title: Human cancer, melanoma metastasis (Met Nr 18/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 66/1)

status: Public on Oct 02 2007

type: RNA

city: cambridge

first: steve

last: shen

state: MA

address: 77 mass ave

country: USA

institute: MIT

description: human clinical tumor tissue sample

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on one U133A human chip and one test chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: raw data (CEL file) were normalized with RMA and further analyzied with GenePatter comparative marker selection module.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: melanoma clinical sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (701025, Revision 3).

extract_protocol: Rneasy mini kit

tag: Genotype

value: melanoma metastasis

tag: Age


title: Human cancer, melanoma metastasis (Met Nr 66/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 66/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 64/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (met Nr 64/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr. 99/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 15/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 67/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 67/6)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 65/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 18/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr. 101/6)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr. 99/2)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 107/5)

description: human clinical tumor tissue sample

value: primary tumor


title: Human cancer, primary melanoma (Prim Nr 107/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 68/4)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 89/6)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 106/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 79/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 103/4)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 106/2)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 102/6)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 103/2)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 102/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 103/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 104/6)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 89/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 71/5 )

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 106/1)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 89/2)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 8/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 90/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 103/1)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 90/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 20/1)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 103/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 72/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 99/6)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 74/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 72/2 )

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 78/2)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 87/3)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 15/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 90/6)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 104/5)

description: human clinical tumor tissue sample


title: Human cancer, primary melanoma (Prim Nr 89/4)

description: human clinical tumor tissue sample


title: NA19145_across_population_normalised

status: Public on Oct 01 2007

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: HapMap YRI_child Male

hyb_protocol: 1.5ug cRNA as per Gene expression on Sentrix Arrays direct hybridization system manual (Illumina Doc. #11161707, Rev. B). Arrays were hybridized for 18 hours and stained with Cy3-Streptavidin.

scan_protocol: Standard Illumina protocol, PMT 638

data_processing: background-corrected values for each single bead type (raw data) were normalized on a log scale using a quantile normalization method (Bolstad et al. Bioinformatics, 2003. 19(2): p. 185-93) across replicates of a single individual, followed by a median normalisation across all 270 individuals of the 4  populations.

source_name: lymphoblastoid cell line

label_protocol: One-quarter scale Message Amp II reactions (Ambion) were performed for each RNA extraction using 200 ng of total RNA. Biotin-16-UTP (Perkin Elmer) made up half of the UTP used in the in vitro transcription (IVT) reaction (37 Celsius for 18 hours).

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80 Celsius.

extract_protocol: RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen).

tag: HapMap YRI_child, Male


title: NA19173_across_population_normalised

description: HapMap YRI_child Male


title: NA19103_across_population_normalised

description: HapMap YRI_child Male


title: NA18914_across_population_normalised

description: HapMap YRI_child Male


title: NA19205_across_population_normalised

description: HapMap YRI_child Male


title: NA19154_across_population_normalised

description: HapMap YRI_child Male


title: NA19194_across_population_normalised

description: HapMap YRI_child Male


title: NA19208_across_population_normalised

description: HapMap YRI_child Male


title: NA19240_across_population_normalised

description: HapMap YRI_child Female

tag: HapMap YRI_child, Female


title: NA19161_across_population_normalised

description: HapMap YRI_child Male


title: NA19129_across_population_normalised

description: HapMap YRI_child Female


title: NA19142_across_population_normalised

description: HapMap YRI_child Male


title: NA19100_across_population_normalised

description: HapMap YRI_child Female


title: NA19211_across_population_normalised

description: HapMap YRI_child Male


title: NA19094_across_population_normalised

description: HapMap YRI_child Female


title: NA19120_across_population_normalised

description: HapMap YRI_child Male


title: NA19221_across_population_normalised

description: HapMap YRI_child Female


title: NA19139_across_population_normalised

description: HapMap YRI_child Male


title: NA19202_across_population_normalised

description: HapMap YRI_child Female


title: NA18863_across_population_normalised

description: HapMap YRI_child Male


title: NA18860_across_population_normalised

description: HapMap YRI_child Male


title: NA18854_across_population_normalised

description: HapMap YRI_child Male


title: NA18857_across_population_normalised

description: HapMap YRI_child Male


title: NA18521_across_population_normalised

description: HapMap YRI_child Male


title: NA18872_across_population_normalised

description: HapMap YRI_child Male


title: NA19132_across_population_normalised

description: HapMap YRI_child Female


title: NA18515_across_population_normalised

description: HapMap YRI_child Male


title: NA18506_across_population_normalised

description: HapMap YRI_child Male


title: NA18503_across_population_normalised

description: HapMap YRI_child Male


title: NA12865_across_population_normalised

description: HapMap CEU_child Female

tag: HapMap CEU_child, Female


title: NA18500_across_population_normalised

description: HapMap YRI_child Male


title: NA12864_across_population_normalised

description: HapMap CEU_child Male

tag: HapMap CEU_child, Male


title: NA12753_across_population_normalised

description: HapMap CEU_child Female


title: NA12802_across_population_normalised

description: HapMap CEU_child Female


title: NA12740_across_population_normalised

description: HapMap CEU_child Female


title: NA10860_across_population_normalised

description: HapMap CEU_child Male


title: NA12801_across_population_normalised

description: HapMap CEU_child Male


title: NA10838_across_population_normalised

description: HapMap CEU_child Male


title: NA12878_across_population_normalised

description: HapMap CEU_child Female


title: NA10857_across_population_normalised

description: HapMap CEU_child Male


title: NA10863_across_population_normalised

description: HapMap CEU_child Female


title: NA10851_across_population_normalised

description: HapMap CEU_child Male


title: NA10861_across_population_normalised

description: HapMap CEU_child Female


title: NA10835_across_population_normalised

description: HapMap CEU_child Male


title: NA10839_across_population_normalised

description: HapMap CEU_child Female


title: NA07348_across_population_normalised

description: HapMap CEU_child Female


title: NA12707_across_population_normalised

description: HapMap CEU_child Male


title: NA07019_across_population_normalised

description: HapMap CEU_child Female


title: NA10856_across_population_normalised

description: HapMap CEU_child Male


title: NA10847_across_population_normalised

description: HapMap CEU_child Female


title: NA10854_across_population_normalised

description: HapMap CEU_child Female


title: NA10855_across_population_normalised

description: HapMap CEU_child Female


title: NA10831_across_population_normalised

description: HapMap CEU_child Female


title: NA10859_across_population_normalised

description: HapMap CEU_child Female


title: NA10830_across_population_normalised

description: HapMap CEU_child Male


title: NA07029_across_population_normalised

description: HapMap CEU_child Male


title: NA10846_across_population_normalised

description: HapMap CEU_child Male


title: NA12752_across_population_normalised

description: HapMap CEU_child Male


title: NA07048_across_population_normalised

description: HapMap CEU_child Male


title: NA19239_across_population_normalised

description: HapMap YRI_parent Male

tag: HapMap YRI_parent, Male


title: NA06991_across_population_normalised

description: HapMap CEU_child Female


title: NA19223_across_population_normalised

description: HapMap YRI_parent Male


title: NA19238_across_population_normalised

description: HapMap YRI_parent Female

tag: HapMap YRI_parent, Female


title: NA19210_across_population_normalised

description: HapMap YRI_parent Male


title: NA19209_across_population_normalised

description: HapMap YRI_parent Female


title: NA19206_across_population_normalised

description: HapMap YRI_parent Female


title: NA19222_across_population_normalised

description: HapMap YRI_parent Female


title: NA19172_across_population_normalised

description: HapMap YRI_parent Female


title: NA19207_across_population_normalised

description: HapMap YRI_parent Male


title: NA19193_across_population_normalised

description: HapMap YRI_parent Female


title: NA19203_across_population_normalised

description: HapMap YRI_parent Male


title: NA19192_across_population_normalised

description: HapMap YRI_parent Male


title: NA19144_across_population_normalised

description: HapMap YRI_parent Male


title: NA19159_across_population_normalised

description: HapMap YRI_parent Female


title: NA19201_across_population_normalised

description: HapMap YRI_parent Female


title: NA19200_across_population_normalised

description: HapMap YRI_parent Male


title: NA19141_across_population_normalised

description: HapMap YRI_parent Male


title: NA19131_across_population_normalised

description: HapMap YRI_parent Female


title: NA19204_across_population_normalised

description: HapMap YRI_parent Female


title: NA19160_across_population_normalised

description: HapMap YRI_parent Male


title: NA19171_across_population_normalised

description: HapMap YRI_parent Male


title: NA19152_across_population_normalised

description: HapMap YRI_parent Female


title: NA19138_across_population_normalised

description: HapMap YRI_parent Male


title: NA19143_across_population_normalised

description: HapMap YRI_parent Female


title: NA19140_across_population_normalised

description: HapMap YRI_parent Female


title: NA19119_across_population_normalised

description: HapMap YRI_parent Male


title: NA19116_across_population_normalised

description: HapMap YRI_parent Female


title: NA19128_across_population_normalised

description: HapMap YRI_parent Male


title: NA19102_across_population_normalised

description: HapMap YRI_parent Female


title: NA19101_across_population_normalised

description: HapMap YRI_parent Male


title: NA19130_across_population_normalised

description: HapMap YRI_parent Male


title: NA19099_across_population_normalised

description: HapMap YRI_parent Female


title: NA19093_across_population_normalised

description: HapMap YRI_parent Female


title: NA18912_across_population_normalised

description: HapMap YRI_parent Female


title: NA19127_across_population_normalised

description: HapMap YRI_parent Female


title: NA18913_across_population_normalised

description: HapMap YRI_parent Male


title: NA18871_across_population_normalised

description: HapMap YRI_parent Male


title: NA18861_across_population_normalised

description: HapMap YRI_parent Female


title: NA18856_across_population_normalised

description: HapMap YRI_parent Male


title: NA19092_across_population_normalised

description: HapMap YRI_parent Male


title: NA18862_across_population_normalised

description: HapMap YRI_parent Male


title: NA18852_across_population_normalised

description: HapMap YRI_parent Female


title: NA19098_across_population_normalised

description: HapMap YRI_parent Male


title: NA18855_across_population_normalised

description: HapMap YRI_parent Female


title: NA18523_across_population_normalised

description: HapMap YRI_parent Female


title: NA18859_across_population_normalised

description: HapMap YRI_parent Male


title: NA18870_across_population_normalised

description: HapMap YRI_parent Female


title: NA18508_across_population_normalised

description: HapMap YRI_parent Female


title: NA18517_across_population_normalised

description: HapMap YRI_parent Female


title: NA18522_across_population_normalised

description: HapMap YRI_parent Male


title: NA18853_across_population_normalised

description: HapMap YRI_parent Male


title: NA18858_across_population_normalised

description: HapMap YRI_parent Female


title: NA18505_across_population_normalised

description: HapMap YRI_parent Female


title: NA18516_across_population_normalised

description: HapMap YRI_parent Male


title: NA18507_across_population_normalised

description: HapMap YRI_parent Male


title: NA18504_across_population_normalised

description: HapMap YRI_parent Male


title: NA18502_across_population_normalised

description: HapMap YRI_parent Female


title: NA19012_across_population_normalised

description: HapMap JPT Male

tag: HapMap JPT, Male


title: NA19005_across_population_normalised

description: HapMap JPT Male


title: NA18997_across_population_normalised

description: HapMap JPT Female

tag: HapMap JPT, Female


title: NA18998_across_population_normalised

description: HapMap JPT Female


title: NA19007_across_population_normalised

description: HapMap JPT Male


title: NA19000_across_population_normalised

description: HapMap JPT Male


title: NA18501_across_population_normalised

description: HapMap YRI_parent Male


title: NA19003_across_population_normalised

description: HapMap JPT Female


title: NA18994_across_population_normalised

description: HapMap JPT Male


title: NA18992_across_population_normalised

description: HapMap JPT Female


title: NA18990_across_population_normalised

description: HapMap JPT Male


title: NA18999_across_population_normalised

description: HapMap JPT Female


title: NA18995_across_population_normalised

description: HapMap JPT Male


title: NA18981_across_population_normalised

description: HapMap JPT Female


title: Wound Biorep 3 Tech Rep 2 dye swap

city: La Jolla

first: Justin

last: Walley

state: CA

address: 9500 Gilman Ave

department: Biological Sciences

institute: UCSD

hyb_protocol: One µg of labeled cRNA (cy3 and cy5 labeled sample) was diluted to 175 µl and defragmented at 60°C for 30 min following the Agilent hybridization protocols (5184-3568; Agilent). Defragmented samples were diluted to 500 µl (30% formamide final concentration) and hybridized for 20 h at 40°C.

scan_protocol: Arrays were washed and dried and scanned on an Agilent G2565BA microarray scanner [82]. The raw TIFF images were analyzed using the Agilent Feature Extraction software v 8.1 using the recommended default settings.

data_processing: The intensities of Cy3- and Cy5-labeled probes were normalized by comparing signal intensities of house keeping genes (positive controls) for both dyes and using the determined ratio as a correction factor for differences in labeling efficiencies (Agilent Feature Extraction v8.1 software)

organism: Arabidopsis thaliana

source_name: Not wound control 3

label_protocol: Five hundred ng of total RNA was used as template for cRNA production and Cyanine dyes were incorporated using the Agilent low RNA input linear amp kit (5198-3523; Agilent). Normal yields from 500 ng total RNA input using a 4 h in vitro transcription were 15 µg cRNA (15 pmol cyanine dye incorporated/µg cRNA)

extract_protocol: RNA was isolated using TRIzol reagent

tag: Ecotype

value: Col

tag: 3 week old rosette leaves

source_name: 5 min wound4


title: NA18987_across_population_normalised

description: HapMap JPT Female


title: Wound Biorep 3 Tech Rep 1 dye swap

source_name: 5 min wound3

source_name: Not wound control3


title: Wound Biorep 3 Tech Rep 1


title: NA18991_across_population_normalised

description: HapMap JPT Female


title: Wound Biorep 3 Tech Rep 2

source_name: Not wounded control 3


title: CS823L

city: Kobe

first: Anthony

middle: CF

last: Perry

state: Hyogo-ken

address: 2-2-3 Minatojima-minamimachi

department: Center for Developmental Biology

country: Japan

institute: RIKEN

hyb_protocol: Essentially as described previously (Amanai et al. 2006; PMID: 16943360).

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: Global Normalization

organism: Mus musculus

extract_protocol: RNA was recovered using the mirVana miRNA isolation kit (Ambion) and analysed essentially as described previously (Amanai et al. 2006; PMID: 16943360).


title: CS823R

label_protocol: Essentially as described previously (Amanai et al. 2006; PMID: 16943360).


title: Wound Biorep 2 Tech Rep 1 dye swap

source_name: Not wound control 2

source_name: 5 min wound2


title: Wound Biorep 1 Tech Rep 2

source_name: 5 min Wound

source_name: Not wounded control


title: Wound Biorep 2 Tech Rep 2 dye swap

source_name: Not wound control2


title: Wound Biorep 1 Tech Rep 2 dye swap

source_name: 5 min Wounded


title: NA18980_across_population_normalised

description: HapMap JPT Female


title: NA18978_across_population_normalised

description: HapMap JPT Female


title: Wound Biorep 2 Tech Rep 2

source_name: Not wounded control 2


title: NA18976_across_population_normalised

description: HapMap JPT Female


title: NA18975_across_population_normalised

description: HapMap JPT Female


title: CS686L


title: CS686R


title: NA18974_across_population_normalised

description: HapMap JPT Male


title: NA19153_across_population_normalised

description: HapMap YRI_parent Male


title: CV608


title: CS809


title: Wound Biorep 1 Tech Rep 1 dye swap

source_name: 5 min wounded


title: NA18972_across_population_normalised

description: HapMap JPT Female


title: CS785


title: NA18973_across_population_normalised

description: HapMap JPT Female


title: CS832


title: CV833


title: NA18968_across_population_normalised

description: HapMap JPT Female


title: NA18971_across_population_normalised

description: HapMap JPT Male


title: Wound Biorep 1 Tech Rep 1


title: Wound Biorep 2 Tech Rep 1


title: NA18966_across_population_normalised

description: HapMap JPT Male


title: NA18969_across_population_normalised

description: HapMap JPT Female


title: NA18961_across_population_normalised

description: HapMap JPT Male


title: NA18970_across_population_normalised

description: HapMap JPT Male


title: NA19137_across_population_normalised

description: HapMap YRI_parent Female


title: NA18965_across_population_normalised

description: HapMap JPT Male


title: NA18959_across_population_normalised

description: HapMap JPT Male


title: NA18964_across_population_normalised

description: HapMap JPT Female


title: NA18967_across_population_normalised

description: HapMap JPT Male


title: NA18956_across_population_normalised

description: HapMap JPT Female


title: NA18951_across_population_normalised

description: HapMap JPT Female


title: NA18953_across_population_normalised

description: HapMap JPT Male


title: NA18952_across_population_normalised

description: HapMap JPT Male


title: NA18948_across_population_normalised

description: HapMap JPT Male


title: NA18960_across_population_normalised

description: HapMap JPT Male


title: NA18947_across_population_normalised

description: HapMap JPT Female


title: NA18636_across_population_normalised

description: HapMap CHB Male

tag: HapMap CHB, Male


title: NA18942_across_population_normalised

description: HapMap JPT Female


title: NA18949_across_population_normalised

description: HapMap JPT Female


title: NA18944_across_population_normalised

description: HapMap JPT Male


title: NA18940_across_population_normalised

description: HapMap JPT Male


title: NA18945_across_population_normalised

description: HapMap JPT Male


title: NA18637_across_population_normalised

description: HapMap CHB Male


title: NA18623_across_population_normalised

description: HapMap CHB Male


title: Rat Retina- chip number 251186834925; 20 weeks vs 5 weeks

city: Jerusalem

first: Dror

last: Sharon

department: Ophthalmology

country: Israel

institute: Hadassah- Hebrew University Medical Center

description: To add

hyb_protocol: 750ng Cy3-labeled and 750ng Cy5-labeled samples were mixed and incubated with an Agilent microarray slide for 17 hours at 16°C following SSC buffer washing. Sample pairs were dye-swapped and processed at the same time.

scan_protocol: The washed slides were immediately dried and scanned.

data_processing: The raw data were generated using GenePix Pro5.1 software (Axon Instruments, Union City, CA).

organism: Rattus norvegicus

source_name: Retina; age: 20 weeks old

label_protocol: High-quality total RNA samples (10 ug each) were amplified and labeled with Cy5-and Cy3-CTP. The dye-incorporation ratio was determined using a Nanodrop spectrophotometer.

extract_protocol: The whole retina was dissected from each eye, placed in an eppendorf tube containing 500 ul RNAlater, and stored at -80°C. Retinal samples were pooled and total RNA was extracted using Qiagen™ RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration was measured using the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Wilmington, DE) and RNA quality was monitored using Agilent 2100 bioanalyzer.

tag: Albino Lewis rats were raised from birth under normal laboratory conditions, in a diurnal environment. age

value: 20 weeks old

source_name: Retina; age: 5 weeks old

value: 5 weeks old


title: NA18635_across_population_normalised

description: HapMap CHB Male


title: NA18943_across_population_normalised

description: HapMap JPT Male


title: NA18632_across_population_normalised

description: HapMap CHB Male


title: NA18621_across_population_normalised

description: HapMap CHB Male


title: NA18611_across_population_normalised

description: HapMap CHB Male


title: Rat Retina- chip number 251186834169; 5 weeks vs 11 weeks

description: To add

source_name: Retina; age: 11 weeks old

value: 11 weeks old


title: NA18633_across_population_normalised

description: HapMap CHB Male

source_name: lymphoblastoid cell line


title: NA18609_across_population_normalised

description: HapMap CHB Male


title: NA18624_across_population_normalised

description: HapMap CHB Male


title: NA18622_across_population_normalised

description: HapMap CHB Male


title: NA18603_across_population_normalised

description: HapMap CHB Male


title: Rat Retina- chip number 251186834168; 11 weeks vs 5 weeks

description: To add


title: NA18620_across_population_normalised

description: HapMap CHB Male


title: NA18608_across_population_normalised

description: HapMap CHB Male


title: NA18605_across_population_normalised

description: HapMap CHB Male


title: NA18594_across_population_normalised

description: HapMap CHB Female

tag: HapMap CHB, Female


title: NA18612_across_population_normalised

description: HapMap CHB Male


title: NA18582_across_population_normalised

description: HapMap CHB Female


title: NA18593_across_population_normalised

description: HapMap CHB Female


title: Sca+Lin-PBM_NA10_rep3

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

description: Retroviral vector coding for NUP98-HOXA10 (NA10) were introduced in primary bone marrow cells.

hyb_protocol: Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1

scan_protocol: Pixel Size	3 Filter	570 Scan Temperature Scan Date Scanner ID Number of Scans	2 Scanner Type	HP

data_processing: MAS 5.0

label: Biotin

source_name: Primary bone marrow

label_protocol: One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions.

growth_protocol:
Bone marrow cells were harvested from mice treated 4 days previously with 150 mg/kg 5-fluorouracil (Faulding, Underdaler, Australia) and prestimulated for 48 hours in Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (IL-3), and 100 ng/mL murine stem cell factor (mSF) (StemCell Technologies, Vancouver, BC, Canada). Cells were infected by co-cultivation with irradiated (4000 cGy x-ray) GP+E86 viral producer cells with the addition of 5 µg/mL protamine sulfate (Sigma, Oakville, ON, Canada). Loosely adherent and nonadherent cells were harvested from the co-cultures after 2 days and were cultured for 24 hours in the same medium without protamine sulfate.
The single cell suspensions collected were blocked for 10 min on ice with 5 μg/ml anti mouse CD16/CD32 (Fc Block, BD Pharmingen) in Phosphate Buffered Saline (STI) + 2% Fetal Bovine Serum (PF). Cells were washed once with PF and then incubated on ice for 20 min with the primary mAb. Cells were then washed once, incubated with the secondary antibody if needed, washed again, and then analysed by flow cytometry using a FACSCalibur™ flow cytometer and CELLQuest™ software (BD Pharmingen).  GFP+ Sca-1+Lin- cells were sorted using a FACSVantage™  (BD Pharmingen). Purity > 90% were confirmed by re-analysis of sorted cells. The forward versus side scatter profile was used to gate on viable cells and an unstained sample was used to determine appropriate gating for expression. Monoclonal antibodies (mAbs) were all purchased from PharMingen (San Diego, CA) (phycoerythrin [PE]–labeled Gr-1, B220, Ter-119, CD4, CD5 and CD8).

extract_protocol: Sorted cells were lyzed in Trizol™ (Invitrogen) and total RNA was extracted according to the manufacturer instructions.

treatment_protocol: Mice were treated with 5-fluorouracil 4 days prior to bone marrow collection.

tag: Donors of primary bone marrow cells were male mice (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) older than 12-weeks.


title: Rat Retina- chip number 251186834924; 5 weeks vs 20 weeks

description: To add


title: NA18577_across_population_normalised

description: HapMap CHB Female


title: Sca+Lin-PBM_MIG_rep3

description: Retroviral vector only coding for GFP (MIG) were introduced as negative control in primary bone marrow cells.


title: Sca+Lin-PBM_ND13N51S_rep3

description: Retroviral vector coding for NUP98-HOXD13 with a mutation (N51S) were introduced in primary bone marrow cells.


title: Sca+Lin-PBM_NA10_rep2


title: NA18576_across_population_normalised

description: HapMap CHB Female


title: NA18572_across_population_normalised

description: HapMap CHB Male


title: Sca+Lin-PBM_ND13_rep3

description: Retroviral vector coding for NUP98-HOXD13 (ND13) were introduced in primary bone marrow cells.


title: NA18573_across_population_normalised

description: HapMap CHB Female


title: NA18570_across_population_normalised

description: HapMap CHB Female


title: NA18579_across_population_normalised

description: HapMap CHB Female


title: Sca+Lin-PBM_ND13_rep2


title: Sca+Lin-PBM_MIG_rep2


title: Sca+Lin-PBM_ND13N51S_rep2


title: Sca+Lin-PBM_ND13N51S_rep1

label_protocol: One hundred ng of total RNA from each sample were double linear amplified with the ENZO BioArray High Yield RNA Transcript Labeling kit and the GeneChip Eukaryotic Small Sample Target Labeling Assay, Version II protocol (Affymetrix, Santa Clara, CA) to produce target for hybridization to Affymetrix MOE430 according to the manufacturer’s instructions and performed at the Genome Science Centre, BC Cancer Agency, Vancouver, Canada.


title: NA18571_across_population_normalised

description: HapMap CHB Female


title: NA18564_across_population_normalised

description: HapMap CHB Female


title: NA18561_across_population_normalised

description: HapMap CHB Male


title: NA18558_across_population_normalised

description: HapMap CHB Male


title: NA18562_across_population_normalised

description: HapMap CHB Male


title: NA18563_across_population_normalised

description: HapMap CHB Male


title: NA18555_across_population_normalised

description: HapMap CHB Female


title: NA18550_across_population_normalised

description: HapMap CHB Female


title: NA18552_across_population_normalised

description: HapMap CHB Female


title: Sca+Lin-PBM_NA10_rep1


title: NA18547_across_population_normalised

description: HapMap CHB Female


title: NA18545_across_population_normalised

description: HapMap CHB Female


title: NA18537_across_population_normalised

description: HapMap CHB Female


title: Sca+Lin-PBM_MIG_rep1


title: NA12892_across_population_normalised

description: HapMap CEU_parent Female

tag: HapMap CEU_parent, Female


title: NA12815_across_population_normalised

description: HapMap CEU_parent Female


title: NA12874_across_population_normalised

description: HapMap CEU_parent Male

tag: HapMap CEU_parent, Male


title: NA18526_across_population_normalised

description: HapMap CHB Female


title: NA12891_across_population_normalised

description: HapMap CEU_parent Male


title: NA12875_across_population_normalised

description: HapMap CEU_parent Female


title: NA12812_across_population_normalised

description: HapMap CEU_parent Male


title: NA12761_across_population_normalised

description: HapMap CEU_parent Female


title: NA18532_across_population_normalised

description: HapMap CHB Female


title: NA18542_across_population_normalised

description: HapMap CHB Female


title: NA18524_across_population_normalised

description: HapMap CHB Male


title: NA12872_across_population_normalised

description: HapMap CEU_parent Male


title: NA12814_across_population_normalised

description: HapMap CEU_parent Male


title: NA12763_across_population_normalised

description: HapMap CEU_parent Female


title: NA12873_across_population_normalised

description: HapMap CEU_parent Female


title: NA18529_across_population_normalised

description: HapMap CHB Female


title: NA18540_across_population_normalised

description: HapMap CHB Female


title: NA12751_across_population_normalised

description: HapMap CEU_parent Female


title: NA12716_across_population_normalised

description: HapMap CEU_parent Male


title: NA12717_across_population_normalised

description: HapMap CEU_parent Female


title: NA12750_across_population_normalised

description: HapMap CEU_parent Male


title: NA12760_across_population_normalised

description: HapMap CEU_parent Male


title: NA12762_across_population_normalised

description: HapMap CEU_parent Male


title: NA12156_across_population_normalised

description: HapMap CEU_parent Female


title: NA12239_across_population_normalised

description: HapMap CEU_parent Female


title: NA12248_across_population_normalised

description: HapMap CEU_parent Male


title: NA12813_across_population_normalised

description: HapMap CEU_parent Female


title: NA12249_across_population_normalised

description: HapMap CEU_parent Female


title: NA12264_across_population_normalised

description: HapMap CEU_parent Male


title: NA12236_across_population_normalised

description: HapMap CEU_parent Female


title: Sca+Lin-PBM_ND13_rep1


title: NA12155_across_population_normalised

description: HapMap CEU_parent Male


title: NA12154_across_population_normalised

description: HapMap CEU_parent Male


title: NA12146_across_population_normalised

description: HapMap CEU_parent Male


title: NA12145_across_population_normalised

description: HapMap CEU_parent Female


title: NA11994_across_population_normalised

description: HapMap CEU_parent Male


title: NA12005_across_population_normalised

description: HapMap CEU_parent Male


title: NA12006_across_population_normalised

description: HapMap CEU_parent Female


title: NA12234_across_population_normalised

description: HapMap CEU_parent Female


title: NA18566_across_population_normalised

description: HapMap CHB Female


title: NA18592_across_population_normalised

description: HapMap CHB Female


title: NA12057_across_population_normalised

description: HapMap CEU_parent Female


title: NA11995_across_population_normalised

description: HapMap CEU_parent Female


title: NA11882_across_population_normalised

description: HapMap CEU_parent Female


title: NA11831_across_population_normalised

description: HapMap CEU_parent Male


title: NA12004_across_population_normalised

description: HapMap CEU_parent Female


title: NA12144_across_population_normalised

description: HapMap CEU_parent Male


title: NA12056_across_population_normalised

description: HapMap CEU_parent Male


title: NA11832_across_population_normalised

description: HapMap CEU_parent Female


title: NA12043_across_population_normalised

description: HapMap CEU_parent Male


title: NA11993_across_population_normalised

description: HapMap CEU_parent Female


title: NA11992_across_population_normalised

description: HapMap CEU_parent Male


title: NA12044_across_population_normalised

description: HapMap CEU_parent Female


title: NA11881_across_population_normalised

description: HapMap CEU_parent Male


title: NA11830_across_population_normalised

description: HapMap CEU_parent Female


title: NA11839_across_population_normalised

description: HapMap CEU_parent Male


title: NA07345_across_population_normalised

description: HapMap CEU_parent Female


title: NA12003_across_population_normalised

description: HapMap CEU_parent Male


title: NA11840_across_population_normalised

description: HapMap CEU_parent Female


title: NA07034_across_population_normalised

description: HapMap CEU_parent Male


title: NA07357_across_population_normalised

description: HapMap CEU_parent Male


title: CS513

description: No.3-Ovary is CS513

source_name: No.3-Ovary is CS513

tag: No.3-Ovary is CS513


title: CS110

description: No.2-Ovary is CS110

source_name: No.2-Ovary is CS110

tag: No.2-Ovary is CS110


title: CV885

description: No.1-Ovary is CV885

source_name: No.1-Ovary is CV885

tag: No.1-Ovary is CV885


title: wt placenta

description: wildtype

source_name: placenta

tag: wildtype


title: NA07056_across_population_normalised

description: HapMap CEU_parent Female


title: wt ovary

description: wildtype

source_name: ovary


title: NA11829_across_population_normalised

description: HapMap CEU_parent Male


title: NA07055_across_population_normalised

description: HapMap CEU_parent Female


title: HEPG; ATCC; DnaseI enriched E_070809_06_DS7812_W D

status: Public on Sep 30 2007

type: genomic

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description:
Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.
DnaseI enriched

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software; linearly scaled to intesity of 500, 2-sided upper quantile normalization. BED files contain Log2 ratio of experimental normalized to control (2-sided Upper and linearly scaled to intensity 500) using the Affymetrix Tiling Analysis Software  (TAS) version 1.1.02).

molecule: genomic DNA

source_name: HEPG; ATCC; DnaseI enriched

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: HEPG; ATCC


title: NA06994_across_population_normalised

description: HapMap CEU_parent Male


title: NA07022_across_population_normalised

description: HapMap CEU_parent Male


title: HEPG; ATCC; DnaseI enriched E_070809_07_DS7816_W D


title: HEPG; ATCC; DnaseI enriched E_070809_01_DS7605_W D


title: NA06993_across_population_normalised

description: HapMap CEU_parent Male


title: NA06985_across_population_normalised

description: HapMap CEU_parent Female


title: NA07000_across_population_normalised

description: HapMap CEU_parent Female


title: HEPG; ATCC; DnaseI enriched E_070809_03_DS7768_W D


title: HEPG; ATCC; DnaseI enriched E_070808_12_DS7601_W D


title: HEPG; ATCC; DnaseI enriched E_070809_05_DS7809_W D


title: HEPG; ATCC; DnaseI enriched E_070809_04_DS7771_W D


title: HEPG; ATCC; DnaseI enriched E_070808_10_DS7591_W D


title: 2HA NAA, biological rep 1

city: Canberra

first: Peta

last: Holmes

state: Australian Capital Territory

address: Building 46, Australian National University

department: Reseach School of Biological Sciences

country: Australia

institute: Genomic Interactions Group

description: Gene expression data from Medicago truncatula 2HA leaf explants after 1 week of auxin treatment

hyb_protocol: Fifteen to 20 µg of each biotin-labeled fragmented cRNA sample was used to prepare 300 µL of hybridization mixture. Aliquots of each sample (100 µL) were hybridized for 16 hours at 45 degrees celcius onto Test3 arrays to check the quality of the samples prior to hybridization (200 µL) onto the Medicago GeneChip arrays

scan_protocol: GeneChips were scanned with the Agilent GeneArray Scanner (Affymetrix)

data_processing: To remove certain systematic biases from microarray, the raw Affymetrix data (.cel files) were normalized with the GCRMA (GC content – Robust Multi-Array Average) algorithm (ver. 2.2.0) including quantile normalization and variance stabilisation, using the affy package of the bioconductor software. The normalized average of the replicates was then log transformed in base 2 to reduce the proportional relationship between random error and signal intensity. Differentially expressed genes were identified by evaluating the log2 ratio between the two conditions

organism: Medicago truncatula

source_name: Medicago truncatula 2HA leaf explants, 1 week on NAA

label_protocol: Biotinylated cRNA was generated using the Enzo BioArray kit (Affymetrix), purified using RNeasy spin columns (Qiagen), according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Medicago truncatula 2HA (Nolan et al, Plant Cell Rep 8: 278–281), plants were used for the collection of leaves and for the preparation of leaf explants for tissue culture. The basal medium used for tissue culture was P4, which is based on Gamborg's B5 medium as described by Thomas et al (Plant Sci 69: 189–198).

extract_protocol: Total RNA was extracted and purified from plant tissues using the Qiagen RNeasy plant mini kit (Qiagen).

treatment_protocol: Young leaves were collected from plants that were 2 hours into a regular day cycle. Leaf explants were plated onto P4 medium containing 10 µM NAA 1 week and were grown in the dark.


title: HEPG; ATCC; DnaseI enriched E_070809_02_DS7764_W D


title: HEPG; ATCC; DnaseI enriched E_070808_11_DS7596_W D


title: HEPG; ATCC; Control genomic dna C_070424_06_PDS276_W D

description:
Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer
Control genomic dna (untreated)

source_name: HEPG; ATCC; Control genomic dna (untreated)

extract_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K


title: HEPG; ATCC; Control genomic dna C_070827_04_PDS276_W D


title: 2HA NAA, biological rep 2


title: HEPG; ATCC; Control genomic dna C_070827_05_PDS276_W D


title: 2HA, biological rep 1

description: Gene expression data from Medicago truncatula 2HA leaves

source_name: Medicago truncatula 2HA leaf


title: 2HA NAA, biological rep 3


title: CHD Patient 2631

city: Berlin

first: Fikret

last: Erdogan

address: Ihnestr. 73

country: Germany

institute: Max-Planck-Institute

description: Array CGH analysis of a patient with congenital heart disease

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure  (Grimberg J, Nawoschik S, Belluscio L, McKee R, Turck A, Eisenberg A. A simple and efficient non-organic procedure for the isolation of genomic DNA from blood. Nucleic Acids Res. 1989 Oct 25;17(20):8390), PMID: 2813076, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=2813076

tag: DNA isolated from blood of a patient with congenital heart disease.  Gender

value: female

extract_protocol: DNA was extracted from peripheral blood by a salting out procedure (Blin N, Stafford DW. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976 Sep;3(9):2303-8), PMID: 987581, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=987581

tag: DNA isolated from the blood of a healthy female donor


city: London

first: Maria

last: Ocampo-Hafalla

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK London Research Institute

description: SUPernatant file for chromosome VI (rikDACF) tiling arrays. [Figures 1, 4, 5 and Supplementary Figure 1]

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Reference: Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4).

organism: Saccharomyces cerevisiae

source_name: SUPernatant fraction (equal to Whole Cell Extract)

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

extract_protocol:
Extraction was performed as previously described (Katou et al. 2003).
Reference:
Katou Y, Kanoh Y, Bando M, Noguchi H, Tanaka H, Ashikari T, Sugimoto K and Shirahige K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424: 1078-1083.

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before temperature shift.

tag: Strain 2272 = Scc1-9PK-TRP, rat1-1


title: 2HA, biological rep 2


title: GAL-Scc1-HA3 distribution (HU-loaded; -NOC)

description: GAL-Scc1-HA3 distribution (HU-loaded) on chromosome VI in metaphase-arrested cells in the absence of nocodazole. [Figure 4, 2nd panel]

source_name: Chromatin-immunoprecipitated DNA

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase. From there cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Loading of ectopic, HA epitope-tagged cohesin was induced by induction of the GAL1 promoter for 1 hour during the time in the HU arrest (HU-loaded). Nocodazole was then washed out to allow spindle assembly and centromere breathing.

tag: Strain 3267 = Scc1-9PK-TRP, leu:GAL-SCC1-HA3:LEU2, MET-HA3-CDC20-URA3


title: Scc1-HA6 distribution (-Cdc20)

description: Scc1-HA6 distribution on chromosome VI in metaphase-arrested cells in the absence of nocodazole. [Figure 1, bottom panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into metaphase arrest by Cdc20 depletion in the absence of nocodazole.

tag: Strain 379 = Scc1-HA6::HIS3, MET-HA3-CDC20::TRP


title: Smc3-HA3 distribution (-Cdc20)

description: Smc3-HA3 distribution on chromosome VI in metaphase-arrested cells in the absence of nocodazole. [Supplementary Figure 1, bottom panel]

tag: Strain 3235 = Scc1-PK3::HIS, Smc3-HA3::URA, MET-HA3-CDC20-TRP


title: GAL-Scc1-HA3 distribution (noc-loaded; -NOC)

description: GAL-Scc1-HA3 distribution (noc-loaded) on chromosome VI in metaphase-arrested cells in the absence of nocodazole. [Figure 4, bottom panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase. From there cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Loading of ectopic, HA epitope-tagged cohesin was induced by induction of the GAL1 promoter for 1 hour during the time in the metaphase arrest (noc-loaded). Nocodazole was then washed out to allow spindle assembly and centromere breathing.


title: Scc1-HA6 distribution (-Cdc20; +NOC)

description: Scc1-HA6 distribution on chromosome VI in metaphase-arrested cells in the presence of nocodazole. [Figure 1, top panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into metaphase arrest by Cdc20 depletion in the presence of nocodazole.


title: GAL-Scc1-HA3 distribution (noc-loaded; +NOC)

description: GAL-Scc1-HA3 distribution (noc-loaded) on chromosome VI in metaphase-arrested cells in the presence of nocodazole. [Figure 4, 3rd panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase. From there cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Loading of ectopic, HA epitope-tagged cohesin was induced by induction of the GAL1 promoter for 1 hour during the time in the metaphase arrest (noc-loaded).


title: Scc1-HA6 distribution (-NOC)

description: Scc1-HA6 distribution on chromosome VI in metaphase-arrested cells in the absence of nocodazole. [Figure 5, top panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before Scc2 was inactivated by temperature shift. From there cells were released into metaphase arrest by Cdc20 depletion.

tag: Strain 3138 = Scc1-HA6-HIS, scc2-4, leu2::LEU2 tetR-GFP, 1.4kb left of CEN5:

value: tetO2X112 ::HIS3, MET-HA3-CDC20::TRP1, ura3::GAL-CDC14-3Pk::URA3


title: Scc1-HA6 distribution (+NOC)

description: Scc1-HA6 distribution on chromosome VI in metaphase-arrested cells in the presence of nocodazole. [Figure 5, bottom panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before Scc2 was inactivated by temperature shift. From there cells were released into metaphase arrest by Cdc20 depletion. Centromere breathing was then stopped, and centromere re-association was facilitated by addition of nocodazole.


title: N_terminal Wor1 ChIP wor1D

type: mixed

city: San Francisco

first: David

middle: J

last: Galgoczy

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

description: RZY219 white a_a wor1D/wor1D cells grown at 25deg in SD + aa media.

hyb_protocol: Agilent custom 244K DNA microarray hybridization protocol.

scan_protocol: Axon GenePix 4000B Scanner, 5micron resolution.

data_processing: Raw scanned data from GenePix gpr file, unnormalized.  Spots that have multiple BLAST hits in the contigs 20 Candida sequence assembly are flagged.

molecule: other

organism: Candida albicans

source_name: N_terminal Wor1 ChIP DNA from RZY219 Candida albicans white a_a wor1D/wor1D cells

label_protocol: ChIP DNA was amplified by random_primed 3 step PCR amplification.  Aminoallyl d_UTP was incorporated in the final PCR step.  5 micrograms of product were labeled with Cy5 fluorescent dye, and desalted using a Zymo DNA Clean & Concentrator_25 column (Zymo Research).

extract_protocol: Cells were formaldehyde crosslinked and lysed following cell wall digestion with lyticase.  ChIPs were performed using 5microl affinity purified antibodies raised against N_Terminal Wor1 peptide (near N terminus)_ QVLDKQLEPVSRRPHERER

tag: RZY219 a_a white wor1D cells

source_name: Total DNA from RZY219 Candida albicans white a_a wor1D/wor1D cells

label_protocol: Total DNA was diluted to the same concentration as the matched ChIP DNA and amplified by random_primed 3 step PCR amplification.  Aminoallyl d_UTP was incorporated in the final PCR step.  5 micrograms of product were labeled with Cy5 fluorescent dye, and desalted using a Zymo DNA Clean & Concentrator_25 column (Zymo Research).


title: C_terminal Wor1 ChIP wt Replicate 1

description: Biological replicate 1 of 2.  RZY511 opaque a_a cells grown at 25deg in SD + aa media.

source_name: C_terminal Wor1 ChIP DNA from RZY511 Candida albicans opaque a_a cells

extract_protocol: Cells were formaldehyde crosslinked and lysed following cell wall digestion with lyticase.  ChIPs were performed using 5microl affinity purified antibodies raised against C_Terminal Wor1 peptide (near C terminus)_ DDAVGNSSGSYYTGT

tag: RZY511 a_a opaque cells

source_name: Total DNA from RZY511 Candida albicans opaque a_a cells


title: Smc3-HA3 distribution (-Cdc20; +NOC)

description: Smc3-HA3 distribution on chromosome VI in metaphase-arrested cells in the presence of nocodazole. [Supplementary Figure 1, top panel]


title: N_terminal Wor1 ChIP wt Replicate 2

source_name: N_terminal Wor1 ChIP DNA from RZY511 Candida albicans opaque a_a cells

extract_protocol: Cells were formaldehyde crosslinked and lysed following cell wall digestion with lyticase


title: SHED206

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

country: France

institute: Institut national de la santé et de la recherche médicale

description: We analyzed the gene expression profiles of subcutaneous white adipose tissue from 29 obese subjects during very low calorie diet (VLCD) using cDNA microarray. The patterns of expression were compared with that of 17 non-obese subjects.

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software.

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized using Stanford Microarray Database Online resources (http://genome-www5.stanford.edu/).The VALUE field represents the log(base2) of the print-tip loess normalized R/G ratio (mean).

source_name: Pool

label_protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit (Ambion, Austin, TX), and 3 µg aRNA was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit (Amersham Biosciences, Orsay, France) (available at http://cmgm.stanford.edu/pbrown/protocols/index).

extract_protocol: Total RNA from scWAT was prepared using the RNeasy RNA Mini Kit (Qiagen, Courtaboeuf, France).

tag: Pool of human subcutaneous adipose tissue

source_name: Obese

tag: Obese subcutaneous adipose tissue (ZEMB)


title: C_terminal Wor1 ChIP wor1D Replicate 2

description: Biological replicate 2 of 2.  RZY219 white a_a wor1D/wor1D cells grown at 25deg in SD + aa media.

source_name: C_terminal Wor1 ChIP DNA from RZY219 Candida albicans white a_a wor1D/wor1D cells


title: GAL-Scc1-HA3 distribution (HU-loaded; +NOC)

description: GAL-Scc1-HA3 distribution (HU-loaded) on chromosome VI in metaphase-arrested cells in the presence of nocodazole. [Figure 4, top panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase. From there cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Loading of ectopic, HA epitope-tagged cohesin was induced by induction of the GAL1 promoter for 1 hour during the time in the HU arrest (HU-loaded).


title: C_terminal Wor1 ChIP wt Replicate 2


title: SHED129

tag: Obese subcutaneous adipose tissue (NGO)


title: HL60; ATCC; DnaseI enriched E_070809_12_DS7694_W A

description:
Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.
DnaseI enriched

source_name: HL60; ATCC; DnaseI enriched

tag: HL60; ATCC


title: C_terminal Wor1 ChIP wor1D Replicate 1

description: Biological replicate 1 of 2.  RZY219 white a_a wor1D/wor1D cells grown at 25deg in SD + aa media.


title: SHED096

tag: Obese subcutaneous adipose tissue (VAR)


title: HL60; ATCC; DnaseI enriched E_070809_10_DS7686_W A


title: HL60; ATCC; DnaseI enriched E_070809_09_DS7682_W A


title: GM69; DnaseI enriched E_070808_09_DS7784_W E

source_name: GM69; DnaseI enriched


title: HL60; ATCC; DnaseI enriched E_070809_11_DS7691_W A


title: K562; ATCC; DnaseI enriched E_070807_06_DS7678_W F

source_name: K562; ATCC; DnaseI enriched

tag: K562; ATCC


title: SHEA143

tag: Obese subcutaneous adipose tissue (KAM)


title: SHED098

tag: Obese subcutaneous adipose tissue (ZEAU)


title: SHEA200

tag: Obese subcutaneous adipose tissue (LEF)


title: Aortic endothelial RNA, 21 day diabetes, replicate 2, dye reversal

city: Honolulu

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: The GPR data was uploaded to Acuity, normalized, and a dataset was generated with 2 biological replicate experiments with dye reversal microarrays for each was generated (4 microarrays total)

hyb_protocol: The microarrays were hybridized with the ASAP Micromax hybridization buffer system 16 hours at 50 degrees C. Washing was at room temp: 5 minutes in 2X SSC, 0.1% SDS, then 5 minutes in .1 X SSC, 0.1% SDS, then 5 minutes in .1 X SSC.

data_processing: The log 2 fold change represents the log 2 of experimental/control ratio of normalized 2 channel feature values (ratio of median normalization determined with the default settings of Acuity).

source_name: Cy5-labeled RNA of control aortic endothelium

label_protocol: Perkin Elmer Micromax ASAP system

growth_protocol: 4-6 week-old male mice were exposed to saline injection and their endothelium isolated from their aortae by FACS after 21 days

extract_protocol: TRIZOL, Qiagen microrneasy column

treatment_protocol: RNA was extracted, amplified with the oligodT-T7 method, labeled with Cy5 with Perkin Elmer Micromax ASAP system

tag: Cy5-labeled, amplified RNA isolated from endothelium of aortae of mice of strain Tie 2 GFP freshly obtained by FACS. This channel represents control, non-diabetic mice 21 days after saline injection. (Experimental mice in channel 2 were exposed to streptozotocin-induced diabetes for 21 days).

source_name: Cy3-labeled RNA of diabetic aortic endothelium

growth_protocol: 4-6 week-old male mice were exposed to streptozotocin injection and their endothelium isolated from their aortae by FACS after 21 days.

treatment_protocol: RNA was extracted, amplified with the oligodT-T7 method, labeled with Cy3 with Perkin Elmer Micromax ASAP system.

tag: Cy3-labeled, amplified RNA isolated from endothelium of aortae of mice of strain Tie 2 GFP freshly obtained by FACS. This channel represents diabetic mice 21 days after streptozotocin injection at 180 mg/kg. (Experimental mice in channel 1 were control mice 21 days after saline injection).


title: N_terminal Wor1 ChIP wt Replicate 1


title: Aortic endothelial RNA, 21 day diabetes, replicate 1

scan_protocol: Genepix 4000B was used.  The power gain settings were chosen to maintain minimal number of saturated pixils in either channel.

source_name: Cy3-labeled RNA of control aortic endothelium

growth_protocol: 4-6 week-old male mice were exposed to saline injection and their endothelium isolated from their aortae by FACS after 21 days.

extract_protocol: TRIZOL,  Qiagen microrneasy column

tag: Cy3-labeled, amplified RNA isolated from endothelium of aortae of mice of strain Tie 2 GFP freshly obtained by FACS. This channel represents control, non-diabetic mice 21 days after saline injection. (Experimental mice in channel 2 were exposed to streptozotocin-induced diabetes for 21 days).

source_name: Cy5-labeled RNA of diabetic aortic endothelium

treatment_protocol: RNA was extracted, amplified with the oligodT-T7 method, labeled with Cy5 with Perkin Elmer Micromax ASAP system.

tag: Cy5-labeled, amplified RNA isolated from endothelium of aortae of mice of strain Tie 2 GFP freshly obtained by FACS. This channel represents diabetic  mice 21 days after streptozotocin  injection at 180 mg/kg. (Experimental mice in channel 1 were control mice 21 days after saline injection).


title: Aortic endothelial RNA, 21 day diabetes, replicate 1, dye reversal

scan_protocol: Genepix 4000B was used. The power gain settings were chosen to maintain minimal number of saturated pixils in either channel.


title: SHEA110

tag: Obese subcutaneous adipose tissue (DAR)


title: Aortic endothelial RNA, 21 day diabetes, replicate 2

tag: Cy5-labeled, amplified RNA isolated from endothelium of aortae of mice of strain Tie 2 GFP freshly obtained by FACS. This channel represents diabetic mice 21 days after streptozotocin injection at 180 mg/kg. (Experimental mice in channel 1 were control mice 21 days after saline injection).


title: 2HA, biological rep 3

description: Gene expression data from Medicago truncatula 2HA leaves

source_name: Medicago truncatula 2HA leaf


title: HL60; ATCC; DnaseI enriched E_070809_05_DS7832_W A


title: K562; ATCC; DnaseI enriched E_070807_05_DS7674_W F


title: GM69; DnaseI enriched E_070808_08_DS7779_W E


title: SHEA108

tag: Obese subcutaneous adipose tissue (CAR)


title: GM69; DnaseI enriched E_070808_06_DS7748_W E


title: K562; ATCC; DnaseI enriched E_070807_03_DS7666_W F


title: HL60; ATCC; DnaseI enriched E_070809_06_DS7837_W A


title: GM69; DnaseI enriched E_070808_07_DS7788_W E


title: K562; ATCC; DnaseI enriched E_070807_02_DS7664_W F


title: K562; ATCC; DnaseI enriched E_070807_04_DS7671_W F


title: K562; ATCC; DnaseI enriched E_070807_01_DS7649_W F


title: GM69; DnaseI enriched E_070808_05_DS7743_W E


title: GM69; DnaseI enriched E_070808_03_DS7646_W E


title: HL60; ATCC; DnaseI enriched E_070809_03_DS7824_W A


title: HL60; ATCC; DnaseI enriched E_070809_01_DS7724_W A


title: SHEA139

tag: Obese subcutaneous adipose tissue (DEP)


title: HL60; ATCC; DnaseI enriched E_070809_04_DS7830_W A


title: K562; ATCC; DnaseI enriched E_070801_08_DS7630_W F


title: K562; ATCC; DnaseI enriched E_070801_07_DS7625_W F


title: GM69; DnaseI enriched E_070808_02_DS7637_W E


title: HL60; ATCC; Control genomic dna C_070827_07_DS7457_W A

description:
Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer
Control genomic dna (untreated)

source_name: HL60; ATCC; Control genomic dna (untreated)


title: GM69; DnaseI enriched E_070808_04_DS7739_W E


title: HL60; ATCC; DnaseI enriched E_070809_02_DS7728_W A


title: HL60; ATCC; Control genomic dna C_070827_06_DS7457_W A


title: GM69; DnaseI enriched E_070808_01_DS7633_W E


title: K562; ATCC; DnaseI enriched E_070801_06_DS7621_W F


title: K562; ATCC; DnaseI enriched E_070801_02_DS7564_W F


title: K562; ATCC; Control genomic dna C_070827_02_PDS277_W F

source_name: K562; ATCC; Control genomic dna (untreated)


title: K562; ATCC; DnaseI enriched E_070801_05_DS7568_W F


title: GM69; DnaseI enriched E_070807_07_DS7584_W E


title: GM69; DnaseI enriched E_070801_02_DS7582_W E


title: K562; ATCC; Control genomic dna C_070425_07_PDS277_W F


title: K562; ATCC; DnaseI enriched E_070801_01_DS7562_W F


title: HEPG; ATCC; DnaseI enriched E_070809_08_DS7822_W D

source_name: HEPG; ATCC; DnaseI enriched

tag: HEPG; ATCC


title: GM69; Control genomic dna C_070827_03_PDS274_W E

source_name: GM69; Control genomic dna (untreated)


title: HL60; ATCC; Control genomic dna C_070423_01_DS7457_W A


title: GM69; DnaseI enriched E_070801_01_DS7576_W E


title: Scc1-HA6 distribution along the whole genome (-Cdc20; -NOC; +Cdc14)

description: Scc1-HA6 distribution along the whole genome in metaphase-arrested cells in the absence of nocodazole and in the presence of ectopic Cdc14 expression. [Figure 2, bottom panel; Figure 3]

source_name: Chromatin-immunoprecipitated DNA

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before Scc2 was inactivated by temperature shift. Cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Nocodazole was then washed out to allow spindle assembly and centromere splitting, and Cdc14 expression was induced by galactose addition to stabilise split centromeres.

tag: Strain 3138 = Scc1-HA6-HIS, scc2-4, leu2::LEU2 tetR-GFP, 1.4kb left of CEN5:


title: K562; ATCC; DnaseI enriched E_070801_05_DS7617_W F


title: Scc1-HA6 distribution along the whole genome (-Cdc20; +NOC)

description: Scc1-HA6 distribution along the whole genome in metaphase-arrested cells in the presence of nocodazole. [Figure 2, top panel; Figure 3]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before Scc2 was inactivated by temperature shift. Cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole.


title: GM69; DnaseI enriched E_070807_08_DS7590_W E


title: GM69; Control genomic dna C_070418_02_PDS274_W E


title: GM69; Control genomic dna C_070405_02_PDS274_W E


title: K562; ATCC; Control genomic dna C_070827_01_PDS277_W F


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #3; technical replicate #2

status: Public on Sep 29 2007

city: Hobart

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

institute: University of Tasmania

description: Biological replicate #3 (out of 3 biological replicates, Technical replicate #2 (out of 2 technical replicates per biological replicate)

hyb_protocol: Slides were pre-hybridised in a hybrisation solution (25% vol./vol. formamide, 5 x SSC buffer – 0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0, 0.1% sodium dodecyl sulfate) containing 10 mg ml-1 bovine serum albumin for 45 min at 42°C. Slides were then rinsed twice in distilled water and air-dryed followed by gentle drying with an air gun. Hybridisation was performed in a humid hybridisation chamber at 42°C for 16-20 h using a hybridisation solution containing 0.42 ug ul-1 human Cot1 DNA, 0.62 ug ul-1 polyA and 0.83 ug ul-1 salmon sperm DNA. Slides were washed at room temperature in 1 X SSC buffer containing 0.2% SDS for 5 min and again in 0.1 x SSC buffer containing 0.2% SDS for 5 min. The slides were then further washed twice in 0.1 X SSC buffer at room temperature for 2 min. Slides were then dried by plate centrifugation (10 minutes, 1000xg, 550rpm) with then gently with an air gun.

scan_protocol: Scanning: Genepix 4000B scanner Gridding and signal intensity acquisition: GenePix Pro 5.0 Data saved as GPR file

data_processing:
Biological and technical replicate GPR files were submitted to WebArray for analysis
http://bioinformatics.skcc.org/webarray/
Xia, X., McClelland, M. & Wang, Y. 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306-311
Settings used for dual-colored array analysis:
1. Background subtraction applied.
2. Spot quality index - default
3. Within array normalization - Global Loess method
4. Between array normalization - Quantile method
5. Linear Model Statistical Analysis (including FDR calculation with SPLOSH)

organism: Listeria monocytogenes

source_name: L. monocytogenes S2542, 600 MPA 5 min treatment

label_protocol: Conversion of RNA to cDNA and postlabelling was performed using the SuperScript Indirect cDNA Labeling System (protocol Version D; Cat. L1014-01).

growth_protocol:
Media used for growth: tryptone soy yeast extract broth (Oxoid)
Growth state: mid exponential phase
Temperature: 25 C

extract_protocol: Cells underwent a 2-3 hour (25°C) enzymatic treatment in TE buffer (10 mM Tris HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg ml-1 lysozyme and 10 mg ml-1 proteinase K. Cells were fully lysed by bead beating using 0.1 mm zirconium-silica sand in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1% beta-mercaptoethanol. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at -80°C. RNA quality was assessed with electrophoresis using a RNA bioanalyser 2100 (Agilent Technologies) with gels stained with picogreen and scanned with a laser. Electrophoretograms were assessed for intact 16S and 23S rRNA bands before progression to microarray hybridization.

treatment_protocol: High pressure treatment: 600 MPa lasting 5 minutes at 25 C (temperature controlled to negate adiabatic heating). Samples then immediately frozen in liquid nitrogen following treatment. Samples were stored at -70 C until processed.

tag: Strain

tag: Serotype

tag: Source

value: smoked salmon

source_name: L. monocytogenes S2542, atmospheric pressure

treatment_protocol: Incubated under atmospheric pressure for 5 minutes at 25 C (temperature controlled to negate adiabatic heating). Samples then immediately frozen in liquid nitrogen following treatment. Samples were stored at -70 C until processed.


title: Brain Normal_TspR1-ExoIII-rep1

city: Taipei

first: Ming-Ta

last: Hsu

address: 155, Li-Nong St., Sec.2, Peitou, Taipei, Taiwan, R.O.C.

country: Taiwan

institute: National Yang-Ming University

description:
Protected from Exonuclease III digestion by TspRI ends.
1~2μg DNA was digested with methylation sensitive restriction enzyme in 10μl of total volume for 2hrs, 1μl(10units) TspR I was then added and reacted at 65℃ for two hours using hot top PCR machine. 10unit of Exonuclease III enzyme was then added and total volume was brought to 20μl by addition of water and 10X buffer. Reaction was carried out at 30℃ for 1hr. Exonuclease III was heat inactive by 70℃ for 20min. 30units RecJf was added to remove single-strand DNA and the enzyme was inactivated by heating at 65℃ for 20min. DNA was then phenol/chloroform extracted and ethanol precipitate.

hyb_protocol: According to the manual of Agilent protocol (http://www.agilent.com)

scan_protocol: Scanning was performed as the manual of Agilent protocol (http://www.agilent.com)

data_processing: The Cy3 hybridization intensity was normalized to Cy5 for comparison among samples. The log2 ratio(log2 Cy5/Cy3) were calculated and compared. Agilent software was used.

source_name: Brain-MOCK

label_protocol: According to the manual of Agilent Oligo Microarray Kit.

extract_protocol: This genomic DNA was purchased from BioChain (Catalog No.: D1234035)

treatment_protocol: Genomic DNA was first digested with TspR I, which created DNA fragments with 9-base 3’ extension and were resistant for exonuclease III digestion. The DNA was NOT digested with methylation-sensitive restriction enzyme Hpa II. Then treatment with exonuclease III and RecJf exonuclease, DNA were purified and labeled with Cy3 and Cy5 fluorescence dyes respectively. The Cy3 hybridization intensity was normalized to Cy5 for comparison among samples.

tag: This genomic DNA was purchased from BioChain. (Catalog No.

tag: Human, Normal Brain, Male, 41 years old

tag: Genomic DNA was NOT digested with HpaII

source_name: Brain-HpaII

treatment_protocol: Genomic DNA was first digested with TspR I, which created DNA fragments with 9-base 3’ extension and were resistant for exonuclease III digestion. The DNA were then digested with methylation-sensitive restriction enzyme Hpa II. After treatment with exonuclease III and RecJf exonuclease, DNA were purified and labeled with Cy3 and Cy5 fluorescence dyes respectively. The Cy3 hybridization intensity was normalized to Cy5 for comparison among samples.


title: MCF7_TspR1-ExoIII_rep1

extract_protocol: Cells were grown to 90 % confluence in 10 cm tissue culture dish. Each 10 cm dish was washed with 1X PBS for three times, and resuspended with 700μl of cell lysis buffer. Suspensions were collected in a 1.5ml eppendorf tube and treated with 0.1 mg/ml of RNase A for an hour at 37 ℃ and then with 0.3 mg/ml of proteinase K for 12-16 hours at 50℃. An equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1) was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. The aqueous phase was collected carefully, and then repeated the extraction procedure until the interface is clean. The aqueous phase again was collected and an equal volume of chloroform was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. This procedure was repeated until the intersurface was clean. Finally, total genomic DNA in the aqueous phase was precipitated by the addition of 1/10 volume of 7.5 M ammonium acetate (pH: 5.2) and two volume of absolute ethanol. The mixture was incubated at -70℃ overnight and centrifuged at 13000 rpm, 4℃ for 30 min. Supernatant was removed and the pellet was washed by proper amount of 70 % ethanol and then centrifuged. In the end, the pellet was redissolved in d3H20 and then stored at -20℃. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry.

treatment_protocol: Genomic DNA was first digested with TspR I, which created DNA fragments with 9-base 3’ extension and were resistant for exonuclease III digestion. The DNA were NOT digested with methylation-sensitive restriction enzyme Hpa II. Then treatment with exonuclease III and RecJf exonuclease, DNA were purified and labeled with Cy3 and Cy5 fluorescence dyes respectively. The Cy3 hybridization intensity was normalized to Cy5 for comparison among samples.

tag: Cell line

tag: Gender

value: Female

tag: Age

tag: Tissue

value: Breast tumor

source_name: MCF-HpaII


title: MDA-MB-231_TspR1-ExoIII-rep1


title: Breast Tumor_TspR1-ExoIII_rep1

source_name: Breast Tumor-MOCK

extract_protocol: This genomic DNA was purchased from BioChain (Catalog No.: D1235086)

tag: Species

value: Human

value: Breast Tumor (Invasive Ductal Carcinoma)

source_name: Breast Tumor-HpaII

tag: Genomic DNA was digested with HpaII


title: Leukocyte Normal_TspR1 contain HpaII_rep1

source_name: Leukocyte-MOCK

extract_protocol: This genomic DNA was purchased from BioChain (Catalog No.: D1234148)

tag: Human, Normal Peripheral Blood Leukocyte, Male, 44 years old

source_name: Leukocyte-HpaII


title: Luc RNAi biological rep6

city: Singapore

first: Huck

middle: Hui

last: Ng

state: Singapore

address: Biopolis street

department: Stem Cell and Development biology

country: Singapore

institute: Genone Institute of Singapore

description: Gene expression data from Luc shRNA treated E14 embryonic stem cells

hyb_protocol: 1.5 ug of cRNA were hybridized to Illumina Mouse-6 Expression BeadChip v1 for 20 hr at 55oC on Ilumina Hybridization Oven.

scan_protocol: Illumina Mouse-6 Expression BeadChip v1 were washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was chosen to obtain the signal intensity.

source_name: E14 mouse embryonic stem cells

label_protocol: Biotinylated cRNA were prepared from 500 ng of total RNA according to the standard protocol (TotalPrep RNA Amplification Kit, Instruction Manual, Catalog #IL1791, Illumina).

growth_protocol: Feeder-free E14 mouse embryonic stem cells were cultured at 37°C with 5% CO2. All cells were maintained on gelatin-coated dishes in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM Beta-mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon)

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified with RNeasy minikit (Qiagen).

treatment_protocol: 2 ug of Luc shRNA (targeting Firefly luciferase transcript) was cloned in pSUPER puro vector (OligoEngine, Seattle, WA) and transfected into E14 mouse embryonic stem cells cells on 60mm plates. Puromycin (Sigma) selection was introduced 1 day after transfection at 1.0 µg/ml, and maintained for 4 days prior to harvesting RNA

tag: Luc shRNA (targeting Firefly luciferase transcript) transfected E14 mouse embryonic stem cells


title: Jmjd2c RNAi biological rep3

description: Gene expression data from Jmjd2c shRNA treated E14 embryonic stem cells

growth_protocol: Feeder-free E14 mouse embryonic stem cells were cultured at 37°C with 5% CO2. All cells were maintained on gelatin-coated dishes in Dulbecco’s modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovi

treatment_protocol: 2 ug of Jmjd2c shRNA (targeting Jumonji domain containing 2C transcript) was cloned in pSUPER puro vector (OligoEngine, Seattle, WA) and transfected into E14 mouse embryonic stem cells cells on 60mm plates. Puromycin (Sigma) s

tag: Jmjd2c shRNA (targeting Jumonji domain containing 2C transcript) transfected E14 mouse embryonic stem cells


title: Scc1-HA6 distribution along the whole genome (-Cdc20; -NOC)

description: Scc1-HA6 distribution along the whole genome in metaphase-arrested cells in the absence of nocodazole. [Figure 2, middle panel]

treatment_protocol: Cells were synchronized in G1 with α-factor and released into HU arrest in early S-phase, before Scc2 was inactivated by temperature shift. Cells were released into metaphase arrest by Cdc20 depletion in the presence of nocodazole. Nocodazole was then washed out to allow spindle assembly and centromere splitting.


title: Testis Normal_TspRI-ExoIII_rep1

source_name: Testis-MOCK

extract_protocol: This genomic DNA was purchased from BioChain (Catalog No.: D1234260)

tag: Human, Normal Testis, Male, 27 years old

source_name: Testis-HpaII


title: Breast Normal_TspR1-ExoIII-rep1

source_name: Breast-MOCK

extract_protocol: This genomic DNA was purchased from BioChain (Catalog No.: D1234086)

tag: This DNA was purchased from BioChain. (Catalog No.

tag: Human, Normal Breast, Female, 83 years old.

source_name: Breast-HpaII


title: SHEA141

source_name: Pool

tag: Pool of human subcutaneous adipose tissue

source_name: Obese

tag: Obese subcutaneous adipose tissue (GAN)


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #3; technical replicate #1

description: Biological replicate #3 (out of 3 biological replicates, Technical replicate #1 (out of 2 technical replicates per biological replicate)

tag: Strain

tag: Serotype

tag: Source


title: Human Ntera2 cells, Kap1 WG Array, 94009_ratio.gff

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

institute: University of California Davis

description: A complete genomic analysis of KAP1 binding in human Ntera2 testicular carcinoma cells using a 38 array tiling set, identifying ~7000 KAP1 binding sites.

hyb_protocol: The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.

scan_protocol: The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).

data_processing: log base 2 ratios; specifically, fluorescence intensity raw data were obtained from scanned images of the oligonucleotide tiling arrays using NIMBLESCAN 2.0 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure is approximately equivalent to mean-normalization of each channel.

source_name: Ntera2 cells

label_protocol: The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

tag: KAP1 antibody immunoprecipitated DNA

label_protocol: see labeling protocol for channel 1

extract_protocol: see extract protocol for channel 1

tag: control total input


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #2; technical replicate #2

description: Biological replicate #2 (out of 3 biological replicates, Technical replicate #2 (out of 2 technical replicates per biological replicate)

source_name: L. monocytogenes S2542, 600 MPA 5 min treatment


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #2; technical replicate #1

description: Biological replicate #2 (out of 3 biological replicates, Technical replicate #1 (out of 2 technical replicates per biological replicate)

source_name: L. monocytogenes S2542, atmospheric pressure


title: Jmjd2c RNAi biological rep1


title: Luc RNAi biological rep5


title: Jmjd2c RNAi biological rep2


title: Human Ntera2 cells, Kap1 WG Array, 71055_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 73429_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 82962_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 72220_ratio.gff_GPL5204


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #1; technical replicate #2

description: Biological replicate #1 (out of 3 biological replicates, Technical replicate #2 (out of 2 technical replicates per biological replicate)


title: Human Ntera2 cells, Kap1 WG Array, 82980_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 71318_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 94008_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 83263_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 83146_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 95470_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 63776_ratio.gff


title: Jmjd1a RNAi biological rep3

description: Gene expression data from Jmjd1a shRNA treated E14 embryonic stem cells

treatment_protocol: 2 ug of Jmjd1a shRNA (targeting Jumonji domain containing 1A transcript) was cloned in pSUPER puro vector (OligoEngine, Seattle, WA) and transfected into E14 mouse embryonic stem cells cells on 60mm plates. Puromycin (Sigma) selection was

tag: Jmjd1a shRNA (targeting Jumonji domain containing 1A transcript) transfected E14 mouse embryonic stem cells


title: Human Ntera2 cells, Kap1 WG Array, 73439_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 83305_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 70990_ratio.gff


title: Luc RNAi biological rep4


title: Human Ntera2 cells, Kap1 WG Array, 95066_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 99119_ratio.gff


title: L. monocytogenes S2542; 600 MPa 5 min; biological replicate #1; technical replicate #1

description: Biological replicate #1 (out of 3 biological replicates); Technical replicate #1 (out of 2 technical replicates for each biological replicate)

data_processing:
Combined biological replicate (including duplicated technical replicate) GPR files were submitted to WebArray for analysis:
http://bioinformatics.skcc.org/webarray/
Xia, X., McClelland, M. & Wang, Y. 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306-311
Settings used for dual-colored array analysis:
1. Background subtraction applied.
2. Spot quality index - default
3. Within array normalization - Global Loess method
4. Between array normalization - Quantile method
5. Linear Model Statistical Analysis (including FDR calculation with SPLOSH)

tag: Strain S2542

tag: Serotype 1/2A

tag: Source; smoked salmon


title: Human Ntera2 cells, Kap1 WG Array, 71652_ratio.gff


title: L. monocytogenes S2542, 400 MPa, 5 min., biological replicate #2

description: Biological replicate #2 out of a total of 3

data_processing:
Biological replicate GPR files were submitted to WebArray for analysis
http://bioinformatics.skcc.org/webarray/
Xia, X., McClelland, M. & Wang, Y. 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306-311
Settings used for dual-colored array analysis:
1. Background subtraction applied.
2. Spot quality index - default
3. Within array normalization - Global Loess method
4. Between array normalization - Quantile method
5. Linear Model Statistical Analysis (including FDR calculation with SPLOSH)

source_name: L. monocytogenes S2542, 400 MPa, 5 min (replicate #2)

label_protocol: Conversion of RNA to cDNA and Cy5 postlabelling was performed using the SuperScript Indirect cDNA Labeling System (protocol Version D; Cat. L1014-01).

growth_protocol:
Medium: tryptone soy yeast extract broth
Exponential growth phase
Temperature 25 C

treatment_protocol: High pressure treatment: 400 MPa lasting 5 minutes at 25 C (temperature controlled to negate adiabatic heating). Samples then immediately frozen in liquid nitrogen following treatment. Samples were stored at -70 C until processed.

tag: Strain serotype

source_name: L. monocytogenes S2542, atmospheric pressure (replicate #2)

treatment_protocol: Held at atmospheric pressure for 5 minutes at 25 C. Samples then immediately frozen in liquid nitrogen. Samples were stored at -70 C until processed.


title: Human Ntera2 cells, Kap1 WG Array, 73449_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 78225_ratio.gff


title: L. monocytogenes S2542, 400 MPa 5 min, biological replicate #3

description: Biological replicate #3 out of 3 replicates

data_processing:
All biological replicate GPR files were submitted to WebArray for analysis
http://bioinformatics.skcc.org/webarray/
Xia, X., McClelland, M. & Wang, Y. 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306-311
Settings used for dual-colored array analysis:
1. Background subtraction applied.
2. Spot quality index - default
3. Within array normalization - Global Loess method
4. Between array normalization - Quantile method
5. Linear Model Statistical Analysis (including FDR calculation with SPLOSH)

growth_protocol:
Medium: tryptone soy yeast extract broth (Oxoid)
Exponential growth phase
Temperature 25 C

source_name: L. monocytogenes S2542, atmospheric pressure, biological replicate #3

treatment_protocol: Held at atmospheric pressure for 5 minutes at 25 C. Samples then immediately frozen in liquid nitrogen following treatment. Samples were stored at -70 C until processed.


title: Human Ntera2 cells, Kap1 WG Array, 77217_ratio.gff


title: Luc RNAi biological rep3

tag: Luc shRNA (targeting Firefly luciferase transcript) transfected E14 mouse embryonic stem cells


title: Human Ntera2 cells, Kap1 WG Array, 82958_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 72220_ratio.gff_GPL5212


title: Luc RNAi biological rep2


title: Jmjd1a RNAi biological rep2


title: Vector_transduced_rep2

status: Public on Sep 28 2007

first: Paul

last: Kellam

state: London

address: 46 Cleveland Street

department: Infection

institute: UCL

description: Biological replicate 1 of 3

hyb_protocol: The array slides were post-processed and hybridized with the Cy5/Cy3 mix under coverslips in array hybridization chamber (Ambion) at 65oC for 20h

scan_protocol: Scanned using an Axon GenePix 4000B and GenePix and GenePix Pro 4.0.1.23 software

data_processing: Briefly, data were extracted from microarray image files using GENEPIX PRO 4.0 software (Axon Instruments).  The signal to noise ratio (SNR) for individual spots was calculated by dividing the spot signal by the local background.  The log2 median of ratios (Cy5/Cy3) were filtered to remove all flagged data and spots with SNR<2 in both the Cy3 and Cy5 channel.  The median expression ratio from the quadruplicate spots of each array probe was used for subsequent analysis.  The expression ratios generated from each array were assembled and filtered for genes present in all the arrays.  The filtered data were median centered for both genes and arrays in Cluster (12) to normalize both the host and viral genes.

source_name: Total RNA from vector control transduced JSC1 PEL cells repeat 2 labelled with Cy5

label_protocol: Total RNA (25µg) was primed using anchored oligo(dT) and a pool of KSHV gene specific 3' primers (0.2 µmol), and reverse transcribed into Cy5-dCTP labelled cDNA using the CyScribe First Strand cDNA labelling kit (GE Healthcare) according to the manufacturer's protocol.  Following cDNA labelling, residual RNA was denatured, and unincorporated nucleotides were removed by filtering through Microcon YM-30 columns (Millipore).  Cy5-labelled cDNA was mixed 1:1 with Cy3-labelled cDNA synthesized from a custom-made reference RNA (batched mixture of TPA-induced JSC-1 and HeLa total RNA)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: PEL cell line JSC1

source_name: Common reference RNA labelled with Cy3

tag: to be added


title: Vector_transduced_rep3

description: Biological replicate 1 of 3

source_name: Total RNA from vector control transduced JSC1 PEL cells repeat 3 labelled with Cy5


title: L. monocytogenes S2542 400 MPa 5 min treatment, biological replicate #1

description: Biological replicate #1 out of 3 replicates.

source_name: L. monocytogenes strain S2542, 400 MPa treated, 5 min., biological replicate #1

source_name: L. monocytogenes strain S2542, atmospheric pressure, biological replicate 31

extract_protocol: Cells underwent a 2-3 hour (25°C) enzymatic treatment in TE buffer (10 mM Tris HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg ml-1 lysozyme and 10 mg ml-1 proteinase K. Cells were fully lysed by bead beating using 0.1 mm zirconium-silica sand in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1% -mercaptoethanol. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at -80°C. RNA quality was assessed with electrophoresis using a RNA bioanalyser 2100 (Agilent Technologies) with gels stained with picogreen and scanned with a laser. Electrophoretograms were assessed for intact 16S and 23S rRNA bands before progression to microarray hybridization.

treatment_protocol: Maintained at atmospheric pressure 5 min. at 25 C. Samples then immediately frozen in liquid nitrogen following treatment. Samples were stored at -70 C until processed.


title: Human Ntera2 cells, Kap1 WG Array, 83167_ratio.gff


title: XBP-1u_transduced_rep1

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1u transduced JSC1 PEL cells repeat 1 labelled with Cy5


title: Vector_transduced_rep1

description: Biological replicate 1 of 3

source_name: Total RNA from vector control transduced JSC1 PEL cells repeat 1 labelled with Cy5


title: Untreated_rep2

description: Biological replicate 1 of 3

source_name: Total RNA untreated control JSC1 PEL cells repeat 2 labelled with Cy5


title: Luc RNAi biological rep1

source_name: E14 mouse embryonic stem cells


title: TPA_induced_rep3

description: Biological replicate 1 of 3

source_name: Total RNA from TPA induced JSC1 PEL cells repeat 3 labelled with Cy5


title: TPA_induced_rep2

description: Biological replicate 1 of 3

source_name: Total RNA from TPA induced JSC1 PEL cells repeat 2 labelled with Cy5


title: Untreated_rep1

description: Biological replicate 1 of 3

source_name: Total RNA untreated control JSC1 PEL cells repeat 1 labelled with Cy5


title: XBP-1u_transduced_rep2

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1u transduced JSC1 PEL cells repeat 2 labelled with Cy5


title: Human Ntera2 cells, Kap1 WG Array, 71054_ratio.gff

source_name: Ntera2 cells


title: Human Ntera2 cells, Kap1 WG Array, 71049_ratio.gff


title: XBP-1u_transduced_rep3

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1u transduced JSC1 PEL cells repeat 3 labelled with Cy5


title: XBP-1s_transduced_rep2

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1s transduced JSC1 PEL cells repeat 2 labelled with Cy5


title: XBP-1s_transduced_rep1

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1s transduced JSC1 PEL cells repeat 1 labelled with Cy5


title: TPA_induced_rep1

description: Biological replicate 1 of 3

source_name: Total RNA from TPA induced JSC1 PEL cells repeat 1 labelled with Cy5


title: Jmjd1a RNAi biological rep1


title: XBP-1s_transduced_rep3

description: Biological replicate 1 of 3

source_name: Total RNA from XBP1s transduced JSC1 PEL cells repeat 3 labelled with Cy5

source_name: Common reference RNA labelled with Cy3


title: Human Ntera2 cells, Kap1 WG Array, 73446_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 76890_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 83329_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 89691_ratio.gff


title: Human Ntera2 cells, Kap1 WG Array, 71010_ratio.gff


title: Untreated_rep3

description: Biological replicate 1 of 3

source_name: Total RNA untreated control JSC1 PEL cells repeat 3 labelled with Cy5


title: Human Ntera2 cells, Kap1 WG Array, 71321_ratio.gff