title: Breed = Occidental, Day 30 Fetus, PG2

status: Public on Feb 06 2009

city: Raleigh

first: Nicholas

middle: Eldon

last: Hardison

state: NC

address: 4700 Hillsborough St., Room 318A

institute: North Carolina State University

description: parthenote

hyb_protocol: The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 min, incubated at 45°C for 5 min and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hr in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in a GeneChip® Scanner 3000.

data_processing: Expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.

label: biotin-cRNA, streptavidin-phycoerythrin

source_name: placenta

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

extract_protocol: The RNA was extracted using RNAqueous Kit (Ambion) as per the instructions of the manufacturer. Briefly, media was removed from the plates and cells were lysed in 1 ml lysis buffer. To this was added 1 ml of 64% alcohol. The contents were mixed and passed through the column. The RNA bound to the column was washed once with wash solution 1 and twice with wash solution 2/3. Finally RNA was eluted in 40 ul of hot elution buffer. RNA was quantified by spectrophotometry and quality verified by running 5 ug of RNA on 1% agarose gel. The resulting RNA was used for microarray analyses.

tag: Breed = Occidental, Day 30 Fetus


title: Breed = Occidental, Day 30 Fetus, PC3

type: RNA

country: USA

description: control

molecule: total RNA

organism: Sus scrofa


title: Breed = Occidental, Day 30 Fetus, PG1

description: parthenote


title: Breed = Occidental, Day 30 Fetus, PC2

description: control


title: DP thymocytes 1

status: Public on Mar 31 2009

city: Boston

first: Young

middle: IL

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from N15TCR+/+Rag2-/- DP thymocytes

hyb_protocol: The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h.  After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.

scan_protocol: The chips were scanned in an HIP chip scanner (Affymetrix)

data_processing:
the scanned results were analyzed by dChip
cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline

label: biotin

organism: Mus musculus

source_name: CD4+CD8+ immature thymocytes

label_protocol: Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.

growth_protocol: Mice at the specific age were kept in DanaFarber Cancer Institute animal facility

extract_protocol: Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide

treatment_protocol: Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies

tag: Age

value: 5-6 weeks old


title: Breed = Occidental, Day 30 Fetus, PC1

description: control


title: Breed = Occidental, Day 30 Fetus, LC3

description: control

source_name: liver


title: Breed = Occidental, Day 30 Fetus, LG1

description: parthenote


title: Breed = Occidental, Day 30 Fetus, PG3

description: parthenote


title: Breed = Occidental, Day 30 Fetus, FG2

description: parthenote

source_name: fibroblast


title: Breed = Occidental, Day 30 Fetus, FC1

description: control


title: Breed = Occidental, Day 30 Fetus, LC2

description: control


title: Breed = Occidental, Day 30 Fetus, BC2

description: control

source_name: brain


title: Breed = Occidental, Day 30 Fetus, LG3

description: parthenote


title: Breed = Occidental, Day 30 Fetus, FC3

description: control


title: Breed = Occidental, Day 105 Fetus, 105W_C

source_name: Placenta

tag: Breed = Occidental, Day 105 Fetus


title: Breed = Occidental, Day 30 Fetus, FC2-1

description: control


title: Breed = Occidental, Day 105 Fetus, 105W_A


title: Breed = Meishan, Day 105 Fetus, 105M_C

tag: Breed = Meishan, Day 105 Fetus


title: Breed = Occidental, Day 30 Fetus, FC2-2

description: control


title: Breed = Occidental, Day 30 Fetus, BC3

description: control


title: Breed = Occidental, Day 30 Fetus, FG3

description: parthenote


title: Breed = Occidental, Day 30 Fetus, FG1

description: parthenote


title: Breed = Occidental, Day 30 Fetus, BC1

description: control


title: Breed = Occidental, Day 30 Fetus, BG2

description: parthenote


title: Breed = Occidental, Day 30 Fetus, LC1

description: control


title: Breed = Occidental, Day 30 Fetus, BG1

description: parthenote


title: Breed = Occidental, Day 30 Fetus, FC2-3

description: control


title: Breed = Occidental, Day 85 Fetus, 85W_C

tag: Breed = Occidental, Day 85 Fetus


title: Breed = Occidental, Day 105 Fetus, 105W_B


title: Breed = Meishan, Day 105 Fetus, 105M_B


title: Breed = Meishan, Day 105 Fetus, 105M_A


title: Breed = Occidental, Day 85 Fetus, 85W_B


title: Breed = Occidental, Day 85 Fetus, 85W_A


title: Breed = Occidental, Day 65 Fetus, 65W_B

tag: Breed = Occidental, Day 65 Fetus


title: Breed = Meishan, Day 85 Fetus, 85M_B

tag: Breed = Meishan, Day 85 Fetus


title: Cowpea_null_infected_9dpi_Replicate2

status: Public on Feb 01 2009

city: RIVERSIDE

first: Sayan

last: Das

state: CA

address: 900 University Avenue

department: Botany and Plant Sc.

institute: University of California-Riverside

hyb_protocol: 12 to 16 μg labeled cRNA was fragmented by metal-induced hydrolysis to 35–200 base fragments following Affymetrix protocols. Ten micrograms labeled, fragmented cRNA was then hybridized at 45°C with rotation for 16 h in an Affymetrix microarray Hybridization Oven 320 on Affymetrix soybean genome arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned on a Hewlett-Packard GeneArray scanner. cRNA synthesis and array hybridizations were  performed in the Genomics Core Facility (http://www.genomics.ucr.edu) at the University of California, Riverside.

data_processing: Expression signals were first analyzed in Microarray Suite 5.0 software (MAS 5, Affymetrix Inc.) to determine the “present” probe set list. The detection algorithm uses probe pair intensities to generate a detection p-value and assign a “present”, “marginal”, or “absent” call. Each probe pair in a probe set has a potential vote in determining whether the measured transcript is or is not “present”. The vote is described by the discrimination score (R). R is calculated for each probe pair and compared to a predefined threshold, Tau. Probe pairs with R higher than Tau vote “present” and the voting result is summarized as a p-value. The greater the number of discrimination scores (R) that are above Tau, the smaller the p-value and the more likely the given transcript is truly present in the sample. Only probe sets with a “present” call in all three replicates of at least one treatment was considered to be expressed.

label: Biotin

organism: Vigna unguiculata

source_name: Cowpea root tissue harvested at  9 days post  inoculation with root-knot nematode juveniles

label_protocol: Double-stranded complementary deoxyribonucleicacid (cDNA) was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and T7-oligo (dT) promoter primers. The BioArray High-Yield RNATranscript Labeling Kit (Enzo Diagnostics) was then usedto synthesize biotin-labeled complementary RNA (cRNA) from template cDNA by in vitro transcription.

extract_protocol: RNA from nematode infected and non-infected root tissue was isolated using RNeasy plant mini kit (QIAGEN Inc., Valencia, CA, USA) according to manufacturer’s protocol. 1 volume of Plant RNA Isolation Aid (Ambion, Austin, TX, USA) per unit mass of frozen tissue (ml/gm) was added before the tissue homogenization step for removal of common contaminants like polysaccharides and polyphenolics.  RNA was treated with RNase-Free DNase Set (QIAGEN Inc., Valencia, CA, USA) to digest any genomic DNA which might be present.  RNA was quantified using a UV-spectrophotometer. RNA quality and integrity was examined using RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA, USA) evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

tag: Cowpea genotype null-Rk root tissue


title: Breed = Occidental, Day 65 Fetus, 65W_C


title: Cowpea_null_infected_9dpi_Replicate3


title: Cowpea_null_control_9dpi_Replicate2

source_name: Cowpea root tissue harvested at 9 days post mock inoculation


title: Breed = Meishan, Day 65 Fetus, 65M_A

tag: Breed = Meishan, Day 65 Fetus


title: Cowpea_null_infected_3dpi_Replicate1

source_name: Cowpea root tissue harvested at  3 days post  inoculation with root-knot nematode juveniles


title: Cowpea_null_control_9dpi_Replicate3


title: Cowpea_null_infected_3dpi_Replicate2


title: Breed = Occidental, Day 45 Fetus, 45W_A

tag: Breed = Occidental, Day 45 Fetus


title: Cowpea_null_control_3dpi_Replicate2

source_name: Cowpea root tissue harvested at 3 days post mock inoculation


title: Cowpea_null_control_9dpi_Replicate1


title: Cowpea_null_infected_9dpi_Replicate1


title: Breed = Occidental, Day 45 Fetus, 45W_C


title: Breed = Meishan, Day 85 Fetus, 85M_A


title: Breed = Occidental, Day 45 Fetus, 45W_B


title: Breed = Meishan, Day 65 Fetus, 65M_C


title: Breed = Meishan, Day 25 Fetus, 25M_A

tag: Breed = Meishan, Day 25 Fetus


title: Cowpea_null_control_3dpi_Replicate1


title: Breed = Occidental, Day 25 Fetus, 25W_A

tag: Breed = Occidental, Day 25 Fetus


title: Breed = Meishan, Day 45 Fetus, 45M_B

tag: Breed = Meishan, Day 45 Fetus


title: Breed = Occidental, Day 25 Fetus, 25W_C


title: Breed = Meishan, Day 45 Fetus, 45M_C


title: Breed = Occidental, Day 65 Fetus, 65W_A


title: Breed = Meishan, Day 65 Fetus, 65M_B


title: Breed = Meishan, Day 45 Fetus, 45M_A


title: Breed = Meishan, Day 85 Fetus, 85M_C


title: Breed = Occidental, Day 25 Fetus, 25W_B


title: Cowpea_CB46_infected_9dpi_Replicate2

tag: Cowpea variety CB46 root tissue


title: Breed = Meishan, Day 25 Fetus, 25M_B


title: Breed = Meishan, Day 25 Fetus, 25M_C


title: Cowpea_CB46_infected_3dpi_Replicate1


title: Cowpea_CB46_control_9dpi_Replicate3


title: Cowpea_CB46_infected_9dpi_Replicate1


title: liver; KO; 4051964005_E

city: ST Lucia

first: Johanna

last: Barclay

state: Queensland

address: Building 80, University of Queensland

country: Australia

institute: Institute for Molecular Bioscience

description: Growth hormone receptor was truncated at amino acid 569, amino acid 391, mutated within the Box1 region, or removed altogether (KO) and transgenic mice were created.  At 4 months of age male mice were starved overnight and sacrificed.

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: The raw data were uploaded into GeneSpring GX for analysis

source_name: KO

label_protocol: Illumina protocol

extract_protocol:
3ug of total RNA was extracted from frozen tissue using QIAGEN Rneasy mini kit.  This was submitted to the SRC Microarray Facility at the Institute for Molecular Bioscience at the University of Queensland for processing using Illuminar technology
Illumina protocol

tag: liver

tag: C57B6J mouse

tag: overnight starve

tag: 4 month old


title: Cowpea_CB46_control_9dpi_Replicate2


title: Cowpea_CB46_control_9dpi_Replicate1


title: liver; Box1; 4051964011_C

source_name: mutated within the Box1 region


title: liver; 391; 4051964005_C

source_name: truncated at amino acid 391


title: Cowpea_CB46_control_3dpi_Replicate1

source_name: Vigna unguiculata root RNA extracted at 3 days post mock inoculation


title: liver; 391; 4051964005_A


title: liver; Box1; 4051964011_B


title: liver; 569; 4051964004_F

source_name: truncated at amino acid 569


title: liver; 569; 4051964004_D


title: liver; Wild type (WT); 4051964004_C

source_name: WT


title: liver; Box1; 4051964011_A


title: Cowpea_CB46_infected_3dpi_Replicate2


title: subcutaneous fat; KO; 4051964012_E

extract_protocol:
Illumina protocol
3ug of total RNA was extracted from frozen tissue using QIAGEN Rneasy mini kit.  This was submitted to the SRC Microarray Facility at the Institute for Molecular Bioscience at the University of Queensland for processing using Illuminar technology

tag: subcutaneous fat


title: subcutaneous fat; 391; 4051964012_D


title: subcutaneous fat; Box1; 4051964011_F


title: liver; KO; 4051964005_F


title: liver; 391; 4051964005_B


title: subcutaneous fat; Box1; 4051964011_D


title: liver; 569; 4051964004_E


title: subcutaneous fat; 391; 4051964012_A


title: liver; Wild type (WT); 4051964004_B


title: subcutaneous fat; KO; 4051964012_C


title: liver; Wild type (WT); 4051964004_A


title: subcutaneous fat; Box1; 4051964011_E


title: subcutaneous fat; 569; 4051964006_D

source_name: truncated at amino acid 569,


title: subcutaneous fat; 569; 4051964006_F


title: subcutaneous fat; KO; 4051964012_F


title: subcutaneous fat; Wild type (WT); 4051964006_A


title: subcutaneous fat; 569; 4051964006_E


title: Slow-dried vs. hydrated gametophyte polysomal RNA fraction (slide 85)

status: Public on Jan 31 2009

city: Lubbock

first: Paxton

last: Payton

state: TX

address: 3810 4th Street

institute: USDA-ARS

description: The controls used were cDNAs for that encode four separate ribosomal proteins L17, S14, S16, and S3 from T. ruralis. The transcript levels for all four genes are unaffected by the desiccation treatments (Wood et al., 2000, Zeng and Wood 2000).

hyb_protocol: Target cDNAs were hybridized at 60C for 12 hours in a water bath. Slides were washed 15 minutes at 60C in the dark in 2X SSC with 0.1% SDS, 15 minutes at room temperature in 2XSSC with 0.05% SDS, and 10 minutes at room temperature in 2X SSC. Slides were rinsed briefly in 100% ethanol and dried by centrifugation.

scan_protocol: Slides were scanned using an Axon4000B array scanner. Image analysis and spot quantification were performed with Imagen 4.2 software.

data_processing: Image analysis was performed with Imagene 4.2 (Biodiscovery, Inc). Selection criteria for "good" spots was as follows: 1) signal strength-processed signal (minus background) < 3 x standard deviation of the mean local background 2) signal uniformity-pixel to pixel signal variation < 20% 3) replicate uniformity-mean processed signal (minus background) must have a coefficient of variance < 0.2 4) replicate mean signal strength-one channel must have processed signal > 1.5% of the quantifiable maximum signal. Data analysis was performed using GeneSpring 5.1 (Silicon Genetics, Inc.). Signal was normalized to the 50th percentile of the positive control values.

organism: Syntrichia ruralis

source_name: polysomal RNA fraction from rapid-dried rehydrated gametophyte

label_protocol: Cy3 and Cy5 labeled probes for hybridization were made from 300-450ng of poly (A)+ mRNA using the 3DNA Submicro EX Expression Array Detection Kit (Genisphere, Hatfield, PA, USA) as described by the manufacturer. Hybridizations were performed at 60ºC in hybridization chambers (2551, Corning, Corning, NY, USA) under water using the 2-step hybridization protocol described by the manufacture.

growth_protocol: T. ruralis ([Hedw.] Gaertn, Meyer and Scherb) gametophytes were collected and stored dry at room temperature. For experiments, gametophyte tissue was hydrated for 48h as described previously (Oliver, 1991; Scott and Oliver, 1994) to ensure recovery of the tissue to full activity from its exposure to drying environments in the field.

extract_protocol: Total RNA was isolated using a series of phenol extractions as described by Lane and Tumaitis-Kennedy (1981). The final nucleic acid pellet obtained by this procedure was resuspended in 5ml of 1 X TE buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA), 0.73g of NaCl was added, and the sample was placed at 4ºC overnight to precipitate RNA. This NaCl precipitation was repeated again prior to resuspension in 1 X TE for analysis or water for Poly A RNA fractionation.

treatment_protocol: Rapid-dried moss was prepared by placing fresh gametophyte on filter paper over activated silica gel in a petri dish as described previously (Bewley and Thorpe, 1974).  The rehydrated state was obtained by immediately flash freezing in liquid nitrogen following 2h of rehydration.  Samples were flash frozen in liquid nitrogen.

tag: T. ruralis ([Hedw.] Gaertn, Meyer and Scherb) rapid-dried rehydrated gametophytes

source_name: polysomal RNA fraction from hydrated gametophyte

treatment_protocol: Gametophyte tissue was hydrated for 48h as described previously (Oliver, 1991; Scott and Oliver, 1994) to ensure recovery of the tissue to full activity from its exposure to drying environments in the field and flash frozen in liquid nitrogen.

tag: T. ruralis ([Hedw.] Gaertn, Meyer and Scherb) hydrated gametophytes


title: Slow-dried vs. hydrated gametophyte polysomal RNA fraction (slide 93)

source_name: polysomal RNA fraction from slow-dried gametophyte

treatment_protocol: Slow-dried moss was prepared by placing fresh gametophytes of known weights on a nylon mesh in a closed chamber over a stirred saturated solution of sodium nitrite at 20˚C (RH 66%) for 24 h. Using this regime the air-dried weight (ca. 20% of original fresh weight) was obtained within 6h (Oliver, 1991). Samples were flash frozen in liquid nitrogen.

tag: T. ruralis ([Hedw.] Gaertn, Meyer and Scherb) slow-dried gametophytes


title: subcutaneous fat; 391; 4051964012_B


title: Rapid-dried rehydrated vs. hydrated gametophyte polysomal RNA fraction (slide 73)


title: subcutaneous fat; Wild type (WT); 4051964006_C


title: Rapid-dried rehydrated vs. hydrated gametophyte total RNA fraction (slide 2)

source_name: total RNA fraction from rapid-dried rehydrated gametophyte

extract_protocol: Total RNA was isolated using a series of phenol extractions as described by Lane and Tumaitis-Kennedy (1981).  The final nucleic acid pellet obtained by this procedure was resuspended in 5ml of 1 X TE buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA), 0.73g of NaCl was added, and the sample was placed at 4ºC overnight to precipitate RNA. This NaCl precipitation was repeated again prior to resuspension in 1 X TE for analysis or water for Poly A RNA fractionation.

source_name: total RNA fraction from hydrated gametophyte


title: Cowpea_CB46_infected_9dpi_Replicate3


title: Slow-dried vs. hydrated gametophyte polysomal RNA fraction (slide 105)


title: Rapid-dried Rehydrated vs. hydrated gametophyte total RNA fraction (slide 3)


title: Cowpea_CB46_control_3dpi_Replicate2


title: Slow-dried vs. hydrated gametophyte total RNA fraction (slide 5)

source_name: total RNA fraction from slow-dried gametophyte


title: Favorable Histology Wilms Tumor_WT01-269

status: Public on Jan 30 2009

city: Chicago

first: Elizabeth

last: Perlman

state: IL

address: 2373 North Lincoln Avenue Room A.204

department: Department of Pathology and Laboratory Medicine

institute: Children's Memorial Research Center

hyb_protocol: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols.

scan_protocol: Washing, staining, and scanning - The hybridized microarrays were washed using pre-programmed Affymetrix protocols and individual reagents purchased from Sigma. The arrays were stained with streptavidin-phycoerythrin (S(SAPE, Molecular Probes, Eugene, OR) and the signal amplified using an antibody solution containing 0.1 mg/ml normal goat IgG (Sigma), and 3 µg/ml biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA). Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols. The arrays were scanned in an HP GeneArray Scanner at the excitation wavelength of 488 nm. The amount of light emitted at 570 nm is proportional to the bound target at each location on the microarray.

data_processing: Positional-dependent-nearest-neighbor model (PDNN) software was used to translate the scanned images into expression analysis files and to normalize the data across all arrays (http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/).  Genes with maximum expression less than a log scale of 6 across all tumors and Affymetrix control genes were excluded, resulting in 20,931 probe sets for analysis.

organism: Homo sapiens

source_name: Pretreatment tumor tissue

label_protocol:
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Specifically, cDNA synthesis wasperformed by SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen). The manufacturer’s protocol was modified by the use of an HPLC- purified T7-(dT)24 primer (GenSet Oligos, Proligo, Boulder, CO) and incubation at 42C. The double-stranded cDNA product was purified by phenol/chloroform extraction using Phase Lock Gels (Eppendorf Scientific, Westbury, NY) followed by ethanol precipitation. The resulting pellet was washed twice in 80% ethanol, dried, and re-suspended in 22 µl of RNAse-free water. Biotin-labeled cRNA synthesis –22 µl of purified cDNA underwent an in vitro transcription (IVT) using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY).  The resulting biotin-labeled cRNA was purified using RNeasy Mini Kit (Qiagen) and quantified using a GeneQuant DNA/RNA calculator (Amersham Biosciences).  Labeled cRNA (17 µg) was fragmented according to Affymetrix protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: RNA isolation - Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).   The RNA was purified by RNeasy Mini Kit (Qiagen, Valencia, CA) and the concentration determined by optical density as measured by a GeneQuant DNA/RNA calculator (Amersham Biosciences, Piscataway, NJ).  Samples with A260/A280 of less than 1.8 were excluded. The quality of the RNA was further assessed by electrophoresis on a 1% agarose gel and samples rejected if significant RNA degradation was observed.

tag: Relapse


title: Favorable Histology Wilms Tumor_WT01-286


title: subcutaneous fat; Wild type (WT); 4051964006_B


title: Favorable Histology Wilms Tumor_WT01-260


title: Favorable Histology Wilms Tumor_WT01-258

tag: Non-relapse


title: Favorable Histology Wilms Tumor_WT01-256


title: Favorable Histology Wilms Tumor_WT01-291


title: Favorable Histology Wilms Tumor_WT01-255


title: Favorable Histology Wilms Tumor_WT01-290


title: Favorable Histology Wilms Tumor_WT01-254


title: Favorable Histology Wilms Tumor_WT01-275


title: Slow-dried vs. hydrated gametophyte total RNA fraction (slide 6)


title: Favorable Histology Wilms Tumor_WT01-270


title: Favorable Histology Wilms Tumor_WT01-242


title: Favorable Histology Wilms Tumor_WT01-276


title: Favorable Histology Wilms Tumor_WT01-250


title: Favorable Histology Wilms Tumor_WT01-246


title: Favorable Histology Wilms Tumor_WT01-216


title: Favorable Histology Wilms Tumor_WT01-249


title: Favorable Histology Wilms Tumor_WT01-218


title: Favorable Histology Wilms Tumor_WT01-224


title: Favorable Histology Wilms Tumor_WT01-233


title: Favorable Histology Wilms Tumor_WT01-235


title: Favorable Histology Wilms Tumor_WT01-211


title: Favorable Histology Wilms Tumor_WT01-206


title: liver; KO; 4051964005_D


title: Favorable Histology Wilms Tumor_WT01-194


title: Favorable Histology Wilms Tumor_WT01-189


title: Favorable Histology Wilms Tumor_WT01-181


title: Favorable Histology Wilms Tumor_WT01-141


title: Favorable Histology Wilms Tumor_WT01-177


title: Favorable Histology Wilms Tumor_WT01-138


title: Favorable Histology Wilms Tumor_WT01-131


title: Favorable Histology Wilms Tumor_WT01-165


title: Favorable Histology Wilms Tumor_WT01-114


title: Favorable Histology Wilms Tumor_WT01-171


title: Favorable Histology Wilms Tumor_WT01-122


title: Favorable Histology Wilms Tumor_WT01-125


title: Favorable Histology Wilms Tumor_WT01-142


title: Favorable Histology Wilms Tumor_WT01-164


title: Favorable Histology Wilms Tumor_WT01-119


title: Favorable Histology Wilms Tumor_WT01-117


title: Favorable Histology Wilms Tumor_WT01-107


title: Favorable Histology Wilms Tumor_WT01-137


title: Favorable Histology Wilms Tumor_WT01-118


title: Favorable Histology Wilms Tumor_WT01-095


title: Favorable Histology Wilms Tumor_WT01-092


title: Favorable Histology Wilms Tumor_WT01-111


title: Favorable Histology Wilms Tumor_WT01-077


title: Favorable Histology Wilms Tumor_WT01-130


title: Favorable Histology Wilms Tumor_WT01-099


title: Favorable Histology Wilms Tumor_WT01-097


title: Favorable Histology Wilms Tumor_WT01-129


title: Favorable Histology Wilms Tumor_WT01-295


title: Favorable Histology Wilms Tumor_WT01-058


title: Favorable Histology Wilms Tumor_WT01-053


title: Favorable Histology Wilms Tumor_WT01-049


title: Favorable Histology Wilms Tumor_WT01-022


title: Favorable Histology Wilms Tumor_WT01-006


title: Favorable Histology Wilms Tumor_WT01-046


title: Favorable Histology Wilms Tumor_WT01-045


title: Favorable Histology Wilms Tumor_WT01-021


title: Favorable Histology Wilms Tumor_WT00-252


title: Favorable Histology Wilms Tumor_WT01-002


title: Favorable Histology Wilms Tumor_WT01-062


title: Favorable Histology Wilms Tumor_WT00-291


title: Favorable Histology Wilms Tumor_WT01-005


title: Favorable Histology Wilms Tumor_WT01-027


title: Favorable Histology Wilms Tumor_WT00-254


title: Favorable Histology Wilms Tumor_WT00-262


title: Favorable Histology Wilms Tumor_WT01-031


title: Favorable Histology Wilms Tumor_WT00-277


title: Favorable Histology Wilms Tumor_WT01-015


title: Favorable Histology Wilms Tumor_WT00-266


title: Favorable Histology Wilms Tumor_WT01-016


title: Favorable Histology Wilms Tumor_WT01-074


title: Favorable Histology Wilms Tumor_WT00-268


title: Favorable Histology Wilms Tumor_WT00-248


title: Favorable Histology Wilms Tumor_WT00-267


title: Favorable Histology Wilms Tumor_WT00-250


title: Favorable Histology Wilms Tumor_WT00-283


title: Favorable Histology Wilms Tumor_WT00-245


title: Favorable Histology Wilms Tumor_WT00-294


title: Favorable Histology Wilms Tumor_WT00-244


title: Favorable Histology Wilms Tumor_WT00-234


title: Favorable Histology Wilms Tumor_WT00-249


title: Favorable Histology Wilms Tumor_WT00-237


title: Favorable Histology Wilms Tumor_WT00-231


title: Favorable Histology Wilms Tumor_WT00-224


title: Favorable Histology Wilms Tumor_WT00-229


title: Favorable Histology Wilms Tumor_WT00-223


title: Favorable Histology Wilms Tumor_WT00-209


title: Favorable Histology Wilms Tumor_WT00-212


title: Favorable Histology Wilms Tumor_WT00-219


title: Favorable Histology Wilms Tumor_WT00-227


title: Favorable Histology Wilms Tumor_WT00-225


title: Favorable Histology Wilms Tumor_WT00-189


title: Favorable Histology Wilms Tumor_WT00-206


title: Favorable Histology Wilms Tumor_WT00-213


title: Favorable Histology Wilms Tumor_WT00-183


title: Favorable Histology Wilms Tumor_WT00-204


title: Favorable Histology Wilms Tumor_WT00-184


title: Favorable Histology Wilms Tumor_WT00-198


title: Favorable Histology Wilms Tumor_WT00-144


title: Favorable Histology Wilms Tumor_WT00-187


title: Favorable Histology Wilms Tumor_WT00-145


title: Favorable Histology Wilms Tumor_WT00-123


title: Favorable Histology Wilms Tumor_WT00-140


title: Favorable Histology Wilms Tumor_WT00-142


title: Favorable Histology Wilms Tumor_WT00-124


title: Favorable Histology Wilms Tumor_WT00-192


title: Favorable Histology Wilms Tumor_WT00-122


title: Favorable Histology Wilms Tumor_WT01-020


title: Favorable Histology Wilms Tumor_WT00-141


title: Favorable Histology Wilms Tumor_WT00-136


title: Favorable Histology Wilms Tumor_WT00-108


title: Favorable Histology Wilms Tumor_WT00-099


title: Favorable Histology Wilms Tumor_WT00-103


title: Favorable Histology Wilms Tumor_WT00-104


title: Favorable Histology Wilms Tumor_WT00-120


title: Favorable Histology Wilms Tumor_WT00-115


title: Favorable Histology Wilms Tumor_WT00-069


title: Favorable Histology Wilms Tumor_WT00-105


title: Favorable Histology Wilms Tumor_WT00-089


title: Favorable Histology Wilms Tumor_WT00-088


title: Favorable Histology Wilms Tumor_WT00-170


title: Favorable Histology Wilms Tumor_WT00-092


title: Favorable Histology Wilms Tumor_WT00-112


title: Favorable Histology Wilms Tumor_WT00-076


title: Favorable Histology Wilms Tumor_WT00-073


title: Favorable Histology Wilms Tumor_WT00-068


title: Favorable Histology Wilms Tumor_WT00-062


title: Favorable Histology Wilms Tumor_WT00-063


title: Favorable Histology Wilms Tumor_WT00-121


title: Favorable Histology Wilms Tumor_WT00-051


title: Favorable Histology Wilms Tumor_WT00-047


title: Favorable Histology Wilms Tumor_WT00-040


title: Favorable Histology Wilms Tumor_WT00-064


title: Favorable Histology Wilms Tumor_WT00-044


title: Favorable Histology Wilms Tumor_WT00-039


title: Favorable Histology Wilms Tumor_WT00-036


title: Favorable Histology Wilms Tumor_WT00-049


title: Favorable Histology Wilms Tumor_WT00-022


title: Favorable Histology Wilms Tumor_WT00-009


title: Favorable Histology Wilms Tumor_WT00-032


title: Favorable Histology Wilms Tumor_WT00-001


title: Wheat var. Kennedy_Fp inoculated_rep3

status: Public on Jan 01 2009

city: St Lucia

first: Brendan

last: Kidd

state: QLD

address: 306 Carmody Road

department: Plant Industry

institute: CSIRO

hyb_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.

data_processing: GeneSpring 7.3 (Agilent Technologies) was used for data analysis. Each CHP file was imported into GeneSpring running the Wheat GeneChip Genome and then associated with its matching CEL file. A final normalised ratio was obtained by applying an additional “per probe set” normalisation. This was achieved by dividing the raw value for each probe set by the median value for that probe set in the whole experiment. This centred the data near a value of 1 and ensured ease of identification of differentially expressed probe sets. Statistical analysis was performed to identify differentially expressed genes in Fp inoculated samples compared to mock inoculated samples using ANOVA with a p<0.05 across all replicates. Induction or repression of differentially expressed genes was determined by dividing each replicate raw signal value from Fp inoculated tissue by the average of the raw signal from the mock inoculated tissue. Genes were classes as induced or repressed if their change in expression was greater than 1.5 fold.

organism: Triticum aestivum

source_name: Crown tissue of Wheat variety Kennedy, F. pseudograminearum inoculated, 24hr

growth_protocol: Plants were grown in a controlled environment growth room under 500umol/m/s PAR with a 7hr photoperiod. Day/night conditions were 25C/15C and 65/95% relative humidity, respectively. Plants were grown in small pots, approximately 5cm, filled with sterile soil containing two seeds sown below the surface. Plants were watered every second day.

extract_protocol: Total RNA was isolated using the caesium chloride extraction method described by Chirgwin et al., 1979. RNA extraction was followed by a DNase treatment using a RNase-free DNase kit (QIAGEN) and column purified using a MiniElute kit (QIAGEN) according to manufacturer's instructions. Samples were dissolved in nuclease free water and sent to the Australian Genome Research Facility for cDNA synthesis, labelling, hybridisation to the Affymetrix GeneChip Wheat Genome Array, washing and scanning.

treatment_protocol: Two week old wheat plants were inoculated by placing the pots horizontally and applying 10uL of a 10^6 spores/ml spore suspension of F. pseudograminearum or water to the leaf sheaf approximately 2cm from the soil surface. The plants were kept horizontal at saturating humidity using perspex hoods for 24hrs before the crown tissue was harvested.

tag: Fusarium pseudograminearum isolate CS3096 or water was used to inoculate the crown tissue of the wheat (Triticum aestivum) cultivar Kennedy. RNA was extracted from 2cm of crown tissue, 24hr after mock or fungal inoculation.


title: microdevice 1544923026_G

city: gaithersburg

first: audrey

middle: n

last: player

state: MD

address: 8717 grovemont circle

department: microarray facility

institute: national cancer institute

description:
microdevice; Illumina 1544923026_G
L device 2.27 repeat

hyb_protocol: Hybridization, washing and staining was performed as documented in 11162460_Illumina GEX-BeadChip_System_Manual _Rev_C

scan_protocol: Scanning was performed as suggested in 11162460_Illumina GEX-BeadChip_System_Manual _Rev_C

data_processing: The archived Human RefSeq-8.xml manifest file was used for data extraction (http://www.switchtoi.com/annotationprevfiles.ilmn ; Illumina's BeadStudio). The raw data signal intensities (between samples) were directly compared to determine transcripts detected under the various experimental conditions.

label: biotin UTP

source_name: 0.053ng microdevice

label_protocol: Biotinylated aRNA was generated using the Ambion / Applied Biosystems Message Amp II aRNA Amplification Kit (1751 and 1791) per manufacturer's suggestion

extract_protocol: not performed; cell line Jurkat T-cell total RNA purchased from Stratagene cat# 54107

tag: cell line

value: Jurkat T-cell


title: Wheat var. Kennedy_control_rep3

scan_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.

source_name: Crown tissue of Wheat variety Kennedy, mock inoculated, 24hr


title: benchtop 1544923026_B

description:
benchtop; Illumina 1544923026_B
M bench 2.28 repeat

source_name: 1.0ng benchtop


title: microdevice 1544923026_C

description:
microdevice; Illumina 1544923026_C
M device 2.28 repeat

source_name: 0.026ng microdevice


title: benchtop 1544923026_A

description:
benchtop; Illumina 1544923026_A
L bench 2.28 repeat

source_name: 0.100ng benchtop


title: benchtop 1544923026_F

description:
benchtop; Illumina 1544923026_F
M bench 2.27 repeat


title: Wheat var. Kennedy_Fp inoculated_rep2

label_protocol: Refer to the AGRF website http://www.agrf.org.au for details of the protocol used.


title: microdevice 1544923003_C

description:
microdevice; Illumina 1544923003_C
L device 2.18 repeat

source_name: 0.040ng microdevice


title: Wheat var. Kennedy_Fp inoculated_rep1


title: microdevice 1544923026_D

description:
microdevice; Illumina 1544923026_D
L device 2.28 repeat

source_name: 0.360ng microdevice


title: microdevice 1544923026_H

description:
microdevice; Illumina 1544923026_H
M device 2.27 repeat

source_name: 0.330ng microdevice


title: Wheat var. Kennedy_control_rep2


title: benchtop 1544923003_F

description:
benchtop; Illumina 1544923003_F
N bench 2.20 repeat

source_name: 10ng benchtop


title: microdevice 1544923003_H

description:
microdevice; Illumina 1544923003_H
N device 2.20 repea

source_name: 2.60ng microdevice


title: Wheat var. Kennedy_control_rep1


title: blank 1544923003_E

description:
NA; Illumina 1544923003_E
blank 2

source_name: 0ng benchtop


title: benchtop 1544923097_A

description:
benchtop; Illumina 1544923097_A
L bench 2.28.08


title: microdevice 1544923097_D

description:
microdevice; Illumina 1544923097_D
L device 2.28.08


title: microdevice 1544923003_G

description:
microdevice; Illumina 1544923003_G
M device 2.20 repeat

source_name: 0.260ng microdevice


title: microdevice 1544923097_H

description:
microdevice; Illumina 1544923097_H
M device 2.27.08


title: blank 1544923003_A

description:
NA; Illumina 1544923003_A
Blank 1


title: benchtop 1544923097_E

description:
benchtop; Illumina 1544923097_E
L bench 2.27.08

source_name: 0.10ng benchtop


title: microdevice 154492087_H

description:
microdevice; Illumina 154492087_H
N device 2.20.08


title: Favorable Histology Wilms Tumor_WT00-029


title: micrdodevice 1544923097_G

description:
micrdodevice; Illumina 1544923097_G
L device 2.27.08


title: benchtop 1544923097_F

description:
benchtop; Illumina 1544923097_F
M bench 2.27.08


title: microdevice 1544923097_C

description:
microdevice; Illumina 1544923097_C
M device 2.28.08


title: microdevice 154492087_C

description:
microdevice; Illumina 154492087_C
L device 2.18.08

source_name: 0.078ng microdevice


title: benchtop 154492087_A

description:
benchtop; Illumina 154492087_A
L bench 2.18.08


title: benchtop 154492087_E

description:
benchtop; Illumina 154492087_E
M bench 2.20.08


title: microdevice 154492087_B

description:
microdevice; Illumina 154492087_B
L2 device 2.26.08


title: microdevice 154492087_G

description:
microdevice; Illumina 154492087_G
M device 2.20.08

source_name: 0.50ng microdevice


title: benchtop 1544923078_G

description:
benchtop; Illumina 1544923078_G
B sample 2


title: microdevice 1544923003_B

description:
microdevice; Illumina 1544923003_B
L2 device 2.26 repeat

source_name: 0.020ng microdevice


title: benchtop 1544923078_H

description:
benchtop; Illumina 1544923078_H
B sample 3


title: benchtop 1544923097_B

description:
benchtop; Illumina 1544923097_B
M bench 2.28.08


title: microdevice 1544923078_D

description:
microdevice; Illumina 1544923078_D
L sample 6

source_name: 3.8ng microdevice


title: microdevice 1544923078_C

description:
microdevice; Illumina 1544923078_C
L sample 5

source_name: 0.250ng microdevice


title: benchtop 154492087_F

description:
benchtop; Illumina 154492087_F
N bench 2.20.08


title: microdevice 1544923078_F

description:
microdevice; Illumina 1544923078_F
B sample 1


title: Heps_APAP5_donor5

city: Bilthoven

first: Anne

middle: Susan

last: Kienhuis

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

hyb_protocol: For microarray hybridization, Cy5-labeled samples and Cy3-labeled samples were combined. cRNAs were fragmented at 60 degrees Celsius for 30 min with fragmentation solution followed by hybridization on Agilent 22K format 60-mer oligo microarrays (G4110B from Agilent Technologies, Palo Alto, CA) for 17h at 60 degrees Celsius with Agilent hybridization solution. Arrays were washed according to manufacturer's instruction.

scan_protocol: Microarrays were scanned using a Packard Scanarray Express confocal laser scanner (PerkinElmer, Boston, MA).

data_processing: RFlagged spots, consisting of poor quality spots and negative and positive control spots, were excluded. For each spot, median local background intensity was subtracted from the median spot intensity and spots from low expression genes (with a net intensity of < 40 in both channels), were excluded from further analysis. These background-corrected median intensities were log transformed base 2. Data were normalized using the Lowess algorithm.

source_name: primary hepatocytes, sandwich-cultured, 5 mM APAP, 24h

label_protocol: RNA samples from control hepatocyte cultures and cultures exposed to APAP were labeled with cyanine 5-CTP (Cy5). Cy5 labeled samples from one individual were hybridized against cyanine 3-CTP (Cy3) labeled RNA samples from control hepatocyte cultures of the same individual. As a result, control samples labeled with Cy5 hybridized agains Cy3 samples can be considered a self-self hybridization. Labeling was performed using Agilent's low RNA input fluorescent linear amplification kit followin manufacturer's instruction. Briefly, double-stranded cDNA was synthesized using molony murine leukemia virus-reverse transcriptase (MMLV-RT) with T7 promoter primer, starting with 1 µg of total RNA. Cyanine-labeled cRNA targets were transcribed using T7 RNA Polymerase. The amlified cRNA was purified using RNeasy mini spin columns. Synthesized cRNA products were quantified spectrophotometrically.

growth_protocol: Human hepatocytes were obtained from resection specimens of patients undergoing partial hepatectomy for colorectal metastases in an otherwise normal liver at the University Hospital Maastricht, the Netherlands. Surgery was performed as described before (Dejong and Garden, 2003) and in none of the cases hepatic inflow occlusion was applied during liver transaction. All patients provided written informed consent and the study was approved by the Medical Ethics Committee of the University Hospital Maastricht. Isolation of human hepatocytes from resection specimens was performed according to the method described by LeCluyse et al. (LeCluyse et al., 2005). Hepatocyte preparations with viability greater than 75% were included for further studies. Cell suspensions with viability below 85% were purified using a Percoll gradient, as previously described (LeClusye et al., 2005). Cells were cultured on collagen gel precoated 12-well plates at a density of 6.5 x 10-5 cells per well. Human hepatocyte sandwich cultures were essentially prepared according to the method of Beken et al. (Beken et al., 2004). After attachment for 4 h in attachment medium, dead cells were removed by washing and the upper collagen layer was applied. Thereafter, cells were kept in DMEM containing 0.1 µM DEX, 6.25 µg/ml insulin, 6.25 µg/ml transferin, and 6.25 ng/ml selenium (Hamilton et al. 2001). Cultures were incubated 37 degrees Celsius in a humidified incubator gassed with 5% CO-2 in air. Medium was changed on a daily basis during a period of 72h.

extract_protocol: After 24h exposure time, culture medium of sandwich-cultured hepatocytes was removed, Trizol was added onto the upper collagen layer and cells were collected. RNA was purified using the RNeasy MinElute kit including an additional DNA digestion step. RNA quality was determined using the Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples contained intact total RNA with a 28S/18S rRNA ratio > 1.5 and a RIN number > 8. RNA extractions of five human individuals were used for microarray analysis.

treatment_protocol: After 72h of culture, five independent human hepatocyte cultures (biological replicates) were exposed to two concentrations of APAP (5 and 10 mM) for 24h. APAP was dissolved in culture medium.

tag: Donor 5, female, Age

value: 75 years, Cell viability 94%

source_name: primary hepatocytes, sandwich-cultured, non-exposed


title: Heps_APAP10_donor4

source_name: primary hepatocytes, sandwich-cultured, 10 mM APAP, 24h

tag: Donor 4, female, Age

value: 42 years, Cell viability 86%


title: microdevice 1544923078_B

description:
microdevice; Illumina 1544923078_B
L sample 4

source_name: 6.3ng microdevice


title: Heps_APAP0_donor5


title: Heps_APAP10_donor5


title: Heps_APAP0_donor6

tag: Donor 6, male, Age

value: 68 years, Cell viability 96%


title: Heps_APAP10_donor3

tag: Donor3, male, Age

value: 73 years, Cell viability 90%


title: Heps_APAP0_donor4


title: Heps_APAP10_donor6


title: Heps_APAP5_donor6


title: Heps_APAP5_donor3


title: Heps_APAP5_donor4


title: Heps_APAP0_donor2

tag: Donor2, male, Age

value: 74 years, Cell viability 91%


title: Heps_APAP5_donor2


title: MOLM14_GFPcontrolsh_control_rep2

first: Joerg

last: Faber

address: 1 Blackfan Circle

institute: Children's Hospital Boston

description: Human t(9;11) MOLM-14 AML cells transduced with non targeting pLKO.1 lentiviral GFPshRNA control construct.

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a Affymetrix U133A 2.0 microarray chip overnight at 45°C.  The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a Genchip 3000 confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured using GeneChip operating software.

data_processing: The data were analyzed with Genepattern Suite version 3.0 (The Broad Institute, Cambridge MA) using the dCHIP (Li and Wong) algorithm.

source_name: MOLM-14, GFPcontrolshRNA, 44h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were incubated at 37 degC, 5% CO2.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit according to the manufacturers protocol.

treatment_protocol: Lentiviral transduction of 1F3- or 2A5 - HOXA9shRNA or GFPcontrol shRNA construct was performed 44h prior to RNA collection.  In detail, 1x10e5 cells  were seeded in 96-well tissue culture plates (100 μl per well) in the appropriate culture  media. Polybrene (Hexadimethrine bromide, Sigma) was added at a final concentration of  7μg/ml. After adding 150 μl lentiviral particles (titer of each lentiviral shRNA construct  adjusted to 1.6x10e6 TU/ml to achieve a MOI of 2.4 TU/cell), spinoculation was  performed at 2250 RPM for 90 minutes at 37 °C. 8 hours after infection, the media was  replaced with 100 μl of the appropriate fresh culture media.

tag: human acute myeloid leukemia, AML FAB M5a, carries internal tandem duplication of FLT3 and MLLAF9 rearrangement


title: MOLM14_2A5HOXA9sh_suppression_rep3

description: Human t(9;11) MOLM-14 AML cells transduced with pLKO.1 lentiviral shRNA construct "2A5" targeting human HOXA9.

source_name: MOLM-14, HOXA9suppression, 44h


title: Heps_APAP0_donor3


title: MOLM14_GFPcontrolsh_control_rep3


title: MOLM14_GFPcontrolsh_control_rep4


title: Heps_APAP10_donor2


title: MOLM14_GFPcontrolsh_control_rep5


title: MOLM14_GFPcontrolsh_control_rep6


title: MIRA vs Input Set 35 of 38

type: genomic

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: hybridized at Nimblegen facilities in Iceland

hyb_protocol: NimbleGen Kit

scan_protocol: NimbleGen Protocol

data_processing: NimbleGen protocol

molecule: genomic DNA

source_name: MIRA

label_protocol: NimbleGen Kit

extract_protocol: Genomic DNA was purified from B cells by standard procedures by using proteinase K digestion, phenol chloroform extraction and ethanol precipitation.

tag: MIRA enriched

source_name: Input

tag: Input genomic DNA


title: MOLM14_GFPcontrolsh_control_rep1


title: MOLM14_2A5HOXA9sh_suppression_rep1


title: MOLM14_1F3HOXA9sh_suppression_rep3

description: Human t(9;11) MOLM-14 AML cells transduced with pLKO.1 lentiviral shRNA construct "1F3" targeting human HOXA9.


title: microdevice 1544923078_A

description:
microdevice; Illumina 1544923078_A
L sample 3- exp 1


title: MOLM14_1F3HOXA9sh_suppression_rep2


title: MIRA vs Input Set 33 of 38


title: neurons_naive_13div_3

city: Pasadena

middle: M

last: Taylor

institute: Caltech

description: neurons isolated in compartmentalized microfluidic platform

hyb_protocol: 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA).  Batch normalized to axonal controls (sample 1-7).

molecule: polyA RNA

organism: Rattus norvegicus

source_name: cortical neurons, uninjured

label_protocol: The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.

growth_protocol: Neurobasal E medium supplemented with B27

extract_protocol: Cellular material from 3 microfluidic platforms were pooled for each Genechip sample.  RNA was isolated using Ambion RNAqueous®-Micro kit.  Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).

treatment_protocol: Axons from samples 8-10 were axotomized after 11 days in culture.

tag: E18 dissociated cortical and hippocampal neurons, cultured 13 days


title: MIRA vs Input Set 14 of 38


title: axons_naive_13div_7

description: axons isolated in compartmentalized microfluidic platform

source_name: cortical axons, uninjured


title: axons_regen_13div_2

source_name: cortical axons, 2 days after axotomy


title: axons_naive_13div_4


title: axons_regen_13div_1


title: axons_regen_13div_3


title: MOLM14_1F3HOXA9sh_suppression_rep1


title: MOLM14_2A5HOXA9sh_suppression_rep2


title: neurons_naive_13div_1


title: neurons_naive_13div_2


title: axons_naive_13div_5


title: axons_naive_13div_6


title: Alveolar Macrophages vs. Dendritic Cells

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

description: Trafficking of monocytes into lung tissue and their differentiation into lung resident macrophages and dendritic cells is supposed to be regulated by the expression of specific gene clusters, which promote cell-cell interaction, migration and matrix degradation and the acquisition of tissue specific cellular phenotypes. Traffic related gene clusters include chemokines, integrins, and tissue-degrading matrix metallopeptidases, for all of which members have been shown to be functionally important. A complete picture, however, of the gene clusters that are regulated during in vivo migration and differentiation of peripheral blood monocytes under non-inflammatory conditions has not been obtained yet. Currently, adaptive changes of cellular phenotypes cannot be directly assessed by cell fate mapping during the slow trafficking of mononuclear phagocytes to lung tissue under steady-state conditions. Therefore, as an alternative approach to gain a better insight into the genetic programs that drive the mononuclear phagocyte migration and differentiation processes, the transcriptomes of circulating monocytes were compared with their lung tissue mononuclear phagocyte progeny.

hyb_protocol: The labeled RNA pools were hybridized overnight at 60°C in Agilent in.situ hybridization buffer using Agilent Hybridization chambers.

scan_protocol: Slides were scanned using a GenePix 4100A Scanner (Axon Instruments, Downingtown, PA). PMT gains were adjusted to get a use the entire dynamic range of the scanner. Image analysis was performed with GenePix Pro 5.0 software.

data_processing: Data were evaluated using the R software and the limma package from BioConductor. The spot intensities were corrected for local background using the method of Edwards with an offset of 64 to stabilize the variance of low-intensity spots. The M/A data were LOESS normalized before averaging. Genes were ranked for differential expression using a moderated t-statistic.

label: Cy3, Cy5

source_name: Alveolar Macrophages

label_protocol: Labelling was performed according to the Two-Color Microarray-Based Gene Expression Analysis Protocol version 5.5 (Agilent) using an Agilent RNA Spike-In Kit, a Low RNA Input Linear Amp Kit and a Cyanine CTP2-color dye pack (Agilent Technologies, Wilmington, DE). Per reaction, 1 µg of total RNA was used. RNA was pooled using comparable amounts of total RNA (as assessed by Nanodrop analysis) from four animals.

extract_protocol: After sorting, cells were frozen at -80°C in RLT lysis buffer (Qiagen) with 1% beta-mercaptoethanol (Sigma). RNA from highly purified cell populations was isolated using an RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Quantification and purity of RNA was determined with an Agilent Bioanalyzer 2100 (Agilent Biosystems). Only those RNA preparations exceeding absorbance ratios of A260/280 nm > 1.90 and of a total amount of RNA greater than 200 ng were used for microarray experiments.

tag: wild-type C57BL/6N mice

tag: gender

value: male and female

tag: age

value: six to nine weeks

tag: cells isolated by FACS

label: Cy5, Cy3

source_name: Dendritic Cells


title: Dendritic Cells vs. Peripheral Blood Monocyctes

source_name: Peripheral Blood Monocytes


title: axons_naive_13div_2


title: axons_naive_13div_1


title: axons_naive_13div_3


title: Heps_Mod_APAP10_rat4

description: Mod_Modified culture medium

hyb_protocol: For microarray hybridization, Cy5-labeled samples and Cy3-labeled samples were combined. cRNAs were fragmented at 60 degrees Celsius for 30 min with fragmentation solution followed by hybridization on Agilent 22K format 60-mer oligo microarrays (G4130A from Agilent Technologies, Palo Alto, CA) for 17h at 60 degrees Celsius with Agilent hybridization solution. Arrays were washed according to manufacturer's instruction.

data_processing: Flagged spots, consisting of poor quality spots and negative and positive control spots, were excluded. For each spot, median local background intensity was subtracted from the median spot intensity and spots from low expression genes (with a net intensity of < 40 in both channels), were excluded from further analysis. These background-corrected median intensities were log transformed base 2. Data were normalized using the Lowess algorithm.

label_protocol: RNA samples from control hepatocyte cultures and cultures exposed to APAP were labeled with cyanine 5-CTP (Cy5). Cy5 labeled samples from one rat were hybridized against cyanine 3-CTP (Cy3) labeled RNA samples from control hepatocyte cultures of the same rat. As a result, control samples labeled with Cy5 hybridized agains Cy3 samples can be considered a self-self hybridization. Labeling was performed using Agilent's low RNA input fluorescent linear amplification kit followin manufacturer's instruction. Briefly, double-stranded cDNA was synthesized using molony murine leukemia virus-reverse transcriptase (MMLV-RT) with T7 promoter primer, starting with 1 µg of total RNA. Cyanine-labeled cRNA targets were transcribed using T7 RNA Polymerase. The amlified cRNA was purified using RNeasy mini spin columns. Synthesized cRNA products were quantified spectrophotometrically.

growth_protocol: Male Wistar rats (Crl: (WI) WU BR), 9-12 weeks of age, were obtained from Charles River GmbH, Sulzfeld, Germany. During the acclimatization period and until sacrifice, animals were housed individually in macrolon cages with wire tops and sawdust bedding at 22 degrees Celsius and 50-60% humidity. The light cycle was 12 h light and 12 h dark. Feed and tap water were available ad libitum. Animal protocols for hepatocyte isolation were approved by the institutional Animal Ethics Committee. Hepatocytes were isolated acording to a two-step collagenase perfusion technique as described by Seglen (Seglen, 1976) with minor modifications. Hepatocyte preparations with viability greater than 85% as determined by Trypan Blue exclusion were used and cultured on collagen gel precoated 6-well plates at a density of 1.3 x 10-E6 cells per well. Sandwich-cultures of rat hepatocytes were essentially prepared according to the method of Beken (Beken et al., 2004) with culture conditions as described by Kienhuis (Kienhuis et al., 2006, Kienhuis et al., 2007). After attachment for 4 h in attachment medium, dead cells were removed by washing and the upper collagen layer was applied. Thereafter, cells were kept in DMEM containing either standard culture medium (St.) consisting of DMEM supplemented with 0.5 U/ml insulin, 7 ng/ml glucagon, 7.5 µg/ml hydrocortisone hemisuccinate, and 50 µg/ml gentamycin, or modified culture medium (Mod.) consisting of standard culture medium (St.) supplemented with 1 mM phenobarbital (PB), 10 µM dexamethasone (DEX), and 5 µM β-naphthoflavone (β-NF) (Kienhuis et al., 2007). PB was added as a concentrated stock solution in PBS. DEX and β-NF were added as concentrated stock solutions in DMSO. The final DMSO concentration was equalized in all culture media (St. and Mod.) and did not exceed 0.2% (v/v). Cultures were incubated at 37 degrees Celsius in a humidified incubator gassed with 5% CO-2 in air. Medium was changed on a daily basis during a period of 72 h.

extract_protocol: After 24h exposure time, culture medium of sandwich-cultured hepatocytes was removed, Trizol was added onto the upper collagen layer and cells were collected. RNA was purified using the RNeasy MinElute kit including an additional DNA digestion step. RNA quality was determined using the Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples contained intact total RNA with a 28S/18S rRNA ratio > 1.5 and a RIN number > 8. RNA extractions of three rats cultured in two conditions (St. and Mod.) were used for microarray analysis.

treatment_protocol: After 72h of culture, three independent rat hepatocyte cultures (biological replicates) cultured in two conditions (St. and Mod.) were exposed to two concentrations of APAP (5 and 10 mM) for 24h. APAP was dissolved in culture medium.

tag: Male Wistar (Crl

value: (WI) WU BR), 9-12 weeks of age, 180-250 g


title: Heps_Mod_APAP_5_rat4

description: Mod_Modified culture medium


title: Heps_St_APAP_5_rat4

description: St_Standard culture medium


title: Heps_St_APAP10_rat4

description: St_Standard culture medium


title: Alveolar Macrophages vs. Peripheral Blood Monocyctes


title: Heps_Mod_APAP0_rat4

description: Mod_Modified culture medium


title: Heps_Mod_APAP0_rat3

description: Mod_Modified culture medium


title: Heps_Mod_APAP10_rat3

description: Mod_Modified culture medium


title: Heps_St_APAP0_rat4

description: St_Standard culture medium


title: Heps_St_APAP0_rat3

description: St_Standard culture medium


title: Heps_St_APAP5_rat3

description: St_Standard culture medium


title: Heps_St_APAP10_rat3

description: St_Standard culture medium


title: Heps_Mod_APAP5_rat3

description: Mod_Modified culture medium


title: SA, 12h vs 24h, biol rep 2

city: Pretoria

first: Bridget

middle: Genevieve

last: Crampton

address: PO Box 395

country: South Africa

institute: CSIR Biosciences

description: Biological replicate 2, technical replicate 1

hyb_protocol: Probes were prepared by combining selected Cy3 and Cy5 labelled samples, which were then dried in a vacuum desiccator, and resuspended in 45 µl hybridisation buffer [50% formamide, 25% hybridisation buffer (Amersham Biosciences), 25% deionised water].  Probes were denatured at 92ºC for 5 min.The glass slide was initially incubated in pretreatment solution (3.5X SSC; 0.2% SDS; 1% bovine serum albumin) without probe at 60ºC for 20 min.  Thereafter, the slide was placed in a HybUP hybridisation chamber (NB Engineering, Pretoria, South Africa) with the denatured probe solution at 42ºC for 16 h.  After hybridisation, slides were washed for 4 min at 42ºC with 1 X SSC/0.2% SDS, 0.1 X SSC/0.2% SDS (twice) followed by three washes in 0.1 X SSC for 1 min at room temperature.  Slides were rinsed with distilled water, and dried by centrifugation (2000Xg for 2 min).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: Scanned images (tiff images) were imported into GenePix Pro 5.0 (Axon Instruments), and fluorescence intensity in both red (CyanineTM-5 dye) and green (CyanineTM-3 dye) channels for each spot was quantified.  Grids were predefined and manually adjusted to ensure optimal spot recognition, and spots with dust or locally high background were flagged as bad.  Fluorescence data from a total of 12 slides were imported into limmaGUI (linear models for microarray data Graphical User Interface) (Wettenhall and Smyth, 2004) in the R computing environment where data was normalised (within array global loess normalisation and between array quantile normalisation), and linear models were fitted in order to contrast post treatment expression values with the non-treated sample (time = 0 h). Differentially expressed genes for each treatment were defined as those with a fold-change (expression ratio) greater than or equal to two between a particular time point and t=0, and were significant at P ≤ 0.05 (moderated t test as implemented in limmaGUI with Bonferonni correction for multiple testing (Wettenhall and Smyth 2004).

organism: Cenchrus americanus

source_name: SA-treated leaves, 12 hpt

label_protocol: 15 µg total RNA was reverse transcribed using SuperScript™II (Invitrogen) in the presence of 6 µg random hexamers (Invitrogen), 1 ug oligo(dT)20 (Invitrogen), and 1 X aminoallyl-dNTP labelling mix (0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, 0.2 mM aminoallyl-dUTP).  Reactions were incubated at 42ºC overnight.  Thereafter, RNA was hydrolysed at 65ºC for 15 min by the addition of 0.2 N NaOH and 0.1 mM EDTA.  Tris, pH7.4 (0.3 M) was added to neutralise the reaction before cDNA was purified using a modified Qiaquick PCR Purification kit (Qiagen) protocol. Manufacturer’s instructions were followed except that columns were washed with phosphate wash buffer (5 mM KPO4, pH 8.5 in 80% ethanol), and cDNA was eluted in 4 mM KPO4, pH 8.5.  cDNA samples were vacuum dried and resuspended in 4.5 µl 0.1 M sodium carbonate buffer (Na2CO3), pH 9.0, to which an equal volume of NHS-Cy dye (Amersham BioSciences, Little Chalfont, UK) (prepared in DMSO) was added.  The dye coupling reaction was incubated for 1 h in the dark at room temperature.  Thirty five microlitres 100 mM sodium acetate, pH 5.2 was added to neutralise the reaction, and uncoupled dye was removed by purifying the sample using a Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: Pearl millet seeds (line ICML12 = P7) were surface sterilised, germinated on half strength Murashige and Skoog medium for one week, transferred to vermiculite in seedling trays, and grown for six weeks at constant temperature (25°C) and 85% relative humidity.

extract_protocol: Total RNA was isolated from leaves using Qiazol Lysis Reagent according to the manufacturer's instructions.

treatment_protocol: Seven week plants were sprayed until runoff with 5 mM sodium salicylate (Sigma) prepared in 0.1% Tween20.  Leaf tissue was harvested 0, 12, 24 and 48 h post treatment.

tag: Pearl millet line ICML12 = P7

source_name: SA-treated leaves, 24 hpt


title: Heps_Mod_APAP10_rat2

description: Mod_Modified culture medium


title: SA, 24h vs 48h, biol rep 2

source_name: SA-treated leaves, 48 hpt


title: SA, 0h vs 12h, biol rep 2

source_name: SA-treated leaves, 0 hpt


title: Heps_Mod_APAP5_rat2

description: Mod_Modified culture medium

source_name: primary hepatocytes, sandwich-cultured, 5 mM APAP, 24h

source_name: primary hepatocytes, sandwich-cultured, non-exposed


title: Heps_Mod_APAP0_rat2

description: Mod_Modified culture medium


title: MIRA vs Input Set 36 of 38


title: Heps_St_APAP10_rat2

description: St_Standard culture medium

source_name: primary hepatocytes, sandwich-cultured, 10 mM APAP, 24h


title: SA, 48h vs Oh, biol rep 2


title: SA, 12h vs 24h, biol rep 1, tech rep 2

description: Biological replicate 1, technical replicate 2 (dye swap)


title: SA, 24h vs 48h, biol rep 1, tech rep 2


title: Heps_St_APAP5_rat2

description: St_Standard culture medium


title: SA, 48h vs Oh, biol rep 1, tech rep 2


title: Dictyostelium discoideum amoeba stage SAGE library

type: SAGE

anchor: NlaIII

city: Pocatello

first: Maureen

last: Brandon

state: ID

address: Mail Stop 8007

department: Biological Sciences

institute: Idaho State University

description: Reduce the amount of 26 bp ditags in concatemer ligation by 25%

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum amoeba

growth_protocol: HL5 liquid culture, shaking to density of 2.4 X 10 (7) cells/ml

extract_protocol: Ambion RNAqueous RNA isolation kit; modified Invitrogen SAGE protocol

tag: AX2 strain


title: Heps_St_APAP0_rat2

description: St_Standard culture medium


title: MIRA vs Input Set 15 of 38


title: SA, 48h vs Oh, biol rep 1, tech rep 1

description: Biological replicate 1, technical replicate 1


title: MIRA vs Input Set 20 of 38


title: MIRA vs Input Set 13 of 38


title: SA, 24h vs 48h, biol rep 1, tech rep 1


title: SA, 12h vs 24h, biol rep 1, tech rep 1


title: SA, 0h vs 12h, biol rep 1, tech rep 1


title: MIRA vs Input Set 7 of 38


title: SA, 0h vs 12h, biol rep 1, tech rep 2


title: rust, 8d vs 0h, biol rep 1, tech rep 2

source_name: rust-treated leaves, 0 hpi

growth_protocol: Pearl millet seeds (line ICML12 = P7) were surface sterilised, germinated on half strength Murashige and Skoog medium for one week, transferred to vermiculite in seedling trays, and germinated for a further week at constant temperature (25°C) and 85% relative humidity.

treatment_protocol: For inoculations, 50 ul uredospores were gently rubbed onto the adaxial surface of 2-week-old pearl millet (ICML12=P7) seedlings that had been misted by spraying sterile double-distilled water from an “atomiser” spray bottle.  Seedlings were incubated in the dark for two days, and were thereafter maintained under 16 h light (140 umol/m2/s) and 8 h dark cycles at a constant temperature of 25ºC and 85% relative humidity.  Rust-infected pearl millet leaf material was harvested 0, 20, 120 and 8 d post inoculation.

source_name: rust-treated leaves, 8 dpi


title: rust, 5d vs 8d, biol rep 1, tech rep 2

source_name: rust-treated leaves, 5 dpi


title: MIRA vs Input Set 5 of 38

source_name: MIRA

source_name: Input


title: rust, 20h vs 5d, biol rep 1, tech rep 2

source_name: rust-treated leaves, 20 hpi


title: rust, 0h vs 20h, biol rep 2


title: rust, 20h vs 5d, biol rep 2


title: rust, 8d vs 0h, biol rep 2


title: rust, 5d vs 8d, biol rep 2


title: rust, 0h vs 20h, biol rep 1, tech rep 2


title: rust, 8d vs 0h, biol rep 1, tech rep 1


title: rust, 5d vs 8d, biol rep 1, tech rep 1


title: MIRA vs Input Set 6 of 38


title: rust, 20h vs 5d, biol rep 1, tech rep 1


title: MeJA, 48h vs Oh, biol rep 1, tech rep 2

source_name: MeJA-treated leaves, 0 hpt

growth_protocol: Pearl millet seeds (line ICML12) were surface sterilised, germinated on half strength Murashige and Skoog medium for one week, transferred to vermiculite in seedling trays, and grown for six weeks at constant temperature (25°C) and 85% relative humidity.

treatment_protocol: Seven week plants were sprayed until runoff with 500 uM MeJA in 0.1% ethanol, 0.1% Tween 20.  Leaf tissue was harvested 0, 12, 24 and 48 h post treatment.

source_name: MeJA-treated leaves, 48 hpt


title: rust, 0h vs 20h, biol rep 1, tech rep 1


title: MIRA vs Input Set 37 of 38


title: MIRA vs Input Set 34 of 38


title: MIRA vs Input Set 12 of 38


title: MeJA, 24h vs 48h, biol rep 1, tech rep 2

source_name: MeJA-treated leaves, 24 hpt


title: MIRA vs Input Set 22 of 38


title: MIRA vs Input Set 21 of 38


title: MeJA, 12h vs 24h, biol rep 1, tech rep 2

source_name: MeJA-treated leaves, 12 hpt


title: MIRA vs Input Set 27 of 38


title: MeJA, 0h vs 12h, biol rep 1, tech rep 2


title: MIRA vs Input Set 24 of 38


title: MIRA vs Input Set 31 of 38


title: MIRA vs Input Set 25 of 38


title: MIRA vs Input Set 26 of 38


title: MeJA, 48h vs Oh, biol rep 2


title: MIRA vs Input Set 9 of 38


title: MIRA vs Input Set 23 of 38


title: MIRA vs Input Set 1 of 38


title: MIRA vs Input Set 30 of 38


title: MIRA vs Input Set 11 of 38


title: MIRA vs Input Set 8 of 38


title: MeJA, 12h vs 24h, biol rep 2


title: MIRA vs Input Set 29 of 38


title: MIRA vs Input Set 10 of 38


title: MeJA, 24h vs 48h, biol rep 2


title: MeJA, 48h vs Oh, biol rep 1, tech rep 1


title: MeJA, 0h vs 12h, biol rep 2


title: MeJA, 12h vs 24h, biol rep 1, tech rep 1


title: MeJA, 24h vs 48h, biol rep 1, tech rep 1


title: MIRA vs Input Set 4 of 38


title: msg5-wt

status: Public on Dec 31 2008

city: Madrid

first: Maria

last: Molina

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia II Fcc Farmacia

country: Spain

institute: Universidad Complutense de Madrid

description: Image analysis and data segmentation were done using GenePix Pro software 5.0 (Axon Instruments) obtaining a txt file to proceed with the data analysis.

hyb_protocol: treated and control cDNA labeled with different dyes are mixed, dried in speed vac and resuspended in hybridation solution: 50% Formamide, 6x SSC, 0.5% SDS, 5x Denhardt´s, 20 microgrammes PolyA (Sigma) and salmon sperm (Gibco) 100 microgrammes/ml. Hybridation of slides with labeled cDNA is carried out for 18 hours at 42ºC in a fluidic station LucideaTM SlidePro (Amersham Biosciences) followed by several washes and drying of slides.

scan_protocol: Microarrays were scanned using GenePix 4000B scanner (Axon Instruments) at 5 micron/píxel, using laser excitation between 550 and 700 PMT and 100% laser power.

data_processing:
Filtering of low neat intensity and inconsistent spot data was followed by Lowess normalization and calculation of ratios. Statistical t-student test was carried out to determine the significance of the induction and repression ratios.
The Data table represents results condensed from four microarrays (coming from two different biological samples labeled using dye swapping strategy)

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: Labelling with Cy3 or Cy5 groups of the corresponding cDNA was achieved using CyScribeTM Post-Labelling kit (Amersham Biosciences) incubating the samples in the dark for two hours. Fluorocrome incorporation was measured using espectophotometer.

growth_protocol: S. cerevisiae was grown on YPD overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. At this point time 0 begins. Cells were collected at 2 hours of growth, frozen at -80 °C and processed for RNA extraction.

extract_protocol: Saccharomyces cerevisiae total RNA was extracted by mechanical disruption following the instructions of RNeasy Midi kit manufacturer (QIAGEN). Total concentration of RNA obtained was measured at 260 nm and sample quality was checked using RNA Nano Labchips in a Bioanalyzer 2100B (Agilent Technologies, Palo Alto, CA). cDNA synthesis and incorporation of aminoallyl nucleotides is carried out by retrotranscription from 25-30 microgrames of total RNA using Amersham Bioscienceskit .

treatment_protocol: growth at conditions 24 °C 200rpm

tag: BY4741 Strain (Control mRNA

value: no treatment)

growth_protocol: msg5 delta strain was grown on YPD overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. At this point time 0 begins. Cells were collected at 2 hours of growth, frozen at -80 °C and processed for RNA extraction.

tag: msg5 strain (experimental condition)


title: MIRA vs Input Set 32 of 38


title: MIRA vs Input Set 28 of 38


title: 721_EBNA1_IP

city: Madison

first: Bill

last: Sugden

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

hyb_protocol: Hybridization was carried out by Nimblegen Systems, Inc at 42C overnight using proprietary buffers. Arrays were washed using proprietary Wash buffers I, II and III.

scan_protocol: Scanning was carried out by Nimblegen Systems, Inc.

data_processing: Data processing was carried out by Nimblegen Systems, Inc with NimbleScan software version 2.2. using default settings. NimbleScan provides ChIP-Chip analysis as described in B. Ren, et al. (2000), Genome-wide location and function of dna-binding proteins. Science, 290:2306-2309.

source_name: chromatin immunoprecipitated with anti-EBNA1 antibody (IH4)

label_protocol: Chromatin samples from ChIP experiments were amplified by two rounds of linker-mediated PCR, following the protocol provided by NimbleGen Systems, Inc.  Amplifed chromatin samples from three independent ChIP experiments were pooled for submission to NimbleGen. Total, non-immunoprecipitated DNA was labelled with Cy3, EBNA1-immunoprecipitated DNA or non-specific IgG-immunoprecipitated DNA was labelled with Cy5 by NimbleGen Systems, Inc.

growth_protocol: The lymphoblastoid cell line 721 was grown in RPMI-1640 supplemented with 10% fetal bovine serum, 200 U of penicillin, and 200 μg of streptomycin sulfate per mL.

extract_protocol: Chromatin immunoprecipation was carried out as described in Wang, J., S. E. Lindner, E. R. Leight, and B. Sugden. 2006. Essential elements of a licensed, mammalian plasmid origin of DNA synthesis. Mol. Cell. Biol. 26:1124-1134.

tag: 721 lymphoblastoid cell line, growing in log phase

source_name: Total, non-immunoprecipitated DNA


title: 721_Non-specific IgG_IP

description:
This sample served as a negative control. It was hybridized only to the HG17_promoter1 array and not the HG17_promoter2 array.
NA

source_name: chromatin immunoprecipitated with rabbit anti-rat IgG antibody (R3756, Sigma)

treatment_protocol: Chromatin immunoprecipation was carried out as described in Wang, J., S. E. Lindner, E. R. Leight, and B. Sugden. 2006. Essential elements of a licensed, mammalian plasmid origin of DNA synthesis. Mol. Cell. Biol. 26:1124-1134.


title: MIRA vs Input Set 17 of 38


title: S. pombe Rad21 binding pattern in anaphase cells after release from cdc25-22 imposed arrest

city: Bethesda

first: Christine

middle: Katrin

last: Schmidt

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included only one step with SAPE.

scan_protocol: Microarray scanning was performed with an Affymetrix Gene Chip Scanner 3000.

data_processing: The Affymetrix Gene Chip Operating Software GCOS, version 1.4,  was used for data processing.

label: biotin-11-ddATP (NEL548)

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-11-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells were released from G2 in minimal EMM2 medium at 25°C after a 6 h cdc25-22 imposed arrest at 36.5°C. The sample was taken 30 min after release when most cells were in anaphase.

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-HA mouse monoclonal 16B12 antibody (Babco) against the HA-tagged cohesin subunit Rad21 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y2699

value: h- leu1-32 cdc25-22 rad21-Pk9-kanMX6 SV40p-GFP-atb2-LEU2


title: MIRA vs Input Set 38 of 38


title: MIRA vs Input Set 3 of 38


title: S. pombe Fhl1 binding pattern in cycling cells

description: no additional information

growth_protocol: Cells were exponentially grown in rich YE4S medium at 25°C.

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged forkhead domain containing protein Fhl1 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3403

value: h90 leu1-32 fhl1-Pk9-kanMX6


title: S. pombe untagged Pk binding pattern in cycling cells

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymetrix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included only one step with SAPE.

growth_protocol: Cells were exponentially grown in rich medium (YE4S) at 25°C.

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal antibody (SV5-Pk1, Serotec) in conjunction with protein A magnetic dynabeads (Dynal). The eluates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y2460


title: S. pombe Sfc6 binding pattern in cycling cells

description: no additional information

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged TFIIIC subunit Sfc6 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3351

value: h90 leu1-32 mis4-Pk9-kanMX6 sfc3-GFP-hygMX6


title: 721_EBNA1_IP


title: Pombe Sup/WCE fraction

description: no additional information

data_processing: The Affymetrix Gene Chip Operating Software GCOS, version 1.4, was used for data processing.

source_name: genomic DNA

extract_protocol:
Genomic DNA was prepared essentially as previously described (Katou et al., 2003, see below). 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and a small fraction was directly taken for DNA purification, amplification and labeling (SUP sample).
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.

tag: Normalisation for pombe ChIP chip patterns GSM333163, GSM333230 & GSM334197, whole genomic DNA was used for hybridisation


title: S. pombe Ssl3 binding pattern in cycling cells

description: no additional information

growth_protocol: Cells were exponentially grown in rich medium (YE4S) at 25°C

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged cohesin loader subunit Ssl3 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3071

value: h+ ssl3-Pk9-kanMX6


title: MIRA vs Input Set 16 of 38

tag: MIRA enriched

tag: Input genomic DNA


title: MIRA vs Input Set 18 of 38


title: S. pombe Cnd2 binding pattern in metaphase-arrested cells

description: no additional information

growth_protocol: Cells were arrested at 20°C in rich medium (YE4S) for 6 h using the nda3-KM311 cold-sensitive allele.

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged condensin subunit Cnd2 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3250 h90 leu1-32 cdc25-22 cnd2-Pk9-kanMX6 SV40p-GFP-atb2-LEU2


title: S. pombe Mis4 binding pattern in cycling cells in the absence of SPBTRNAGLY.05 and SPBTRNAARG.04

description: no additional information

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged cohesin loader subunit Mis4 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3650

value: h- leu1-32 ura4-D18 ade6-M210 mis4-Pk9-kanMX6 SPBTRNAGLY.05Δ SPBTRNAARG.04Δ


title: MIRA vs Input Set 2 of 38


title: S. pombe Rad21 binding pattern in anaphase cells after release from cdc25-22 imposed arrest, ark1-as3 plus 1NM-PP1

description: no additional information

growth_protocol: To inhibit Ark1 kinase activity, 5µM of 1NM-PP1 were added 15 min before cells were released from G2 in minimal EMM2 medium at 25°C after a 6 h cdc25-22 imposed arrest at 36.5°C. The sample was taken 30 min after release when most cells were in anaphase.

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal SV5-Pk1 antibody (Serotec) against the Pk-tagged cohesin subunit Rad21 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y3586

value: h- leu1-32 ark1-as3-hygMX6 cdc25-22 rad21-Pk9-kanMX6 SV40p-GFP-atb2-LEU2


title: S. pombe Rad21 binding pattern in G2-arrested cells in the absence of SPBTRNAGLY.05 and SPBTRNAARG.04

description: no additional information

growth_protocol: Cells were arrested in G2 in minimal EMM2 medium at 36.5°C using the cdc25-22 thermosensitive allele.

tag: Strain Y3724

value: h90 leu1-32 ura4-D18 cdc25-22 rad21-Pk9-kanMX6 SPBTRNAGLY.05Δ SPBTRNAARG.04Δ


title: S. pombe Rad21 binding pattern, swi6 deleted, G2 (cdc25-22)

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included one step with SAPE.

source_name: chromatin-immunoprecipitated DNA

growth_protocol: Cells were arrested for 6 h at 36°C in EMM2 plus supplements in G2 using the thermosensitive cdc25-22 allele.

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Anti-Pk antibodies (SV5-Pk1, Serotec), in conjunction with protein-A coupled magnetic Dynabeads were used against the Pk-tagged cohesin subunit Rad21. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
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.

tag: Strain Y3272

value: h- leu1-32 ura4-D18 cdc25-22 rad21-Pk9-kanMX6 SV40p-GFP-atb2-LEU2 swi6::ura4+


title: S. pombe Mis4 binding pattern in cycling cells

description: no additional information

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-Pk mouse monoclonal antibody (SV5-Pk1, Serotec) against the Pk-tagged cohesin loader subunit Mis4 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
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.

tag: Strain Y2468

value: h90 leu1-32 mis4-Pk9-kanMX6


title: S. pombe Pds5 binding pattern in cycling cells

description: no additional information

growth_protocol: Cells were grown in YE4S at 25°C.

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Anti-Pk antibodies (SV5-Pk1, Serotec), in conjunction with protein-A coupled magnetic Dynabeads were used against the Pk-tagged cohesin subunit Pds5. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
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.

tag: Strain Y2828 h- pds5-Pk9-kanMX6


title: S. pombe Psc3 binding pattern in cycling cells

description: no additional information

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Anti-Pk antibodies (SV5-Pk1, Serotec), in conjunction with protein-A coupled magnetic Dynabeads were used against the Pk-tagged cohesin subunit Psc3. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
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.

tag: Strain

value: Y2447 h90 leu1-32 psc3-Pk9-kanMX6


title: S. pombe Rad21 binding pattern in metaphase cells after release from cdc25-22 imposed arrest

description: no additional information

growth_protocol: Cells were released from G2 in minimal EMM2 medium at 25°C after a 6 h cdc25-22 imposed arrest at 36.5°C. The sample was taken 20 min after release when most cells were in metaphase.


title: MIRA vs Input Set 19 of 38

extract_protocol: Genomic DNA was purified from B cells by standard procedures by using proteinase K digestion, phenol chloroform extraction and ethanol precipitation.


title: S. pombe Rad21 binding pattern in cycling cells

description: no additional information

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Monoclonal anti-HA antibodies (16B12, Roche), in conjunction with protein-A coupled magnetic Dynabeads were used against the HA-tagged cohesin subunit Rad21. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
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.

tag: Strain Y2197

value: h90 leu1-32 ade6-M216 rad21-HA3-kanMX6


title: KM_AG_47145_24h_3uM_BP2_DF

status: Public on Dec 30 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 24h DMSO v 24h 3 BaP BP2 DF

hyb_protocol: Hybridization and washing were performed according to the Agilent manual.

scan_protocol: Scanner: Axon4000A. Voltage: 100%

data_processing: Regions were used for normalizing samples 1-32. To account for dye swap, the signal channel and control channel measurements for sample(s) 1, 3, 5, 7, 9-10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: MS-HepG2 24 h 3 uM BaP BP2(24 h 3 uM BaP BP2)

label_protocol: Labelling and hybridization was carried out according to the Agilent manual for microarrays with minor modifications. Total RNA (0.5 ug) was transcribed into cDNA and labelled with either Cyanine 5 (Cy5) or Cyanine 3 (Cy3). If dye-incorporation was above 7 pmol/µg RNA, 2 µg of BaP treated-cRNA and 2 µg DMSO control-cRNA were applied on the Agilent Human 1A (V2) Oligo Microarray.

extract_protocol: Total RNA was isolated and purified from the Trizol fraction with the RNeasy Mini Kit (Qiagen Westburg bv., Leusden, The Netherlands).

tag: tissue type

value: tumor

source_name: MS-HepG2 24 h DMSO BP2(24 h DMSO BP2 )


title: S. pombe Rad21 binding pattern, G2 (cdc25-22)

description: no additional information

growth_protocol: Cells were arrested for 6 h at 36.5°C in minimal medium (EMM2 + supplements) in G2 using the thermosensitive cdc25-22 mutant.

tag: Strain Y2699


title: KM_AG_43088_24h_3uM_BP2

description: 24h DMSO v 24h 3 BaP BP2


title: KM_AG_41210_24h_3uM_BP1

description: 24h DMSO v 24h 3 BaP BP1

source_name: MS-HepG2 24 h DMSO BP1(25 h DMSO BP1)

source_name: MS-HepG2 24 h 3 uM BaP BP1(24 h 3 uM BaP BP1)


title: KM_AG_42974_24h_3uM_BP1_DF

description: 24h DMSO v 24h 3 BaP BP1 DF


title: KM_AG_47141_6h_3uM_BP2_DF

description: 6h DMSO v 5h 3 BaP BP2 DF

source_name: MS-HepG2 6 h 3 uM BaP BP2(6 h 3 uM BaP BP2)

source_name: MS -HepG2 6 h DMSO BP2(6 h DMSO BP2)


title: KM_AG_43079_6h_3uM_BP1_DF

description: 6h DMSO v 6h 3 BaP BP1 DF

source_name: MS-HepG2 6 h 3 uM BaP BP1(6 h 3 uM BaP BP1)

source_name: MS-HepG2 6 h DMSO BP1(6 h DMSO BP1)


title: SH-3000100879_24h_3 BaP_BP1

description: 24h DMSO v 24h 3 BaP exp.1

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 μl hybridisation mix (19 μl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150μl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000A. Voltage: 3.68 and 3.57. Resolution (micrometers): 10.

label_protocol: Total RNA (4 μg) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 μg Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.


title: SH-3000100880_6h_3_BaP_BP1_DF #2

description: 6h DMSO v 6h 3 BaP exp.1 DF

scan_protocol: Scanner: Axon4000A. Voltage: 3.7 and 3.5. Resolution (micrometers): 10.