2O2-treated Sk-Mel-147 (3 h) 2

description: gene expression of H2O2-treated control


title: Imprinting_G2R_MGC_DEHP_1

description: Chip ID: Imprinting_G2R_MGC_DEHP_1

tag: mouse cross to generate experimental fetus


title: NM-401 Dose 164 Time Point 1 ID 686


title: H2O2-treated Sk-Mel-147 (3 h) 1

description: gene expression of H2O2-treated control


title: NRCWE-26 Dose 54 Time Point 1 ID 788


title: NRCWE-26 Dose 18 Time Point 1 ID 782


title: Imprinting_G2R_MGC_VZ_2

description: Chip ID: Imprinting_G2R_MGC_VZ_2

source_name: MIRA-chip in G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero

tag: age

value: VZ

source_name: Input DNA of G21R prospermatogonia that was derived from G1R prospermatogonia treated with VZ in utero


title: Imprinting_G2R_MGC_BPA_2

description: Chip ID: Imprinting_G2R_MGC_BPA_2

source_name: MIRA-chip in G2R prospermatogoniat hat was derived from G1R prospermatogonia treated with BPA in utero

tag: cell type

value: mouse fetal prospermatogonia

value: BPA

source_name: Input DNA of G2R prospermatogoniat hat was derived from G1R prospermatogonia treated with BPA in utero


title: untreated SK-Mel-147 1

description: gene expression of untreated control

source_name: SK-Mel-147 untreated control

value: control

tag: cell line


title: Human_fibroblast_P18

status: Public on Feb 17 2015

city: Brescia

first: Nadia

last: Cattane

state: BS

address: Viale Europa 11

department: Department of Translational and Molecular Medicine

institute: University of Brescia

description: Cell line was cultured until the 5th passage

hyb_protocol: Following fragmentation, 5.5 µg of ssDNA were hybridized for 20 hours at 48°C on Human Gene 1.1 ST Array Strip. Array Strips were washed and stained using the GeneAtlas instrument.

scan_protocol: Array Strips were scanned using the GeneAtlas instrument.

data_processing: Data processing was performed using R/Bioconductor. Oligo package was used to read CEL files and compute the log intensities of gene expression by exploiting Robust Multi-array Average (RMA) algorithm. Linear models fitting (LmFit) and Empirical Bayes method (eBayes) from the BioConductor limma package were used to test the differences in mRNA levels.

source_name: patient 18

label_protocol: ssDNA was labelled with biotin according to the standard Affymetrix protocol (GeneAtlasTM WT Expression Kit User Manual)

growth_protocol: Skin biopsies (3 mm2) were collected under local anaesthesia from the scapular region using aseptic conditions and immediately immersed in a saline solution (PBS). All primary cultures were grown in Eagle’s minimum essential medium supplemented with 10% of foetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 μg/ml), non-essential amino acids (1% v/v) and glutamine (1% v/v) under optimal conditions (37° C, 5% CO2).

extract_protocol: RNA from fibroblasts was extracted using the NucleoSpin kit (MACHEREY-NAGEL, Düren , Germany) according to the manufacturer’s instructions.

tag: disease state

value: schizophrenia

tag: tissue

value: skin

value: fibroblast

value: Female


title: Human_fibroblast_P20

source_name: patient 20

tag: gender


title: Human_fibroblast_P19

source_name: patient 19


title: NRCWE-26 Dose 0 Time Point 1 ID 350

source_name: Left lung

source_name: 11 mouse cell lines

tag: vendor


title: Human_fibroblast_P17

source_name: patient 17


title: Imprinting_G2R_MGC_OIL_3

description: Chip ID: Imprinting_G2R_MGC_OIL_3

source_name: MIRA-chip in G2R prospermatogonia that was derived from G1R prospermatogonia treated with OIL in utero

value: DNA methylation

tag: generation of germ cell

tag: treatment in utero of g0 mother

source_name: Input DNA of G2R prospermatogonia that was derived from G1R prospermatogonia treated with OIL in utero


title: Human_fibroblast_P16

source_name: patient 16


title: Imprinting_G2R_MGC_BPA_3

description: Chip ID: Imprinting_G2R_MGC_BPA_3


title: Imprinting_G2R_MGC_OIL_2

description: Chip ID: Imprinting_G2R_MGC_OIL_2


title: Imprinting_G2R_MGC_OIL_1

description: Chip ID: Imprinting_G2R_MGC_OIL_1


title: Imprinting_G2R_MGC_VZ_3

description: Chip ID: Imprinting_G2R_MGC_VZ_3


title: Human_fibroblast_P15

source_name: patient 15


title: Human_fibroblast_P8

source_name: patient 8

value: Male


title: Human_fibroblast_P14

source_name: patient 14


title: Imprinting_G2R_MGC_BPA_1

description: Chip ID: Imprinting_G2R_MGC_BPA_1


title: Human_fibroblast_P12

source_name: patient 12


title: Human_fibroblast_P11

source_name: patient 11


title: Human_fibroblast_P13

source_name: patient 13