title: B6 naive vs. B6 3%DSS d4

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5.1, Agilent) using standard protocol according the supplier's recommendations.

hyb_protocol: After precipitation, purification and quantification, 1.25 µg of each labeled cRNA was fragmented and hybridized to whole mouse genome 44k microarrays according to the supplier’s protocol (Agilent Technologies). Microarrays were washed with a SSC protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 6.1 (Rosetta Biosoftware). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: B6 naive

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: C57Bl/6 mice (WT) were purchased from Charles River Laboratories (Berlin, Germany).

extract_protocol: Samples of proximal colon were cut longitudinally, washed in PBS, shortly incubated in 4M Guanidinium-isothiocyanat and transferred to TRIzol (Invitrogen). Total RNA was isolated according to manufacturer´s instructions using Glycogen as carrier. RNA samples of three mice per group and time point were pooled for the analysis.

treatment_protocol: Mice at age (9-11 weeks) and sex matched (female) were untreated. The control animals were given water only.

tag: tissue

value: proximal colon

value: female

value: WT

tag: treatment

tag: time

value: 4 days

source_name: B6 3%DSS d4

treatment_protocol: Mice at age (9-11 weeks) and sex matched (female) and 3% (w/v) DSS (mol weight range 35.000-50.000 kDa, Biochemicals) was administered via the drinking water ad libidum for 5 days, followed by drinking water until the end of the experiment.

value: DSS


title: trichocyst_discharge_T40, biological rep3

status: Public on Jul 07 2010

type: RNA

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

description: Time point 40 minutes after trichocyst discharge.

hyb_protocol: Hybridization by NimbleGen company.

scan_protocol: Scanning by NimbleGen company.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447192.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

label: biotin

molecule: total RNA

organism: Paramecium tetraurelia

label_protocol: SuperScript Invitrogen (double strand labeling)

extract_protocol: Trizol

treatment_protocol: A pellet of living paramecia (routinely 0.5 ml) is transferred drop by drop in a small beaker containing 5 ml of aminoethyl dextran 0.05%  in TrisHCl 10mM pH 7.2, CaCl2 1mM under mild rotary agitation, diluted to 100 ml of the same buffer without aminoethyl dextran and centrifuged 1 min. 1000g. The pellet is essentially composed of living paramecia having discharged all of their trichocysts (secretory granules) that are transferred to fresh culture medium. Aliquots are taken and pelleted at desired times after the treatment for total RNA extraction.

tag: strain

value: 7s d4-2 self VB mt7-2A

value: Wild type

tag: caryonide

value: polycaryonide

tag: medium

value: Klebsiella pneumoniae BHB

value: stationary phase


title: trichocyst_discharge_T210, biological rep4

description: Time point 210 minutes after trichocyst discharge.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447196.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: B6 3%DSS d4 vs. B6 naive

country: Germany

organism: Mus musculus

tag: gender

tag: genotype


title: trichocyst_discharge_T0, biological rep3

description: Time point before trichocyst discharge.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447191.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

source_name: Time point before trichocyst discharge


title: LMP7 3%DSS d4 vs. LMP7 naive

source_name: LMP7 3%DSS d4

growth_protocol: Breeding pairs of lmp7-/- mice, originally described by Fehling et. al. (Fehling et al., 1994), were bred in the animal facilities of the Max-Planck-Institute for Infection Biology (Berlin, Germany).

treatment_protocol: Age (9-11 weeks) and sex matched (female) lmp7-/- mice were used. 3% (w/v) DSS (mol weight range 35.000-50.000 kDa, Biochemicals) was administered via the drinking water ad libidum for 5 days, followed by drinking water until the end of the experiment.

source_name: LMP7 naive


title: starved cells, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 1870 cells/mL; 35% vegetative cells; 39% meiotic cells; 18% cells with skeins; 7% cells with fragmented old macronucleus and no visible anlagen; 2% post autogamous cells

hyb_protocol: Hybridization by NimbleGen company

scan_protocol: Scanning by NimbleGen company

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450350.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450350_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Starved cells

growth_protocol: Strain 51 is an entirely homozygous Paramecium tetraurelia strain. Its mating type was checked to be E (=mt8) before autogamy. Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae bacteria, and supplemented with 0.8 µg/L of beta-sitosterol (Merck, Darmstadt, FRG). Cells were maintained at 27°C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

treatment_protocol: At each time-point, 200 to 400 mL of Paramecium cells were centrifuged at 170 to 200 xg for 1 min and total RNA was extracted from unwashed cell pellets.

value: 51 new mt8

value: stock 37c09

value: monocaryonide

value: Klebsiella pneumoniae WGP

value: autogamy competent


title: HD766-Tu-Primary_Colorectal_Cancer_Patient_No.17

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

hyb_protocol: According to the Illumina® Protocol for Human Sentrix-6 Beat-Chips

data_processing: Data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. All data was then used for the mean expression value calculation within one array. Next, outliers were removed when their expression value dropped below a threshold of median + 3*MAD expression of all negative control beads. Individual bead types were also flagged as filtered when their bead replicate count dropped below 17. Finally, we discarded a bead type when the bead type’s filter flag was set across all samples. 18.184 features passed quality controls and further data analysis was done by variance stabilization and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

organism: Homo sapiens

source_name: Primary Colorectal Cancer

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: Extraction of high molecular weight DNA and RNA from frozen CRC and liver metastases samples was carried out by ultracentrifugation in cesium chloride as previously described in van den Boom et al., 2003 Am J Pathol.


title: trichocyst_discharge_T40, biological rep4

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447195.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

source_name: Time point 40 minutes after trichocyst discharge


title: HD779-LM-Liver_Metastasis_Patient_No.18

scan_protocol: According to the Illumina® Protocol for Human Sentrix-6 Beat-Chips

source_name: Liver metastasis of Colorectal Cancer

tag: Liver Metastasis of a Colorectal Cancer from Sigma;pT2;pN1;(1/13);G2;null;L1


title: patient 5, reperfusion

city: Erlangen

first: Stefan

last: Schnürer

address: Schuhstr. 37

department: Plastic and Handsurgery

institute: University of Erlangen-Nuremberg

description: Gene expression data from muscle tissue during reperfusion.

hyb_protocol: Following fragmentation, human HG U133 A2.0 oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C.

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

data_processing: The data were analyzed with GeneChip Operating Software 1.4 (GCOS 1.4, Affymetrix). Standard Affymetrix internal control genes were used to check the quality of the assay quality by comparing the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios smaller 3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.

source_name: gracilis muscle

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

growth_protocol: Muscle tissue was shock frozen in liqid nitrogen and stored in an -80°Celsius freezer.

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

tag: age

value: male

tag: race

value: caucasian

tag: time of sample harvesting

value: reperfusion


title: trichocyst_discharge_T210, biological rep2

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447190.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

source_name: Time point 210 minutes after trichocyst discharge


title: trichocyst_discharge_T0, biological rep2

description: Time point before trichocyst discharge.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447188.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: patient 5, ischemia

description: Gene expression data from muscle tissue during ischemia.

value: ischemia


title: trichocyst_discharge_T210, biological rep3

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447193.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: HD766-LM-Liver_Metastasis_Patient_No.17

tag: Liver Metastasis of a Colorectal Cancer from Sigma;pT3;pN1;(1/15);G2;null;null


title: Nova2 KO cortex 2

city: New York

first: Masato

last: Yano

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

country: USA

institute: The Rockefeller University

hyb_protocol: Affymetrix WT Sense Target Labeling Assay

scan_protocol: Affymetrix GeneChip Operating Software (GCOS) v1.4; GeneChip Scanner 3000 7G.

data_processing:
The average probe values used by ASPIRE version 3 (RMA signal estimates from Expression Console 1.1). All exon (PSR) and junction (JUC) probe values were analysed by the second and third step of ASPIRE version 3 (see supplemental methods, Licatalosi et al., Nature 456, 464-469, 2008). The median value of background probes with the same GC content was subtracted from each probe value. Probe values with high variability and weak signal were removed from analysis before calculating the median value of all probes within a probeset.
probe group file: mjay.r1.pgf

source_name: mouse Nova2 knockout cortex

extract_protocol: Trizol Extraction

tag: genotype/variation

value: Nova2 knockout

tag: developmental stage


title: patient 5, normoxia

description: Gene expression data from muscle tissue during normoxia.

value: normoxia


title: patient 4, reperfusion


title: LMP7 naive vs. LMP7 3%DSS d4

value: proximal colon

value: female

value: 4 days

value: DSS


title: HD687-Tu-Primary_Colorectal_Cancer_Patient_No.15


title: patient 4, normoxia


title: HD713-Tu-Primary_Colorectal_Cancer_Patient_No.16


title: HD713-LM-Liver_Metastasis_Patient_No.16

tag: Liver Metastasis of a Colorectal Cancer from Colon ascendens;pT4;pN2;(5/5);G3;null;L1


title: HD687-LM-Liver_Metastasis_Patient_No.15

tag: Liver Metastasis of a Colorectal Cancer from Rekto-Sigmoid;pT3;pN2;(6/16);G2;V1;L1


title: patient 4, ischemia


title: trichocyst_discharge_T40, biological rep2

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447189.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

value: 7s d4-2 self VB mt7-2A

value: Wild type

value: polycaryonide

value: Klebsiella pneumoniae BHB


title: patient 3, reperfusion


title: HD668-Tu-Primary_Colorectal_Cancer_Patient_No.14


title: Nova2 KO cortex 3

label_protocol: Affymetrix WT Sense Target Labeling Assay


title: autogamy_T0, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 22% vegetative cells; 21% meiotic cells; 12% cells with skeins; 43% cells with fragmented old macronucleus and no visible anlagen; 2% cells with two anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450357.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450357_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T0 (first point in autogamy time course)

value: 51 new mt8

value: stock 37c09

value: monocaryonide


title: C1S/84 - repeat 4 - rev. label - mAdbID:107314

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

description: mAdb experiment ID: 107314

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.

organism: Nakaseomyces glabratus

source_name: WT 84 Control - cy5

label_protocol:
Cy5 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log phase culture of C. glabrata grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

value: log-phase culture

value: Wild Type

source_name: Complemented strain C1S- cy3

label_protocol:
Cy3 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).

value: CgPDR1 complemented


title: trichocyst_discharge_T40, biological rep1

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447186.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

value: stationary phase


title: Nova2 KO cortex 1

value: Nova2 knockout


title: Wild type cortex 3

source_name: mouse wild type cortex

value: wild type


title: Wild type cortex 1


title: trichocyst_discharge_T210, biological rep1

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447187.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: vegetative cells, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 750 cells/mL; 99% vegetative cells, 1% cells with fragmented old macronucleus and no visible anlagen

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450349.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450349_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Vegetative cell before autogamy

value: Klebsiella pneumoniae WGP

value: log-phase growth


title: trichocyst_discharge_T0, biological rep1

description: Time point before trichocyst discharge.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447185.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: C16R/84 - repeat 4 - rev. label - mAdbID:105756

description: mAdb experiment ID: 105756

source_name: Complemented strain C16R- cy3


title: patient 2, reperfusion

source_name: latissimus dorsi muscle

value: female

value: caucasian

value: reperfusion


title: patient 3, normoxia

value: normoxia


title: patient 3, ischemia

value: ischemia


title: C16R/84 - repeat 3 - mAdbID:105754

description: mAdb experiment ID: 105754

source_name: WT 84 Control - cy3

source_name: Complemented strain C16R- cy5


title: HD590-Tu-Primary_Colorectal_Cancer_Patient_No.13


title: Wild type cortex 2


title: HD668-LM-Liver_Metastasis_Patient_No.14

tag: Liver Metastasis of a Colorectal Cancer from Rekto-Sigmoid;pT4;pN2;(22/22);G3;V1;L1


title: HD590-LM-Liver_Metastasis_Patient_No.13

tag: Liver Metastasis of a Colorectal Cancer from Colon ascendens;pT3;pN2;(5/10);G2;V1;null


title: C16R/84 - repeat 2 - mAdbID:105752

description: mAdb experiment ID: 105752


title: patient 2, ischemia


title: HD569-Tu-Primary_Colorectal_Cancer_Patient_No.12


title: HD569-LM-Liver_Metastasis_Patient_No.12

tag: Liver Metastasis of a Colorectal Cancer from Flexura coli dextra;pT3;pN1;(2/17);G2;null;null


title: C16R/84 - repeat 1 - mAdbID:105750

description: mAdb experiment ID: 105750

tag: strain


title: LMP7 naive vs. LMP7 3%DSS d8

data_processing: The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 6.1 (Rosetta Biosoftware). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: LMP7 naive

tag: tissue

value: proximal colon

tag: treatment

tag: time

value: 8 days

source_name: LMP7 3%DSS d8

value: DSS


title: HD555-Tu-Primary_Colorectal_Cancer_Patient_No.11

source_name: Primary Colorectal Cancer


title: C1S/84 - repeat 3 - mAdbID:105746

description: mAdb experiment ID: 105746

source_name: Complemented strain C1S- cy5


title: patient 1, reperfusion

tag: gender


title: B6 3%DSS d8 vs. B6 naive

source_name: B6 3%DSS d8

tag: genotype

value: WT

source_name: B6 naive


title: LMP7 3%DSS d8 vs. LMP7 naive


title: KM4_224

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

hyb_protocol: Agilent manufactured Fathead minnow microarrays based on the EcoArray platform (15K probes) were hybridized with 1 µg Cy5-labelled hypothalamic RNA and 1 µg Cy3-labelled pooled reference RNA, used as a common reference on all arrays.  Arrays were incubated overnight at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned on a Agilent Technologies Scanner G2505B US22502706

data_processing: The data were normalized by lowess curve (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002; 30:

organism: Pimephales promelas

source_name: Total RNA from FHM hypothalamus labeled with Cyanine-5 (red)

label_protocol: Individual total RNA samples each tank (pool of 4 hypothalami) or pooled reference were labelled with Cyanine 5-CTP or Cyanine 3-CTP, respectively (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc.)

extract_protocol: Total RNA was extracted from the hypothalamus using the Qiagen RNeasy mini kit (Qiagen, Mississauga, ON) following the manufacturer’s directions including on-column Dnase treatment, and quantified using the NanoDrop ND-1000.  Quality was accessed using the Agilent Bioanalyzer 2100 and RIN numbers were greater than 8.2.

value: hypothalamus

value: Female

tag: exposure

tag: time post treatment

value: 5 days

tag: method of termination

value: Spinal transection

tag: microarray id

tag: hyb date

source_name: pooled reference from 96 samples, males and females, pimephales promelas, hypothalamus and telencephalon

tag: reference

value: Total RNA from 96 samples, males and females, pimephales promelas, hypothalamus and telencephalon


title: KM4_221


title: TM5_223


title: C1S/84 - repeat 2 - mAdbID:105744

description: mAdb experiment ID: 105744

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild Type

value: CgPDR1 complemented


title: HD529-LM-Liver_Metastasis_Patient_No.9

source_name: Liver metastasis of Colorectal Cancer

tag: Liver Metastasis of a Colorectal Cancer from Colon ascendens;pT3;pN2;(5/10);G3;null;null


title: patient 1, normoxia

tag: age

value: female

tag: race

tag: time of sample harvesting


title: IR29 Root Salt, biological rep 1

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

description: Gene expression data from rice root

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

organism: Oryza sativa

source_name: IR29 Root Salt 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: hydroponics

extract_protocol: Trizol extraction of total RNA

treatment_protocol: salt root

tag: stress

value: salt

tag: tissue

value: root tip


title: C1S/84 - repeat 1 - mAdbID:105742

description: mAdb experiment ID: 105742

tag: strain


title: HD529-Tu-Primary_Colorectal_Cancer_Patient_No.9

data_processing: Data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. All data was then used for the mean expression value calculation within one array. Next, outliers were removed when their expression value dropped below a threshold of median + 3*MAD expression of all negative control beads. Individual bead types were also flagged as filtered when their bead replicate count dropped below 17. Finally, we discarded a bead type when the bead type’s filter flag was set across all samples. 18.184 features passed quality controls and further data analysis was done by variance stabilization and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.


title: HD536-Tu-Primary_Colorectal_Cancer_Patient_No.10


title: HD555-LM-Liver_Metastasis_Patient_No.11

tag: Liver Metastasis of a Colorectal Cancer from Colon descendens;ypT4;ypN0;0/10);;null;null


title: IR29 Root Salt, biological rep 2

description: Gene expression data from rice root

source_name: IR29 Root Salt 2

tag: genotype


title: IR29 Root Salt, biological rep 3

description: Gene expression data from rice root

source_name: IR29 Root Salt 3


title: patient 2, normoxia

tag: gender

value: caucasian

value: normoxia


title: TM6_213

tag: exposure

tag: time post treatment


title: B6 naive vs. B6 3%DSS d8

value: proximal colon

tag: treatment

tag: time


title: TM6_222

tag: method of termination

tag: microarray id

tag: hyb date

tag: reference


title: HD524-LM-Liver_Metastasis_Patient_No.8

tag: Liver Metastasis of a Colorectal Cancer from Flexura coli sinistra;pT3;pN1;(2/10);G3;null;L1


title: CNHF_214

description: CNHF

value: Control(un-exposed)


title: HD524-Tu-Primary_Colorectal_Cancer_Patient_No.8


title: IR29 Root Control, biological rep 2

description: Gene expression data from rice root

source_name: IR29 Root Control 2

treatment_protocol: control root

value: control


title: TM5_212


title: IR29 Root Control, biological rep1

description: Gene expression data from rice root

source_name: IR29 Root Control 1


title: FL478 Root Salt, biological rep 3

description: Gene expression data from rice root

source_name: FL478 Root Salt 3


title: HD522-Tu-Primary_Colorectal_Cancer_Patient_No.7


title: HD522-LM-Liver_Metastasis_Patient_No.7

tag: Liver Metastasis of a Colorectal Cancer from Flexura coli sinistra;pT3;pN0;(0/16);G3;V1;null


title: CNHF_211

description: CNHF


title: HD517-NC-Normal_Colon_Control_No.7

source_name: Normal Colon Epithelium

tag: normal colonic epithelium


title: HD510-NC-Normal_Colon_Control_No.6


title: patient 1, ischemia

source_name: latissimus dorsi muscle

tag: age

tag: race

tag: time of sample harvesting

value: ischemia


title: TM5_122

tag: tissue

value: hypothalamus


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 8h #2

city: Stony Brook

first: Hana

middle: S.

last: Fukuto

address: CMM rm350, Stony Brook University

department: Microbiology and Molecular Genetics/Center for Infectious Diseases

institute: Stony Brook University

description: Yersinia pestis KIM5 in DMEM vs. J774A.1, 8h

hyb_protocol: cDNA with 250 pmol Cy3 and cDNA with 150 pmol Cy5 was included in 55 µl total hybridization solution (25% v/v formamide, 5x SSC, 0.1% SDS, and 100 µg/ml of sonicated salmon sperm DNA). Hybridizations were performed under 25 x 60 mm lifter cover slips (Erie Scientific) at 50 ˚C in a humidified chamber for 16–20 h. Hybridized arrays were washed by gently shaking as follows: twice briefly with 2x SSC/0.1% SDS (50 ˚C), twice for 10 min with 2x SSC/0.1% SDS (50 ˚C), twice briefly with 0.1x SSC/0.1% SDS (50 ˚C), twice for 10 min with 0.1x SSC/0.1% SDS and four times briefly with 0.1x SSC at room temperature. Arrays were dried by placing them into a 50 ml blue cap Falcon tube containing tissue paper in the bottom, and centrifuged at 2500 x g for 2 min at room temperature.

scan_protocol: Arrays were scanned using an Axon 4000B scanner, controlled by GenePix Pro 6 software with a pixel size of 10 µm and two-pass sequential line averaging. Laser power was set to 100%, and PMT gains were subjectively adjusted during prescan to maximize effective dynamic range and to limit image saturation. Lossless image files were stored for later analysis.

data_processing: The microarray data were analyzed using the Limma module of the Bioconductor package for the R statistical environment. The “normexp” method was used for background correction, followed by print tip loess normalization and between-array normalization of intensities. The microarray data for each gene were fitted to a linear model, and statistics were generated using the lmFit and eBayes functions.

organism: Yersinia pestis

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #12

label_protocol: Fluorescent cDNA probes were prepared by an indirect aminoallyl labeling method according to protocols from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) with following changes: 2-5 µg of total RNA was used for cDNA synthesis, and the reaction contained 300 µM aminoallyl-dUTP and 200 µM dTTP. RNA was degraded after the cDNA synthesis using 0.8 µg of RNaseA (Boehringer Mannheim) and 1 U of RNaseH (Invitrogen) instead of NaOH.

growth_protocol: 25 mL of DMEM was inoculated with 1 x 10^8 bacteria that have been grown overnight at 28°C in HI broth supplemented with ampicillin and placed in 10 cm tissue culture plate.  The bacteria were grown for 4 hours (to logarithmic phase) in DMEM under the same conditions without macrophages or gentamicin.  After 4 hours of incubation, bacteria were collected by centrifugation at 3,800 xg for ~5 minutes.

extract_protocol: Y. pestis growing in DMEM was collected by centrifugation at room temperature at 3,800 xg for ~5 minutes, and the bacterial RNA was stabilized by incubation in 0.1% SDS, 0.1% acidic phenol and 19% ethanol on ice, as previously described by Eriksson et al (Mol Microbiol. 2003 Jan;47(1):103-18).  The bacterial cells were lysed with 3-5mg/mL lysozyme (Boehringer Mannheim) in Tris-EDTA for 5 minutes at room temperature and total RNA was isolated using a Qiagen RNeasy Mini kit.  On-column digestion of genomic DNA was performed using an RNase-free DNase set (Qiagen).

tag: strain

value: Yersinia pestis KIM5

tag: location

value: in DMEM

tag: sample

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 8h sample #4

growth_protocol: J774A.1 macrophage-like cells were seeded on 10 cm tissue culture plates at 4 x 10^6/plate and grown overnight. Approximately 2x10^7 J774A.1 cells were infected at an MOI of 50 with Y. pestis KIM5 that had been grown overnight at 28°C in HI broth supplemented with ampicillin. After 20 minutes of infection, 8 micrograms/mL of gentamicin was added to inhibit extracellular growth. Gentamicin concentration was reduced to 2 micrograms/mL at 1.5 hour post infection. Toal RNA of the intracellular bacteria was islolated at 1.5, 4, or 8 hours post infection.

extract_protocol: The infected macrophages were lysed and the RNA was stabilized by incubation in 0.1% SDS, 0.1% acidic phenol and 19% ethanol on ice, as previously described by Eriksson et al (Mol Microbiol. 2003 Jan;47(1):103-18). The intracellular bacteria were collected by centrifugation at 4°C at 3,800 xg for ~20 minutes. The bacterial cells were lysed with 3-5mg/mL lysozyme (Boehringer Mannheim) in Tris-EDTA for 5 minutes at room temperature and total RNA was isolated using a Qiagen RNeasy Mini kit. On-column digestion of genomic DNA was performed using an RNase-free DNase set (Qiagen).

value: inside J774A.1

value: gentamicin


title: HD536-LM-Liver_Metastasis_Patient_No.10

tag: Liver Metastasis of a Colorectal Cancer from Colon ascendens;pT3;pN2;(4/25);G3;null;null


title: HD495-NC-Normal_Colon_Control_No.3


title: CNHF_121

description: CNHF

tag: gender

value: Female

tag: exposure

tag: time post treatment

value: 5 days

value: Spinal transection

value: Total RNA from 96 samples, males and females, pimephales promelas, hypothalamus and telencephalon


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 4h #1

description: Yersinia pestis KIM5 in J774A.1 vs. DMEM, 4h

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #6

tag: time

source_name: Yersinia pestis KIM5 strain in J774A.1 cells, 4h sample #2

tag: treatment


title: TM6_113

tag: method of termination

tag: microarray id

tag: hyb date

tag: reference


title: TM6_114


title: TM5_112


title: HD499-NC-Normal_Colon_Control_No.4

tag: normal colonic epithelium


title: CNHF_124

description: CNHF


title: HD491-NC-Normal_Colon_Control_No.2


title: FL478 Root Salt, biological rep 2

description: Gene expression data from rice root

source_name: FL478 Root Salt 2

tag: genotype

tag: stress

value: salt


title: KM4_111

tag: tissue


title: HD508-NC-Normal_Colon_Control_No.5


title: FL478 Root Control, biological rep1

description: Gene expression data from rice root

source_name: FL478 Root Control 1

value: root tip


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 8h #1

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #10

tag: strain

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 8h sample #2


title: FL478 Root Control, biological rep 3

description: Gene expression data from rice root

source_name: FL478 Root Control 3


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 8h #2

description: Yersinia pestis KIM5 in J774A.1 vs. DMEM, 8h

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 8h sample #3

tag: location

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #11


title: HD485-NC-Normal_Colon_Control_No.1


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 4h #2

description: Yersinia pestis KIM5 in DMEM vs. J774A.1, 4h

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #8

tag: sample

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 4h sample #4


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 8h #1

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 8h sample #1

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #9


title: HD482-LM-Liver_Metastasis_Patient_No.6

source_name: Liver metastasis of Colorectal Cancer

tag: Liver Metastasis of a Colorectal Cancer from Rektum;pT3;pN0;(0/18);G2;V0;null


title: HD482-Tu-Primary_Colorectal_Cancer_Patient_No.6

source_name: Primary Colorectal Cancer


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 4h #1

description: Yersinia pestis KIM5 in DMEM vs inside J774A.1, 4h

hyb_protocol: cDNA with 250 pmol Cy3 and cDNA with 150 pmol Cy5 was included in 55 µl total hybridization solution (25% v/v formamide, 5x SSC, 0.1% SDS, and 100 µg/ml of sonicated salmon sperm DNA). Hybridizations were performed under 25 x 60 mm lifter cover slips (Erie Scientific) at 50 ˚C in a humidified chamber for 16–20 h. Hybridized arrays were washed by gently shaking as follows: twice briefly with 2x SSC/0.1% SDS (50 ˚C), twice for 10 min with 2 SSC/0.1% SDS (50 ˚C), twice briefly with 0.1x SSC/0.1% SDS (50 ˚C), twice for 10 min with 0.1x SSC/0.1% SDS and four times briefly with 0.1x SSC at room temperature. Arrays were dried by placing them into a 50 ml blue cap Falcon tube containing tissue paper in the bottom, and centrifuged at 2500 x g for 2 min at room temperature.

source_name: Yersinia pestis KIM5 strain in J774A.1 cells, 4h sample #1

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #5


title: HD469-Tu-Primary_Colorectal_Cancer_Patient_No.5


title: HD346-Tu-Primary_Colorectal_Cancer_Patient_No.4


title: CVMMS126R_8WG16_N2_L4_2B extraction3_array4

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Ab:8WG16:JL:CVMMS126R;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing:
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180

label: Cy3 dye

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Worm_L4_growth_and_harvest_vSE1.doc. Worms were grown in standard S-basal media liquid culture. The culture was synchronized by starving hatched embryos at L1 stage and grown at 20C in liquid culture until they reach L4 stage. Worms were collected over 34 uM Nitex membrane, and washed with M9 Buffer + protease inhibitors (Calbiochem). Worms were resuspended in 1 pellet volume of M9, frozen as ?popcorn? in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_germlineless_adult_soma_extract_v2.2. Frozen worms were ground to a powder using mortar and pestle. Worm powder was diluted in M9 + 1% formaldehyde+1mM PMSF and fixed 5 or 10 minutes. Fixing was quenched by the addition of 125 mM glycine for 5 minutes. Cells were collected by centrifuging 5 minutes at 4000 g at 4C. Samples were washed and resuspended in FA Buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and 10 mgs were used per ChIP.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

tag: developmental stage

value: L4 Larva

value: wild type

tag: sex

value: mixed Male and Hermaphrodite population

label: Cy5 dye


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 4h #2

source_name: Yersinia pestis KIM5 strain in J774A.1 cells, 4h sample #3

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #7


title: HD469-LM-Liver_Metastasis_Patient_No.5

tag: Liver Metastasis of a Colorectal Cancer from Sigma;pT4;pN1;(3/26);G2;null;L1


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 1.5h #2

description: Yersinia pestis KIM5 in DMEM vs inside J774A.1, 1.5h

data_processing: The microarray data were analyzed using the Limma module of the Bioconductor package for the R statistical environment. The “normexp” method was used for background correction, followed by print tip loess normalization and between-array normalization of intensities.  The microarray data for each gene were fitted to a linear model, and statistics were generated using the lmFit and eBayes functions.

source_name: Yersinia pestis KIM5 strain in DMEM, 4h, sample #4

tag: time

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 1.5h sample #4

growth_protocol: J774A.1 macrophage-like cells were seeded on 10 cm tissue culture plates at 4 x 10^6/plate and grown overnight.  Approximately 2x10^7 J774A.1 cells were infected at an MOI of 50 with Y. pestis KIM5 that had been grown overnight at 28°C in HI broth supplemented with ampicillin.  After 20 minutes of infection, 8 micrograms/mL of gentamicin was added to inhibit extracellular growth.  Gentamicin concentration was reduced to 2 micrograms/mL at 1.5 hour post infection.  Toal RNA of the intracellular bacteria was islolated at 1.5, 4, or 8 hours post infection.

extract_protocol: The infected macrophages were lysed and the RNA was stabilized by incubation in 0.1% SDS, 0.1% acidic phenol and 19% ethanol on ice, as previously described by Eriksson et al (Mol Microbiol. 2003 Jan;47(1):103-18).  The intracellular bacteria were collected by centrifugation at 4°C at 3,800 xg for ~20 minutes.  The bacterial cells were lysed with 3-5mg/mL lysozyme (Boehringer Mannheim) in Tris-EDTA for 5 minutes at room temperature and total RNA was isolated using a Qiagen RNeasy Mini kit.  On-column digestion of genomic DNA was performed using an RNase-free DNase set (Qiagen).


title: CVMMS126R_8WG16_N2_L4_2A extraction2_array4

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: Ab:8WG16:JL:CVMMS126R;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: HD346-LM-Liver_Metastasis_Patient_No.4

tag: Liver Metastasis of a Colorectal Cancer from Rekto-Sigmoid;pT4;pN2;(9/16);G2;null;null


title: HD301-Tu-Primary_Colorectal_Cancer_Patient_No.2


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 1.5h #2

source_name: Yersinia pestis KIM5 strain inside J774A.1 cells, 1.5h sample #3

tag: treatment

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #3


title: HD301-LM-Liver_Metastasis_Patient_No.2

tag: Liver Metastasis of a Colorectal Cancer from Rekto-Sigmoid;pT3;pN0;(0/10);G2;null;null


title: HD324-Tu-Primary_Colorectal_Cancer_Patient_No.3


title: Yersinia pestis KIM5- in DMEM vs inside J774A.1, 1.5h #1

description: Yersinia pestis KIM5 in J774A.1 vs in DMEM, 1.5h

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #2

label_protocol: Fluorescent cDNA probes were prepared by an indirect aminoallyl labeling method according to protocols from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) with following changes: 2-5 microgrmas of total RNA was used for cDNA synthesis, and the reaction contained 300 µM aminoallyl-dUTP and 200 µM dTTP. RNA was degraded after the cDNA synthesis using 0.8 micrgrams of RNaseA (Boehringer Mannheim) and 1 U of RNaseH (Invitrogen) instead of NaOH.

source_name: Yersinia pestis KIM5 strain in DJ774A.1 cells, 1.5h sample #2


title: Yersinia pestis KIM5- inside J774A.1 vs in DMEM, 1.5h #1

description: Yersinia pestis KIM5 in J774A.1 vs in DMEM, 1.5h.

source_name: Yersinia pestis KIM5 strain in J774A.1 cells, 1.5h sample #1

growth_protocol: J774A.1 macrophage-like cells were seeded on 10 cm tissue culture plates at 4 x 10^6/plate and grown overnight.  Approximately 2x10^7 J774A.1 cells were infected at an MOI of 50 with Y. pestis KIM5 that had been grown overnight at 28°C in HI broth supplemented with ampicillin.  After 20 minutes of infection, 8 micrograms/mL of gentamicin was added to inhibit extracellular growth.  Gentamicin concentration was reduced to 2 microgram/mL at 1.5 hour post infection.  Toal RNA of the intracellular bacteria was islolated at 1.5, 4, or 8 hours post infection.

source_name: Yersinia pestis KIM5 strain in DMEM, 4h sample #1


title: HD293-Tu-Primary_Colorectal_Cancer_Patient_No.1


title: HD324-LM-Liver_Metastasis_Patient_No.3

tag: Liver Metastasis of a Colorectal Cancer from Coecum;pT4;pN2;(10/15);G2;null;null


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, REH cell line (Sty)

city: Lund

first: Henrik

last: Lilljebjörn

address: Lund University Hospital

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Hybridized to 250K_Sty

hyb_protocol: The protocol provided by the manufacturer (Affymetrix) was used

scan_protocol: The chips were washed and stained according to the manufacturer's instructions and scanned using a GeneChip Scanner 3000

data_processing:
CEL files containing raw signal intensities were exported from the GeneChip Operating Software. The CEL files were imported into GeneChip Genotyping Analysis Software to produce genotype calls using the BRLMM algorithm (CHP-files).
Signal: Summarized signal; Call = Genotype Call (SNP call): AA, AB, BB, and NoCall

label: Biotin

growth_protocol: The cell line was grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from leukemic blasts obtained from bone marrow at diagnosis using standard methods. Genomic DNA from the REH cell line was extracted from cultured cells using standard methods. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: cell type

value: Acute lymphoblastic leukemia

tag: cell line

value: REH


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 23 (Sty)

description: Hybridized to 250K_Sty

label_protocol: The protocol provided by the manufacturer (Affymetrix) was used


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 22 (Sty)

description: Hybridized to 250K_Sty


title: HD293-LM-Liver_Metastasis_Patient_No.1

tag: Liver Metastasis of a Colorectal Cancer from Flexura coli sinistra;pT4;pN1;(3/15);G3;null;null


title: FL478 Root Salt, biological rep 1

description: Gene expression data from rice root

source_name: FL478 Root Salt 1

tag: genotype

tag: stress


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 14 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 21 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 20 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 16 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 18 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 19 (Sty)

description: Hybridized to 250K_Sty


title: OD00079_HCP3_N2_MXEMB_4 extraction4_array2

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l.  Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added.  50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 °C.  Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C.  Eluates were incubated over night at 65 °C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 °C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 °C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 °C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.

tag: strain

value: Mixed Embryo


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 17 (Sty)

description: Hybridized to 250K_Sty


title: OD00079_HCP3_N2_MXEMB_3 extraction3_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 12 (Sty)

description: Hybridized to 250K_Sty


title: Cells + DOPA 72 h rep 3

city: Aberdeen

first: Frank

middle: C

last: Odds

address: Institute of Medical Sciences

department: School of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: Cells + DOPA 72 h rep 3

hyb_protocol: For each of the four time points, four independent hybridizations were done for labelled RNA from L-DOPA-grown cells versus the labelled, pooled  control samples. Samples  were pre-hybridized in 5x SSC/1% SDS/1% BSA for 45 min at 42 °C, washed five times in water, once in isopropanol and air-dried. The labelled samples were added to 20 mL of hybridization solution (50% formamide/10x SSC/0.2% SDS), boiled to denature for 3 min and carefully added to the printed part of the microarray slide and the lifter slip placed on the slide.  The slides were incubated at 42 °C overnight.  Slides were washed at room temperature in 2x SSC/1% SDS for 15 min, 1x SSC/0.2% SDS for 8 min and 0.1x SSC/0.2% SDS for 5 min.  The slides were dried by centrifugation.

scan_protocol: The slides were scanned at different wavelengths so that when the dual images were opened together, each spot lit up either as a yellow colour or in varying shades of green or red, depending on the relative level of expression of the individual gene in each spot.  Signals on the slides were located with a ScanArray 4000 Microarray Analysis System, and quantified with QuantArray AcquisitionSoftware.

data_processing: The raw data were normalized according to the Lowess algorithm, using the program GeneSpring to generate ratio data for further analysis.  For each set of quadruplicate data, the median ratio of experimental/control was calculated.  A cutoff of 2-fold or greater ratio change indicating up- or down-regulation of a gene was regarded as significant.

organism: Candida albicans

source_name: Fungal cells, no DOPA, 72 h

label_protocol: To each control RNA sample, 15mL of labelling master mix (1x RT buffer,1 mM DTT, 500 mM dATP, 500 mM dCTP, 500 mM dGTP,100 mM dTTP) was added followed by 3 mL of Cy3-dUTP (Amersham Biosciences). The triplicate samples from cells grown in L-DOPA were individually labelled with Cy5-dUTP (Amersham Biosciences) by the same method.  Following the addition of the label, 2 mL of Superscript II reverse transcriptase (Invitrogen) was added, mixed thoroughly and incubated at 42 °C for2  h. The reaction was stopped by  addition of 1.5 mL of 20 mM EDTA, followed by 1.5 mL of 500 mM NaOH and incubated for 10 min at 70 °C to degrade the RNA. This reaction was neutralized by addition of 1.5 mL of 500 mM HCl.  Following reverse transcription, the samples were mixed  and purified in a GFX purification column (Amersham Biosciences) following the manufacturer’s procedure, then concentrated in a Speed Vac to 20 mL.

growth_protocol: C. albicans strain SC5314 was grown in the dark for 72 h at 35 °C in cultures with and without addition of L-DOPA to 1 mM.  Samples were taken at 6, 24, 48 and 72 h.

extract_protocol: RNA was extracted as described by Hayes et al (Methods 2002;26:281-290).  cDNA was prepared from the RNA samples by reverse transcription. In brief, 2mg of oligo (dT)12-18 primer (500mg/mL)(Promega) was added to 50mg of RNA and made up to 10mL with RNase-free H2O, incubated for 10 min at 70 °C and snap-cooled on ice for 1 min.

treatment_protocol: The cells were flash frozen in liquid nitrogen and RNA was extracted as described by Hayes et al (Methods 2002;26:281-290)

tag: reference

value: pooled control samples

source_name: Fungal cells, plus DOPA, 72 h

tag: agent

value: 1 mM L-DOPADOPA

tag: time point


title: Cells + DOPA 48 h rep 4

description: Cells + DOPA 48 h rep 4

source_name: Fungal cells, no DOPA, 48 h

source_name: Fungal cells, plus DOPA, 48 h


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 15 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 7 (Sty)

description: Hybridized to 250K_Sty


title: Cells + DOPA 72 h rep 1

description: Cells + DOPA 72 h rep 1


title: Rom silenced replicate 2

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Epigenetically silenced for the Rhomboid protease, EhRom1. Isolated mid-log phase

hyb_protocol: Standard Affymetrix protocol using GeneChip® Hybridization Oven 640 and GeneChip® Fluidics Station 450.

scan_protocol: Standard Affymetrix protocol GeneChip® Scanner 3000 7G.

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: Trophozoites of strain G3, silenced for EhRom1

label_protocol: Affymetrix single amplification using the GeneChip IVT labeling kit.

tag: media

value: TYI

tag: growth

value: Long term axenic growth

tag: genotype/variation

value: Rom-silenced


title: Cells + DOPA 72 h rep 4

description: Cells + DOPA 72 h rep 4


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 2 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 6 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 3 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 10 (Sty)

description: Hybridized to 250K_Sty


title: OD00079_HCP3_N2_MXEMB_2 extraction2_array2

tag: developmental stage

tag: sex


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 9 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 13 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 4 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 11 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 8 (Sty)

description: Hybridized to 250K_Sty


title: Cells + DOPA 48 h rep 3

description: Cells + DOPA 48 h rep 3


title: Rom silenced replicate 1


title: ABAB5408_4H8_N2_MXEMB_2 extraction2_array2

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;antigen: Synthetic peptide YSPTSpPS;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: ab5408;reference: Abcam website and references therein;short description: This antibody recognises the C-terminal repeat of the largest subunit of RNA polymerase II.  It recognises both unphosphorylated and phosphorylated forms.;


title: ABAB5408_4H8_N2_MXEMB_1 extraction1_array2


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 1 (Sty)

description: Hybridized to 250K_Sty


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 5 (Sty)

description: Hybridized to 250K_Sty


title: Cells + DOPA 48 h rep 1

description: Cells + DOPA 48 h rep 1


title: 5 week_Lpr_B  cells

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

description:
the purity of cell >94%
pool of 6 MRL/lpr mouse B cells

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples.  Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous housekeeping snoRNA202. [delta] CT =  CT_sample - CT_reference.

label: FAM

source_name: 5 week MRL/lpr primary B cells

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

value: MRL/lpr

tag: disease state

value: lupus

tag: tissue

value: spleen

value: B cells

tag: age

value: 5 weeks


title: 16 week_Ctrl_B  cells

description:
the purity of cell >94%
pool of 6 BALB/c mouse B cells

source_name: 16 week BALB/c primary B cells

value: BALB/c

value: control

tag: cell type

value: 16 weeks


title: 16 week_Lpr_B  cells

source_name: 16 week MRL/lpr primary B cells


title: Cells + DOPA 48 h rep 2

description: Cells + DOPA 48 h rep 2


title: G3 replicate 1

description: Trophozoites after long term axenic growth. Isolated mid-log phase

source_name: Trophozoites of strain G3


title: Cells + DOPA 24 h rep 4

description: Cells + DOPA 24 h rep 4

source_name: Fungal cells, no DOPA, 24 h

source_name: Fungal cells, plus DOPA, 24 h


title: Cells + DOPA 24 h rep 1

description: Cells + DOPA 24 h rep 1


title: Cells + DOPA 6 h rep 4

description: Cells + DOPA 6 h rep 4

source_name: Fungal cells, no DOPA, 6 h

source_name: Fungal cells, plus DOPA, 6 h

value: 6 h


title: Cells + DOPA 24 h rep 2

description: Cells + DOPA 24 h rep 2


title: Cells + DOPA 24 h rep 3

description: Cells + DOPA 24 h rep 3


title: 16 week_Lpr_CD4+T cells

description:
the purity of cell >94%
pool of 6 MRL/lpr mouse CD4+T cells

source_name: 16 week MRL/lpr primary CD4+T cells

value: CD4+T cells


title: 16 week_Ctrl_CD4+T cells

description:
the purity of cell >94%
pool of 6 BALB/c mouse CD4+T cells

source_name: 16 week BALB/c primary CD4+T cells


title: Cells + DOPA 6 h rep 3

description: Cells + DOPA 6 h rep 3


title: G3 replicate 2


title: Cells + DOPA 6 h rep 2

description: Cells + DOPA 6 h rep 2


title: FL478 Root Control, biological rep 2

description: Gene expression data from rice root

source_name: FL478 Root Control 2

value: root tip


title: 5 week_Lpr_CD4+T cells

source_name: 5 week MRL/lpr primary CD4+T cells


title: Cells + DOPA 6 h rep 1

description: Cells + DOPA 6 h rep 1


title: 5 week_Ctrl_B  cells

source_name: 5 week BALB/c primary B cells


title: Resting vs. activated

city: Boston

first: john

last: Iacomini

state: MA

address: 221 Longwood Ave. LMRC 303

department: renal division

institute: brigham and womens hospital

description: Cells were activated in culture for 72 hours with 1microgram/ml anti-CD3 and CD28

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: mus musculus splenic T cells

label_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: Cells were cultured in DMEM supplemented with L-glutamine, penicillin-streptomycin, sodium pyruvate, nonessential amino acids  and 10% fetal calf serum

extract_protocol: Total RNA was extracted from unstimulated and stimulated (activated) T cells using the miRNeasy kit

treatment_protocol: Cells were activated with 2µg/mL anti-CD3 (2C11) and 1µg/mL CD28 (37.51)

tag: gender

value: Female

value: splenic resting T cell

source_name: mus musculus splenic T cells activated 72 hrs

value: female

value: splenic activated T cell


title: 5 week_Ctrl_CD4+T cells

source_name: 5 week BALB/c primary CD4+T cells


title: Cells + DOPA 72 h rep 2

description: Cells + DOPA 72 h rep 2

source_name: Fungal cells, no DOPA, 72 h

value: pooled control samples

source_name: Fungal cells, plus DOPA, 72 h

value: 1 mM L-DOPADOPA


title: Matched normal for tumor PT207SYN

status: Public on Jul 06 2010

first: Barry

middle: Stephen

last: Taylor

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

description: Hybridized to 250K_Sty

hyb_protocol: Per manufacturer's instructions

scan_protocol: After hybridization, arrays were washed with Affymetrix fluidics station and scanned with the Gene Chip Scanner 3000 7G and Affymetrix Genotyping Tools Version 2.0

data_processing:
Signal instensities were were quantified and normalized with the Affymetrix Chromosomal Copy Number Analysis Tool (CNAT 4.0, 1.5.6_v3.1) and copy number was converted to tumor-to-normal log2 ratios using the algorithm described in Taylor BS, et al PLoS ONE 2008; 3(9):e3179. Cell line signal intensities were normalized to a baseline array with median intensity and quantile normalization in GenePattern based on the dChipSNP algorithm. SNP-level inteisities were obtained for these using the model-based PM/MM method. Data from each were compared to data from 1800 normal datasets, and the 5 normal samples with noise profiles most similar to each cell line were used to determine log2 ratios at each SNP locus.
The normalized tumor/normal ratio data described above are presented in the Sample data tables of the Tumor sample (normal Samples therefore do not have data tables).  The matrix of ratio data is also available as a text file on the Series record.

label: Cy3 and Cy5

source_name: matched normal DNA

label_protocol: PCR projects, after pooling, concentration, and fragmentation with Dnase I were labeled and denatured as per manufacturer's instructions with Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5.

extract_protocol: Genomic DNA was extracted from cyromoled-macrodissected tumor samples and from blood or normal adjacent tissue and digested with the StyI restriction enzyme

value: Matched normal tissue

tag: disease status

value: normal

tag: sample id


title: Matched normal for tumor PT206SYN

description: Hybridized to 250K_Sty


title: R. palustris wild-type (CGA009) NF Replicate #2

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix Microarray Suite was used for initial data acquisition and processing.

label: Biotinylated GeneChip DNA labeling reagent

organism: Rhodopseudomonas palustris

source_name: Photosyntheic bacterium Rhodopseudomonas palustris

growth_protocol: Photosynthetically grown with acetate and without ammonium (nitrogen-fixing conditions).

extract_protocol: Rhodopseudomonas palustris cells were disrupted by treatment with by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: R. palustris wild-type (CGA009) grown under nitrogen-fixing conditions Replicate #2


title: Matched normal for tumor PT202SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT205SYN

description: Hybridized to 250K_Sty


title: R. palustris wild type (CGA009) NF Replicate #1

scan_protocol: As recommended by the manufacturer (Affymetrix)

source_name: Photosynthetic bacterium Rhodopseudomonas palustris

tag: R. palustris wild type (CGA009) grown under nitrogen-fixing conditions Replicate #1


title: Matched normal for tumor PT201SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT195SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT197SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT196SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT198SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT200SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT199SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT194SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT193SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT192SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT188SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT190SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT189SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT191SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT186SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT187SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT204SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT183SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT184SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT203SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT182PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT185SYN

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT180PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT181PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT174PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT173PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT175PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT179PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT172PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT178PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT169PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT165PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT171PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT170PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT168PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT166PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT163PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT162PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT159PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT157MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT160PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT158MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT154MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT156MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT155MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT151MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT150MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT152MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT176PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT167PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT164PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT148MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT147MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT146MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT144MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT141MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT142MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT143MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT161PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT137MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT140MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT139MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT138MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT136MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT135MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT129MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT127MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT128MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT130MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT133MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT131MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT134MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT125MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT124MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT153MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT145MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT123MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT149MRC

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT122MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT121MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT126MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT119MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT118MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT116MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT117MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT114MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT115MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT113MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT110MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT112MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT111MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT106MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT107MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT104MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT105MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT101MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT102MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT103MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT99LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT95LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT109MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT94LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT120MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT97LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT98LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT177PL

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT96LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT91LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT92LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT90LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT89LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT108MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT87LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT85LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT82LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT84LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT100MF

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT81LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT80LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT78LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT79LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT77LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT75LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT73LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT74LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT72GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT93LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT71GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT70GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT67GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT66GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT68GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT65GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT88LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT86LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT62GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT83LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT63GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT60GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT57GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT56GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT58GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT76LMS

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT53GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT55GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT54GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT52GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT50DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT51GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT43DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT44DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT45DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT48DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT47DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT64GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT49DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT40DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT38DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT42DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT41DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT61GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT37DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT39DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT36DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT59GT

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT35DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT34DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT33DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT46DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT32DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT28DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT25DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT29DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT26DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT27DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT31DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT30DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT23DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT24DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT22DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT21DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT16DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT17DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT11DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT14DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT12DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT19DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT15DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT9DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT18DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT20DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT10DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT7DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT4DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT6DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT2DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT3DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT13DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT1DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT8DD

description: Hybridized to 250K_Sty


title: Matched normal for tumor PT5DD

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT203SYN

description: Hybridized to 250K_Sty

source_name: tumor DNA

value: Soft-tissue sarcoma


title: Sarcoma tumor PT205SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT201SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT207SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT199SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT204SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT200SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT202SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT195SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT190SYN

description: Hybridized to 250K_Sty


title: Cell line LPS141

description: Hybridized to 250K_Sty

source_name: Cell line LPS141

tag: cell line


title: Cell line DDLS8817

description: Hybridized to 250K_Sty

source_name: Cell line DDLS8817


title: Sarcoma tumor PT181PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT193SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT182PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT196SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT191SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT192SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT197SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT187SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT185SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT184SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT183SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT206SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT186SYN

description: Hybridized to 250K_Sty


title: Cell line FU-DD-LS1

description: Hybridized to 250K_Sty

source_name: Cell line FU-DD-LS1


title: Sarcoma tumor PT189SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT194SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT180PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT198SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT176PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT178PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT177PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT174PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT188SYN

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT173PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT175PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT171PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT170PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT168PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT169PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT179PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT165PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT164PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT166PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT167PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT163PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT162PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT158MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT154MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT159PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT161PL

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT152MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT153MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT151MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT148MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT143MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT156MRC

description: Hybridized to 250K_Sty


title: Sarcoma tumor PT155MRC

description: Hybridized to 250K_Sty