title: Embryonic Drosophila cells, Kc167 cells, D1 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing D1-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. Full length D1 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).

tag: D1-Dam (EXPERIMENTAL)


title: Postnatal lungs at 21 Days (Mu11KA)

status: Public on Apr 07 2008

type: RNA

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Avenue Box 850

department: Pediatrics

country: USA

institute: University of Rochester Medical Center

description: Lung

hyb_protocol: Twenty-five micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mu11K sub A and B chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Standard Affymetrix protocol

data_processing: Chips were scanned and the intensity of signal was computed using GeneChip Analysis Suite version 3.3 (Affymetrix, Santa Clara, CA). All chip intensities were scaled to an average of 1,500 units for comparison (inter-experiment scaling) purposes.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: normal lung

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: Ten micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of three individual lungs. This step was performed to minimize both biologic variability and the number of microarrays necessary to generate informative data. After pooling, RNA was re-purified using Qiagen purification kits (Valencia, CA). Target cRNA was synthesized according to manufacturer's protocol. Briefly, total RNA was reverse transcribed into a complete cDNA library (SuperScript Choice kit; Invitrogen) using a T7/T24 primer (Genset Corp., La Jolla, CA). This cDNA was subsequently in vitro transcribed into biotin-labeled cRNA (High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The resulting cRNA was fragmented and assessed for quality by gel electrophoresis.  Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols

tag: Strain

value: Swiss webster, Age:post natal 21 days,Tissue:normal lung


title: Ago2 Hek293 FLAG-Ago2 IP (3)

status: Public on Apr 08 2008

city: Stanford

first: Daniel

last: Hogan

state: CA

address: 279 Campus Dr B439

institute: Stanford University

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67821.gif
Measurement: mass(absolute) 10 ug

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.13; Parameter Scan Time = 20:07:24; Parameter PMT Volts = 461; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.13; Parameter Scan Time = 20:07:24; Parameter PMT Volts = 505; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: amplified RNA from HEK293T cell lysate

label_protocol: not provided

extract_protocol: not provided

tag: amplified RNA from HEK293T cell lysate

source_name: amplified RNA after FLAG-Ago2 affinity purification

tag: Measurement

value: mass(absolute) 10 ug


title: Embryonic Drosophila cells, Kc167 cells, D1 DamID, replicate 2

type: genomic

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 to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed in four subsequent steps. The respective washing buffers were: 1X SSC/0.03% SDS (arrays were submerged once), 1XSSC (arrays were submerged 15 times), 0.2XSSC (20 minutes), 0.05XSSC (10 minutes).

data_processing: After removal of low quality, redundant or ambiguous proves, hybridization data of 9,993 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: Sample labeling 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)

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)

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).

tag: Dam (REFERENCE)


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 5

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing H1-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. Full length H1 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).

tag: H1-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, Sir2 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Sir2-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. Full length Sir2 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).

tag: Sir2-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Sir2 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Su(var)3-7-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. Full length Su(var)3-7 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).

tag: Su(var)3-7-Dam (EXPERIMENTAL)


title: Postnatal lungs at 10 Days (Mu11KA)

description: Lung

value: Swiss webster, Age:post natal 10 days,Tissue:normal lung


title: Ago2 Hek293 FLAG-Ago2 Expression (2)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72488.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 250, 1940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.00; Parameter Scan Time = 13:29:42; Parameter PMT Volts = 360; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58761; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.00; Parameter Scan Time = 13:29:42; Parameter PMT Volts = 358; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58760; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: UNIVERSAL REFERENCE

tag: UNIVERSAL REFERENCE

source_name: amplified RNA from HEK293T cells

tag: amplified RNA from HEK293T cells


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Postnatal lungs at 1 Day (Mu11KA)

description: Lung

value: Swiss webster, Age:post natal 1 day,Tissue:normal lung


title: Postnatal lungs at 14 Days (Mu11KA)

description: Lung

value: Swiss webster, Age:post natal 14 days,Tissue:normal lung


title: Embryonic Drosophila cells, Kc167 cells, Mnt DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Mnt-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. Full length Mnt 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).

tag: Mnt-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, Mnt DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Mnt DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, DSP1 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing DSP1-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. Full length DSP1 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).

tag: DSP1-Dam (EXPERIMENTAL)


title: Postnatal lungs at 4 Days (Mu11KA)

description: Lung

value: Swiss webster, Age:post natal 4 days,Tissue:normal lung


title: Embryonic Drosophila cells, Kc167 cells, D1 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Postnatal lungs at 7 Days (Mu11KA)

description: Lung

value: Swiss webster, Age:post natal 7 days,Tissue:normal lung


title: Embryonic lungs at 14 Days (Mu11KA)

description: Embryonic lung

value: Swiss webster, Age:embryonic 14 days,Tissue:normal lung


title: Embryonic lungs at 18 Days (Mu11KA)

description: Embryonic lung

value: Swiss webster, Age:embryonic 18 days,Tissue:normal lung


title: Embryonic Drosophila cells, Kc167 cells, D1 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Gro DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Gro-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. Full length Gro 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).

tag: Gro-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, Gro DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Sin3 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Sin3-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. Full length Sin3 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).

tag: Sin3-Dam (EXPERIMENTAL)


title: Embryonic lungs at 16 Days (Mu11KA)

description: Embryonic lung

value: Swiss webster, Age:embryonic 16 days,Tissue:normal lung


title: Embryonic Drosophila cells, Kc167 cells, DSP1 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Sin3 DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Sin3 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Adult lungs (Mu11KB)

description: Lung

value: Swiss webster, Age:adult,Tissue:normal lung


title: Embryonic Drosophila cells, Kc167 cells, MBD-like DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MBD-like-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. Full length MBD-like 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).

tag: MBD-like-Dam (EXPERIMENTAL)


title: Embryonic lungs at 12 Days (Mu11KA)

description: Embryonic lung

value: Swiss webster, Age:embryonic 12 days,Tissue:normal lung


title: Postnatal lungs at 14 Days (Mu11KB)

description: Lung


title: Postnatal lungs at 10 Days (Mu11KB)

description: Lung


title: Postnatal lungs at 21 Days (Mu11KB)

description: Lung


title: Embryonic Drosophila cells, Kc167 cells, Gro DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Postnatal lungs at 7 Days (Mu11KB)

description: Lung


title: Embryonic Drosophila cells, Kc167 cells, MBD-like DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Postnatal lungs at 4 Days (Mu11KB)

description: Lung


title: Embryonic Drosophila cells, Kc167 cells, GAGA DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing GAGA-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. Full length GAGA 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).

tag: GAGA-Dam (EXPERIMENTAL)


title: Embryonic Drosophila cells, Kc167 cells, GAGA DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, MBD-like DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Postnatal lungs at 1 Day (Mu11KB)

description: Lung


title: Embryonic lungs at 12 Days (Mu11KB)

description: Embryonic lung


title: Embryonic lungs at 18 Days (Mu11KB)

description: Embryonic lung


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Brm DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Brm-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. Full length Brm 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).

tag: Brm-Dam (EXPERIMENTAL)


title: Embryonic lungs at 14 Days (Mu11KB)

description: Embryonic lung


title: Embryonic Drosophila cells, Kc167 cells, Bicoid DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Bicoid-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. Full length Bicoid 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).

tag: Bicoid-Dam (EXPERIMENTAL)


title: Embryonic lungs at 16 Days (Mu11KB)

description: Embryonic lung

source_name: normal lung

tag: Strain


title: Embryonic Drosophila cells, Kc167 cells, Bicoid DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Bicoid DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Brm DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Brm DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP1 (HyQ) DamID, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

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

growth_protocol: Drosophila Kc cells were grown in HyClone SFX-Insect medium (HyClone) 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).

tag: HP1-Dam (EXPERIMENTAL)

growth_protocol: Drosophila Kc cells were grown in HyClone SFX-Insect medium (HyClone) 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).


title: Embryonic Drosophila cells, Kc167 cells, HP1 (HyQ) DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, HP1 (HyQ) DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: MN16_swap

status: Public on Apr 05 2008

city: São Paulo

first: Nádia

middle: Pereira

last: Castro

state: SP

address: R: Prof Antônio Prudente, 211

country: Brazil

institute: Hospital AC Camargo

description: Fresh-frozen human breast samples were retrieved from the Tumor Tissue Biobank of the Medical and Research Center - Hospital A. C. Camargo, São Paulo. This research was approved by Ethic Committee of the Medical and Research Center - Hospital A. C. Camargo under number 587/04 and a written informed consent signed by all participants. All patients had presented at least 5 years of follow-up. Thirty samples were evaluated, 4 non-neoplastic breast samples, 5 pure DCIS (stage 0), 11 DCIS with co-existing IDC and 10 IDC. The non-neoplastic samples were obtained from perilesional mammary specimens from patients submitted to resection of benign lesions. All cells types were laser capture microdissected using PixCell II LCM system (Arcturus Engineering, Mountain View, CA). HB4a normal luminal epithelial mammary cell line (O’Hare et al 1991) was used as reference for microarray hybridizations. Dye swap was performed for each sample analyzed and used as replicate samples.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:5 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:10 min / Washing Number: 2 Washing - Round 3 - Solution: 0,1 X SSC / Temperature:sol 42C / Lavagem TA / Time:2,5 min / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Sample VALUEs represent Lowess-normalized, log2(test/ref) ratios.

label_protocol: A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP.

extract_protocol: Trizol

tag: Normal luminal epithelial mammary cell line

extract_protocol: The total RNA was extracted by using the PicoPureä RNA Isolation kit (Arcturus Engineering # KT0204).


title: Embryonic Drosophila cells, Kc167 cells, DSP1 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

tag: Dam (REFERENCE)


title: 86DCIS_control

tag: Age


title: MN19_swap

tag: perilesional mammary specimens from patients submitted to resection of benign lesions


title: 85DCIS_control

tag: Stage I, Age


title: MN19_control


title: MN18_control


title: MN18_swap


title: MN14_control


title: 87DCIS_swap

tag: Stage

value: IIa, Age:48, T2N1M0, Nuclear Grade:3, ER-, PR-, p53 -, HER2 + (2+)


title: 85DCIS_swap


title: 81IDC_control

value: IIb, Age:31, T2N1M0, Nuclear Grade:3, ER-, PR-, p53+, HER2 + (3+)


title: MN16_control


title: 86DCIS_swap


title: 87DCIS_control


title: 83IDC_swap

value: IIa, Age:48, T2N0M0, Nuclear Grade:2, ER+, PR+, p53-, HER2 + (2+)


title: 81IDC_swap


title: MN14_swap


title: 80IDC_swap

value: IIa, Age:44, T1cN1M0, Nuclear Grade:3, ER+, PR+, p53-, HER2 -


title: 80IDC_control


title: 83IDC_control


title: 75DCIS_control

tag: Stage IIb, Age


title: 75DCIS_swap


title: 66DCIS_swap

tag: Stage IIIb, Age

value: 44, T4bN1M0, Nuclear Grade:3, ER+, PR+, p53 +, HER2 - (1+)


title: 69DCIS_swap

tag: Stage IIIa, Age

value: 57, T2N2M0, Nuclear Grade:2, ER+, PR+, HER2 + (2+)


title: 66DCIS_control

source_name: HB4a - Reference


title: 53IDC_control

value: IIIa, Age:43, T2N2M0, Nuclear Grade:3, ER+, PR+, HER2 + (2+)


title: 69DCIS_control


title: 49DCIS-0_control

value: 0, Age:58, T1cN0M0, Nuclear Grade:3, ER-, PR-, p53-, HER2 + (3+)


title: 56IDC_control

value: I


title: 50IDC_control

value: IIIb, Age:71, T4N2M0, Nuclear Grade:3, ER+, PR+, p53+, HER2 + (2+)


title: 51IDC_control

value: IIa, Age:43, T2N0M0, Nuclear Grade:3, ER-, HER2 + (3+)


title: 56IDC_swap


title: 48DCIS-0_swap


title: 51IDC_swap


title: 53IDC_swap


title: 46DCIS-0_control


title: 50IDC_swap


title: 48DCIS-0_control


title: LThio-LS Slide S20

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

description: The objective of this study is to identify the genes differentially expressed in dissimilatory sulfate reduction by D. vulgaris using thiosulfate as the electron acceptor as compared to sulfate as the electron donor. Lactate was the sole electron donor under both culturing conditions.

data_processing: Lowess intensity-based normalization.  He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Cells grown with Lactate + Thiosulfate

growth_protocol: D. vulgaris (DSM 644) was grown in a modified medium C at 37ºC, under an anoxic atmosphere of N2. The modified medium C contained 25 micromolar FeSO4.7H2O and 1 micromolar NiCl2.6H2O. Medium C-LS contained 40 mM lactate and 40 mM sulfate, and was used as a control. Pyruvate (40 mM) and thiosulfate (40 mM) were used as an alternative electron donor and acceptor, respectively. Fermentative growth was carried out with pyruvate (40 mM). Media (1000-ml) were dispensed in 2000-ml DURAN® SHOTT bottles, flushed with N2 and sealed with butyl rubber stoppers. Cultures with hydrogen as electron donor were grown in a 3L fermentor containing 2L of growth medium with 40 mM acetate, gassed with a mixture of 80 % (vol/vol) H2, 20 % (vol/vol) CO2 at 900 ml/min, stirred at 250 rpm and with a constant pH of 6.8. As a control, D. vulgaris was grown in the same conditions but in Medium C-LS, and gassed with N2. In both procedures a 10% (vol/vol) inoculum of a freshly grown culture of D. vulgaris in the same conditions of the experiment was used, with exception to pyruvate culture where the inoculum was grown in pyruvate/sulfate medium. The optical density of the cultures at 600 nm (OD600) was determined with a Shimadzu UV-1603 spectrophotometer.

treatment_protocol: Cells grown with thiosulfate as the electron acceptor for sulfate reduction

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with lactate as the only electron donor and thiosulfate as the only electron acceptor.

source_name: Cells grown with Lactate + Sulfate

treatment_protocol: Cells grown with sulfate as the electron acceptor for sulfate reduction

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with lactate as the only electron donor and sulfate as the only electron acceptor.


title: LThio-LS Slide W

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: LThio-LS Slide F

scan_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: LThio-LS Slide AV

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: 45DCIS_swap

value: 55, T1N0M0, Nuclear Grade:3, ER-, PR-, p53 +, HER2 (3+)


title: 46DCIS-0_swap


title: LThio-LS Slide AU

extract_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Embryonic Drosophila cells, Kc167 cells, Mnt DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

tag: Mnt-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam


title: 49DCIS-0_swap


title: LThio-LS Slide X


title: 45DCIS_control


title: 44DCIS-0_control

value: 0, Age:44, T0N0M0, Nuclear Grade:3, ER+, PR+, p53-, HER2 +


title: 44DCIS-0_swap


title: PyrS-LS Slide U

description: The objective of this study is to identify the genes differentially expressed in dissimilatory sulfate reduction by D. vulgaris using pyruvate as the electron donor as compared to lactate as the electron donor.

source_name: Cells grown with pyruvate as the electron donor during sulfate reduction

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with pyruvate as the only electron donor and sulfate as the only electron acceptor.

source_name: Cells grown with lactate as the electron donor during sulfate reduction

treatment_protocol: Cells grown with lactate as the electron donor.


title: LThio-LS Slide AT


title: 43DCIS-0_swap


title: PyrS-LS Slide V

treatment_protocol: Cells grown with pyruvate as the electron donor


title: 3IDC_swap

value: IIa, Age:43, T1cN0M0, Nuclear Grade:3, ER+, PR-, p53 -, HER2 + (3+)


title: Embryonic Drosophila cells, Kc167 cells, GAGA DamID, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

tag: GAGA-Dam (EXPERIMENTAL)


title: 43DCIS-0_control


title: PyrS-LS Slide AY


title: 33DCIS_swap

value: 38, T1cN0M0, Nuclear Grade:3, ER+, PR-, p53 -, HER2 -


title: PyrS-LS Slide AX


title: PyrS-LS Slide E


title: 33DCIS_control


title: PyrS-LS Slide B


title: H2-LS Slide Y

description: The objective of this study is to identify the genes differentially expressed in dissimilatory sulfate reduction by D. vulgaris using hydrogen as the electron donor as compared to lactate as the electron donor.

data_processing: Lowess intensity-based normalization. He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

source_name: Cells grown with hydrogen as the electron donor during sulfate reduction

growth_protocol: D. vulgaris (DSM 644) was grown in a modified medium C at 37ºC, under an anoxic atmosphere of N2. The modified medium C contained 25 micromolar FeSO4.7H2O and 1 micromolar NiCl2.6H2O. Medium C-LS contained 40 mM lactate and 40 mM sulfate, and was used as a control. Pyruvate (40 mM) and thiosulfate (40 mM) were used as an alternative electron donor and acceptor, respectively. Fermentative growth was carried out with pyruvate (40 mM). Media (1000-ml) were dispensed in 2000-ml DURAN® SHOTT bottles, flushed with N2 and sealed with butyl rubber stoppers. Cultures with hydrogen as electron donor were grown in a 3L fermentor containing 2L of growth medium with 40 mM acetate, gassed with a mixture of 80 % (vol/vol) H2, 20 % (vol/vol) CO2 at 900 ml/min, stirred at 250 rpm and with a constant pH of 6.8.  As a control, D. vulgaris was grown in the same conditions but in Medium C-LS, and gassed with N2. In both procedures a 10% (vol/vol) inoculum of a freshly grown culture of D. vulgaris in the same conditions of the experiment was used, with exception to pyruvate culture where the inoculum was grown in pyruvate/sulfate medium. The optical density of the cultures at 600 nm (OD600) was determined with a Shimadzu UV-1603 spectrophotometer.

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with hydrogen as the only electron donor and sulfate as the only electron acceptor.

treatment_protocol: Cells grown with lactate as the electron donor


title: 2DCIS_control

tag: Stage IIa, Age

value: 48, T2N0M0, Nuclear Grade:3, ER+, PR+, p53+, HER2 +


title: 24IDC_swap

value: IIa, Age:54, T2N0M0, Nuclear Grade:3, ER+, PR+, p53+, HER2 + (3+)


title: H2-LS Slide G

treatment_protocol: Cells grown with hydrogen as the electron donor


title: 25DCIS_swap

value: 34, T2N0M0, Nuclear Grade:3, ER+, PR+, p53+, HER2 (3+)


title: H2-LS Slide Z


title: PyrS-LS Slide AW


title: H2-LS Slide S19


title: 3IDC_control


title: 2DCIS_swap


title: 25DCIS_control


title: 1IDC_control

value: IIa, Age:45, T2N0M0, Nuclear Grade:2, ER-, PR-, p53 -, HER2 + (3+)


title: H2-LS Slide AR

description: The objective of this study is to identify the genes differentially expressed in dissimilatory sulfate reduction by D. vulgaris using hydrogen as the electron donor as compared to lactate as the elctron donor.


title: 24IDC_control


title: H2-LS Slide AQ


title: H2-LS Slide AS


title: 1IDC_swap


title: H2-LS Slide AP


title: 13DCIS_control

value: 75, T2N0M0, Nuclear Grade:2, ER+, PR+, p53+, HER2 (2+)


title: Pyr-LS Slide S

description: The objective of this study is to identify the genes differentially expressed in D. vulgaris under fermentative growth as compared to growth via dissimilatory sulfate reduction.

source_name: Cells grown with pyruvate fermentation

growth_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

treatment_protocol: Growth with pyruvate fermentation

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with pyruvate as the only substrate; no sulfate was added.

source_name: Cells grown with sulfate reduction

treatment_protocol: Growth with sulfate reduction

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with sulfate as the only electron acceptor and lactate as the only electron donor


title: E.coli-DH10B_Human-BAC clone P8 transformed_v1

city: Vancouver

first: Rene

middle: Louis

last: Warren

state: British Columbia

address: 570 West 7th avenue Suite 100

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Agency

description: E.coli DH10B transformed with Human clone P8 - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

data_processing: Perfect match probe intensity that has been further normalized by Nimblegen using some tools available through the Bioconductor project using quantile normalization (see:Bolstad B, Irizarry R, Astrand M, Speed T (2003)).  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

organism: Escherichia coli

source_name: E. coli DH10B transformed with Human clone P8

growth_protocol: Cells were grown at 37C in 5ml in Brain-heard infusion broth (BHI) containing Hemin (10ug/ml), NAD (2ug/ml). H. influenzae 883 cells were grown in the presence of Kanamycin (10ug/ml) and E. coli DH10B T1 cells were cultured in the absence of antibiotic.  All BAC clones were grown in the same media at 37C in the presence of Chloramphenicol (10ug/ml).

extract_protocol: Total RNA was purified from 1ml of 20hr bacteria culture as per protocols from RNAprotect reagent (Qiagen) and RNeasy Mini Kit (Qiagen) including on-column DNase digestion. 2ml RNAprotect reagent was combined with 1ml bacteria culture in 5ml tubes and immediately vortexed 5sec and incubated at R.T. 5min. Samples were split into 2 X 1.5ml microfuge tubes and cells pelleted 10min, 5000 x g, at R.T. Supernatant was decanted and tubes tapped on Kimwipe towels. 200ul TEpH8 (30mM Tris-Cl, 1mM EDTA, pH8) containing 15mg/ml lysozyme and 750ug/ml proteinase K was added to each tube. Pellets were carefully resuspended by pipetting up and down several times and then mixed by vortexing 10sec and incubated at R.T. (15C-25oC), 10min. Tubes were vortexed for 10sec every 2min during incubation. 700ul Buffer RLT containing 10ul of B-mercaptoethanol per 1ml Buffer RLT was added and vortexed to mix well. 500ul 96-100% ethanol is then added and mixed by pipetting or shaking vigorously. 700ul lysate was transferred to each of two RNeasy Mini spin columns (Qiagen) placed in 2ml collection tubes and centrifuged 15sec, 8000 x g and the flow-through was discarded. 350ul Buffer RW1 was added and tubes were spun 15sec, 8000 x g and the flow-through was discarded. 80ul DNase I incubation mix (DNase I in Buffer RDD) was added to the membrane of each spin column and tubes were incubated 20-30oC for 15min. DNase I stock solution was made by dissolving 1500 Kunitz units DNase I in 550ul RNase-free water. DNase I incubation mix was made by combining 10ul DNase I stock solution with 70ul Buffer RDD and mixing by gently inverting the tube. Spin columns were then washed with 350ul Buffer RW1, incubated 5min, spun 15sec at 8000 x g and the collection tubes were discarded. Spin columns were placed in new 2ml collection tubes and 500ul Buffer RPE was added. Tubes were spun 15sec at 8000 x g and flow-through was discarded. Another 500ul Buffer RPE was added to each spin column and spun 2min at 8000 x g to wash membranes. RNA was eluted into new collection tubes with two additions of 30ul RNase-free water directly to the spin column membrane, spinning each time for 1min at 8000 x g.  Each pair of eluted RNA sample was pooled, 2ul RNA aliquots were measured for yield and quality by A260 measurement (Nanodrop ND-1000) and another 2ul aliquot was diluted in RNase-free water to ~100ng/ul and measured by RNA 6000 Nano Assay (Agilent Bioanalyzer). 1ul RNaseOUT (Invitrogen) was added to the remaining samples and stored at –80oC. 40ug of each RNA sample was dehydrated to 1ug/ul in a speedvac and sent to NimbleGen for gene transcription assay.

tag: E.coli DH10B transformed with Human clone P8 spanning genomic coordinates 108550285-108670449 on chromosome 6


title: 0.5% oxgall_30 min exposure_37C_rep1

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description: Signal intensities were quantified, background subtracted, and data normalized using the QuantArray 3.0 software package (Perkin-Elmer).  Two slides, each containing triplicate arrays, were hybridized reciprocally to Cy3 and Cy5 labeled probes per experiment (dye swapping).

hyb_protocol: Coupling of the Cy3 and Cy5 dyes to the AA-dUTP-labeled cDNA and hybridization of samples to microarrays was performed according to the protocols outlined by TIGR (www.tigr.org/tdb/microarray/protocolsTIGR.shtml).  Cy5- and Cy3-labeled cDNA probes were hybridized to the arrays for 16 hours at 42°C.  After hybridization, the slides were washed twice in high stringency buffer (1X SSC with 0.2% sodium dodecyl sulfate) for 5 min each.  The first wash was performed at 42°C and the second at room temperature.  Slides were then washed in a low stringency buffer (0.1 X SSC containing 0.2% sodium dodecyl sulfate) for five min at room temperature and finally in 0.1 X SSC for two 2.5 min washes at room temperature.

scan_protocol: Immediately after washing, fluorescence intensities were acquired at 10 μM resolution using a ScanArray 4000 microarray scanner (Packard Biochip BioScience; Biochip Technologies LLC) and stored as TIFF images.

data_processing: Spots were analyzed by adaptive quantitation.  The data were median normalized.  When the local background intensity was higher than the spot signal, no data were recorded for those spots.  The mean of the six ratios per gene was recorded, and the ratio between the average absolute pixel values for the replicated spots of each gene, with or without treatment, represented the fold change in gene expression.  Genes in potential operons were considered for analysis if at least one gene of the operon showed significant expression changes and the remaining genes showed trends towards that expression.  Confidence intervals and P values on the fold change were also calculated with the use of a two-sample t test.  P values of < 0.05 were considered significant.

organism: Lactobacillus acidophilus NCFM

source_name: Early log phase cells, MRS broth, 30 minutes

label_protocol: Twenty-five μg of RNA were aminoallyl-labeled by reverse transcription with random hexamers in the presence of aminoallyl dUTP (Sigma Chemical Co.) using Superscript II reverse transcriptase (Life Technologies) followed by fluorescent labeling with N-hydroxysuccinimide activated Cy3 or Cy5 esters (Amersham Biotech).  Labeled cDNA probes were purified using a PCR purification kit (QIAGEN).

extract_protocol: NCFM cells were grown to an OD600nm between 0.2 and 0.3 (representing early log phase.)  Cells were then pelleted at room temperature and resuspended in either MRS or MRS with 0.5% (w/v) Oxgall (Difco) and incubated 30 minutes at 37ºC.  Cells were then cold shocked in an ethanol/dry ice bath, pelleted at 4ºC, flash frozen, and stored at -80ºC.  Total RNA was isolated using a Trizol (Invitrogen)/chloroform extraction and samples were DNAsed using DNAseI, Amplification Grade (Invitrogen) according to manufacturer’s directions.  RNA concentration and quality were determined by spectrophotometry and agarose gel electrophoresis.

tag: Strain

value: NCFM

value: Early log-phase (OD600=0.3)

tag: Culture medium

value: MRS broth

source_name: Early log phase cells, MRS broth containing 0.5% Oxgall, 30 minutes

value: MRS broth containing 0.5% Oxgall (Difco)


title: E.coli-DH10B_H.influenzae-Pooled BAC clones from tiling path-transformed individually_v1

description: E.coli DH10B transformed with all H.influenzae clones from a BAC tiling path - total pooled RNA =~20 ug.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with all H.influenzae clones from a BAC tiling path


title: Pyr-LS Slide S3


title: normal_stroma_rep5

status: Public on Apr 03 2008

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

description: Our objective was to analyze transcriptome differences between stromal and epithelial cells in normal breast tissue and invasive breast cancer to define the role stroma plays in invasion.

hyb_protocol: Standard Affymetrix protocols were used at 45°C, for 16h, at 60 rpm

scan_protocol: Standard Affmetrix protocols were followed using GS300.

data_processing: Robust Multi-array Average (RMA)

label: Biotin

source_name: stromal cells

label_protocol: Target preparation was accomplished using NuGen Ribo-SPIA Ovation Technology with a 10 minute increase in the incubation time for the first strand cDNA synthesis reaction and SPIA amplification step in order to generate enough products for the Affymetrix HG U133A 2.0 GeneChip.

extract_protocol: Total RNA was isolated using Arcturus Picopure kit (Arcturus Engineering) following manufacturer's protocol for laser captured frozen tissue.  The DNase step was ommitted to prevent unnecessary losses of the limited RNA.

tag: stromal cells from normal patient


title: 13DCIS_swap

tag: Normal luminal epithelial mammary cell line


title: Pyr-LS Slide H

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with sulfate as the only electron acceptor and lactate as the only electron donor.


title: Pyr-LS Slide T


title: E.coli-DH10B_P.aeruginosa-cloneE6-transformed_v1

description: E.coli DH10B transformed with P.aeruginosa clone E6 - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with P. aeruginosa clone E6

tag: E.coli DH10B transformed with P.aeruginosa clone E6 spanning genomic coordinates 4157241-4266531


title: E.coli-DH10B_P.aeruginosa-cloneE5-transformed_v1

description: E.coli DH10B transformed with P.aeruginosa clone E5 - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with P. aeruginosa clone E5

tag: E.coli DH10B transformed with P.aeruginosa clone E5 spanning genomic coordinates 4071201-4186030


title: normal_epithelial_rep5

source_name: normal epithelium

tag: epithelium from normal patient


title: normal_stroma_rep4


title: normal_epithelial_rep3


title: normal_epithelial_rep2


description: Pseudomonas aeruginosa native cells - RNA extract.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa native cells

tag: Strain PA01


title: normal_stroma_rep1


title: E.coli-DH10B_H.influenzae-cloneS-transformed_v1

description: E.coli DH10B transformed with H.influenzae clone S - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with H. influenzae clone S

tag: E.coli DH10B transformed with Hinfluenzae clone S, spanning genomic coordinates 1687344-1785178


title: 0.5% oxgall_30 min exposure_37C_rep2

tag: Stage


title: normal_epithelial_rep1


title: normal_stroma_rep3


title: normal_stroma_rep2


title: E.coli-DH10B_P.aeruginosa-cloneE4-transformed_v1

description: E.coli DH10B transformed with P.aeruginosa clone E4 - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with P. aeruginosa clone E4

tag: E.coli DH10B transformed with P.aeruginosa BAC clone E4 spanning genomic coordinates 3897404-4071194


title: E.coli-DH10B_H.influenzae-cloneQtransformed_v1

description: E.coli DH10B transformed with H.influenzae clone Q - total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B transformed with H. influenzae clone Q

tag: Strain DH10B transformed with H.influenzae BAC clone spanning genome coordinate 1509405-1613444


title: cancer_epithelial_rep28

source_name: invasive breast cancer, tumor epithelium

tag: tumor epithelium from breast cancer patient


title: cancer_stroma_rep28

source_name: invasive breast cancer, stromal cells

tag: stromal cells from breast cancer patient


title: cancer_stroma_rep26


title: cancer_epithelial_rep24


title: cancer_stroma_rep22


title: cancer_epithelial_rep27


title: cancer_stroma_rep24


title: cancer_stroma_rep25


title: cancer_stroma_rep23


title: cancer_stroma_rep20


title: cancer_stroma_rep19


title: cancer_stroma_rep21


title: cancer_epithelial_rep23


title: cancer_stroma_rep18


title: cancer_stroma_rep27


title: cancer_epithelial_rep21


title: cancer_epithelial_rep25


title: cancer_stroma_rep17


title: cancer_epithelial_rep17


title: cancer_epithelial_rep20


title: Hinfluenzae RNA - native state - v1.0

description: Haemophilus influenzae native cells - RNA extract.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

organism: Haemophilus influenzae

source_name: Haemophilus influenzae native cells

tag: Strain 883


title: cancer_epithelial_rep18


title: cancer_stroma_rep16


title: cancer_epithelial_rep15


title: cancer_epithelial_rep14


title: cancer_epithelial_rep22


title: cancer_epithelial_rep16


title: cancer_stroma_rep11


title: cancer_epithelial_rep13


title: cancer_stroma_rep14


title: cancer_epithelial_rep11


title: cancer_stroma_rep10


title: cancer_stroma_rep12


title: cancer_stroma_rep13


title: E.coli-DH10B_nativeState_v1

description: native E.coli DH10B total RNA from 1ml of 20hr bacterial culture.  All array processing by NimbleGen, Inc. See www.nimblegen.com for details.

source_name: E. coli DH10B native cells

tag: Strain DH10B


title: cancer_stroma_rep15


title: cancer_epithelial_rep12


title: cancer_epithelial_rep8


title: cancer_epithelial_rep7


title: cancer_stroma_rep8


title: cancer_epithelial_rep10


title: cancer_epithelial_rep9


title: normal_epithelial_rep4


title: cancer_epithelial_rep5


title: cancer_stroma_rep5


title: cancer_stroma_rep6


title: cancer_stroma_rep9


title: cancer_stroma_rep7


title: cancer_epithelial_rep6


title: cancer_epithelial_rep26


title: cancer_stroma_rep4


title: cancer_stroma_rep3


title: cancer_stroma_rep1


title: cancer_epithelial_rep1


title: cancer_epithelial_rep3


title: cancer_epithelial_rep4


title: HF1585P+N, chip HG-U133A

status: Public on Apr 02 2008

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S398
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_398
Short description:			Three week old platelet-derived growth factor and neurotrophin-3-generated neurospheres cultured from 22 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			248ng/ul
Sample volume:				~50 ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

source_name: PDGF-responsive precursors, fetal brain tissue

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2%B27
Culture conditions:			PDGF-AA 100ng/ul, NT-3 100ng/ul for 21 days

extract_protocol:
RNA prep method:				PNeasy
Amplification method:			N/A
Cell purification method:			Isolation based on neurosphere formation in response to PDGF-AA +NT-3
Contaminating cell type:			unknown
Method for estimating purity:		N/A

tag: Strain:

tag: Defining markers:				PDGFR-alpha


title: HF1588P+N, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S397
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_397
Short description:			Three week old platelet-derived growth factor and neurotrophin-3-generated neurospheres cultured from 20 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			165ng/ul
Sample volume:				~50 ul


title: LLNL virulence mechanism array version 2A LOD experiment: 310 fg S.aureus DNA

city: Livermore

first: Crystal

last: Jaing

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

hyb_protocol: For each hybridization, 4 μg of labeled DNA was mixed with Cy3- and Cy5-labeled CPK6 oligomers, NimbleGen hybridization components and hybridization buffer according to the manufacturer's protocols. The Arrays were hybridized with labeled DNA on a MAUI hybridization station (BioMicro Systems, Salt Lake City, UT) at 42 deg C for 16 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Arrays were scanned using an Axon GenePix 4000B scanner at 5 μm resolution.

data_processing: Data were analyzed using custom software based on the R programming environment and BioConductor packages. Each probe was randomly spotted in three to five replicates to control for positional effects on the array. Data from replicate probes were summarized by the median of the log2-transformed intensities. No normalization or background correction was performed.

organism: Staphylococcus aureus subsp. aureus Mu50

source_name: S.aureus genomic DNA

label_protocol: DNA from one filter was used as a common background, to which varying quantities of fragmented S. aureus DNA were added. S. aureus DNA was quantified using a Quant-iT PicoGreen ds DNA kit (Invitrogen, Carlsbad, CA), serially diluted, and then spiked into 10 ng of aerosol sample DNA in quantities of 0.31 fg, 3.1 fg, 31 fg, 310 fg or 3.1 pg. We performed whole genome amplification of the combined samples (aerosol samples with spiked-in S. aureus DNA, plus one control pure aerosol sample) at 30oC for 16 hr using the REPLI-g whole genome amplification kit (Qiagen, Valencia, CA). The amplified material was inactivated at 65oC for 3 min and then purified using the QiaQuick PCR purification kit (Qiagen) to remove the primers and dNTPs. The entire amplified product was labeled with Cy3-random primer using the Klenow fragment.

growth_protocol: The bacterial culture pellets were grown according to the instructions from ATCC.

extract_protocol: Genomic DNA was extracted using the Epicentre DNA extraction kit according to the manufacturer's protocols.

tag: strain Mu50; GenBank accession NC_002758.2


title: cancer_epithelial_rep2


title: LLNL virulence mechanism array version 2A LOD experiment: 31 fg S.aureus DNA


title: LLNL virulence mechanism array version 2A LOD experiment: 3.1 fg S.aureus DNA


title: cancer_stroma_rep2


title: HF1585P+N, chip HG-U133B


title: HF1588P+N, chip HG-U133A


title: LLNL virulence mechanism array version 2A LOD experiment: 3.1 pg S.aureus DNA

organism: Staphylococcus aureus


title: LLNL virulence mechanism array version 2A LOD experiment: background only

organism: unidentified

source_name: Aerosol background sample

extract_protocol: DNA was extracted using the MoBio UltraClean Soil DNA kit (MoBio Laboratories, Carlsbad, CA), as described in Radosevich JL, Wilson WJ, Shinn JH, DeSantis TZ, Anderson GL (2002), Development of a high-volume aerosol collection system for the identification of air-borne micro-organisms, Let in Appl Micro 34: 162-167.

tag: Aerosol sample collection filter


title: HF1585PDGF, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S396
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_396
Short description:			Three week old platelet-derived growth factor-generated neuropsheres cultured from 22 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			109ng/ul
Sample volume:				~50 ul

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2%B27
Culture conditions:			PDGF-AA 100ng/ul for 21 days

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			N/A
Cell purification method:			Isolation based on neurosphere formation in response to PDGF-AA, !Sample_extract_protocol = Contaminating cell type:			unknown
Method for estimating purity:		N/A


title: HF1588PDGF, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S395
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_395
Short description:			Three week old platelet-derived growth factor-generated neuropsheres cultured from 20 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			77.3ng/ul
Sample volume:				~50 ul


title: LLNL virulence mechanism array version 2A LOD experiment: 0.31 fg S.aureus DNA


title: HF1585PDGF, chip HG-U133A


title: cancer_epithelial_rep19


title: S.saprophyticus genomic DNA hybridization to LLNL virulence mechanism array v2A

organism: Staphylococcus saprophyticus

source_name: S.saprophyticus genomic DNA

label_protocol: DNA samples were sonicated to fragment the DNA to a size range of 500-2000 bp, and then labeled using nick translation with Cy3-labeled random nonamer primers (TriLink Biotechnologies, San Diego, CA) and Klenow DNA polymerase at 37 deg C for 3 hr. The labeled DNA was precipitated in isopropanol, and the pellet washed, dried, reconstituted and quantified.

tag: strain ATCC 15305; GenBank accession NC_007350.1


title: HF1585EGF, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S394
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_394
Short description:			Three week old epidermal growth-factor generated neurospheres cultured from 22 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			278 ng/ul
Sample volume:				~50 ul

source_name: EGF-responsive neural stem cell, Fetal Brain

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2%B27
Culture conditions:			EGF 20ng/ul for 21 days

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			N/A
Cell purification method:			Isolation based on neurosphere formation in response to EGF
Contaminating cell type:			unknown
Method for estimating purity:		N/A


title: HF1585EGF, chip HG-U133A


title: S.pyogenes genomic DNA hybridization to LLNL virulence mechanism array v2A

organism: Streptococcus pyogenes MGAS5005

source_name: S.pyogenes genomic DNA

tag: strain MGAS5005; GenBank accession NC_007297.1


title: HF1588EGF, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S393
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_393
Short description:			Three week old epidermal growth-factor generated neurospheres cultured from 20 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			150 ng/ul
Sample volume:				~50 ul


title: HF1588PDGF, chip HG-U133A


title: HF1583P+N, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S378
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_392
Short description:			Three week old platelet-derived growth factor and neurotrophin-3-generated neurospheres cultured from 18 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			80ng/ul
Sample volume:				~50ul


title: human_MCF10A_siRNA-eIF4GI_total RNA_R3

status: Public on Apr 01 2008

city: New York

first: Robert

middle: J

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

description: Overall transcriptome changes were determined for control or eIF4GI silenced cells.

hyb_protocol: 10 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the MBEI algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Total RNA MCF10A cells 72 hrs post eIF4GI siRNA transfection

label_protocol: Fragmented cDNA labeled with biotin at the 3' terminus by terminal deoxynucleotidyl transferase (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: 48 h after siRNA transfection, MCF10A cells were seeded in 15 cm plates and harvested at 50% confluency 24 h later and either treated with cycloheximide to fractionate polysome bound mRNA in a 10-50% sucrose gradient or subjected to trizol reagent (Invitrogen) to extract total RNA.

extract_protocol: Polysome-bound mRNA was extracted using  phenol:chloroform after fractionation on sucrose gradient.  Total RNA was extracted with trizol (Invitrogen) followed by further purification using RNeasy mini-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: Cells were transfected with either control or eIF4GI siRNA using oligofectamine (invitrogen).

tag: eIF4GI siRNA


title: HF1583EGF, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S376
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_390
Short description:			Three week old epidermal growth-factor generated neurospheres cultured from 18 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			353ng/ul
Sample volume:				~50ul


title: human_MCF10A_siRNA-control_total RNA_R1

source_name: Total RNA MCF10A cells 72 hrs post control siRNA transfection

tag: Control siRNA


title: human_MCF10A_siRNA-eIF4GI_total RNA_R2


title: human_MCF10A_siRNA-control_total RNA_R3


title: E.coli O157:H7 EDL 933 genomic DNA hybridization to LLNL virulence mechanism array v2A

organism: Escherichia coli O157:H7 str. EDL933

source_name: E.coli O157:H7 EDL 933 genomic DNA

tag: serovar O157:H7 strain EDL933; GenBank accession NC_002655.2


title: E.faecalis genomic DNA hybridization to LLNL virulence mechanism array v2A

hyb_protocol: For each hybridization, 4 μg of labeled DNA was mixed with Cy3- and Cy5-labeled CPK6 oligomers, NimbleGen hybridization components and hybridization buffer according to the manufacturer’s protocols. The arrays were hybridized with labeled DNA on a MAUI hybridization station (BioMicro Systems, Salt Lake City, UT) at 42oC for 16 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols

organism: Enterococcus faecalis V583

source_name: E.faecalis genomic DNA

label_protocol: DNA samples were sonicated to fragment the DNA to a size range of 500-2000 bp, and then labeled using nick translation with Cy3-labeled random nonamer primers (TriLink Biotechnologies, San Diego, CA) and Klenow DNA polymerase at 37oC for 3 hr. The labeled DNA was precipitated in isopropanol, and the pellet washed, dried, reconstituted and quantified.

extract_protocol: Genomic DNA was extracted using the Epicentre DNA extraction kit according to the manufacturer’s protocols.

tag: strain V583


title: E.coli CFT073 genomic DNA hybridization to LLNL virulence mechanism array v2A

organism: Escherichia coli CFT073

source_name: E.coli CFT073 genomic DNA

tag: strain CFT073; GenBank accession AE014075.1


title: human_MCF10A_siRNA-control_polysomal RNA_R3

type: other

description: Polysome bound mRNAs were compared between control and eIF4GI silenced cells.

molecule: other

source_name: Polysomal RNA of MCF10A Cells, 72 h post control siRNA transfection, 50% confluent.


title: S.enterica serovar paratyphi genomic DNA hybridization to LLNL virulence mechanism array v2A

organism: Salmonella enterica

tag: serovar paratyphi A strain ATCC 9150; GenBank accession NC_006511.1


title: HF1583P+N, chip HG-U133A


title: HF1583EGF, chip HG-U133A


title: human_MCF10A_siRNA-control_polysomal RNA_R2


title: HF1583PDGF, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S377
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_391
Short description:			Three week old platelet-derived growth factor-generated neuropsheres cultured from 18 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			29ng/ul
Sample volume:				~50ul


title: human_MCF10A_siRNA-control_polysomal RNA_R1


title: human_MCF10A_siRNA-eIF4GI_total RNA_R1


title: human_MCF10A_siRNA-eIF4GI_polysomal RNA_R2

source_name: Polysomal RNA of MCF10A Cells, 72 h post eIF4GI siRNA transfection, 50% confluent.


title: human_MCF10A_siRNA-control_total RNA_R2


title: human_MCF10A_siRNA-eIF4GI_polysomal RNA_R3


title: H3K9me3_1_WT

status: Public on Mar 16 2008

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, H3K9me3 ChIP(chromatin immunoprecipitation)-on-chip replicate 2

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformadehyde at 18C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

tag: Chromatin DNA not enriched for H3K9me3

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

tag: Chromatin DNA enriched for H3K9me3


title: Raf1_1_WT

description: Schizosaccharomyces pombe cells, Flag-Raf1 ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Flag-Raf1

tag: Chromatin DNA enriched for Flag-Raf1


title: Raf2_1_WT

description: Schizosaccharomyces pombe cells, Raf2-Myc ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Raf2-Myc

tag: Chromatin DNA enriched for Raf2-Myc


title: Cul4_1_WT

description: Schizosaccharomyces pombe cells, Flag-Cul4 ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Flag-Cul4

tag: Chromatin DNA enriched for Flag-Cul4


title: Fly heads, beta-eliminated, 8 mismatches tolerated on the pair of adapters

status: Public on Jan 22 2008

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description: This sample was beta-eliminated before adapter ligation. The .sff files are not available for this submission.

hyb_protocol: (not applicable)

scan_protocol: (not applicable)

data_processing:
Inserts were extracted from the 454 reads, tolerating 0 mismatch on the pair of adapters (5´ adapter: AUCGUAGGCACCUGAAA; 3´ adapter: CACUCGGGCACCAAGGA); inserts of 18 to 30 nt long were selected.
The "ID_REF" column indicates the sequence of the small RNA; "VALUE" indicates the number of times that small RNA was detected in this sample.

source_name: Fly heads (with a transgene expressing an inverted repeat of a fragment of the white gene)

label_protocol: (not applicable)

extract_protocol: Total RNA was extracted using the miRVana kit (Ambion), then small RNAs (18 to 30-nt long) were gel-purified. 2S ribosomal RNA was depleted with a biotinylated, anti-2S DNA oligo, captured with streptavidin-coated paramagnetic beads (Dynal, M-270 beads).

treatment_protocol: Heads were dissociated from the rest of the body by shaking liquid nitrogen-frozen flies on a mesh.

tag: Mixed male and female adult flies (expressing an inverted repeat of a fragment of the white gene; strain described in Lee et al. (2004) Cell 117(1):1-3).


title: S2 cells, not beta-eliminated, 9 mismatches tolerated on the pair of adapters

description: This sample was not beta-eliminated before adapter ligation. The .sff files are not available for this submission.

data_processing:
Inserts were extracted from the 454 reads, tolerating 0 mismatch on the pair of adapters (5´ adapter: AUCGUAGGCACCUGAAA; 3´ adapter: UUUAACCGCGAAUUCCAG); inserts of 18 to 30 nt long were selected.
The "ID_REF" column indicates the sequence of the small RNA; "VALUE" indicates the number of times that small RNA was detected in this sample.

source_name: S2 cells (with a stable transgene expressing mini-white and GFP, and: transiently transfected with a double-stranded RNA against GFP)

tag: S2 cells containing the stably-integrated pKF63 construct (expressing the mini-white gene and GFP; described in Förstemann et al. (2005) PLoS Biol 3(7):e236) were transfected with a double-stranded RNA against GFP (described in Horwich et al. (2007) Curr. Biol. 17(14):1265).


title: Fly heads, beta-eliminated, 7 mismatches tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 9 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 5 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 6 mismatches tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 9 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 8 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 7 mismatches tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 6 mismatches tolerated on the pair of adapters


title: Clr4_1_WT

description: Schizosaccharomyces pombe cells, Flag-Clr4 ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Flag-Clr4

tag: Chromatin DNA enriched for Flag-Clr4


title: S2 cells, beta-eliminated, 5 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 8 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 7 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 6 mismatches tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 7 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 9 mismatches tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 8 mismatches tolerated on the pair of adapters


title: Rik1_1_WT

description: Schizosaccharomyces pombe cells, Rik1-Myc ChIP(chromatin immunoprecipitation)-on-chip replicate 1

tag: Chromatin DNA not enriched for Rik1-Myc

tag: Chromatin DNA enriched for Rik1-Myc


title: Fly heads, not beta-eliminated, 5 mismatches tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 3 mismatch tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 3 mismatch tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 3 mismatch tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 3 mismatch tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 2 mismatches tolerated on the pair of adapters

treatment_protocol: Heads were dissociated from the rest of the body by shaking liqui nitrogen-frozen flies on a mesh.


title: Fly heads, not beta-eliminated, 4 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 4 mismatches tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 1 mismatch tolerated on the pair of adapters


title: Sprague Dawley I/R rep1

status: Public on Dec 28 2007

city: Barcelona

first: Jose Luis

last: Viñas

address: rosellon 161 7ª

department: Experimental Pathology

country: Spain

institute: IIBB-CSIC

description: Tissue from Sprague Dawley rat

hyb_protocol: Digoxigenin-labelled cRNA targets were hybridized to Applied Biosystems Rat Whole Genome Survey Microarrays using the Applied Biosystems Chemiluminescent Detection Kit. Briefly, 15 μg of labelled cRNA targets were fragmented via incubation for 30 min at 60 ◦C with fragmentation buffer provided in the kit. Fragmented targets were hybridized to microarrays during 16 h of incubation at 55 ◦C with buffers and reagents from the Chemiluminescent Detection Kit. Post-hybridization washes and anti-digoxigenin-alkaline phosphatase binding were performed according to the kit protoco

scan_protocol: Chemiluminescence detection, image acquisition and analysis were performed using the Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer’s protocols. Images were autogridded and the chemiluminescent signals were quantified, corrected for background and, finally, spot- and spatially normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software version 1.1 (for more information see Applied Biosystems 1700 Chemiluminescent Microarray Analyzer user bulletin in ABI's website)

data_processing: The data obtained after the process described in the scan protocol section were normalized by LOWESS (Locally weighted least mean squares scatter Plot smoother), this was the statistical algorithm for performing a non linear normalization and corrects deviations of the backbone of the data cloud from the expected main diagonal. Data were LOWESS normalized excluding the controls on the microarray and using only the transcripts with a S/N ratio to > 2.

label: Digoxigenin-labelled cRNA

organism: Rattus norvegicus

source_name: Sprague Dawley I/R

label_protocol: All RNA targets were labelled using the Applied Biosystems RT-IVT Labelling Kit Version 2.0. Briefly, 1.5 μg of the total RNA sample was reverse transcribed via 2 h incubation at 42 ◦C with ArrayScript RT enzyme (Ambion, Austin, TX, USA) and oligo dT-T7 primer. Double-stranded cDNA was produced following 2 h incubation with E. coli DNA polymerase and RNase H at 16 ◦C. Double-stranded cDNA was purified according to the RT-IVT kit protocol. In vitro transcription was performed by incubation of the cDNA product with T7 RNA polymerase, 0.75 mM digoxigenin-11-UTP (Roche Applied Science, Indianapolis, IN, USA) and all other NTPs for 9 h. Labelled cRNA was purified according to the RT-IVT kit protocol and analyzed for quality and quantity using standard UV spectrometry and the Bioanalyzer.

extract_protocol:
Total RNA from cells was isolated using an RNeasy system (Qiagen, Valencia, CA, USA) and were further purified by passage through RNeasy mini-columns (QIAGEN, Valencia, CA) according to manufacturer’s protocols for RNA clean-up. Final RNA preparations were resuspended in RNase-free water and stored at -80°C.
The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm. The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Only high-quality RNA with RNA integrity numbers (RINs) greater than 7.5 were used for microarray experiments

tag: Tissue from Sprague Dawley rat strain.


title: Sprague Dawley I/R rep2

description: Tissue from Sprague Dawley rat

tag: Tissue from Sprague Dawley rat strain


title: HF1583PDGF, chip HG-U133A

organism: Homo sapiens

source_name: PDGF-responsive precursors, fetal brain tissue

tag: Strain:

tag: Defining markers:				PDGFR-alpha


title: Fly heads, beta-eliminated, 5 mismatches tolerated on the pair of adapters

organism: Drosophila melanogaster


title: S2 cells, beta-eliminated, 2 mismatches tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 2 mismatches tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 4 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 0 mismatch tolerated on the pair of adapters


title: S2 cells, beta-eliminated, 0 mismatch tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 0 mismatch tolerated on the pair of adapters


title: Brown Norway I/R rep2

description: Tissue from Brown Norway rat

source_name: Brown Norway I/R

tag: Tissue from Brown Norway strain rat


title: Fly heads, non beta-eliminated, 0 mismatch tolerated on the pair of adapters


title: Brown Norway Control rep2

description: Tissue from Brown Norway rat

source_name: Brown Norway Control

tag: kidney tissue from Brown Norway strain rat


title: Brown Norway I/R rep1

description: Tissue from Brown Norway rat

tag: Tissue from Brown Norway strain rat.


title: Fly heads, non beta-eliminated, 1 mismatch tolerated on the pair of adapters


title: Fly heads, not beta-eliminated, 6 mismatches tolerated on the pair of adapters


title: S2 cells, not beta-eliminated, 2 mismatches tolerated on the pair of adapters


title: Sprague Dawley Control rep2

description: Tissue from Brown Norway rat

source_name: Sprague Dawley Control

tag: kidney tissue from Brow Norway rat strain


title: Sprague Dawley Control rep1

description: Tissue from Sprague Dawley rat

tag: Kidney tissue from Sprague Dawley rat strain.


title: S2 cells, not beta-eliminated, 1 mismatch tolerated on the pair of adapters


title: Fly heads, beta-eliminated, 1 mismatch tolerated on the pair of adapters


title: human_MCF10A_siRNA-eIF4GI_polysomal RNA_R1

tag: eIF4GI siRNA


title: NF-VGB (Replicate 4-Dye Swap)

status: Public on Oct 05 2007

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: Array Number: 12926014. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

scan_protocol: Slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

source_name: Drosophila melanogaster, unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials containing normal food, for three days..

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of untreated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in normal food for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

tag: Strain

value: Oregon R

tag: Sex

value: Male

tag: Tissue

value: Head

source_name: Drosophila melanogaster, unmated, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials with food containing 24 mg/ml of VGB, for three days..

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of VGB treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 24 mg/ml of Vigabatrin (VGB) for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Brown Norway Control rep1

description: Tissue from Brown Norway rat

tag: cortico-medullar renal  tissue from brown norway rat strain .


title: NF-GBP (Replicate 3-Dye Swap)

description: Array Number: 12926026. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials containing normal food, for three days.

source_name: Drosophila melanogaster, unmated, gabapentin treated

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials with food containing 16 mg/ml of GBP, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of GBP treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 16 mg/ml of Gabapentin (GBP) for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

value: oragon R


title: NF-VGB (Replicate 2)

description: Array Number: 12926450. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials with food containing 24 mg/ml of VGB, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of VGB treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol