title: Field Isolate 4138_rep1, Human Clinical

description: 4138 - 09Apr10

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 4138

tag: C. jejuni Field Isolate 4138, Human Clinical


title: Field Isolate 2699_rep1, Bovine

status: Public on Oct 17 2008

type: genomic

city: Lethbridge

first: Eduardo

middle: N

last: Taboada

state: Alberta

address: PO Box 640, TWP Rd. 9-1

country: Canada

institute: Public Health Agency of Canada

description: 2699 - 04Mar28

hyb_protocol: In a fresh 1.5 ml amber tube, amounts corresponding to 40 pmol of both the reference strain (Cy3) and test strain (Cy5) were combined in a total volume of 20 µl. Labeled targets were prepared by addition of 55µl of SlideHyb Buffer #2 (Ambion, Austin, TX, USA) to the 20 µl volume obtained after the quantification step, mixing gently and heating for 5 min (65-67˚C). Arrays were prepared by submerged in warm prehybridization solution (Genicon Sciences Corporation, now part of Invitrogen, Carlsbad, CA, USA) and incubating for 30 min at 42˚C. Each array was then washed in fresh distilled H2O 10 times and in 100% isopropanol 10 times. Arrays were then dried with filtered air. Denatured targets were then added to the array under a Lifter Slip. Each array was hybridized at 42˚C in a humidified chamber for 18-24 h. After incubation, the Lifter Slips were removed, and the arrays immersed in fresh wash 1 solution (1x sodium chloride-sodium citrate (SSC)/0.1% sodium dodecyl sulfate, 42˚C for 5 min.) This step was then repeated twice. Arrays were then immersed in wash solution 2 (1xSSC) at 42˚C for 5 min (repeated twice), and then in wash solution 3 (0.1xSSC) at 42˚C for 5 min (repeated twice). Slides were then rinsed in warm distilled H2O (42˚C), dried with filtered air, placed into clean slide mailers and protected from direct light until scanned.

scan_protocol: Arrays were scanned using GenePix Pro version 4.1 (GenePix 4000B scanner, MDS Analytical Technologies, Mississauga, ON, Canada) or Jaguar, 2.0 (ArrayScanner 428, Affymetrix Inc, Santa Clara, CA,USA). Cy 3 and Cy 5 were scanned at wavelengths of approximately 532 and 635 respectively, both with 100% power.

data_processing: Primary image analysis was performed with ArrayVision version 8.0, rev. 3.0 (Imaging Research Inc.). The background was then subtracted from the raw spot intensity for both reference and test strain, giving a net intensity for each spot. Prior to all subsequent analyses, anomalous spots resulting from printing errors were removed from the dataset. The average net intensity data in reference and test channels for each ORF on the array was then obtained by averaging the net intensity of remaining replicate spots. Global loess normalization was performed with ArrayPipe (http://www.pathogenomics.ca/arraypipe/). Preliminary analysis of our data set revealed that low intensity data reduced the concordance of data from replicate arrays. A custom script was written in VBA for Microsoft Office Excel to test pixel intensity cut-offs from 200 to 1200 pixel units (in 20 unit increments) while monitoring concordance of replicate data. This analysis allowed us to determine intensity and log ratio cut-offs which would maximize the amount of reliable data retained for subsequent analysis and minimize the adverse effects of low signal data on replicate concordance. ORFs and arrays in which greater than 5% of the data yielded less than 500 pixel units in the reference channel were excluded from subsequent analysis.

molecule: genomic DNA

organism: Campylobacter jejuni

label_protocol: To perform random priming reaction 9 µg of random primers (Invitrogen Corporation, Carlsbad, CA, USA) were added to approximately 6 µg of genomic C. jejuni DNA in a volume of 40.5 µl, denatured at 95-97˚C for 6 min, and snap cooled on ice. The random priming reaction was set-up by adding 5 microlitres of 10 x Klenow reaction buffer, 1.5 µl Cy labeled dCTP, 1 µl dNTP, and 20 units exonuclease-free Klenow; tubes were incubated at 37˚C for 2h. Cleanup of probes was carried out using the Qiagen MinElute Reaction Cleanup Kit as per manufacturer’s specifications with a final elution volume of 13 µl distilled H2O. Labeled DNA and dye incorporation efficiency was quantified using a spectrophotometer (Ultrospec® 3000, Pharmacia Biotech) and equivalent Cy3 (control) and Cy5 (tester) molarities were used in each hybridization.

growth_protocol: Isolates were plated onto Mueller-Hinton (MH) agar for 48 hours at 43°C to ensure pure culture, and then streaked onto three MH plates and incubated for 16-18 hours at 37°C (10%CO2, 5% O2, 85% N2). Growth from three plates per strain was then suspended in a 50% brain-heart infusion-25% glycerol mixture and frozen to -70C for genotyping at a later date. Prior to DNA isolation, glycerol stocks were used to grow a confluent lawn on an M-H plate and grown as described above.

extract_protocol: Genomic DNA isolation was done using a modification of the hexadecyktrimethyl ammonium bromide (CTAB) procedure (Current Protocols in Molecular Biology section 2.4.2). Briefly, cells were suspended in 567 µL of TE (10mM Tris HCl and 1 mM EDTA pH 8.0).  Proteinase K and sodium dodecyl sulfate were added to a final concentration of 100 µg/mL and 0.5% respectively. After incubation for 1 h at 37οC 100 µL of 5 M NaCl was added and the suspension was mixed thoroughly. 80 µL of 10% CTAB in 0.7 M NaCl the solution added and the mixture was incubated at 65 οC for 10 min. An equal volume of chloroform/isoamyl alcohol (24:1) was added and after thorough mixing the CTAB-protein/polysaccharide complex was removed by centrifugation. The aqueous supernatant was transferred to a fresh tube and the remaining protein was extracted with phenol/chloroform/isoamyl alcohol (25:24:1). The supernatant was precipitated with 0.6 volumes of isopropanol and the precipitate was dissolved in 250 µL of water.

treatment_protocol: No treatment

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 2699

tag: C. jejuni Field Isolate 2699, Bovine


title: Field Isolate 2603_rep1, Bovine

description: 2603 - 02Apr10

source_name: genomic DNA from strain Field Isolate 2603

tag: C. jejuni Field Isolate 2603, Bovine


title: Field Isolate 4125_rep1, Human Clinical

description: 4125 - 18Sep25

source_name: genomic DNA from strain Field Isolate 4125

tag: C. jejuni Field Isolate 4125, Human Clinical


title: Field Isolate 4123_rep1, Human Clinical

description: 4123 - 03Apr22

source_name: genomic DNA from strain Field Isolate 4123

tag: C. jejuni Field Isolate 4123, Human Clinical


title: Field Isolate 4128_rep1, Human Clinical

description: 4128 - 05Apr24

source_name: genomic DNA from strain Field Isolate 4128

tag: C. jejuni Field Isolate 4128, Human Clinical


title: Field Isolate 4127_rep1, Human Clinical

description: 4127 - 04Apr24

source_name: genomic DNA from strain Field Isolate 4127

tag: C. jejuni Field Isolate 4127, Human Clinical


title: Field Isolate 2371_rep1, Bovine

description: 2371 - 01Sep22

source_name: genomic DNA from strain Field Isolate 2371

tag: C. jejuni Field Isolate 2371, Bovine


title: Field Isolate 2699_rep2, Bovine

description: 2699 - 12Sep25


title: Field Isolate 2719_rep1, Bovine

description: 2719 - 22Apr24

source_name: genomic DNA from strain Field Isolate 2719

tag: C. jejuni Field Isolate 2719, Bovine


title: Field Isolate 2808_rep1, Bovine

description: 2808 - 04Oct21

source_name: genomic DNA from strain Field Isolate 2808

tag: C. jejuni Field Isolate 2808, Bovine


title: Field Isolate 4140_rep1, Human Clinical

description: 4140 - 08Apr10

source_name: genomic DNA from strain Field Isolate 4140

tag: C. jejuni Field Isolate 4140, Human Clinical


title: Field Isolate 4121_rep1, Human Clinical

description: 4121 - 09Sep20

source_name: genomic DNA from strain Field Isolate 4121

tag: C. jejuni Field Isolate 4121, Human Clinical


title: Field Isolate 4122_rep1, Human Clinical

description: 4122 - 01Oct18

source_name: genomic DNA from strain Field Isolate 4122

tag: C. jejuni Field Isolate 4122, Human Clinical


title: Field Isolate 2808_rep2, Bovine

description: 2808 - 07Apr05


title: Field Isolate 2202_rep1, Bovine

description: 2202 - 03Sep22

source_name: genomic DNA from strain Field Isolate 2202

tag: C. jejuni Field Isolate 2202, Bovine


title: Field Isolate 2360_rep1, Bovine

description: 2360 - 06Sep22

source_name: genomic DNA from strain Field Isolate 2360

tag: C. jejuni Field Isolate 2360, Bovine


title: Field Isolate 2106_rep2, Bovine

description: 2106 - 04Apr10

source_name: genomic DNA from strain Field Isolate 2106

tag: C. jejuni Field Isolate 2106, Bovine


title: Field Isolate 2202_rep2, Bovine

description: 2202 - 04Oct18

source_name: genomic DNA from strain Laboratory strain NCTC11168


title: Field Isolate 2326_rep1, Bovine

description: 2326 - 17Apr24

source_name: genomic DNA from strain Field Isolate 2326

tag: C. jejuni Field Isolate 2326, Bovine


title: Cell body Expt 3_AFFY494B

type: RNA

city: Vancouver

first: Ivan

middle: Robert

last: Nabi

state: British columbia

address: LSI, 2350 health sciences Mall

department: CPS

institute: University of British Columbia

description: no additional information

hyb_protocol: 15 μg of labeled cRNA was hybridized to Canine GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA).  GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)

data_processing: RMA normalization was performed on the 6 Affymetrix Canine arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7.  263 pseudopod-enriched genes were selected. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 6 samples.

label: biotin

molecule: total RNA

organism: Canis lupus familiaris

source_name: MSV-MDCK-INV cell body fraction

label_protocol: Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP.    RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA).  Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)

growth_protocol: MSV-MDCK-INV cells were grown in high glucose Dulbecco’s modified Eagle’s medium supplemented with nonessential amino acids, glutamine, and vitamins and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).

extract_protocol: Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers

treatment_protocol: 107 MSV-MDCK-INV cells were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).

tag: Cell line


title: Pseudopod Expt 3_AFFY493B

description: no additional information

source_name: MSV-MDCK-INV cell pseudopod fraction


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t240min] (biol. repl. 1 - tech. repl. 1)

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Medical School

description: KCN118 cells (S288C ade2) were growin to mid-log in complete medium (SD+amino acids+inositol), rapidly vacuum-filtered to remove media and washed with PBS, then shifted to the indicated media for the indicated amount of time. Cells were rapidly pelleted and mRNA was extracted. mRNA was competetively hybridized against mRNA from t=0 to yeast whole-genome cDNA gene expression arrays.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and poly A+ mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

tag: Strain

source_name: mRNA, KCN118 (wt) Sgal+ino [t240min]

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa+ino [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa+ino [t240min]


title: Pseudopod Expt 1_AFFY446B

description: no additional information


title: Cell body Expt 2_AFFY478B

description: no additional information


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa+ino [t60min]


title: Pseudopod Expt 2_AFFY477B

description: no additional information


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa+ino [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa+ino [t15min]


title: Field Isolate 2046_rep1, Bovine

description: 2046 - 03Apr05

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 2046

tag: C. jejuni Field Isolate 2046, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+ino [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+ino [t120min]


title: Cell body Expt 1_AFFY447B

description: no additional information


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t60min] (biol. repl. 1 - tech. repl. 1, ojgrid)


title: Field Isolate 1888_rep1, Bovine

description: 1888 - 17Sep25

source_name: genomic DNA from strain Field Isolate 1888

tag: C. jejuni Field Isolate 1888, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+ino [t30min]


title: Field Isolate 1676_rep2, Bovine

description: 1676 - 20Sep25

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 1676

tag: C. jejuni Field Isolate 1676, Bovine


title: Field Isolate 2106_rep1, Bovine

description: 2106 - 02Oct18

source_name: genomic DNA from strain Field Isolate 2106


title: Field Isolate 1826_rep1, Bovine

description: 1826 - 05Sep22

source_name: genomic DNA from strain Field Isolate 1826

tag: C. jejuni Field Isolate 1826, Bovine


title: Field Isolate 1676_rep1, Bovine

description: 1676 - 10Sep22


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

source_name: mRNA, KCN118 (wt) Sgal+aa [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal [t60min]


title: Field Isolate 1716_rep1, Bovine

description: 1716 - 09Jul22

source_name: genomic DNA from strain Field Isolate 1716

tag: C. jejuni Field Isolate 1716, Bovine


title: Field Isolate 1645_rep1, Bovine

description: 1645 - 09Sep22

source_name: genomic DNA from strain Field Isolate 1645

tag: C. jejuni Field Isolate 1645, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+aa [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+aa [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal [t30min]


title: Field Isolate 1393_rep1, Bovine

description: 1393 - 24Apr10

source_name: genomic DNA from strain Field Isolate 1393

tag: C. jejuni Field Isolate 1393, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+ino [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t30min] (biol. repl. 1 - tech. repl. 2)

source_name: mRNA, KCN118 (wt) SEtOH+ino [t30min]


title: Field Isolate 1302_rep1, Bovine

description: 1302 - 06Mar16

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 1302

tag: C. jejuni Field Isolate 1302, Bovine


title: Field Isolate 1302_rep2, Bovine

description: 1302 - 11Sep28


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t240min] (biol. repl. 1 - tech. repl. 2)

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

source_name: mRNA, KCN118 (wt) SEtOH+ino [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t240min] (biol. repl. 1 - tech. repl. 1)


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+ino [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t30min] (biol. repl. 1 - tech. repl. 1)


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+ino [t15min] (biol. repl. 1 - tech. repl. 2)


title: Field Isolate 1111_rep1, Bovine

description: 1111 - 01Apr22

source_name: genomic DNA from strain Field Isolate 1111

tag: C. jejuni Field Isolate 1111, Bovine


title: Field Isolate 1243_rep1, Bovine

description: 1243 - 18Apr10

source_name: genomic DNA from strain Field Isolate 1243

tag: C. jejuni Field Isolate 1243, Bovine


title: Field Isolate 1133_rep1, Bovine

description: 1133 - 12Sep22

source_name: genomic DNA from strain Field Isolate 1133

tag: C. jejuni Field Isolate 1133, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) Sgal+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) Sgal+ino [t15min]


title: Field Isolate 1046_rep1, Bovine

description: 1046 - 08Sep22

source_name: genomic DNA from strain Field Isolate 1046

tag: C. jejuni Field Isolate 1046, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa+ino [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa+ino [t60min]


title: Field Isolate 1016_rep1, Bovine

description: 1016 - 04Sep22

source_name: genomic DNA from strain Field Isolate 1016

tag: C. jejuni Field Isolate 1016, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa+ino [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa+ino [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t60min] (biol. repl. 1 - tech. repl. 2)

source_name: mRNA, KCN118 (wt) SEtOH+aa [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa+ino [t30min]


title: Field Isolate 1006_rep1, Bovine

description: 1006 - 11Sep22

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 1006

tag: C. jejuni Field Isolate 1006, Bovine


title: Field Isolate 0791_rep1, Bovine

description: 0791 - 09Apr05

source_name: genomic DNA from strain Field Isolate 0791

tag: C. jejuni Field Isolate 0791, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

tag: Strain


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t120min] (biol. repl. 1 - tech. repl. 2)

source_name: mRNA, KCN118 (wt) SEtOH+aa [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH+aa [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH+aa [t120min] (biol. repl. 1 - tech. repl. 1)


title: Field Isolate 0875_rep1, Bovine

description: 0875 - 16Apr22

tag: C. jejuni Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 0875

tag: C. jejuni Field Isolate 0875, Bovine


title: Field Isolate 0697_rep1, Bovine

description: 0697 - 12Apr10

source_name: genomic DNA from strain Field Isolate 0697

tag: C. jejuni Field Isolate 0697, Bovine


title: Field Isolate 0773_rep2, Bovine

description: 0773 - 05Oct18

source_name: genomic DNA from strain Field Isolate 0773

tag: C. jejuni Field Isolate 0773, Bovine


title: Field Isolate 0442_rep1, Bovine

description: 0442 - 13Apr22

source_name: genomic DNA from strain Field Isolate 0442

tag: C. jejuni Field Isolate 0442, Bovine


title: Field Isolate 0773_rep1, Bovine

description: 0773 - 02Sep22


title: Field Isolate 0381_rep1, Bovine

description: 0381 - 07Mar16

source_name: genomic DNA from strain Field Isolate 0381

tag: C. jejuni Field Isolate 0381, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+ino [t30min]


title: Field Isolate 0321_rep1, Bovine

description: 0321 - 11Apr22

source_name: genomic DNA from strain Laboratory strain NCTC11168

source_name: genomic DNA from strain Field Isolate 0321

tag: C. jejuni Field Isolate 0321, Bovine


title: Field Isolate 0356_rep1, Bovine

description: 0356 - 12Apr22

source_name: genomic DNA from strain Field Isolate 0356

tag: C. jejuni Field Isolate 0356, Bovine


title: Field Isolate 0213_rep1, Bovine

description: 0213 - 10Apr22

source_name: genomic DNA from strain Field Isolate 0213

tag: C. jejuni Field Isolate 0213, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t240min] (biol. repl. 1 - tech. repl. 1, ojgrid)

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

source_name: mRNA, KCN118 (wt) SD+ino [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:LIVWHM+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:LIVWHM+ino [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t240min] (biol. repl. 1 - tech. repl. 1)


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:LIVWHM+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:LIVWHM+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t60min]


title: Field Isolate 0179_rep1, Bovine

description: 0179 - 10Apr05

source_name: genomic DNA from strain Field Isolate 0179

tag: C. jejuni Field Isolate 0179, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:LIVWHM+ino [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:LIVWHM+ino [t30min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+ino [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:LIVWHM+ino [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:LIVWHM+ino [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SEtOH [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SEtOH [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+ino [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:LIVWHM+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:LIVWHM+ino [t15min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t15min]


title: Field Isolate 0179_rep2, Bovine

description: 0179 - 13Sep25

source_name: genomic DNA from strain Laboratory strain NCTC11168


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa+ino [t0min]

source_name: mRNA, KCN118 (wt) SD+aa [t240min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa:ARNCQGKPSDEFTY+ino [t120min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa [t60min]


title: Field Isolate 0100_rep1, Bovine

description: 0100 - 09Apr22

source_name: genomic DNA from strain Field Isolate 0100

tag: C. jejuni Field Isolate 0100, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa [t30min]


title: Field Isolate 0100_rep2, Bovine

description: 0100 - 25Apr24


title: Field Isolate 0122_rep1, Bovine

description: 0122 - 05Apr05

source_name: genomic DNA from strain Field Isolate 0122

tag: C. jejuni Field Isolate 0122, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t240min] (biol. repl. 1 - tech. repl. 2)


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa [t120min]


title: Daphnia_1/10LC50_WO4_exp3,rep2

status: Public on Oct 16 2008

city: Boston

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: 164 mg/L WO4

hyb_protocol: The labeled cDNA pools from the unexposed and exposed D. magna werehybridized the the Daphnia magna microarry using reagents and protocols from Genisphere 3DNA 350 labeling and hybridization kit (Genisphere, Hatfield, PA).

scan_protocol: Scanning and quantification was performed using an arrayWoRx Biochip Reader (Applied Precision, Issaquah, WA) and GenePix software version 6.0 (Axon Instruments, Union City, CA).

data_processing: Technical replicates were normalized to remove possible non-linearity, if any, and checked for homogeneity using boxplots.  As an alternative to between-slide normalization we applied an approach based on sequential single-slide data analysis and utilized the α-outlier-generating model and outlier regions approach to identify differentially expressed cDNAs.  Details of the method can be found in: Loguinov, A. V., Mian, I. S. & Vulpe, C. D. (2004) Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome Biol. 5, R18.

organism: Daphnia magna

label_protocol: cDNA was synthesized from 5 ug of total RNA using Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, CA) and labeled following the protocols of the Genisphere 3DNA 350 labeling kit (Genisphere, Hatfield, PA).  The dyes were switched for each technical replicate so that the control cDNA was labeled with Cy3 in one hybridization and Cy5 in the other.

growth_protocol: Genetically homogeneous Daphnia magna, purchased from Aquatic Research Organisms (Hampton, NH), were cultured in MHRW and maintained at 23.50 C according to standard protocols (Weber, 1993; Lewis et al., 1994).  Weber, C. I. (1993) Methods for Measuring the Acute Toxicity of Effluent and Receiving Waters to Freshwater and Marine Organisms. U.S. Environmental Protection Agency: EPA/600/4-90/027F; Lewis, P. A., Klemm, D. J., Lazorchak, J. M., Norberg-King, T. J., Peltier, W. H. & Heber, M. A. (1994) Short-term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Waters to Freshwater Organisms. US Environmental Protection Agency: EPA/600/4-91/002

extract_protocol: Whole daphnids (40 pooled for each exposure) were initally preserved in RNAlater (Ambion).  They were later transferred to liquid nitrogen and ground with a morter and pestle. RNA was isolated using Trizol according to standard methods (Invitrogen, Carlsbad, CA).

treatment_protocol: All exposures to the ORCs were conducted on adult female daphnids 14-16 days old and occurred at 23.50 C for 24 hours


title: Field Isolate 0084_rep2, Bovine

description: 0084 - 13Sep22

source_name: genomic DNA from strain Field Isolate 0084

tag: C. jejuni Field Isolate 0084, Bovine


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD+aa [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD+aa [t15min]


title: Daphnia_1/10LC50_WO4_exp3,rep1

description: 164 mg/L WO4


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD [t60min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD [t60min]


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD [t30min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD [t30min]


title: Daphnia_1/10LC50_WO4_exp2,rep1

description: 164 mg/L WO4


title: Daphnia_1/10LC50_WO4_exp1,rep2

description: 164 mg/L WO4


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD [t240min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD [t240min]


title: Daphnia_1/10LC50_WO4_exp2,rep2

description: 164 mg/L WO4


title: Daphnia_1/10LC50_Pb_exp2,rep2

description: 0.871 mg/L Pb


title: Daphnia_1/10LC50_Zn_exp3,rep2

description: 0.603 mg/L Zn


title: Daphnia_1/10LC50_Pb_exp3,rep2

description: 0.871 mg/L Pb


title: Daphnia_1/10LC50_WO4_exp1,rep1

description: 164 mg/L WO4


title: Daphnia_1/10LC50_Pb_exp3,rep1

description: 0.871 mg/L Pb


title: Daphnia_1/10LC50_Pb_exp2,rep1

description: 0.871 mg/L Pb


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD [t120min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD [t120min]


title: S2 cell infected with FHV deltaB2 particle

type: other

city: Riverside

first: Qingfa

last: Wu

state: CA

address: 900 University Ave

institute: UC Riverside

description: no additional information

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Only sequences containing both 5' and 3' adaptors were analyzed. The sequences of both 5' and 3' linker were computationally removed.

molecule: other

organism: Drosophila melanogaster

source_name: Drosophila melanogaster S2 cell

label_protocol: not applicable

extract_protocol:
Total RNA was isolated with Trizol.
Small RNAs were then separated on a denaturing 15% polyacrylamide gel. Then the eluted 18~28 nt RNA was dephosphorylated before 3’ linker ligation. The ligation product was recovered from the gel, 5' phosphorylated, and the RNA was recovered by ethanol precipitation. Next, the 5' adapter was ligated to the phosphorylated ligation product as described above. The ligation products from the second ligation reaction were excised and eluted from the gel. RT and PCR reaction were performed sequentially.

tag: S2 cells were infected with FHV deltaB2 particle and the S2 cells were harvested to isolate total RNA at 96 hpi


title: Daphnia_1/10LC50_Zn_exp1,rep2

description: 0.603 mg/L Zn


title: Daphnia_1/10LC50_Zn_exp3,rep1

description: 0.603 mg/L Zn


title: Field Isolate 0084_rep1, Bovine

description: 0084 - 03Apr10


title: Daphnia_1/10LC50_Zn_exp2,rep1

description: 0.603 mg/L Zn


title: Daphnia_1/10LC50_Zn_exp2,rep2

description: 0.603 mg/L Zn


title: Daphnia_1/10LC50_Pb_exp1,rep1

description: 0.871 mg/L Pb


title: Daphnia_1/10LC50_Cu_exp1,rep2

description: 4 ug/L Cu


title: Daphnia_1/10LC50_Cu_exp2,rep1

description: 4 ug/L Cu


title: Daphnia_1/10LC50_Pb_exp1,rep2

description: 0.871 mg/L Pb


title: Daphnia_1/10LC50_Zn_exp1,rep1

description: 0.603 mg/L Zn


title: Daphnia_1/10LC50_Cu_exp3,rep2

description: 4 ug/L Cu


title: KCN118 (wt) SD+aa+ino [t0min] vs. KCN118 (wt) SD [t15min] (biol. repl. 1 - tech. repl. 1)

source_name: mRNA, KCN118 (wt) SD [t15min]


title: Daphnia_1/10LC50_Cu_exp2,rep2

description: 4 ug/L Cu


title: Daphnia_1/10LC50_DNB_exp2,rep1

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_DNB_exp3,rep1

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_DNB_exp3,rep2

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_DNB_exp2,rep2

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_TNB_exp2,rep2

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_Cu_exp1,rep1

description: 4 ug/L Cu


title: Daphnia_1/10LC50_DNB_exp1,rep1

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_DNB_exp1,rep2

description: 14.6 mg/L DNB


title: Daphnia_1/10LC50_TNB_exp1,rep1

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_2,6-DNT_exp3,rep2

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_TNB_exp3,rep1

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_TNB_exp3,rep2

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_TNB_exp2,rep1

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_TNB_exp1,rep2

description: 0.454 mg/L TNB


title: Daphnia_1/10LC50_2,6-DNT_exp3,rep1

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_2,6-DNT_exp2,rep2

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_2,6-DNT_exp2,rep1

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_2,6-DNT_exp1,rep1

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_2,6-DNT_exp1,rep2

description: 1.537 mg/L 2,6-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp2,rep1

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp3,rep1

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp3,rep2

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp1,rep2

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp1,rep1

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_2,4-DNT_exp2,rep2

description: 2.018 mg/L 2,4-DNT


title: Daphnia_1/10LC50_4ADNT_6

description: 0.895 mg/L 4ADNT

hyb_protocol: The labeled cDNA pools from the unexposed and exposed D. magna were mixed and hybridized to the Daphnia microarray (protocols available at http://cmgm.stanford.edu/pbrown/mguuide).

scan_protocol: Scanning and quantification was performed using an arrayWoRx Biochip Reader (Applied Precision, Issaquah, WA) and GenePix software version 3.01 (Axon Instruments, Union City, CA).

label_protocol: cDNA was synthesized using Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, CA) from total RNA in the presence of aminoallyl labeled dUTP. Fluorescence labeling proceeded by incubating the aminoallyl labeled cDNA with Cy5 or Cy3 fluorescent dyes (Amersham Biosciences, Piscataway, NJ). The dyes were switched for each technical replicate so that the control cDNA was labeled with Cy3 in one hybridization and Cy5 in the other.


title: Daphnia_1/10LC50_4ADNT_4

description: 0.895 mg/L 4ADNT


title: Daphnia_1/10LC50_4ADNT_3

description: 0.895 mg/L 4ADNT


title: Daphnia_1/10LC50_4ADNT_5

description: 0.895 mg/L 4ADNT


title: Daphnia_1/10LC50_4ADNT_2

description: 0.895 mg/L 4ADNT


title: Embryos uninjected biological repl. 1 (15uM)

city: Dübendorf

first: Mirjam

last: Föhlicher

address: überlandstrasse 133

country: Switzerland

institute: eawag

description: gene expression in 72hpf zebrafish embryos

hyb_protocol: Affymetrix Gene Expression protocol using Fragmentation Buffer (Affymetrix Inc., P/N 900371), Hybridization Mix (Affymetrix Inc., P/N 900720), Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Arrays were washed using an Affymetrix Fluidics Station 450 (FS450_0004 protocol)

scan_protocol: Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.), according to manufacturer

data_processing: Raw data processing was performed using the Affymetrix AGCC software. After hybridization and scanning, probe cell intensities were calculated by means of the MAS5 algorithm. The data were then analyzed with Genespring. The data were normalized per chip (50th percentil) and per gene (to median). They were finally filtered by fold change (fold change data files are on the Series record).

organism: Danio rerio

source_name: 72hpf zebrafish embryos

label_protocol: biotin-labeling using a IVT Labeling Kit (Affymetrix Inc.)

growth_protocol: Eggs were pooled from different aquaria, washed with a E3 medium and injected with ERbeta2 MO or coMO at 15uM until the 4 cell stage. After they were raised in petri dishes until 72hpf at 28°C.

extract_protocol: RNA isolation was performed with Rneasy Mini Kit, Qiagen, according to the manufacturer's instructions.

treatment_protocol: When embryo reached 72hpf they were euthanized in MS222 and put in RNAlater solution at 4°C overnight. The samples were stored until RNA isolation at -20°C

tag: wild type

tag: blank


title: Embryos injected with 50uM ERbeta2 MO biological repl. 1

growth_protocol: Eggs were pooled from different aquaria, washed with a E3 medium and injected with ERbeta2 MO or coMO at 50uM until the 4 cell stage. After they were raised in petri dishes until 72hpf at 28°C.

tag: ERbeta2 morpholinos


title: Daphnia_1/10LC50_4ADNT_1

description: 0.895 mg/L 4ADNT


title: Embryos injected with 50uM coMO biological repl. 1

tag: control morpholinos


title: Embryos uninjected biological repl. 2 (15uM)


title: Embryos injected with 15uM ERbeta2 MO biological repl. 2


title: Embryos injected with 15uM ERbeta2 MO biological repl. 1


title: Embryos uninjected biological repl. 1 (50uM)


title: Embryos injected with 15uM coMO biological repl. 2


title: Daphnia_1/10LC50_2ADNT_6

description: 0.600 mg/L 2ADNT


title: Daphnia_1/10LC50_2ADNT_3

description: 0.600 mg/L 2ADNT


title: Daphnia_1/10LC50_2ADNT_4

description: 0.600 mg/L 2ADNT


title: Embryos injected with 50uM ERbeta2 MO biological repl. 2


title: Daphnia_1/10LC50_2ADNT_1

description: 0.600 mg/L 2ADNT


title: Daphnia_1/10LC50_2ADNT_2

description: 0.600 mg/L 2ADNT


title: Daphnia_1/10LC50_2ADNT_5

description: 0.600 mg/L 2ADNT


title: Embryos injected with 50uM coMO biological repl. 2


title: Embryos injected with 15uM coMO biological repl. 1


title: Daphnia_1/10LC50_TNT_5

description: 1.194 mg/L TNT


title: Daphnia_1/10LC50_TNT_4

description: 1.194 mg/L TNT


title: Daphnia_1/10LC50_TNT_2

description: 1.194 mg/L TNT


title: S. aureus_control _45min_replicate3

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

description: Control

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_control

label_protocol: Conversion to cDNA and labeling was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., 2004 July, 186(14):4665-4684

treatment_protocol: Dimethyl sulfoxide (DMSO, 1% (vol/vol))

tag: Standard strain ATCC25923


title: Daphnia_1/10LC50_TNT_1

description: 1.194 mg/L TNT


title: Daphnia_1/10LC50_RDX_6

description: 30 mg/L RDX


title: S. aureus_cryptotanshinone_45min_replicate1

description: cryptotanshinone treatment

source_name: Staphylococcus aureus_cryptotanshinone

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. (iii) 500 µl of a 12800 µg /ml cryptotanshinone stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the cultures, giving a final concentration of 1/2× MIC (2 µg/ml), and the final concentration of DMSO was 1% (vol/vol). Then, the bacterial suspensions were further incubated for 45 min at 37°C

treatment_protocol: cryptotanshinone (2 µg/ml)


title: Daphnia_1/10LC50_RDX_2

description: 30 mg/L RDX


title: FEMX-I melanoma cells CD133 knockdown (II)

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

institute: Currently unaffilliated

hyb_protocol: Biotinylated UTP complementary RNA (cRNA) probes were prepared, fragmented and hybridized to the microarrays for 16-18 h with constant rotation.

scan_protocol: The microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen), and scanned using an Axon GenePix 4000B scanner.

data_processing: For data analyses, the local background was subtracted and the spot intensities were log2-transformed. The spot intensities were then normalized by subtracting the 70th percentile of spot intensity of the probes against human constitutive exons and adding back a scaling factor (grand mean of 70th percentiles).

organism: Homo sapiens

source_name: lymph node melanoma metastasis

label_protocol: Biotin incorporated during in vitro transcription.

growth_protocol: Cultured in RPMI (Mediatech Inc. Herndon, VA) supplemented with 10% FBS (Atlanta Biologicals, Lawrenceville, GA) at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Trizol phenol-based extraction.

tag: Originating from a lymph node metastasis in a patient, uniquely and selectively produced extrapulmonary metastases after i.v. injection of cells prepared from xenografts into adult, nude mice.


title: Daphnia_1/10LC50_RDX_1

description: 30 mg/L RDX


title: Daphnia_1/10LC50_RDX_4

description: 30 mg/L RDX


title: Daphnia_1/10LC50_RDX_3

description: 30 mg/L RDX


title: Embryos uninjected biological repl. 2 (50uM)


title: Daphnia_1/10LC50_RDX_5

description: 30 mg/L RDX


title: S. aureus_cryptotanshinone_45min_replicate3

description: cryptotanshinone treatment


title: Neuroblastoma tumor NB99

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

country: France

institute: Institut Curie

hyb_protocol: Affymetrix SNP array protocol

scan_protocol: Hewlett-Packard scanner

data_processing: Data were normalized using the ITALICS algorithm (Rigaill et al, Bioinformatics, 2008)

source_name: neuroblastic tumor

label_protocol: Affymetrix SNP array protocol

extract_protocol: Standard DNA extraction protocol

tag: neuroblastoma tumor with ALK amplification

tag: stage 4 tumor


title: S. aureus_cryptotanshinone_45min_replicate2

description: cryptotanshinone treatment


title: S. aureus_control _45min_replicate2

description: Control

growth_protocol: (i) S. aureus strain ATCC25923 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of MHB II, (ii) after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of MHB II in 250-ml Erlenmeyer flasks, the bacteria were grown at 37°C at 200 rpm to an OD600 of 0.3. and (iii) 1% (vol/vol) dimethyl sulfoxide (DMSO) was added to the culture, the bacterial suspensions were further incubated for 45 min at 37°C.


title: FEMX-I control melanoma cells (II)

description: FEMX-I control melanoma cells (II)


title: Daphnia_1/10LC50_TNT_3

description: 1.194 mg/L TNT


title: S. aureus_control _45min_replicate1

description: Control


title: FEMX-I melanoma cells CD133 knockdown

description: FEMX-I melanoma cells CD133 knockdown


title: Adenoma (F68A_s65_b47)

status: Public on Oct 15 2008

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: as described by Carvalho et al, Cell Oncol. 2006;28(5-6):283-94.

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the July 2003 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.

source_name: colon

label_protocol: as described by Snijders et al, Nat Genetics, volume 29, p 263-4

extract_protocol: protocol available on www.vumc.nl/microarrays

tag: Adenoma

source_name: Female Reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: A pool of ten normal individuals


title: Adenoma (F65A_s62_b47)


title: FEMX-I control melanoma cells

description: FEMX-I control melanoma cells


title: Adenoma (F66A_s63_b47)


title: Adenoma (F62A_s58_b47)


title: Carcinoma (F67C_s64_b47)

tag: Carcinoma


title: Adenoma (F63A_s59_b47)


title: Adenoma (F64A_s60_b47)


title: Carcinoma (F2C_s64_b21)

source_name: male Reference DNA


title: Carcinoma (F3C_s65_b21)


title: Adenoma (F56A_s36_b47)


title: Adenoma (F7A_s66_b21)


title: Adenoma component of a progressed adenoma (P34A_s50_b21)

extract_protocol: as described in Weiss et al, Mol Pathol. 1999 Oct;52(5):243-51.


title: Adenoma component of a progressed adenoma (P20A_s57_b21)

source_name: female Reference DNA


title: Adenoma (F61A_s41_b47)


title: Carcinoma component of a progressed adenoma (P20C_s58_b21)


title: Adenoma 1 (F58A1_s37_b47)

tag: Adenoma 1


title: Adenoma 2 (F38A2_s32_b47)

tag: Adenoma 2


title: Adenoma component of a progressed adenoma (P33A_s52_b21)


title: Carcinoma (F4C_s76_b21)


title: Adenoma (F48A_s34_b47)


title: Carcinoma component of a progressed adenoma (P34C_s54_b21)


title: Adenoma component of a progressed adenoma (P31A_s48_b21)


title: Carcinoma (F9C_s68_b21)


title: Adenoma (F52A_s30_b47)


title: Adenoma (F60A_s40_b47)


title: Adenoma 2 (F58A2_s38_b47)


title: Adenoma component of a progressed adenoma (P35A_s56_b21)


title: Adenoma (F59A_s39_b47)


title: Adenoma component of a progressed adenoma (P30A_s46_b21)


title: Adenoma component of a progressed adenoma (P1A_s11_b14)


title: Adenoma component of a progressed adenoma (P29A_s33_b21)


title: Carcinoma component of a progressed adenoma (P4C1_s20_b14)


title: Adenoma component of a progressed adenoma (P2A_s13_b14)


title: Adenoma component of a progressed adenoma (P28A_s31_b21)


title: Adenoma component of a progressed adenoma (P3A1_s22_b14)


title: Adenoma component of a progressed adenoma (P3A2_s17_b14)


title: Carcinoma component of a progressed adenoma (P1C_s12_b14)


title: Adenoma component of a progressed adenoma (P21A_s56_b16)


title: Carcinoma component of a progressed adenoma (P21C_s57_b16)


title: Adenoma component of a progressed adenoma (P4A1_s19_b14)


title: Carcinoma component of a progressed adenoma (P3C1_s16_b14)


title: Adenoma component of a progressed adenoma (P23A_s54_b16)


title: Carcinoma component of a progressed adenoma (P3C2_s18_b14)


title: Carcinoma component of a progressed adenoma (P30C_s47_b21)


title: carcinoma component of a progressed adenoma (P19C1_s15_b17)


title: Adenoma component of a progressed adenoma (P22A_s66_b16)


title: Carcinoma component of a progressed adenoma (P17C_s65_b16)


title: Carcinoma (F54C_s55_b47)


title: Carcinoma component of a progressed adenoma (P28C_s32_b21)


title: Adenoma component of a progressed adenoma (P27A_s59_b21)


title: Carcinoma component of a progressed adenoma (P16C_s18_b17)


title: Adenoma component of a progressed adenoma (P18A_s60_b16)


title: Carcinoma component of a progressed adenoma (P31C_s49_b21)


title: Adenoma component of a progressed adenoma (P13A_s06_b17)


title: Carcinoma (F24C_s24_b14)


title: Carcinoma component of a progressed adenoma (P12C_s63_b16)


title: Adenoma component of a progressed adenoma (P17A_s64_b16)


title: Carcinoma component of a progressed adenoma (P15C_s11_b17)


title: Carcinoma component of a progressed adenoma (P33C_s53_b21)


title: Adenoma component of a progressed adenoma (P16A_s12_b17)


title: Adenoma component of a progressed adenoma (P15A_s10_b17)


title: Carcinoma component of a progressed adenoma (P13C_s07_b17)


title: Adenoma component of a progressed adenoma (P12A_s62_b16)


title: Carcinoma component of a progressed adenoma (P26C2_s29_b21)


title: Adenoma component of a progressed adenoma (P10A_s22_b16)


title: Adenoma (F50A_s61_b47)


title: Adenoma (F55A_s31_b47)


title: Carcinoma (F57C_s56_b47)


title: Adenoma component of a progressed adenoma (P11A1_s24_b16)


title: Carcinoma (F25C_s25_b14)


title: Adenoma (F16A_s29_b47)


title: Carcinoma component of a progressed adenoma (P11C1_s25_b16)


title: Adenoma component of a progressed adenoma (P19A1_s19_b17)


title: Adenoma component of a progressed adenoma (P14A_s08_b17)


title: Carcinoma component of a progressed adenoma (P19A2_s16_b17)


title: Adenoma component of a progressed adenoma (P9A_s20_b16)


title: Adenoma component of a progressed adenoma (P7A_s11_b16)


title: Carcinoma component of a progressed adenoma (P19C2_s17_b17)


title: Carcinoma component of a progressed adenoma (P5C_s07_b16)


title: Carcinoma component of a progressed adenoma (P7C_s12_b16)


title: Carcinoma component of a progressed adenoma (P11C2_s27_b16)


title: Carcinoma (F6C_s38_b16)


title: Carcinoma component of a progressed adenoma (P6C_s10_b16)


title: Adenoma component of a progressed adenoma (P6A_s09_b16)


title: Adenoma component of a progressed adenoma (P8A_s18_b16)


title: Adenoma component of a progressed adenoma (P11A2_s26_b16)


title: Adenoma (F44A_s62_b17)


title: Adenoma component of a progressed adenoma (P26A2_s28_b21)


title: Adenoma component of a progressed adenoma (P5A_s06_b16)


title: Adenoma (F40A_s59_b17)


title: Carcinoma (F34C_s49_b16)


title: Adenoma (F25A_s44_b16)


title: Adenoma 1 (F23A1_s13_b16)


title: Adenoma (F37A_s67_b17)


title: Adenoma 1 (F38A1_s68_b16)


title: Adenoma (F47A_s66_b17)


title: Adenoma 2 (F23A2_s31_b16)


title: Adenoma (F21A_s29_b17)


title: Carcinoma (F33C_s50_b16)


title: Carcinoma (F31C_s47_b16)


title: Adenoma (F26A_s35_b17)


title: Carcinoma (F19C_s15_b16)


title: Carcinoma (F28C_s16_b16)


title: Adenoma (F17A_s14_b16)


title: Carcinoma (F15C_s46_b16)


title: Carcinoma (F13C_s45_b16)


title: Adenoma component of a progressed adenoma (P36A_s55_b17)


title: Adenoma (F41A_s65_b17)


title: Adenoma (F22A_s30_b16)


title: Adenoma (F49A_s52_b16)


title: Adenoma component of a progressed adenoma (P37A_s57_b17)


title: Carcinoma component of a progressed adenoma (P37C_s58_b17)


title: Adenoma component of a progressed adenoma (P24A_s20_b17)


title: Carcinoma (F14C_s17_b16)


title: Adenoma component of a progressed adenoma (P26A1_s24_b17)


title: Adenoma (F20A_s28_b17)


title: Adenoma component of a progressed adenoma (P32A_s53_b17)


title: Carcinoma component of a progressed adenoma (P32C_s54_b17)


title: Caricinoma component of a progressed adenoma (P26C1_s25_b17)


title: Adenoma component of a progressed adenoma (P25A_s23_b17)


title: Adenoma (F59A_expr_s90_b34)

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings, as described in Carvalho et al, submitted

label_protocol: As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47.

extract_protocol: protocol available on wwww.vumc.nl/microarrays/

source_name: universal human reference RNA, Stratagene

extract_protocol: See www.stratagene.com

tag: comprised of 10 cell lines for human giving broad gene coverage


title: Adenoma (F66A_expr_s16_b34)

hyb_protocol: As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47


title: Carcinoma (F57C_expr_s94_b34)

label_protocol: As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47


title: Adenoma (F58A2_expr_s89_b34)


title: Adenoma (F63A_expr_s06_b34)


title: Adenoma (F58A1_expr_s95_b34)


title: Adenoma (F62A_expr_s05_b34)


title: Adenoma (F68A_expr_s97_b34)


title: Adenoma (F61A_expr_s96_b34)


title: Adenoma (F55A_expr_s87_b34)


title: Adenoma (F65A_expr_s08_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL15)

city: Tsu

first: Kana

last: Miyazaki

state: Mie

address: 2-174 Edobashi

department: Department of Hematology and Oncology

country: Japan

institute: Mie University

description: Gene expression data from lymphoma tissue of an angioimmunoblastic T-cell lymphoma patient

hyb_protocol: The probe consisted of a mixture of Cy5-labeled patient's cRNA and Cy3-labeled control cRNA was hybridized for 17 hours at 65C on the Agilent 44K human oligo microarray.

scan_protocol: Hybridized array slides were scanned at 10-um resolution using an Agilent G2565BA fluorescence dual laser scanner for Cy3 and Cy5 excitation.

data_processing: Image intensity data were recorded and transferred into text files using Feature Extraction software, version 9.1.

source_name: Human Universal Reference Total RNA (Beckton Dickinson)

label_protocol: Cy3-labeled cRNA was generated from 0.5 ug of total RNA according to the manufacturer's protocol (Agilent Technology).

tag: Human Universal Reference Total RNA

source_name: Total RNA from frozen lymph node tissue

label_protocol: Cy5-labeled cRNA was generated from 0.5 ug of total RNA according to the manufacturer's protocol (Agilent Technology).

extract_protocol: Frozen lymphoma tissues were ground to powder and lysed in lysis buffer Trizol reagent (Invitrogen).

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL15)


title: Adenoma (F60A_expr_s91_b34)


title: Adenoma (F64A_expr_s07_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL14)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL14)


title: Adenoma (F7A_expr_s30_b34)


title: Carcinoma (F58C_expr_s12_b34)


title: Carcinoma (F67C_expr_s09_b34)


title: Adenoma (F56A_expr_s88_b34)


title: Carcinoma (F54C_expr_s15_b34)


title: Adenoma (F52A_expr_s86_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL12)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL12)


title: Adenoma (F50A_expr_s04_b34)


title: Carcinoma (F53C_expr_s14_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL13)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL13)


title: Adenoma (F49A_expr_s63_b34)


title: Carcinoma (F51C_expr_s13_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL8)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL8)


title: Angioimmunoblastic T-cell lymphoma patient (AITL11)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL11)


title: Angioimmunoblastic T-cell lymphoma patient (AITL10)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL10)


title: Adenoma (F48A_expr_s85_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL7)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL7)


title: Angioimmunoblastic T-cell lymphoma patient (AITL5)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL5)


title: Angioimmunoblastic T-cell lymphoma patient (AITL9)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL9)


title: Follicular Lymphoma tissue 40 snap frozen

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

description: 41 frozen follicular lymphoma tissues were profiled, then correlated to 5 year follow up survival data.

hyb_protocol: labeled RNA was hybridized to Agilent 44K Human Whole Genome microarays at 65°C for 17h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 1 minute each.

scan_protocol: Images was scanned with Agilent scanner at 10µm resolution

data_processing: 1)Of the 23,216 features remaining after removing the features with >10% missing values, there are 12,390 genes with no below-threshold values, and 10,826 genes with below-threshold values.2) For the 10,826 genes with below-threshold values, we substituted the below threshold values with the minimum determined from all the above threshold values.3) We determined the trimmed mean for each chip based on the expression values of 12,390 genes with no below-threshold values.  The trimmed mean is the average of the measurements that are within +/- 1 stdev of the measured mean (again, only taking into account genes with no below threshold substitutions).4) Then we subtracted the trimmed mean from all 23,216 features (including the sub-threshold minimum substitutions), which generated the final dataset we used

source_name: Follicular Lymphoma tissue

label_protocol: 200ng total RNA was amplified and labeled with Cy3 using Agilent low input RNA amplification kit following manufacturer's protocol

growth_protocol: 41 tissues were snap frozen in cryovials containing Tissue Tek optimal cutting temperature compound in an isopentane bath shortly after excision and maintained thereafter at -80

extract_protocol: Total RNA was extracted from each sample using Trizol (Qiagen) according to the manufacturer's protocol. RNA was then further purified using a RNEasy column (Qiagen).

tag: death after 5 years


title: Follicular Lymphoma tissue 41 snap frozen

tag: alive after 5 years


title: Adenoma (F47A_expr_s84_b34)

tag: Adenoma


title: Adenoma (F45A_expr_s61_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL4)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL4)


title: Angioimmunoblastic T-cell lymphoma patient (AITL3)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL3)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u11)

description: Gene expression data from lymphoma tissue of a peripheral T-cell lymphoma, unspecified patient

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u11)


title: Follicular Lymphoma tissue 38 snap frozen


title: Adenoma (F41A_expr_s83_b34)

tag: comprised of 10 cell lines for human giving broad gene coverage


title: Carcinoma (F46C_expr_s11_b34)

tag: Carcinoma


title: Adenoma (F43A_expr_s60_b34)


title: Carcinoma (F39C_expr_s62_b34)


title: Adenoma (F44A_expr_s54_b34)


title: Follicular Lymphoma tissue 37 snap frozen


title: Follicular Lymphoma tissue 39 snap frozen


title: Hepatosplenic alpha beta T-cell lymphoma patient (PTCL hs12)

description: Gene expression data from lymphoma tissue of a hepatosplenic alpha beta T-cell lymphoma patient

tag: Human Universal Reference Total RNA

source_name: Total RNA from frozen spleen tissue

tag: Spleen from hepatosplenic alpha beta T-cell lymphoma patient (PTCL hs12)


title: Angioimmunoblastic T-cell lymphoma patient (AITL2)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL2)


title: Angioimmunoblastic T-cell lymphoma patient (AITL1)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL1)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u8)

source_name: Total RNA from frozen stomach tissue

tag: Stomach from peripheral T-cell lymphoma, unspecified patient (PTCL u8)


title: Adenoma (F40A_expr_s59_b34)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u10)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u10)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u9)

source_name: Total RNA from frozen tonsil tissue

tag: Tonsil from peripheral T-cell lymphoma, unspecified patient (PTCL u9)


title: Adenoma (F42A_expr_s42_b34)


title: Angioimmunoblastic T-cell lymphoma patient (AITL6)

tag: Lymph node from angioimmunoblastic T-cell lymphoma patient (AITL6)


title: Follicular Lymphoma tissue 36 snap frozen


title: Adenoma (F38A2_expr_s93_b34)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u7)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u7)


title: Adenoma (F38A1_expr_s58_b34)


title: Follicular Lymphoma tissue 35 snap frozen


title: Follicular Lymphoma tissue 33 snap frozen


title: Adenoma (F37A_expr_s82_b34)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u6)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u6)


title: Follicular Lymphoma tissue 34 snap frozen

tag: alive after 5 years


title: Follicular Lymphoma tissue 32 snap frozen


title: Carcinoma (F36C_expr_s53_b34)


title: Carcinoma (F34C_expr_s41_b34)


title: Follicular Lymphoma tissue 29 snap frozen

tag: death after 5 years


title: Follicular Lymphoma tissue 30 snap frozen


title: Peripheral T cell lymphoma, unspecified patient (PTCL u4)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u4)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u5)

tag: Stomach from peripheral T-cell lymphoma, unspecified patient (PTCL u5)


title: Carcinoma (F35C_expr_s25_b34)


title: Carcinoma (F33C_expr_s37_b34)


title: Peripheral T cell lymphoma, unspecified patient (PTCL u2)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u2)


title: Follicular Lymphoma tissue 31 snap frozen


title: Carcinoma (F32C_expr_s52_b34)

tag: comprised of 10 cell lines for human giving broad gene coverage


title: Carcinoma (F31C_expr_s51_b34)

tag: Carcinoma


title: Follicular Lymphoma tissue 28 snap frozen


title: Peripheral T cell lymphoma, unspecified patient (PTCL u3)

tag: Human Universal Reference Total RNA

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u3)


title: Adenoma (F30C_expr_s10_b34)

tag: Adenoma


title: Follicular Lymphoma tissue 27 snap frozen


title: Peripheral T cell lymphoma, unspecified patient (PTCL u1)

tag: Lymph node from peripheral T-cell lymphoma, unspecified patient (PTCL u1)


title: Carcinoma (F29C_expr_s40_b34)


title: Thyroidal gamma delta T cell lymphoma patient (GD-nhs7)

description: Gene expression data from lymphoma tissue of a thyroidal gamma delta T-cell lymphoma patient

source_name: Total RNA from frozen thyroid tissue

tag: Thyroid from thyroidal gamma delta T-cell lymphoma patient (GD-nhs7)


title: Follicular Lymphoma tissue 25 snap frozen


title: Follicular Lymphoma tissue 26 snap frozen


title: Cutaneous gamma delta T cell lymphoma patient (GD-nhs6)

description: Gene expression data from lymphoma tissue of a cutaneous gamma delta T-cell lymphoma patient

tag: Lymph node from cutaneous gamma delta T-cell lymphoma patient (GD-nhs6)


title: Hepatosplenic gamma delta T cell lymphoma patient (GD-hs4)

description: Gene expression data from lymphoma tissue of a hepatosplenic gamma delta T-cell lymphoma patient

tag: Spleen from hepatosplenic gamma delta T-cell lymphoma patient (GD-hs4)


title: Carinoma (F28C_expr_s36_b34)

tag: Carinoma


title: Carcinoma (F27C_expr_s24_b34)


title: EPY338/EPY330_72h_E

city: Emeryville

first: Mario

last: Ouellet

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

description: Replicate E

hyb_protocol: Hybridization and washes were carried using an hybridization station (TECAN). Slides were pre-hybridized with SlideHyb#3 (ArrayIt) at 55°C for 15 minutes and hybridized with the labeled cDNA diluted in SlideHyb#3 at 55°C for 16h. The slides were washed 3 times with [1X SSC, 0.1%SDS] at 55°C (30s soak, 2 minutes wash), then 3 times with 1X SSC at 25°C (30s soak, 1 minute wash) and 3 times with 0.1X SSC (wash 30s), before drying at 30°C for 3 minutes.

scan_protocol: Images were acquired with a GenePix Professional 4200A scanner (Axon Instruments) and feature fluorescence intensities [F532 median-B532 and F635 median-B635] were extracted with the GenePix Pro 6.1 software.

data_processing: Artifactual or aberrant spots were excluded, as well as spots with low signal in both channels and spots for which more than 50% of the values across all slides were missing. Dulicate spots on the slide were averaged and Lowess normalization was performed using BRB-ArrayTools version 3.5.0 developed by Dr. Richard Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html). The VALUE column represent the normalized Log2 (EPY338/EPY330) ratio.

label_protocol: Twenty (20) µg of a pool of total RNA containing equal amounts of RNA extracted from 5 independent biological replicates were used for reverse transcription and fluorescent labeling with SuperScript Plus Indirect cDNA Labeling System (Invitrogen) following the manufacturer’s recommendations, except for the chemical hydrolysis of RNA and cDNA purifications, which were carried according to standard protocols (http://cmgm.stanford.edu/pbrown/protocols/amino-allyl.htm).

extract_protocol: Total RNA from 5 independent transformants was prepared by hot acid phenol extraction [Ausubel, F. Current Protocol in Molecular Biology. 2004.] and further purified on an RNEasy Mini column (QIAgen). The RNA integrity was verified using a 2100 Bioanalyzer (Agilent).

tag: Strain EPY330 (artemisinic acid producer) after 72h of growth in galactose-inducing medium.

tag: Strain EPY338 (inactivated AMO) after 72h of growth in galactose-inducing medium.


title: Intestinal gamma delta T cell lymphoma patient (GD-nhs5)

description: Gene expression data from lymphoma tissue of an intestinal gamma delta T-cell lymphoma patient

source_name: Total RNA from frozen jejunum tissue

tag: Jejunum from intestinal gamma delta T-cell lymphoma patient (GD-nhs5)


title: Follicular Lymphoma tissue 20 snap frozen

tag: alive after 5 years


title: Hepatosplenic gamma delta T cell lymphoma patient (GD-hs3)

source_name: Total RNA from frozen liver tissue

tag: Liver from hepatosplenic gamma delta T-cell lymphoma patient (GD-hs3)


title: Follicular Lymphoma tissue 21 snap frozen

tag: death after 5 years


title: Follicular Lymphoma tissue 23 snap frozen


title: EPY338/EPY330_72h_D

description: Replicate D


title: Hepatosplenic gamma delta T cell lymphoma patient (GD-hs2)

tag: Lymph node from hepatosplenic gamma delta T-cell lymphoma patient (GD-hs2)


title: Follicular Lymphoma tissue 24 snap frozen


title: Adenoma (F23A1_expr_s26_b34)

tag: comprised of 10 cell lines for human giving broad gene coverage


title: Carcinoma (F25C_expr_s50_b34)

tag: Carcinoma


title: EPY338/EPY330_72h_B

description: Replicate B


title: Follicular Lymphoma tissue 19 snap frozen


title: Adenoma (F26A_expr_s28_b34)


title: EPY338/EPY330_72h_C

description: Replicate C


title: EPY338/EPY330_72h_A

description: Replicate A


title: Adenoma (F25A_expr_s81_b34)


title: Follicular Lymphoma tissue 18 snap frozen


title: Follicular Lymphoma tissue 17 snap frozen


title: Hepatosplenic gamma delta T cell lymphoma patient (GD-hs1)

tag: Human Universal Reference Total RNA

tag: Spleen from hepatosplenic gamma delta T-cell lymphoma patient (GD-hs1)


title: Adenoma (F23A2_expr_s27_b34)

tag: Adenoma


title: Adenoma (F22A_expr_s23_b34)


title: Carcinoma (F21A_expr_s22_b34)


title: Adenoma (F20A_expr_s31_b34)


title: EPY338/EPY330_48h_E

description: Replicate E

tag: Strain EPY330 (artemisinic acid producer) after 48h of growth in galactose-inducing medium.

tag: Strain EPY338 (inactivated AMO) after 48h of growth in galactose-inducing medium.


title: Carcinoma (F19C_expr_s80_b34)


title: EPY338/EPY330_48h_D

description: Replicate D


title: Follicular Lymphoma tissue 22 snap frozen


title: Follicular Lymphoma tissue 16 snap frozen


title: Follicular Lymphoma tissue 13 snap frozen


title: Follicular Lymphoma tissue 15 snap frozen


title: EPY338/EPY330_48h_C

description: Replicate C


title: EPY338/EPY330_48h_B

description: Replicate B


title: EPY338/EPY330_24h_C

description: Replicate C

tag: Strain EPY330 (artemisinic acid producer) after 24h of growth in galactose-inducing medium.

tag: Strain EPY338 (inactivated AMO) after 24h of growth in galactose-inducing medium.


title: EPY338/EPY330_48h_A

description: Replicate A


title: EPY338/EPY330_24h_D

description: Replicate D


title: Follicular Lymphoma tissue 12 snap frozen


title: Follicular Lymphoma tissue 9 snap frozen


title: Follicular Lymphoma tissue 14 snap frozen


title: Follicular Lymphoma tissue 11 snap frozen


title: Follicular Lymphoma tissue 10 snap frozen


title: Follicular Lymphoma tissue 8 snap frozen


title: EPY338/EPY330_24h_B

description: Replicate B


title: Adenoma (F16A_expr_s98_b34)


title: Adenoma (F17A_expr_s56_b34)


title: Carcinoma (F18C_expr_s49_b34)


title: Follicular Lymphoma tissue 7 snap frozen


title: Carcinoma (F11C_expr_s22_b34)


title: Follicular Lymphoma tissue 6 snap frozen


title: Carcinoma (F12C_expr_s21_b34)


title: Carcinoma (F10C_expr_s33_b34)


title: Follicular Lymphoma tissue 5 snap frozen


title: Carcinoma (F9C_expr_s55_b34)


title: Carcinoma (F15C_expr_s35_b34)


title: Carcinoma (F14C_expr_s34_b34)


title: Follicular Lymphoma tissue 3 snap frozen


title: Follicular Lymphoma tissue 4 snap frozen


title: Carcinoma (F6C_expr_s39_b34)


title: Carcinoma (F3c_expr_s29_b34)


title: Carcinoma (F1C_expr_s92_b34)


title: Carcinoma (F8C_expr_s32_b34)


title: Olfactory Epithlium-Emx2 Knockout-replicate 3

city: Lexington

first: Jeremy

last: McIntyre

state: KY

address: 800 Rose St

department: Physiology

institute: University of Kentucky

description: Gene expression data from the olfactory epithelium of ED18.5 Emx2 Knockout mice

hyb_protocol: Biotin labeled probes were hybridized overnight in Affymetrix GeneChip Hybridization Oven 640, then washed and stained with Affymetrix GeneChip Fluidics Station 450

scan_protocol: Chips scanned with Affymetrix GCS 3000 7G scanner

data_processing: Data was analyzed by RMA with Expression Console software. Data was analyzed at the gene level, using the core annotation level (Limits analysis to exon-level probe sets that map to BLAT alignments of mRNA with annotated full-lenths CDS regions) . Gene level data is obtained by aggregation of multiple exon level porbe sets.

organism: Mus musculus

source_name: Olfactory epithelium of Emx2 knockout mice

label_protocol: Biotin-labelled probes were prepared using Affymetrix Whole Transcript Sense target labelling protocol from 2.7ug total RNA.

growth_protocol: Females were mated overnight, morning of vaginal plug detection was ED0.5. Embryos were collected at ED18.5

extract_protocol: Olfactory epithelium of ED18.5 embryos was dissected out and RNA was extracted with TRI-reagent following manufacturers protocol(Molecular Research Center, Inc)

tag: Age

tag: Genotype

value: Emx2 Knockout


title: Olfactory Epithlium-Emx2 Knockout-replicate 1


title: Follicular Lymphoma tissue 2 snap frozen


title: Olfactory Epithelium-Emx2 Wildtype_replicate 2

description: Gene expression data from the olfactory epithelium of ED18.5 Emx2 wildtype mice

source_name: Olfactory epithelium of Emx2 wildtype mice

value: Emx2 Homozygous Wildtype


title: Follicular Lymphoma tissue 1 snap frozen


title: Olfactory Epithlium-Emx2 Knockout-replicate 2


title: Olfactory Epithelium-Emx2 Wildtype_replicate 1


title: Olfactory Epithelium-Emx2 Wildtype_replicate 3


title: brain_homozygous_Insm1_knockout_rep3

status: Public on Oct 14 2008

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max-Planck-Institute of Evolutionary Anthropology

description: dorsal telencephanlon, homozygous_Insm1_knockout

hyb_protocol: Hybridisation (16 hours), washing and staining were done by following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix).

scan_protocol: The chips were scanned with a GeneChip scanner 3000 7G system. Image analysis was done with the GeneChip® Command Console™ Software Version 1.0 (Affymetrix).

data_processing: Low level data analysis, such as the calculation of expression values (RMA) and the calculation of detection P-values for the genes that are annotated in the core set of probes (23238 transcript clusters) on the Mouse Exon 1.0 ST Array was carried out with the Expression Console Software version 1.1 (Affymetrix). A gene was considered as expressed if at least 60% of the exons of a gene were significantly (P<=0.05) higher expressed than the background signals in 80% of the samples.   High level data analysis was done in R. Gene by gene t-tests were carried between the control and the Insm1 over expressed samples and between wt and Insm1 KO mice.  To adjust P-values for multiple hypothesis testing, we chose to control the false discovery rate (FDR), which is less conservative and more powerful than other adjustments. FDR adjustments were performed to reduce the number of false significant genes to fewer than 5%.

label_protocol: The RNA samples were processed following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix) which is optimized for the use of 1µg total RNA as input.

extract_protocol: Total RNA was extracted from mice brain tissues using TRIZOL (GibcoBRL)  reagent following the protocol according to the manufacturers  instructions. Quality was assessed by running nano assays on a Bioanalyzer (Agilent). Ribosomal RNA was reduced following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix) which is optimized for the use of 1µg total RNA.


title: brain_homozygous_Insm1_knockout_rep4


title: brain_homozygous_Insm1_knockout_rep2


title: stop 0 time point sample 5

city: Charlottesville

first: Carol

middle: A

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

description: EF compare to STOP at 0 and 9 hours time points

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCRMA

organism: Entamoeba histolytica

source_name: stop 0 time point sample 5

label_protocol: SPIA

tag: stop 0 time point sample 5


title: brain_homozygous_Insm1_knockout_rep1


title: EF 9 hour time point sample 3

source_name: EF 9 hour time point sample 3

tag: EF 9 hour time point sample 3


title: stop 0 time point sample 3

source_name: stop 0 time point sample 3

tag: stop 0 time point sample 3


title: brain_heterozygous_Insm1_knockout_rep5

description: dorsal telencephanlon, heterozygous_Insm1_knockout


title: stop at 9 hour time poine sample 3

source_name: stop at 9 hour time poine sample 3

tag: stop at 9 hour time poine sample 3


title: EPY338/EPY330_24h_A

description: Replicate A


title: brain_heterozygous_Insm1_knockout_rep1


title: brain_Insm1_wildtype_rep8

description: dorsal telencephanlon, wildtype

source_name: dorsal telencephanlon, wildtype


title: brain_heterozygous_Insm1_knockout_rep2


title: EF 9 hour time point sample 1

source_name: EF 9 hour time point sample 1

tag: EF 9 hour time point sample 1


title: brain_heterozygous_Insm1_knockout_rep6


title: EF at 9hour time point sample 2

source_name: EF at 9hour time point sample 2

tag: EF at 9hour time point sample 2


title: stop  9hour time point sample1

source_name: stop at 9hour time point sample1

tag: stop  9hour time point sample1


title: brain_Insm1_wildtype_rep7

description: dorsal telencephanlon, wildtype


title: EF 0 time point sample 3

source_name: EF 0 time point sample 3

tag: EF 0 time point sample 3


title: brain_heterozygous_Insm1_knockout_rep3


title: brain_Insm1_wildtype_rep6

description: dorsal telencephanlon, wildtype


title: EF time 0 point sample 5

source_name: EF time 0 point sample 5

tag: EF time 0 point sample 5


title: brain_Insm1_wildtype_rep4

description: dorsal telencephanlon, wildtype


title: brain_heterozygous_Insm1_knockout_rep4


title: stop 9hour time point sample2

source_name: stop 9hour time point sample2

tag: stop 9hour time point sample2


title: BEAS-2B_IL4-TNF3

city: Houston

first: David

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

description: BEAS-2B cells were seeded 24 h before extraction

hyb_protocol: Illumina protocol, overnight

scan_protocol: Beadscan

data_processing: Beadstudio v3, bkg subtracted, cubic spline normalization

label: biotin - Streptavadin Cy3

source_name: BEAS-2B cells treated with IL4 and TNfa - 3

label_protocol: 200 ng biotin labelled according to Illumina protocol

growth_protocol: BEAS-2B cells were  cultured in DMEM/F-12 medium containing heat-inactivated fetal calf serum (5%), L-glutamine (2mM), penicillin (100 U/ml) and streptomycin (100 ug/ml) at 37 C, 5% CO2.

extract_protocol: cytoplasmic RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer's protocol.

treatment_protocol: The cells were treated with TNF-a/IL-4 (50 ng/ml of each) for 18 h.

tag: BEAS-2B bronchial epithelial cells


title: brain_Insm1_wildtype_rep5

description: dorsal telencephanlon, wildtype


title: EF 0 time point sample 2

source_name: EF 0 time point sample 2

tag: EF 0 time point sample 2


title: BEAS-2B_IL4-TNF1

source_name: BEAS-2B cells treated with IL4 and TNfa - 1


title: BEAS-2B_IL4-TNF2

source_name: BEAS-2B cells treated with IL4 and TNfa - 2


title: brain_Insm1_wildtype_rep1

description: dorsal telencephanlon, wildtype


title: BEAS-2B_Control3

source_name: BEAS-2B cells control - 3

treatment_protocol: vehicle treated sample


title: BEAS-2B_Control2

source_name: BEAS-2B cells control - 2


title: brain_Insm1_wildtype_rep3

description: dorsal telencephanlon, wildtype


title: S10A Sporadic-frontal

status: Public on Oct 11 2008

city: Philadelphia

first: Alice

last: Chen-Plotkin

state: PA

address: 3600 Spruce Street 3rd Floor Maloney

department: Pathology and Neurology

institute: University of Pennsylvania

hyb_protocol: cRNA was hybridized for 16 hr at 45C on the Affymetrix Human U133A array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: RMA

source_name: S10A Sporadic-frontal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: postmortem brain


title: brain_Insm1_wildtype_rep2

description: dorsal telencephanlon, wildtype


title: S9C Sporadic-hippocampus

source_name: S9C Sporadic-hippocampus


title: S10B Sporadic-cerebellum

source_name: S10B Sporadic-cerebellum


title: S8A Sporadic-frontal

source_name: S8A Sporadic-frontal


title: S9B Sporadic-cerebellum

source_name: S9B Sporadic-cerebellum


title: BEAS-2B_Control1

description: BEAS-2B cells were seeded 24 h before TNF-a/IL-4 (50 ng/ml) treatment

source_name: BEAS-2B cells control - 1


title: S6A Sporadic-frontal

source_name: S6A Sporadic-frontal


title: S8C Sporadic-hippocampus

source_name: S8C Sporadic-hippocampus


title: S9A Sporadic-frontal

source_name: S9A Sporadic-frontal


title: S7C Sporadic-hippocampus

source_name: S7C Sporadic-hippocampus


title: S6B Sporadic-cerebellum

source_name: S6B Sporadic-cerebellum


title: S6C Sporadic-hippocampus

source_name: S6C Sporadic-hippocampus


title: S5A Sporadic-frontal

source_name: S5A Sporadic-frontal


title: S7A Sporadic-frontal

source_name: S7A Sporadic-frontal


title: S3A Sporadic-frontal

source_name: S3A Sporadic-frontal


title: S4C Sporadic-hippocampus

source_name: S4C Sporadic-hippocampus


title: S4A Sporadic-frontal

source_name: S4A Sporadic-frontal


title: S4B Sporadic-cerebellum

source_name: S4B Sporadic-cerebellum


title: S3B Sporadic-cerebellum

source_name: S3B Sporadic-cerebellum


title: S3C Sporadic-hippocampus

source_name: S3C Sporadic-hippocampus


title: S2B Sporadic-cerebellum

source_name: S2B Sporadic-cerebellum


title: S1C Sporadic-hippocampus

source_name: S1C Sporadic-hippocampus


title: S2C Sporadic-hippocampus

source_name: S2C Sporadic-hippocampus


title: S1A Sporadic-frontal

source_name: S1A Sporadic-frontal


title: P7A Progranulin-frontal

source_name: P7A Progranulin-frontal


title: P4B Progranulin-cerebellum

source_name: P4B Progranulin-cerebellum


title: P4C Progranulin-hippocampus

source_name: P4C Progranulin-hippocampus


title: S2A Sporadic-frontal

source_name: S2A Sporadic-frontal


title: P5B Progranulin-cerebellum

source_name: P5B Progranulin-cerebellum


title: P2C Progranulin-hippocampus

source_name: P2C Progranulin-hippocampus


title: P3B Progranulin-cerebellum

source_name: P3B Progranulin-cerebellum


title: Female E9.5-3d

city: Geelong

first: Stephanie

last: Bannister

state: Victoria

address: 5 Portarlington Road

department: Livestock Industries

country: Australia

institute: CSIRO

description:
small RNA <200nt
26 spots excluded from data extraction: probe no see additional file sample25-ex.txt
Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC).  Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction.  E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos.  E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction.
PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138).  Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes.  Digested tissue samples cooled to room temperature.  1ul of digested sample added to each PCR (see paper ref. for reaction mix).  RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction.  PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium).  Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller).  Male positive samples give only 18S control band (no W chromosome in males).

hyb_protocol: CombiMatrix CustomArray 4x2k miRNA microarrays (design #4166) stored at room temperature prior to use.  Rehydrated and prehybridised according to CombiMatrix hybridisation and imaging protocol.  Hybridisation solutions prepared from concentrated, labelled miRNA samples adjusting volume of nuclease-free water (NF-H2O) used according to volume of miRNA sample.  Hybridisations carried out at 37degrees celcius in rotating hybridisation oven for 4hours or overnight.  Post-hybridisation wash steps and array preparation for imaging performed according to manufacturer's protocol.  Arrays were stripped following hybridisation and scanning according to manufacturer's protocol and stored in glad-wrap at 4degrees prior to re-hybridisation.  Individual array slides were stripped and re-hybridised between 4-10 times

scan_protocol: Arrays scanned using arrayWorx e microarray scanner (Applied Precision) and arrayWorx e scanning software.  Single Cy-5 channel used.  Resolution setting: High SNR 3.252um/pixel.  Focus adjusted manually per array.  Each array hybridisation was scanned at 5 exposure levels: a = 0.1sec; b = 0.2sec; c - 0.5sec; d = 1.0sec; e = 2.0sec.  Each exposure image saved as 24bit RGB colour image in TIFF format.

data_processing: CombiMatrix microarray imager software used to analyse scanned array images and extract data.  Briefly, chip design file #4166 opened as probe 1 and TIFF image opened at 100% size. Array template overlaid manually and data extracted for each individual array panel (Arrays 1-4).  Data for each individual array exported to text file and saved with array number, date, chip used and hybridisation number.  Data for arrays 1-4 imported into Microsoft Excel Spreadsheet template using an in-house macro, and background, subtraction, negative correction and normalisation was carried out using macro encompassing the following steps:  (1) Probe signal intensity values ranked from highest to lowest to identify 80th percentile value (2) 80th percentile value per sample subtracted from intensity value for each probe to give background-subtracted data set. (3) Negative numbers in background subtracted set made equal to zero (0). (4) Background subtracted values multipled by constant of 2 million (2.0E+6) to give normalised signal intensity.  Fold change analysis performed in Excel eg: by dividing sample 1 by sample 2 to give ratio sample1:sample2.

organism: Gallus gallus

source_name: Embryonic gonad

label_protocol: 500ng aliquot of miRNA sample was used per microarray hybridisation.  500ng volume of RNA sample was concentrated by vacuum drying using SpeedVac and resuspended in 17ul of Rnase-free water (Promega).  miRNA samples were labelled with ULS™-Cy5 using ULS™ Small RNA labelling kit (Kreatech Diagnostics).  This labels guanine (G) residues within miRNA sequence.  Therefore some G-bias in labelling. Protocol carried out as per manufacturers instructions.  Labelled samples purified using KreaPure columns (Kreatech Diagnostics) according to manufacturer's instructions and concentrated to less than 5.1ul using Microcon centrifugal filter columns (YM-30) (Microcon Bioseparations, Millipore) according to manufacturer's instructions.

extract_protocol: miRNA was extracted from pooled gonad lysates using the mirVana miRNA isolation kit (Ambion) protocol for enrichment of small RNAs <200nt, according to the manufacturer's instructions.  High-molecular weight (HMW) RNA fractions were also collected separately for all samples.  miRNA and HMW eluted in 100ul of RNase-free water (Ambion) pre-heated to 95degrees, quantified by nanodrop and stored at -20degrees celcius prior to microarray analysis.

tag: Sex

value: Female

tag: Stage

tag: Sexed

value: Manual

tag: exposure

tag: array chip #


title: P5C Progranulin-hippocampus

source_name: P5C Progranulin-hippocampus


title: Mouse PUER exon 24h-2

city: Regensburg

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

description: Gene expression data from PUER cells 24h after induction of PU.1 expression with 100nM OHT

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Mouse Exon 1.0 ST Arrays (exon arrays) according to manufacturer’s protocols at the KFB Regensburg

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 Blank7G (Affymetrix).

data_processing:
The data were analyzed with Affymetrix Expression console and Genomatix ChipInspector using Affymetrix default analysis settings and global scaling as normalization method.
MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1,5 μg total RNA method according to the manufacturer’s protocols (Affymetrix, GeneChip WT terminal labelling kit 900671). Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: PUER cells were cultivated in IMDM supplemented with penicillin/streptomycin (10,000 U/ml), glutamin (200 mM),  ß-ME (50  M), mouse IL-3 (5 ng/ml, Biosource, Camarillo, CA, USA), puromycin (1  g/ml), and 10% FCS.

extract_protocol: Total RNA from the PUER cells was extracted according to the manufacter's instructions using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)

treatment_protocol: To activate the PU.1-ER fusion protein, PUER cells were centrifuged and resuspended in medium containing 100nM tamoxifen [4-hydroxytamoxifen (OHT)]

tag: PU.1 -/- deficient myeloid progenitors with PU-ER fusion protein


title: Mouse PUER exon 24h-1

source_name: PUER cells 24h after induction of PU.1 expression with 100nM OHT


title: P7B Progranulin-cerebellum

source_name: P7B Progranulin-cerebellum


title: N14B Normal-cerebellum

source_name: N14B Normal-cerebellum


title: P5A Progranulin-frontal

source_name: P5A Progranulin-frontal


title: Mouse PUER exon 24h-3


title: Mouse PUER exon 0h-3

description: Gene expression data from PU-ER cells without expression of PU.1.

source_name: PU-ER cells without expression of PU.1


title: P7C Progranulin-hippocampus

source_name: P7C Progranulin-hippocampus


title: P2A Progranulin-frontal

source_name: P2A Progranulin-frontal


title: N12A Normal-frontal

source_name: N12A Normal-frontal


title: P1C Progranulin-hippocampus

source_name: P1C Progranulin-hippocampus


title: P3A Progranulin-frontal

source_name: P3A Progranulin-frontal


title: N13B Normal-cerebellum

source_name: N13B Normal-cerebellum


title: P1A Progranulin-frontal

source_name: P1A Progranulin-frontal


title: P4A Progranulin-frontal

source_name: P4A Progranulin-frontal


title: N11B Normal-cerebellum

source_name: N11B Normal-cerebellum


title: Mouse PUER exon 0h-2


title: Female E9.5-2d

description:
small RNA <200nt
5 spots excluded from data extraction: probe no; 320;774;922;1256;1370
Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC).  Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction.  E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos.  E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction.
PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138).  Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes.  Digested tissue samples cooled to room temperature.  1ul of digested sample added to each PCR (see paper ref. for reaction mix).  RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction.  PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium).  Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller).  Male positive samples give only 18S control band (no W chromosome in males).