title: Cfin_High-Low food comparison_rep4

city: Groton

first: Ebru

last: Unal

state: CT

address: 1080 Shennecossett Road

department: Department of Marine Sciences

institute: University of Connecticut

hyb_protocol: Printed slides were pre-hybridized following the manufacturer’s instructions (Pronto Microarray Hybridization Kit, Corning). After addition of the hybridization buffer (Pronto, Corning), the samples were loaded into slides and incubated in a MAUI Hybridization Chamber (BioMicro) overnight at 42ºC for 14-16 hours.

scan_protocol: The slides were scanned by using Genepix Pro Ver. 4.1 (Molecular Devices, Union City, CA) scanner with AutoPMT setting. At the completion of each scan, images were visually checked to align the features in a specific block to their appropriate location on a deconvolution file.

data_processing: The normalization, quality control and gene filtering of the microarray data were performed by using Acuity 4.0 Microarray Informatics Software (Molecular Devices, Inc.). The Lowess normalization (with data centering) was performed for individual slides by using print-tip (block-by-block) normalization, with a smoothing factor of 0.4 for 4 iterations. The Lowess normalized median Log2 ratios of the individual dye intensities were used for subsequent analysis. Following normalization of each slide, pre-processing of the microarrays was performed, including the spot quality analysis and array scaling.

label: Alexa Fluor 555-aha-dUTP

organism: Calanus finmarchicus

source_name: High food_Sample 4

label_protocol: Fluorescently labeled cDNA was generated using the Invitrogen SurperScriptTM Plus Direct cDNA Labeling System. First-strand cDNA synthesis was performed on samples containing 5 to 15 µg of total RNA using SuperScript III RT and labeled using either Alexa Fluor 555-aha-dUTP nucleotide with green fluorescent emission.

growth_protocol: The incubation period was 7 days, and food was added daily at the two feeding levels. Groups of animals were kept at 7-10 individuals per liter in 3.5 L jars.  At the end of the incubation period, 10 to 15 individuals were preserved in RNAlater as a group.

extract_protocol: Qiagen RNeasy Mini Kit (in conjunction with the Qiashredder column [Qiagen]), following the instructions of the manufacturer, with a final elution volume of either 30 or 40 µl.

treatment_protocol: C. finmarchicus adult females were maintained in the laboratory at 8°C at 12:12 light:dark cycle at 5000 cells/ml of Tetraselmis sp.  (Reed Mariculture paste).

tag: Stage

value: Adult female

value: High food

value: Whole copepod, multiple individuals pooled

label: Alexa Fluor 647-aha-dUTP

source_name: Low food_Sample 9

label_protocol: Fluorescently labeled cDNA was generated using the Invitrogen SurperScriptTM Plus Direct cDNA Labeling System. First-strand cDNA synthesis was performed on samples containing 5 to 15 µg of total RNA using SuperScript III RT and labeled using either Alexa Fluor 647-aha-dUTP nucleotide with green fluorescent emission.

treatment_protocol: C. finmarchicus adult females were maintained in the laboratory at 8°C at 12:12 light:dark cycle at 500 cells/ml of Tetraselmis sp.  (Reed Mariculture paste).

value: Low food


title: WAT from Zucker Lean control Replicate3

status: Public on Mar 23 2012

type: RNA

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University

hyb_protocol: labeled two cDNA probe solutions containing hybridization buffer (Genocheck, Korea) were mixed on equal amount and HybriWell FL Sealing System (Grace bio-labs, U.S.A) were applied to the microarrays and placed in a humidified chamber at 62℃ for 14 h. Then, the microarrays were sequentially washed

scan_protocol: Scanned on an Axon GenePix scanarray 4000(Axon 4000, USA) Software

data_processing: All analysis of microarray data was carried the limma package in R. Log2 ratios were calculated using print-tip loess normalization method and quantile normalization was applied across arrays

molecule: total RNA

organism: Rattus norvegicus

source_name: Epididimal Fat of ZLC rat

label_protocol: we used the Superscript TMⅡ (Invitrogen, U.S.A) RNase H Reverse Transcriptase to synthesize cDNA. The reverse transcription mixture included 400 U Superscript RNase H-reverse transcriptase, 15 mM dATP, dTTP and dGTP, 0.6 mM dCTP and 3 mM Cy3 or Cy5 labeled dCTP (NEN Life Science Product Inc.  MA, USA).

extract_protocol: Total RNA was extracted from the different tissues after drug treatment using Trizol reagent (Invitrogen Co., U.S.A) according to the manufacturer’s instructions.

treatment_protocol: Metformin (Glucophage, 300mg/kg/day) and glimepiride (Amaryl, 200mg/kg/day) were given by oral injection to ZDF rats for 2 weeks in each groups and rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) was given to ZDF rats for 1 week according to the manufacture’s protocols and recommendations

tag: tissue

value: Epididimal Fat

tag: age

value: 12-weeks old

tag: gender

value: Male

tag: strain

value: ZDF lean control rat(Crl:ZUC-Leprfa)

tag: treatment

source_name: Epididimal Fat of ZDF rat

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: EoE patient #6_after treatment [miRNA]

city: Providence

first: Shaolei

last: Lu

state: Rhode Island

address: 593 Eddy Steet

department: Pathology

country: USA

institute: Rhode Island Hospital

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-6A

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions of ABI HT7900.
Original Ct values were normalized based on mammalian U6 as housekeeping gene control.
Target gene signals (delta Ct) normalized to housekeeping genes; delta Ct = (Ct_Target − Ct_HKG)
The folder change of each miRNA is calculated using 2^-delta delta Ct (before/after treatment ratios).

label: FAM

organism: Homo sapiens

source_name: EoE patient_after treatment

label_protocol: Five nanograms of total RNA was reverse-transcribed using the Taqman MicroRNA Reverse Transcription Kit and the Megaplex RT primer Human Pool A (Applied Biosystems).  The reverse-transcribed cDNA was then pre-amplified in 12 cycles of PCR using Taqman PreAmp Master Mix and the Megaplex PreAmp primers, Human Pool A (Applied Biosystems).  The cDNA’s were then diluted and loaded on to a Taqman Human miRNA Array card A (Applied Biosystems), which contains probes for 377 distinct miRNAs.  The Array cards were run on an ABI HT7900 qPCR instrument.

extract_protocol: Tissue sections (10mm) were cut and mounted onto plain glass slides.  If the biopsy section contained only epithelium, the sections were scraped from the slides and RNA was extracted using the RecoverAll Total Nucleic Acid Extraction kit for FFPE tissues (Ambion).  If biopsy sections contained sub-epithelium, the sections were deparaffinized, stained, dehydrated through graded alcohols using the Paradise FFPE reagent System (Applied Biosystems, Foster City, CA) and subjected to LCM within 2 hr of deparaffinization.  About 20000 epithelial cells were captured on LCM Macro CapSure caps (Applied Biosystems) using the Arcturus XT LCM instrument (Applied Biosystems).  Total RNA was extracted from the caps also using the RecoverAll kit as above, and subjected to analysis by the Agilent Bioanalyzer using an RNA 6000 Nano or Pico LabChip (Agilent Technologies)

tag: age range

value: Pediatric patient

tag: clinical procedure

value: Biopsy

tag: disease status

value: After glucocorticoid steroid treatment

value: epithelium

tag: histology procedure

value: Formalin-fixed paraffin-embedded


title: EoE patient #6_before treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-6B

source_name: EoE patient_before treatment

value: Before glucocorticoid steroid treatment


title: 13552313 - N25C15-2 vs N25C30-2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: How does the C/N balance act in cells ?

hyb_protocol: N25C30-2 Cy5 / N25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: cell culture/primary cell - Cells are grown in 50ml of Gamborg medium + 0.1mg/l 2,4-D in sterile 250 ml erlenmeyers.

extract_protocol: N25C30-2:34ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N25C30 - growth conditions - carbon concentration,sucrose:quantity 30g/l time 1week . Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

value: cell culture

extract_protocol: N25C15-2:17ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N25C15 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.


title: 12h_Gem_IC10_R2

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

country: India

institute: Piramal Lifesciences India Limited

hyb_protocol: The microarray slides were processed for pre-hybridization using the Pronto hybridization kit as described by the manufacturer. The slides were loaded onto the GeneTac automated hybridization station and primed with the labeled cDNA as per the manufacturer's instructions. A step down hybridization was performed for 18 hours with the following protocol – 6 hrs at 42 degree centigrade, 6 hours at 35 degree centigrade and 6 hours at 30 degree centigrade. At the end of the hybridization cycle, the slides were removed from the hybridization station, washed and processed for scanning as described by the manufacturer (Corning Pronto, USA). The slides were spun dry by centrifugation at 1600 rpm for 10 minutes and loaded onto a laser scanner for scanning the Cy3 and Cy5 intensities.

scan_protocol: The microarray slides were scanned with the “autogain” function of the scanner (GeneTAC UC4) so as to optimize the laser power for amplifying the low intensity spots versus avoiding the over-saturation of the high intensity spots on the slide. The resultant scanned tiff image files were gridded using the GAL file generated from the spotting run with use of the GeneTac Integrator software.

data_processing: Foreground and background intensity values were recorded for every gene in the array using a fixed threshold boundary by GeneTAC Integrator software. Background intensity values were subtracted from the foreground and normalized using global normalization algorithm used by GeneTAC Integrator software. The resultant comma separated file with the background subtracted, globally normalized intensity ratio between the treated versus control (Cy5/Cy3) values were used for statistical analysis.

source_name: pancreatic cancer cell line PANC-1

label_protocol: The total RNA from control PANC-1 cells were labeled with fluorescent dyes Cy3, whereas total RNA from treated cells were labelled with Cy5 using the indirect labeling method. Briefly, twenty micrograms of total RNA from PANC-1 cells were converted to cDNA using modified amino-allyl dUTP. The resultant cDNA was purified using the silica columns provided by the kit and subsequently used for dye conjugation. The purified cDNA was eluted in binding buffer and incubated with the DMSO dissolved Cy3 dye suspension for 3 hours in a thermo mixer at room temperature. Excess dye was quenched using 20mM hydroxylamine and the resultant labeled cDNA was again purified using the silica columns as provided by the kit. The purified and labeled cDNA was eluted using 65μL elution buffer. The exultant was dried under vacuum and resuspended in 65μl of hybridization buffer. The resuspended cDNA was heated at 95 degree centigrade for 5 minutes, flash chilled on ice and microfuged on ice before use in hybridization.

growth_protocol: The pancreatic cancer cell line PANC-1 (ATCC, Manassas, VA) was maintained in RPMI 1640 containing 10% heat inactivated fetal bovine serum (Sigma-Aldrich) and 1% antibiotic and antimycotic solution (Mediatech Inc) at 370C in a humidified atmosphere of 5% CO2.

extract_protocol: On assay completion, PANC-1 cells (treated & control) were harvested with chilled Trizol reagent (Invitrogen Corp, Carlsbad, USA). The volume of Trizol was maintained at 1 ml for every 1 x 106 cells. The cells with Trizol were stored at -80 degree centigrade until used for RNA extraction. The lysates were thawed at room temperature and passed through a 21-gauge needle for 10 times. This ensured that the lysates was uniformly homogenized. Post homogenization, the lysates were allowed to settle for 5 minutes at room temperature. The lysates were then spun at 12000 rpm for 15 minutes in a fixed angle rotor centrifuge at 4 degree centigrade. The upper aqueous phase was then transferred to a new microfuge tube and equal volumes of chilled 70% ethanol were added to the tubes. The ethanol-aqueous phase was mixed gently with a pipette and total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, USA). The lysates were then transferred to a purification column and spun at 10,000 rpm for 10 seconds. The flow-through is discarded and the column is filled with 500μl of RW1 buffer provided by the kit. The columns are spun at 10,000 rpm for 10 seconds and the flow-through is discarded. The columns are then filled with 500μl of RPE buffer and spun at 10,000 rpm for 10 seconds. The RPE buffer spin is repeated once more and a dry spin is performed by centrifugation of the empty column at 13,000 rpm for 2 minutes. The final elution step was performed by adding 32μl of nuclease free water and spinning the column for 5 minutes at 13,000 rpm. The concentration of the RNA is determined using 1μl of RNA with a Nanodrop spectro-photometer (ND-1000,).

treatment_protocol: PANC-1 cells were treated with single treatment of gemcitabine or P276-00 for 12 hours according to respective dosage (IC10, IC50). For combination treatment, the cells were pre-treated with Gemcitabine [(IC10 (100 nM)] followed by P276-00 [IC50 (1000 nM)] for 12 hours. The control cells were treated with vehicle control for 12 hours.

value: Control (Untreated)

tag: dose

value: Gemcitabine


title: 13552314 - N25C15-2 vs N2.5C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-2 Cy5 / N25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N2.5C15-2:39ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C15 - growth conditions - nitrogen concentration,nitrate:quantity 2.5mM time 1week . Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.


title: Atf3KO.oxLDL.1

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

hyb_protocol: Biotinylated cRNA was hybridized to an Affymetrix Mouse Exon 1.0 ST GeneChip using standard protocols and reagents from Affymetrix.

scan_protocol: Imaging was performed with the Affymetrix GeneChip Scanner 3000.

data_processing:
Scanned GeneChip images were processed into probe-level intensities (CEL files) using the Affymetrix GeneChip Operating Software.
Probe intensities were quantile normalized and probeset-summarized (at both exon and transcript levels) using the Affymetrix PLIER algorithm, with no background adjustment, as implemented in the Affymetrix Power Tools software suite. The probeset summarization was carried out using probe-to-probeset mappings from the CustomCDF Project based on the Ensembl Transcript databases (CustomCDF Version 13). Values are in log2 scale.
MoEx10stv1_Mm_ENST.pgf

label: biotin

organism: Mus musculus

label_protocol: Sample mRNA was amplified and labeled with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay protocol and reagents.

growth_protocol: Bone marrow cells collected from femurs were plated on non-tissue culture-treated plastic in complete RPMI medium [RPMI 1640 (Invitrogen) containing L-glutamine, supplemented with 10% (v/v) FBS (Invitrogen, cat #10437), 100 IU/mL penicillin and 100 μg/mL streptomycin (all from Cellgro)] plus 50 ng/mL recombinant human macrophage colony-stimulating factor (rhM-CSF, Chiron) (hereafter, BMDM medium). On day four, the medium was replaced, and on day six, adherent cells were lifted in PBS + 1 mM EDTA, counted, pelleted, resuspended in BMDM medium, and plated into six-well tissue culture plates.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent 2100 Bioanalyzer.

treatment_protocol: On day seven, for samples intended for oxLDL stimulation, oxidized LDL (CuSO4-oxidized human low density lipoprotein, from Intracel) was introduced into the culture medium, at 25 ug/mL (protein concentration). Cells were then incubated for 24 hours.

tag: strain background

tag: genotype/variation

value: Atf3-/- (Aft3 KO)

value: female

value: 8-12 weeks

tag: diet

value: normal chow

tag: cell type

value: Bone marrow-derived macrophages

tag: stimulus

value: oxidized low-density lipoprotein (oxLDL)

tag: stimulus concentration

value: 25 ug/mL

tag: stimulus duration


title: EoE patient #5_after treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-5A

value: Pediatric patient

tag: tissue


title: WT.unstim.3

value: wild type

tag: gender

tag: age


title: Cfin_High-Low food comparison_rep3

source_name: High food_Sample 3

tag: Stage

value: Adult female

tag: treatment

value: High food

value: Whole copepod, multiple individuals pooled

source_name: Low food_Sample 5

value: Low food


title: WT.unstim.2


title: Cfin_High-Low food comparison_rep1

source_name: High food_Sample 1


title: Cfin_High-Low food comparison_rep2

source_name: High food_Sample 2

source_name: Low food_Sample 7


title: EoE patient #5_before treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-5B

tag: age range

tag: clinical procedure

value: Biopsy

tag: disease status

value: Before glucocorticoid steroid treatment

value: epithelium

value: Formalin-fixed paraffin-embedded


title: WAT from Zucker Lean control Replicate2

value: Epididimal Fat

value: 12-weeks old

value: Male

tag: strain

value: ZDF lean control rat(Crl:ZUC-Leprfa)

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: 13552310 - N25C7.5-2 vs N25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-2 Cy5 / N25C7.5-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

value: cell culture

value: Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.

extract_protocol: N25C7.5-2:8ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N25C7.5 - growth conditions - carbon concentration,sucrose:quantity 7.5g/l time 1week . Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13561254 - N25C15-2 vs N25C7.5-2

description: How does the C/N balance act in cells ?

hyb_protocol: N25C7.5-2 Cy5 / N25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13561252 - N25C30-2 vs N25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-2 Cy5 / N25C30-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Pancreas from Zucker Lean control Replicate3

source_name: Pancreas of ZLC rat

value: Pancreas

source_name: Pancreas of of ZDF rat


title: Liver from Rosiglitazone-treated Zucker diabetic fatty rat Replicate1

source_name: Liver of Rosiglitazone-treated ZDF rat

value: liver

value: rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) daily for 2weeks by oral gavage

source_name: Liver of ZDF rat


title: WAT from Zucker Lean control Replicate1


title: 13550744 - N25C7.5-1 vs N25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-1 Cy5 / N25C7.5-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

extract_protocol: N25C15-1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: N25C7.5-1:19ug. (Qiagen_RNeasy.pdf)


title: 12h_Gem_IC10_R1

value: Control (Untreated)

tag: dose

value: Gemcitabine


title: Pancreas from Zucker Lean control Replicate2


title: WT.unstim.1

tag: strain background

tag: genotype/variation

value: wild type

value: female

value: 8-12 weeks

tag: diet

value: normal chow

value: Bone marrow-derived macrophages


title: EoE patient #4_after treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-4A

value: Pediatric patient

value: Biopsy

value: After glucocorticoid steroid treatment

value: epithelium

tag: histology procedure

value: Formalin-fixed paraffin-embedded


title: Cfin_Fat-Thin comparison_rep5R

source_name: Lipid-poor (thin) stage CV

treatment_protocol: Lipid-poor (lipid sac ≈ 5% by volume) C. finmarchicus juveniles (CV stage) were collected from the Gulf of Maine in June 5, 2009 and preserved in RNAlater in pools of 15 to 25 individuals.

value: Juvenile (CV)

tag: morphotype

value: Lipid-poor (thin)

value: Whole copepod, multiple individuals pooled

source_name: Lipid-rich (fat) stage CV

treatment_protocol: Lipid-rich (lipid sac ≈ 20% by volume) C. finmarchicus juveniles (CV stage) were collected from the Gulf of Maine in June 5, 2009 and preserved in RNAlater in pools of 15 to 25 individuals.

value: Lipid-rich (fat)


title: EoE patient #4_before treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-4B

value: Before glucocorticoid steroid treatment

tag: tissue


title: Cfin_Fat-Thin comparison_rep4R


title: Cfin_Fat-Thin comparison_rep5


title: EoE patient #2_after treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-2A


title: EoE patient #1_after treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-1A


title: EoE patient #2_before treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-2B


title: 13550742 - N2.5C30-1 vs N2.5C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-1 Cy5 / N2.5C30-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N2.5C15-1:8ug. (Qiagen_RNeasy.pdf)

value: cell culture

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

extract_protocol: N2.5C30-1:6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C30 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 2.5 mM Sucrose : 30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:2.5 mM Sucrose:30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: Cfin_Fat-Thin comparison_rep4


title: Cfin_Fat-Thin comparison_rep2


title: Cfin_Fat-Thin comparison_rep3


title: EoE patient #1_before treatment [miRNA]

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-1B


title: 13550743 - N25C15-1 vs N25C7.5-1

description: How does the C/N balance act in cells ?

hyb_protocol: N25C7.5-1 Cy5 / N25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.


title: Cfin_Fat-Thin comparison_rep1


title: 13550741 - N2.5C15-1 vs N2.5C30-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C30-1 Cy5 / N2.5C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Pancreas from Zucker Lean control Replicate1

value: Pancreas

value: 12-weeks old

tag: gender

value: Male

value: ZDF lean control rat(Crl:ZUC-Leprfa)

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: 13550738 - N2.5C15-1 vs N25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-1 Cy5 / N2.5C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550740 - N2.5C7.5-1 vs N2.5C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-1 Cy5 / N2.5C7.5-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N2.5C7.5-1:24ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C7.5 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 2.5 mM Sucrose : 7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:2.5 mM Sucrose:7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13550737 - N25C15-1 vs N2.5C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-1 Cy5 / N25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550739 - N2.5C15-1 vs N2.5C7.5-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C7.5-1 Cy5 / N2.5C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Muscle from Zucker Lean control Replicate2

source_name: Gastronemious of ZLC rat

value: Gastronemious

tag: age

source_name: Gastronemious of ZDF rat


title: Muscle from Zucker Lean control Replicate3


title: Liver from Zucker Lean control Replicate2

source_name: Liver of ZLC rat

value: liver


title: Liver from Zucker Lean control Replicate1


title: Liver from Zucker Lean control Replicate3


title: Muscle from Zucker Lean control Replicate1


title: Cold and warm perfusion supplemented with heparin

status: Public on Mar 22 2012

city: Sunderland

first: Noel

middle: Mark

last: Carter

state: Tyne and Wear

address: Wharnecliffe St

department: Pharmacy, Health and Wellbeing

country: United Kingdom

institute: University of Sunderland

description: Gene expression data from donor kidney after 3 hours hypothermic machine perfusion with cold UW solution (supplemented with heparin)  followed by 30 minutes of oxygenated warm perfusion with modified Krebs-Henseleit buffer (supplemented with heparin)

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

scan_protocol: GeneChips were scanned using an Affymetrix genechip scanner.

data_processing: Data was processed using GCRMA from simpleaffy (BioConductor)

label: Biotin

source_name: Kidneys from heparin group

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: Animals were housed and fed under normal conditions prior to experimental treatments

extract_protocol: Trizol extraction according to manufactureres instructions. The RNA was stored in 1X RNA secure storage solution (Ambion). Due to a restriction in funding available the RNA from three kidneys from the control, warm, heparin and PPS treated groups were pooled in an equimolar ratio to be used for labelling and hybridisation. Changes in gene expression are to be statistically verified by  Q-PCR performed of RNA from individual kidneys.

treatment_protocol: Animals were exsanguinated under schedule 1 of the animal experimentation act 1976. The animals were left for 29 minutes to simulate the period of primary warm ischemia suffered by organs in DCD donors. The left kidney was then removed and flushed. The kidney was then preserved by hypothermic machine perfusion for a period of 3 hours in cold University of Wisconsin (UW) organ preservation solution. After this storage period ischemia reperfusion injury was simulated by warm perfusion with oxygenated modified Krebs-Henseleit buffer. Control animal (n=3) were machine perfused for 3 hours using cold UW preservation solution and test animals (n=3 each group) were further perfused with warm oxygenated modified Krebs-Henseleit buffer for 30 minutes. In the treated groups, perfusates were supplemented with either low molecular weight heparin or PPS both during the cold and warm perfusion at a final concentration of 10 IU ml-1. After the period of warm oxygenated perfusion the kidneys were removed and used to extract RNA for gene expression analysis

value: Kidney

tag: Sex

tag: weight

value: Wistar


title: Cold perfusion only

description: Gene expression data from donor kidney after 3 hours hypothermic machine perfusion with cold University of Wisconsin (UW) solution

source_name: Kidneys from cold perfusion group


title: Cold and warm perfusion supplemented with PPS

description: Gene expression data from donor kidney after 3 hours hypothermic machine perfusion with cold UW solution (supplemented with PPS)  followed by 30 minutes of oxygenated warm perfusion with modified Krebs-Henseleit buffer (supplemented with PPS)

source_name: Kidneys from PPS group


title: ZR-75-30-BMP7/vehicle-12h

city: Tampere

first: Alejandra

last: Rodriguez-Martinez

address: Biokatu 6

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

hyb_protocol: The labeled cRNAs were hybridized to the 44K Whole Human Genome oligo microarrays (Agilent Technologies) according to the manufacturer’s protocol.

scan_protocol: Microarray slides were scanned (Agilent Microarray Scanner) after hybridization, and data were extracted using the Feature Extraction software, version A.7.5.1 (Agilent Technologies).

data_processing: Data were subjected to linear normalization to allow comparison between arrays. The normalized ratio data was obtained with the software named Anduril (version 1.1.0).

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 12 h

label_protocol: Total RNA (500 ng) was used to generate fluorescent Cy-3-(vehicle treated cells) or Cy-5-labeled cRNA (BMP7-treated cells) using the Agilent Low RNA Input Fluorescence Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) and the quality of RNA was validated using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Cells were seeded on 24-well plates, allowed to adhere for 24h, and treated with vehicle for 30min, 1h, 3h, 6h, 12h and 24h. Experiments were performed in triplicate and collected cells were pooled.

tag: cell line

tag: agent

value: vehicle

tag: time point

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 12 h

treatment_protocol: Cells were seeded on 24-well plates, allowed to adhere for 24h, and treated with recombinant human BMP7 protein for 30min, 1h, 3h, 6h, 12h and 24h. Experiments were performed in triplicate and collected cells were pooled.


title: T-47D-BMP7/vehicle-1h

source_name: T-47-D human breast cancer cell line, treated with vehicle, 1 h

source_name: T-47-D human breast cancer cell line, treated with BMP7, 1 h


title: ZR-75-30-BMP7/vehicle-6h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 6 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 6 h


title: MDA-MB-361-BMP7/vehicle-12h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 12 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 12 h


title: ZR-75-30-BMP7/vehicle-1h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 1 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 1 h


title: Cold and warm perfusion

description: Gene expression data from donor kidney after 3 hours hypothermic machine perfusion with cold UW solution followed by 30 minutes of oxygenated warm perfusion with modified Krebs-Henseleit buffer

source_name: Kidneys from warm perfusion group

tag: strain


title: ZR-75-30-BMP7/vehicle-24h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 24 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 24 h


title: ZR-75-30-BMP7/vehicle-30min

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 30 min

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 30 min


title: T-47D-BMP7/vehicle-6h

source_name: T-47-D human breast cancer cell line, treated with vehicle, 6 h

source_name: T-47-D human breast cancer cell line, treated with BMP7, 6 h


title: T-47D-BMP7/vehicle-30min

source_name: T-47-D human breast cancer cell line, treated with vehicle, 30 min

source_name: T-47-D human breast cancer cell line, treated with BMP7, 30 min


title: T-47D-BMP7/vehicle-12h

source_name: T-47-D human breast cancer cell line, treated with vehicle, 12 h

source_name: T-47-D human breast cancer cell line, treated with BMP7, 12 h


title: MDA-MB-231-BMP7/vehicle-30min

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 30 min

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 30 min


title: MDA-MB-361-BMP7/vehicle-6h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 6 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 6 h


title: MDA-MB-231-BMP7/vehicle-6h

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 6 h

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 6 h


title: T-47D-BMP7/vehicle-24h

source_name: T-47-D human breast cancer cell line, treated with vehicle, 24 h

source_name: T-47-D human breast cancer cell line, treated with BMP7, 24 h


title: T-47D-BMP7/vehicle-3h

source_name: T-47-D human breast cancer cell line, treated with vehicle, 3 h

source_name: T-47-D human breast cancer cell line, treated with BMP7, 3 h


title: MDA-MB-361-BMP7/vehicle-30min

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 30 min

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 30 min


title: ZR-75-30-BMP7/vehicle-3h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 3 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP7, 3 h


title: MDA-MB-361-BMP7/vehicle-24h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 24 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 24 h


title: MDA-MB-361-BMP7/vehicle-1h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 1 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 1 h


title: MDA-MB-231-BMP7/vehicle-1h

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 1 h

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 1 h


title: MDA-MB-231-BMP7/vehicle-12h

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 12 h

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 12 h


title: HCC1954-BMP7/vehicle-12h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 12 h

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 12 h


title: MDA-MB-231-BMP7/vehicle-24h

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 24 h

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 24 h


title: HCC1954-BMP7/vehicle-6h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 6 h

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 6 h


title: MDA-MB-231-BMP7/vehicle-3h

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 3 h

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP7, 3 h


title: HCC1954-BMP7/vehicle-30min

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 30 min

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 30 min


title: HCC1954-BMP7/vehicle-24h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 24 h

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 24 h


title: ZR-75-30-BMP4/vehicle-6h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 6 h

label_protocol: Total RNA (500 ng) was used to generate fluorescent Cy-3-(vehicle treated cells) or Cy-5-labeled cRNA (BMP4-treated cells) using the Agilent Low RNA Input Fluorescence Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions.

value: 6 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 6 h

treatment_protocol: Cells were seeded on 24-well plates, allowed to adhere for 24h, and treated with recombinant human BMP4 protein for 30min, 1h, 3h, 6h, 12h and 24h. Experiments were performed in triplicate and collected cells were pooled.


title: ZR-75-30-BMP4/vehicle-30min

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 30 min

value: 30 min

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 30 min


title: HCC1954-BMP7/vehicle-3h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 3 h

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 3 h


title: ZR-75-30-BMP4/vehicle-24h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 24 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 24 h


title: MDA-MB-361-BMP7/vehicle-3h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 3 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP7, 3 h


title: ZR-75-30-BMP4/vehicle-1h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 1 h

value: 1 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 1 h


title: SK-BR-3-BMP4/vehicle-12h

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 12 h

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 12 h


title: ZR-75-30-BMP4/vehicle-12h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 12 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 12 h


title: SK-BR-3-BMP4/vehicle-30min

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 30 min

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 30 min


title: SK-BR-3-BMP4/vehicle-1h

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 1 h

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 1 h


title: MDA-MB-361-BMP4/vehicle-12h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 12 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 12 h


title: MDA-MB-361-BMP4/vehicle-6h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 6 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 6 h


title: ZR-75-30-BMP4/vehicle-3h

source_name: ZR-75-30 human breast cancer cell line, treated with vehicle, 3 h

value: 3 h

source_name: ZR-75-30 human breast cancer cell line, treated with BMP4, 3 h


title: MDA-MB-361-BMP4/vehicle-30min

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 30 min

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 30 min


title: SK-BR-3-BMP4/vehicle-3h

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 3 h

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 3 h


title: HCC1954-BMP4/vehicle-12h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 12 h

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 12 h


title: SK-BR-3-BMP4/vehicle-6h

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 6 h

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 6 h


title: HCC1954-BMP4/vehicle-6h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 6 h

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 6 h


title: MDA-MB-361-BMP4/vehicle-3h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 3 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 3 h


title: MDA-MB-361-BMP4/vehicle-1h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 1 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 1 h


title: MDA-MB-361-BMP4/vehicle-24h

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 24 h

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 24 h


title: HCC1419-BMP4/vehicle-1h

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 1 h

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 1 h


title: 13561512 - RSt24h-2 vs RSt4d-2

description: Do nitrogen starvation and resupply change miRNAs ?

hyb_protocol: RSt4d-2 Cy5 / RSt24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

growth_protocol: roots - STANDARD MEDIUM

extract_protocol: RSt4d-2:4.6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:St4d - growth conditions - nitrogen concentration,nitrate:quantity 0.08mM time 4day. Plants are grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 4 days.

tag: ecotype

tag: treatment

value: roots

extract_protocol: RSt24h-2:13.2ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:St24h - growth conditions - nitrogen concentration,nitrate:quantity 0.08mM time 24hour. Plants are grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 24h.


title: 13552417 - LSt24h-1 vs LCo24h-1

hyb_protocol: LCo24h-1 Cy5 / LSt24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: rosette - STANDARD MEDIUM

extract_protocol: LCo24h-1:30.7ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Co24h - growth conditions - control,nitrate:quantity 8mM time 24hour. Plants are grown on normal medium until Boyes stage 1.04 and transfered on normal medium for 1 more day.

tag: dev.stage (boyes et al. plant cell 2001)

value: rosette

extract_protocol: LSt24h-1:27.7ug. (Qiagen_RNeasy.pdf)

value: grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 24h.


title: 13561492 - RSt4d-2 vs RSt24h-2

hyb_protocol: RSt24h-2 Cy5 / RSt4d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 4 days.


title: 13552419 - LSt4d-2 vs LSt10d-2

hyb_protocol: LSt10d-2 Cy5 / LSt4d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LSt10d-2:57ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:St10d - growth conditions - nitrogen concentration,nitrate:quantity 0.08mM time 10day. Plants are grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 10 days.

extract_protocol: LSt4d-2:74.8ug. (Qiagen_RNeasy.pdf)


title: HCC1954-BMP4/vehicle-24h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 24 h

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 24 h


title: HCC1954-BMP4/vehicle-3h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 3 h

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 3 h


title: 13561494 - LSt10d-2 vs LSt4d-2

hyb_protocol: LSt4d-2 Cy5 / LSt10d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: grown on normal medium until Boyes stage 1.04 and transfered on starvation medium for 10 days.


title: HCC1954-BMP4/vehicle-30min

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 30 min

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 30 min


title: HCC1419-BMP4/vehicle-12h

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 12 h

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 12 h


title: HCC1419-BMP4/vehicle-30min

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 30 min

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 30 min


title: HCC1954-BMP4/vehicle-1h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 1 h

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 1 h


title: HCC1419-BMP4/vehicle-24h

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 24 h

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 24 h


title: SK-BR-3-BMP4/vehicle-24h

source_name: SK-BR-3 human breast cancer cell line, treated with vehicle, 24 h

source_name: SK-BR-3 human breast cancer cell line, treated with BMP4, 24 h


title: 13552409 - LSt24h-1 vs LSt4d-1

hyb_protocol: LSt4d-1 Cy5 / LSt24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LSt4d-1:16.5ug. (Qiagen_RNeasy.pdf)


title: 13552402 - LSt10d-1 vs LSt4d-1

hyb_protocol: LSt4d-1 Cy5 / LSt10d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LSt10d-1:51.8ug. (Qiagen_RNeasy.pdf)


title: 13552323 - LSt24h-2 vs LCo24h-2

hyb_protocol: LCo24h-2 Cy5 / LSt24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LCo24h-2:61.7ug. (Qiagen_RNeasy.pdf)

value: grown on normal medium until Boyes stage 1.04 and transfered on normal medium for 1 more day.

extract_protocol: LSt24h-2:29.1ug. (Qiagen_RNeasy.pdf)


title: 13552416 - LCo24h-1 vs LSt24h-1

hyb_protocol: LSt24h-1 Cy5 / LCo24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13552401 - LSt4d-1 vs LSt10d-1

hyb_protocol: LSt10d-1 Cy5 / LSt4d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550762 - LSt4d-2 vs LSt24h-2

hyb_protocol: LSt24h-2 Cy5 / LSt4d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13552327 - LSt24h-2 vs LSt4d-2

hyb_protocol: LSt4d-2 Cy5 / LSt24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550759 - LCo24h-2 vs LSt24h-2

hyb_protocol: LSt24h-2 Cy5 / LCo24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550758 - RSt10d-2 vs RSt4d-2

hyb_protocol: RSt4d-2 Cy5 / RSt10d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: RSt10d-2:9ug. (Qiagen_RNeasy.pdf)


title: 13552410 - LSt4d-1 vs LSt24h-1

hyb_protocol: LSt24h-1 Cy5 / LSt4d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550761 - RSt4d-2 vs RSt10d-2

hyb_protocol: RSt10d-2 Cy5 / RSt4d-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561269 - RSt24h-2 vs RCo24h-2

hyb_protocol: RCo24h-2 Cy5 / RSt24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: RCo24h-2:9.4ug. (Qiagen_RNeasy.pdf)


title: 13550752 - RSt24h-1 vs RSt4d-1

hyb_protocol: RSt4d-1 Cy5 / RSt24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: RSt4d-1:14.3ug. (Qiagen_RNeasy.pdf)

extract_protocol: RSt24h-1:6.1ug. (Qiagen_RNeasy.pdf)


title: 13550754 - RSt4d-1 vs RSt10d-1

hyb_protocol: RSt10d-1 Cy5 / RSt4d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: RSt10d-1:46.4ug. (Qiagen_RNeasy.pdf)


title: HCC1419-BMP4/vehicle-3h

hyb_protocol: The labeled cRNAs were hybridized to the 44K Whole Human Genome oligo microarrays (Agilent Technologies) according to the manufacturer’s protocol.

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 3 h

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 3 h


title: 13550749 - RCo24h-1 vs RSt24h-1

hyb_protocol: RSt24h-1 Cy5 / RCo24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: RCo24h-1:5.1ug. (Qiagen_RNeasy.pdf)


title: 13550755 - RSt10d-1 vs RSt4d-1

hyb_protocol: RSt4d-1 Cy5 / RSt10d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550753 - RSt4d-1 vs RSt24h-1

hyb_protocol: RSt24h-1 Cy5 / RSt4d-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HCC1419-BMP4/vehicle-6h

source_name: HCC1419 human breast cancer cell line, treated with vehicle, 6 h

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) and the quality of RNA was validated using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA).

source_name: HCC1419 human breast cancer cell line, treated with BMP4, 6 h


title: 13550751 - RSt24h-1 vs RCo24h-1

hyb_protocol: RCo24h-1 Cy5 / RSt24h-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13550756 - RCo24h-2 vs RSt24h-2

hyb_protocol: RSt24h-2 Cy5 / RCo24h-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3T3-Pax6-p15

city: Tromso

first: Ingvild

last: Mikkola

address: 9037 Tromso

department: Department of Pharmacy

country: Norway

institute: University of Tromso

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data: The numerical results were extracted with Bead Studio v3.2.3 without any normalization or background subtraction. Normalized data: Normalized using quantile normalisation with limma in R

source_name: Flp-In-3T3 cells expressing Pax6, passage nr 15

label_protocol: For the Illumina gene expression analysis, 300 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: DMEM (high glucose), 10% FBS, 2 mM L-glutamine, 1% Pen-Strep, with 100 ug/ml Zeozin for the unmodified Flp-In-3T3 cells and 150 ug/ml Hygromycine for the Pax6 and Pax6(5a) cells.

extract_protocol: Trizol (Invitrogen)

treatment_protocol: No special treatment before harvesting.

tag: cell type

value: embryonic fibroblast


title: 3T3-K-p13-1

source_name: Flp-In-3T3 cells (Invitrogen), passage nr 13, replicate1

tag: genotype/variation

value: no Pax6 or Pax(5a)


title: 3T3-Pax6(5a)-p13

source_name: Flp-In-3T3 cells expressing Pax6(5a), passage nr 13


title: 3T3-K-p13-2

source_name: Flp-In-3T3 cells (Invitrogen), passage nr 13, replicate2


title: 3T3-Pax6(5a)-p8-2

source_name: Flp-In-3T3 cells expressing Pax6(5a), passage nr 8, replicate2


title: 3T3-K-19

source_name: Flp-In-3T3 cells (Invitrogen), passage nr 19


title: 3T3-Pax6-p9

source_name: Flp-In-3T3 cells expressing Pax6, passage nr 9


title: 3T3-Pax6(5a)-p8-1

source_name: Flp-In-3T3 cells expressing Pax6(5a), passage nr 8, replicate1


title: BXD83_M

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: Gene expression data from adult hypothalamus

hyb_protocol: The wash and staining are done on a Affymetrix Fluidics Station 450 and hybed and scanned using Affymetrix manufactures protocols for the Mouse Gene ST 1.0

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000

data_processing: Probe intensity values were extracted using the Affymetrix GeneChip Operating Software and RMA normalized

source_name: Hypothalamus, BXD83, M

label_protocol: 100ng of total RNA were amplified and labeled according to Affymetrix manufactures protocols for the Mouse Gene ST 1.0. Samples were amplified using the Ambion Whole Transcriptome Amplification Kit using manufactures protocols and the fragmentation and labeling was done according to Affymetrix manufactures protocols.

extract_protocol: RNA was purified using the RNAeasy micro kit on the QIAcube system (Qiagen, www.qiagen.com).

value: Hypothalamus

value: M

tag: age (days)


title: BXD92A_F

source_name: Hypothalamus, BXD92A, F

value: F


title: BXD70_F

source_name: Hypothalamus, BXD70, F


title: BXD85_M

source_name: Hypothalamus, BXD85, M


title: BXD83_F

source_name: Hypothalamus, BXD83, F


title: BXD56_F

source_name: Hypothalamus, BXD56, F


title: BXD85_F

source_name: Hypothalamus, BXD85, F


title: BXD68_F

source_name: Hypothalamus, BXD68, F


title: BXD70_M

source_name: Hypothalamus, BXD70, M


title: BXD68_M

source_name: Hypothalamus, BXD68, M


title: BXD87_F

source_name: Hypothalamus, BXD87, F


title: BXD95_F

source_name: Hypothalamus, BXD95, F


title: BXD92A_M

source_name: Hypothalamus, BXD92A, M


title: BXD90_M

source_name: Hypothalamus, BXD90, M


title: BXD32_F

source_name: Hypothalamus, BXD32, F


title: BXD79_F

source_name: Hypothalamus, BXD79, F


title: BXD90_F

source_name: Hypothalamus, BXD90, F


title: BXD87_M

source_name: Hypothalamus, BXD87, M


title: BXD101_M

source_name: Hypothalamus, BXD101, M


title: BXD101_F

source_name: Hypothalamus, BXD101, F


title: BXD97_F

source_name: Hypothalamus, BXD97, F


title: BXD50_M

source_name: Hypothalamus, BXD50, M


title: HCC1954-BMP7/vehicle-1h

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 1 h

source_name: HCC1954 human breast cancer cell line, treated with BMP7, 1 h


title: BXD97_M

source_name: Hypothalamus, BXD97, M


title: BXD63_F

source_name: Hypothalamus, BXD63, F


title: BXD56_M

source_name: Hypothalamus, BXD56, M


title: BXD48_M

source_name: Hypothalamus, BXD48, M


title: BXD71_F

source_name: Hypothalamus, BXD71, F


title: BXD99_M

source_name: Hypothalamus, BXD99, M


title: BXD50_F

source_name: Hypothalamus, BXD50, F


title: DBA/2J_M

source_name: Hypothalamus, DBA/2J, M


title: BXD65_F

source_name: Hypothalamus, BXD65, F


title: BXD48_F

source_name: Hypothalamus, BXD48, F


title: B6D2_F

source_name: Hypothalamus, B6D2, F


title: C57BL/6J_M

source_name: Hypothalamus, C57BL/6J, M


title: D2B6F1_M

source_name: Hypothalamus, D2B6F1, M


title: DBA/2J_F

source_name: Hypothalamus, DBA/2J, F


title: BXD99_F

source_name: Hypothalamus, BXD99, F


title: BXD89_M

source_name: Hypothalamus, BXD89, M


title: BXD65_M

source_name: Hypothalamus, BXD65, M


title: BXD95_M

source_name: Hypothalamus, BXD95, M


title: BXD71_M

source_name: Hypothalamus, BXD71, M


title: BXD89_F

source_name: Hypothalamus, BXD89, F


title: D2B6F1_F

source_name: Hypothalamus, D2B6F1, F


title: BXD40_M

source_name: Hypothalamus, BXD40, M


title: BXD40_F

source_name: Hypothalamus, BXD40, F


title: B6D2_M

source_name: Hypothalamus, B6D2, M


title: C57BL/6J_F

source_name: Hypothalamus, C57BL/6J, F


title: BXD100_F

source_name: Hypothalamus, BXD100, F


title: BXD62_M

source_name: Hypothalamus, BXD62, M