title: H1963

tag: SCLC cell line H1963 from ATCC


title: 35 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours

status: Public on Apr 10 2007

type: RNA

city: Milan

first: Stefano

last: Berri

address: via Celoria 26

department: biomolecular sciences and biotechnology

country: Italy

institute: University of Milan

hyb_protocol: For array hybridisation, Cy3 and Cy5 labelled cDNA probes were mixed with Calf thymus DNA (Sigma) and EGT hybridization buffer (Eurogentec) and hybridised to the microarray (Eurogentec) at 42°c in a humid chamber (Corning) for 16 hours. Arrays were washed 5min in a 0.2xSSC-0.1% sodium dodecyl sulfate solution then 5min in 0.2xSSC. The arrays were spin-dried.

scan_protocol: The arrays were scanned using the Axon 4100A Scanner. The hybridisation data were collected and normalization performed using the GenePix Pro 3.0 software.

data_processing: Data were normalized using Limma, a package of Bioconductor, using loess, but giving different weight do spots. Weight of each spot is reported in the data table.

molecule: total RNA

organism: Oryza sativa Japonica Group

label_protocol: 10 µg of total RNAs were used for Cy3 or Cy5 labelling using the Cyscribe First-Strand cDNA Labelling kit (Amersham). The labelled cDNA samples were purified using the CyScribe GFX Purification Kit (Amersham) and concentrated using a microcon YM-30 filter (Millipore). 5 ng of Luciferase RNA (Promega) was added to each RNA samples prior labelling and used as spiking / normalization control.!Sample_label_protocol_ch2 = 10 µg of total RNAs were used for Cy3 or Cy5 labelling using the Cyscribe First-Strand cDNA Labelling kit (Amersham). The labelled cDNA samples were purified using the CyScribe GFX Purification Kit (Amersham) and concentrated using a microcon YM-30 filter (Millipore). 5 ng of Luciferase RNA (Promega) was added to each RNA samples prior labelling and used as spiking / normalization control.

growth_protocol:
Seeds of rice genotype Nipponbarre were obtained from the International Rice Research Institute (IRRI). Dehisced seeds were sterilized with 15% (v/v) sodium hypochlorite for 30 min and then rinsed with distilled water. Seeds were germinated in Petri dishes at 28oC on Whatman® paper soaked in deionized water. After 4 days, rice seedlings were transferred in pots containing pouzzolane and allowed to growth under controlled conditions with a 28°C/25°C day/night temperatures, 12 hr photoperiod and 55-65% humidity for 2 weeks in Yoshida’s modified solution (1981): 0.7 mM KNO3, 1.2 mM Ca(NO3)2, 1.6 mM MgSO4, 0.5 mM (NH4)2SO4, 0.8 mM KH2PO4, 60 µM FeEDTA, 20µM MnSO4, 0.32 µM(NH4)6Mo7O24, 1.4 µM ZnSO4, 1.6 µM CuSO4, 45.2 µM H3BO3. Medium pH was adjusted to 5.0 twice a day. Seedlings at the 5 leaves stage without any visible tiller were carefully selected for stress treatments.
Seeds of rice genotype Nipponbarre were obtained from the International Rice Research Institute (IRRI). Dehisced seeds were sterilized with 15% (v/v) sodium hypochlorite for 30 min and then rinsed with distilled water. Seeds were germinated in Petri dishes at 28oC on Whatman® paper soaked in deionized water. After 4 days, rice seedlings were transferred in pots containing pouzzolane and allowed to growth under controlled conditions with a 28°C/25°C day/night temperatures, 12 hr photoperiod and 55-65% humidity for 2 weeks in Yoshida’s modified solution (1981): 0.7 mM KNO3, 1.2 mM Ca(NO3)2, 1.6 mM MgSO4, 0.5 mM (NH4)2SO4, 0.8 mM KH2PO4, 60 µM FeEDTA, 20µM MnSO4, 0.32 µM(NH4)6Mo7O24, 1.4 µM ZnSO4, 1.6 µM CuSO4, 45.2 µM H3BO3. Medium pH was adjusted to 5.0 twice a day. Seedlings at the 5 leaves stage without any visible tiller were carefully selected for stress treatments.

extract_protocol: TRIZOL protocol (Invitrogen, Carlsbad, CA), as indicated by the manufacturer.

treatment_protocol: 100 mM of mannitol was added in the hydroponic solution. Root and shoot tissues were harvested 1 hr or 5 hr after the beginning of stress treatment

tag: Tissue

value: 2-weeks old rice seedling Leaves. Treatment:Osmotic

treatment_protocol: Water was added in the hydroponic solution. Root and shoot tissues were harvested 1 hr or 5 hr after the beginning of stress treatment

value: 2-weeks old rice seedling Leaves. Treatment:Mock treatment


title: 36 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: Control treated cells Rep1

status: Public on Apr 19 2007

city: Boston

first: Geoffrey

last: Girnun

state: MA

address: One Jimmy Fund Way

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

description: Nothing more to add

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a 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 confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

label: biotinylated

organism: Homo sapiens

source_name: NSCLC adenocarcinoma cell line

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).

extract_protocol: Samples were scraped into trizol and transfered to phaselock tubes.  RNA was extracted according to manufactures directions.

treatment_protocol: Cells were cultured overnight in DMEM 10% FBS (pen/strep).  Media was changed with cells receiving either control media, 1 micromolar rosiglitazone, 10 micromolar carboplatin or combination of carboplatin and rosiglitazone.

tag: A549 NSCLC cell line


title: DMS79

status: Public on Apr 15 2007

type: genomic

city: Abbott Park

first: Dimitri

last: Semizarov

state: IL

address: 100 Abbott Park Rd, bld AP10, dept R4CD

institute: Abbott Laboratories

description: gDNA from cell line profiled on Affymetrix 100K arrays using the standard protocol

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Standard Affymetrix data generation protocol: CEL, CHP files generated by the GCOS and GTYPE programs.

label: Biotin

molecule: genomic DNA

source_name: cell line

label_protocol: Affymetrix 100K protocol

extract_protocol: Qiagen DNAeasy kit

tag: SCLC cell line DMS79


title: 34 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: 33 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: H209

tag: SCLC cell line


title: 32 BR29 Rice Pathogen(BR29) Leaves 1 day

growth_protocol: Plants were grown from seeds in a greenhouse in trays of 40 x 29 x 7 cm filled with compost (7/8 Neuhaus compost N° 9, 1/8 pouzzolane) under a day-time temperature of 27°C, a night-time temperature of 22°C, 60 % humidity. Twenty seeds were sown in rows with 6 rows per genotype. Nitrogen fertilisation with 8.6 g of nitrogen equivalent was done at 7 and 2 days before inoculation.

treatment_protocol: Thirty ml of sterile water with 0.5% gelatine were sprayed on each tray (60 plants). Rice plants were then kept for 16 h in a controlled climatic chamber at 25 °C and 95 % relative humidity.

treatment_protocol: Fungal isolates of BR29 were chosen from the M. grisea (Hebert) Barr strain collection (CIRAD, Montpellier). These strains were cultured in Petri dishes containing 20 mL of medium composed with 20 g.L-1 rice seed flour, 2.5 g.L-1 yeast extract, 1.5 % agar (Merck). After autoclaving, 500,000 units of Penicillin G (Sigma) were added aseptically by filter sterilising. The cultures were then placed in a growth chamber with a 12 h photoperiod and a constant temperature of 25 °C for 7 to 9 days prior to inoculation. Inoculation method: Conidia were harvested from plates by rinsing with sterile distilled water and filtering through two layers of gauze. Inoculations with M. grisea Hebert (Barr) strains were performed with rice plantlets 2 weeks after sowing by spraying with conidial suspensions. Thirty ml of either a 100,000 (for FR13) or 300,000 (for BR29 or BR32) conidia*ml-1 suspension with 0.5% gelatine were sprayed on each tray (60 plants). Rice plants were then kept for 16 h in a controlled climatic chamber at 25 °C and 95 % relative humidity.

value: 2-weeks old rice seedling Leaves. Treatment:Pathogen


title: H69


title: H524

tag: SCLCcell line H524


title: DMS 53


title: H711

tag: SCLC cell line H711


title: H146

tag: SCLC cell line from ATCC


title: H211

tag: SCLC cell line H211


title: H889

tag: SCLC cell line H889 from ATCC


title: 31 BR29 Rice Pathogen(BR29) Leaves 1 day


title: H345

tag: SCLC cell line H345


title: H748

tag: SCLC cell line H748


title: 27 BR32 Rice Pathogen(BR32) Leaves 1 day

treatment_protocol: Fungal isolates of BR32 were chosen from the M. grisea (Hebert) Barr strain collection (CIRAD, Montpellier). These strains were cultured in Petri dishes containing 20 mL of medium composed with 20 g.L-1 rice seed flour, 2.5 g.L-1 yeast extract, 1.5 % agar (Merck). After autoclaving, 500,000 units of Penicillin G (Sigma) were added aseptically by filter sterilising. The cultures were then placed in a growth chamber with a 12 h photoperiod and a constant temperature of 25 °C for 7 to 9 days prior to inoculation. Inoculation method: Conidia were harvested from plates by rinsing with sterile distilled water and filtering through two layers of gauze. Inoculations with M. grisea Hebert (Barr) strains were performed with rice plantlets 2 weeks after sowing by spraying with conidial suspensions. Thirty ml of either a 100,000 (for FR13) or 300,000 (for BR29 or BR32) conidia*ml-1 suspension with 0.5% gelatine were sprayed on each tray (60 plants). Rice plants were then kept for 16 h in a controlled climatic chamber at 25 °C and 95 % relative humidity.


title: 24 FR13 Rice Pathogen(FR13) Leaves 1 day

treatment_protocol: Fungal isolates of FR13 were chosen from the M. grisea (Hebert) Barr strain collection (CIRAD, Montpellier). These strains were cultured in Petri dishes containing 20 mL of medium composed with 20 g.L-1 rice seed flour, 2.5 g.L-1 yeast extract, 1.5 % agar (Merck). After autoclaving, 500,000 units of Penicillin G (Sigma) were added aseptically by filter sterilising. The cultures were then placed in a growth chamber with a 12 h photoperiod and a constant temperature of 25 °C for 7 to 9 days prior to inoculation. Inoculation method: Conidia were harvested from plates by rinsing with sterile distilled water and filtering through two layers of gauze. Inoculations with M. grisea Hebert (Barr) strains were performed with rice plantlets 2 weeks after sowing by spraying with conidial suspensions. Thirty ml of either a 100,000 (for FR13) or 300,000 (for BR29 or BR32) conidia*ml-1 suspension with 0.5% gelatine were sprayed on each tray (60 plants). Rice plants were then kept for 16 h in a controlled climatic chamber at 25 °C and 95 % relative humidity.


title: 26 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 29 BR29 Rice Pathogen(BR29) Leaves 1 day


title: 30 BR29 Rice Pathogen(BR29) Leaves 1 day


title: H187


title: 28 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 22 FR13 Rice Pathogen(FR13) Leaves 1 day


title: H526

tag: SCLC cell line H526


title: 23 FR13 Rice Pathogen(FR13) Leaves 1 day


title: 21 FR13 Rice Pathogen(FR13) Leaves 1 day


title: H510

tag: SCLC cell line H510


title: 20 BR29 Rice Pathogen(BR29) Leaves 1 day


title: 19 BR29 Rice Pathogen(BR29) Leaves 1 day


title: 25 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 18 BR29 Rice Pathogen(BR29) Leaves 1 day


title: 17 BR29 Rice Pathogen(BR29) Leaves 1 day


title: 13 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 14 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 8 Or1h Rice Osmotic(Or1h) Roots 1 hour

growth_protocol: Seeds of rice genotype Nipponbarre were obtained from the International Rice Research Institute (IRRI). Dehisced seeds were sterilized with 15% (v/v) sodium hypochlorite for 30 min and then rinsed with distilled water. Seeds were germinated in Petri dishes at 28oC on Whatman® paper soaked in deionized water. After 4 days, rice seedlings were transferred in pots containing pouzzolane and allowed to growth under controlled conditions with a 28°C/25°C day/night temperatures, 12 hr photoperiod and 55-65% humidity for 2 weeks in Yoshida’s modified solution (1981): 0.7 mM KNO3, 1.2 mM Ca(NO3)2, 1.6 mM MgSO4, 0.5 mM (NH4)2SO4, 0.8 mM KH2PO4, 60 µM FeEDTA, 20µM MnSO4, 0.32 µM(NH4)6Mo7O24, 1.4 µM ZnSO4, 1.6 µM CuSO4, 45.2 µM H3BO3. Medium pH was adjusted to 5.0 twice a day. Seedlings at the 5 leaves stage without any visible tiller were carefully selected for stress treatments.

value: 2-weeks old rice seedling Roots. Treatment:Mock treatment

value: 2-weeks old rice seedling Roots. Treatment:Osmotic


title: 11 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: 12 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: 5 Or1h Rice Osmotic(Or1h) Roots 1 hour


title: 16 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 6 Or1h Rice Osmotic(Or1h) Roots 1 hour


title: 15 BR32 Rice Pathogen(BR32) Leaves 1 day


title: 10 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: 3 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: H1417

tag: SCLC cell line H1417


title: 7 Or1h Rice Osmotic(Or1h) Roots 1 hour


title: 4 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: 2 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: 9 Or5h Rice Osmotic(Or5h) Roots 5 hours


title: Ca11968

status: Public on Apr 07 2007

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

hyb_protocol: Labeled targets were pooled and combined with blocking agents (12 ug poly-dA, 6 ug yeast tRNA, 20 ug Cot-1 DNA), and hybridized to microarray using the Pronto Universal Hybridization System (Corning) for 18 hours in a humidified chamber (Corning) submerged in a 42 C water bath.  Slide was washing using the Pronto Universal Hybridization System.

scan_protocol: Scanned using the Agilent DNA Microarray Scanner at 10 micron resolution.  The TIFF image was split and analyzed with GenePix 4.1.1.4.  Result files were loaded into BioArray Software Environment.  Cy3=channel 1, Cy5=channel 2.

data_processing: Data was preprocessed in the BioArray Software Environment. For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad/missing during image analysis were removed. Poorly measured features with A<1.5 (A defined as log10(sqrt(Ch1*Ch2))) were removed. Data was normalized using pin-based LOWESS (6 groups of 8 pins/group).  Features that were present in at least 80% of the 105 tumors in the series were kept, all other features were removed.

label_protocol: 25 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).

extract_protocol: Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by 2nd round of purification using RNeasy kit (Qiagen).

tag: See supplemental datasheet attached to the associated GEO series GSE5325.

source_name: Stratagene Universal Human Reference

label_protocol: 15 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).

growth_protocol: See Stratagene product # 740000.

extract_protocol: See Stratagene product # 740000.

treatment_protocol: See Stratagene product # 740000.

tag: See Stratagene product # 740000.


title: Ca11522


title: Ca11570


title: 1 Ol5h Rice Osmotic(Ol5h) Leaves 5 hours


title: Ca11829


title: Ca11442


title: Ca10591


title: Ca11379


title: Ca13351


title: Ca11591


title: Ca11205


title: Ca11620


title: Ca11460


title: Ca10481


title: Ca10960


title: Ca9765


title: Ca10419


title: Ca10289


title: Ca10879


title: Ca10426


title: Ca10109


title: Ca10335


title: Ca10607


title: Ca9909


title: Ca10580


title: Ca9795


title: Ca9732


title: Ca9552


title: Ca9298


title: Ca9174


title: Ca9159


title: Ca9539


title: Ca9126


title: Ca9079


title: Ca8800


title: Ca9701


title: Ca8477


title: Ca8582


title: Ca8610


title: Ca8290


title: Ca8676


title: Ca8860


title: Ca8212


title: Ca8237


title: Ca8560


title: Ca8174


title: Ca9077


title: Ca8401


title: Ca7845


title: Ca8333


title: Ca8537


title: Ca7921


title: Ca7732


title: Ca7722


title: Ca8196


title: Ca7982


title: Ca7811


title: Ca8173


title: Ca7609


title: Ca7589


title: Ca7604


title: Ca7583


title: Ca7495


title: Ca7461


title: Ca7549


title: Ca7493


title: Ca7367


title: Ca7398


title: Ca7244


title: Ca7366


title: Ca7357


title: Ca7170


title: Ca7214


title: Ca7246


title: Ca6773


title: Ca6687


title: Ca6617


title: Ca6716


title: Ca7106


title: Ca7168


title: Ca7408


title: Ca7151


title: Ca7102


title: Ca6537


title: Ca7632


title: Ca6474


title: Ca6516


title: Ca6366


title: Ca6318


title: Ca6219


title: Ca6464


title: Ca6257


title: Ca6165


title: Ca6125


title: Ca6188


title: Ca6146


title: 20 weeks sample 5

status: Public on Apr 01 2007

city: Oslo

first: Esten

last: Nakken

address: Kirkeveien 166

department: Ulleval university Hospital

country: Norway

institute: Institute for Experimental Medical Research

description: Hepatic gene expression was examined in abcb4 (-/-)mice (FVB.129P2-Abcb4tm1Bor/J) at 3, 6, 9 and 20 weeks after weaning, using spotted cDNA microarrays; FVB/NJ abcb4 (+/+) mice serving as controls.

hyb_protocol: Agilent Hybridization Procedure, Version 4.1, SureHyb enabled, SSC wash

scan_protocol: The arrays were controlled for spatial and intensity dependent effects by visual inspections of the array images and of ratio/intensity (RI) plots. To retain saturated spots (with more than half of the pixels in saturation) we performed additional lower scans of the arrays and modified the saturated intensities according to the algorithm described in Lyng, Badiee et al (2004). As measures of the spot intensities we used the median of the foreground pixel intensities, and log-transformed them to obtain approximate normality. No further normalisation was done because this is taken care of in our model-based analysis described below.

data_processing:
Our model is based on a log-linear mixed effect model according to Kerr et al (2000).The base2 logarithm of each of the measured fluorescent intensity was modelled as a sum of dye, gene and array effects plus effects of the interaction terms array*gene (i.e. spot effects), dye*gene and time*variety*gene (the time-dependent effect of the specific variety - here abcb4 (-/-) orcontrol - on each gene). The latter is the parameter of main concern, and we note that the difference here for a given gene between abcb4 (-/-) and control is the log2 ratio (normalised for experimental noise) in gene expression between the two types. Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al (2002), for the statistical language R. We set a rather conservative threshold of significance of at least two-fold change and p<0.01, which corresponds to false discovery rates (FDR), i.e. the proportion of falsely claimed differentially expressed genes, of 2.6%, 2.5%, 2.7% and 2.2%, for the four time points, respectively, calculated in SAM (Tusher et al 2001).

The Gene Ontology (GO) based data mining tool High Throughput GoMiner (Zeeberg et al 2005) was used to find GO categories, i.e. molecular functions, biological processes, and cellular components, overrepresented by regulated genes.

organism: Mus musculus

source_name: Mouse liver abcb4 (+/+) 3 weeks

label_protocol: FairPlay Microarray Labeling Kit, Stratagene

extract_protocol: RNeasy protocol from Qiagene

tag: Mouse FVB/NJ, Male, Age 3 weeks, Liver, Healthy control

source_name: Mouse liver abcb4 (-/-) 3 weeks

tag: Mouse FVB.129P2-Abcb4tm1Bor/J, Male, Age 3 weeks, Liver, Sclerosing cholangitis


title: Ca6144


title: Ca6110


title: Ca6206


title: Ca6388


title: 20 weeks sample 4


title: Ca6042


title: Ca6061


title: 20 weeks sample 3


title: Ca6012


title: Ca6021


title: 20 weeks sample 2


title: 20 weeks sample 6


title: 20 weeks sample 1


title: Ca6014


title: 9 weeks sample 6


title: 9 weeks sample 5


title: 9 weeks sample 4


title: 9 weeks sample 2


title: 9 weeks sample 3


title: 9 weeks sample 1


title: Ca7422


title: 6 weeks sample 4

hyb_protocol: Agilent Hybridization Procedure (cDNA labeled targets) Version 4.1, SureHyb enabled, SSC Wash


title: 6 weeks sample 6


title: C9701

city: New York

first: Sofia

middle: K

last: Gruvberger-Saal

state: NY

address: 1130 St. Nicholas Ave., ICRC 406

department: Institute for Cancer Genetics

institute: Columbia University

description: Human breast tumor sample

hyb_protocol: Labeled targets were pooled and combined with blocking agents (12 ug poly-dA, 6 ug yeast tRNA, 20 ug Cot-1 DNA), and hybridized to microarray using the Pronto Universal Hybridization System (Corning) for 18 hours in a humidified chamber (Corning) submerged in a 42 C water bath. Slide was washing using the Pronto Universal Hybridization System.

scan_protocol: Scanned using the Agilent DNA Microarray Scanner at 10 micron resolution. The TIFF image was split and analyzed with GenePix 4.1.1.4. Result files were loaded into BioArray Software Environment. Cy3=channel 1, Cy5=channel 2.

data_processing: Data was preprocessed in the BioArray Software Environment. For each channel, the Median FG - Median BG intensity value was used. Features flagged bad/missing during image analysis were removed. Data was normalized using pin-based LOWESS (6 groups of 8 pins/group). Filtering on median Signal-to-Noise ratio was applied, keeping only those datapoints with a ch1median or ch2median SNR>=3. Features that were present in at least 80% of the 88 tumors in the series were kept, all other features were removed. Features with a variation <0.45 SD of log2(ratio) were removed. Genes and arrays were then median centered 1X.

source_name: C9701 tumor biopsy

tag: ERalpha Negative;ERbeta Positive


title: 3 weeks sample 4


title: 3 weeks sample 5


title: 6 weeks sample 1


title: 6 weeks sample 3


title: 3 weeks sample 2


title: 6 weeks sample 5


title: C9732

description: Human breast tumor sample

source_name: C9732 tumor biopsy

tag: ERalpha Negative;ERbeta Negative


title: 6 weeks sample 2


title: C9552

description: Human breast tumor sample

source_name: C9552 tumor biopsy


title: 3 weeks sample 1


title: C9765

description: Human breast tumor sample

source_name: C9765 tumor biopsy


title: 3 weeks sample 3


title: Nur77-/-_brown adipose tissue_rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Nur77-/-, brown adipose tissue

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Nur77-/-, brown adipose tissue, RNA pool of 7 knock out individuals

source_name: Wildtype, brown adipose tissue

tag: Wildtype, brown adipose tissue, pool of 7 individuals


title: 3 weeks sample 6


title: Nur77-/-_brown adipose tissue_rep2


title: Nur77-/-_brown adipose tissue_rep3


title: C9029

description: Human breast tumor sample

source_name: C9029 tumor biopsy

tag: ERalpha Positive;ERbeta Positive


title: C9077

description: Human breast tumor sample

source_name: C9077 tumor biopsy


title: C8800

description: Human breast tumor sample

source_name: C8800 tumor biopsy


title: Nur77-/-_brown adipose tissue_rep1


title: C8610

description: Human breast tumor sample

source_name: C8610 tumor biopsy


title: C8860

description: Human breast tumor sample

source_name: C8860 tumor biopsy


title: C8676

description: Human breast tumor sample

source_name: C8676 tumor biopsy


title: Nur77-/-_heart_rep4

source_name: Nur77-/-, heart

tag: Nur77-/-, heart, RNA pool of 7 knock out individuals

source_name: Wildtype, heart

tag: Wildtype, heart, pool of 7 individuals


title: C8560

description: Human breast tumor sample

source_name: C8560 tumor biopsy

tag: ERalpha Negative;ERbeta strong_Positive

source_name: Stratagene Universal Human Reference


title: C8582

description: Human breast tumor sample

source_name: C8582 tumor biopsy

tag: ERalpha Positive;ERbeta Negative


title: C8537

description: Human breast tumor sample

source_name: C8537 tumor biopsy

tag: ERalpha Positive;ERbeta strong_Positive


title: C8477

description: Human breast tumor sample

source_name: C8477 tumor biopsy


title: C8212

description: Human breast tumor sample

source_name: C8212 tumor biopsy


title: C8290

description: Human breast tumor sample

source_name: C8290 tumor biopsy


title: Nur77-/-_heart_rep1


title: C8401

description: Human breast tumor sample

source_name: C8401 tumor biopsy


title: C7845

description: Human breast tumor sample

source_name: C7845 tumor biopsy


title: Nur77-/-_heart_rep2

source_name: Wildtype, skeleton muscle


title: Nur77-/-_heart_rep3


title: C7956

description: Human breast tumor sample

source_name: C7956 tumor biopsy


title: C7921

description: Human breast tumor sample

source_name: C7921 tumor biopsy


title: Nur77-/-_skeleton muscle_rep3

source_name: Nur77-/-, skeleton muscle

tag: Nur77-/-, skeleton muscle, RNA pool of 7 knock out individuals

tag: Wildtype, skeleton muscle, pool of 7 individuals


title: C7688

description: Human breast tumor sample

source_name: C7688 tumor biopsy


title: C7604

description: Human breast tumor sample

source_name: C7604 tumor biopsy


title: C7609

description: Human breast tumor sample

source_name: C7609 tumor biopsy


title: C7811

description: Human breast tumor sample

source_name: C7811 tumor biopsy


title: Nur77-/-_skeleton muscle_rep4


title: C7583

description: Human breast tumor sample

source_name: C7583 tumor biopsy


title: C7632

description: Human breast tumor sample

source_name: C7632 tumor biopsy

source_name: Stratagene Universal Human Reference


title: C7589

description: Human breast tumor sample

source_name: C7589 tumor biopsy


title: Nur77-/-_testis_rep3

source_name: Nur77-/-, testis

tag: Nur77-/-, testis, RNA pool of 7 knock out individuals

source_name: Wildtype, testis

tag: Wildtype, testis, pool of 7 individuals


title: Nur77-/-_skeleton muscle_rep2


title: Nur77-/-_testis_rep4


title: C7549

description: Human breast tumor sample

source_name: C7549 tumor biopsy

tag: See Stratagene product # 740000.


title: Nur77-/-_testis_rep2


title: C7461

description: Human breast tumor sample

source_name: C7461 tumor biopsy


title: Nur77-/-_testis_rep1


title: C7490

description: Human breast tumor sample

source_name: C7490 tumor biopsy


title: C7519

description: Human breast tumor sample

source_name: C7519 tumor biopsy


title: Nur77-/-_skeleton muscle_rep1

source_name: Wildtype, skeleton muscle


title: C7495

description: Human breast tumor sample

source_name: C7495 tumor biopsy


title: C7367

description: Human breast tumor sample

source_name: C7367 tumor biopsy


title: Nur77-/-_spleen_rep4

source_name: Nur77-/-, spleen

tag: Nur77-/-, spleen, RNA pool of 7 knock out individuals

source_name: Wildtype, spleen

tag: Wildtype, spleen, pool of 7 individuals


title: C7422

description: Human breast tumor sample

source_name: C7422 tumor biopsy


title: C7408

description: Human breast tumor sample

source_name: C7408 tumor biopsy


title: Nur77-/-_spleen_rep3


title: Nur77-/-_spleen_rep2


title: C7246

description: Human breast tumor sample

source_name: C7246 tumor biopsy

tag: ERalpha Negative;ERbeta Positive


title: Nur77-/-_spleen_rep1


title: C7357

description: Human breast tumor sample

source_name: C7357 tumor biopsy

tag: ERalpha Negative;ERbeta Negative


title: C7168

description: Human breast tumor sample

source_name: C7168 tumor biopsy

source_name: Stratagene Universal Human Reference


title: Nur77-/-_lung_rep3

source_name: Nur77-/-, lung

tag: Nur77-/-, lung, RNA pool of 7 knock out individuals

source_name: Wildtype, lung

tag: Wildtype, lung, pool of 7 individuals


title: C7104

description: Human breast tumor sample

source_name: C7104 tumor biopsy

tag: ERalpha Positive;ERbeta Positive


title: C7244

description: Human breast tumor sample

source_name: C7244 tumor biopsy


title: C7214

description: Human breast tumor sample

source_name: C7214 tumor biopsy


title: C7102

description: Human breast tumor sample

source_name: C7102 tumor biopsy


title: C7151

description: Human breast tumor sample

source_name: C7151 tumor biopsy


title: C7170

description: Human breast tumor sample

source_name: C7170 tumor biopsy


title: C7106

description: Human breast tumor sample

source_name: C7106 tumor biopsy


title: C7035

description: Human breast tumor sample

source_name: C7035 tumor biopsy


title: Nur77-/-_lung_rep4


title: Nur77-/-_lung_rep2


title: C6716

description: Human breast tumor sample

source_name: C6716 tumor biopsy


title: C6773

description: Human breast tumor sample

source_name: C6773 tumor biopsy


title: Nur77-/-_lung_rep1


title: C6687

description: Human breast tumor sample

source_name: C6687 tumor biopsy


title: C6464

description: Human breast tumor sample

source_name: C6464 tumor biopsy


title: C6557

description: Human breast tumor sample

source_name: C6557 tumor biopsy


title: C6594

description: Human breast tumor sample

source_name: C6594 tumor biopsy


title: C6474

description: Human breast tumor sample

source_name: C6474 tumor biopsy

source_name: Stratagene Universal Human Reference


title: C6516

description: Human breast tumor sample

source_name: C6516 tumor biopsy


title: C6219

description: Human breast tumor sample

source_name: C6219 tumor biopsy


title: C6537

description: Human breast tumor sample

source_name: C6537 tumor biopsy


title: C6318

description: Human breast tumor sample

source_name: C6318 tumor biopsy


title: C6144

description: Human breast tumor sample

source_name: C6144 tumor biopsy


title: C6125

description: Human breast tumor sample

source_name: C6125 tumor biopsy


title: C6110

description: Human breast tumor sample

source_name: C6110 tumor biopsy


title: C6061

description: Human breast tumor sample

source_name: C6061 tumor biopsy


title: C6146

description: Human breast tumor sample

source_name: C6146 tumor biopsy


title: C6366

description: Human breast tumor sample

source_name: C6366 tumor biopsy


title: C6257

description: Human breast tumor sample

source_name: C6257 tumor biopsy


title: C6047

description: Human breast tumor sample

source_name: C6047 tumor biopsy


title: C6188

description: Human breast tumor sample

source_name: C6188 tumor biopsy


title: C6158

description: Human breast tumor sample

source_name: C6158 tumor biopsy


title: C6021

description: Human breast tumor sample

source_name: C6021 tumor biopsy


title: C6165

description: Human breast tumor sample

source_name: C6165 tumor biopsy


title: C11968

description: Human breast tumor sample

source_name: C11968 tumor biopsy

source_name: Stratagene Universal Human Reference


title: C6042

description: Human breast tumor sample

source_name: C6042 tumor biopsy


title: C6014

description: Human breast tumor sample

source_name: C6014 tumor biopsy


title: C11620

description: Human breast tumor sample

source_name: C11620 tumor biopsy


title: C11591

description: Human breast tumor sample

source_name: C11591 tumor biopsy


title: C10881

description: Human breast tumor sample

source_name: C10881 tumor biopsy


title: C11570

description: Human breast tumor sample

source_name: C11570 tumor biopsy


title: C10580

description: Human breast tumor sample

source_name: C10580 tumor biopsy


title: C10607

description: Human breast tumor sample

source_name: C10607 tumor biopsy


title: C10481

description: Human breast tumor sample

source_name: C10481 tumor biopsy


title: C10335

description: Human breast tumor sample

source_name: C10335 tumor biopsy


title: C10426

description: Human breast tumor sample

source_name: C10426 tumor biopsy


title: C10289

description: Human breast tumor sample

source_name: C10289 tumor biopsy


title: C10419

description: Human breast tumor sample

source_name: C10419 tumor biopsy


title: C11379

description: Human breast tumor sample

source_name: C11379 tumor biopsy


title: C6616

description: Human breast tumor sample

source_name: C6616 tumor biopsy


title: C10109

description: Human breast tumor sample

source_name: C10109 tumor biopsy


title: C11460

description: Human breast tumor sample

source_name: C11460 tumor biopsy

source_name: Stratagene Universal Human Reference


title: C10879

description: Human breast tumor sample

source_name: C10879 tumor biopsy


title: ZR-75-1 Breast cancer cell line

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: Array CGH data for the ZR-75-1 breast cancer cell line.

hyb_protocol: Arrays were hybridized and washed as described in Jönsson et al. (Genes, Chromosomes and Cancer 2007)

scan_protocol: Arrays were scanned in Agilent Microarray scanner

data_processing: Image analysis was performed using Genepix v4.0. Results file were uploaded into BASE where they were filtered and pin-based lowess normalized

label_protocol: Samples were labeled using the Invitrogen BioPrime array CGH labeling module

growth_protocol: Cells were grown according to ATCC recommendations

extract_protocol: Proteinase K treatment of cells followed by phenol-chloroform extraction

tag: ZR-75-1 breast cancer cell line

source_name: Promega reference male DNA

tag: pooled lymphoblastoid genomic DNA from ten male individuals


title: BT-474 Breast cancer cell line

description: Array CGH data for the BT-474 breast cancer cell line.

hyb_protocol: Hybridized and washed as described in Jönsson et al. (Genes, Chromosomes and Cancer 2007)

tag: BT-474 breast cancer cell line


title: JIMT Breast cancer cell line

description: Array CGH data for the JIMT breast cancer cell line.

source_name: JIMT

growth_protocol: Cells were grown according to DSMZ recommendations

tag: JIMT breast cancer cell line


title: SK-BR-3 Breast cancer cell line

description: Array CGH data for the SK-BR-3 breast cancer cell line.

tag: SK-BR-3 breast cancer cell line


title: MDA-MB-231 Breast cancer cell line

description: Array CGH data for the MDA-MB-231 breast cancer cell line.

tag: MDA-MB-231 breast cancer cell line


title: HCC1937 Breast cancer cell line

description: Array CGH data for the HCC1937 breast cancer cell line.

scan_protocol: Scanned in Agilent Microarray scanner

tag: HCC1937 breast cancer cell line


title: HCC218 Breast cancer cell line

description: Array CGH data for the HCC218 breast cancer cell line.

tag: genomic DNA was provided by ATCC


title: L56Br-C1 Breast cancer cell line

description: Array CGH data for the L56Br-C1 breast cancer cell line.

growth_protocol: Cells were grown according to suppliers recommendations

tag: L56Br-C1 breast cancer cell line


title: MDA-MB-361 Breast cancer cell line

description: Array CGH data for the MDA-MB-361 breast cancer cell line.

tag: MDA-MB-361 breast cancer cell line


title: Cell line derived from normal breast epithelium from a women with fibrocystic disease

description: Array CGH data for the MCF-10A cell line.

tag: MCF-10A cell line


title: Sasa kidney sample on day9 after waterborne challenged by IHN, replicate 5

status: Public on Mar 31 2007

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description: kidney tissue from a single fish exposed to the IHN virus in a waterborne challenge compared to a major reference pool of kidney from all collected samples, treated and untreated (n=72).

hyb_protocol: The microarray slides were prepared by washing in 0.01% SDS and 3 water washes, followed by a denaturation step at 80 oC for 3 min.  The slides were then directly placed into a pre-hybridization solution (5X SSC, 0.01% SDS; 0.2% BSA) V) at 43 oC for 1h.  The slides were washed 3 times in water and centrifuged dry using 50 ml falcon tubes and a bench top centrifuge (1600xg).  The slides were assembled into the Corning slide chambers and 3X SSC were added to the reservoirs.  The denatured targets (sample and pooled reference) were added to the slides and slide covers and chambers were assembled immediately.  The slides were incubated for 16 hr at 45 oC.  Slides were then washed at low (0.01% SDS; 1xSSC) and high (0.1X SSC) stringency, centrifuged to dry.

scan_protocol: All arrarys were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA) , adjusting the PMT gain for optimized visualization of each image.

data_processing: The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com) and processed to GeneSight (version 4.1, BioDiscovery, Inc. El Segundo, CA, www.biodiscovery.com).  Data was prepared in GeneSight as following steps: correct for background intensity using  local background correction; omit multiple spots with flags(1,2,3,4,5,6,7); raise all values below a specified value to the minimum threshold (20.0), replace missing values by the experimental means for each gene, LOWESS normalization is done locally with smoothing parameter of 0.2 and linear degree of fitness, finally calculate the log base 2 and the difference of the log2 of 2 channels. This pairMean log difference (VALUE) was used for all subsequent data analysis.

label: Alexa 555

organism: Salmo salar

source_name: kidney tissue from a fish sampled on day9 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 5

label_protocol: Twenty micrograms of total RNA were reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer’s instructions.

extract_protocol: The -80oC samples were removed and processed immediately by adding 0.75 ml of Trizol (Invitrogen) and one stainless steel 3 mm ball.  The tubes were placed in a Retsch mixer mix for two cycles of 3 min/20Hz.  Chloroform (0.3 ml) was added to the resulting homogenate and vortexed for 30 sec.  The phases were separated by centrifugation at 13000 rpm at 5 ºC for 15 min. The aqueous phase was transferred to a tube containing 0.2 ml isopropanol and mixed.  The RNA was precipitated for 5 min and then centrifuged as before. The total RNA pellet was washed with 80% cold ethanol, centrifuged, and incubated with 1 U of DNase for 15 min followed by gel electrophoresis and spectrophotometric analysis for quality and quantity.

treatment_protocol: challenged individuals were immersion challenged with the IHN virus by lowering the water level to 100 L and adding 100 ml of stock IHN virus, giving an exposure level 8.0 x 103 pfu/ml for 1 hr, kidney tissue was collected from individuals 1-14 day post-injection.

tag: Number of individuals

value: 1;  mean weight: 55.3 g; Tissue:hematopoietic end of the kidney (the anterior 1/3rd including the head and mid kidney)

label: Alexa 647

source_name: pooled reference sample from all individuals collected

label_protocol: the same as channel 1 sample

extract_protocol: kidney tissue from each individual was extracted separately as described for channel 1 sample. Equal quantities of RNA from each sample were mixed for the pooled sample.

treatment_protocol: challenged individuals were exposed to 100 ml of IHN, control individuals were exposed to100 ml of Hank’s balanced salt solution.

value: 72;  mean weight: 55.3 g; Tissue:hematopoietic end of the kidney (the anterior 1/3rd including the head and mid kidney)


title: Sasa kidney sample on day9 after waterborne challenged by IHN, replicate 2

source_name: kidney tissue from a fish sampled on day9 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 2


title: Sasa kidney sample on day5 after waterborne challenged by IHN, replicate 3

source_name: kidney tissue from a fish sampled on day5 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 3


title: Sasa kidney sample on day9 after waterborne challenged by IHN, replicate 3

source_name: kidney tissue from a fish sampled on day9 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 3


title: MCF-7 Breast cancer cell line

description: Array CGH data for the MCF-7 breast cancer cell line.

tag: MCF-7 breast cancer cell line


title: Sasa kidney sample on day9 after waterborne challenged by IHN, replicate 4

source_name: kidney tissue from a fish sampled on day9 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 4


title: Sasa kidney sample on day9 after waterborne challenged by IHN, replicate 1

source_name: kidney tissue from a fish sampled on day9 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 1


title: Sasa kidney sample on day5 after waterborne challenged by IHN, replicate 4

source_name: kidney tissue from a fish sampled on day5 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 4


title: Sasa kidney sample on day5 after waterborne challenged by IHN, replicate 5

source_name: kidney tissue from a fish sampled on day5 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 5


title: Sasa kidney sample on day5 after waterborne challenged by IHN, replicate 1

source_name: kidney tissue from a fish sampled on day5 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 1


title: Sasa kidney sample on day1 after waterborne challenged by IHN, replicate 1

source_name: kidney tissue from a fish sampled on day1 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 1


title: Sasa kidney sample on day1 after waterborne challenged by IHN, replicate 2

source_name: kidney tissue from a fish sampled on day1 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 2


title: Sasa kidney sample on day1 after waterborne challenged by IHN, replicate 5

source_name: kidney tissue from a fish sampled on day1 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 5


title: Sasa kidney sample on day5 after waterborne challenged by IHN, replicate 2

source_name: kidney tissue from a fish sampled on day5 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 2


title: Sasa kidney sample on controls, replicate 5

source_name: kidney tissue from a control fish , replicate 5

treatment_protocol: The same procedure as challenged samples was followed for the fish in a control tank except they were exposed to 100 ml of Hank’s balanced salt solution.


title: Sasa kidney sample on controls, replicate 1

source_name: kidney tissue from a control fish , replicate 1


title: Bpre_I24Rep3

status: Public on Mar 15 2007

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

country: France

institute: INRA

description: Spots positions in the 5x5 grid within the 384 blocks generated by the arrayer were retrieved in scanned 16-bits TIFF images by using the XDotsReader spot finder software (COSE, Paris France). In the raw file generated by XDotsReader, the spot position (1 to 23, odd numbers) is followed by block position (A to P; 1 to 24) in the 'def.coord' column and the raw signal intensity is given in the 'sel' column

hyb_protocol: Nylon arrays were preincubated in 30 ml of a hybridization solution (5XSSC, 5XDenhardt’s solution, 0.5% SDS, 50µg/ml shared salmon sperm DNA) for 4 h at 65°C in a rotating hybridization incubator. The arrays were then incubated in 10 ml of fresh hybridization solution containing the 33P-labeled probe at 65°C for 22 h. The hybridized arrays were washed successively for 3 x 5 min in 2X SSC at room temperature; 2 x 20 min in 2X SSC, 0.05% SDS (65°C); 2 X 20 min in 1X SSC, 0.1% SDS (65°C); and 2 x 20 min in 0.1X SSC, 0.1% SDS (65°C).

scan_protocol: Arrays were exposed to phosphorimaging screen (Eastman Kodak Company) and cDNA spots intensities were visualized by scanning at a resolution of 50 µm per pixel in a Personal Molecular Imager FX (Bio-Rad).

data_processing: Data were processed as follow: the mean value of all empty spots positions was calculated and then a flag-limit corresponding to 2 x this value was set; all spots that showed raw intensities below this flag-limit in all treatments were removed from the analysis; remaining spots intensities were centered-normalized to mean intensity value within each experiment. Statistical analyses between replicates were further processed with the CyberT statistical framework (http://visitor.ics.uci.edu/genex/cybert/index.shtml)

label: [33P]dCTP, [33P]dATP

organism: Populus trichocarpa x Populus deltoides

source_name: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain, 24 hours post-inoculation (Incompatible, I24)

label_protocol: Total RNA were treated with DNase and cDNA were aplified with SMART-PCR cDNA Synthesis Kit (BD BioSciences). cDNA probes were labelled with 30 µCi [33P]dCTP and 30 µCi [33P]dATP using the Prime-a-Gene Kit (Promega). The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN).

extract_protocol: Leaves were ground in liquid nitrogen, bead beat in QIAgen buffer RLT and then RNA were isolated with QIAgen RNeasy kit

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 93ID6 avirulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 24 hours post-inoculation


title: Bpre_I48Rep3

source_name: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain, 48 hours post-inoculation (Incompatible, I48)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 93ID6 avirulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation


title: histone H1R deletion mutant #1

status: Public on Mar 21 2007

city: Atlanta

first: Hideharu

last: Hashimoto

state: GA

address: 1510 Clifton

department: Biochemistry

institute: Emory University

data_processing: GCOS

label: standard affymetrix protcol

organism: Gallus gallus

source_name: chicken DT40

tag: histone H1R deletion mutant chicken DT40


title: Sasa kidney sample on controls, replicate 2

source_name: kidney tissue from a control fish , replicate 2

source_name: pooled reference sample from all individuals collected


title: Bpre_I24Rep2


title: Bpre_I48Rep1


title: Bpre_I12Rep1

source_name: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain, 12 hours post-inoculation (Incompatible, I12)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 93ID6 avirulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 12 hours post-inoculation


title: Bpre_I48Rep2


title: Bpre_I12Rep2


title: Sasa kidney sample on controls, replicate 4

source_name: kidney tissue from a control fish , replicate 4


title: histone H1R deletion mutant #2


title: histone H1L deletion mutant #1

tag: histone H1L deletion mutant, chicken DT40 cell


title: wild type #1

tag: wild type chicken DT40


title: Bpre_I12Rep3


title: wild type #2


title: Sasa kidney sample on day1 after waterborne challenged by IHN, replicate 4

source_name: kidney tissue from a fish sampled on day1 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 4


title: Sasa kidney sample on controls, replicate 3

source_name: kidney tissue from a control fish , replicate 3


title: Bpre_I24Rep1


title: Bpre_C48Rep2

source_name: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain, 48 hours post-inoculation (Compatible, C48)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 98AG31 virulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation


title: Bpre_C24Rep3

source_name: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain, 24 hours post-inoculation (Compatible, C24)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 98AG31 virulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 24 hours post-inoculation


title: Bpre_C48Rep1


title: Sasa kidney sample on day1 after waterborne challenged by IHN, replicate 3

source_name: kidney tissue from a fish sampled on day1 after challenged by waterborne exposure to Infectious hematopoietic necrosis (IHN)  virus, strain 93-057, replicate 3


title: Bpre_C24Rep1


title: Bpre_C48Rep3


title: Bpre_C12Rep2

source_name: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain, 12 hours post-inoculation (Compatible, C12)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 98AG31 virulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 12 hours post-inoculation


title: Bpre_C12Rep3


title: Bpre_C24Rep2


title: Bpre_T48Rep2

source_name: Beaupré leaves mock-inoculated with water, 48 hours post-inoculation (control, T48)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were mock-inoculated with water, maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation


title: Bpre_T48Rep3


title: Bpre_C12Rep1


title: Bpre_T48Rep1


title: Bpre_T24_Rep2

source_name: Beaupré leaves mock-inoculated with water, 24 hours post-inoculation (control, T24)

label_protocol: Total RNA were treated with DNase and cDNA were aplified with SMART-PCR cDNA Synthesis Kit (BD BioSciences). cDNA probes were labelled with 30 ?Ci [33P]dCTP and 30 ?Ci [33P]dATP using the Prime-a-Gene Kit (Promega). The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN).

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were mock-inoculated with water, maintained in vitro under constant illumination at 24°C and harvested 24 hours post-inoculation


title: Bpre_T24_Rep1


title: Bpre_T12_Rep1

hyb_protocol: Nylon arrays were preincubated in 30 ml of a hybridization solution (5XSSC, 5XDenhardt’s solution, 0.5% SDS, 50µg/ml  shared salmon sperm DNA) for 4 h at 65°C in a rotating hybridization incubator. The arrays were then incubated in 10 ml of fresh hybridization solution containing the 33P-labeled probe at 65°C for 22 h. The hybridized arrays were washed successively for 3 x 5 min in 2X SSC at room temperature; 2 x 20 min in 2X SSC, 0.05% SDS (65°C); 2 X 20 min in 1X SSC, 0.1% SDS (65°C); and 2 x 20 min in 0.1X SSC, 0.1% SDS (65°C).

scan_protocol: Arrays were  exposed to phosphorimaging screen (Eastman Kodak Company) and cDNA spots intensities were visualized by scanning at a resolution of 50 µm per pixel in a Personal Molecular Imager FX (Bio-Rad).

source_name: Beaupré leaves mock-inoculated with water, 12 hours post-inoculation (control, T12)

label_protocol: Total RNA were treated with DNase and cDNA were aplified with SMART-PCR cDNA Synthesis Kit (BD BioSciences). cDNA probes were labelled with 30 μCi [33P]dCTP and 30 μCi [33P]dATP using the Prime-a-Gene Kit (Promega). The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN).

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were mock-inoculated with water, maintained in vitro under constant illumination at 24°C and harvested 12 hours post-inoculation


title: Bpre_T12_Rep3


title: Bpre_T12_Rep2


title: MA-10 stably transfected with human LHR mutation Asp578His 2

status: Public on Mar 08 2007

city: Bethesda

first: TIN-LAP

last: LEE

state: MD

address: 2C08 Building 49

department: NICHD

institute: National Institutes of Health

description: cDNA from the subject (Cy3) was co-hybridized with control MA-10 cDNA labelled with (Cy5). The ratio between Cy3 and Cy5 signal was normalized and in log scale.

hyb_protocol: Microarrays were prehybridized in 1% bovine serum albumin, 5× SSC, 0.1% SDS for 45 min at 42°C, washed in H2O and dried by centrifugation. Cy3 and Cy5 labeled cDNA samples were mixed with 50 μl of hybridization buffer and applied to the microarrays for hybridization at 37°C for 16 hours in a hybridization chamber in the dark with gentle agitation. Slides were washed for 10 minutes at 50°C in 1× SSC and 0.1% SDS in shaking incubator, followed by a 1 minute wash in 1× SSC, three 1 minute washes in 0.1× SSC, and one rinse in H2O, at room temperature. Slides were dried by centrifugation.

scan_protocol: Images were acquired for Cy3 and Cy5 channels in a 16-bit TIFF format using ScanArray Express v2.2 software. Laser power and the gain on the photomultiplier tube (PMT) were kept constant during scanning of each individual slide. The PMT setting was chosen so that the highest intensity values lied below the saturation point. Spot intensity and background signals were quantified for each channel and used to generate spreadsheet data for Microsoft Excel.

data_processing: The acquired image was processed in ScanArray Express v2.2 software. All bad spots were flagged. Data obtained from each hybridization were stored in a database for analysis. Cy3/Cy5 ratios were normalized with respect to the median ratio value of all of the spots in the array. After normalization, spots with intensities for both channels (sum of medians) less than that of the local background were discarded. The ratios of the remaining spots were log transformed (base 2), and duplicated spots on the OncoChip were averaged to the median. Biological functions of selected genes were assigned by Gene Ontology databases.

source_name: MA-10 Asp578His 2

label_protocol: An indirect labeling method using aminoallyl-dUTP and amino-reactive fluorescent dyes overnight.

extract_protocol: Total RNA was extracted by Trizol reagent (invitrogen).

source_name: MA-10 cell

tag: MA-10 cell


title: Bpre_T24_Rep3


title: MA-10 control 1 transfected with empty vector

hyb_protocol: Microarrays were prehybridized in 1% bovine serum albumin, 5× SSC, 0.1% SDS for 45 min at 42°C, washed in H2O and dried by centrifugation. Cy3  and Cy5 labeled cDNA samples were mixed with 50 μl of hybridization buffer and applied to the microarrays for hybridization at 37°C for 16 hours in a hybridization chamber in the dark with gentle agitation. Slides were washed for 10 minutes at 50°C in 1× SSC and 0.1% SDS in shaking incubator, followed by a 1 minute wash in 1× SSC, three 1 minute washes in 0.1× SSC, and one rinse in H2O, at room temperature. Slides were dried by centrifugation.

data_processing: The acquired image was processed in ScanArray Express v2.2 software. All bad spots were flagged.  Data obtained from each hybridization were stored in a database for analysis. Cy3/Cy5 ratios were normalized with respect to the median ratio value of all of the spots in the array. After normalization, spots with intensities for both channels (sum of medians) less than that of the local background were discarded. The ratios of the remaining spots were log transformed (base 2), and duplicated spots on the OncoChip were averaged to the median. Biological functions of selected genes were assigned by Gene Ontology databases.

label_protocol: An indirect labeling method using 3-aminoallyl-dUTP and amino-reactive fluorescent dyes overnight.

tag: MA-10 cell stably transfected with vector only

label_protocol: An indirect labeling method using 5-aminoallyl-dUTP and amino-reactive fluorescent dyes overnight.


title: MA-10 stably transfected with human LHR mutation Asp578Gly 2

source_name: MA-10 Asp578Gly 2


title: MA-10 stably transfected with human LHR mutation Asp578Gly 1

source_name: MA-10 Asp578Gly 1


title: MA-10 control 3 transfected with empty vector


title: MA-10 stably transfected with human LHR mutation Asp578His 3

source_name: MA-10 Asp578His 3


title: MA-10 control 2 transfected with empty vector

scan_protocol: Images were acquired for Cy3 and Cy5 channels in a 16-bit TIFF format using ScanArray Express v2.2 software. Laser power and the gain on the photomultiplier tube (PMT) were kept constant during scanning of each individual slide. The PMT setting was chosen so that the highest intensity values lied below the saturation point. Spot intensity and background signals were quantified for each channel and used to generate excel table.


title: MA-10 stably transfected with human LHR mutation Asp578Gly 3

source_name: MA-10 Asp578Gly 3


title: MA-10 stably transfected with human LHR mutation Asp578His 1

source_name: MA-10 Asp578His 1


title: Beaupre_I48vsT48_Rep2

description: Detection of spots was done using the GenePix Pro 5 software coming with the Axon GenePix 4000B scanning device using implemented tools

hyb_protocol: Array hybridization was performed with hybridization buffer (GE Amersham) with 50% deionized formamide for 14h at 42°C in humid hybridization chambers (Corning) then washed 25 minutes each in 1XSSC; 0,2%SDS then 0,1XSSC; 0,2%SDS then 0,2XSSC and 3 times briefly in milliQ water (1 min) and finally dried by centrifugation at 500 rpm for 4 min

scan_protocol: Axon GenePix 4000B scanning device at 10µm resolution

data_processing: For each spot, spot mean value was subtracted by background value and ratio of means (channel1 / channel 2) was calculated. Data in the VALUE column corresponded of LogRatio normalized through RegressionRatio normalization procedure implemented in the GenePix Pro 5 software (NormalizationMethod=RegressionRatio, AllFeatures, MeanValue:1.000000; NormalizationFactors=0.701999	1.4245)

source_name: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain, 48 hours post-inoculation (Incompatible, I48)

label_protocol: After DNase treatment, RNA were amplified and Cy5-labelled with SMART cDNA synthesis kit and Custom Atlas SMART fluorescent probe labelling kit (BD BioSciences); probes were purified with QIAgen QIAquick PCR purification kit

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 93ID6 avirulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation

label_protocol: After DNase treatment, RNA were amplified and Cy3-labelled with SMART cDNA synthesis kit and Custom Atlas SMART fluorescent probe labelling kit (BD BioSciences); probes were purified with QIAgen QIAquick PCR purification kit

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were mock-inoculated with water, maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation


title: Beaupre_I48vsT48_Rep1

data_processing: For each spot, spot mean value was subtracted by background value and ratio of means (channel1 / channel 2) was calculated. Data in the VALUE column corresponded of LogRatio normalized through RegressionRatio normalization procedure implemented in the GenePix Pro 5 software (NormalizationMethod=RegressionRatio, AllFeatures, MeanValue:1.000000; NormalizationFactors=0.666326	1.50077)


title: rgt1- C. albicans 37 degrees C Slide 55 low PMT

status: Public on Mar 01 2007

city: Santa Barbara

first: Jessica

last: Sexton

state: CA

address: UCSB/MCDB

institute: UCSB

description: An additional scan was done for each slide with the PMT such that <1% of the elements are saturated in order to characterize spots which were saturated at the higher PMT setting. This is referred to here as the low PMT scan.

hyb_protocol: The labeled RNA was resuspended in a formamide based hybridization buffer (MWG “Coverslips Hybridization Buffer”), hybridized to the microarrays at 42ºC overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each.

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence. Laser power was kept constant and photomultiplier tube values were set for optimal intensity with minimal background. Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer).

data_processing: What is submitted is the raw output of ScanArray. VALUE = log2 (test/ref)

organism: Candida albicans

source_name: Total RNA from rgt1- C. albicans cultured in SC media/5% glycerol 37 degrees C

label_protocol: 5ug of total RNA was labeled using Micromax ASAP (PerkinElmer) according to the manufacturer’s instructions.

growth_protocol: For all RNA preparations, C. albicans cells from overnight cultures were diluted to an OD600 of 0.2 and grown ~ 4h in synthetic medium containing 5% glycerol as a carbon source to an OD600 of about 1.0. Cells were then diluted to an OD600 of 0.25 in 50 ml synthetic media containing various carbon sources, grown for two hours, harvested, flash frozen, and stored at -80º C until needed.

extract_protocol: To extract RNA, C. albicans cell pellets (~25 OD600 units) were resuspended in 0.5 ml TES (10 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and immediately added to 0.5 ml acid phenol. This mixture was incubated at 65º for 15 minutes, vortexed for 20 s at 3 minute intervals, and centrifuged at 4º C, 13,000 x g for 5 minutes. The aqueous phase was transferred and extracted with 0.5 ml phenol/chloroform/isoamyl alcohol, centrifuged as above, then extracted with chloroform in the same manner. RNA was precipitated overnight at -20º C in 0.1 M ammonium acetate and 70% ethanol, collected by centrifugation at 4º C, 13,000 x g for 20 minutes, washed with 70% ethanol, air dried, and resuspended in 100 µl of sterile, deionized, nuclease-free water. A typical yield for this preparation was ~ 50 µg. Each RNA preparation was further purified using the RNeasy kit from Qiagen according to the manufacturer’s recommendation. RNA was eluted in a 30 µl volume of sterile, deionized, nuclease-free water.

tag: Strain CM18

source_name: Total RNA from WT C. albicans cultured in SC media/5% glycerol 37 degrees C

tag: Strain BWP17


title: rgt1- C. albicans 37 degrees C Slide 56 low PMT


title: rgt1- C. albicans 37 degrees C Slide 57 low PMT


title: rgt1- C. albicans 37 degrees C Slide 57


title: Beaupré leaves mock-inoculated with water (control, T48 Bpre_T48_Rep1)

description: Procedure for spot detection was performed by NimbleGen Company

hyb_protocol: Hybridization by NimbleGen Company

scan_protocol: Scanning by NimbleGen Company

data_processing: Expression values reflect accross-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA) expressed as log2. For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

organism:
Populus trichocarpa
Populus deltoides

label_protocol: Labelling by NimbleGen Company


title: rgt1- C. albicans 37 degrees C Slide 54 low PMT


title: rgt1- C. albicans 37 degrees C Slide 54


title: rgt1- C. albicans 37 degrees C Slide 55


title: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain (Compatible, C48 Bpre_C48_Rep1)

source_name: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain, 48 hours post-inoculation (Compatible, C48)

tag: Detached leaves of Populus trichocarpa x Populus deltoides 'Beaupré' cuttings grown in greenhouses were inoculated with Melampsora larici-populina 98AG31 virulent strain (100000 spores/ml), maintained in vitro under constant illumination at 24°C and harvested 48 hours post-inoculation


title: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain (Incompatible, I48 Bpre_I48_Rep2)


title: rgt1- C. albicans 37 degrees C Slide 56


title: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain (Incompatible, I48 Bpre_I48_Rep3)


title: Beaupré leaves mock-inoculated with water (control, T48 Bpre_T48_Rep3)


title: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain (Compatible, C48 Bpre_C48_Rep2)


title: rgt1- C. albicans 30 degrees C Slide 24 low PMT

source_name: Total RNA from rgt1- C. albicans cultured in SC media/5% glycerol 30 degrees C

source_name: Total RNA from WT C. albicans cultured in SC media/5% glycerol 30 degrees C


title: Beaupré leaves inoculated with Melampsora larici-populina 93ID6 avirulent strain (Incompatible, I48 Bpre_I48_Rep1)


title: Beaupré leaves inoculated with Melampsora larici-populina 98AG31 virulent strain (Compatible, C48 Bpre_C48_Rep3)


title: rgt1- C. albicans 30 degrees C Slide 23 low PMT


title: H3K27Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 2

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against H3K27Ac and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27Ac antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: HeLa immunoprecipitated chromatin

source_name: Input Chromatin HeLa cells.

extract_protocol: input chromatin

value: HeLa input chromatin


title: Beaupré leaves mock-inoculated with water (control, T48 Bpre_T48_Rep2)

source_name: Beaupré leaves mock-inoculated with water, 48 hours post-inoculation (control, T48)


title: Embryonic Drosophila cells, Kc167 cells, High resolution HP1 DamID, replicate 2

status: Public on Mar 02 2007

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Embryonic Drosophila cells, Kc167 cells

hyb_protocol: Samples were hybridized by NimbleGen Systems, Reykjavik, Iceland

scan_protocol: Arrays were scanned and analyzed by NimbleGen Systems, Reykjavik, Iceland

data_processing: The log2-ratio of Dam-Fusion signal over Dam-only signal was calculated and the median over the the entire array was subtracted from the data

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP1-Dam

label_protocol: Samples were labeled by NimbleGen Systems, Reykjavik, Iceland

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length HP1 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 17, 2825-38, 2003)

tag: HP1-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Dam (REFERENCE)


title: H3K27me3 HeLa ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27me3 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27me3 antibody


title: Embryonic Drosophila cells, Kc167 cells, High resolution HP1 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, High resolution HP1 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: H3K18Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K18Ac and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K18Ac antibody


title: rgt1- C. albicans 30 degrees C Slide 21 low PMT


title: H3K27me3 HeLa ENCODE NimbleGen hg17 tiling array replicate 2


title: H3K27me3 HeLa ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K27Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 3


title: AML-ID49_Cy3L-Cy5C

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

source_name: AML patient ID49 leukemic fraction

tag: CD34+ leukemic fraction

source_name: AML patient ID49 control fraction

tag: CD34- control fraction


title: rgt1- C. albicans 30 degrees C Slide 24


title: AML-ID49_Cy3C-Cy5L


title: rgt1- C. albicans 30 degrees C Slide 21

description: An additional scan was done for each slide with the PMT such that <1% of the elements are saturated in order to characterize spots which were saturated at the higher PMT setting.  This is referred to here as the low PMT scan.

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer) to detect Cy3 and Cy5 fluorescence.  Laser power was kept constant and photomultiplier tube values were set for optimal intensity with minimal background.  Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer).

data_processing: What is submitted is the raw output of ScanArray.  VALUE = log2 (test/ref)

growth_protocol: For all RNA preparations, C. albicans cells from overnight cultures were diluted to an OD600 of 0.2 and grown ~ 4h in synthetic medium containing 5% glycerol as a carbon source to an OD600 of about 1.0.  Cells were then diluted to an OD600 of 0.25 in 50 ml synthetic media containing various carbon sources, grown for two hours, harvested, flash frozen, and stored at -80º C until needed.

extract_protocol: To extract RNA, C. albicans cell pellets (~25 OD600 units) were resuspended in 0.5 ml TES (10 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and immediately added to 0.5 ml acid phenol.  This mixture was incubated at 65º for 15 minutes, vortexed for 20 s at 3 minute intervals, and centrifuged at 4º C, 13,000 x g for 5 minutes.  The aqueous phase was transferred and extracted with 0.5 ml phenol/chloroform/isoamyl alcohol, centrifuged as above, then extracted with chloroform in the same manner.  RNA was precipitated overnight at -20º C in 0.1 M ammonium acetate and 70% ethanol, collected by centrifugation at 4º C, 13,000 x g for 20 minutes, washed with 70% ethanol, air dried, and resuspended in 100 µl of sterile, deionized, nuclease-free water.  A typical yield for this preparation was ~ 50 µg.  Each RNA preparation was further purified using the RNeasy kit from Qiagen according to the manufacturer’s recommendation.  RNA was eluted in a 30 µl volume of sterile, deionized, nuclease-free water.


title: AML-ID48_Cy3L-Cy5C

source_name: AML patient ID48 leukemic fraction

source_name: AML patient ID48 control fraction


title: AML-ID48_Cy3C-Cy5L


title: rgt1- C. albicans 30 degrees C Slide 22 low PMT


title: rgt1- C. albicans 30 degrees C Slide 22


title: rgt1- C. albicans 30 degrees C Slide 23


title: AML-ID47_Cy3L-Cy5C

source_name: AML patient ID47 leukemic fraction

source_name: AML patient ID47 control fraction


title: AML-ID44_Cy3L-Cy5C

source_name: AML patient ID44 leukemic fraction

source_name: AML patient ID44 control fraction


title: AML-ID36_Cy3L-Cy5C

source_name: AML patient ID36 leukemic fraction

source_name: AML patient ID36 control fraction


title: AML-ID44_Cy3C-Cy5L


title: AML-ID43_Cy3L-Cy5C

source_name: AML patient ID43 leukemic fraction

source_name: AML patient ID43 control fraction


title: AML-ID43_Cy3C-Cy5L


title: H3K9Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K9Ac and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K9Ac antibody

source_name: Input Chromatin HeLa cells.


title: AML-ID47_Cy3C-Cy5L


title: AML-ID36_Cy3C-Cy5L


title: H3K18Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 2


title: AML-ID32_Cy3L-Cy5C

source_name: AML patient ID32 leukemic fraction

source_name: AML patient ID32 control fraction


title: AML-ID32_Cy3C-Cy5L


title: AML-ID28_Cy3C-Cy5L

source_name: AML patient ID28 control fraction

source_name: AML patient ID28 leukemic fraction


title: AML-ID28_Cy3L-Cy5C


title: H3K9Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 2


title: CTCF HeLa ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from HeLa cells using CTCF antibody


title: CTCF HeLa ENCODE NimbleGen hg17 tiling array replicate 3


title: AML-ID29_Cy3L-Cy5C

source_name: AML patient ID29 leukemic fraction

source_name: AML patient ID29 control fraction


title: AML-ID13_Cy3L-Cy5C

source_name: AML patient ID13 leukemic fraction

source_name: AML patient ID13 control fraction


title: AML-ID29_Cy3C-Cy5L


title: AML-ID09_Cy3L-Cy5C

source_name: AML patient ID09 leukemic fraction

source_name: AML patient ID09 control fraction


title: AML-ID13_Cy3C-Cy5L


title: H3K18Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K18Ac antibody


title: AML-ID10_Cy3C-Cy5L

source_name: AML patient ID10 control fraction

source_name: AML patient ID10 leukemic fraction


title: AML-ID10_Cy3L-Cy5C


title: AML-ID07_Cy3C-Cy5L

source_name: AML patient ID07 control fraction

source_name: AML patient ID07 leukemic fraction


title: H3K27Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27Ac antibody

source_name: Input Chromatin HeLa cells.


title: H3K9Ac HeLa ENCODE NimbleGen hg17 tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K9Ac antibody


title: AML-ID05_Cy3L-Cy5C

source_name: AML patient ID05 leukemic fraction

source_name: AML patient ID05 control fraction


title: AML-ID05_Cy3C-Cy5L


title: AML-ID09_Cy3C-Cy5L


title: AML-ID06_Cy3C-Cy5L

source_name: AML patient ID06 control fraction

source_name: AML patient ID06 leukemic fraction


title: AML-ID06_Cy3L-Cy5C


title: 3 hrs Post-clamp sample 5

city: Malmö

first: Hemang

last: Parikh

address: Building 91, Plan 12, CRC, Entrance 72, Malmö University Hospital

department: Department of Clinical Sciences-Diabetes and Endocrinology

description: Skeletal muscle biopsy was obtained after a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data was normalized via means scaling

label: biotin

source_name: Skeletal muscle biopsy

label_protocol: standard Affymetrix procedures

extract_protocol: Muscle biopsy was extracted by guadinium thiocyanate method

tag: Muscle biopsy was obtained from the vastus lateralis muscle


title: AML-ID07_Cy3L-Cy5C


title: 3 hrs Pre-clamp sample 5

description: Skeletal muscle biopsy was obtained before a 3-hour hyperinsulinemic (infusion rate 40 mU/m2/min) euglycemic clamp


title: 3 hrs Post-clamp sample 6


title: 3 hrs Pre-clamp sample 6


title: AML-ID04_Cy3L-Cy5C

source_name: AML patient ID04 leukemic fraction

source_name: AML patient ID04 control fraction


title: 3 hrs Post-clamp sample 3


title: CTCF HeLa ENCODE NimbleGen hg17 tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HeLa cells using CTCF antibody


title: 3 hrs Post-clamp sample 4


title: AML-ID04_Cy3C-Cy5L


title: 3 hrs Pre-clamp sample 3


title: 3 hrs Pre-clamp sample 4


title: 3 hrs Post-clamp sample 2


title: 3 hrs Pre-clamp sample 1


title: 3 hrs Post-clamp sample 1


title: 3 hrs Pre-clamp sample 2


title: Ptdsr_embryo_E12.5_rep10

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

source_name: Ptdsr-/- Embryo, E12.5

tag: Ptdsr-/- Embryo, E12.5  #20

source_name: Ptdsr+/+ Embryo, E12.5


title: Ptdsr_embryo_E12.5_rep9

tag: Ptdsr-/- Embryo, E12.5 #20


title: Ptdsr_embryo_E13.5_rep1

source_name: Ptdsr-/- Embryo, E13.5

tag: Ptdsr-/- Embryo, E13.5 #36

source_name: Ptdsr+/+ Embryo, E13.5


title: Ptdsr_embryo_E12.5_rep13


title: Ptdsr_embryo_E13.5_rep2


title: Ptdsr_embryo_E13.5_rep4


title: Ptdsr_embryo_E12.5_rep6

tag: Ptdsr-/- Embryo, E12.5 #59

tag: Ptdsr+/+ Embryo, E12.5 pool


title: Ptdsr_embryo_E12.5_rep11


title: Ptdsr_embryo_E12.5_rep2

tag: Ptdsr-/- Embryo, E12.5 #60


title: Ptdsr_embryo_E12.5_rep1


title: Ptdsr_embryo_E12.5_rep8


title: Ptdsr_embryo_E12.5_rep4


title: Ptdsr_embryo_E11.5_rep3

source_name: Ptdsr-/- Embryo, E11.5

tag: Ptdsr-/- Embryo, E11.5  #10

source_name: Ptdsr+/+ Embryo, E11.5

tag: Ptdsr+/+ Embryo, E11.5 #4


title: Ptdsr_embryo_E12.5_rep3


title: Ptdsr_embryo_E13.5_rep3


title: Ptdsr_embryo_E11.5_rep2

tag: Ptdsr-/- Embryo, E11.5 #2


title: Ptdsr-/- fibroblast_rep13

source_name: Ptdsr-/- fibroblast

tag: k.o. fibroblast cell culture

source_name: Wt fibroblast

tag: Wt fibroblast cell culture


title: Ptdsr_embryo_E12.5_rep7


title: Ptdsr_embryo_E12.5_rep5

tag: Ptdsr-/- Embryo, E12.5  #59


title: Ptdsr-/- fibroblast_rep14


title: Ptdsr_embryo_E11.5_rep1

tag: Ptdsr-/- Embryo, E11.5 #10


title: Ptdsr-/- fibroblast_rep12


title: Ptdsr_embryo_E11.5_rep4

tag: Ptdsr-/- Embryo, E11.5  #2


title: Ptdsr-/- fibroblast_rep11


title: Ptdsr-/- fibroblast_rep10


title: H3K18Ac K562 RenLab ENCODE PCR tiling array replicate 4 ENC1879

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K18Ac antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: NimbleGen

source_name: Input DNA from K562 cells

tag: Input DNA from K562 cells


title: MPSS profiling of embryonic gonad in chicken

type: MPSS

city: Seoul

first: heebal

last: kim

address: San 56-1 Sillim-dong Gwanak-gu

country: South Korea

institute: Seoul National University

description:
The abundance for each signature was converted to transcripts per million (TPM).
Total number of sequenced signatures were 1,012,533.
The sequencing runs were merged and the expression level of each signature were normalized in units of transcripts per million signatures (TPM) (Meyers, Tej et al. 2004)
Brenner, S., M. Johnson, et al. (2000). "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays." Nat Biotechnol 18(6): 630-4.
Brenner, S., S. R. Williams, et al. (2000). "In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs." Proc Natl Acad Sci U S A 97(4): 1665-70.
Meyers, B. C., S. S. Tej, et al. (2004). "The use of MPSS for whole-genome transcriptional analysis in Arabidopsis." Genome Res 14(8): 1641-53.
Ruan, Y., P. Le Ber, et al. (2004). "Interrogating the transcriptome." Trends Biotechnol 22(1): 23-30.
Wallis, J. W., J. Aerts, et al. (2004). "A physical map of the chicken genome." Nature 432(7018): 761-4.

data_processing: normalization method

source_name: embryonic gonad

extract_protocol: Total RNA was isolated from 4 samples by TRIzol® Reagent and checked by Agilent 2100 Bioanlyzer. After quality check, 4 samples of Sample#2(G) were mixed respectively. The mixed RNAs were treated with RNase-free DNase I and checked by Agilent 2100 Bioanalyzer. The RNAs were processed according to the MPSS protocol as outlined in the references (Brenner, Johnson et al. 2000; Brenner, Williams et al. 2000; Ruan, Le Ber et al. 2004). Briefly, each total RNA was reverse transcribed and the cDNA was digested with DpnII. MmeI site-containing adapter was ligated and the 3’-most DpnII fragment (signature) was obtained and cloned into a Tag vector. The resulting libraries, more than 1.3M total complexity for each sample, were amplified and loaded onto microbeads. More than 1.0 million microbeads were loaded into each flowcell and the signature sequences were determined by a series of enzymatic reactions as outlined in the references (Brenner, Johnson et al. 2000; Brenner, Williams et al. 2000; Man, Wang et al. 2000; Ruan, Le Ber et al. 2004).

tag: gonads of 6.5-day-old (stage 29) White Leghorn (WL) embryos


title: Ptdsr-/- fibroblast_rep9

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562


title: CTCF K562 RenLab ENCODE PCR tiling array replicate 3 ENC1880

source_name: Chromatin immunoprecipitated DNA from K562 cells using CTCF antibody


title: MPSS profiling of primordial germ cells in chicken

source_name: primordial germ cells (PGCs)

extract_protocol: Total RNA was isolated from 7 samples by TRIzol® Reagent and checked by Agilent 2100 Bioanlyzer. After quality check, 7 samples of Sample#1(P) were mixed respectively. The mixed RNAs were treated with RNase-free DNase I and checked by Agilent 2100 Bioanalyzer. The RNAs were processed according to the MPSS protocol as outlined in the references (Brenner, Johnson et al. 2000; Brenner, Williams et al. 2000; Ruan, Le Ber et al. 2004). Briefly, each total RNA was reverse transcribed and the cDNA was digested with DpnII. MmeI site-containing adapter was ligated and the 3’-most DpnII fragment (signature) was obtained and cloned into a Tag vector. The resulting libraries, more than 1.3M total complexity for each sample, were amplified and loaded onto microbeads. More than 1.0 million microbeads were loaded into each flowcell and the signature sequences were determined by a series of enzymatic reactions as outlined in the references (Brenner, Johnson et al. 2000; Brenner, Williams et al. 2000; Man, Wang et al. 2000; Ruan, Le Ber et al. 2004).


title: Ptdsr-/- fibroblast_rep8


title: Ptdsr-/- fibroblast_rep4


title: H3K18Ac K562 RenLab ENCODE PCR tiling array replicate 2 ENC1877

tag: Chromatin immunoprecipitated DNA from K562 cells using H3K18Ac antibody


title: Ptdsr-/- fibroblast_rep2


title: H3K18Ac K562 RenLab ENCODE PCR tiling array replicate 3 ENC1878


title: Ptdsr-/- fibroblast_rep6


title: Ptdsr-/- fibroblast_rep1

source_name: wt fibroblast


title: Ptdsr-/- fibroblast_rep5


title: p300(C-20) K562 RenLab ENCODE PCR tiling array replicate 3 ENC1858

source_name: Chromatin immunoprecipitated DNA from K562 cells using p300(C-20) antibody


title: p300(C-20) K562 RenLab ENCODE PCR tiling array replicate 2 ENC1857

tag: Chromatin immunoprecipitated DNA from K562 cells using p300(C-20) antibody


title: H3K4me3 K562 RenLab ENCODE PCR tiling array replicate 1 ENC1806

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3 antibody


title: Ptdsr-/- fibroblast_rep7


title: H3K18Ac HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1836

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K18Ac antibody

source_name: Input DNA from HeLa cells

tag: Input DNA from HeLa cells


title: Ptdsr-/- fibroblast_rep3


title: CTCF K562 RenLab ENCODE PCR tiling array replicate 2 ENC1862

tag: Chromatin immunoprecipitated DNA from K562 cells using CTCF antibody


title: H3K4me3 K562 RenLab ENCODE PCR tiling array replicate 2 ENC1807

tag: Chromatin immunoprecipitated DNA from K562 cells using H3K4me3 antibody


title: CTCF K562 RenLab ENCODE PCR tiling array replicate 1 ENC1861


title: p300(C-20) K562 RenLab ENCODE PCR tiling array replicate 1 ENC1856


title: H3K27Ac HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1837

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27Ac antibody


title: H3K4me2 K562 RenLab ENCODE PCR tiling array replicate 1 ENC1808

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me2 antibody


title: H3K4me3 K562 RenLab ENCODE PCR tiling array replicate 3 ENC1844


title: H3K4me2 K562 RenLab ENCODE PCR tiling array replicate 3 ENC1810

tag: Chromatin immunoprecipitated DNA from K562 cells using H3K4me2 antibody


title: H3K27Ac K562 RenLab ENCODE PCR tiling array replicate 3 ENC1784

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K27Ac antibody


title: H3K4me2 K562 RenLab ENCODE PCR tiling array replicate 2 ENC1809


title: H3K9Ac HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1764

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K9Ac antibody


title: H3K18Ac K562 RenLab ENCODE PCR tiling array replicate 1 ENC1746


title: H3K4me1 K562 RenLab ENCODE PCR tiling array replicate 1 ENC1738

source_name: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: H3K27Ac K562 RenLab ENCODE PCR tiling array replicate 1 ENC1782

tag: Chromatin immunoprecipitated DNA from K562 cells using H3K27Ac antibody


title: H3K27Ac K562 RenLab ENCODE PCR tiling array replicate 2 ENC1783


title: H3K4me1 K562 RenLab ENCODE PCR tiling array replicate 2 ENC1739

tag: Chromatin immunoprecipitated DNA from K562 cells using H3K4me1 antibody


title: H3K9Ac HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1763

tag: Chromatin immunoprecipitated DNA from HeLa cells using H3K9Ac antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 15 ENC1759

source_name: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody


title: H3K4me1 K562 RenLab ENCODE PCR tiling array replicate 3 ENC1740


title: TAFII p250 (6B3) K562 RenLab ENCODE PCR tiling array replicate 2 ENC1734

source_name: Chromatin immunoprecipitated DNA from K562 cells using TAFII p250 (6B3) antibody


title: H4K20me3 HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1704

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me3 antibody


title: TAFII p250 (6B3) K562 RenLab ENCODE PCR tiling array replicate 3 ENC1735

tag: Chromatin immunoprecipitated DNA from K562 cells using TAFII p250 (6B3) antibody

source_name: Input DNA from K562 cells


title: H3K27me3 HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1714

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27me3 antibody


title: H3K27me3 HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1715

tag: Chromatin immunoprecipitated DNA from HeLa cells using H3K27me3 antibody


title: p300(C-20) IMR90 RenLab ENCODE PCR tiling array replicate 4 ENC1683

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using p300(C-20) antibody

source_name: Input DNA from IMR90 cells

tag: Input DNA from IMR90 cells


title: H4K20me1 HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1702

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me1 antibody


title: TAFII p250 (6B3) K562 RenLab ENCODE PCR tiling array replicate 1 ENC1733


title: H4K20me2 HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1703

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me2 antibody


title: H3K27Ac HeLa RenLab ENCODE PCR tiling array replicate 4 ENC1712

tag: Chromatin immunoprecipitated DNA from HeLa cells using H3K27Ac antibody


title: H3K27me3 HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1713


title: H3K27Ac HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1677


title: H3K9Ac HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1676


title: H3K18Ac HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1711

tag: Chromatin immunoprecipitated DNA from HeLa cells using H3K18Ac antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 12 ENC1667

tag: Chromatin immunoprecipitated DNA from HeLa cells using TAFII p250 (6B3) antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 13 ENC1668


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 14 ENC1669


title: p300(C-20) IMR90 RenLab ENCODE PCR tiling array replicate 2 ENC1636

tag: Chromatin immunoprecipitated DNA from IMR90 cells using p300(C-20) antibody


title: H2A.Z HeLa RenLab ENCODE PCR tiling array replicate 3 ENC1645

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H2A.Z antibody


title: p300(C-20) IMR90 RenLab ENCODE PCR tiling array replicate 1 ENC1633


title: H3K4me1 IMR90 RenLab ENCODE PCR tiling array replicate 2 ENC1634

source_name: Chromatin immunoprecipitated DNA from IMR90 cells using H3K4me1 antibody


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 10 ENC1588

source_name: Input DNA from HeLa cells


title: TAFII p250 (6B3) HeLa RenLab ENCODE PCR tiling array replicate 11 ENC1589


title: H4K20me3 HeLa RenLab ENCODE PCR tiling array replicate 2 ENC1578

tag: Chromatin immunoprecipitated DNA from HeLa cells using H4K20me3 antibody