title: 249 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
249 10% Power (600-530)


title: 201 10% Power

status: Public on Mar 21 2013

type: RNA

city: Albuquerque

first: shannon

last: bruse

state: New Mexico

address: 2425 ridgecrest drive SE

country: USA

institute: lovelace respiratory research institute

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
201 10% Power (610-500)

hyb_protocol: Samples were hybridized to the array at 37˚C overnight using the hybridization buffer included with the labeling kit.

scan_protocol: Image analysis was performed on a GenePix 4000B microarray scanner.  A marked difference in pixel intensity was observed between Sanger miRNAs and the novel features exclusively present on the NCode V3 arrays, with many of the latter approaching saturation.  Photomultiplier tube (PMT) settings were adjusted so as to balance signal intensity in the red and green channels, and maximize pixel intensity without saturation at 10% power.  Arrays were then rescanned at 100% power without PMT adjustment.

data_processing: Images were exported and processed using the Acuity 4.0 software package.  Data filtering parameters were established to include only features with (1) at least 70% of pixels greater than 2 standard deviations above background in either the red or green channel, (2) regression R2 greater than 0.5 to ensure feature uniformity, (3) less than 20% of pixels saturated in both the red and the green channels, and (4) no flags upon visual inspection.  Normalization was performed with the LOWESS (locally weighted regression) method, and expression log ratios were used for statistical analysis.

molecule: total RNA

organism: Homo sapiens

source_name: Brain, cerebral tissue

label_protocol: On each array, a single Cy3 labeled total RNA sample was competitively hybridized against a Cy5 labeled control pool.  The control pool was a mixture of all RNA samples, where each developmental time point was equally represented, and each individual sample was equally represented within a given time point.  For each channel, 1 μg of total RNA was labeled with the Label IT® miRNA Labeling Kit, Version 2 (Mirus Bio, Madison, WI) according to manufacturer’s protocol.

growth_protocol: Frozen brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders, housed at the University of Maryland.  Brain sectioning (described at http://medschool.umaryland.edu/btbank/NICHD-BTB-ProtocolMethods.asp) began with separation of the cerebral hemispheres, followed by removal of the midbrain/pons/cerebellum. The remaining cerebrum (from the left hemisphere) was sectioned coronally at approximately 1 cm intervals.

extract_protocol: Tissue homogenization and RNA extraction procedures were performed using the mirVana PARIS kit (Ambion) according to the manufacturer’s protocol.  RNA yield and quality were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment

tag: tissue

value: Brain, cerebral tissue

tag: gestational age, weeks

tag: taqman pool by age

tag: Sex

value: male

tag: race

value: African American

tag: post-mortem interval (hours)

source_name: Brain

tag: sample type

value: Control pool (a mixture of all RNA samples, where each developmental time point was equally represented, and each individual sample was equally represented within a given time point)


title: P53-wildetype without Del17p, biological rep163

city: Basel

first: Giuseppe

last: Palermo

address: wettsteinallee 76

country: Switzerland

institute: F. Hoffman-La Roche Ltd.

hyb_protocol: Hybridization was performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Controls were omitted from the hybridization.

scan_protocol: Imaging and signal extraction were performed according to Affymetrix-recommended procedures. GCOS 1.3 was used

data_processing: The probe intensities of miRNA arrays were background-subtracted, quantile normalized and summarized using the RMA method. All data were log2-transformed

label: biotin

source_name: Patient WITHOUT P53-mutation and WITHOUT Del17p

label_protocol: The 3’ ends of RNA molecules in total RNA samples (400ng total RNA per sample) were labeled with biotin according to the company’s standard protocol

extract_protocol: RNA of CD19 selected B-cells was isolated using Ambion miRVANA total RNA extraction kit

tag: p53 mutation

value: NO


title: 280 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
280 10% Power (600-520)

value: female


title: 4609 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4609 10% Power (590-510)


title: P53-wildetype without Del17p, biological rep167


title: 1742 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1742 10% Power (600-490)

tag: age, years

tag: age, days


title: 1521 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1521 10% Power (600-530)


title: 1488 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1488 10% Power (610-510)


title: 46 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
46 10% Power (600-520)

value: Caucasian


title: P53-wildetype without Del17p, biological rep158


title: P53-wildetype without Del17p, biological rep155


title: P53-wildetype without Del17p, biological rep159


title: P53-wildetype without Del17p, biological rep157


title: P53-wildetype without Del17p, biological rep162


title: 1453 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1453 10% Power (600-550)


title: P53-wildetype without Del17p, biological rep156


title: P53-wildetype without Del17p, biological rep154


title: P53-wildetype without Del17p, biological rep160


title: 14 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
14 10% Power (600-570)


title: 1388 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1388 10% Power (620-560)


title: 1296 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1296 10% Power (590-480)


title: 113 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
113 10% Power (590-510)


title: 1185 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1185 10% Power (600-530)


title: 1499 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1499 10% Power (600-520)

value: Asian


title: P53-wildetype without Del17p, biological rep153


title: P53-wildetype without Del17p, biological rep161


title: 12 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
12 10% Power (610-570)


title: 1063 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1063 10% Power (620-490)


title: 1055 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1055 10%


title: P53-wildetype without Del17p, biological rep152


title: P53-wildetype without Del17p, biological rep149


title: Reference Pool 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
Reference Pool 100% Power (590-520)

source_name: Total Brain, multisample [FirstChoice Human Brain Reference RNA (Ambion)]


title: P53-wildetype without Del17p, biological rep148


title: P53-wildetype without Del17p, biological rep151


title: P53-wildetype without Del17p, biological rep150


title: First Choice 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
First Choice 100% Power (570-510)

source_name: Total Brain [FirstChoice Human Brain Total RNA (Ambion)]


title: P53-wildetype without Del17p, biological rep147


title: 633 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
633 100%


title: 66 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
66 100% Power (620-560)


title: 779 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
779 100% Power (590-520)


title: 9 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
9 100% Power (610-500)


title: P53-wildetype without Del17p, biological rep143


title: P53-wildetype without Del17p, biological rep140


title: 4825 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4825 100% Power


title: 4823 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4823 100% Power


title: 4889 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4889 100% Power


title: 4934 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4934 100% Power (610-540)


title: P53-wildetype without Del17p, biological rep141


title: 4799 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4799 100% Power (600-530)


title: 4912 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4912 100% Power (610-510)

value: African AmerincaAmerican


title: P53-wildetype without Del17p, biological rep139


title: P53-wildetype without Del17p, biological rep142


title: P53-wildetype without Del17p, biological rep135


title: 4794 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4794 100% Power (610-570)


title: P53-wildetype without Del17p, biological rep137


title: P53-wildetype without Del17p, biological rep144


title: P53-wildetype without Del17p, biological rep136


title: 4715 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4715 100% Power (600-530)


title: P53-wildetype without Del17p, biological rep134


title: P53-wildetype without Del17p, biological rep145


title: 57 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
57 100% power


title: P53-wildetype without Del17p, biological rep133


title: 4670 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4670 100% Power (620-550)


title: 4654 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4654 100% Power

value: unknown


title: P53-wildetype without Del17p, biological rep132


title: P53-wildetype without Del17p, biological rep131


title: 4573 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4573 100% Power (600-530)


title: 4609 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4609 100% Power (590-510)


title: 46 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
46 100% Power (600-520)


title: 396 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
396 100% Power (590-520)


title: 43 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
43 100% Power (590-490)


title: 45 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
45 100% Power (600-530)


title: P53-wildetype without Del17p, biological rep130


title: 391 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
391 100% Power


title: 392 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
392 100% Power


title: P53-wildetype without Del17p, biological rep126


title: 42 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
42 100% Power


title: P53-wildetype without Del17p, biological rep128


title: P53-wildetype without Del17p, biological rep127


title: P53-wildetype without Del17p, biological rep146


title: 33 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
33 100% Power (620-490)


title: P53-wildetype without Del17p, biological rep129


title: P53-wildetype without Del17p, biological rep120


title: P53-wildetype without Del17p, biological rep121


title: P53-wildetype without Del17p, biological rep125


title: P53-wildetype without Del17p, biological rep123


title: P53-wildetype without Del17p, biological rep122


title: P53-wildetype without Del17p, biological rep124


title: P53-wildetype without Del17p, biological rep119


title: 31 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
31 100% Power (600-520)


title: 291 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
291 100% Power (620-570)


title: 280 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
280 100% Power (600-520)


title: 311 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
311 100% Power (600-450)


title: P53-wildetype without Del17p, biological rep117


title: P53-wildetype without Del17p, biological rep115


title: 250 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
250 100% Power (620-560)


title: 261 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
261 100% Power (590-520)


title: 249 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
249 100% Power (600-530)


title: 201 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
201 100% Power (610-500)


title: P53-wildetype without Del17p, biological rep116


title: 1521 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1521 100% Power (600-530)


title: 1488 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1488 100% Power (610-510)


title: 279 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
279 100% Power (590-520)


title: P53-wildetype without Del17p, biological rep114


title: 1499 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1499 100% Power (600-520)


title: P53-wildetype without Del17p, biological rep110


title: P53-wildetype without Del17p, biological rep112


title: P53-wildetype without Del17p, biological rep111


title: P53-wildetype without Del17p, biological rep118


title: P53-wildetype without Del17p, biological rep164


title: P53-wildetype without Del17p, biological rep108


title: 278 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
278 100% Power (600-540)


title: P53-wildetype without Del17p, biological rep107


title: P53-wildetype without Del17p, biological rep106


title: 1388 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1388 100% Power (620-560)


title: 14 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
14 100% Power (600-570)


title: 1742 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1742 100% Power (600-490)


title: P53-wildetype without Del17p, biological rep113


title: P53-wildetype without Del17p, biological rep105


title: P53-wildetype without Del17p, biological rep104


title: P53-wildetype without Del17p, biological rep109


title: 1296 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1296 100% Power (590-480)


title: 1453 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1453 100% Power (600-550)


title: 12 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
12 100% Power (610-570)


title: 113 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
113 100% Power (590-510)


title: 1055 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1055 100%


title: 1063 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1063 100% Power (620-490)


title: 1185 100% Power

description:
This is the 100% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
1185 100% Power (600-530)


title: P53-wildetype without Del17p, biological rep102


title: P53-wildetype without Del17p, biological rep98


title: P53-wildetype without Del17p, biological rep103


title: P53-wildetype without Del17p, biological rep100


title: P53-wildetype without Del17p, biological rep101


title: P53-wildetype without Del17p, biological rep99


title: P53-wildetype without Del17p, biological rep95


title: P53-wildetype without Del17p, biological rep96


title: P53-wildetype without Del17p, biological rep89


title: P53-wildetype without Del17p, biological rep97


title: P53-wildetype without Del17p, biological rep91


title: P53-wildetype without Del17p, biological rep94


title: P53-wildetype without Del17p, biological rep93


title: P53-wildetype without Del17p, biological rep88


title: P53-wildetype without Del17p, biological rep92


title: P53-wildetype without Del17p, biological rep90


title: P53-wildetype without Del17p, biological rep174


title: P53-wildetype without Del17p, biological rep87


title: P53-wildetype without Del17p, biological rep83


title: P53-wildetype without Del17p, biological rep85


title: P53-wildetype without Del17p, biological rep84


title: P53-wildetype without Del17p, biological rep86


title: P53-wildetype without Del17p, biological rep82


title: P53-wildetype without Del17p, biological rep138


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep1

type: genomic

city: Martinsried/Munich

first: Jörg

last: Renkawitz

address: Am Klopferspitz 18

department: Molecular Cell Biology

country: Germany

institute: Max Planck Institute of Biochemistry

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: Raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor as described ((Prestel et al., 2010) and Tobias Straub Epigenome project PROT43, http://www.epigenesys.eu/).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Input DNA

label_protocol: standard NimbleGen protocol

growth_protocol: YP lactate

extract_protocol: Chromatin extract preparation and chromatin immunoprecipitation were performed as described in (Kalocsay et al., 2009). Briefly, 200ml cultures of every time point were cross-linked by the addition of 1% (final concentration) formaldehyde for 16 min, and subsequent quenching with 375 mM (final concentration) glycine for at least 10 min. Cells were lysed using Silica beads, the chromatin was enriched by centrifugation and sonicated (water bath sonification: Bioruptor UCD-200, Diagenode) to shear the DNA to an average size of 250-500 bp. After RNase treatment and ligation of linker oligonucleotides, DNA was amplified two times for 14 PCR cycles (using the GenomePlex Whole Genome Amplification (WGA) and reamplifications kits (Sigma)), as described in the Farnham Lab protocol for WGA amplification of DNA (O'Geen et al., 2006). Subsequent labeling of input and IP samples (either Cy3 or Cy5), hybridization to custom-made high-density whole S. cerevisiae genome NimbleGen arrays, array scanning and raw data extraction was done by imaGenes (www.imaGenes-bio.de).

treatment_protocol: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr

tag: chip antibody

value: Input DNA

tag: strain

tag: treatment

source_name: gamma-H2A ChIP


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep2

value: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr


title: P53-wildetype without Del17p, biological rep80


title: P53-wildetype without Del17p, biological rep81


title: P53-wildetype without Del17p, biological rep79


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep1

treatment_protocol: Without addition of 2% Galactose

value: Without addition of 2% Galactose


title: P53-wildetype without Del17p, biological rep78


title: P53-wildetype without Del17p, biological rep76


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep2


title: P53-wildetype without Del17p, biological rep75


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep1

source_name: Myc ChIP DNA

value: Myc


title: P53-wildetype without Del17p, biological rep73


title: P53-wildetype without Del17p, biological rep72


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep1


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep2

source_name: Rad52 ChIP DNA


title: P53-wildetype without Del17p, biological rep65


title: gammaH2A_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep2


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep1


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep2


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep1


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep2


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep2


title: P53-wildetype without Del17p, biological rep62


title: P53-wildetype without Del17p, biological rep71


title: P53-wildetype without Del17p, biological rep61


title: P53-wildetype without Del17p, biological rep74


title: P53-wildetype without Del17p, biological rep63


title: P53-wildetype without Del17p, biological rep68


title: P53-wildetype without Del17p, biological rep66


title: P53-wildetype without Del17p, biological rep64


title: P53-wildetype without Del17p, biological rep67


title: P53-wildetype without Del17p, biological rep59


title: P53-wildetype without Del17p, biological rep60


title: P53-wildetype without Del17p, biological rep58


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep1


title: Rad52_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep1


title: P53-wildetype without Del17p, biological rep56


title: P53-wildetype without Del17p, biological rep55


title: P53-wildetype without Del17p, biological rep54


title: P53-wildetype without Del17p, biological rep70


title: P53-wildetype without Del17p, biological rep52


title: P53-wildetype without Del17p, biological rep53


title: P53-wildetype without Del17p, biological rep77


title: P53-wildetype without Del17p, biological rep51


title: P53-wildetype without Del17p, biological rep49


title: P53-wildetype without Del17p, biological rep46


title: P53-wildetype without Del17p, biological rep47


title: P53-wildetype without Del17p, biological rep50


title: P53-wildetype without Del17p, biological rep45


title: P53-wildetype without Del17p, biological rep44


title: P53-wildetype without Del17p, biological rep42


title: P53-wildetype without Del17p, biological rep43


title: P53-wildetype without Del17p, biological rep40


title: P53-wildetype without Del17p, biological rep48


title: P53-wildetype without Del17p, biological rep38


title: P53-wildetype without Del17p, biological rep41


title: iLN_InVivo_Rep2_DyeSwap2-1_4

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

country: Belgium

institute: University of Liege

hyb_protocol: Hybridization was performed according to the VIB Leuven Microarray facility's standard protocol: hybridization was carried out at 65°C for 17 hours at 10 rpm, after 17 h the glass slides were washed without triton.

scan_protocol: After hybridization, the glass slides were dried and scanned using a Scanner G2505C (Agilent Technologies, USA, VIB Leuven Microarray facility).

data_processing: The data was analyzed in R using the 'limma' package from the Bioconductor project. The two-colour arrays were first background corrected with the 'norm exp' method and an offset of 50 and then normalized with a 'loess' normalization.

molecule: polyA RNA

organism: Bos taurus

source_name: Inguinal lymphnode from AlHV-1 infected individual 718

label_protocol: Samples were prepared with the standard RNA Gene Expression Agilent Kit (QuickAmp) which includes a poly-dT amplification and Cy3 or Cy5 labeling (cyanine) steps.

growth_protocol: Calves were selected from a Bovine herpesvirus 1, 4 and Bovine Viral Diarrhea virus (BVDV)-free herd in the Czech Republic. All calves were screened one week after transportation at the Veterinary and Agrochemical Research Institute (Brussels, Belgium) and confirmed to be negative for the three viral infections mentioned above. The animals were allowed to acclimatize for 6 weeks and maintained on a diet of hay supplemented with minerals and concentrates.

extract_protocol: RNA samples were obtained from cultured inguinal LN biopsies using the RNeasy miniprep kit with on-column DNAse I treatment (Qiagen). The absence of contaminating genomic viral DNA was determined by PCR on all RNA samples and RNA quality was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: inguinal lymphnode

tag: gender

tag: breed

value: Holstein-Friesan

tag: age

value: 4-6 months

tag: infection

value: AlHV-1 C500 strain

source_name: Inguinal lymphnode from Mock infected individual 969

value: mock-infection


title: P53-wildetype without Del17p, biological rep37


title: iLN_InVivo_Rep4_DyeSwap1-2_3

source_name: Inguinal lymphnode from Mock infected individual 846

tag: tissue

value: male

source_name: Inguinal lymphnode from AlHV-1 infected individual 911


title: MDBK_InVitro_Rep4_DyeSwap2-2_4

source_name: AlHV-1 infected MDBK cells

growth_protocol: Madin-darby bovine kidney cells (MDBK, ATCC) were cultured in Dulbecco’s modified Essential Medium (DMEM, Life technologies) containing 10 % foetal calf serum (FCS, Bio Wittaker). The pathogenic AlHV-1 C500 strain isolated from an ox with MCF and the AlHV-1 BAC clone were used throughout this study . The virus strains were maintained by limited passage (<5).

extract_protocol: RNA samples were obtained from cultured MDBK cells using the RNeasy miniprep kit with on-column DNAse I treatment (Qiagen). The absence of contaminating genomic viral DNA was determined by PCR on all RNA samples and RNA quality was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: MDBK cells from ATCC (CCL-22)

source_name: Mock infected MDBK cells


title: P53-wildetype without Del17p, biological rep36

value: NO


title: MDBK_InVitro_Rep4_DyeSwap1-2_3


title: iLN_InVivo_Rep4_DyeSwap2-2_4


title: iLN_InVivo_Rep3_DyeSwap1-2_1

source_name: Inguinal lymphnode from Mock infected individual 619

source_name: Inguinal lymphnode from AlHV-1 infected individual 273


title: P53-wildetype without Del17p, biological rep39


title: iLN_InVivo_Rep3_DyeSwap2-2_2


title: iLN_InVivo_Rep2_DyeSwap1-1_3


title: iLN_InVivo_Rep1_DyeSwap1-1_1

source_name: Inguinal lymphnode from Mock infected individual 436

source_name: Inguinal lymphnode from AlHV-1 infected individual 617


title: MDBK_InVitro_Rep3_DyeSwap1-2_1


title: iLN_InVivo_Rep1_DyeSwap2-1_2


title: P53-wildetype without Del17p, biological rep35

source_name: Patient WITHOUT P53-mutation and WITHOUT Del17p


title: P53-wildetype without Del17p, biological rep31


title: P53-wildetype without Del17p, biological rep69


title: P53-wildetype without Del17p, biological rep34


title: P53-wildetype without Del17p, biological rep33


title: P53-wildetype without Del17p, biological rep32


title: P53-wildetype without Del17p, biological rep30


title: P53-wildetype without Del17p, biological rep28


title: P53-wildetype without Del17p, biological rep27


title: MDBK_InVitro_Rep2_DyeSwap1-1_3


title: P53-wildetype without Del17p, biological rep29


title: p3143_rep4

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: The hybridization was done according to manufacturer´s instructions and using the protocol One-Color Microarray-Based Gene Expression Analysis -protocol version 5.5, February 2007.

scan_protocol: Microarrays were washed and scanned with Agilent Scanner  using manufacturer provided protocols. Feature Extraction software was used for image analysis.

data_processing: BioConductor Limma package.

source_name: CaCo2 cells

label_protocol: The labeling was done according to manufacturer´s instructions and using the protocol One-Color Microarray-Based Gene Expression Analysis -protocol version 5.5, February 2007.

growth_protocol: Caco-2 cells (American Cell Type Collection, HTB-37, Rockville, MD, USA) were kindly provided by Prof. M. Mäki (University of Tampere, Tampere, Finland). Cells were maintained in minimum essential medium (MEM, 31095-029 GIBCO) supplemented with 1X sodium pyruvate (NaPy 100X, 11360-039 GIBCO), 1% Pen-Strep (Pen-Strep, 15070-063 GIBCO), 1X non-essential amino acids (NEAA 100X, 11140-035 GIBCO) and 10% fetal calf serum (FCS, C-37350 PROMOCELL) in 75cm2 flasks (353136 BD Biosciences) and were routinely split every 5 days. For stimulations, 3x105 cells were seeded in 25 cm2 flasks (156367, nunc) in 3ml MEM+1% FCS and incubated at 37°C with 5% CO2 in the air. On the third day of seeding, before stimulations the undifferentiated Caco-2 cells were washed once with 1X phosphate-buffered saline (PBS).

extract_protocol: The cells were collected by adding 1ml 1X trypsin-EDTA (Trypsin 10X, 15400-054 Invitrogen) to the flasks followed by 4-5 min incubation at 37°C. Trypsin was inhibited by adding 1ml MEM+10% FCS and the cells were collected by centrifugation at 9.600x g for 5 min. The pellet was washed with 500µl 1X PBS and RNA was extracted using RNeasy Plus Mini kit (74134, QIAGEN).

treatment_protocol: Bovine serum albumin (BSA) was obtained from Sigma Aldrich (Albumin, bovine fraction V powder, A8806-1G Sigma Aldrich) and contained endotoxin at ≤ 0.1ng/mg. Lactalbumin was also obtained from Sigma Aldrich (Alpha-lactalbumin from bovine milk, 61289-50MG Sigma Aldrich), however information on endotoxin level in lactalbumin was not available. Pepsin- and trypsin- digested BSA (PT-BSA), pepsin- and trypsin- digested lactalbumin (PT-L), a blank pepsin- and trypsin- control (PT), where no substrate was used for digestion, and PT-G were prepared as described earlier (Lindfors,K. 2008). An endotoxin test was performed on PT-G and PT-BSA using a Limulus Amebocyte Lysate (LAL), Pyrogent plus single test kit (cat no. N289-06, CAMBREX). No endotoxin was found in PT-G, but PT-BSA tested positive for endotoxin.  Lyophilised PT, PT-BSA, PT-L and PT-G were dissolved in MEM+1% FCS and filter sterilised by passing through 0.22µm pore filter (SLGS033SS, Millipore). Similarly the synthetic peptides p31-43 (LGQQQPFPPQQPY) and the immunogenic peptide p57-68 (QLQPFPQPQLPY) (New England Peptide LLC, USA) were dissolved in MEM+1% FCS to achieve a final concentration of 150µg/ml. PT, PT-BSA and PT-L were used as negative controls for PT-G treatment. The cells were stimulated for six hours with a particular stimulant dissolved in 2ml MEM+1% FCS. The control cells (MED-CTL) were kept in MEM+1% FCS for six hours. In total, four identical but independent experiments were performed with cells differing in 1-2 passages between each experiment.

tag: agent


title: MDBK_InVitro_Rep3_DyeSwap2-2_2


title: MDBK_InVitro_Rep2_DyeSwap2-1_4


title: MDBK_InVitro_Rep1_DyeSwap1-1_1


title: P53-wildetype without Del17p, biological rep24


title: P53-wildetype without Del17p, biological rep22


title: MEDIUM_rep4

value: MEDIUM


title: PT_rep4

value: PT


title: PTG_rep3

value: PTG


title: P53-wildetype without Del17p, biological rep25


title: MDBK_InVitro_Rep1_DyeSwap2-1_2


title: PTG_rep4


title: P53-wildetype without Del17p, biological rep23


title: P53-wildetype without Del17p, biological rep26


title: PTG_rep2


title: PT_rep3


title: MEDIUM_rep3


title: P53-wildetype without Del17p, biological rep21


title: p3143_rep3


title: P53-wildetype without Del17p, biological rep20


title: PT_rep2


title: P53-wildetype without Del17p, biological rep17


title: MEDIUM_rep1


title: P53-wildetype without Del17p, biological rep18


title: P53-wildetype without Del17p, biological rep19


title: PTG_rep1


title: p3143_rep2


title: P53-wildetype without Del17p, biological rep57


title: P53-wildetype without Del17p, biological rep8


title: p3143_rep1


title: P53-wildetype without Del17p, biological rep14


title: P53-wildetype without Del17p, biological rep9


title: P53-wildetype without Del17p, biological rep15


title: PT_rep1


title: P53-wildetype without Del17p, biological rep13


title: Huh7 cells_SOR+CELE treated_48h vs untreated HepG2 cells_rep1

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

department: Medicine

country: Canada

institute: Laval university

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Control Huh7 cells (DMSO-treated)

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: HepG2 and Huh7 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: The human HCC cell lines HepG2 and Huh7 were treated simultaneously with 50 µM celecoxib and 7.5 µM sorafenib for 48 hours.

tag: cell type

value: hepatocellular carcinoma (HCC)

source_name: Huh7 cells, simultaneously treated with 50 µM celecoxib and 7.5 µM sorafenib for 48 hours


title: P53-wildetype without Del17p, biological rep10


title: Huh7 cells_SOR+CELE treated_48h vs untreated HepG2 cells_rep2 (dye swap)


title: P53-wildetype without Del17p, biological rep16


title: MEDIUM_rep2


title: P53-wildetype without Del17p, biological rep11


title: P53-wildetype without Del17p, biological rep12


title: HepG2 cells_SOR+CELE treated_48h vs untreated HepG2_rep2 (dye swap)

source_name: HepG2 cells, simultaneously treated with 50 µM celecoxib and 7.5 µM sorafenib for 48 hours

source_name: Control HepG2 cells (DMSO-treated)


title: pCAGGS-IRES-CFP transfected HeLa cell

city: Wako

first: Yoko

last: Aida

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

country: Japan

institute: RIKEN

description: Control

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip Command Console Software (AGCC) were used for processing scanning data. Normalization was performed using MAS5.0.

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: RNA from total cell extracts was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instruction.

value: HeLa

tag: transiently transfected with

value: pCAGGS vector


title: control diet, biological rep 5

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.

label: Biotin

organism: Rattus norvegicus

source_name: Liver of rat fed iron-deficient diet

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n = 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).

value: 5 weeks

value: liver

value: control diet


title: HepG2 cells_SOR+CELE treated_48h vs untreated HepG2_rep1


title: P53-wildetype without Del17p, biological rep7


title: control diet, biological rep 4


title: P53-wildetype without Del17p, biological rep4


title: P53-wildetype without Del17p, biological rep2


title: HFD [D918]

city: Nashville

first: Kasey

middle: C

last: Vickers

state: TN

address: 2220 Pierce Ave   358 PRB

institute: Vanderbilt Univ. School of Medicine

description: mouse liver mRNA

hyb_protocol: Samples were hybridized to GeneChip.MOuse430_2 arrays, washed, stained (Affymetrix Fluidics Station)

scan_protocol: Affymetrix GeneChip Scanner

data_processing: GeneSpring GX 12.0 (CEL input,RMA (summarization algorithm) and quantile normalized, data was baseline transformed to median of all samples)

organism: Mus musculus

source_name: Liver

label_protocol: Affymetrix GeneChip microarray assays were completed according to manufacture protocols (Affymetrix). Briefly, 1 microgram total RNA was reverse transcribed (T-7 dT primers), amplified and biotinylated (Affymetrix IVT Labeling Kit).

growth_protocol: Chow diets until study

extract_protocol: miRNAEasy Kits

treatment_protocol: HFD (21% fat; 42% calories from fat) Harlan-Teklad

tag: diet

value: high-fat diet (21% fat)


title: P53-wildetype without Del17p, biological rep1


title: pCAGGS-Tax-IRES-CFP transfected HeLa cell

description: HTax

value: pCAGGS-HTLV-1 tax gene amplified from HTLV-1 infectious molecular clone K30-FLAG tagged vector


title: iron-deficient diet, biological rep 5

value: iron-deficient diet


title: HFD [D921]

description: mouse liver mRNA


title: iPS4 [11899]

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA    * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)    * Priming: 5xSSC, 0.1%SDS    * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul    * Hybridization: 45 min at 42C.    * Wash 2x: milliQ    * Wash: 5xSSC, 0.1%SDS    * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)    * Hybridization: 16 hours at 42C.    * Wash 2x: 1xSSC, 0.2%SDS at 23C    * Wash 2x: 0.1xSSC, 0.2%SDS at 23C    * Wash 2x: 0.1xSSC at 23C    * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. Data processing :  maanova : running Wu & Churchill's MAANOVA to obtain estimates for sample effect. In a fixed effect analysis, sample, array and dye effects are modeled. P-values are determined by a permutation F2-test, in which residuals are shuffled 5000 times globally. Genes with p < 0.05 after family wise error correction are considered significantly changed.!Sample_data_row_count = 45220

label_protocol: robot amplification and labeling v1.0 All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).        mRNA amplification protocol description:    * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.    * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.    * plate is incubated @ 70C for 10 mins, cooled to 48C.    * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.    * plate is incubated @ 48C for 2 hours and cooled to room temperature.    * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well.    * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .    * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).    * Plate is incubated @37C for 4 hours.    * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.     * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.    * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.        Labeling protocol description:     * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).      All subsequent steps are performed by the robot script :    * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).    * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.    * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.    * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.    * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.    * RNA concentration and labeling incorporation are measured (SpectraMax 190).    * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.    * Samples are stored at -20C until hybridization.

growth_protocol: iPS cells were obtained by transduction of OG2 MEFs with a mixture of pMX retroviruses expressing Oct4, Sox2, Klf4, c-Myc, TAF3, TAF4, TAF4b, TAF5, TAF6, TAF7, TAF9, TAF10, TAF11, TAF12, TAF13, and TBP. After 12 days, GFP+ colonies were picked and expanded. Three lines, iPS#1, iPS#4, and iPS#5 were used for microarray analysis. OG2 ES cells or iPS cells derived from OG2 mouse embryonic fibroblasts (MEFs) 3 were cultured on irradiated MEF feeder cells in the following medium: DMEM high glucose (4.5g/l) (Invitrogen), 10% FBS gold (PAA), heat inactivated for 30 min at 56° C, 5% Serum replacement (Gibco), 2 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 0.1 mM ?-mercaptoethanol (Sigma), 50 ?g/ml penicillin/streptomycin (Invitrogen), and LIF.

extract_protocol: 1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.     2. Incubate 5 min at room temperature.     3. Add chloroform (200 Âµl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.     4. Centrifuge 20 min at 14000 rpm 4Â°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.     5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.     6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 Âµg/column)     7. Adjust each sample to a volume of 300 Âµl with sterile MilliQ water. Add 160 Âµl buffer RLT to the samples, and mix (= lysis buffer).     8. Add 240 Âµl ethanol (100% stored at -20 Â°C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.     9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 Âµl/reaction): add 10 Âµl DNase I stock solution to 70 Âµl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 Âµl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30Â°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.     10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 Âµl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.    11. Pipet 500 Âµl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.     12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).     13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 Âµl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 Âµl milliQ.     14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 Â°C.

value: ES

value: MEF


title: HFD [D915]

description: mouse liver mRNA


title: P53-wildetype without Del17p, biological rep3


title: control diet, biological rep 3

value: male


title: iron-deficient diet, biological rep 4


title: iPS5 [11904]


title: P53-wildetype without Del17p, biological rep6


title: control diet, biological rep 1


title: iPS5 [11900]


title: P53-mutated with Del17p, biological rep19

source_name: Patient WITH P53-mutation and WITH Del17p

value: YES

tag: multiple p53 mutation


title: P53-wildetype without Del17p, biological rep5

tag: p53 mutation

value: NO


title: Control [C975]

description: mouse liver mRNA

value: Control


title: Control [C978]

description: mouse liver mRNA


title: iron-deficient diet, biological rep 3


title: HFD [D917]

description: mouse liver mRNA


title: control diet, biological rep 2


title: HFD [D922]

description: mouse liver mRNA


title: Control [C976]

description: mouse liver mRNA


title: Zym_rep3

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

institute: National Food Rsearch Institute

description:
Zym_3
Gene expression data from yeast treated with zymolyase.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Signals were calculated by MAS5.0 using Affymetrix GeneChip Operating Software Version 1.4.

source_name: BY4743, zymolyase

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets using the Affymetrix 3' IVT Express Kit.

growth_protocol: The S. cerevisiae BY4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) strain was incubated in YPD medium at 25C for 2 days.

extract_protocol: Each sample of total RNA was extracted using the FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Yeast cells were treated with final 30 U/ml of zymolyase, and was incubated at 37 ℃ for 10 min. Non-treated samples were prepared as a control. Each condition was replicated three times.

tag: background/strain

value: zymolyase


title: iron-deficient diet, biological rep 2


title: Control [C977]

description: mouse liver mRNA


title: P53-mutated with Del17p, biological rep18

tag: dominant p53 mutation


title: iPS4 [11903]


title: P53-mutated with Del17p, biological rep16


title: P53-mutated with Del17p, biological rep17


title: iPS1 [11898]


title: Zym_rep2

description:
Zym_2
Gene expression data from yeast treated with zymolyase.


title: iron-deficient diet, biological rep 1


title: iPS1 [11902]


title: Control_untreated_rep2

description:
CON_2
Gene expression data from untreated yeast.

source_name: BY4743, control


title: Control_untreated_rep3

description:
CON_3
Gene expression data from untreated yeast.


title: Primary ESCC tissue from patient 3 with ESCC

city: Calgary

first: Wei

last: Wu

address: 3330 Hospital Dr. NW

institute: 1.Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China; 2. University of Calgary

description: primary ESCC tissue

hyb_protocol: 1600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately with acetonitrile for 1 min.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 20 bit tiff file, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11and Grid:028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: surgical speciment from normal esophageal tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using  One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0 (Agilent) following manufacture's instruction, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs were extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary  tumours and adjacent non-neoplastic tissues were obtained from patients with esophageal squamous cell cancer who underwent surgical treatment, the samples were immeidately stored in liquid nitroge tank.

value: primary esophageal sqaumous cell cancer (ESCC)

value: Male


title: Primary ESCC tissue from patient 4 with ESCC

description: primary ESCC tissue


title: PP002-H-1

growth_protocol: Stable control knock down or TAF5 knock down cell lines were obtained after transduction with pLKO-puro lentivirus expressing shRNA followed by selection with 1.8 mg/ml puromycin. Resistant colonies were picked after 10 days and expanded. IB10 E14 mouse ES cells and clonal knock down cell lines derived from these cells were cultured on gelatinized plates in medium containing Dulbecco's minimal medium (DMEM) with high glucose (Lonza), 15% fetal bovine serum (Hyclone), 1 U/ml penicillin/streptavidin (Lonza), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate (Lonza), 0.1 mM  -mercaptoethanol, and LIF

value: E14, subclone IB10

value: ES cells

tag: genetic modification


title: P53-mutated with Del17p, biological rep14


title: Normal esophageal tissue from patient 3 with ESCC

description: normal esophageal tissue

source_name: surgical speciment from ESCC adjacent normal tissue

value: normal esophageal


title: Primary ESCC tissue from patient 2 with ESCC

description: primary ESCC tissue


title: Normal esophageal tissue from patient 4 with ESCC

description: normal esophageal tissue


title: PP002-F-2


title: PP002-H-2


title: Control_untreated_rep1

description:
CON_1
Gene expression data from untreated yeast.


title: P53-mutated with Del17p, biological rep13


title: P53-mutated with Del17p, biological rep12


title: Zym_rep1

description:
Zym_1
Gene expression data from yeast treated with zymolyase.


title: Normal esophageal tissue from patient 2 with ESCC

description: normal esophageal tissue


title: PP002-B-2


title: P53-mutated with Del17p, biological rep11


title: P53-mutated with Del17p, biological rep15


title: PP002-B-1


title: Primary ESCC tissue from patient 1 with ESCC

description: primary ESCC tissue


title: PP002-F-1


title: Normal esophageal tissue from patient 1 with ESCC

description: normal esophageal tissue


title: P53-mutated with Del17p, biological rep8


title: P53-mutated with Del17p, biological rep9


title: P53-mutated with Del17p, biological rep10


title: P53-mutated with Del17p, biological rep6


title: PP002-A-1

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. Data processing :  maanova : running Wu & Churchill's MAANOVA to obtain estimates for sample effect. In a fixed effect analysis, sample, array and dye effects are modeled. P-values are determined by a permutation F2-test, in which residuals are shuffled 5000 times globally. Genes with p < 0.05 after family wise error correction are considered significantly changed.


title: P53-mutated with Del17p, biological rep7


title: PP002-A-2


title: P53-mutated with Del17p, biological rep4


title: P53-mutated with Del17p, biological rep5


title: P53-mutated with Del17p, biological rep3


title: P53-mutated with Del17p, biological rep1


title: P53-mutated without Del17p, biological rep12

source_name: Patient WITH P53-mutation and WITHOUT Del17p


title: P53-mutated with Del17p, biological rep2


title: P53-mutated without Del17p, biological rep10


title: MVR4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Gene expression in Right heart ventricle of adult male mouse
MVR_3-4.txt
raw data file:
WT_MV_R34_US83300186_252665512247_S01_GE2_1100_Jul11_1_3.txt

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: Right heart ventricle

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: heart was removed from adult male mice and each ventricle was isolated and minced

tag: strain

tag: develomental stage

value: adult

value: right heart ventricle


title: SNP105ZX3

city: changsha

first: xiong

last: bo

address: xiangya road

country: China

institute: xiangya

description:
Hybridized to 250K_Nsp
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.

scan_protocol: The arrays were scanned using the GeneChip Scanner 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using the DNAcopy package for R Bioconductor on raw data.

source_name: whole genome amplification product of trophectoderm cells

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

extract_protocol: Whole genome amplification of the biopsied trophectoderm cells was performed using a WGA4 GenomePlex Single Cell Whole Genome Amplification kit (Sigma-Aldrich, MO, USA) according to the manufacturer's instructions.

treatment_protocol: Blastocyst cultivation and biopsy reference to clinical standard procedure. The normal/balance embryos detected by SNP-array would have been transferred to patients as clinical stantard ptocedure.

value: trophectoderm cells

tag: karyotype of patient donor

tag: karyotype classification

value: reciprocal translocation

tag: analysis result

tag: result classification

value: normal female


title: P53-mutated without Del17p, biological rep11


title: SNP087SLM3


title: SNP086ZYW1


title: SNP090TWJ5


title: MVR3

tag: gender

tag: tissue


title: MVR2

description:
Gene expression in Right heart ventricle of adult male mouse
MVR_1-2.txt
raw data file:
WT_MV_R12_US83300186_252665512247_S01_GE2_1100_Jul11_1_4.txt


title: P53-mutated without Del17p, biological rep8


title: SNP086ZYW2


title: MVR1


title: SNP066CX4


title: SNP079LJM1


title: SNP070LJM12


title: SNP070LJM2


title: P53-mutated without Del17p, biological rep7


title: SNP077HLF2


title: SNP076SL2


title: MVL4

description:
Gene expression in Left heart ventricle of adult male mouse
MVL_3-4.txt
raw data file:
WT_MV_L34_US83300186_252665512247_S01_GE2_1100_Jul11_1_1.txt

source_name: Left heart ventricle

value: left heart ventricle


title: P53-mutated without Del17p, biological rep6


title: MVL3


title: P53-mutated without Del17p, biological rep9


title: P53-mutated without Del17p, biological rep5


title: SNP067CY2


title: SNP066CX1

value: Robertsonian translocation


title: SNP105ZX1


title: P53-mutated without Del17p, biological rep4


title: BN_testis_blood

first: Victor

last: Guryev

address: Uppsalalaan 8

institute: Hubrecht Institute

hyb_protocol: Hybridization was done at 37C according to Nimblegen standard aCGH protocol

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

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

source_name: BN testis

label_protocol: Labelling was done using standard Nimblegen protocol for aCGH

extract_protocol: DNA was extracted from 100 milligrams of liver tissue using Qiagen DNAEasy blood and tissue DNA isolation kit

value: testis

value: brown norway

source_name: BN blood

value: blood


title: SNP066CX5


title: MVL2

description:
Gene expression in Left heart ventricle of adult male mouse
MVL_1-2.txt
raw data file:
WT_MV_L12_US83300186_252665512247_S01_GE2_1100_Jul11_1_2.txt

value: male


title: 3 day dpi, Mock Anthers, Cy5, Rep 4

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
3 day dpi, mock-injected anther compared to 3 day dpi infected anther
Cy5-8_4

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities. Dual-channel hybridizations were analyzed as single channel only.

organism:
Zea mays
Mycosarcoma maydis

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford greenhouse.  Tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

treatment_protocol: Host anthers were ~0.1-0.2 mm at the time of infection and 0.3 - 0.6 mm at the time of dissection three days after pathogen inoculation.  Approximately 1 mL of water containing U. maydis (Absorbance 600nm = 1) was injected into the air space surrounding immature maize tassels of 30-day old greenhouse plants to initiate the infection.  One anther of each group of 3 per floret was checked by microscopy to verify that the floret was infected. Pools of ~50 infected anthers were used in each sample.

value: Mock Anthers

tag: time post infection

value: 3 day dpi


title: P53-mutated without Del17p, biological rep3

value: YES

value: NO


title: P53-mutated without Del17p, biological rep2


title: MVL1


title: BN_liver_blood

source_name: BN liver

value: liver


title: P53-mutated without Del17p, biological rep1


title: 3 day dpi, Infected Anthers, Cy5, Rep 4

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
3 day dpi, infected anthers compared to 3 day dpi mock-injected anthers
Cy5-8_2

value: Infected Anthers


title: 3 day dpi, Infected Anthers, Cy5, Rep 3

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
3 day dpi, infected anthers compared to 3 day dpi mock-injected anthers
Cy5-8_1


title: 3 day dpi, Mock Anthers, Cy5, Rep 3

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
3 day dpi, mock-injected anther compared to 3 day dpi infected anther
Cy5-8_3


title: 3 day dpi, Mock Anthers, Cy3, Rep 2

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_4.txt
3 day dpi, mock-injected anther compared to 3 day dpi infected anther
Cy3-8_4


title: BN_brain_testis

source_name: BN brain

value: brain


title: BN_liver_testis


title: BN_brain_liver


title: BN_testis_liver


title: BN_brain_blood


title: BN_liver_brain


title: Colorectal tissue-tumor-ID245

status: Public on Mar 20 2013

city: Hong Kong

first: Yujuan

last: Dong

address: Ngan Shing Street

department: Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Tumor tissue

data_processing: Results were analyzed by the SDS RQ Manager 1.2 software (Applied Biosystems, Foster City, CA).The relative miRNA expression level in each group was normalized to the housekeeping gene RNU6B and given by 2-ΔΔCt method. The formulae for the relative quantification of each of the miRNA were as follows: (dCt of each miRNA) = (Ct of each miRNA) − (Ct of internal control), and (relative quantification of each miRNA) = 2−(dCt of each miRNA). The Ct value was read according to the number of cycles at which the fluorescence signal passes a manual threshold. The Ct value of 39 was used as a cut-off point for defining a miRNA as not expressed.

label: FAM

source_name: Colorectal tissue-tumor-ID245

label_protocol: Reverse transcription for miRNA microarray was carried out using Megaplex Primer pools, Human Pools A v2.1and B v3.0 (Applied Biosystems, Foster City, CA). The cDNA product was used to perform miRNA Array.

growth_protocol: Fresh human colorectal tissues were used for RNA extraction.

extract_protocol: Total RNA was extracted with miRNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: The specimens (both tumour and adjacent normal) were processed immediately after the section and snap-frozen in liquid nitrogen for RNA extraction.

tag: age

value: Male

tag: tnm stage

tag: recurrence

value: Yes


title: BN_blood_testis


title: Colorectal tissue-tumor-ID218

description: Tumor tissue

source_name: Colorectal tissue-tumor-ID218

value: No


title: 3 day dpi, Infected Anthers, Cy3, Rep 2

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_2.txt
3 day dpi, infected anthers compared to 3 day dpi mock-injected anthers
Cy3-8_2


title: Colorectal tissue-normal-ID158

description: Normal tissue

source_name: Colorectal tissue-normal-ID158


title: Cplus vs Input

city: Debrecen

first: Zsuzsanna

middle: S.

last: Nagy

address: Nagyerdei krt. 98

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Technical replicates

hyb_protocol: Approximately 8.25μg of DNA was hybridzed per array using the Affymetrix hybridization kit at the EMBL Genomics Core Facility in Heidelberg, Germany.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Data was analyzed using MAT at http://liulab.dfci.harvard.edu/MAT/
CplusInp.bed.txt contains all 1581 high quality STAT5 binding sites.

source_name: STAT5 ChIP DNA

label_protocol: To generate libraries from ChIP-ed DNA, random amplification was carried out as described at http://research.stowers-institute.org/gertonlab/protocols/RandomPCRamplification.pdf by the DeRisi lab at the UC San Francisco.

growth_protocol: Cells were maintained in RPMI-1640 medium containing 10% fetal calf serum, 2 mM L-glutamine and penicillin-streptomycin (50 IU/ml and 50 μg/ml, respectively). Kit225 media was supplemented with 20 U/ml human recombinant IL-2 (NCI Preclinical Repository).

extract_protocol: Chromatin immunoprecipitations were performed from approximately 5 x 107 Kit225 cells as described by our group earlier (Nagy et al Mol. Cancer. 2009) with anti-STAT5A/B antibodies (mixing sc-1081 and sc-835 (C-terminal STAT5A and STAT5B antibodies, respectively)) or normal rabbit serum (IgG control) for 3h at 4 ºC. To confirm that the assays were successful, PCR amplification of the known STAT5 binding site located 5’ to the human IL2RA gene within the Positive Regulatory Region III  (Forward: 5’-ACG TCT AGA AAG AAA GTG GTC-3’ Reverse: 5’- CTG TCC CTG GAT GAA CCT AGT-3’) was performed using quantitative real time PCR.

treatment_protocol: Prior to IL-2 stimulation, Kit225 cells were made quiescent for 24 h in their regular medium without IL-2. Cell stimulations were carried out with 10 nM IL-2.

tag: cell type

value: leukemia cell

tag: cell line

tag: antibody

value: STAT5 C-term polyclonal

source_name: Input DNA

value: input, none


title: Colorectal tissue-tumor-ID150

description: Tumor tissue

source_name: Colorectal tissue-tumor-ID150


title: Colorectal tissue-tumor-ID158

description: Tumor tissue

source_name: Colorectal tissue-tumor-ID158


title: 3 day dpi, Infected Anthers, Cy3, Rep 1

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_1.txt
3 day dpi, infected anthers compared to 3 day dpi mock-injected anthers
Cy3-8_1


title: Colorectal tissue-normal-ID150

description: Normal tissue

source_name: Colorectal tissue-normal-ID150


title: 3 day dpi, Mock Anthers, Cy3, Rep 1

description:
raw data filename: US84703594_252361510008_S01_GE2-v5_95_Feb07_2_JF_1_3.txt
3 day dpi, mock-injected anther compared to 3 day dpi infected anther
Cy3-8_3


title: BN_testis_brain

value: testis


title: 15598-1

city: Iowa City

first: Alexey

middle: A

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

description:
Gene expression data from dissected ovaries 4-6 hours old, i.e. before stage 9 egg chambers
ovaries at 4-6 hours post-eclosion, replicate 1

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix hybridization buffer, placed onto Drosophila 2.0 arrays (Cat #900532), and incubated at 45º C for 18 h with 60 rpm rotation in Affymetrix Model 640 GeneChip Hybridization Oven.  Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes). Signal was amplified with anti-streptavidin antibody (Vector Laboratories), followed by staining with streptavidin-phycoerythrin (Molecular Probes) using the Affymetrix Model 450 Fluidics Station (Affymetrix).

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade.

data_processing: The data was analyzed with Partek 6.5 Suite using GCRMA analyses settings (GCRMA background correction, quantile normalization, median polish probeset summarization)

organism: Drosophila melanogaster

source_name: BL15598 virgin female ovaries dissected 4-6 hours post-eclosion

label_protocol: Fifty nanograms of total RNA was converted to cDNA using the Ovation RNA Amplification System v2 (NuGEN). The cDNA product was purified using QIAquick PCR Purification column (Qiagen) and 3.75 µg were fragmented to an average size of 85 bases and biotin labeled using the FL-Ovation cDNA Biotin Module (NuGEN) per the manufacturer’s protocol.

growth_protocol: Flies were raised at 25ºC, 70% humidity on standard cornmeal/agar medium supplemented with yeast.

extract_protocol: Total RNA was isolated from approximately 100 pairs of frozen ovaries per biological replicate using TRIzol reagent (Invitrogen), treated with DNaseI (Qiagen DNaseI) and purified using RNeasy columns (Qiagen) according to the manufacturer instructions.

treatment_protocol: Ovaries were dissected in ice-cold PBS and stored at -80C until RNA isolation

value: ovary

tag: genotype

value: 4-6 hours post-eclosion


title: CS-3

description:
Gene expression data from dissected ovaries 4-6 hours old, i.e. before stage 9 egg chambers
ovaries at 4-6 hours post-eclosion, replicate 3

source_name: Canton S virgin female ovaries dissected 4-6 hours post-eclosion

value: Canton S


title: 15598-3


title: Pb2-1

source_name: su(Hw)Pb/2 virgin female ovaries dissected 4-6 hours post-eclosion


title: 2663v-3

source_name: su(Hw)A2663/v virgin female ovaries dissected 4-6 hours post-eclosion


title: Pb2-2

description:
Gene expression data from dissected ovaries 4-6 hours old, i.e. before stage 9 egg chambers
ovaries at 4-6 hours post-eclosion, replicate 2


title: 15598-2


title: Pb2-3


title: CS-2


title: BN_blood_brain

value: blood

value: brown norway


title: CS-1


title: U87MG_hypoxia_rep2

city: Lund

first: Paulina

last: Kucharzewska

address: Barngatan 2B

department: Clinical Sciences

country: Sweden

institute: Lund University

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using q-quantile normalisation with BASE (BioArray Software Environment) application. BASE is described in Vallon-Christersson J, Nordborg N, Svensson M, Häkkinen J. BMC Bioinformatics 2009, 10:330. doi:10.1186/1471-2105-10-330.

source_name: U87 MG glioblastoma cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit.

growth_protocol: Routine culture medium: High Glucose DMEM supplemented with 10% FBS, 2 mM L-glutamine and 100 U/ml penicillin and 100 µg/ml streptomycin. Experiment medium: High glucose DMEM supplemented with 1% BSA, 2 mM L-glutamine and 100 U/ml penicillin and 100 µg/ml streptomycin. Routine culture was done in a humidified incubator maintained at 37 °C with 5% CO2 and 95% air. For hypoxia experiments, cells were incubated in a humidified 5% CO2 InVivo2 Hypoxia Work station 400 (Ruskinn Technology Ltd) set at 37 ºC and 1% O2.

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment with DNA-free™ Kit (Ambion) in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: U87 MG glioblastoma cells were grown at normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 48 hours. Conditioned media from normoxic and hypoxic cells were then used to isolate exosomes by differential centrifugation. Both cells and exosomes were lysed in Trizol reagent and RNA was isolated.

value: Brain

tag: treatment

value: hypoxic (1% oxygen)

tag: isolate

value: cells


title: U87MG_hypoxia_rep3

description: Replicate 3


title: 2663v-2


title: Colorectal tissue-normal-ID245

description: Normal tissue

source_name: Colorectal tissue-normal-ID245


title: BN_blood_liver

source_name: BN blood

tag: strain

value: liver


title: Colorectal tissue-normal-ID218

description: Normal tissue

source_name: Colorectal tissue-normal-ID218


title: U87MG_normoxia_rep2

description: Replicate 2

value: normoxic (21% oxygen)


title: Exosomes_hypoxia_rep2

description: Replicate 2

value: exosomes


title: U87MG_normoxia_rep3

description: Replicate 3


title: U87MG_normoxia_rep1

description: Replicate 1


title: 2663v-1


title: Exosomes_hypoxia_rep1

description: Replicate 1


title: MAR3

description:
Gene expression in heart right atrium of adult male mouse
MAR_3-4.txt
WT_MA_R34_US83300186_252665513679_S01_GE2_1100_Jul11_1_3.txt

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Right heart atrium _Replicate 3

treatment_protocol: heart was removed from adult male mice and each atrium was isolated and minced

tag: Sex

value: male

value: right heart atrium

tag: develomental stage

value: adult


title: MAR4

source_name: Right heart atrium _Replicate 4


title: ACI_testis_brain

source_name: ACI testis

value: ACI

source_name: ACI brain

value: brain


title: MEF_re

city: Seoul

first: MIN JUNG

last: KIM

address: 605-21 YeokSamDong

country: South Korea

institute: CHA University

description: Sample name: MEF.2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: embryonic fibroblast

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: NSC expansion medium, comprising NS-A media supplemented with N2 supplement, 10 ng/ml of each epidermal growth factor and basic fibroblast growth factor, 50 µg/ml bovine serum albumin, 1X  penicillin/streptomycin/glutamine, and 1X nonessential amino acids

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

value: embryonic fibroblast

tag: genotype/variation

value: female


title: MAR2

description:
Gene expression in heart right atrium of adult male mouse
MAR_1-2.txt
WT_MA_R12_US83300186_252665513679_S01_GE2_1100_Jul11_1_4.txt

source_name: Right heart atrium _Replicate 2


title: ACI_liver_testis

source_name: ACI liver

value: testis


title: ACI_testis_blood

source_name: ACI blood


title: U87MG_hypoxia_rep1

description: Replicate 1


title: ACI_liver_brain


title: miPS-NSC_re

description: Sample name: pips-NSC P8_re

source_name: neural stem cell

value: miPS-NSC


title: miPS-NSC

description: Sample name: pips-NSC P8


title: parthenogenetic NSC_re

description: Sample name: PNSC  P18_re

value: pNSC


title: MEF

description: Sample name: MEF.1


title: Exosomes_hypoxia_rep3

description: Replicate 3


title: Exosomes_normoxia_rep2

description: Replicate 2


title: ACI_testis_liver


title: MAR1

source_name: Right heart atrium _Replicate 1


title: parthenogenetic NSC

description: Sample name: PNSC  P18


title: ACI_liver_blood

value: blood


title: ACI_brain_blood


title: ACI_brain_testis


title: Exosomes_normoxia_rep3

description: Replicate 3

value: Brain


title: female NSC_re

description: Sample name: NSC P27_re

value: fNSC


title: female NSC

description: Sample name: NSC P27


title: Exosomes_normoxia_rep1

description: Replicate 1


title: ACI_blood_liver


title: II+ROP16I infected intestine

city: Cambridge

first: Kirk

last: Jensen

state: MA

address: 77 Massachusetts Ave. Bldg 68-270

institute: MIT

description: R11_1338_Type II +ROP16I Intestine

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings. All normalized RMA intensities (Log2)that were below 6.5 were set as 6.5.

source_name: The middle third portion of the small intestine (with Peyer's patches removed) from a II+ROP16I orally infected mouse on Day 5

label_protocol: biotin

growth_protocol: Tissue cysts were obtained from the brains of chronically infected C57BL/6 mice, enumerated and resuspended in PBS at a concentraion of 1000 cysts per 200 ul PBS.

extract_protocol: The samples were crushed using a sterile 16 G needle in tubes on dry ice.  In the case of the intestine, the sample was resuspended in TRizol and extruded through a 16 G needle using a syringe and RNA was isolated according to manufacturer's protocol; for the Peyer's patch, the sample was suspended in cell lysis buffer and RNA isolated using the RNeasey kit (Invitrogen) according to the manufacter's protocol.

treatment_protocol: C57BL/6 female mice were orally gavaged with 1000 cysts and on Day 5 individual Peyer's patches and small intestines were dissected and analyzed for parasite burden by bioluminescence imaging. Individual Peyer's patches and intestinal sections (with the Peyer's patches removed), corresponding to the middle third of the intestine (~jejuem), that had equivalent parasite burden were snap frozen in liquid nitrogen.

value: intestine

tag: toxoplasma parasite strain

value: type II (Pru A7) +ROP16I


title: slide 15 - Tel sulpiride

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

institute: University of Ottawa

description: Slide #48

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS and GPA methods.

organism: Carassius auratus

source_name: control

extract_protocol: RNeasy Mini Plus kit (Qiagen) including optional on-column DNase I treatment. RNA quantity was evaluated using the NanoDrop ND-1000. RNA integrity was evaluated using the BioAnalyzer (Agilent); RIN for each sample was > 8.4.

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.

tag: sex

source_name: sulpiride 6 ug/g

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 6 ug/g sulpiride 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.


title: Naïve Peyer's Patch

description: R11_1335_Naive Peyer's Patch

source_name: A Peyer's patch from a naïve mouse

tag: tissue

value: Peyer's Patch


title: ACI_brain_liver

value: liver


title: MAL3

description:
Gene expression in heart left atrium of adult male mouse
MAL_3-4.txt
WT_MA_L34_US83300186_252665513679_S01_GE2_1100_Jul11_1_1.txt

source_name: Left heart atrium _Replicate 3

value: male

value: left heart atrium


title: MAL4

source_name: Left heart atrium _Replicate 4

value: adult


title: ACI_blood_testis

value: ACI


title: slide 37 - Tel sulpiride

description: Slide #37

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)


title: slide 26 - Tel sulpiride

description: Slide #26


title: Type II infected Intestine

description: R11_1339_Type II Intestine

source_name: The middle third portion of the small intestine (with Peyer's patches removed) from a type II orally infected mouse on Day 5

value: type II (Pru A7)


title: ACI_blood_brain

value: brain


title: II Δgra15+ROP16I Stat3 deficient

description: AA447_type II dgra15 +ROP16I STAT3 deficient

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

source_name: 18hr infected Stat3 deficient BMDMs with the type II Δgra15+ROP16I strain

growth_protocol: BMDMs were plated at 3x10^6 cells per well in 6-well plates. They were generated by incubated bonemarrow cells in 20% L929 medium for 6-7 days before harvesting.

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

treatment_protocol: BMDMs were infected with parasite strains at the indicated Multiplicity of Infection (MOI) for 18 hours before RNA harvesting; the actual MOI of viable parasites after plaque assays for this series of experiments was between 1 and 2.

value: Bone marrow-derived macrophages (BMDMs)

value: Stat3fl/fl mLysCre (B6)

value: type II (Pru A7) Δgra15+ROP16I


title: Naïve Intestine

description: R11_1340_Naive Intestine

source_name: The middle third portion of the small intestine (with Peyer's patches removed) from a naïve mouse


title: II+ROP16I infected Peyer's patch

description: R11_1337_Type II +ROP16I Peyer's Patch

source_name: A parasitized Peyer's patch from a II+ROP16I orally infected  mouse on Day 5


title: Type II infected Peyers

description: R11_1336_Type II Peyer's Patch

source_name: A parasitized Peyer's patch from a type II orally infected  mouse on Day 5


title: II Δgra15 Stat3 deficient

description: AA448_type II dgra15 STAT3 deficient

source_name: 18hr infected Stat3 deficient BMDMs with the type II Δgra15 strain

value: type II (Pru A7) Δgra15


title: MAL1

description:
Gene expression in heart left atrium of adult male mouse
MAL_1-2.txt
WT_MA_L12_US83300186_252665513679_S01_GE2_1100_Jul11_1_2.txt

source_name: Left heart atrium _Replicate 1


title: II+ROP16I Stat6-/-

description: AA371_type II+ROP16I Stat6KO

source_name: 18 hr Infected Stat6-/- BMDMs with the II+ROP16I strain


title: MAL2

source_name: Left heart atrium _Replicate 2


title: Uninfected Stat3 deficient

description: AA444_uninfected STAT3 deficient

source_name: Uninfected (18hr) Stat3 deficient BMDMs


title: II+ROP16I Stat3 deficient

description: AA446_type II +ROP16I STAT3 deficient

source_name: 18hr infected Stat3 deficient BMDMs with the type II+ROP16I strain


title: slide 28 - Hyp sulpiride

description: Slide #28

value: female


title: slide 15 - Hyp sulpiride

description: Slide #15


title: Type II Stat3 deficient

description: AA445_type II STA3 deficient

source_name: 18hr infected Stat3 deficient BMDMs with the type II strain


title: slide 12 - Tel sulpiride

description: Slide #12

source_name: control


title: II+ROP16I B6

description: AA370_type II+ROP16I B6

source_name: 18 hr Infected BMDMs with the II+ROP16I strain

value: type II (Pru A7) +ROP16I (2C4)


title: slide 52 - Hyp MPTP + aMPT

description:
Sexually mature (mid-May) adult female goldfish received a single injection of MPTP (50 ug/g body weight at 5 uL/g body weight) or 0.6% saline on day 0 and a single injection of alpha-MPT (240 ug/g body weight at 5 uL/g body weight) or 0.6% saline on Day 5.
Hypothalamus tissue was extracted on Day 6.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS method.

source_name: MPTP (50 ug/g) + aMPT (240ug/g)

extract_protocol: Total RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) as per the manufacturer's protocol. Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada). RNA quantity was evaluated using the NanoDrop ND-1000. RNA integrity was evaluated using the BioAnalyzer (Agilent); RIN for each sample was > 8.4.

tag: developmental stage

value: sexually mature (mid-May) adult

tag: gender

tag: agent

value: MPTP, alpha-MPT

value: Hypothalamus

source_name: Control

value: saline (control)


title: Uninfected Stat6-/-

description: AA369_unifected Stat6KO

source_name: Uninfected (18hr) Stat6-/- BMDMs


title: slide 21 - Hyp MPTP + aMPT (dye swap)

label_protocol:
Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)
This slide is a dye-swap


title: slide 39 - Tel SCH

description: Slide #36

treatment_protocol:
sexually regressing (mid-june) female adult goldfish received 2 injections at 5 ul/g body weight:
1) 40 ug/g SCH 233090 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline
Animals were anaesthetized in MS222 5h post-injection, and tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.