title: Normal_adjacent_tissue_3

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

institute: Sun Yat-sen Memorial Hospital

description:
NAT3
Gene expression without treatment.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using the Gene Expression Hybridization Kit (Agilent) in the Hybridization Oven (Agilent), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon) with the Gene Expression Wash Buffer Kit (Agilent), following the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent) with default settings, Dye channel: Green, Scan resolution=3 μm, 20 bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by the Quantile algorithm, GeneSpring Software 11.0 (Agilent).

source_name: Normal adjacent tissue, patient 3

label_protocol: Total RNA was then amplified and labeled by the Low Input Quick Amp Labeling Kit, One-Color (Agilent), following the manufacturer's instructions. Labeled cRNA were purified by the RNeasy mini kit (QIAGEN).

extract_protocol: Total RNA from cells was isolated using Trizol reagent (Life Technologies). RNA purity and integrity were analyzed by Agilent Bioanalyzer 2100 (Agilent). Qualified total RNA was further purified by the RNeasy mini kit (QIAGEN) and RNase-free DNase set (QIAGEN).

treatment_protocol: Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were used directly for total RNA extraction.

value: adjacent normal bladder

tag: patient


title: MPM_infected_2h_rep2

status: Public on Mar 15 2013

type: RNA

city: Beijing

first: Feng

last: Xue

state: Beijing

address: No. 95, Yong'an Road

department: Department of Microbiology and Parasitology

country: China

institute: Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University

hyb_protocol: The labeled samples were hybridized to the OneArrayTM whole genome microarray with Phalanx hybridization buffer using cover slides. After overnight hybridization at 50°C, non-specific binding targets were washed away using 3 different washing steps.

scan_protocol: The slides were dried using centrifugation and scanned using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed using GenePix Pro 6.0 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the immediate surroundings. Spots which flag <0 and SNR <3, and the control probes were filtered out.

data_processing: Spots that passed the above-mentioned criteria were normalized using quantile normalization according to the manufacturer’s recommendation and tested for differential expression. The differential expressed genes were further analyzed using Agilent GeneSpring GX software (version 10.0). Considering that primary cells were a mixture of several related cell types with limited purity, regulated genes with more than 3 folds (P<0.05) of up-regulation or down-regulation were defined as significantly regulated genes.

molecule: total RNA

organism: Mus musculus

label_protocol: For each sample, about 10 μg of total RNA was mixed with 600 ng of random hexamer primers (TaKaRa, Otsu, Japan) and denaturalized at 65℃ for 5 min. Then the first strand cDNA was synthesized using 2 μl (400 U) SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) according to the protocol recommended by the manufacturer. The double strand cDNA (ds cDNA) sample was then synthesized using 2nd Strand Synthesis section of M-MLV RTase cDNA Synthesis Kit (TaKaRa, Otsu, Japan) according to the manufacturers’ instructions. Following RNase H (Invitrogen, Carlsbad, CA) and RNase A (Ambion, Texas) digestion for 1 h, ds cDNA sample was purified using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany) according to QIAquick Spin handbook. The double-stranded cDNA templates were labeled using Amersham Mono-functional Cy5 CyDye.

growth_protocol: Murine peritoneal macrophages (MPMs) were isolated from male BALB/c mice (6 to 8 weeks old) by washing the peritoneal cavities with cold RPMI 1640 medium. Macrophages were seeded in 75cm2 tissue culture flasks (Corning. Inc., Big Flats, NY) and the cell numbers were counted in a haemocytometer. The cells were cultured in RPMI 1640 medium (supplemented with 10% heat-inactivated fetal bovine serum, 100 μg/ml of penicillin, and 100 μg/ml of streptomycin) for 2 h at 37°C under a humidified atmosphere containing 5% CO2. After the pre-incubation, non-adherent cells were removed gently by washing with PBS (0.01M, pH 7.4), and the purity of the remaining macrophages was tested by Wright’s staining. Human peripheral blood monocytes (HBMs) were isolated from 6 healthy donors using standard Ficoll-Hypaque gradient centrifugation as previously described. The monocytes were seeded and counted according to the above-mentioned protocol of MPM, then pre-incubated overnight at 37°C under a humidified atmosphere containing 5% CO2. After the pre-incubation, the monocytes was thoroughly washed with autocleaved PBS to remove non-adherent cells, and then continuously incubated for 5 days in a medium containing 500 U/ml of granulocyte-macrophage colony stimulating factor (GM-CSF; eBioscience, CA, USA) to differentiate the cells into macrophages.

extract_protocol: At sample harvesting, MPM and HBM cell cultures were washed 3 times using autocleaved PBS to remove leptospiral cells. The total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA), then purified using RNeasy Mini Kit (QIAGEN, Hilden, Germany) with on-column DNase digestion (QIAGEN, Hilden, Germany) according to the RNeasy Mini handbook. RNA quantity and integrity was determined using RNA 6000 Nano Laboratory-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The MPM and HBM cell cultures were washed 3 times with autocleaved PBS, renewed with new medium without antibiotics, and further cultured for 12 h before infection. Leptospiral cells were harvested by centrifugation at 8,000 g for 10 min at 20℃, and then washed twice with PBS. The bacterial pellets were re-suspended in 37℃ RPMI 1640 medium to final concentration of 108 per ml. Then 10 ml of leptospiral suspension (10^9) were added into 10^7 cells (bacteria: cell = 100:1) and incubated at 37°C under a humidified atmosphere containing 5% CO2. Cell samples were collected at 3 intervals (1, 2 and 4 hours) respectively in the cell infection models, and 3 biological replicates were designed for each sample. Previous cytokine mRNA kinetic expression research showed that most of the cytokine transcripts can be detected as early as 1h after infection in animal infection model, which indicated that the rapid gene regulation of innate immune response can be detected within 4-hour window period in this study. The MPM and HBM cell cultures not infected by L. interrogans were used as negative controls.

tag: strain

value: BALB/c

tag: gender

value: male

tag: age

value: 6-8 wks

tag: cell type

value: Murine peritoneal macrophages (MPM)

tag: infected with

value: pathogenic Leptospira

tag: time point

value: 2h after infection


title: ST88-14 Cell Replicate 2

city: Detroit

first: Michael

middle: A

last: Tainsky

state: MI

address: 110 E Warren  Room 311

department: Center for Molecular Medicine and Genetics

country: USA

institute: Wayne State University

description: Comparison 1

hyb_protocol: standard hybridization methods described by the manufacturer

scan_protocol: Agilent Technologies Scanner G2505B US45102939

data_processing: Images were quantified using Agilent Feature Extraction Software. Microarray data was normalized within arrays using loess normalization followed by normalizing between arrays using quantile normalization as implemented in the Bioconductor library limma.

organism: Homo sapiens

source_name: Malignant Peripheral Nerve Sheath Tumor

label_protocol: Labeled targets were synthesized from the purified RNA using linear amplification and indirect labeling by incorporation of aminoallyl-labeled nucleotide with the TargetAmp 1-round aminoallyl-aRNA amplification kit 101 (Epicentre Technologies), which was subsequently modified by the covalent addition of Alexa dye (Epicentre Technologies).

growth_protocol: Human MPNST ST88-14(Nf1-/-) cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 5% fetal bovine serum (Hyclone Laboratories). Normal human Schwann cell lines were cultured in DMEM supplemented with 10% FBS, 2 μM forskolin, and 10nM heregulin.

extract_protocol: Total RNA was extracted from the cells using RNeasy mini Kit (#74106, Qiagen) with genomic DNA removal by RNase-Free DNase Set (#79254, Qiagen).  RNA integrity was determined by an Agilent Bioanalyzer 2100.

treatment_protocol: normal culture

tag: cell line

tag: protocol

source_name: Universal Human Reference RNA

tag: tissue

value: mixture of 10 human cell lines


title: Bladder_cancer_tissue_3

description:
BCa3
Gene expression without treatment.

source_name: Bladder cancer tissue, patient 3

value: bladder cancer


title: Donor 113-Neg versus Donor 113-Pos

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Paired RNA samples from p24+ (latently infected) and p24- (uninfected) cells from 4 donors (4 biological replicas) were labeled using a two-color design with dye-swap control. Thus, paired RNA samples from p24+ cells and p24- cells of two donors were labeled with Cy3 and Cy5, respectively; whereas, paired RNA samples from p24+ cells and p24- cells of the other two donors were labeled with Cy5 and Cy3, respectively. Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on 4 Whole Human Genome Microarray 44K (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2505B microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 10 micrometer resolutions. Data was extracted using Feature Extraction Software version 10.5.1.1 (Agilent Technologies).

data_processing: Within-array dye effects were corrected by the 'loess' normalization method, while the ”scale” method was applied to standardize the log2 fold change distributions across the arrays, by using the median-absolute-value as scale estimator. No background subtraction was performed prior to normalization. Positive and negative microarray control features were not used to compute the 'loess' smoothing and were not considered in subsequent analyses. Data pre-processing was performed using the R/Bioconductor package 'limma'.

source_name: CD4+ cells from healthy donor: 113 ; HIV infection status: NEGATIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy5, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 mircrogram of Cy5-labeled sample was mixed with control targets (G4112F, Agilent Technologies).

extract_protocol: Cells were washed with PBS, fixed in 1% paraformaldehyde (PFA, Sigma-Aldrich) in PBS at 4°C for 20 minutes, permeabilized with 0.1% saponin (Sigma-Aldrich) for 5 minutes at 4°C, stained for the detection of intracellular HIV-1 p24gag with FITC-labeled KC57 antibody (Beckman Coulter) for 20 minutes on ice, and finally washed twice with ice-cold PBS. Latently infected (HIV-1 p24+) and uninfected cells (HIV-1 p24-) from the same culture were then sorted by Flow Cytometry with a DAKO-Cytomation MoFlo High Speed cell sorter. Total RNA was isolated from sorted cells using the RNeasy FFPE Kit (Qiagen) following manufacturer’s protocol with a few modifications. The treatment with xylene and the subsequent ethanol precipitation step were omitted. The incubation steps at 55°C, and at 80°C were shortened (12 minutes instead of 15) to reduce RNA degradation. RNA was eluted from the column with RNase-free water, quantified by NanoDrop, and stored at -80°C. RNA quality was confirmed by UV spectrophotometry and by analysis with an Agilent 2100 Bioanalyzer.

treatment_protocol: Anonymized cells were obtained from an HIV-1 negative, healthy volunteer. CD4+ T cells latently infected with HIV-1 were generated as previously described (Marini et al., 2008). Briefly, PBMCs were isolated from peripheral blood of healthy volunteers by Ficoll-Paque PLUS (GE Healthcare). Total CD4+ T cells were enriched by negative selection (CD4+ T Cell Isolation Kit from Miltenyi Biotec), and activated in plates coated with anti-CD3 (eBioscience) and anti-CD28 (Beckman Coulter) in the presence of 50 U/ml IL-2 (Roche Biochemicals). Activated cells were infected 3 days post-activation with 5,000 50% tissue culture infective dose (TCID50) per 1,000,000 cells of gradient-purified HIV-1IIIB (Advanced Biotechnologies Inc.) for 2 h at 37°C. Finally, cells were plated at 0.5x1,000,000 cells/ml in fresh RPMI 1640 supplemented with 1% penicillin/streptomycin, 1% glutamine, 1% nonessential amino acids, 1% sodium pyruvate, 50 uMolar 2-mercaptoethanol (all from Invitrogen), 50 ug/ml gentamicin (Sigma), 10% human AB serum (Cellgro), 50 U/ml IL-2, and cultured until 10-15% cells were infected, followed by intracellular FACS on HIV-1 p24gag. Cells were then allowed to rest for a week in the presence of 1 ng/ml IL-7 (R&D Systems).

value: CD4+ lymphocytes purified from PBMCs

tag: hiv-1 infection status

value: negative

tag: healthy donor

source_name: Resting primary CD4+ T cells generated in vitro from healthy donor: 113 ; HIV infection status: POSITIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy3, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 mircrogram of Cy3-labeled sample was mixed with control targets (G4112F, Agilent Technologies).

value: positive


title: MPM_uninfected_control_rep2

value: none (uninfected control)


title: Normal Human Schwann Cell Replicate 2

description: Comparison 1

source_name: Human Schwann cell

value: HSC


title: Normal Human Schwann Cell Replicate 3

description: Comparison 1


title: Bladder_cancer_tissue_2

description:
BCa2
Gene expression without treatment.

source_name: Bladder cancer tissue, patient 2


title: Normal_adjacent_tissue_2

description:
NAT2
Gene expression without treatment.

source_name: Normal adjacent tissue, patient 2


title: Donor 3-Pos versus Donor 3-Neg

source_name: Resting primary CD4+ T cells generated in vitro from healthy donor: 3 ; HIV infection status: POSITIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy5, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 microgram of Cy5-labeled sample was mixed with control targets (G4112F, Agilent Technologies).

source_name: CD4+ cells from healthy donor: 3 ; HIV infection status: NEGATIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second-strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. The labeled cRNA was purified using RNeasy mini kit (Qiagen) and followed by quantification on both concentrations of cRNA and dye labeled. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 microgram of each sample labeled with Cy3 was mixed with control targets (G4112F, Agilent Technologies).


title: MPM_uninfected_control_rep1


title: ST88-14 Cell Replicate 1

description: Comparison 1


title: Normal Human Schwann Cell Replicate 1

description: Comparison 1


title: Normal_adjacent_tissue_1

description:
NAT1
Gene expression without treatment.

source_name: Normal adjacent tissue, patient 1

value: female


title: Cdc5l_72h_shRNAtrasient #1

status: Public on Mar 14 2013

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: shRNA transient transfection

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 246 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: shRNA transient transfection

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: The samples were dissolved in the well with TRIzol reagent 1 mL.  They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample.  They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate  for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun  for 5 minutes, then the ethanol was dumped out.  Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer.  ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

treatment_protocol: Cells (2,000,000 cells) were co-transfected with 1.6ug of shRNA expression vector and 0.4ug of expression vector for puromycine resistant gene and plated onto 1 well of 6 well plate. After 24h and 48h, medium was changed to medium containing puromycine (1.5ug/ml). At 72 hours after the transfection, the cells were harvested in Trizol.For time couse experiments, cell were harvetsed  at 48h, 72h, and 96h. For rescue experiments, NIA mouse ES cell bank clone were co-trasnfeteced with shRNA expression vector and expression vector for Blasticidin S and cultured in presence of puromycine (0.5 or 1.5 ug/ml) and presence/absence of doxycyclin (0.2 ug/ml). Blasticidin S (40 or 100 ug/ml) was used for selection. ZHtc6 cells were cultured with doxycyclin and Zeocin (20 ug/ml) and co-transfected wuith shRNA expression vector and expression vector for puromycine resistant gene in presence/absence of doxycyclin. puromycine (1.5 ug/ml) was used for selection.

value: Embryonic Stem Cells

tag: individual identifier

value: Cdc5l shRNA transient transfection , 72h, Replictaion 1; Cdc5l_72h_shRNAtrasient #1; 251508710879A3

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: Cdc5l_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Cdc5l shRNA transient transfection , 72h, Replictaion 2; Cdc5l_72h_shRNAtrasient #2; 251508710879A4


title: Bladder_cancer_tissue_1

description:
BCa1
Gene expression without treatment.

source_name: Bladder cancer tissue, patient 1


title: Adult, acetone, replicate B

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by Quantile normalization and baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.

organism: Daphnia magna

source_name: Whole daphnia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All experiments were performed using a well-characterized single clone of Daphnia magna (Clone F), maintained indefinitely as pure parthenogenetic cultures. Individual or bulk cultures of 10 animals/L were maintained in ASTM hard synthetic water. Individual or bulk cultures were fed daily with Chorella vulgaris Beijerinck (5x105 cells/mL, respectively, corresponding to 1.8 mg C/mL; [24]). C. vulgaris was grown axenically in Jaworski/Euglena gracilis 1: 1 medium (CCAP, 1989). The culture medium was changed every day, and neonates were removed within 24 h. Photoperiod was set to 14h light: 10h dark cycle and temperature at 20 ± 1oC.

extract_protocol: Qiagen Rneasy

treatment_protocol: Groups of twenty juveniles < 24 h old were exposed to selected exposure levels in 0.5 L of ASTM hard water with food present (5x105 cells/mL of C. vulgaris) during 3 consecutive days. Contaminants were dosed using acetone as a carrier (0.1 ml/L). Treatments were quadruplicated. At the end of exposure the 20 juveniles of each treatment per replicate were collected, pooled in an eppendorf, flash- frozen in liquid N2 and preserved at -80 oC until RNA extraction.For adult reproductive tests, exposures started with 8-9 day old gravid females, which were exposed during three consecutive broods to the studied chemicals (10-14 days). Just after releasing their fourth clutch into the brood pouch, eggs were gently flushed from the brood pouch and females were immediately flash- frozen in liquid N2 and preserved at 80oC until RNA extraction.

tag: Stage

value: adult

tag: treatment

value: acetone


title: Tcfap2c_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tcfap2c shRNA transient transfection , 72h, Replictaion 2; Tcfap2c_72h_shRNAtrasient #2; 251508710878A4


description: shRNA transient transfection

value: Nanog shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNanog; Nanog_Dox-_shRNA_04-22-2010_72h_shRNAtrasient #2; 251508710797A4


title: Aff1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Aff1 shRNA transient transfection , 72h, Replictaion 1; Aff1_72h_shRNAtrasient #1; 251508710878A1


title: Aire_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Aire shRNA transient transfection , 72h, Replictaion 1; Aire_72h_shRNAtrasient #1; 251508710879A1


title: Aff1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Aff1 shRNA transient transfection , 72h, Replictaion 2; Aff1_72h_shRNAtrasient #2; 251508710878A2


title: Tcfap2c_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tcfap2c shRNA transient transfection , 72h, Replictaion 1; Tcfap2c_72h_shRNAtrasient #1; 251508710878A3


title: Esrrb_72h_shRNAtrasient #2

description: Esrrb_shRNA 72h

source_name: Esrrb_shRNA 72h

value: ES Cells

value: male

value: Esrrb shRNA transient transfection , 72h, Replictaion 2; Esrrb_72h_shRNAtrasient #2; 251508710826A4


title: Aire_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Aire shRNA transient transfection , 72h, Replictaion 2; Aire_72h_shRNAtrasient #2; 251508710879A2


title: Esrrb_72h_shRNAtrasient #1

description: Esrrb_shRNA 72h

value: Esrrb shRNA transient transfection , 72h, Replictaion 1; Esrrb_72h_shRNAtrasient #1; 251508710826A3


description: shRNA transient transfection

value: Embryonic Stem Cells

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNan; Nanog_Dox-_control_04-22-2010_72h_shRNAtrasient #2; 251508710795A4


description: shRNA transient transfection

value: Nanog shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNanog; Nanog_Dox+_shRNA_04-22-2010_72h_shRNAtrasient #1; 251508710797A1

value: Universale Mouse Reference


description: shRNA transient transfection

value: Nanog shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNanog; Nanog_Dox+_shRNA_04-22-2010_72h_shRNAtrasient #2; 251508710797A2


title: Zfp292_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zfp292 shRNA transient transfection , 72h, Replictaion 2; Zfp292_72h_shRNAtrasient #2; 251508710788A2


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNan; Nanog_Dox+_control_04-22-2010_72h_shRNAtrasient #1; 251508710795A1


title: Stat3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Stat3 shRNA transient transfection , 72h, Replictaion 2; Stat3_72h_shRNAtrasient #2; 251508710788A1


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNan; Nanog_Dox-_control_04-22-2010_72h_shRNAtrasient #1; 251508710795A3


title: Ctnnb1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Ctnnb1 shRNA transient transfection , 72h, Replictaion 2; Ctnnb1_72h_shRNAtrasient #2; 251508710788A3


title: Zfp281_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zfp281 shRNA transient transfection , 72h, Replictaion 1; Zfp281_72h_shRNAtrasient #1; 251508710780A1


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNan; Nanog_Dox+_control_04-22-2010_72h_shRNAtrasient #2; 251508710795A2


title: Pou5f1-N_96h_shRNAtrasient #2

description: shRNA transient transfection

value: Pou5f1 96h shRNA transient transfection, time course experiments , 96h, Replicta; Pou5f1-N_96h_shRNAtrasient #2; 251508710787A4


title: Zscan4c_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zscan4c shRNA transient transfection , 72h, Replictaion 1; Zscan4c_72h_shRNAtrasient #1; 251508710788A4


title: Control_04-08-2010_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Control shRNA transient transfection , 72h, Replictaion 1; Control_04-08-2010_72h_shRNAtrasient #1; 251508710781A3


title: Control_04-08-2010_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Control shRNA transient transfection , 72h, Replictaion 2; Control_04-08-2010_72h_shRNAtrasient #2; 251508710781A4


title: Pou5f1-N_48h_shRNAtrasient #2

description: shRNA transient transfection

value: Pou5f1 72h shRNA transient transfection for batch control, time course experimen; Pou5f1-N_48h_shRNAtrasient #2; 251508710787A2


title: Lin28_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Lin28 shRNA transient transfection , 72h, Replictaion 1; Lin28_72h_shRNAtrasient #1; 251508710779A3


title: Cdyl_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Cdyl shRNA transient transfection , 72h, Replictaion 2; Cdyl_72h_shRNAtrasient #2; 251508710777A2


title: Eomes_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Eomes shRNA transient transfection , 72h, Replictaion 2; Eomes_72h_shRNAtrasient #2; 251508710777A4

value: Universale Mouse Reference


title: Zfp281_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zfp281 shRNA transient transfection , 72h, Replictaion 2; Zfp281_72h_shRNAtrasient #2; 251508710780A2


title: Foxd3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Foxd3 shRNA transient transfection , 72h, Replictaion 1; Foxd3_72h_shRNAtrasient #1; 251508710779A1


title: Pou5f1-N_96h_shRNAtrasient #1

description: shRNA transient transfection

value: Pou5f1 96h shRNA transient transfection, time course experiments , 96h, Replicta; Pou5f1-N_96h_shRNAtrasient #1; 251508710787A3


title: Fbxo15_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Fbxo15 shRNA transient transfection , 72h, Replictaion 1; Fbxo15_72h_shRNAtrasient #1; 251508710778A3


description: shRNA transient transfection

value: Nanog shRNA transient transfection, rescue experiment using ES[MC1R(20):tetNanog; Nanog_Dox-_shRNA_04-22-2010_72h_shRNAtrasient #1; 251508710797A3


title: Pou5f1-N_48h_shRNAtrasient #1

description: shRNA transient transfection

value: Pou5f1 72h shRNA transient transfection for batch control, time course experimen; Pou5f1-N_48h_shRNAtrasient #1; 251508710787A1


title: Etv1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Etv1 shRNA transient transfection , 72h, Replictaion 1; Etv1_72h_shRNAtrasient #1; 251508710778A1


title: Fbxo15_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Fbxo15 shRNA transient transfection , 72h, Replictaion 2; Fbxo15_72h_shRNAtrasient #2; 251508710778A4


title: Foxd3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Foxd3 shRNA transient transfection , 72h, Replictaion 2; Foxd3_72h_shRNAtrasient #2; 251508710779A2


title: Lin28_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Lin28 shRNA transient transfection , 72h, Replictaion 2; Lin28_72h_shRNAtrasient #2; 251508710779A4


title: Cdyl_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Cdyl shRNA transient transfection , 72h, Replictaion 1; Cdyl_72h_shRNAtrasient #1; 251508710777A1


title: Dmrt1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dmrt1 shRNA transient transfection , 72h, Replictaion 2; Dmrt1_72h_shRNAtrasient #2; 251508710776A2


title: Btbd14b_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Btbd14b shRNA transient transfection , 72h, Replictaion 1; Btbd14b_72h_shRNAtrasient #1; 251508710776A3


title: Foxg1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Foxg1 shRNA transient transfection , 72h, Replictaion 1; Foxg1_72h_shRNAtrasient #1; 251508710775A3


title: Grhl2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Grhl2 shRNA transient transfection , 72h, Replictaion 2; Grhl2_72h_shRNAtrasient #2; 251508710775A2


title: Btbd14b_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Btbd14b shRNA transient transfection , 72h, Replictaion 2; Btbd14b_72h_shRNAtrasient #2; 251508710776A4

value: Universale Mouse Reference


title: D1pas1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: D1pas1 shRNA transient transfection , 72h, Replictaion 2; D1pas1_72h_shRNAtrasient #2; 251508710774A4


title: Dmrt1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dmrt1 shRNA transient transfection , 72h, Replictaion 1; Dmrt1_72h_shRNAtrasient #1; 251508710776A1


title: Etv1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Etv1 shRNA transient transfection , 72h, Replictaion 2; Etv1_72h_shRNAtrasient #2; 251508710778A2


title: Grhl2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Grhl2 shRNA transient transfection , 72h, Replictaion 1; Grhl2_72h_shRNAtrasient #1; 251508710775A1


title: Gbx2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Gbx2 shRNA transient transfection , 72h, Replictaion 1; Gbx2_72h_shRNAtrasient #1; 251508710773A1


title: Control-04-01-2010_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Control shRNA transient transfection , 72h, Replictaion 2; Control-04-01-2010_72h_shRNAtrasient #2; 251508710772A4


title: Gbx2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Gbx2 shRNA transient transfection , 72h, Replictaion 2; Gbx2_72h_shRNAtrasient #2; 251508710773A2


title: D1pas1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: D1pas1 shRNA transient transfection , 72h, Replictaion 1; D1pas1_72h_shRNAtrasient #1; 251508710774A3


title: Foxg1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Foxg1 shRNA transient transfection , 72h, Replictaion 2; Foxg1_72h_shRNAtrasient #2; 251508710775A4


title: Ebf1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Ebf1 shRNA transient transfection , 72h, Replictaion 2; Ebf1_72h_shRNAtrasient #2; 251508710774A2


title: Dmrt2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dmrt2 shRNA transient transfection , 72h, Replictaion 1; Dmrt2_72h_shRNAtrasient #1; 251508710773A3


title: Ebf1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Ebf1 shRNA transient transfection , 72h, Replictaion 1; Ebf1_72h_shRNAtrasient #1; 251508710774A1


title: Dmrt2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dmrt2 shRNA transient transfection , 72h, Replictaion 2; Dmrt2_72h_shRNAtrasient #2; 251508710773A4


title: Eomes_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Eomes shRNA transient transfection , 72h, Replictaion 1; Eomes_72h_shRNAtrasient #1; 251508710777A3


title: Dppa2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dppa2 shRNA transient transfection , 72h, Replictaion 2; Dppa2_72h_shRNAtrasient #2; 251508710771A2


title: Batf3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Batf3 shRNA transient transfection , 72h, Replictaion 2; Batf3_72h_shRNAtrasient #2; 251508710769A4

value: Universale Mouse Reference


title: Sox1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sox1 shRNA transient transfection , 72h, Replictaion 2; Sox1_72h_shRNAtrasient #2; 251508710772A2


title: Sox1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sox1 shRNA transient transfection , 72h, Replictaion 1; Sox1_72h_shRNAtrasient #1; 251508710772A1


title: Rpap1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Rpap1 shRNA transient transfection , 72h, Replictaion 1; Rpap1_72h_shRNAtrasient #1; 251508710770A1


title: Tcfap4_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tcfap4 shRNA transient transfection , 72h, Replictaion 2; Tcfap4_72h_shRNAtrasient #2; 251508710769A2


title: Mbd3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Mbd3 shRNA transient transfection , 72h, Replictaion 2; Mbd3_72h_shRNAtrasient #2; 251508710770A4


title: Sall1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sall1 shRNA transient transfection , 72h, Replictaion 2; Sall1_72h_shRNAtrasient #2; 251508710768A2


title: Foxp1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Foxp1 shRNA transient transfection , 72h, Replictaion 2; Foxp1_72h_shRNAtrasient #2; 251508710771A4


title: Dppa2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dppa2 shRNA transient transfection , 72h, Replictaion 1; Dppa2_72h_shRNAtrasient #1; 251508710771A1


title: Foxp1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Foxp1 shRNA transient transfection , 72h, Replictaion 1; Foxp1_72h_shRNAtrasient #1; 251508710771A3


title: Zfp292_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zfp292 shRNA transient transfection , 72h, Replictaion 1; Zfp292_72h_shRNAtrasient #1; 251508710768A3


title: Batf3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Batf3 shRNA transient transfection , 72h, Replictaion 1; Batf3_72h_shRNAtrasient #1; 251508710769A3


title: Sall1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sall1 shRNA transient transfection , 72h, Replictaion 1; Sall1_72h_shRNAtrasient #1; 251508710768A1


title: Control-04-01-2010_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Control shRNA transient transfection , 72h, Replictaion 1; Control-04-01-2010_72h_shRNAtrasient #1; 251508710772A3


title: Rpap1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Rpap1 shRNA transient transfection , 72h, Replictaion 2; Rpap1_72h_shRNAtrasient #2; 251508710770A2


title: Mbd3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mbd3 shRNA transient transfection , 72h, Replictaion 1; Mbd3_72h_shRNAtrasient #1; 251508710770A3


title: Trim28_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Trim28 shRNA transient transfection , 72h, Replictaion 1; Trim28_72h_shRNAtrasient #1; 251508710767A1

value: Universale Mouse Reference


title: Prdm5_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Prdm5 shRNA transient transfection , 72h, Replictaion 2; Prdm5_72h_shRNAtrasient #2; 251508710766A4


title: Tcfap4_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tcfap4 shRNA transient transfection , 72h, Replictaion 1; Tcfap4_72h_shRNAtrasient #1; 251508710769A1


title: Mkrn1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mkrn1 shRNA transient transfection , 72h, Replictaion 1; Mkrn1_72h_shRNAtrasient #1; 251508710766A1


title: Mkrn1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Mkrn1 shRNA transient transfection , 72h, Replictaion 2; Mkrn1_72h_shRNAtrasient #2; 251508710766A2


title: Dppa3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dppa3 shRNA transient transfection , 72h, Replictaion 1; Dppa3_72h_shRNAtrasient #1; 251508710767A3


title: NCI-HPN-M2C Blad_passage 5, 1 technical replicate 2

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

address: 50 South Drive

department: Genetics Branch

institute: NCI

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 GneChip micorarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS2v5 protocol.

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

data_processing: The gene expression data were processed using the Affymetrix GCOS (Gene Chip Operating software v 1.2) and using internal control genes beta-actin and Gapdh. Data was normalized with rma method from bioconductor package of R (v.2.5.0) .

label: biotin

source_name: bladder epithelial cells_passage 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The epithelial cells were grown in DMEM/F12 media supplemented with low fetal bovine serum (2-5%).The cells were fed every 10 days to promote in vitro cellular transformation (Padilla Nash et al., 2012).

extract_protocol: Trizol extraction of total RNA from the uncultured epithelial bladder and kidney cells and from the spontaneously transformed cultures was performed according to the manufacturer's instructions.

value: male

value: bladder

value: epithelial cells

value: pre-immortal

tag: passage


title: NCI-HPN-M2C Blad_passage 14, 1 technical replicate 2

source_name: bladder epithelial cells_passage 14

value: immortal


title: NCI-HPN-M1C Kid_passage 8, 1 technical replicate 2

source_name: kidney epithelial cells_passage 8

value: kidney


title: NCI-HPN-M1C Kid_passage 44, 1 technical replicate 1

source_name: kidney epithelial cells_passage 44

value: transformed


title: Prdm5_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Prdm5 shRNA transient transfection , 72h, Replictaion 1; Prdm5_72h_shRNAtrasient #1; 251508710766A3


title: NCI-HPN-M1I Blad_passage 12, 1 technical replicate 1

source_name: bladder epithelial cells_passage 12


title: Mycl1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Mycl1 shRNA transient transfection , 72h, Replictaion 2; Mycl1_72h_shRNAtrasient #2; 251508710764A4


title: Ncoa3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Ncoa3 shRNA transient transfection , 72h, Replictaion 2; Ncoa3_72h_shRNAtrasient #2; 251508710765A2


title: Trim28_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Trim28 shRNA transient transfection , 72h, Replictaion 2; Trim28_72h_shRNAtrasient #2; 251508710767A2

value: Universale Mouse Reference


title: Dppa3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dppa3 shRNA transient transfection , 72h, Replictaion 2; Dppa3_72h_shRNAtrasient #2; 251508710767A4


title: NCI-HPN-M1C Kid_passage 8, 1 technical replicate 1


title: Hmga1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Hmga1 shRNA transient transfection , 72h, Replictaion 1; Hmga1_72h_shRNAtrasient #1; 251508710765A3


title: Ncoa3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Ncoa3 shRNA transient transfection , 72h, Replictaion 1; Ncoa3_72h_shRNAtrasient #1; 251508710765A1


title: NCI-HPN-M1C Blad_passage 66, 1 technical replicate 2

source_name: bladder epithelial cells_passage 66


title: NCI-HPN-M1C Kid_passage 14, 1 technical replicate 1

source_name: kidney epithelial cells_passage 14


title: NCI-HPN-M1C Kid_passage 14, 1 technical replicate 2


title: NCI-HPN-M1I Blad_passage 55, 1 technical replicate 1

source_name: bladder epithelial cells_passage 55


title: Hmga1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Hmga1 shRNA transient transfection , 72h, Replictaion 2; Hmga1_72h_shRNAtrasient #2; 251508710765A4


title: NCI-HPN-M1I Blad_passage 12, 1 technical replicate 2

value: male


title: Mycl1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mycl1 shRNA transient transfection , 72h, Replictaion 1; Mycl1_72h_shRNAtrasient #1; 251508710764A3


title: NCI-HPN-M2C Blad_passage 5, 1 technical replicate 1

value: bladder

value: epithelial cells


title: NCI-HPN-M1I Blad_passage 55, 1 technical replicate 2


title: NCI-HPN-M1C Kid_passage 44, 1 technical replicate 2


title: NCI-HPN-M1C Blad_passage 14, 1 technical replicate 2

value: immortal


title: NCI-HPN-M2C Blad_passage 14, 1 technical replicate 1


title: NCI-HPN-M1C Blad_passage 14, 1 technical replicate 1


title: NCI-HPN-M1C Blad_passage 66, 1 technical replicate 1


title: Nanog-B_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Nanog shRNA transient transfection with 2nd shRNA , 72h, Replictaion 2; Nanog-B_72h_shRNAtrasient #2; 251508710761A4


title: Nr0b1-B_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Nr0b1 shRNA transient transfection with 2nd shRNA , 72h, Replictaion 2; Nr0b1-B_72h_shRNAtrasient #2; 251508710762A2


title: Nr0b1-B_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Nr0b1 shRNA transient transfection with 2nd shRNA , 72h, Replictaion 1; Nr0b1-B_72h_shRNAtrasient #1; 251508710762A1


title: NCI-HPN-M1C Blad_passage 2, 1 technical replicate 2

source_name: bladder epithelial cells_passage 2

value: pre-immortal


title: Ell2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Ell2 shRNA transient transfection , 72h, Replictaion 1; Ell2_72h_shRNAtrasient #1; 251508710763A3


title: NCI-HPN-F2G Kid_passage 27, 1 technical replicate 2

source_name: kidney epithelial cells_passage 27

value: female

value: kidney

value: transformed


title: Ell2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Ell2 shRNA transient transfection , 72h, Replictaion 2; Ell2_72h_shRNAtrasient #2; 251508710763A4

value: Universale Mouse Reference


title: Zscan4c_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zscan4c shRNA transient transfection , 72h, Replictaion 2; Zscan4c_72h_shRNAtrasient #2; 251508710764A2


title: NCI-HPN-F2G Kid_passage 15, 1 technical replicate 2

source_name: kidney epithelial cells_passage 15


title: NCI-HPN-F2G Kid_passage 4, 1 technical replicate 2

source_name: kidney epithelial cells_passage 4


title: Nanog-B_72h_shRNAtrasient #1

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Nanog shRNA transient transfection with 2nd shRNA , 72h, Replictaion 1; Nanog-B_72h_shRNAtrasient #1; 251508710761A3


title: Pou5f1-B_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Pou5f1 shRNA transient transfection with 2nd shRNA , 72h, Replictaion 2; Pou5f1-B_72h_shRNAtrasient #2; 251508710761A2

source_name: Universal Mouse Reference 129ES Cell


title: NCI-HPN-M1C Blad_passage 2, 1 technical replicate 1

value: male

value: bladder


title: NCI-HPN-F2G Kid_passage 4, 1 technical replicate 1

value: epithelial cells


title: Pou5f1-B_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Pou5f1 shRNA transient transfection with 2nd shRNA , 72h, Replictaion 1; Pou5f1-B_72h_shRNAtrasient #1; 251508710761A1


title: NCI-HPN-F2G Kid_passage 27, 1 technical replicate 1


title: Sall4_Dox-_shRNA_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sall4 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSall4; Sall4_Dox-_shRNA_72h_shRNAtrasient #2; 251508710759A4


title: Sall4_Dox-_control_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSal; Sall4_Dox-_control_72h_shRNAtrasient #2; 251508710759A2


title: NCI-HPN-F2G Kid_passage 15, 1 technical replicate 1

value: immortal


title: NCI-HPN-F2G Blad_passage 4, 1 technical replicate 2

source_name: bladder epithelial cells_passage 4

value: pre-immortal


title: NCI-HPN-F2G Blad_passage 53, 1 technical replicate 2

source_name: bladder epithelial cells_passage 53

value: female


title: NCI-HPN-F2G Blad_passage 4, 1 technical replicate 1


title: Sall4_Dox+_shRNA_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sall4 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSall4; Sall4_Dox+_shRNA_72h_shRNAtrasient #1; 251508710758A3


title: Sall4_Dox+_shRNA_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sall4 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSall4; Sall4_Dox+_shRNA_72h_shRNAtrasient #2; 251508710758A4


title: Sall4_Dox-_shRNA_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sall4 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSall4; Sall4_Dox-_shRNA_72h_shRNAtrasient #1; 251508710759A3


title: Sall4_Dox+_control_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSal; Sall4_Dox+_control_72h_shRNAtrasient #1; 251508710758A1

value: Universale Mouse Reference


title: NCI-HPN-F1G Kid_passage 5, 1 technical replicate 2

source_name: kidney epithelial cells_passage 5

value: kidney


title: NCI-HPN-F2G Blad_passage 53, 1 technical replicate 1

value: transformed


title: Sall4_Dox-_control_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSal; Sall4_Dox-_control_72h_shRNAtrasient #1; 251508710759A1


title: NCI-HPN-F1G Kid_passage 16, 1 technical replicate 2

source_name: kidney epithelial cells_passage 16


title: Pou5f1_Dox-_shRNA_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Pou5f1 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou5; Pou5f1_Dox-_shRNA_72h_shRNAtrasient #2; 251508710757A4


title: NCI-HPN-F1G Kid_passage 35, 1 technical replicate 2

source_name: kidney epithelial cells_passage 35

value: epithelial cells


title: NCI-HPN-F2G Blad_passage 10, 1 technical replicate 1

source_name: bladder epithelial cells_passage 10

value: bladder


title: NCI-HPN-F1G Blad_passage 6, 1 technical replicate 1

source_name: bladder epithelial cells_passage 6


title: Sall4_Dox+_control_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetSal; Sall4_Dox+_control_72h_shRNAtrasient #2; 251508710758A2


title: Pou5f1_Dox+_shRNA_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Pou5f1 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou5; Pou5f1_Dox+_shRNA_72h_shRNAtrasient #2; 251508710756A4


title: NCI-HPN-F1G Blad_passage 6, 1 technical replicate 2


title: NCI-HPN-F1G Kid_passage 5, 1 technical replicate 1


title: NCI-HPN-F1G Blad_passage 51, 1 technical replicate 2

source_name: bladder epithelial cells_passage 51


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou; Pou5f1_Dox+_control_72h_shRNAtrasient #2; 251508710756A2


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou; Pou5f1_Dox-_control_72h_shRNAtrasient #2; 251508710757A2


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou; Pou5f1_Dox-_control_72h_shRNAtrasient #1; 251508710757A1


title: NCI-HPN-F2G Blad_passage 10, 1 technical replicate 2

value: female

value: immortal


title: NCI-HPN-F1G Kid_passage 35, 1 technical replicate 1


title: NCI-HPN-F1B Kid_passage 4, 1 technical replicate 2

value: pre-immortal


title: NCI-HPN-F1G Blad_passage 10, 1 technical replicate 1


title: Gtf2i_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Gtf2i shRNA transient transfection , 72h, Replictaion 1; Gtf2i_72h_shRNAtrasient #1; 251508710749A3


title: Gtf2i_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Gtf2i shRNA transient transfection , 72h, Replictaion 2; Gtf2i_72h_shRNAtrasient #2; 251508710749A4

value: Universale Mouse Reference


description: shRNA transient transfection

value: Control shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou; Pou5f1_Dox+_control_72h_shRNAtrasient #1; 251508710756A1


title: Hells_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Hells shRNA transient transfection , 72h, Replictaion 1; Hells_72h_shRNAtrasient #1; 251508710749A1


title: NCI-HPN-F1B Kid_passage 29, 1 technical replicate 1

source_name: kidney epithelial cells_passage 29

value: kidney

value: transformed


title: NCI-HPN-F1G Blad_passage 51, 1 technical replicate 1

value: bladder

value: epithelial cells


title: NCI-HPN-F1G Blad_passage 10, 1 technical replicate 2


title: NCI-HPN-F1B Kid_passage 18, 1 technical replicate 2

source_name: kidney epithelial cells_passage 18


title: NCI-HPN-F1B Kid_passage 4, 1 technical replicate 1


title: Pou5f1_Dox-_shRNA_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Pou5f1 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou5; Pou5f1_Dox-_shRNA_72h_shRNAtrasient #1; 251508710757A3


title: Hells_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Hells shRNA transient transfection , 72h, Replictaion 2; Hells_72h_shRNAtrasient #2; 251508710749A2


title: Trim24_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Trim24 shRNA transient transfection , 72h, Replictaion 1; Trim24_72h_shRNAtrasient #1; 251508710748A3


title: Tbl1x_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tbl1x shRNA transient transfection , 72h, Replictaion 2; Tbl1x_72h_shRNAtrasient #2; 251508710748A2


title: Tcl1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tcl1 shRNA transient transfection , 72h, Replictaion 2; Tcl1_72h_shRNAtrasient #2; 251508710746A2


title: Male kidney cells pooled, samples 1 and 2, 3 technical replicate 2

source_name: kidney epithelial cells from 2 normal male kidneys

value: male

value: normal


title: Female bladder cells pooled, 2 technical replicate 1

source_name: bladder epithelial cells from 3 normal female bladders

value: female


title: Male kidney cells pooled, samples 5 and 6, 2 technical replicate 2


title: Trim24_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Trim24 shRNA transient transfection , 72h, Replictaion 2; Trim24_72h_shRNAtrasient #2; 251508710748A4


title: Male kidney cells pooled, samples 5 and 6, 2 technical replicate 1


title: Female bladder cells pooled, 1 technical replicate 2


title: Female bladder cells pooled, 2 technical replicate 2


title: Klf2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Klf2 shRNA transient transfection , 72h, Replictaion 1; Klf2_72h_shRNAtrasient #1; 251508710746A3

value: Universale Mouse Reference


title: Male bladder cells pooled, 1 technical replicate 2

source_name: bladder epithelial cells from 3 normal male bladders


title: Male kidney cells pooled, samples 1 and 2, 1 technical replicate 2


title: Male bladder cells pooled, 1 technical replicate 1


title: Male bladder cells pooled, 2 technical replicate 1


title: NCI-HPN-F1G Kid_passage 16, 1 technical replicate 1

value: immortal


title: Male kidney cells pooled, samples 1 and 2, 3 technical replicate 1

value: kidney


title: Klf2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Klf2 shRNA transient transfection , 72h, Replictaion 2; Klf2_72h_shRNAtrasient #2; 251508710746A4


title: Male kidney cells pooled, samples 1 and 2, 1 technical replicate 1


title: NCI-HPN-F1B Kid_passage 18, 1 technical replicate 1


title: Gli1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Gli1 shRNA transient transfection , 72h, Replictaion 1; Gli1_72h_shRNAtrasient #1; 251508710744A3


title: Zic3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zic3 shRNA transient transfection , 72h, Replictaion 1; Zic3_72h_shRNAtrasient #1; 251508710743A3


title: Tbx3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Tbx3 shRNA transient transfection , 72h, Replictaion 2; Tbx3_72h_shRNAtrasient #2; 251508710745A4


title: Tcl1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tcl1 shRNA transient transfection , 72h, Replictaion 1; Tcl1_72h_shRNAtrasient #1; 251508710746A1


title: Tbl1x_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tbl1x shRNA transient transfection , 72h, Replictaion 1; Tbl1x_72h_shRNAtrasient #1; 251508710748A1


title: Zic3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zic3 shRNA transient transfection , 72h, Replictaion 2; Zic3_72h_shRNAtrasient #2; 251508710743A4


title: Rest_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Rest shRNA transient transfection , 72h, Replictaion 1; Rest_72h_shRNAtrasient #1; 251508710744A1


title: Female kidney cells pooled, samples 5 and 6, 2 technical replicate 2

source_name: kidney epithelial cells from 2 normal female kidneys

value: epithelial cells


title: 4932441K18Rik_72h_shRNAtrasient #2

description: shRNA transient transfection

value: 4932441K18Rik shRNA transient transfection , 72h, Replictaion 2; 4932441K18Rik_72h_shRNAtrasient #2; 251508710745A2


title: Male bladder cells pooled, 2 technical replicate 2

value: male

value: bladder

value: normal


title: NCI-HPN-F1B Kid_passage 29, 1 technical replicate 2

value: female

value: transformed


title: Rest_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Rest shRNA transient transfection , 72h, Replictaion 2; Rest_72h_shRNAtrasient #2; 251508710744A2

value: Universale Mouse Reference


title: Tbx3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tbx3 shRNA transient transfection , 72h, Replictaion 1; Tbx3_72h_shRNAtrasient #1; 251508710745A3


title: Cdyl2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Cdyl2 shRNA transient transfection , 72h, Replictaion 2; Cdyl2_72h_shRNAtrasient #2; 251508710742A4


title: Pdlim1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Pdlim1 shRNA transient transfection , 72h, Replictaion 1; Pdlim1_72h_shRNAtrasient #1; 251508710743A1


title: Female kidney cells pooled, samples 5 and 6, 2 technical replicate 1

value: kidney


title: 4932441K18Rik_72h_shRNAtrasient #1

description: shRNA transient transfection

value: 4932441K18Rik shRNA transient transfection , 72h, Replictaion 1; 4932441K18Rik_72h_shRNAtrasient #1; 251508710745A1


title: Female bladder cells pooled, 1 technical replicate 1


title: Cdyl2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Cdyl2 shRNA transient transfection , 72h, Replictaion 1; Cdyl2_72h_shRNAtrasient #1; 251508710742A3


title: Zfp206_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zfp206 shRNA transient transfection , 72h, Replictaion 2; Zfp206_72h_shRNAtrasient #2; 251508710742A2


title: Gli1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Gli1 shRNA transient transfection , 72h, Replictaion 2; Gli1_72h_shRNAtrasient #2; 251508710744A4


title: Female kidney cells pooled, samples 1 and 2, 1 technical replicate 1

value: epithelial cells


title: Fgfbp1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Fgfbp1 shRNA transient transfection , 72h, Replictaion 2; Fgfbp1_72h_shRNAtrasient #2; 251508710741A4


title: Female kidney cells pooled, samples 1 and 2, 1 technical replicate 2


title: Pou5f1_Dox+_shRNA_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Pou5f1 shRNA transient transfection, rescue experiment using ES[MC1R(20):tetPou5; Pou5f1_Dox+_shRNA_72h_shRNAtrasient #1; 251508710756A3


title: Pdlim1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Pdlim1 shRNA transient transfection , 72h, Replictaion 2; Pdlim1_72h_shRNAtrasient #2; 251508710743A2


title: Nr6a1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Nr6a1 shRNA transient transfection , 72h, Replictaion 2; Nr6a1_72h_shRNAtrasient #2; 251508710741A2


title: NCI-HPN-M2G Kid_passage 5, 1 technical replicate 2

value: male

value: pre-immortal


title: Zfp206_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zfp206 shRNA transient transfection , 72h, Replictaion 1; Zfp206_72h_shRNAtrasient #1; 251508710742A1

value: Universale Mouse Reference


title: Sox15_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sox15 shRNA transient transfection , 72h, Replictaion 2; Sox15_72h_shRNAtrasient #2; 251508710740A4


title: NCI-HPN-M2G Kid_passage 13, 1 technical replicate 2

source_name: kidney epithelial cells_passage 13

value: immortal


title: Fgfbp1_72h_shRNAtrasient #1

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Embryonic Stem Cells

value: Fgfbp1 shRNA transient transfection , 72h, Replictaion 1; Fgfbp1_72h_shRNAtrasient #1; 251508710741A3


title: NCI-HPN-M2G Kid_passage 13, 1 technical replicate 1

value: kidney


title: NCI-HPN-M2G Kid_passage 24, 1 technical replicate 1

source_name: kidney epithelial cells_passage 24

value: transformed


title: NCI-HPN-M2G Kid_passage 24, 1 technical replicate 2


title: Nr6a1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Nr6a1 shRNA transient transfection , 72h, Replictaion 1; Nr6a1_72h_shRNAtrasient #1; 251508710741A1

source_name: Universal Mouse Reference 129ES Cell


title: NCI-HPN-M2C Kid_passage 6, 1 technical replicate 2

source_name: kidney epithelial cells_passage 6


title: NCI-HPN-M2C Kid_passage 6, 1 technical replicate 1


title: Klf5_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Klf5 shRNA transient transfection , 72h, Replictaion 1; Klf5_72h_shRNAtrasient #1; 251508710740A1


title: NCI-HPN-M2C Kid_passage 14, 1 technical replicate 1

source_name: kidney epithelial cells_passage 14

value: epithelial cells


title: NCI-HPN-M2G Kid_passage 5, 1 technical replicate 1

source_name: kidney epithelial cells_passage 5


title: NCI-HPN-M2C Kid_passage 14, 1 technical replicate 2


title: NCI-HPN-M2C Kid_passage 54, 1 technical replicate 2

source_name: kidney epithelial cells_passage 54


title: Klf5_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Klf5 shRNA transient transfection , 72h, Replictaion 2; Klf5_72h_shRNAtrasient #2; 251508710740A2


title: NCI-HPN-M2C Blad_passage 66, 1 technical replicate 1

source_name: bladder epithelial cells_passage 66

value: bladder


title: NCI-HPN-M2C Blad_passage 66, 1 technical replicate 2


title: Tle4_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tle4 shRNA transient transfection , 72h, Replictaion 2; Tle4_72h_shRNAtrasient #2; 251508710738A4


title: NCI-HPN-M2C Kid_passage 54, 1 technical replicate 1


title: Elf2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Elf2 shRNA transient transfection , 72h, Replictaion 2; Elf2_72h_shRNAtrasient #2; 251508710739A2


title: Tle4_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tle4 shRNA transient transfection , 72h, Replictaion 1; Tle4_72h_shRNAtrasient #1; 251508710738A3


title: Sox15_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sox15 shRNA transient transfection , 72h, Replictaion 1; Sox15_72h_shRNAtrasient #1; 251508710740A3


title: Zfp57_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Zfp57 shRNA transient transfection , 72h, Replictaion 1; Zfp57_72h_shRNAtrasient #1; 251508710738A1


title: Elf2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Elf2 shRNA transient transfection , 72h, Replictaion 1; Elf2_72h_shRNAtrasient #1; 251508710739A1

value: Universale Mouse Reference


title: Jmjd1a_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Jmjd1a shRNA transient transfection , 72h, Replictaion 1; Jmjd1a_72h_shRNAtrasient #1; 251508710737A3


title: BLaER1 168h_2

city: Barcelona

first: Francesca

last: Rapino

address: dr.aiguader 88

country: Spain

institute: center for genomic regulation

description:
GF200_024
B cells containing C/EBPa, induced with E2 for 168h, replicate 2.

hyb_protocol: Labeled cRNA was hybridized to the Agilent Human SurePrint G3 (8x60K) oligo microarray (G4858A-028004).

scan_protocol: The arrays were scanned on an Agilent G2565CA microarray scanner at 110% PMT and 5 μm resolution. Intensity data was extracted using the Feature Extraction software (Agilent).

data_processing: Extracted log2-transformed intensities were background corrected with the normexp method and quantile normalized to make all data comparable. All analyses were performed using R/Bioconductor.

source_name: Seraphina cells C/EBPa ER GFP induced 168h with E2

label_protocol: 500ng of RNA was labeled using Agilent's QuickAmp Labeling Kit.

growth_protocol: Burkitt lymphoma cells, seraphina containing the C/eBPa ER GFP retrovirus were grown at 37°C in 5% CO2 in RPMI 1640 Hepes (Lonza) with 10% FBS, Pen-Strep and L-Glutamine (Gibco).

extract_protocol: Total RNA was extracted with the RNeasy mini Kit (Qiagen).

treatment_protocol: Freshly isolated CD71+ CB/CC B-cells were sorted from the tonsils of a healthy donor and used for total RNA extraction. Primary macrophages were differentiated from the peripheral blood of a healthy donor and cultured in RPMI 1640 Hepes (Lonza) with 10% FBS, Pen-Strep and L-Glutamine (Gibco) in the presence of 50ng/ml of hr-MCSF-1. C/EBPα was induced in the Burkitt Lymphoma Seraphina cells containing the transgeneL by addition of 100 nM E2 (Calbiochem) and grown in the medium decribed before with 10ng/ml of hrIL-3 (Peprotech) and 10ng/ml hr-CSF-1 (M-CSF). Biological duplicates of BLaER1 cells were harvested for RNA extraction at various times thereafter.

value: Burkitt lymphoma cells

tag: treatment duration


title: Primary B cells_2

description:
GF200_026
CD71+ cells from the tonsils, replicate 2.

source_name: CD71+ primary CB/CC B-cells from the tonsils of a donor

value: tonsils

value: primary B cells


title: Jmjd1a_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Jmjd1a shRNA transient transfection , 72h, Replictaion 2; Jmjd1a_72h_shRNAtrasient #2; 251508710737A4


title: BLaER1 168h_1

description:
GF200_023
B cells containing C/EBPa, induced with E2 for 168h, replicate 1.


title: Primary macrophages_1

description:
GF200_027
primary macrophages differentiated from peripheral blood, replicate 1.

source_name: macrophages differentiated from peripheral blood of a donor, cultured for 7 days with 50ng/ml of hr-CSF-1

value: peripheral blood

value: primary macrophages


title: Zfp57_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zfp57 shRNA transient transfection , 72h, Replictaion 2; Zfp57_72h_shRNAtrasient #2; 251508710738A2


title: Inppl1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Inppl1 shRNA transient transfection , 72h, Replictaion 2; Inppl1_72h_shRNAtrasient #2; 251508710739A4


title: Inppl1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Inppl1 shRNA transient transfection , 72h, Replictaion 1; Inppl1_72h_shRNAtrasient #1; 251508710739A3


title: Primary macrophages_2

description:
GF200_028
primary macrophages differentiated from peripheral blood, replicate 2.


title: Utf1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Utf1 shRNA transient transfection , 72h, Replictaion 2; Utf1_72h_shRNAtrasient #2; 251508710736A4


title: Gabpa_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Gabpa shRNA transient transfection , 72h, Replictaion 2; Gabpa_72h_shRNAtrasient #2; 251508710737A2


title: BLaER1 120h_2

description:
GF200_022
B cells containing C/EBPa, induced with E2 for 120h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 120h with E2


title: Primary B cells_1

description:
GF200_025
CD71+ cells from the tonsils, replicate 1.


title: Gabpa_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Gabpa shRNA transient transfection , 72h, Replictaion 1; Gabpa_72h_shRNAtrasient #1; 251508710737A1


title: BLaER1 120h_1

description:
GF200_021
B cells containing C/EBPa, induced with E2 for 120h, replicate 1.


title: BLaER1 72h_2

description:
GF200_020
B cells containing C/EBPa, induced with E2 for 72h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 72h with E2


title: Pml_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Pml shRNA transient transfection , 72h, Replictaion 2; Pml_72h_shRNAtrasient #2; 251508710736A2


title: Utf1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Utf1 shRNA transient transfection , 72h, Replictaion 1; Utf1_72h_shRNAtrasient #1; 251508710736A3


title: BLaER1 48h_1

description:
GF200_017
B cells containing C/EBPa, induced with E2 for 48h, replicate 1.

source_name: Seraphina cells C/EBPa ER GFP induced 48h with E2


title: BLaER1 48h_2

description:
GF200_018
B cells containing C/EBPa, induced with E2 for 48h, replicate 2.


title: Mtf2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Mtf2 shRNA transient transfection , 72h, Replictaion 2; Mtf2_72h_shRNAtrasient #2; 251508710735A2

value: Universale Mouse Reference


title: Mtf2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mtf2 shRNA transient transfection , 72h, Replictaion 1; Mtf2_72h_shRNAtrasient #1; 251508710735A1


title: BLaER1 24h_1

description:
GF200_013
B cells containing C/EBPa, induced with E2 for 24h, replicate 1.

source_name: Seraphina cells C/EBPa ER GFP induced 24h with E2

value: Burkitt lymphoma cells


title: BLaER1 72h_1

description:
GF200_019
B cells containing C/EBPa, induced with E2 for 72h, replicate 1.


title: BLaER1 36h_2

description:
GF200_016
B cells containing C/EBPa, induced with E2 for 36h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 36h with E2


title: Phc1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Phc1 shRNA transient transfection , 72h, Replictaion 1; Phc1_72h_shRNAtrasient #1; 251508710733A1


title: Tlk1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Tlk1 shRNA transient transfection , 72h, Replictaion 2; Tlk1_72h_shRNAtrasient #2; 251508710734A2


title: BLaER1 36h_1

description:
GF200_015
B cells containing C/EBPa, induced with E2 for 36h, replicate 1.


title: Tcfcp2l1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tcfcp2l1 shRNA transient transfection , 72h, Replictaion 1; Tcfcp2l1_72h_shRNAtrasient #1; 251508710735A3


title: Phc1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Phc1 shRNA transient transfection , 72h, Replictaion 2; Phc1_72h_shRNAtrasient #2; 251508710733A2


title: Jmjd2c_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Jmjd2c shRNA transient transfection , 72h, Replictaion 2; Jmjd2c_72h_shRNAtrasient #2; 251508710734A4


title: Parp1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Parp1 shRNA transient transfection , 72h, Replictaion 2; Parp1_72h_shRNAtrasient #2; 251508710733A4


title: Parp1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Parp1 shRNA transient transfection , 72h, Replictaion 1; Parp1_72h_shRNAtrasient #1; 251508710733A3


title: Tlk1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tlk1 shRNA transient transfection , 72h, Replictaion 1; Tlk1_72h_shRNAtrasient #1; 251508710734A1


title: BLaER1 18h_2

description:
GF200_012
B cells containing C/EBPa, induced with E2 for 18h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 18h with E2


title: BLaER1 12h_1

description:
GF200_009
B cells containing C/EBPa, induced with E2 for 12h, replicate 1.

source_name: Seraphina cells C/EBPa ER GFP induced 12h with E2


title: BLaER1 6h_2

description:
GF200_006
B cells containing C/EBPa, induced with E2 for 6h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 6h with E2


title: BLaER1 12h_2

description:
GF200_010
B cells containing C/EBPa, induced with E2 for 12h, replicate 2.


title: BLaER1 18h_1

description:
GF200_011
B cells containing C/EBPa, induced with E2 for 18h, replicate 1.


title: BLaER1 9h_1

description:
GF200_007
B cells containing C/EBPa, induced with E2 for 9h, replicate 1.

source_name: Seraphina cells C/EBPa ER GFP induced 9h with E2


title: BLaER1 6h_1

description:
GF200_005
B cells containing C/EBPa, induced with E2 for 6h, replicate 1.


title: BLaER1 24h_2

description:
GF200_014
B cells containing C/EBPa, induced with E2 for 24h, replicate 2.


title: BLaER1 9h_2

description:
GF200_008
B cells containing C/EBPa, induced with E2 for 9 h, replicate 2.


title: Ctbp2_72h_shRNAtrasient #2

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Ctbp2 shRNA transient transfection , 72h, Replictaion 2; Ctbp2_72h_shRNAtrasient #2; 251508710732A4

source_name: Universal Mouse Reference 129ES Cell


title: BLaER1 3h_2

description:
GF200_004
B cells containing C/EBPa, induced with E2 for 3h, replicate 2.

source_name: Seraphina cells C/EBPa ER GFP induced 3h with E2


title: RNA_top3-105_36C

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description:
Total RNA from top3-105 cells after 8 hours at 36C
RNA_top3-105_36C

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing: CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. One sample analysis of replicates A+B and linear scaling to 100 was applied. Linear probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2007) and reported in BAR files (Fwd and Rev strands).

organism: Schizosaccharomyces pombe

source_name: Total RNA, top3-105, 36C

label_protocol: RNA was treated according to the Affymetrix total RNA labelling protocol (http://www.affymetrix.com).

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm. The temperature sensitive top3-105 mutant and wild type controls were grown at the permissive temperature (25 °C) over night and then for 8 hours at the nonpermissive temperature (36°C) before harvesting. All other strains were grown at 30 °C.

extract_protocol: Total RNA was extracted from mid-logarithmic phase cells after 8 hours at 36C using the hot-phenol method. Briefly, cells were harvested by centrifugation at RT, resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to preheated acid phenol (65 °C).  After 60 min shaking incubation at 65 °C, RNA was isolated by phenol-chloroform extraction.

tag: genotype/variation

tag: temperature


title: Ctbp2_72h_shRNAtrasient #1

description: shRNA transient transfection

tag: strain

value: Ctbp2 shRNA transient transfection , 72h, Replictaion 1; Ctbp2_72h_shRNAtrasient #1; 251508710732A3


title: BLaER1 3h_1

description:
GF200_003
B cells containing C/EBPa, induced with E2 for 3h, replicate 1.


title: ChIP_Cnp1_WT_36C

type: genomic

description:
test CEL files:
Cnp1 WT 8h 36C A.CEL
Cnp1 WT 8h 36C B.CEL
ctrl CEL files:
Input WT 8h 36C B.CEL
Cnp1 ChIP DNA from WT cells after 8 hours at 36C
ChIP_Cnp1_WT_36C

data_processing:
CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated vs. input samples, quantile normalization (separate) and linear scaling to 100 was applied. Linear probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2007 and Sanger 2004) and reported in BAR files (Fwd and Rev strands).
All result files are also provided in .txt format: 2007 Transcription Hu303 A+B (one sample PM MM) Fwd_linear signal.txt, 2007 Transcription Hu303 A+B (one sample PM MM) Rev_linear signal.txt, 2007 Transcription Hu2027 A+B (one sample PM MM) Fwd_linear signal.txt, 2007 Transcription Hu2027 A+B (one sample PM MM) Rev_linear signal.txt, Top3myc_A+B_Input_1+2 (separate) 2004 Fwd_signal.txt, Top3myc_A+B_Input_1+2 (separate) 2004 Rev_signal.txt, Top3myc_A+B_Input_1+2 (separate) 2007 Fwd_signal.txt, Top3myc_A+B_Input_1+2 (separate) 2007 Rev_signal.txt, Cnp1 WT 36C_A+B_Input WT 36C_B (separate) 2004 Fwd_signal.txt, Cnp1 WT 36C_A+B_Input WT 36C_B (separate) 2004 Rev_signal.txt, Cnp1 WT 36C_A+B_Input WT 36C_B (separate) 2007 Fwd_signal.txt, Cnp1 WT 36C_A+B_Input WT 36C_B (separate) 2007 Rev_signal.txt, Cnp1 Top3-105 36C_A+B_Input Top3-105 36C_B (separate) 2004 Fwd_signal.txt, Cnp1 Top3-105 36C_A+B_Input Top3-105 36C_B (separate) 2004 Rev_signal.txt, Cnp1 Top3-105 36C_A+B_Input Top3-105 36C_B (separate) 2007 Fwd_signal.txt, Cnp1 Top3-105 36C_A+B_Input Top3-105 36C_B (separate) 2007 Rev_signal.txt
Results file in .BAR and .txt formats were generated using  Affymetrix Tiling Analysis Software (TAS) v1.1. and contains linear values for transcription in arbitrary units or relative enrichment (ChIP vs. input) for each probe.

molecule: genomic DNA

source_name: ChIP DNA, Cnp1, WT, 36C

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the precence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.  Immunoprecipitation Assay Protocol

extract_protocol: Cnp1 was immunoprecipitated from chromatin extracts prepared from mid-logarithmic phase cells after 8 hours at 36C. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine,  and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with anti-Cnp1 serum for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

value: WT

tag: chip antibody

value: anti-Cnp1 serum

tag: sample type

value: ChIP DNA

source_name: ChIP input DNA, WT, 36C

value: input DNA


title: ChIP_Top3-Myc_30C

description:
test CEL files:
WT Top3-myc 30C A.CEL
WT Top3-myc 30C B.CEL
ctrl CEL files:
JW_1 WT 30C.CEL
JW_2_2 WT 30C.CEL
Top3-myc ChIP DNA from cells expressing Top3-Myc from the endogenous promoter at 30C
ChIP_Top3-Myc_30C

source_name: ChIP DNA, Top3-Myc, 30C

extract_protocol: Top3-Myc was immunoprecipitated from chromatin extracts prepared from mid-logarithmic phase cells at 30C. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine,  and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with 9E10 mouse anti-Myc for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

value: WT Top3-myc

value: 9E10 mouse anti-Myc

source_name: ChIP input DNA, WT, 30C


title: ChIP_Cnp1_top3-105_36C

description:
test CEL files:
Cnp1 Top3-105 8h 36C A.CEL
Cnp1 Top3-105 8h 36C B.CEL
ctrl CEL files:
Input Top3-105 8h 36C B.CEL
Cnp1 ChIP DNA from top5-105 cells after 8 hours at 36C
ChIP_Cnp1_top3-105_36C

source_name: ChIP DNA, Cnp1, top3-105, 36C

source_name: ChIP input DNA, top3-105, 36C


title: Sfrs6_72h_shRNAtrasient #1

description: shRNA transient transfection

tag: cell type

value: Sfrs6 shRNA transient transfection , 72h, Replictaion 1; Sfrs6_72h_shRNAtrasient #1; 251508710731A3

value: Universale Mouse Reference


title: Jarid2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Jarid2 shRNA transient transfection , 72h, Replictaion 2; Jarid2_72h_shRNAtrasient #2; 251508710731A2


title: Sfrs6_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sfrs6 shRNA transient transfection , 72h, Replictaion 2; Sfrs6_72h_shRNAtrasient #2; 251508710731A4


title: Jmjd2c_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Jmjd2c shRNA transient transfection , 72h, Replictaion 1; Jmjd2c_72h_shRNAtrasient #1; 251508710734A3


title: Dnmt3l_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dnmt3l shRNA transient transfection , 72h, Replictaion 1; Dnmt3l_72h_shRNAtrasient #1; 251508710732A1


title: RNA_WT_36C

description:
Total RNA from WT cells after 8 hours at 36C
RNA_WT_36C

source_name: Total RNA, WT, 36C


title: Trp53_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Trp53 shRNA transient transfection , 72h, Replictaion 2; Trp53_72h_shRNAtrasient #2; 251508710730A2


title: Zfp42_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Zfp42 shRNA transient transfection , 72h, Replictaion 2; Zfp42_72h_shRNAtrasient #2; 251508710730A4


title: Dnmt3l_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dnmt3l shRNA transient transfection , 72h, Replictaion 2; Dnmt3l_72h_shRNAtrasient #2; 251508710732A2


title: Jarid2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Jarid2 shRNA transient transfection , 72h, Replictaion 1; Jarid2_72h_shRNAtrasient #1; 251508710731A1


title: Liver_Cancer-HCC_QD344_C_C3vsN5

city: Shanghai

first: Lin

last: Wei

address: No.25/Ln.2200, Xie Tu Road

institute: Shanghai Cancer Institute

description: Cancer liver tissue (Cy3) from HCC patient QD344 vs. Normal liver tissue mixed (Cy5)

hyb_protocol: Labeled controls and test samples labeled with Cy5-dCTP and Cy3-dCTP were dissolved in 80 µL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixer II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned with a confocal LuxScan scanner and the images obtained were then analyzed using LuxScan 3.0 software (Both from CapitalBio).

data_processing: Faint spots (intensity < 400) removed, background subtracted data were normalized by LOWESS program.

source_name: Liver tissue, Hepatocellular carcinoma

label_protocol: Eberwine’s linear RNA amplification method and subsequent enzymatic reaction

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA).

value: C, Cancer

tag: gender

value: Male

tag: age

tag: survival

value: No

tag: recurrence

value: Yes

tag: cirrhosis

tag: edmonson

tag: metastasis

source_name: Liver tissue, Normal

tag: tissue type

value: N, Normal


title: BLaER1 0h_1

description:
GF200_001
B cells containing C/EBPa, uninduced, replicate 1.

source_name: Seraphina cells C/EBPa ER GFP, uninduced

value: Burkitt lymphoma cells

tag: treatment


title: BLaER1 0h_2

description:
GF200_002
B cells containing C/EBPa, uninduced, replicate 2.


title: Liver_Pericancer_QD344_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD344 vs. Normal liver tissue mixed (Cy5)

source_name: Liver tissue, Pericancer

value: P, Pericancerous


title: Liver_Pericancer_QD338_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD338 vs. Normal liver tissue mixed (Cy5)


title: Zfp42_72h_shRNAtrasient #1

description: shRNA transient transfection

tag: individual identifier

value: Zfp42 shRNA transient transfection , 72h, Replictaion 1; Zfp42_72h_shRNAtrasient #1; 251508710730A3

value: Universale Mouse Reference


title: Liver_Pericancer_QD341_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD341 vs. Normal liver tissue mixed (Cy5)

value: Female


title: Liver_Cancer-HCC_QD338_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD338 vs. Normal liver tissue mixed (Cy5)


title: Trp53_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Trp53 shRNA transient transfection , 72h, Replictaion 1; Trp53_72h_shRNAtrasient #1; 251508710730A1


title: Liver_Cancer-HCC_QD323_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD323 vs. Normal liver tissue mixed (Cy5)


title: Liver_Pericancer_QD321_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD321 vs. Normal liver tissue mixed (Cy5)


title: Liver_Cancer-HCC_QD341_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD341 vs. Normal liver tissue mixed (Cy5)


title: Trp63 cKO vagina, rep4

city: Columbus

first: Takeshi

last: Kurita

state: OH

address: 460 W. 12th Avenue,

department: Molecular Virology, Immunology & Medical Genetics

institute: Ohio State University

description: Total RNA was extracted from the vaginae of 3 Trp63 cKO mice.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The average signal intensity for each array was normalized to the average total signal intensity of all 12 arrays by average normalization utilizing Excel.

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

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

tag: strain/background

value: mixed (C57BL/6, S129/5 and CD-1)

tag: genotype

value: Trp63 flox/floxt ; Pax2-cre

tag: tissue

value: vagina

value: female

value: postnatal day 3


title: Ash2l_72h_shRNAtrasient #2

description: shRNA transient transfection

tag: strain

value: Ash2l shRNA transient transfection , 72h, Replictaion 2; Ash2l_72h_shRNAtrasient #2; 251508710729A2


title: Ncl_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Ncl shRNA transient transfection , 72h, Replictaion 2; Ncl_72h_shRNAtrasient #2; 251508710729A4


title: Liver_Pericancer_QD323_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD323 vs. Normal liver tissue mixed (Cy5)

value: Male

value: No


title: Trp63 cHet vagina, rep4

description: Total RNA was extracted from the vaginae of 3 Trp63 cHet mice.

value: Trp63 flox/wt ; Pax2-cre


title: Liver_Cancer-HCC_QD318_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD318 vs. Normal liver tissue mixed (Cy5)

value: C, Cancer

value: Yes

value: N, Normal


title: Liver_Cancer-HCC_QD317_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD317 vs. Normal liver tissue mixed (Cy5)


title: PC-3 7days dye-swap

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

country: Japan

institute: SHIMA Institution for Quantum Medicine

description: PC-3  7days  non RB-treated vs RB-treated

hyb_protocol: The Cy3-labeled probe using RNA from cells treated with DMSO and the Cy5-labeled probe using RNA from cells treated with DNCB for 4.5 hr were mixed, fragmented, and then suspended in GE hybridization buffer in the Gene Expression Hybridization Kit (Agilent). The probes were applied to Whole Human Genome Oligo array (Agilent), and hybridization (70 degree centigrade, 14 hr) , washing, and scanning by Agilent Microarray Scanner were performed according to the manufacturer’s recommended protocol.

scan_protocol: Scanned on an Agilent Affymetrix 428 Array scanner. The images were processed using Feature Extraction Software (ver9.5.3.1, Agilent), and scanned by Affymetrix 428 Array Scanner.

data_processing:
For each hybridized spot, background intensity was subtracted and normalized by the global LOWESS normalization method.
Data analysis was performed using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland). Functional analyses were performed and the networks were generated using Ingenuity Pathways Analysis (Ingenuity Systems, CA, USA).

source_name: prostate cancer cells, untreated

label_protocol: Aliquots of 200 ng of total RNAs were labeled with Cy3- or Cy5- UTP using Agilent Quick Amp Labeling Kit (Agilent Technologies Inc.) according to the manufacture’s instructions.

growth_protocol: PC-3 (human prostate cancer cells) were  maintained  in F-12K medium (10%heat-inactivated FCS, 2mM L-glutamine, 100U/ml penicilin G, 0.1mM non-essencial aminoacid ) added  in an atomosphere of 5% CO2 at 37 ºC.

extract_protocol: Total RNA extracted using Isogen kit (NIPPON GENE CO., LTD, Osaka, Japan) from PC-3 cells with or without RB on the 7th and 12th day.

treatment_protocol: The culture dish was sandwiched with RB (Yamamoto Corporation, Osaka Japan) , far-infrared rays emitter,  Another set of culture dish was　not covered with RB, which was used as reference sample. The subculture was done properly at 70-80 % confluency.

tag: cell line

value: Prostate, adenocarcinoma

tag: sex

source_name: prostate cancer cells, RB-treated


title: PC-3 12 days dye-swap

description: PC-3 12 days  non RB-treated vs RB-treated

tag: cell type


title: Tcfcp2l1_72h_shRNAtrasient #2

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Tcfcp2l1 shRNA transient transfection , 72h, Replictaion 2; Tcfcp2l1_72h_shRNAtrasient #2; 251508710735A4

value: Universale Mouse Reference


title: Ash2l_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Ash2l shRNA transient transfection , 72h, Replictaion 1; Ash2l_72h_shRNAtrasient #1; 251508710729A1

source_name: Universal Mouse Reference 129ES Cell


title: Trp63 cHet uterus, rep4

description: Total RNA was extracted from the uteri of 3 Trp63 cHet mice.

value: mixed (C57BL/6, S129/5 and CD-1)

value: uterus

tag: gender


title: Ncl_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Ncl shRNA transient transfection , 72h, Replictaion 1; Ncl_72h_shRNAtrasient #1; 251508710729A3


title: Liver_Pericancer_QD317_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD317 vs. Normal liver tissue mixed (Cy5)

value: P, Pericancerous

tag: age


title: Liver_Cancer-HCC_QD321_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD321 vs. Normal liver tissue mixed (Cy5)

tag: survival


title: PC-3 7days

description: PC-3  7days RB-treated vs non RB-treated


title: Trp63 cHet vagina, rep3

value: vagina

value: female

value: postnatal day 3


title: Liver_Pericancer_QD318_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD318 vs. Normal liver tissue mixed (Cy5)

value: Female

value: No

tag: recurrence


title: PC-3 12 days

description: PC-3 12 days  RB-treated vs non RB-treated

value: Male


title: Sub1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sub1 shRNA transient transfection , 72h, Replictaion 1; Sub1_72h_shRNAtrasient #1; 251508710728A3


title: Liver_Cancer-HCC_QD316_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD316 vs. Normal liver tissue mixed (Cy5)

value: C, Cancer

tag: cirrhosis

value: Yes

value: N, Normal


title: Liver_Pericancer_QD316_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD316 vs. Normal liver tissue mixed (Cy3)

tag: edmonson


title: Sub1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sub1 shRNA transient transfection , 72h, Replictaion 2; Sub1_72h_shRNAtrasient #2; 251508710728A4

value: Universale Mouse Reference


title: Liver_Pericancer_QD133_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD133 vs. Normal liver tissue mixed (Cy3)

tag: metastasis


title: Liver_Cancer-HCC_QD314_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD314 vs. Normal liver tissue mixed (Cy5)

tag: tissue type


title: Pml_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Pml shRNA transient transfection , 72h, Replictaion 1; Pml_72h_shRNAtrasient #1; 251508710736A1


title: Liver_Pericancer_QD315_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD315 vs. Normal liver tissue mixed (Cy5)


title: Trp63 cKO vagina, rep3

description: Total RNA was extracted from the vaginae of 3 Trp63 cKO mice.

value: mixed (C57BL/6, S129/5 and CD-1)

value: Trp63 flox/floxt ; Pax2-cre


title: Liver_Cancer-HCC_QD313_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD313 vs. Normal liver tissue mixed (Cy5)


title: Liver_Pericancer_QD313_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD313 vs. Normal liver tissue mixed (Cy5)

value: P, Pericancerous


title: Liver_Pericancer_QD314_P_P3vsN5

description: Periancerous liver tissue (Cy3) from HCC patient QD314 vs. Normal liver tissue mixed (Cy5)


title: Liver_Pericancer_QD131_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD131 vs. Normal liver tissue mixed (Cy3)


title: Otx2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Otx2 shRNA transient transfection , 72h, Replictaion 1; Otx2_72h_shRNAtrasient #1; 251508710727A3


title: Sap30_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sap30 shRNA transient transfection , 72h, Replictaion 2; Sap30_72h_shRNAtrasient #2; 251508710728A2


title: Trp63 cHet vagina, rep2

description: Total RNA was extracted from the vaginae of 3 Trp63 cHet mice.

value: Trp63 flox/wt ; Pax2-cre

value: vagina

value: female

value: postnatal day 3


title: Trp63 cHet uterus, rep2

description: Total RNA was extracted from the uteri of 3 Trp63 cHet mice.

value: uterus


title: Liver_Cancer-HCC_QD315_C_C3vsN5

description: Cancer liver tissue (Cy3) from HCC patient QD315 vs. Normal liver tissue mixed (Cy5)

value: C, Cancer

value: Male

value: No


title: Trp63 cHet uterus, rep3


title: Liver_Cancer-HCC_QD132_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient QD132 vs. Normal liver tissue mixed (Cy3)

value: Yes

value: N, Normal


title: Trp63 cKO vagina, rep1


title: Trp63 cKO vagina, rep2


title: Liver_Pericancer_QD130_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD130 vs. Normal liver tissue mixed (Cy3)

value: Female


title: Otx2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Otx2 shRNA transient transfection , 72h, Replictaion 2; Otx2_72h_shRNAtrasient #2; 251508710727A4

value: Universale Mouse Reference


title: Sap30_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Sap30 shRNA transient transfection , 72h, Replictaion 1; Sap30_72h_shRNAtrasient #1; 251508710728A1


title: Liver_Cancer-HCC_QD130_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient QD130 vs. Normal liver tissue mixed (Cy3)


title: Liver_Cancer-HCC_QD133_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient QD133 vs. Normal liver tissue mixed (Cy3)


title: Whsc2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Whsc2 shRNA transient transfection , 72h, Replictaion 1; Whsc2_72h_shRNAtrasient #1; 251508710727A1